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Traffic Analysis and Collision Pattern ( Vision Zero) 
Alia Kasem
Lina Kasem

Alia Kasem

and 1 more

June 07, 2021
This analysis will primarily focus on the number of collisions before and after NYC adopting  Vision Zero. In this analysis, the statistical model of K-S testing will be used to compare the two periods;  before and after the adoption of Vision Zero. The study will include a time series of the effectiveness of Vision Zero using the data; based on the cumulative number of accidents. The cumulative number and daily pattern of the collisions will measure probabilities of effectiveness.
Book Review: Inner Animalities: Theology and the End of the Human
Saortua Marbun

Saortua Marbun

December 10, 2018
Saortua MarbunSekolah Tinggi Ilmu Ekonomi Triatma Mulya Bali IndonesiaEmail: saortuam@gmail.com | http://orcid.org/0000-0003-1521-7694.Book Review: Inner Animalities: Theology and the End of the Human, by Eric Daryl Meyer. New York, Fordham University Press, 2018., i-x, 241 pp., $115.00 (Hardcover), ISBN 9780823280155.Eric Daryl Meyer’s book, “Inner Animalities: Theology and the End of the Human” raises an ambiguous question of human animality. He aims to both reveal the flaws of anthropological exceptionalism and show that it does not have to be an integral part of Christian theology. Moreover, in his book, Meyer intends to expand the boundaries of his discussion of human animality to a broader context, namely to reflect upon people’s inability to withstand ecological degradation. In other words, Meyer is interested not only in Christian theology but also in such important issue as ecology. In this regard, he uses human animality to design a new understanding of ecological theology.Meyer’s theological explorations emerge from the idea, which is deeply grounded in Western culture, precisely the concept of human uniqueness. People believe in their specialness, which results in such a distinctive feature of Christian ideology as “a categorical distinction between human beings and all other animals(1)” and plays a vital role in the understanding of the concept of sin, among others. Meyer points out that although even the great philosopher Aristotle defined a human being as a political animal, throughout history, representatives of the Western civilization tried to distance themselves from animals as far as possible, making humans and other living beings opposing creatures. One of the consequences of such perception is not only the emergence of Christian theological anthropology, but also people’s failure to cope with modern ecological disasters, including but not limited to climate change, environmental pollution, and extinction of numerous species. Thus, there is an urgent need of reevaluation of human animality, which might give rise to a better understanding of people’s place in the world and the improvement of their relationship with God and nature alike.With such global objectives in mind, Meyer divides his book into two parts. The first part of “Inner Animalities” is a critical analysis of “Animality and Ascent” by Gregory of Nazianzus and “Reading Animality and Desire” by Gregory of Nyssa, as well as the discussion of the issue of human animality in modern theological anthropology. Meyer shows how human animality makes the theology of Gregory of Nazianzus conflicting. On the one hand, Gregory of Nazianzus fiercely disavows human animality. On the other hand, human salvation appears to be impossible without it. Meyer discusses the main elements of Gregory’s theology, namely mind, flesh, logos through the lens of humanity-animality opposition and proceeds to a discussion of his sermons, “Oration 39” and “Oration 28.”In “Homilies on the Song of Songs,” Gregory of Nyssa struggles with the same challenge. He wishes to deny human animality, yet its exclusion from a proper spiritual understanding of the text seems to deprive it of essential meaning. Therefore, in his interpretation of “The Song of Songs,” Gregory of Nyssa allows, “the desires proper to animality become indispensable to human perfection in an unacknowledged way. (55)” From this point, Meyer can move to contemporary visions of human animality.The second part of the book reconsiders the issue of human animality in the context of three essential notions, the image of God in Chapter 4, sin and redemption in Chapter 5, and eschatological transformation in Chapter 6. In conclusion, Meyer emphasizes that discussion of humanity and animality goes far beyond theological disputes. In particular, this discourse applies to a wide range of important issues, from relations between human thoughts, bodies, desires, social ties, and subjects to the boundaries of class, gender, sexuality, race, citizenship, and ethnicity(173). He invites further researches of this topic, whereas he believes in its significance and relevance.Eric Daryl Meyer’s, “Inner Animalities: Theology and the End of the Human” is interesting literary writing, mostly since it takes seeming purely theological question and turns it on its head. In other words, what begins as a critical reading of fourth-century authors, who are likely to be noteworthy for people who are keen on religious literature only, ends as a meaningful discussion of the future of the humankind in the context of a rapidly deteriorating ecology. Meyer points out to a cause-effect relationship between people’s confidence in their superiority and uniqueness and anthropogenic ecological degradation. It may be difficult to embrace and accept, especially taking into account a long-term tradition of opposing human beings and other living beings, yet it gives the readers a lot to think about and to question.From this perspective, “Inner Animalities” is written for a wide audience and it can be recommended for both theological scholars and people interested in different kinds of literature that nurture reasoning. The book might cause disagreement and even resentment with the readers who firmly believe in the idea of human exceptionalism, yet even in this case, fervent advocates of traditional theological anthropology of Christianity will find something informative and new in it. As for the rest, “Inner Animalities” definitely suggests fresh ideas and unusual approaches to common Christian visions.
Ideologies Behind the Halal Tourism Sector
Saortua Marbun

