Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi

ABSTRACT To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunization programs. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix) into its immunization schedule in 2012. Utilizing a surveillance platform of hospitalized rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 to 2012) and after (2013 to 2014) vaccine introduction. Analysis of whole genomes obtained through next-generation sequencing revealed that all randomly selected prevaccine G1P[8] strains sequenced (n = 32) possessed a Wa-like genetic constellation, whereas postvaccine G1P[8] strains (n = 18) had a DS-1-like constellation. Phylodynamic analyses indicated that postvaccine G1P[8] strains emerged through reassortment events between human Wa- and DS-1-like rotaviruses that circulated in Malawi from the 1990s and hence were classified as atypical DS-1-like reassortants. The time to the most recent common ancestor for G1P[8] strains was from 1981 to 1994; their evolutionary rates ranged from 9.7 × 10−4 to 4.1 × 10−3 nucleotide substitutions/site/year. Three distinct G1P[8] lineages chronologically replaced each other between 1998 and 2014. Genetic drift was the likely driver for lineage turnover in 2005, whereas replacement in 2013 was due to reassortment. Amino acid substitution within the outer glycoprotein VP7 of G1P[8] strains had no impact on the structural conformation of the antigenic regions, suggesting that it is unlikely that they would affect recognition by vaccine-induced neutralizing antibodies. While the emergence of DS-1-like G1P[8] rotavirus reassortants in Malawi was therefore likely due to natural genotype variation, vaccine effectiveness against such strains needs careful evaluation. IMPORTANCE The error-prone RNA-dependent RNA polymerase and the segmented RNA genome predispose rotaviruses to genetic mutation and genome reassortment, respectively. These evolutionary mechanisms generate novel strains and have the potential to lead to the emergence of vaccine escape mutants. While multiple African countries have introduced a rotavirus vaccine, there are few data describing the evolution of rotaviruses that circulated before and after vaccine introduction. We report the emergence of atypical DS-1-like G1P[8] strains during the postvaccine era in Malawi. Three distinct G1P[8] lineages circulated chronologically from 1998 to 2014; mutation and reassortment drove lineage turnover in 2005 and 2013, respectively. Amino acid substitutions within the outer capsid VP7 glycoprotein did not affect the structural conformation of mapped antigenic sites, suggesting a limited effect on the recognition of G1-specific vaccine-derived antibodies. The genes that constitute the remaining genetic backbone may play important roles in immune evasion, and vaccine effectiveness against such atypical strains needs careful evaluation.
How to be a successful app developer: lessons from the simulation of an app ecosystem

App developers are constantly competing against each other to win more downloads for their apps. With hundreds of thousands of apps in these online stores, what strategy should a developer use to be successful? Should they innovate, make many similar apps, optimise their own apps or just copy the apps of others? Looking more deeply, how does a complex app ecosystem perform when developers choose to use different strategies? This paper investigates these questions using AppEco, the first Artificial Life model of mobile application ecosystems. In AppEco, developer agents build and upload apps to the app store; user agents browse the store and download the apps. A distinguishing feature of AppEco is the explicit modelling of apps as artefacts. In this work we use AppEco to simulate Apple's iOS app ecosystem and investigate common developer strategies, evaluating them in terms of downloads received, app diversity, and adoption rate.
A fine-grained understanding of emotions: Young children match within-valence emotional expressions to their causes

Previous research suggests that the ability to make finegrained distinctions among emotions emerges gradually over development. However, such studies have looked primarily at children’s first-person responses to emotional expressions or at whether children can match emotion labels to emotional expressions. Relatively little work has looked at children’s ability to link emotional responses to their probable causes. Here we ask two, three, and four year-old children and adults to identify the causes of vocal expressions. Because we were interested in the ability to make nuanced distinctions, we looked within a single valence and asked whether children could distinguish expressions elicited by exciting, delicious, adorable, funny, and sympathetic events. Our results suggest both an early emerging ability to distinguish within-valence emotions and rapid development; by four, children’s performance mirrored that of the adults. This suggests that very early in development, children have a rich representation of emotions that allows them to link distinct positively valenced emotional expressions to their probable causes.
Perceptual Responses to High- and Moderate-Intensity Interval Exercise in Adolescents

