Miracle-dz/UniFAR-FTUs huggingface dataset:
High GUD Incidence in the Early 20th Century Created a Particularly Permissive Time Window for the Origin and Initial Spread of Epidemic HIV Strains

The processes that permitted a few SIV strains to emerge epidemically as HIV groups remain elusive. Paradigmatic theories propose factors that may have facilitated adaptation to the human host (e.g., unsafe injections), none of which provide a coherent explanation for the timing, geographical origin, and scarcity of epidemic HIV strains. Our updated molecular clock analyses established relatively narrow time intervals (roughly 1880–1940) for major SIV transfers to humans. Factors that could favor HIV emergence in this time frame may have been genital ulcer disease (GUD), resulting in high HIV-1 transmissibility (4–43%), largely exceeding parenteral transmissibility; lack of male circumcision increasing male HIV infection risk; and gender-skewed city growth increasing sexual promiscuity. We surveyed colonial medical literature reporting incidences of GUD for the relevant regions, concentrating on cities, suffering less reporting biases than rural areas. Coinciding in time with the origin of the major HIV groups, colonial cities showed intense GUD outbreaks with incidences 1.5–2.5 orders of magnitude higher than in mid 20th century. We surveyed ethnographic literature, and concluded that male circumcision frequencies were lower in early 20th century than nowadays, with low rates correlating spatially with the emergence of HIV groups. We developed computer simulations to model the early spread of HIV-1 group M in Kinshasa before, during and after the estimated origin of the virus, using parameters derived from the colonial literature. These confirmed that the early 20th century was particularly permissive for the emergence of HIV by heterosexual transmission. The strongest potential facilitating factor was high GUD levels. Remarkably, the direct effects of city population size and circumcision frequency seemed relatively small. Our results suggest that intense GUD in promiscuous urban communities was the main factor driving HIV emergence. Low circumcision rates may have played a role, probably by their indirect effects on GUD.
Multidecadal Indian Ocean Variability Linked to the Pacific and Implications for Preconditioning Indian Ocean Dipole Events

AbstractThe Indian Ocean has sustained robust surface warming in recent decades, but the role of multidecadal variability remains unclear. Using ocean model hindcasts, characteristics of low-frequency Indian Ocean temperature variations are explored. Simulated upper-ocean temperature changes across the Indian Ocean in the hindcast are consistent with those recorded in observational products and ocean reanalyses. Indian Ocean temperatures exhibit strong warming trends since the 1950s limited to the surface and south of 30°S, while extensive subsurface cooling occurs over much of the tropical Indian Ocean. Previous work focused on diagnosing causes of these long-term trends in the Indian Ocean over the second half of the twentieth century. Instead, the temporal evolution of Indian Ocean subsurface heat content is shown here to reveal distinct multidecadal variations associated with the Pacific decadal oscillation, and the long-term trends are thus interpreted to result from aliasing of the low-frequency var.
EnVision , a Vision System for Envirobot

The paper describes EnVision, a vision system created for the Envirobot at Ecole Polytechnique Federale de Lausanne (EPFL)’s BioRobotics laboratory. The project consists of two main tasks. The first is to create some form of visual control, linking input from the cameras to the actuators of the Envirobot. We will primarily be using a biologically inspired feed forward spiking neural network, detailed in the work of Iman Kamali Sarvestani[11]. We will see that a simple network is capable of exhibiting a variety of behaviors depending on how we tune the parameters of the network and its neurons. The second task is to create a functional vision system, defining and prototyping mechanical, electrical and other hardware aspects of the system so that we have a platform upon which we can test our visual model.
Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets

Objective: Build probabilistic topic model representations of hospital admissions processes and compare the ability of such models to predict clinical order patterns as compared to preconstructed order sets. Materials and Methods: The authors evaluated the first 24 hours of structured electronic health record data for > 10 K inpatients. Drawing an analogy between structured items (e.g., clinical orders) to words in a text document, the authors performed latent Dirichlet allocation probabilistic topic modeling. These topic models use initial clinical information to predict clinical orders for a separate validation set of > 4 K patients. The authors evaluated these topic model-based predictions vs existing human-authored order sets by area under the receiver operating characteristic curve, precision, and recall for subsequent clinical orders. Results: Existing order sets predict clinical orders used within 24 hours with area under the receiver operating characteristic curve 0.81, precision 16%, and recall 35%. This can be improved to 0.90, 24%, and 47% (P < 10−20) by using probabilistic topic models to summarize clinical data into up to 32 topics. Many of these latent topics yield natural clinical interpretations (e.g., “critical care,” “pneumonia,” “neurologic evaluation”). Discussion: Existing order sets tend to provide nonspecific, process-oriented aid, with usability limitations impairing more precise, patient-focused support. Algorithmic summarization has the potential to breach this usability barrier by automatically inferring patient context, but with potential tradeoffs in interpretability. Conclusion: Probabilistic topic modeling provides an automated approach to detect thematic trends in patient care and generate decision support content. A potential use case finds related clinical orders for decision support.
History of Anesthesia Patient Safety.