Saortua Marbun

December 07, 2018
Ideologies Behind the Halal Tourism SectorSaortua Marbun Sekolah Tinggi Ilmu Ekonomi Triatma Mulya  AbstractA quick scan of the available literature on the subject of halal tourism reveals that many scholars and laypersons alike misconceive this concept. Whereas some suggest that halal tourism occurs whenever a Muslim individual travels somewhere, others retort that only pilgrimages by Muslim travelers regarded as halal tourism. More careful research of the literature shows that the truth is somewhere in between, as none of the above definitions is correct. Overall, it is this lack of clarity that has prompted an additional inquiry into the essence of halal tourism. This essay is a modest academic endeavor to ascertain what halal tourism is and what ideologies lie at its foundation. To answer these questions, the author employs the literature review research methodology, scrutinizing number sources. Ultimately, this essay has established that halal tourism not confined to religious pilgrimages alone. Indeed, halal tourism occurs whenever a Muslim individual travels for religion, business or leisure and uses only those services and facilities that conform to the teachings of Islam.Keywords: tourism, travel, halal tourism, Islamic tourism, Islamic teachings, Sharia. IntroductionJust half a century ago, travel was an undeniable synonym for adventure and exploration. In the popular imagination, any widely traveled individual associated with an aura of mysteriousness. Today, by contrast, travel and tourism have become more common and mundane, as ever more significant numbers of people flock to both domestic and foreign destinations for business and recreation or to simply quench their wanderlust. The travel industry has evolved correspondingly, learning to cater to the specific needs of different categories of tourists and travelers. Some of the most common and clearly defined subcategories of tourism that have developed in recent decades include green tourism, religious tourism, sports tourism, shopping tourism, wellness tourism, package tours and – pardon the obscenity – even sex tourism. Halal tourism, for its part, is yet another burgeoning subcategory of tourism. Despite its growing dimensions, the concept of halal tourism is often misunderstood and misrepresented in popular media.Given the problem, this essay seeks to understand the concept of halal tourism better. By extension, the piece attempts to ascertain the ideologies behind this subcategory of tourism. In other words, the essay examines the relationships between halal tourism on the one hand and religion, management, economics and politics on the other. By these findings, the article seeks to make an informed assessment if the halal tourism sector is capable of withstanding competition from conventional tourism. The overarching argument is, therefore, straightforward: Halal tourism is designed to enable pious Muslim tourists to pray towards Mecca, use gender-segregated facilities and otherwise abide by the Quranic teachings on vacation without raising eyebrows or causing other discomforts. Although evidence suggests that some Muslims are embracing a capitalist consumer culture, it is reasonable to opine that halal tourism will assume even greater dimensions in the future. MethodologyConsidering the constraints of this paper, no primary data were collected to conduct a more robust and comprehensive research project. This limitation, however, does not vitiate the significance of the present essay. Nor does it significantly diminish the contribution of the present article to the relevant academic scholarship on the subject of halal tourism. The most significant value of this article is that it scrutinizes pertinent academic literature to collect evidence. More specifically, it distills and synthesizes common threads from the reviewed scholarship. Many sources were a review for this article. Although several of the used sources are somewhat outdated, they nonetheless provide valuable insights into the topic. The majority of the sources are, however, more up-to-date. Likewise, while some articles from mass media made their way into this essay, the emphasis was on credible sources like articles from peer-reviewed scholarly journals, books published by authoritative publishing houses, articles from reliable newspapers and official reports. To locate these sources, the author of this essay scanned online databases with such keywords as “halal tourism,” “halal destination,” “Muslim friendly tourism,” etc. ResultsSimply put, halal tourism refers to a tourist sector that caters to the needs and requirements of Muslim travelers. To get a more elaborate idea of what halal tourism is, however, it is essential to cite and deconstruct more detailed definitions adduced by competent organizations and individual commentators. Specialists at the Organization of Islamic Cooperation, for example, contend that halal tourism occurs when Muslim travelers visit predominantly Muslim destinations, with religious motivations representing the main reason why they choose these specific destinations (“Strategic roadmap for the development of Islamic tourism in OIC member countries” 2017). It is crucial to acknowledge that halal tourism is a broader concept and it can occur even in those countries where Islam is not the dominant faith. In the same vein, halal tourism can happen in situations when spiritual fulfillment or pilgrimage is not the main reasons why Muslim travelers come to a particular destination. Henderson (2009) concurs with this judgment, further adding that Muslim tourists who travel abroad for recreation rather than the religion but conform to Islamic teachings at the same time are mainly participating in halal tourism. El-Gohary, Edwards, and Eid (2017), too, believe that it is counterproductive and counter intuitive to limit halal tourism only to pilgrimages dogmatically. Other researchers, including Al-Hamarneh (2008), go even further, surmising that any trip taken by a Muslim tourist is part of halal tourism by default. This approach is, however, ineffective, for it blurs the real boundaries of halal tourism. With the same luck, any trip taken by a Christian could be branding as Christian tourism. But this branding would be meaningless, failing to add any novelty to the field of tourism studies.It should be noted, in an important aside, that the well-established kosher tourism is not solely about demographics. It is more about accommodating the needs of a particular demographic group. As seen from the definitions of Henderson and El-Gohary, Edwards and Eid, halal tourism is even more concrete and specific concept. Overall, what this passage serves to show is that halal tourism requires adherence to Islamic rules of propriety by Muslim travelers for their trips to be duly considered as representing halal tourism.The discussion above already alludes to the idea that halal tourism is integral to religion. Despite the commonly regarded belief to the contrary, moreover, that religion is the mainstay of halal tourism, its lynchpin, its cornerstone. Nathalie Bourgeois (2016) addresses what some commentators – those in the west, mainly – see as the incongruence between tourism and Islam:To many non-Muslim Westerners, the expression “Islamic tourism” might seem an oxymoron, an improbable association between a strict religion and the western idea of carefree idleness in exotic locations. The Prophet himself preached Muslims to go and discover the world: “Travel through the land and observe how He began creation,” says the Quran (p. 1).For Muslim travelers, therefore, halal tourism implies the necessity to organize their trips under the beliefs and practices of Islam. For travel companies, hotels and other service providers, halal tourism suggests the need to offer only such facilities that propagate Islamic teachings. Although no codified standards of halal tourism exist, the consulted authors explain that service providers involved in this industry tend to provide separate swimming pools for males and females, serve halal food and do not serve alcohol, announce prayer timings, have Qurans readily available, and even broadcast religious content as part of entertainment (Shirazi, 2016; Raj & Griffin, 2017). Hashim, Shariff, Mahamood, and Bhari (2018) weigh in to suggest that even charter flights booked for Muslim travelers frequently geared toward Muslim standards. In doing so, these service providers are driven by either the desire to attract more Muslim travelers or by their religious consciousness. One or the other way, it is understood that religious ideologies are ubiquitous in the halal tourism sector.Halal tourism has political implications too. It could say in the very least that halal tourism promotes Islamic solidarity (Reiter, 2008; Kozak & Kozak, 2015). This subcategory of tourism could also potentially have an impact on Islamic nationalism (US Congress, 2009). Pinpointing the exact political effects of halal tourism goes beyond the purposes of this essay. It is instead more important to focus on the economic ideologies undergirding the halal tourism sector. It is imperative to make a reservation in this context that halal tourism is not merely about religion, politics, and thinking. Like any other business enterprise, it is also about income. On the face of things, it seems illogical from the standpoint of economics and fiscal integrity that travel service providers would deliberately limit their services to Muslim individuals, thereby eliminating a vast swath of non-Muslim tourists. Frequently, however, it is just a matter of perspective. If travel service providers reason that Muslim tourists are a more profitable market for them, the consulted authors agree, these service providers can make a volte-face in favor of this market at the expense of the less lucrative non-Muslim market (Demir & Toprak, 2004; Adas, 2006; Eddahar, 2016). Drawing on the example of Turkey, Elaziz and Kurt (2017) explain that the recent rise in Islamic capital experienced by this country has contributed to the burgeoning of the Islamic consumer market. Hence, the conclusion arises that the forces of capitalism are unavoidable in the tourism sector, be it conventional tourism or halal tourism. In essence, businesses involved in the halal tourism sector provide Muslim friendly services to their clients with the goal of deriving financial benefits. As far as Muslim tourists themselves are concerned, a study by Elaziz and Kurt (2017) has found that they have a proclivity to provide excuses for their going on vacation. Elaziz and Kurt (2017) elaborate on these findings to suggest that even some religious devotees have espoused capitalist consumer culture or, in other words, a vacation of tourism culture. Overall, what these tidbits imply is that halal tourism is not necessarily a purely religious phenomenon based on religious ideology. Regarding, there seem to be adequate grounds to assert that the halal travel sector holds a great promise for the future. This special-interest-tourism market is in its infancy at this juncture of history. Mattison’s (2018) article for Euronews shows that this sector is quickly catching up with the broader industry. As a more resilient middle class is emerging in many predominantly Islamic nations, ever more pious Muslims now have the wherewithal to travel (Scott, 2010; Bikramjit, 2014). Mattison (2018) reckons that halal tourism will account for some 14% of global travel expenditure by 2022. El-Gohary, Edwards, and Eid (2017) also agree with the overall idea that halal tourism faces sanguine prospects, further adding: “The growth trajectory of Muslim tourism is expected to continue as Muslim increasingly come from fast-growing economies that include BRICS countries such as China and India” (p. 107). The rise in halal tourism is due to multiple factors. First of all, halal tourism is developing under the stewardship of the Organization of Islamic Cooperation. More specifically, the organization initiates and coordinates regional efforts in policy and regulation development, marketing and promotion, destination and industry growth, capacity building and so on (Agarwal, Busby & Huang, 2017). Besides, individual states and individual companies within states make their efforts to foster halal tourism. The government of Indonesia introduced 12 Muslim friendly destinations in 2013 (Firdausi, Marantika, Firdaus & Sajidah, 2017). All this augurs well for the halal tourism sector. ConclusionRecognizing the diversity of needs and seeking to uphold this diversity by providing specific services to Muslim people, representatives of the travel sector in many parts of the world are now increasingly offering travel services that are in strict conformity with Islamic teachings. This essay has confirmed the tentative hypothesis that the halal travel industry has both religious and economic underpinnings. Businesses involved in this sector aspire both to please its Muslim clients, so that these clients would feel comfortable during their vacations, and to derive large financial dividends from the promising and rapidly growing market. Besides, it is also crucial to note in conclusion that the rapid growth of halal tourism has implications for hotels, restaurants, airlines and other businesses involved in this sector. People in charge of these businesses need to be careful to take full advantage of the recent tendencies in the travel industry, thereby facilitating continuous development of halal tourism, but avoid the potential pitfalls at the same time. Accomplishing this in practice might, however, be challenging, for allegiance to halal tourism at the expense of other subcategories of tourism has the potential to create conflicts of interest. After all, the standards of halal tourism and conventional tourism are often incompatible. It remains to see how such incompatibilities will resolve in the future. ReferencesAdas, A. (2006). The making of entrepreneurial Islam and the Islamic spirit of capitalism.Journal for Cultural Research, 10(2), 113-125.Agarwal, S., Busby, G., & Huang, R. (2017). Special interest tourism: Concepts, contextsand cases. Dublin, Ireland: CABI.Al-Hamarneh, A. (2008). Islamic tourism: A long-term strategy of tourist industries in theArab world after 9/11. Center of Research on the Arab World. Retrieved fromhttps://www.researchgate.net/deref/http%3A%2F%2Fwww.ceraw.uni-mainz.de%2FBikramjit, R. (2014). Islamic perspectives on marketing and consumer behavior: Planning,implementation, and control. New York, NY: IGI Global.Bourgeois, N. (2016, September 14). Islamic tourism: Much more than the pilgrimage toMecca. In Focus. Retrieved from https://infocus.wief.org/islamic-tourism-much-pilgrimage-mecca/Demir, O., & Toprak, M. (2004). Anatolian tigers or Islamic capital: Prospects andchallenges. Middle Eastern Studies, 40(6), 166-188.Eddahar, N. (2016). Muslim friendly tourism branding in the global market. Organization ofIslamic Cooperation. Retrieved from https://www.oic-oci.org/docdown/?docID=1827&refID=1071Elaziz, M., & Kurt, A. (2017). Religiosity, consumerism and halal tourism: A study ofseaside tourism organizations in Turkey. Tourism, 65(1), 115-128.El-Gohary, H., Edwards, D., & Eid, R. (2017). Global perspectives on religious tourism andpilgrimage. New York, NY: IGI Global.Firdausi, I., Marantika, S., Firdaus, Z., & Sajidah, R. (2017). Lombok: Halal tourism as a newIndonesia tourism strategy. 4th Conference on Humanities, Social Sciences andEducation. Retrieved from http://heaig.org/images/proceedings_pdf/H0317447.pdfHashim, N., Shariff, N., Mahamood, S., & Bhari, A. (2018). Proceedings of the 3rdInternational Halal Conference. Berlin, Germany: Springer.Henderson, J. (2009). Islamic tourism reviewed. Tourism Recreation Research, 32(2), 207-212.Kozak, M., & Kozak, N. (2015). Destination marketing: An international perspective.London, UK: Routledge.Mattison, T. (2018, 9 September). How are young Muslims boosting the halal tourismindustry? Euronews. Retrieved from https://www.euronews.com/2018/09/07/how-are-young-muslims-boosting-the-halal-tourism-industryRaj, R., & Griffin, K. (2017). Conflicts, religion and culture in tourism. Dublin, Ireland:CABI.Reiter, Y. (2008). Jerusalem and its role in Islamic solidarity. Berlin, Germany: Springer.Scott, N. (2010). Tourism in the Muslim world. London, UK: Emerald.Shirazi, F. (2016). Brand Islam: The marketing and commodification of piety. Austin, TX:University of Texas Press. Strategic roadmap for development of Islamic tourism in OIC member countries. (2017).Organization of Islamic Cooperation. Retrieved from https://www.oicoci.org/docdown/?docID=1777&refID=1071 US Congress. (2009). Exploring the nature of Uighur nationalism. Washington, DC: USCongress.
The Potential Relationship between Foodborne Illness and Restaurant Inspection Result...
Shenghao Lavender Zhang

