Miracle-dz/UniFAR-FTUs huggingface dataset:
Possible Worlds Explorer: Datalog & Answer Set Programming for the Rest of Us

Datalog and Answer Set Programming (ASP) are powerful languages for rule-based querying and constraint solving, respectively. We have developed Possible Worlds Explorer (PWE), an open source Python-based toolkit that employs Jupyter notebooks to make working with Datalog and ASP systems easier and more productive. PWE can parse output from different reasoners (Clingo and DLV) and then run analytical queries over all answer sets or “possible worlds” (PWs), e.g., to calculate relative frequencies of atoms across PWs or to hierarchically cluster PWs based on user-defined complexity and similarity measures. PWE also has support for well-founded Datalog models (from DLV) and temporal models that use a special state argument. Using simple Python functions, generic as well as user-definable presentation and visualization formats can be easily created, e.g., to display all PWs (world views), the unique three-valued well-founded model (partial views), and temporal models (timelines and time series). We provide containerized versions of PWE that can be run in the cloud or locally. We hope that in this way Datalog and ASP can be made more accessible for a wider audience.
Toxic effect of gestational exposure to nonylphenol on F1 male rats.

OBJECTIVE The purpose of this study was to examine whether gestational exposure to major environmental endocrine-disrupting chemicals, nonylphenol (NP), would lead to nerve behavioral and learning and memory capacity alterations in the male offspring of rats, and reproductive development alterations in the male offspring of rats. METHODS Dams were gavaged with NP at a dose level of 50 mg/kg/day, 100 mg/kg/day or 200 mg/kg/day daily from gestational day 9 to 15, and at a dose level of 40 mg/kg/day, 80 mg/kg/day or 200 mg/kg/day daily from gestational day 14 to 19 (transplacental exposures). RESULTS Exposure to 200 mg/kg/day NP produced a significant decrease in learning and memory functions in offspring rats (P<0.05) in Morris water maze task, as demonstrated by the increased escape latency and number of error. In Step-down Avoidance Test, offspring rats exposed to NP spent more reaction time (RT) and presented lower latency to first step-down than the control offspring (P<0.01). In utero exposure to 80 and 200 mg/kg/day NP produced a significant decrease in the number of live pups per litter and ratio of anogenital distance to body length on PND 0 (P<0.05), and also testes and prostate weight, activities of ALP, plasma testosterone concentration, cauda epididymis sperm counts, daily sperm production et al. respectively on PND 90 (P<0.05). Histopathological examination of the brain biopsy illustrates that exposure to NP at high dose induces the presence of abnormal distribution of spermatozoa showed in lumina of the seminiferous tubules, and absence of spermatogenesis and spermiogenesis. CONCLUSION Gestational exposure to nonylphenol might induce neurotoxic and reproductive toxic effects on F1 male rats.
Significant Reduction of Defect States and Surface Tailoring in ZnO Nanoparticles via Nano-Bio Interaction With Glucose for Bio-Applications

In this study, we have investigated the structural and optical properties of nanoconjugates (NJs) consisting of phase pure zinc oxide (ZnO) nanoparticles (NPs) with glucose biomolecules. All NJs were fabricated using a standard biochemical synthesis process. Structural, optical, vibrational, and biochemical interface properties of nano-bio composites are probed by different complementary characterization techniques. The XRD patterns of the NPs and NJs illustrate a highly phase pure ZnO structure. A visible green emission in the photoluminescence spectrum, mainly associated with the oxygen vacancies on the surface of ZnO nanostructure, is significantly reduced by the incorporation of glucose biomolecules. The strong binding interaction of glucose biomolecule on the surface of ZnO NPs results in the reduction in green-yellow-orange emission intensities. The interaction of glucose molecules modifies oxygen vacancies by capturing free electrons from the ZnO surface region. Significant changes in the peak intensity and relative peak position of some of the glucose and ZnO NPs in Raman spectra refer to the direct binding between these two nano- and bio-components. In the X-ray photoelectron spectroscopy, the binding energy of O 1s core level in NJs increases from 531 eV (O 1s core level position for ZnO) and the increment is more with higher initial glucose concentration in the solution during synthesis. This study serves as a promising platform for the development of new kinds of NJs and investigation of their interfacial properties which can take the frontier forward for integration and multifunctionality.
An Empirical Evaluation of the Effect of Adversarial Labels on Classifier Accuracy Estimation