Anesthesia professionals throughout the world should forever be very proud that the concept of “patient safety” as an entity and an organized effort was created and popularized by anesthesia practitioners. “Patient safety” is now a ubiquitous universal term that permeates health care practice in a multitude of ways. Taken in its broadest terms, the idea is today summarized by the World Health Organization (WHO) as follows: “. patient safety is the prevention of errors and adverse effects to patients associated with health care. ” There is a wide array of dedicated organizations, sections of professional societies and health care institutions, regulatory agencies, program initiatives, and investigators, all devoted to patient safety. All these efforts involve serious hardworking and enthusiastic leaders, officials, staff members, and volunteers —nearly all of whom are not aware that, conceptually, patient safety is a specific paradigm that originated in anesthesia practice; it identifies preventable harm caused by medical care and then attempts to prevent it. Credit, praise, and publicity (while, at times, pleasantly reinforcing) are not necessary for the involved anesthesia practitioners and organizations, as well as the entire profession, to have a significant sense of satisfaction from the past, present, and future accomplishments achieved throughout all patient safety efforts. Outlined briefly here is the history of, specifically, anesthesia patient safety, in order for those interested to better understand how it came about, what happened, and where it may be going. Note that this is a complex subject with a lengthy history that could easily fill this entire volume of historical accounts. Each cited reference in this chapter is a window that opens not only to a long list of further revealing references but is also a snapshot of the past that reflects a particular point in the evolution of anesthesia patient safety and its dramatic positive impact on now generations of patients receiving anesthesia care.
Chemical migration in drinking water stored in polyethylene terephthalate (PET) bottles: a source of controversy

Due to its chemical inertness and physical properties PET is particularly suitable for food packaging applications, especially for drinking water. More bottled water is consumed than other bottled beverages. This article is a survey and toxicological investigation of chemical compounds, which are able to diffuse from PET bottles to water. The exact detailed chemical composition of plastic materials is known only from information provided by manufacturers. A declaration of conformity according to EC regulation no.10/2011 is required to ensure the safety of plastic materials in contact with foodstuffs. This regulation established a positive list of monomers and additives which are authorized for use in plastic materials. Some substances are subject to restrictions and/or specifications according to their toxicological data. However, Non-Intentionally Added Substances (NIAS) not listed in this regulation such as breakdown products from monomers and additives and/or impurities found in initial polymerization reactants may be present in a PET bottle wall. Also, recycled PET can be a source of unknown chemical compounds found in water. All these substances may potentially migrate from the PET bottle wall to bottled water. It is well-known that acetaldehyde and antimony are leached from PET bottles. However, several studies have shown the presence of other substances not expected a priori in bottled water, sometimes in non-negligible concentrations. The origin of these compounds has not been clearly established and remains controversial (PET container, cap sealing resins, background contamination, water processing steps, NIAS, etc). Overall, it is difficult to compare the reported results due to the variety of parameters favoring the release of substances (contact time, type of simulant, temperature, sunlight exposure and bottle color). Considering all these difficulties and controversies, further investigations are needed to clearly identify the migration products from PET and to ensure that the consumption of PETbottled water does not involve any health hazards.
The cautious rule of combination for belief functions and some extensions

Dempster's rule plays a central role in the theory of belief functions. However, it assumes the items of evidence combined to be distinct, an assumption which is not always verified in practice. In this paper, a new operator, the cautious rule of combination, is introduced. This operator is commutative, associative and idempotent. This latter property makes it suitable to combine non distinct items of evidence. Extensions based on triangular norms (some of which allow to define operators whose behavior is intermediate between the Dempster's rule and the cautious rule) are also introduced
Digital Assets on Public Blockchains

Digital asset management is one of promising applications of blockchain technology. Blockchains could provide principal disintermediation between digital asset issuers, application developers and consumers and decouple tasks related to asset management, such as issuance, transaction processing, securing users’ funds and establishing users’ identities. This paper outlines basic components of blockchain-based asset ledgers, as well as their use cases for financial services and for emerging Internet of Things and consumer-to-consumer markets. We describe existing and prospective deployment models for asset ledgers, including multi-asset blockchains, colored coin andmetacoin protocols. This paper focuses primarily on Bitcoin-based services and, to a lesser degree, on public blockchains in general. © 2016 Bitfury Group Limited Without permission, anyone may use, reproduce or distribute any material in this paper for noncommercial and educational use (i.e., other than for a fee or for commercial purposes) provided that the original source and the applicable copyright notice are cited. Digital assets are a relatively recent development related to the spreading use of information technologies in the financial services. Digital asset is a floating claim of a certain service or goods ensured by the asset issuer, which is not linked to a particular account, and is governed using computer technologies and the Internet, including asset issuance, claim of ownership, and transfer. Digital assets have numerous use cases, including: • Shares and financial securities
Mobile Health Technology Using a Wearable Sensorband for Female College Students With Problem Drinking: An Acceptability and Feasibility Study