Shenghao Lavender Zhang

September 12, 2020
In New York City, cultural diversity has promoted the growing number of restaurants. However, food sanitation has always been a concern for public health. The project focuses on discovering whether violation results from restaurants inspections would have any strong correlations with food poisoning. Restaurants inspection results from DOHMH and 311 complains are used and analyzed through random forest ensemble learning method. The results indicate that violations found in food sourcing and restaurant facility design have stronger correlation than other factors regarding foodborne illness incidents. 
Tracing the untraceable: AI network inference for the dark web and crypto privacy coi...
Percy Venegas

Percy Venegas

December 04, 2018
IntroductionOn prepared testimony to the House of Representatives Committee on Financial Services, the Secret Service stated that "Digital currencies have the potential to support more efficient and transparent global commerce and to enhance U.S. economic competitiveness. However, because digital currencies continue to be used to facilitate illicit activity, law enforcement must adapt our investigative tools and techniques \cite{services}". Despite the forensics angle on most investigative tools, applied science can also provide support in the form of early warning systems. Here we describe the algorithmic components for a suite of tools that detect patterns on user behavior, that can inform the authorities where to perform a network intervention. The end product has the form of an education project: a source of information with those tools and datasets. We seek to evolve AIs that can learn what is important to humans. The optimization objective is to minimize error while keeping complexity manageable: we do not seek to eliminate the error (that will model noise as signal, and introduce overfitting). For practical purposes, there is a level of error we can live with, and there are also limits to human cognition (e.g. how many variables we can think of at the same time, and how many variable relationships). Ultimately, we want AIs that can gain situational awareness in the way humans do. Network inference \cite{Tieri_2019} is the discipline concerned with the dynamic modeling of biologicals networks and has been approached with the use of machine learning \cite{Spirtes_1993}  and non-linear modeling techniques (Oates 2012). Using the biological metaphor as inspiration, we use a genetic programming approach. We focus on "inferential sensors" in the points of interest to preserve the integrity of the financial system, the applications include prevention of investment fraud, computer hacking/ransomware scams, identity theft. Inoculation The key idea is that it is easier to cure people in the early stages of infection -influence human behavior, and, prevent machines to learn bad habits. Those users who conduct dark web-related activity in the regular web are still "newbies" (otherwise they would be in the dark web already), and therefore they are more susceptive to an intervention to modify their behavior. Data types The following use cases are based on blockchain and web panel datasets only. At this stage, we use global data and daily time granularity, although detail for specific countries, major US metro areas, and intraday sampling is possible. Those data points can be augmented with government intelligence (e.g. geodata), and/or dark web clickstream datasets, when available. Use cases In the following cases, we symbolically regress TOR browser downloads and cryptocurrencies price action on several real-world time series to find relationships regarding aspects such as deterioration of trust in the traditional financial system \cite{Venegas_2018}, the rise of some types of cyber crimes, among others. The modeling method is genetic programming. As a follow-up step, we investigate causation using several signal processing and AI techniques. 
Mapping the Vulnerability to Flooding of Community-Development Corporations (CDCs) Af...
Veronica Olivotto
Eddy Almonte

Veronica Olivotto

and 1 more

November 17, 2020
New York City’s affordable housing stock is vulnerable to coastal flooding under current and projected climate scenarios. Flood vulnerability in this study, was intended as a factor of the exposure of affordable housing units to current and future floodplains as well as topographical elevation. Variables of socio-economic vulnerability included median household income by census tract, expiring affordability of rent-subsidized housing, and East Harlem’s most recent rezoning . The affordable housing in question is owned by two community-development corporations (CDCs) of the Northern Manhattan Collaborative (NMC), Hope and Ascendant based in East Harlem. Using GIS software and publicly available data from NYC Open Data and Mapluto, large scale mapping was conducted at the Borough-Block-Lot (BBL) scale to understand the exposure to coastal flooding of 101 properties owned by Hope and Ascendant, as well as a Hotspot Analysis of all the remaining units included in the NMC (48 more properties). Results show that Hope properties may flood more than Ascendants', under both current and future floodplain projections. A contributing factor is topographical elevation, where Hope Properties are at lower median elevation (13.2 feet) than Ascendants' (29 feet) and also lower than the median elevation of both Central (22 feet) and East Harlem (15 feet). Results from the hotspot analysis shows that 20 of Hope Properties fall within Hot clusters of socioeconomic vulnerability, as well as 5 of Ascendant Properties. Overall the NMC Properties show a higher socioeconomic vulnerability than all the properties in East Harlem. This result is important considering that New York City’s stock of affordable housing hosts some of the most vulnerable populations in the city, with less ability to move elsewhere before or after a flooding event.
Compton Effect
Forrest Bullard