This paper examines the effect of providing adversarial labels to several algorithms that use noisy labels from multiple experts to estimate classiﬁer accuracy, referred to hereafter as “estimators. ” We propose four adversary labeling strategies and use experiments on synthetic data to gauge their impact on the estimators. Our results show that even a single adversary can considerably impact the effectiveness of an estimator. In addition, we ﬁnd that estimators that weight the input of all experts equally tend to be much more affected by the inclusion of adversaries than those that can separately model each expert and that the impact of adversaries is less-ened when the experts have higher accuracy.
Domestic river water use and risk of typhoid fever: results from a case-control study in Blantyre, Malawi.

BACKGROUND Typhoid fever remains a major cause of morbidity and mortality in low and middle-income settings. In the last 10 years, several reports have described the re-emergence of typhoid fever in southern and eastern Africa, associated with multidrug-resistant H58 Salmonella Typhi. Here, we identify risk factors for pediatric typhoid fever in a large epidemic in Blantyre, Malawi. METHODS A case-control study was conducted between April 2015 and November 2016. Cases were recruited at a large teaching hospital, while controls were recruited from the community, matched by residential ward. Stepwise variable selection and likelihood ratio testing were used to select candidate risk factors for a final logistic regression model. RESULTS Use of river water for cooking and cleaning was highly associated with risk of typhoid fever (OR 4.6 [CI: 1.6-12.5]). Additional risk factors included protective effects of soap in the household (OR 0.6 [CI: 0.4-0.98]) and more than one water sources used in the previous 3 weeks (OR 3.2 [CI: 1.6-6.2]). Attendance at school or other daycare was also identified as a risk factor (OR 2.7 [CI: 1.4-5.3]) and was associated with the highest attributable risk (51.3%). CONCLUSIONS These results highlight diverse risk factors for typhoid fever in Malawi, with implications for control in addition to the provision of safe drinking water. There is an urgent need to improve our understanding of transmission pathways of typhoid fever, both to develop tools for detecting S. Typhi in the environment, and inform water, sanitation, and hygiene interventions.
Assessment of Subcutaneous vs Intravenous Administration of Anti-PD-1 Antibody PF-06801591 in Patients With Advanced Solid Tumors: A Phase 1 Dose-Escalation Trial.

Importance We assessed feasibility of monthly subcutaneous administration of PF-06801591, a humanized immunoglobulin G4 monoclonal antibody that binds to the programmed cell death (PD-1) receptor and blocks its interaction with PD-1 ligands. Objective To evaluate the safety, efficacy, and pharmacokinetics of PF-06801591 administered intravenously vs subcutaneously. Design, Setting, and Participants Ongoing phase 1, open-label, multicenter, dose-escalation study of 40 patients, 18 years or older, with locally advanced or metastatic solid tumors, enrolled between March 8, 2016, and March 5, 2018, from 4 US medical centers. Interventions An intravenous dose of 0.5, 1, 3, or 10 mg/kg of PF-06801591 was administered every 3 weeks or a subcutaneous dose of 300 mg was administered every 4 weeks. Dose escalation occurred after 2 to 4 patients were enrolled per dose level, with additional patients enrolled in each cohort for further assessment. Main Outcomes and Measures The primary end points were dose-limiting toxic effects and safety. Secondary end points included pharmacokinetics, immunogenicity, PD-1 receptor occupancy, and efficacy. Results Of 40 enrolled patients (12 men and 28 women; mean [SD] age, 61 [13] years) in this phase 1 dose-escalation trial, 25 received PF-06801591 intravenously at escalating dose levels (0.5, 1, 3, or 10 mg/kg) and 15 patients received the monoclonal antibody subcutaneously at a single dose level. No dose-limiting toxic effects were observed. Grade 3 or higher treatment-related adverse events occurred in 4 (16%) patients treated intravenously and 1 (6.7%) patient treated subcutaneously. Immune-related adverse events occurred in 10 (40%) patients treated intravenously and 3 (20%) treated subcutaneously. No dose-adverse event associations were observed during intravenous dose escalation, and no serious skin toxic effects occurred with subcutaneous delivery. Responses were seen in 5 patients receiving PF-06801591 intravenously and in 2 patients treated subcutaneously for an overall objective response rate of 18.4%. Median overall survival was not reached with intravenous dosing vs 10.7 months with subcutaneous administration. Exposure to PF-06801591 increased in a dose-proportional manner over the range of intravenous doses. Median time to maximum observed serum concentration was 8 days after subcutaneous administration. Full PD-1 receptor occupancy was seen in all dose cohorts. Conclusions and Relevance Anti-PD-1 antibody PF-06801591 was tolerable and showed antitumor activity in a variety of tumor types across all dose levels of intravenous and subcutaneous administration. Monthly subcutaneous administration of PF-06801591 offers a convenient, effective alternative to currently available intravenously administered checkpoint inhibitors. Trial Registration ClinicalTrials.gov identifier: NCT02573259.
Convolutional Adversarial Latent Factor Model for Recommender System