Background An increasing number of mobile app interventions have been developed for problem drinking among college students; however, few studies have examined the integration of a mobile app with continuous physiological monitoring and alerting of affective states related to drinking behaviors. Objective The aim of this paper was to evaluate the acceptability and feasibility of Mind the Moment (MtM), a theoretically based intervention for female college students with problem drinking that combines brief, in-person counseling with ecological momentary intervention (EMI) on a mobile app integrated with a wearable sensorband. Methods We recruited 10 non-treatment seeking, female undergraduates from a university health clinic who scored a 3 or higher on the Alcohol Use Disorders Identification Test–Consumption (AUDIT-C) to participate in this pilot study. Study activities involved an in-person baseline intake and 1 follow-up assessment, 2 in-person alcohol brief intervention counseling sessions, and use of MtM technology components (sensorband and EMI on a mobile app) for approximately 3-4 weeks. The intervention used motivational interviewing (MI) and cognitive behavioral therapy (CBT) strategies for reducing risks associated with drinking. We used both qualitative and quantitative assessments to measure acceptability of the intervention and feasibility of delivery. Use patterns of the sensorband and mobile app were also collected. Results Quantitative and qualitative data indicated high levels of acceptability for the MtM intervention. Altogether, participants made reports on the app on 26.7% (78/292) the days the technology was available to them and completed a total of 325 reports with wide variation between participants. Qualitative findings indicated that sensorband-elicited alerts promoted an increase in awareness of thoughts, feelings, and behaviors related to current environmental stressors and drinking behaviors in theoretically meaningful ways. Specific challenges related to functionality and form of the sensorband were identified. Conclusions Delivering intervention material “just-in-time,” at the moment participants need to use behavioral strategies has great potential to individualize behavioral interventions for reducing problem drinking and other health behaviors. These findings provide initial evidence for the promise of wearable sensors for increasing potency of theoretically grounded mobile health interventions and point to directions for future research and uptake of these technologies.
Predictors of weight reduction and maintenance in a large cohort of overweight and obese adults in a community setting

AIM In overweight/obese individuals, modest 5% weight loss and its maintenance promotes health; however, it is challenging and typically unachievable, especially in community settings. Established predictors of weight loss outcome in a community setting are lacking, hindering the development of practical interventions and prevention tools. Our aim was to identify predictors associated with 5% weight reduction (initial 6 months) and maintenance (1 year) in overweight and obese adults undergoing weight reduction treatment, free of charge, in a community setting. METHODS Computerised medical files of 11 842 adults aged 50.6 ± 16.3 years, attending 162 primary clinics, were analysed retrospectively. Thirty medical, biochemical and demographic independent variables were tested as potential predictors using multiple logistic regression models. RESULTS Significant predictors of high successful weight reduction were: not being treated with insulin (odds ratio (OR) = 0.53), higher baseline body mass index (OR = 1.05) and younger age (OR = 0.98). Weight maintenance predictors were: successful initial weight reduction (OR = 1.26), short time intervals between weighings (OR = 0.88) and frequent weighing (OR = 0.95). Visits to a dietitian were significantly associated with success during both periods: each visit raised the probability of success by 13.4 and 7.6%, respectively. Type 2 diabetes or use of hypoglycaemic drugs were not significant predictors. CONCLUSIONS In a community-based setting, number of visits to a dietitian is a strong predictor of successful weight reduction and maintenance. Initial success is a critical predictor of weight loss maintenance. Subgroup of older, diabetic patients treated with insulin has a dramatically lower probability of weight reduction success.
Distribution of lower extremity work during clean variations performed with different effort

ABSTRACT The purpose of this research was to investigate how lower extremity work was distributed during the pull of cleans performed lifting the barbell to the minimum height required to receive it in a full squat (minimal height clean); or with maximum effort to elevate the barbell as high as possible and receiving it in either a full (maximal effort clean) or partial (power clean) squat. Eight weightlifters screened for proficient technique performed these clean variations at 80% of one repetition maximum. Work performed on the barbell and by the lower extremity net joint moments (NJM) was computed from marker trajectories and ground reaction forces. Total barbell work, lower extremity NJM work, knee extensor work, and knee joint excursion during the second pull was lower in the minimal height clean than the maximal effort and power cleans (P < 0.05). This research demonstrates that more knee extensor work is performed in the second pull of maximal effort and power cleans compared to the minimal height clean. The larger knee extensor work performed is due to larger knee joint excursion during the second pull of the maximal effort and power cleans, but not larger knee extensor NJM.
Incremental CFS clustering on large data