Forrest Bullard

December 12, 2020
IntroductionIn this experiment we will explore the particle nature of light. In particular we will see that scattered photons have less energy than unscattered photons in accordance with the same equations that can be used in classical elastic collisions. In general we will show that this collision conserves both energy and momentum.MathTo derive the equation necessary to model Compton scattering we will need to use both conservation of energy and momentum.  Conservation of momentum shows us that the initial momentum of the incoming photon  \(\vec{p_1}\) is equal to the final momentum of the photon  \(\vec{p_2}\) plus the momentum of the electron  \(\vec{p_e}\) .
Multi-strain disease dynamics on metapopulation networks
Matthew Michalska-Smith

Matthew Michalska-Smith

and 4 more

October 28, 2022
A much-updated version of this work is now available published open-access at Scientific Reports: https://www.nature.com/articles/s41598-022-12774-5Many pathogens have clusters of variation in their genotypes that we refer to as strain structure. Importantly, when considering related pathogen strains, host immunity to one strain is often neither independent from nor equivalent to immunity to other strains. This partial cross-reactive immunity can thus allow repeated infection with (different strains of) the same pathogen and shapes disease dynamics across a population, in turn influencing the effectiveness of intervention strategies. To better understand the dynamics governing multi-strain pathogens in complex landscapes, we combine two frameworks well-studied in their own right: multi-strain disease dynamics and metapopulation network structure. We simulate the dynamics of a multi-strain disease on a network of populations connected by migration and characterize the joint effects of disease model parametrization and network structure on these dynamics. We find that the movement of (partially) immune individuals tends to have a larger impact than the movement of infectious individuals, dampening infection dynamics in populations further along a chain. When disease parameters differ between populations, we find that dynamics can propagate from one population to another, alternatively stabilizing or destabilizing destinations populations based on the dynamics of origin populations. In addition to providing novel insights into the role of host movement on disease dynamics, this work provides a framework for future predictive modelling of multi-strain diseases across generalized population structures.
Will crypto prices recover?   
Percy Venegas

Percy Venegas

November 25, 2018
Market observers tend to use price action as a reference point to assess the likelihood of future movements.  So inevitably, the current regime will be compared to the exuberant period of December of 2017, when bitcoin prices peaked at around 20.000 in USD terms. And much is being said about market manipulation using the facilities of cryptocurrency in exchanges-- what is less evident, is the actual behavior of investors before a price movement occurs. What we learned after studying daily user activity at thousand of the services that crypto investors used, and the sources of information they were exposed to, during 2017 and 2018 is that there is a boundary after which prices become unpredictable.  And, wittingly or unwittingly, the operators of some of these services had the power to manipulate markets without even be present at the exchanges-- just by hacking attention.       We begin by looking at user behavior at a mining pool with several million users, one of the largest players. Miners are key stakeholders in the crypto ecosystem (with an above average degree of sophistication among market participants), each click they make is a tell.     
Tools in ioChem-BD for Studying Chemical Reactivity: Nickel-Catalysed Borylation of C...
Ana Mateo
Moisés Álvarez

Ana Mateo

and 2 more

August 28, 2019
This manuscript reports a DFT based study on the reaction mechanism of the borylation reaction of aryl fluoride assisted by a nickel catalyst and a base, and the kinetic modelling  of such process. The presence of the base modifies the classical cross-coupling reaction mechanism, by activating the diboron and promoting a boryl transfer reaction. Off-cycle reactions, such as some bis-phosphine/mono-phosphine equilibria showed large effects on the overall kinetics. Data publicly available within the ioChem-BD databases is integrated straightforwardly into the manuscript. We also show how the ioChem-BD Reaction Energy Profile Reports tool can be used for daily work and for accelerating catalyst discovery studies. 
Review: "CoRR — The Cloud of Reproducible Records"
Fernando Chirigati

Fernando Chirigati

November 19, 2018
This is a review of manuscript CiSESI-2018-02-0016 submitted to Computing in Science & Engineering: "CoRR — The Cloud of Reproducible Records" (Congo, Traoré, Hill and Wheeler, 2018).OverviewThe paper presents CoRR (Cloud of Reproducible Records), a Web platform for storing and managing records from different tools that create snapshots of computational environments for reproducibility purposes. The authors refer to these tools as CVC (Computation Version Control) tools. In a nutshell, these tools capture the state of the environment in which computational environments are run (e.g.: OS and hardware information, library dependencies, system variables, etc.), in addition to the code and the data. Examples of CVC tools include Sumatra, ReproZip, and CDE. The authors argue that CVC tools are facing major issues in adoption, and that one of the main reasons is related to the lack of a Web interface for sharing and managing CVC records (similar to what GitHub or BitBucket do for SVC tools). CoRR was designed to fill this gap and to facilitate the integration among these tools by providing a common management platform.A common platform for these tools is indeed interesting and useful for reproducibility. However, the contributions of the manuscript are still not clear. More details are provided in the next section, but here is a summary of the main issues: The differences between CoRR and existing data repositories need to be made more clear. The name CVC is misleading.The way that the metadata is stored in the platform is not clear.Diffs in the platform are manual rather than automatic, and there is no discussion on the challenges related to these diffs.Related work about provenance, workflows, and repositories are missing.My recommendation is "Author Should Prepare A Major Revision For A Second Review".Detailed ReviewI should note that I tried to get access to the platform, but I wasn't able to (no confirmation email was sent as of yet). I also tried to use the search feature in the main Website, but it keeps loading after pressing the return key and no results are returned.1. The differences between CoRR and existing data repositories need to be made more clear.CoRR is a repository of computation records. But what makes it different from other data repositories? This is still not clear to me.It seems that one of the main benefits of CoRR is the ability of exposing the metadata that the CVC tools capture, and allowing these to be queryable. For instance, in a regular data repository, if I want to search for projects that used scikit-learn, I would only be able to find such information if it were present in the description of the artifacts. On the other hand, in CoRR, one could make this information automatically available for querying, since tools like Sumatra or ReproZip capture such dependencies.Are these metadata indeed queryable in CoRR? If yes, this is a major benefit and should be made more explicit in the paper. In general, the paper would benefit from a section where authors explicitly discuss the main differences between CoRR and existing data repositories when it comes to CVC tools, i.e., why would someone choose to use CoRR and not any of the existing repositories?2. The name CVC is misleading.CVC stands for Computation Version Control, but neither ReproZip nor CDE do version control: they do create a snapshot of the computation, but they do not have a mechanism for version control. The authors seem to be referring to tools that capture provenance related to the computational environment, but not necessarily that provide version control, so the nomenclature should be changed.3. The way that the metadata is stored in the platform is not clear.The section "Adaptive and Open Database Model" was not clear enough to me. How are different metadata (from different tools) stored in a single data store? The authors do present the MongoDB's models, but there are no details on how different metadata are integrated into a single model. And why not use some representation like PROV (https://www.w3.org/TR/prov-primer/) for integrating the models?4. Diffs in the platform are manual rather than automatic, and there is no discussion on the challenges related to these diffs.At the end of the paper, the authors discuss the concept of diff as a way to tell whether a computation X is a replicate, a repeat, or a reproduction of a computation Y. This is a really cool feature, but it looks like users in CoRR need to define such diffs manually, which is certainly not scalable when dealing with hundreds of computations. Automatically figuring out if two computations are similar in terms of reproducibility is challenging, in particular if they were captured by different tools. But this is certainly a very useful feature for a repository such as CoRR. I was expecting at least a more detailed discussion about this.5. Related work about provenance, workflows, and repositories are missing.Capturing provenance from computations is certainly not a novel topic, and some references are missing. Authors should acknowledge scientific workflow management systems (e.g.: Taverna \citep{Missier_2010}, Kepler \citep{Ludascher:2006:SWM:1148437.1148454}, and VisTrails \citep{vo2011}), since they are known for capturing provenance from experiments \citep{Davidson_2008} \citep{Freire_2008}. In terms of representing provenance information, the authors should take a look at PROV (https://www.w3.org/TR/prov-primer/). There are also other tools that capture provenance from computational environments: although some might not be widely adopted, it is worth mentioning them. These are: PTU \citep{pham}, CARE \citep{Janin_2014}, Arnold \citep{186206}, and noWorkflow \citep{Murta_2015}.I  also recommend taking a look at the related work section of these papers to see if there are additional relevant references as well.Finally, since CoRR is a repository, it is important to acknowledge existing collaborative data repositories, e.g.: Dataverse, figshare, OSF, etc. Again, as I mentioned before, it is important to provide a detailed comparison against these repositories.Additional CommentsThe authors mention in the Introduction that the lack of a platform for storing and managing computation records is probably one of the main reasons for the slow adoption of CVC tools. However, there is no evidence for that. Is there any reference or further study that the authors can provide to back this up? The motivation is not clear.There are other tools (including noWorkflow) supported by CoRR (Figure 3). Why aren't these tools mentioned in the paper?Using forked repositories from the existing tools might not be ideal. It might be hard to keep updating these repositories as the original ones keep changing. For instance, a user might need the latest features of Sumatra, but the CoRR-related Sumatra repository might be a few commits behind. Are there any thoughts on that? Why not just have a standalone CoRR software that reads project information from Sumatra / ReproZip / CDE and uploads data to the platform?Disclaimer
Lecture 11 - Laser fundamentals
Fred Jendrzejewski