Purpose Continuous high-intensity exercise is proposed to evoke unpleasant sensations as predicted by the dual-mode theory and may negatively impact on future exercise adherence. Previous studies support unpleasant sensations in affective responses during continuous high-intensity exercise, but the affect experience during high-intensity interval exercise (HIIE) involving brief bursts of high-intensity exercise separated by low-intensity activity is poorly understood in adolescents. We examined the acute affective, enjoyment, and perceived exertion responses to HIIE compared with moderate-intensity interval exercise (MIIE) in adolescents. Methods Thirteen adolescent boys (mean ± SD: age, 14.0 ± 0.5 yr) performed two counterbalanced exercise conditions: 1) HIIE: 8 × 1-min work intervals at 90% maximal aerobic speed; and 2) MIIE: between 9 and 12 × 1-min work intervals at 90% ventilatory threshold where the number of intervals performed were distance-matched to HIIE. HIIE and MIIE work intervals were interspersed with 75 s active recovery at 4 km·h−1. Affect, enjoyment, and RPE were recorded before, during, and after exercise. Results Affect responses declined in both conditions but the fall was greater in HIIE than MIIE (P < 0.025, effect size [ES], 0.64 to 0.81). Affect remained positive at the end-work interval for both conditions (MIIE, 2.62 ± 1.50; HIIE, 1.15 ± 2.08 on feeling scale). No enjoyment differences were evident during HIIE and MIIE (P = 0.32), but HIIE elicited greater postexercise enjoyment compared with MIIE (P = 0.01, ES = 0.47). RPE was significantly higher during HIIE than MIIE across all work intervals (all P < 0.03, ES > 0.64). Conclusions Despite elevated RPE, HIIE did not elicit prominent unpleasant feelings as predicted by the dual-mode theory and was associated with greater postexercise enjoyment responses than MIIE. This study demonstrates the feasibility of the application of HIIE as an alternative form of physical activity in adolescents.
The Way We Die Now: A Personal Reflection

My book, The Way We Die Now, was published in May 2016. Since then, the most common question I have been asked is: why is a gastroenterologist writing about death and dying? I work as a gastroenterologist and general physician in a large Irish teaching hospital. Like most physicians doing general medical ‘take’, the majority of patients admitted under my care are frail elderly people with multiple comorbidities. And like most gastroenterologists nowadays, the majority of my speciality in-patients are people with chronic liver disease. Death is a common outcome in both groups of patients. I became increasingly aware that some families harboured unrealistic expectations of the hospital treatment of their sick elderly relatives. I also became concerned that my patients with chronic liver disease – which has a worse prognosis than most cancers – were not generally aware of this prognosis, and were not availing of proper palliative care at the end of life. I have witnessed many deaths from liver failure in relatively young people, yet death is rarely discussed with these patients and their families, who tend to assume that modern medicine can fix broken organs, or if they cannot be fixed, they can be replaced.
Biweekly fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT) for patients with metastatic adenocarcinoma of the stomach or esophagogastric junction: a phase II trial of the Arbeitsgemeinschaft Internistische Onkologie.