The high accuracy of Top-N recommendation task is a challenge in the systems with mainly implicit user feedback considered. Adversarial training has presented successful results in identifying real data distributions in various domains (e.g., image processing). Nonetheless, adversarial training applied to the recommendation is still challenged especially by interpretation of negative implicit feedback causing it to converge slowly as well as affecting its convergence stability. The researchers (He et al. 2018a; Chae et al. 2018) denotes the misinterpretation to high sparsity of the implicit feed-back and discrete values characteristic from items recommendation. To face these challenges, we propose a novel model named convolutional adversarial latent factor model (CALF), which uses adversarial training in generative and discriminative models for implicit feedback recommendations. We assume that users prefer observed items over generated items and then apply the pairwise product to model the user-item interactions. Additionally, the hidden features become input data of our convolutional neural network (CNN) to learn correlations among embedding dimensions. Finally, Rao-Blackwell sampling is adopted to deal with the discrete values optimizing CALF and stabilizing the training step. We conducted extensive experiments on three different benchmark datasets, where our proposed model demonstrates its efﬁciency for item recommendation.
Exploring the associations between shift work disorder, depression, anxiety and sick leave taken amongst nurses

This study aimed to evaluate the association between shift work disorder and mental health in hospital‐based nurses. Staff completed an online survey comprising demographic questions, the Shift Work Disorder Questionnaire, Patient Health‐9 and the General Anxiety Disorder‐7 scale. Sick leave data were collected from archival records from the Human Resources Department. Two hundred and two nurses (95% female; age M = 35.28 years ± SD = 12) participated (42% of eligible staff). Those at high risk of shift work disorder had higher depression (M = 7.54 ± SD = 4.28 vs. M = 3.78 ± SD = 3.24; p < 0.001) and anxiety (M = 5.66 ± SD = 3.82 vs. M = 2.83 ± SD = 3.33, p < 0.001) compared to those at low risk. Linear regression models showed that being at high risk of shift work disorder was the most significant predictor of depression, explaining 18.8% of the variance in depression (R2 = 0.188, adjusted R2 = 0.184, F(1, 200) = 46.20, p < 0.001). Shift work disorder combined with the number of night shifts and alcoholic drinks on non‐work days accounted for 49.7% of the variance in anxiety scores (R2 = 0.497, adjusted R2 = 0.453, F(3, 35) = 11.51, p < 0.001). Mean sick leave in those with high risk of shift work disorder was 136.17 hr (SD = 113.11) versus 103.98 hr (SD = 94.46) in others (p = 0.057). Depression and years of shift work accounted for 18.9% of the variance in sick leave taken (R2 = 0.189, adjusted R2 = 0.180, F(2, 175) = 20.36, p < 0.001). Shift work disorder is strongly associated with depression and anxiety, providing a potential target to improve mental health in shift workers. Depression, in turn, is a significant contributing factor to sick leave.
Gene Selection and Clustering of Breast Cancer Data