Fred Jendrzejewski

November 20, 2018
We will study some basic properties of the laser.
Lecture 10 - Propagation of light in dielectric media
Fred Jendrzejewski

Fred Jendrzejewski

November 14, 2018
In this lecture we will study the propagation of light through a dielectric medium like atomic gases. We will see that it is characterized by the susceptibility and discuss the case of two-level atoms. This sets the stage for the laser.
Live-streamed preprint Journal Club on "EMT network-based feature selection improves...
Daniela Saderi, Ph.D.
Dariusz Murakowski

Daniela Saderi, Ph.D.

and 1 more

December 21, 2018
This is a review of the bioRxiv preprint "EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma" by Borong Shao, Maria Bjaanæs, Åslaug Helland, Christof Schütte, Tim Conrad, doi:10.1101/410472. This review was compiled from a discussion during the live-streamed Bioinformatics preprint journal club as part of an Open Access Week effort organized by the PREreview team and PLOS. Event details can be found here, and the collaborative Etherpad showing all the journal club notes can be found here.In addition to those named as authors above, the participants who wished to be acknowledged for their contributions to this review are as follows: Samantha Hindle, Paul Goetsch, and Bradly Alicea.
Risk scoring for non-bank financial institutions
Percy Venegas

Percy Venegas

November 25, 2018
We propose a method to assess the risk of dealing with non-banking financial institutions that utilizes data mining, machine learning, and, historical proxies of KYC (Know Your Customer) screenings. The risk scores are suitable to evaluate both traditional money services businesses and Fintech companies (including cryptocurrency payments and blockchain infrastructure operators). The main users are banks and businesses worldwide that need to assess counter-party risk under uncertainty, as non-banks are often less regulated than other financial institutions.
Fascinating things to do for tropical tree forest recovery 
Yuri Jorge Peña-Ramirez
Lauren Nelson

Yuri Jorge Peña-Ramirez

and 2 more

February 05, 2020
Forest recovery in degraded landscapes is key to mitigating climate change. Reforestation efforts have been successful in temperate environments, partly due to the limited number of tree species found in those ecosystems (i.e.contrast is, Therefore, up to five species). In contrast, tropical forest reforestation is to date, practically impossible due to the huge biological diversity they harbour. The Maya forest in Campeche, Mexico is estimated to contain 300 to 600 tree species. Hence, each species has a low density within a highly diverse matrix.  Biological diversity of trees is maintained by a very complex network of interactions that scientists are starting to understand. One such interaction is related to how trees choose their partners. Yes, they do that. DNA progeny tests indicate that tropical trees are very promiscuous. In a single season, a Tabebuia rosea understand.  (maculís in Mayan) tree can mate with hundreds of other individuals. Due to the low density in population, pollen (and pollinators) must find a way to connect with other individuals diluted among many other species. Moreover, some individuals are more liked by the community. How do we determine this? DNA from certain individuals is more frequently found in seeds from several trees in a region. Knowing this, what would happen if this particularly "attractive" individual was eliminated? We have to consider these "attractive" individuals as a priority for conservation. However, the "attractive" trees do not necessarily fit the timber industry's parameters. Commercial foresters look for tall, straight trees to produce first-class table cuts. Classic silviculture procedures are totally anthropocentric, ignoring trees mating preferences. As a consequence, tree breeding is complicated as trees may not mate with man-selected individuals, lowering seed production. When a commercially selected plantation is established near a natural forest, the "attractive" individual in the landscape may be overwhelmed by the huge amounts of pollen produced by plantations, contributing to loss of genetic diversity. Fortunately, for the maculís in Campeche, Mexico, foresters seed source was as diverse as the natural populations. DNA from "attractive" individuals was found in the same frequency both in plantations and in natural populations \citep{m2016}. An educated propagation protocol for methods that avoid the risk of loosing "attractive" individuals (or their genes), must be based on the development of an Ideotype. This is an ideal imaginary tree which meets timber industry quality parameters, agronomic traits, and considers the species mating system. A tree that meets industrial, agronomic and biological expectations would, for instance be: straight, tall, fast-growing, pest-resistant, drought-tolerant (to face climate change), "attractive" for other trees, and so on. With knowledge of this desired ideotype, we can look into natural populations which are closer to the ideotype. Employing ideotype-based selection enables us to identify several elite maculis trees in the Maya forest \cite{Sol_s_Guill_n_2017}.  Seed or vegetative collection of materials must be performed to capture genetic diversity, representing at least 90% of the natural genetic diversity of close natural populations. Once the germplasm (i.e. a collection of seeds or parts of the trees) has been sampled, it could be propagated vegetatively. Once plants, we are able to use them for buds and cuttings. In the lab, this ability can be turbo-powered by techniques of tissue culture called micropropagation and somatic embryogenesis. Both tools use plant growth regulators which are added to a nutrient-rich medium, acting as artificial soil. These conditions are optimal and can change the inner programming of tree tissues, switching them to a highly proliferative path, resulting in multiple sprouts from a single piece of tissue. In our group, we focused on another tropical tree: Cedrela odorata (or cigar box Spanish red cedar), another native tree from Mesoamérica. Starting from twigs or seeds from adult trees that had been previously selected with the help of the ideotype, a process for the clonal propagation for this species was established \cite{Pe_a_Ram_rez_2010} \cite{Pe_a_Ram_rez_2010a}. With this tool, thousands or millions of trees can be produced, propagating not only trees but genetic diversity and clones that are able to fit industry quality parameters.  A surprising advantage of using tissue culture, is the ability to induce a rejuvenation process in the tissues. Remember Dolly the sheep? Dolly was a cloned sheep borns old, who carried markers in her DNA (i.e. epigenetic markers) that instruct the body to adopt the age of the donor sheep. Epigenetic markers in the DNA of trees also limit adult tree propagation. Frequently, it is hard to establish twigs that have come from mature trees as individual plants or derived trees, did not develop as a young tree; they remain "vintage". Epigenetic markers are naturally reset from adult to young at the moment of fecundation (i.e.this grown, proliferated tree native to Meso américa : cedar). with born "old", carrying instructed Often "adult" "young" Reserve the plants.  when pollination occurs for trees), but it is also feasible to reset the program employing plant tissue culture combined with grafting mature tissues over young ones. Subsequent rounds of grafting eliminate epigenetic markers linked to adult behaviour such as flowering, or lateral instead of vertical growth. By taking advantage of this technology, we were able to colones and propagate mature elite trees from the Calakmul Biosphere Reserve, in the Maya forest, inducing juvenile traits on derived plantlets. We are currently focused on refining our protocols for scaled-up production of plants. When a planter ventures into silviculture, plant material is paramount as trees are a long-term investment. It is beneficial to have superior quality material derived (i.e. cloned) from strictly selected donor trees with juvenile traits, for fast growth and genetic diversity. This will contribute not only to the economic return, but increasing the resilience of plantations to adverse environmental conditions as a consequence of climate change. Successful plantations will satisfy the market demand, reducing the pressure on natural forests.
Citibike Analysis: Comparing ridership during and after the month of January
vaidehi thete

vaidehi thete

November 10, 2018
AbstractThe aim of the project was to analyse how ridership changes from the month of January to February. Many people take up biking as a mode of exercise to fulfil their New Year resolutions of staying healthy. If there is a trend which proves our hypothesis, then Citibike can incentivize the riders to continue using bikes and help them stick to their resolutions.Hypothesis Description:
Citibike and Gender Trip Duration
Alia Kasem
Lina Kasem