BACKGROUND The combination of docetaxel (Taxotere), cisplatin, and fluorouracil improved efficacy in gastric cancer, but was associated with substantial toxicity. This study was designed to incorporate docetaxel into a tolerable biweekly (once every 2 weeks) oxaliplatin-based chemotherapy regimen. PATIENTS AND METHODS Patients with measurable, metastatic adenocarcinoma of the stomach or esophagogastric junction and no prior chemotherapy received oxaliplatin 85 mg/m(2), leucovorin 200 mg/m(2), and fluorouracil 2600 mg/m(2) as a 24-h infusion in combination with docetaxel 50 mg/m(2) (FLOT) on day 1 every 2 weeks. Prophylactic growth factors were not administered. RESULTS Fifty-nine patients were enrolled; 54 received treatment. Patients had a median age of 60 years (range 29-76) and most (93%) of them had metastatic disease. Objective responses were observed in 57.7% of patients with a median time to treatment response of 1.54 months. Median progression-free survival (PFS) and overall survival were 5.2 and 11.1 months, respectively. Twenty-five percent of patients experienced prolonged (>12 months) PFS. Frequent (>10%) grade 3 or 4 toxic effects included neutropenia in 26 (48.1%), leukopenia in 15 (27.8%), diarrhea in 8 (14.8%), and fatigue in 6 (11.1%) patients. Complicated neutropenia was observed in two (3.8%) patients, only. CONCLUSIONS Biweekly FLOT is active and has a favorable safety profile.
Evaluation of independence between multiple fingerprints for multibiometrics

Multibiometrics provides high recognition accuracy and population coverage by combining different biometric sources. However, some multibiometrics may obtain smaller-than-expected improvement of recognition accuracy if the combined biometric sources are dependent in terms of a false acceptance by mistakenly perceiving biometric features from two different persons as being from the same person. In this paper, we evaluated whether or not features of multiple fingerprints from a same person are statistically independent. By evaluating false acceptance error using matching scores obtained by Verifinger SDK, we confirmed that these features were dependent and the FAR obtained by a fusion of the multiple fingerprints could be affected by the dependence.
Leveraging Big Data From Open Source to Improve Software Project Management

Software engineering management research has been conducted for many years. Researchers have faced a myriad of challenges in obtaining reliable data and associated metrics, developing practical estimating models, and influencing project improvements within industry. Open source software (OSS) can be leveraged to address these issues. This paper explores how big data from OSS can improve software engineering and management practices. The authors begin to explore a select few metrics to predicting process quality. Improved software engineering management methods are identified. It is expected that these tangible research outcomes would be of keen interest to practitioners.
Undecaprenyl Diphosphate Synthase Inhibitors: Antibacterial Drug Leads

There is a significant need for new antibiotics due to the rise in drug resistance. Drugs such as methicillin and vancomycin target bacterial cell wall biosynthesis, but methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) have now arisen and are of major concern. Inhibitors acting on new targets in cell wall biosynthesis are thus of particular interest since they might also restore sensitivity to existing drugs, and the cis-prenyl transferase undecaprenyl diphosphate synthase (UPPS), essential for lipid I, lipid II, and thus, peptidoglycan biosynthesis, is one such target. We used 12 UPPS crystal structures to validate virtual screening models and then assayed 100 virtual hits (from 450,000 compounds) against UPPS from S. aureus and Escherichia coli. The most promising inhibitors (IC50 ∼2 μM, Ki ∼300 nM) had activity against MRSA, Listeria monocytogenes, Bacillus anthracis, and a vancomycin-resistant Enterococcus sp. with MIC or IC50 values in the 0.25–4 μg/mL range. Moreover, one compound (1), a rhodanine with close structural similarity to the commercial diabetes drug epalrestat, exhibited good activity as well as a fractional inhibitory concentration index (FICI) of 0.1 with methicillin against the community-acquired MRSA USA300 strain, indicating strong synergism.
Transforming the social-ecological systems framework into a knowledge exchange and deliberation tool for comanagement