In this work, we ﬁrst attempt to reproduce an earlier study on gene selection and clustering, and then we extend this work by applying a different type of hierarchical clustering to discover interesting subsets of genes from breast cancer data. Reproduction of such studies is a known challenge and an active area of research in bioinformatics. The work presented in this paper is three-fold. First, we reproduce a study conducted at the University of North Carolina to generate an initial set of genes. Second, we apply an approach called Distance Weighted Discrimination to fuse multiple, disparate breast cancer datasets into a single validation set. Third, we perform hierarchical clustering and k-means clustering on this validation set to discover natural groupings and compare the clusters generated by both methods. While applying the hierarchical clustering is part of the reproduction step, we extend the research by trying two different forms of hierarchical clustering. We also apply k-means clustering for the same purpose and compare all three methods using Kaplan-Meier estimation and Cox proportional hazards regression. We discover that among the three methods, k-means clustering gives us the best results.
Trauma-related psychiatric and behavioral conditions are uniquely associated with sustained attention dysfunction.

OBJECTIVE It is increasingly recognized that trauma victims, particularly Veterans, have co-occurring psychological and physical conditions that impact cognition, especially the domains of sustained attention and executive functioning. Although previous work has generally attempted to isolate the unique cognitive effects of common combat-related comorbidities, less work has been done to examine how these conditions co-occur, and whether unique cognitive signatures accompany certain clinical combinations. METHOD To address this gap, we examined how several deployment-related conditions were associated with performance on a well-validated measure of sustained attention (i.e., gradual onset continuous performance task [gradCPT]) and a battery of standard neuropsychological measures in 123 Veterans from the Translational Research Center for TBI and Stress Disorders. Initially, a Principal component analysis was conducted to investigate how comorbid conditions grouped together. RESULTS Several sustained attention measures from the gradCPT were differentially associated with four unique combinations of trauma-related pathology. Specifically, a somatic component representing the combination of current pain, sleep disturbance, and mild traumatic brain injury was associated with a higher rate of failures of attentional engagement. On the other hand, a comorbid posttraumatic stress disorder (PTSD) and mood disorder component (moodPTSD), as well as a substance use disorder component, were associated with higher rates of inhibitory control failures. Increased attentional instability was associated with moodPTSD as well as an anxiety disorder component. In contrast, the cognitive effects of deployment-related trauma were not observed on standard neuropsychological measures. CONCLUSION These findings suggest that unique combinations of trauma-related pathology have dissociable effects on sustained attentional control. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
BAY 41‐2272, a soluble guanylate cyclase agonist, activates human mononuclear phagocytes

Phagocyte function is critical for host defense against infections. Defects in phagocytic function lead to several primary immunodeficiencies characterized by early onset of recurrent and severe infections. In this work, we further investigated the effects of BAY 41‐2272, a soluble guanylate cyclase (sGC) agonist, on the activation of human peripheral blood monocytes (PBM) and THP‐1 cells.
What Is the Next Step? Supporting Architectural Room Configuration Process with Case-Based Reasoning and Recurrent Neural Networks

This paper presents the ﬁrst results of the research into AI-based support of the room conﬁguration process during the early design phases in architecture. Room conﬁguration (also: room layout or space layout) is an essential stage of the initial design phase: its results are crucial for user-friendliness and success of the planned utilization of the architectural object. Our approach takes into account different possible actions of the conﬁguration process, such as adding, removing, or (re)assigning of the room type. Its mode of operation is based on speciﬁc process chain clusters, where each cluster represents a contextual subset of previous conﬁguration steps and provides a recurrent neural network trained on this cluster data only to suggest the next step, and a case base that is used to determine if the current process chain belongs to this cluster. The most similar cluster then tries to suggest the next step of the process. The approach is implemented in a distributed CBR framework for support of early conceptual design in architecture and was evaluated with a high number of process chain queries to prove its general suitability.
An Investigation on the Sampling Frequency of the Upper-Limb Force Myographic Signals