As a popular data mining tool, clustering focuses on revealing underlying patterns embedded in data. However, most existing clustering methods mainly deal with static data, which may not be suitable for analyzing large data in dynamic environments. To tackle this problem, this paper proposes an incremental clustering method based on the CFS, clustering by fast search and find of density peaks, to process large dynamic data. In the proposed method, multiple representatives are identified for each cluster to integrate new objects into previous clustering patterns at first. Then the convex hull theory is employed to modify the representatives accordingly. To further improve the generality and effectiveness, one-time cluster adjustment strategy is explored. Extensive experiments on several real-world image datasets demonstrate that the proposed method outperforms state-of-the-art methods for clustering large data.
Practical and Precise Projector-Camera Calibration

Projectors are important display devices for large scale augmented reality applications. However, precisely calibrating projectors with large focus distances implies a trade-off between practicality and accuracy. People either need a huge calibration board or a precise 3D model [12]. In this paper, we present a practical projector-camera calibration method to solve this problem. The user only needs a small calibration board to calibrate the system regardless of the focus distance of the projector. Results show that the root-mean-squared re-projection error (RMSE) for a 450cm projection distance is only about 4mm, even though it is calibrated using a small B4 (250×353mm) calibration board.
PerformanceHat – Augmenting Source Code with Runtime Performance Traces in the IDE

Performance problems observed in production environments that have their origin in program code are immensely hard to localize and prevent. Data that can help solve such problems is usually found in external dashboards and is thus not integrated into the software development process. We propose an approach that augments source code with runtime traces to tightly integrate runtime performance traces into developer workflows. Our goal is to create operational awareness of performance problems in developers' code and contextualize this information to tasks they are currently working on. We implemented this approach as an Eclipse IDE plugin for Java applications that is available as an open source project on GitHub. A video of PerformanceHat in action is online: https://youtu.be/fTBBiylRhag
Spontaneous Viral Load Decline and Subsequent Clearance of Chronic Hepatitis C Virus in Postpartum Women Correlates With Favorable Interleukin-28B Gene Allele

Background Postpartum hepatitis C viral (HCV) load decline followed by spontaneous clearance has been previously described. Herein we identify predictors for viral decline in a cohort of HCV-infected postpartum women. Methods Pregnant women at Cairo University were screened for anti-HCV antibodies and HCV RNA, and viremic women were tested for quantitative HCV RNA at 3, 6, 9, and 12 months postpartum. Spontaneous clearance was defined as undetectable viremia twice at least 6-months apart. Associations between viral load and demographic, obstetrical, HCV risk factors, and interleukin-28B gene (IL28B) polymorphism (rs12979860) were assessed. Results Of 2514 women, 97 (3.9%) had anti-HCV antibodies, 54 (2.1%) were viremic and of those, 52 (2.1%) agreed to IL28B testing. From pregnancy until 12 months postpartum, IL28B-CC allele women had a significant viral decline (P = .009). After adjusting, the IL28B-CC allele had a near significant difference compared to the CT allele (odds ratio [OR], 0.75; 95% confidence interval [CI], 0.75,1.00; P = .05), but not the TT allele (OR, 0.91; 95% CI, 0.61,1.38; P = .64). All 14/52 (26.9%) women who subsequently cleared were among the 15 with undetectable viremia at 12 months, making that time point a strong predictor of subsequent clearance (sensitivity = 100%, specificity = 97.4%, positive predictive value = 93.3%, negative predictive value = 100%). Conclusions IL28B-CC genotype and 12-month postpartum undetectable viremia were the best predictors for viral decline and subsequent clearance. These 2 predictors should influence clinical decision making.
Interference Scripting : Protocol-aware Interference Generation for Repeatable Wireless Testbed Experiments

Despite its practical importance, interference can still be considered a “black box” in wireless network experiments as it is difficult to generate in a controlled and repeatable manner. Current generation approaches, such as packet storms or pre-recorded interference traces, do not adapt to the transmissions on the channel; the resulting effects of the interference are random and beyond the experimenter’s control. Our solution to this problem is to use channel-aware interferers, allowing them to adapt to the actual packet transmissions on the channel. We implemented a reactive jamming system on the USRP2 that enables this mode of operation as a proof of concept, decoding packets and interfering with them during their transmission. With this capability in mind we propose interference scripting, a way to define protocol-aware interference patterns using both packet content and time, and to repeatably generate these patterns on dedicated devices deployed alongside a testbed. This way, we hope to provide a useful tool to experimenters, adding controllable interference to wireless testbeds.