The social-ecological system framework (SESF) can be useful for applied research and management practice beyond its traditional academic applications. In this article we transform the SESF into an image-based practical tool to facilitate knowledge exchange and deliberation processes within community-based natural resource comanagement settings. We develop a transdisciplinary methodology to transform the SESF into simple and context relevant images that are understandable by nonspecialists, yet the imagebased framework still conveys its core tenets of systems thinking, a checklist for system complexity and conceptualizing social-ecological interactions. We then demonstrate a mixed-method approach for testing the usefulness of the image-based framework for enhancing communication, knowledge exchange, and deliberation processes. We show how the academic uses of the SESF, its core tenets, can serve the same purpose for nonacademic actors. When transformed, the image-based SESF has potential to be a tool that can enhance communication and knowledge exchange between actors in governance settings. We demonstrate our methodology with small-scale fishers involved with comanagement in the Gulf of Nicoya, Costa Rica. In the example, we show how scientists must learn from fishers, to understand how they view their system, in order to make the image-based tool useful in context. We then test its usefulness by exploring the hypothesis that the image-based framework can help fishers discuss with more depth and complexity because it provides a simple conceptual base for systems thinking and a core set of variables to consider as interacting. Furthermore, we explore how using the framework during deliberation may be able to alter the social-psychological outcomes of participants using field experimental methods. We discuss our combined methodology, for transforming the framework and measuring deliberation impacts, while reflecting on new ways of thinking about how the SESF can be useful for applied research and practice.
Spectral Algorithms for Computing Fair Support Vector Machines

Classifiers and rating scores are prone to implicitly codifying biases, which may be present in the training data, against protected classes (i.e., age, gender, or race). So it is important to understand how to design classifiers and scores that prevent discrimination in predictions. This paper develops computationally tractable algorithms for designing accurate but fair support vector machines (SVM's). Our approach imposes a constraint on the covariance matrices conditioned on each protected class, which leads to a nonconvex quadratic constraint in the SVM formulation. We develop iterative algorithms to compute fair linear and kernel SVM's, which solve a sequence of relaxations constructed using a spectral decomposition of the nonconvex constraint. Its effectiveness in achieving high prediction accuracy while ensuring fairness is shown through numerical experiments on several data sets.
Long-Term Impact of Universal Contact Precautions on Rates of Multidrug-Resistant Organisms in ICUs: A Comparative Effectiveness Study

OBJECTIVE To evaluate the impact of universal contact precautions (UCP) on rates of multidrug-resistant organisms (MDROs) in intensive care units (ICUs) over 9 years DESIGN Retrospective, nonrandomized observational study SETTING An 800-bed adult academic medical center in New York City PARTICIPANTS All patients admitted to 6 ICUs, 3 of which instituted UCP in 2007 METHODS Using a comparative effectiveness approach, we studied the longitudinal impact of UCP on MDRO incidence density rates, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and carbapenem-resistant Klebsiella pneumoniae. Data were extracted from a clinical research database for 2006–2014. Monthly MDRO rates were compared between the baseline period and the UCP period, utilizing time series analyses based on generalized linear models. The same models were also used to compare MDRO rates in the 3 UCP units to 3 ICUs without UCPs. RESULTS Overall, MDRO rates decreased over time, but there was no significant decrease in the trend (slope) during the UCP period compared to the baseline period for any of the 3 intervention units. Furthermore, there was no significant difference between UCP units (6.6% decrease in MDRO rates per year) and non-UCP units (6.0% decrease per year; P=.840). CONCLUSION The results of this 9-year study suggest that decreases in MDROs, including multidrug-resistant gram-negative bacilli, were more likely due to hospital-wide improvements in infection prevention during this period and that UCP had no detectable additional impact. Infect Control Hosp Epidemiol 2018;39:534–540
Daily self-reports resulted in information bias when assessing exposure duration to computer use.