Alia Kasem

and 1 more

February 16, 2022
This analysis will be focusing on Citibike ridership in terms of total trip duration based on male and female usage per miles and minutes. The study data period for this project from January 2016 to December 2016. The data explore the trip duration for citibike. The Null Hypothesis, the female duration is higher or equal to the male trip. The analysis relied on uses the T-testing as a statistical method to test the two means of samples.
Review: "CoRR — The Cloud of Reproducible Records"
Andrew P. Davison

Andrew P. Davison

November 03, 2018
This is a review of manuscript CiSESI-2018-02-0016 submitted to Computing in Science & Engineering: "CoRR — The Cloud of Reproducible Records" (Congo, Traoré, Hill and Wheeler, 2018). OVERVIEW While a number of tools have been developed over recent years for run-time capture of computational provenance artefacts and metadata (referred to in the manuscript as "Computation Version Control" or CVC), such as Sumatra, CDE, Reprozip, recipy and noWorkflow, these tools generally lack an easy way to review and share provenance records through a web-based graphical interface, such as is provided by Github, Gitlab, Bitbucket, etc. for software version control systems such as Git or Mercurial. In some cases, no graphical interface is available at all. In others, the graphical interface runs only locally, and is not accessible over the web. Where web-based tools do exist (example) they are (i) difficult to deploy and (ii) specific to a given provenance capture tool: there is essentially no interoperability between such tools. This manuscript reports on CoRR, a collaborative web platform that aims to solve the limitations outlined above by being easy to deploy (using a modern cloud architecture approach) and by providing a common graphical interface for different provenance capture tools. The manuscript outlines the case for CoRR, briefly reviews Sumatra, CDE and Reprozip, presents the CoRR architecture and interface, then presents a case study of using CoRR together with the three provenance capture tools previously reviewed. CoRR clearly fills an important gap in the landscape of tools for reproducible computational research, and has the potential to expand the usage of run-time provenance capture in scientific computation, just as Github has done for usage of version control systems. The manuscript is a very good fit for the Reproducible Research track of CiSE (Barba _et al._, 2017). As such, the manuscript should be ACCEPTED AFTER MINOR REVISIONS. SUGGESTIONS FOR IMPROVING THE MANUSCRIPT. Terminology While almost everyone agrees on the need to distinguish "repeatable", "reproducible" and "replicable", there is considerable disagreement over what each term refers to (Plesser, 2018). While your use of terms seem to be largely consistent with one of the more widely used conventions, to minimize confusion it would be desirable to cite a source for your definitions (e.g. Fabien _et al._, 2018, although there are many others). The term "computational provenance" seems to be well established for what is called "CVC" in the manuscript. Rather than coining a new term, I suggest reusing the existing one. This will better integrate the article into the wider literature on this topic, and make it easier to find through search engines. Structure Overall, I think the manuscript is well structured. However, I think there is a lack of balance between the sections: - The section "The main elements views in CoRR" seems unecessarily detailed, describing toolbox actions with a level of detail appropriate for a user manual, but not for a CiSE article. - The manuscript has almost no information on the REST API. While it would not be appropriate to give detailed documentation, some examples of the REST endpoints and the document format(s) used would be helpful. - The machine learning examples used in the case study are described in considerable detail, but this information is then hardly used in the rest of the manuscript; I think this session could be considerably shortened. - The "Results" section is very minimal; I would expect at least to see some screenshots of how the different records are represented in CoRR. In addition, the "Reproducibility Effort" is not well explained; the phrase "is the tool representation directly reproducible after a download from CoRR" does not give me a clear idea of what steps are involved. Inaccuracies and missing references - _"Sumatra (created in 2009), CDE (created in 2010) and ReproZip (created in 2013) are some of the most used CVC tools."_ What is the source for the assertion that these are among the most used tools? Do you have any numbers for this? - There is a web-accessible API and web UI for Sumatra, "sumatra-server", separate from Sumatra's internal, local web-browser UI. This does support dissemination of records and multiple users. However, it is not widely used and is not interoperable with other provenance capture tools. - It is not true that _"Sumatra makes copies of the output files only if placed in a folder named Data."_ Sumatra does not make copies by default (only if the "archive" option is used), rather it stores the file system path or URL together with a hash of the file contents. It is also not necessary to use a specific folder name, this is fully configurable ("Data" is just the default). Language/style There are frequent minor grammatical errors and some typos (e.g. "ReroZip", "CORRR"). I recommend that all co-authors carefully re-read the manuscript to correct these. Style issues: - Please spell out "OS" in the introduction. From the context, it becomes clear that it means "operating system", but the abbreviation is also often use for "open source". - The sentence _"The uncovering of recent frauds, irreproducibility facts and concerns from major journals publications, have enforced new requirements in scientific results corroborations"_ is hard to understand. What are _"irreproducibility facts and concerns"_? What are _"major journals"_? Who is doing the enforcing? - _"We refer to these software and services as CVC tools"_. The antecedent of this sentence is three sentences earlier, which makes it hard to understand what is being referred to. - It is not usual in a scientific context to explicitly use titles, as in "Dr Rosebrock". I think it would be more appropriate to use the name of the book and the author's surname the first time the book is cited, and then use just the surname ("Rosebrock") subsequently. Discussion of existing literature In the context of interoperability, which is one of the main benefits of CoRR, the authors should discuss previous efforts to enable interoperability of representations of computational provenance, such as the ProvONE data model, which builds on the W3C PROV standard. Would it be possible to support PROV-compatible representations (i.e. some form of RDF) through the CoRR API? DISCLAIMER For the sake of transparency, it should be noted that I am the principal developer of Sumatra, one of the software tools reviewed in the manuscript and used in the case study. REFERENCES Lorena A. Barba & George K. Thiruvathukal (2017). Reproducible Research for Computing in Science & Engineering. _Computing in Science & Engineering_ 19:85–87. http://doi.org/10.1109/mcse.2017.3971172 Plesser, H. E. (2018). Reproducibility vs. replicability: A brief history of a confused terminology. _Frontiers in Neuroinformatics_ 11:76. https://doi.org/10.3389/fninf.2017.00076 Fabien C. Y. Benureau, Nicolas P. Rougier (2018). Re-run Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions. _Frontiers in Neuroinformatics_ 11:69. https://doi.org/10.3389/fninf.2017.00069
PREreview: Systems analysis by mass cytometry identifies susceptibility of latent HIV...
Ibraheem Ali
marielle.cavrois