Force myography (FMG) is an emerging method to register muscle activity of a limb using force sensors for human–machine interface and movement monitoring applications. Despite its newly gained popularity among researchers, many of its fundamental characteristics remain to be investigated. The aim of this study is to identify the minimum sampling frequency needed for recording upper-limb FMG signals without sacrificing signal integrity. Twelve healthy volunteers participated in an experiment in which they were instructed to perform rapid hand actions with FMG signals being recorded from the wrist and the bulk region of the forearm. The FMG signals were sampled at 1 kHz with a 16-bit resolution data acquisition device. We downsampled the signals with frequencies ranging from 1 Hz to 500 Hz to examine the discrepancies between the original signals and the downsampled ones. Based on the results, we suggest that FMG signals from the forearm and wrist should be collected with minimum sampling frequencies of 54 Hz and 58 Hz for deciphering isometric actions, and 70 Hz and 84 Hz for deciphering dynamic actions. This fundamental work provides insight into minimum requirements for sampling FMG signals such that the data content of such signals is not compromised.
Moving in Sync: Hourly Physical Activity and Sedentary Behavior are Synchronized in Couples.

BACKGROUND Overall time spent in moderate-to-vigorous intensity physical activity (MVPA) and sedentary behavior are both correlated in couples. Knowledge about the nature and psychosocial correlates of such dyadic covariation could inform important avenues for physical activity promotion. PURPOSE The present study investigates hour-by-hour covariation between partners (i.e., synchrony) in MVPA and sedentary behavior as partners engage in their daily lives and links it with person-level MVPA/sedentary behavior, temporal characteristics, and relationship variables. METHODS We used 7-day accelerometer data from two couple studies (Study 1, n = 306 couples, aged 18-80 years; Study 2, n = 108 couples, aged 60-87 years) to estimate dyadic covariation in hourly MVPA and sedentary behavior between partners. Data were analyzed using coordinated multilevel modeling. RESULTS In both studies, hourly MVPA and sedentary behavior exhibited similarly sized dyadic covariation between partners in the low-to-medium range of effects. Higher MVPA synchrony between partners was linked with higher individual weekly MVPA and higher individual weekly sedentary levels, whereas higher sedentary synchrony between partners was associated with higher individual weekly MVPA but lower individual weekly sedentary levels. MVPA and sedentary synchrony were higher in the morning and evening, more pronounced on weekends, and associated with more time spent together, longer relationship duration, and time-varying perceptions of higher partner closeness. CONCLUSIONS This study demonstrates that MVPA and sedentary behaviors do not occur in a social vacuum. Instead, they are linked with close others such as partners. Thus, capitalizing on social partners may increase the effectiveness of individual-level physical activity interventions.
How Animacy and Information Status Determine Word Order in Translation of the Passive Voice

English uses the passive voice more frequently than French. One method of translating the passive includes rendering the sentence as active by using an active verb, and changing the placement of the verb’s arguments. We are studying extra-syntactic features that predict where this method of translat- ing the passive voice is used, including animacy and information status. We have obtained data from examining the Hansard, the transactions of the Canadian Parliament, which is published in both languages. This paper presents the results of a small mechanized corpus analysis on the relevance of the relative animacy of the agent (or experiencer) and the theme. This information will help to achieve desired stylistic output in a bilingual surface realizer.
The Potential of Carnosine in Brain-Related Disorders: A Comprehensive Review of Current Evidence

Neurological, neurodegenerative, and psychiatric disorders represent a serious burden because of their increasing prevalence, risk of disability, and the lack of effective causal/disease-modifying treatments. There is a growing body of evidence indicating potentially favourable effects of carnosine, which is an over-the-counter food supplement, in peripheral tissues. Although most studies to date have focused on the role of carnosine in metabolic and cardiovascular disorders, the physiological presence of this di-peptide and its analogues in the brain together with their ability to cross the blood-brain barrier as well as evidence from in vitro, animal, and human studies suggest carnosine as a promising therapeutic target in brain disorders. In this review, we aim to provide a comprehensive overview of the role of carnosine in neurological, neurodevelopmental, neurodegenerative, and psychiatric disorders, summarizing current evidence from cell, animal, and human cross-sectional, longitudinal studies, and randomized controlled trials.