BACKGROUND Self-reported exposure duration to computer use is widely used in exposure assessment, and this study examined the associated information bias in a repeated measures setting. METHODS For 3 weeks, 30 undergraduate students reported daily cumulative computer-use duration and musculoskeletal symptoms at four random times per day. Usage-monitor software installed onto participant's personal computers provided the reference measure. We compared daily self-reported and software-recorded duration, and modeled the effect of musculoskeletal symptoms on observed differences. RESULTS The relationships between daily self-reported and software-recorded computer-use duration varied greatly across subject with Spearman's correlations ranging from -0.22 to 0.8. Self-reports generally overestimated computer use when software-recorded durations were less than 3.6 hr, and underestimated when above 3.6 hr. Experiencing symptoms was related to a 0.15-hr increase in self-reported duration after controlling for software-recorded duration. CONCLUSIONS Daily self-reported computer-use duration had a weak-to-moderate correlation with software-recorded duration, and their relationship changed slightly with musculoskeletal symptoms. Self-reports resulted in both non-differential and differential information bias.
Prospects and Present Situation of Conservation Tillage in Shandong Province

This paper presents the situation of conservation tillage (CT) in Shandong province, analyses the various techniques including straw mulching, no-tillage seeding, raking tillage on the stubble, rotary tillage on the stubble, deep loosening, and control of weeds and insect pests. The paper also presents the ecological and social benefits of CT. It further analyzes questions related to CT such as seeding quality, use of agricultural machinery and agronomy, crop planting technologies, weed control, and fertilizer use. Measures to develop CT in Shandong province are also presented which include strengthening the organization with corresponding policy; reinforcing training interventions to increase the understanding of CT; combining agricultural machinery and agronomy; and enhancing the study on the theory behind CT.
The lived neighborhood: understanding how people with dementia engage with their local environment

ABSTRACT Background: In this paper, we report progress on “Neighborhoods: our people, our places” an international study about how people living with dementia interact with their neighborhoods. The ideas of social health and citizenship are drawn upon to contextualize the data and make a case for recognizing and understanding the strengths and agency of people with dementia. In particular, we address the lived experience of the environment as a route to better understanding the capabilities, capacities, and competencies of people living with dementia. In doing this, our aim is to demonstrate the contribution of social engagement and environmental support to social health. Methods: The study aims to “map” local spaces and networks across three field sites (Manchester, Central Scotland and Linkoping, Sweden). It employs a mix of qualitative and participatory approaches that include mobile and visual methods intended to create knowledge that will inform the design and piloting of a neighborhood-based intervention. Results: Our research shows that the neighborhood plays an active role in the lives of people with dementia, setting limits, and constraints but also offering significant opportunities, encompassing forms of help and support as yet rarely discussed in the field of dementia studies. The paper presents new and distinctive insights into the relationship between neighborhoods and everyday life for people with dementia that have important implications for the debate on social health and policy concerning dementia friendly communities. Conclusion: We end by reflecting on the messages for policy and practice that are beginning to emerge from this on-going study.
Bifurcation Analysis for Dust-Acoustic Waves in a Four-Component Plasma Including Warm Ions

Investigation of linear dust-acoustic (DA) waves was analyzed in a system of collisionless, dissipative, and unmagnetized four-component dusty plasma consisting of cold positively and negatively charged particles of dust, with ions and electrons are of the Boltzmann distribution. The compatibility condition is obtained by using the normal mode analysis. The Korteweg de Vries–Burgers (KdV–Burgers) equation is obtained when the plasma system is nonlinearly analyzed by the reductive perturbation method. To study the nonlinear waves, we obtain some interesting physical solutions. These solutions are in the form of soliton, a combination between a shock and a soliton, and finally monotonic and oscillatory shock waves. Graphical illustration for these solutions was presented. The characteristics of the DA solitary and shock waves are significantly modified by the presence of positive and negative dust ions, the ratio of the ion to electron temperatures, and it is also found that the basic features are affected by the dust kinematic viscosity. The planar dynamical systems bifurcation theory, which was used to establish the existence of solitary wave solutions and periodic traveling wave solutions, has been established. Accordingly, the phase portrait topology and the potential diagram are illustrated for the KdV–Burgers equation. As a result of different phase orbits, there is an advantage to predict different classes of traveling wave solutions. The electric field is determined. Generalization of the obtained results in this paper can be used to investigate the nature of plasma waves in both laboratory and space.