Ibraheem Ali

and 2 more

October 31, 2018
Review authored by Marielle Cavrois, Nadia Roan, and Ibraheem AliGladstone Institute of Virology and ImmunologyUniversity of California San FranciscoThis is a journal club review of Systems analysis by mass cytometry identifies susceptibility of latent HIV-infected T cells to targeting of p38 and mTOR pathways. Fong et al. 2018. bioRxiv doi: https://doi.org/10.1101/371922  Fong and colleagues present a very interesting study investigating signaling pathways and biomarkers that are dysregulated in cells exposed to HIV-1. Using a combination of mass cytometry and pharmacological approaches, the authors find that HIV-1 exposed cells are sensitized to cell death caused by T cell activation through disruption of the p38 and mTOR signaling pathways, and then demonstrate that ex vivo treatment of cells from ART-suppressed HIV-infected individuals with drugs targeting these pathways can decrease the proportion of latently-infected cells. This study is of importance as finding ways to therapeutically eliminate latently-infected cells is needed. Major Comments: Use of CyTOF to study the intracellular signaling pathways elicited during HIV infection is a valuable approach to identify novel ways to target HIV-infected cells therapeutically. Targeting intrinsic cell death pathways in latently-infected cells is an exciting approach to try to eliminate the persistent reservoir. However, since the majority of the experiments conducted were in vitro, and many in vitro models of HIV latency exist, the paper would benefit from a more thorough explanation and justification of this particular model of HIV latency. For example, Figure 1A could have more clearly delineated the experimental timeline of infection and stimulation (e.g., illustrating the fact that two rounds of stimulation were used: one to render cells permissive to infection, the second to reactivate latent cells). This would have been more helpful than images depicting the barcoding and cytof methodology, which could be described in the methods section. Furthermore, it should be acknowledged that the HIV-exposed cells consist of 3 cell populations: those that are productively infected, those that are latently infected, and those that are exposed but remain uninfected (broadly termed “bystander cells”, which can include both cells that fused to virus as well as those that did not). It is important to note that when the authors restimulate the HIV-exposed population of cells, they are restimulating a mixed population of these 3 populations, which can interconvert (e.g., p24- can become p24+). (As a side note, the cells should be called p55Gag – vs. +, since intracellular Gag is not p24). This, along with the fact that p24- cells may be predominantly bystander cells and not latently-infected cells, makes it difficult to assess how specific the identified signaling pathways are for latent cells. Also, the authors should clarify why they used different sets of subpopulations in different sections of the paper: sometimes, analysis was performed on the bulk population of HIV-exposed cells, other times on gated populations of p24+ vs. p24- cells.One valuable tool that exists in the field are the so-called dual-reporter viruses, that distinguish between latently- vs. productively-infected cells, \cite{Battivelli2018,Calvanese2013}. The in vitro part of the study could be markedly strengthened by validating the main results through use of such a system, or another system where a pure population of latently-infected cells can be obtained. One of the main readouts the authors used for sensitization to cell death in HIV exposed cells was Cleaved Caspase 3 (CC3). It would have benefitted the reader to have seen the gating strategy leading up to the population of cells that did or did not express CC3. In particular, it is important to know whether cells were gated from the live population as assessed by a viability dye, since dead/dying cells tend to be non-specifically sticky to antibodies.  Additional markers of cell death would have also been valuable in the FACS and CyTOF analyses. DREVI appears to be a powerful tool to infer associations and identify signaling pathways in play, but as many are not familiar with the nature of this analysis tool, a more thorough explanation of how it works, how it should be interpreted, and how it reveals insights that couldn’t be deciphered from the original datasets, would be helpful. Additional Comments:Regarding Figure 1B, were the productively-infected population pre-gated on the CD4- cells? (since HIV downmodulates CD4 upon productive infection)  Regarding Fie. S1E, are all the position Gag+ cells also expressing TAT?  On a minor note, the text Page 5 line 8 should be edited to read Figure 1B There appears to be overlap between the populations labeled as Uninfected (UI), Exposed-Uninfected (EU), and Latent Infected (LI) (Fig. S2, Fig. 2D-F). As indicated above, the LI contains many bystander cells, a fact that should be taken into consideration during the analysis. What is the advantage of analyzing the data in the way presented in Fig. 2E-F over the methods shown in Fig. 2C? Could the authors give their thoughts as to why p-S6 is only upregulated in only a subset of actively infected cells? In Figure 3E it would have been helpful to have known how many donors were used for each of the conditions in these experiments. In Figure 5 the authors should comment on the dosage of ganetespib and INK128 used and whether these concentrations are those that can be achieved in vivo, and the extent to which these doses were cytotoxic. Cell viability info would have been particularly helpful for Fig. 5 G-H since it appears that the treatment preferentially kills latently infected cells. It is important for the reader to know what is the extent of cell death observed after the 3 days of treatment with ganetespib, INK128, or a combination of the two. The authors could also comment on whether pre-treatment with ganetespib and INK128 might affect the ability of cells to be effectively stimulated by PMA/ionomycin as done in TILDA, since these treatments may target similar pathways? On a minor note there is no panel J in Figure 5 (see text page 14). 
Keunggulan Karakter Yusuf
Saortua Marbun

Saortua Marbun

October 25, 2018
Yusuf patut dijadikan model dalam pengembangan sumber daya manusia masa kini. Menjadi model dalam arti dapat diteladani, ditiru. Yusuf adalah sosok yang beriman, berilmu dan berakhlak mulia. Kompetensinya dapat diandalkan dalam memberi kontribusi positif bagi kehidupan yang ada di sekitarnya. Kualitas unggul yang dimilikinya berbeda dengan saudara-saudaranya dalam berbagai aspek. Yusuf diakui bahwa ia dipenuhi Roh Tuhan, cerdas dan berperilaku seperti Yesus Kristus. Menurut Alkitab, “Tetapi TUHAN menyertai Yusuf, sehingga ia menjadi seorang yang selalu berhasil dalam pekerjaannya; maka tinggallah ia di rumah tuannya, orang Mesir itu.  Setelah dilihat oleh tuannya, bahwa Yusuf disertai TUHAN dan bahwa TUHAN membuat berhasil segala sesuatu yang dikerjakannya, maka Yusuf mendapat kasih tuannya, dan ia boleh melayani dia; kepada Yusuf diberikannya kuasa atas rumahnya dan segala miliknya  diserahkannya pada kekuasaan Yusuf. Sejak ia memberikan kuasa dalam rumahnya dan atas segala miliknya kepada Yusuf, TUHAN memberkati rumah orang Mesir itu karena Yusuf, sehingga berkat TUHAN ada atas segala miliknya, baik yang di rumah maupun yang di ladang. Segala miliknya diserahkannya pada kekuasaan Yusuf, dan dengan bantuan Yusuf ia tidak usah lagi mengatur apa-apapun selain dari makanannya sendiri. Adapun Yusuf itu manis sikapnya dan elok parasnya.” (Kejadian 39:2-6)             Perlu dijelaskan bahwa konteks ayat-ayat tersebut adalah Yusuf seorang budak belian yang bekerja di rumah Potifar, tuannya. Ia dinyatakan berhasil dan menjadi kepercayaan bagi tuannya. Yusuf menampilkan performa kerja dengan kecerdasan yang utuh berimbang, berintegritas, bertaqwa dan sanggup mengalahkan godaan. Ketika Yusuf difitnah dan dipenjarakan, Yusuf pun mampu mempertahankan kualitas personal dan kinerjanya mendapat pujian dari kepala penjara. Iman dan karakternya tidak luntur meski dia mengalami penderitaan sejak ia dijual oleh saudara-saudaranya, dipekerjakan sebagai budak hingga ia dijebloskan ke dalam tahanan. Alkitab mencatat bahwa di penjara, Yusuf menolong mengartikan mimpi rekannya. Bahkan pada saat Yusuf dipromosikan oleh Firaun menjadi pejabat di Mesir mutu karakternya tidak merosot.   Alkitab mempertegas, “Sementara itu Yusuf telah menjadi mangkubumi di negeri itu; dialah yang menjual gandum kepada seluruh rakyat negeri itu. Jadi ketika saudara-saudara Yusuf datang, kepadanyalah mereka menghadap dan sujud dengan mukanya sampai ke tanah.” (Kejadian 42:6) “Ketika Yusuf telah pulang, mereka membawa persembahan yang ada pada mereka itu kepada Yusuf di dalam rumah, lalu sujud kepadanya sampai ke tanah.”(Kejadian 43:26) “Ketika Yehuda dan saudara-saudaranya sampai ke dalam rumah Yusuf, Yusuf masih ada di situ, sujudlah mereka sampai ke tanah di depannya.”(Kejadian 44:14).  Bagian ini memberi konfirmasi bahwa mimpi Yusuf telah menjadi kenyataan. Meski pun mimpi tersebut pada awalnya tidak mendapat dukungan dari pihak keluarganya, namun kini Yusuf tidak berubah. Kepada saudara-saudaranya, Yusuf berkata: “Tetapi sekarang, janganlah bersusah hati dan janganlah menyesali diri, karena kamu menjual aku ke sini, sebab untuk memelihara kehidupanlah Allah menyuruh aku mendahului kamu.  Karena telah dua tahun ada kelaparan dalam negeri ini dan selama lima tahun lagi orang tidak akan membajak atau menuai. Maka Allah telah menyuruh aku mendahului kamu untuk menjamin kelanjutan keturunanmu di bumi ini dan untuk memelihara hidupmu, sehingga sebagian besar dari padamu tertolong.  Jadi bukanlah kamu yang menyuruh aku ke sini, tetapi Allah; Dialah yang telah menempatkan aku sebagai bapa bagi Firaun dan tuan atas seluruh istananya dan sebagai kuasa atas seluruh tanah Mesir.”(Kejadian 45:5-8)   Yusuf menambahkan pula, “Memang kamu telah mereka-rekakan yang jahat terhadap aku, tetapi Allah telah mereka-rekakannya untuk kebaikan, dengan maksud melakukan seperti yang terjadi sekarang ini, yakni memelihara hidup suatu bangsa yang besar.”(Kejadian 50:20) Keluhuran karakter Yusuf tidak luntur oleh situasi di luar dirinya – meski ia dijual oleh saudara-saudara, dijadikan budak, difitnah lalu dipenjara – hingga ia menjadi orang yang terhormat dan berkuasa – karakter Yusuf konsisten, berakhlak mulia, berilmu, beriman tangguh dan terus memberi kontribusi positif bagi kemanusiaan.(*)\citep*{marbun2017}
Damai Sejahtera Dalam Kebhinekaan
Saortua Marbun

Saortua Marbun

October 25, 2018
Firman Tuhan dalam Perayaan Natal 2017 dikutip dari Kitab Kolose 3:15, "Hendaklah damai sejahtera Kristus memerintah dalam hatimu, karena untuk itulah kamu telah dipanggil menjadi satu tubuh. Dan bersyukurlah." Alkitab versi Bahasa Indonesia Sehari-hari, "Hendaklah keputusan-keputusanmu ditentukan oleh kedamaian yang diberikan oleh Kristus di dalam hatimu. Sebab Allah memanggil kalian untuk menjadi anggota satu tubuh, supaya kalian hidup dalam kedamaian dari Kristus itu. Hendaklah kalian berterima kasih."Kata Yunani 'damai sejahtera' "eirene" dari kata dasar "eiro" yang berarti "satu", utuh, tidak kurang. Kata eirene dalam bahasa Ibrani 'shalom' yang artinya "lengkap, sejahtera, damai, aman, sehat, makmur, tenang, bersahabat - hubungan manusia dengan Tuhan. oleh sebab itu maksud ayat tersebut tidak dapat dilepaskan dari ayat 3:1-4, "Karena itu, kalau kamu dibangkitkan bersama dengan Kristus, carilah perkara yang di atas, di mana Kristus ada, duduk di sebelah kanan Allah. Pikirkanlah perkara yang di atas, bukan yang di bumi. Sebab kamu telah mati dan hidupmu tersembunyi bersama dengan Kristus di dalam Allah. Apabila Kristus, yang adalah hidup kita, menyatakan diri kelak, kamupun akan menyatakan diri bersama dengan Dia dalam kemuliaan."Berdasarkan itu, dipahami bahwa damai sejahtera adalah salah satu faedah keselamatan yang diterima oleh orang-orang yang berdamai dengan Allah. Paulus dalam Filipi 4:7 menulis, "Maka sejahtera dari Allah yang tidak mungkin dapat dimengerti manusia, akan menjaga hati dan pikiranmu yang sudah bersatu dengan Kristus Yesus."(BIS) Dengan demikian, jika kita berseru kepada Allah dari hati yang tinggal di dalam Kristus dan Firman-Nya (Yohanes 15:7), maka damai sejahtera Allah akan membanjiri jiwa kita. Damai sejahtera ini adalah kesentosaan batin yang dibawa oleh Roh Kudus (Roma 8:15-16). Perasaan sejahtera itu meliputi keyakinan yang teguh bahwa Yesus dekat. Damai sejahtera itu memberi rasa yakin yang mendalam bahwa kasih Allah sedang dan terus-menerus bekerja di dalam kehidupan kita demi kebaikan.(Roma 8:28) Kata "memerintah" dalam bahasa Yunani "brabeuo" satu istilah atletik yang masa kini disebut "wasit, hakim pertandingan, juri". Pemegang otoritas "memutuskan" sesuai dengan aturan main. Hati manusia sebagai pusat kendali moral, memerlukan damai sejahtera sebagai juri pengendali. Bila hati dipimpin oleh juri yang bernama amarah, benci, dendam, maka buahnya dapat diprediksi. Sebaliknya, bila hati dipimpin oleh juri yang benar bernama damai sejahtera maka jiwa terasa utuh. Hidup terasa baik-baik saja, sebab damai sejahtera bertakhta di dalam pusat kehidupan.Oleh sebab itu, setiap orang harus menjawab pertanyaan ini secara jujur, "Siapa yang sedang memerintah di dalam hatiku?" Apakah semangat damai -- "sudah, sedang, terus menerus" atau "belum" -- memerintah dalam hatimu? Waspadalah karena hati bisa diduduki oleh 'spirit' politik identitas, eksklusivisme, fanatisme dan kaki tangannya. Hati itu juga dapat dirajai oleh 'spirit positif' berupa rasa sayang, persaudaraan, rasa hormat. Hati manusia sepanjang zaman menjadi arena pergulatan berbagai ideologi. Generasi manusia dibesarkan dengan ideologi yang disemaikan dalam dadanya. Buah perilaku tergantung pada 'raja yang memperhamba hati'. Bila damai sejahtera memimpin hati, maka perbedaan menjadi ramah keharmonisan.\citep*{marbun2018}
OIST PREreview JC - "Disentangling unspecific and specific transgenerational immune p...
maggi brisbin
yuka.suzuki

Maggi Brisbin

and 3 more

November 06, 2018
Disentangling unspecific and specific transgenerational immune priming components in host-parasite interactionsFrida Ben-Ami, Christian Orlic, Roland R. Regoes doi: https://doi.org/10.1101/429498bioRxiv, 9/27/2018Overview and take-home messages:In this study, the authors tackle the topic of transgenerational immune priming in invertebrates. The authors designed a large experiment taking advantage of clonal Daphnia to test whether infecting parental generations with different parasite strains improves the offspring's resistance to that parasite overall and if yes, if they resist that specific strain more effectively than other strains. This experiment essentially tests the specificity of immune priming at a very fine "strain" scale. The results did not support parental infection strain differentially affecting offspring resistance to different strains, suggesting that immune priming is not specific to the strain level in this system. However, a mathematical model the authors developed for that study fits the data exceptionally well, which means this model could potentially be used in a predictive manner for this or similar systems. Additionally, the unexpected result that one strain actually facilitates specific infection in the offspring is surprising and opens the door to additional inquiry and future experimentation. Overall this study is very interesting and well-presented, but there are a few concerns that could be addressed and improved in the next version of the manuscript.
Book  Review: Creativity and Critique in Online Learning: Exploring and Examining Inn...
Saortua Marbun

Saortua Marbun

October 17, 2018
Book Review:Creativity and Critique in Online Learning: Exploring and Examining Innovations in Online Pedagogy Edited by Jacqueline Baxter, George Callaghan, and Jean McAvoy. Switzerland: Springer International Publishing, 2018 (xxiii + 278 pages, ISBN 978-3-319-78297-3, € 109,99) Saortua MarbunSekolah Tinggi Ilmu Ekonomi Triatma Mulya Bali Indonesia  saortuam@gmail.com | http://orcid.org/0000-0003-1521-7694  
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