Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations Between MAOA‐uVNTR Genotype, Maltreatment, MAOA Methylation, and Alcohol Consumption in Young Adult Males

BACKGROUND Epigenetic mechanisms are candidate moderators of the effect of maltreatment on brain and behavior. Interactions between maltreatment and the monoamine oxidase A upstream variable number tandem repeat genotype (MAOA-uVNTR) are associated with alcohol-related problems. However, presently it is not known whether DNA methylation moderates this association. The study focused on 53 young adult males and aimed to determine whether MAOA methylation moderated the association of alcohol-related problems with the interaction of MAOA-uVNTR and maltreatment, and whether alcohol consumption moderated the association of MAOA methylation with the interaction of MAOA-uVNTR and maltreatment. METHODS MAOA-uVNTR genotypes with ≤ 3 and > 3 repeats were categorized as short (S) and long (L), respectively. Data on maltreatment were obtained retrospectively, using self-reported questionnaires. DNA methylation of 16 candidate CpGs within part of the MAOA first exon and intron was assessed and grouped based on principal component analyses. Alcohol-related problems were assessed using the Alcohol Use Disorders Identification Test (AUDIT). Alcohol consumption was measured using AUDIT-C. Moderation effects were assessed and probed using the moderated moderation model and Johnson-Neyman's method, respectively. RESULTS Carriers of the S allele, who experienced maltreatment and displayed lower Component 1 (mean of CpGs 13-16 in the first intron) MAOA methylation levels, reported higher AUDIT score in contrast to L-allele carriers. Carriers of the S allele, who reported higher AUDIT-C score and experienced maltreatment, displayed lower Component 3 (mean of CpGs 2-6 in the first exon) MAOA methylation levels than L-allele carriers. CONCLUSIONS Intronic methylation moderated the association of alcohol-related problems with the interaction of MAOA-uVNTR and maltreatment. Alcohol consumption moderated the association of exonic methylation with the interaction of MAOA-uVNTR and maltreatment. These results suggest that epigenetic factors as well as genotype and maltreatment play a role in the development of alcohol misuse among young adult males.
Identification and Validation of SAA4 as a Rheumatoid Arthritis Prescreening Marker by Liquid Chromatography Tandem-mass Spectrometry

Rheumatoid arthritis (RA) is a chronic autoimmune disease that progresses into systemic inflammation and joint deformity. RA diagnosis is a complicated procedure, and early diagnostic methods are insufficient. Therefore, in this study, we attempted to identify new markers to improve the accuracy of RA prescreening. e identified differentially expressed proteins (DEPs) by using liquid chromatography tandem-mass spectrometry in health-prescreening sera with high rheumatoid factor (RF) values, and compared the findings with those from sera with normal RF values. We identified 93 DEPs; of these, 36 were upregulated, and 57 were downregulated in high-RF sera. Pathway analysis revealed that these DEPs were related to immune responses. Additionally, four DEPs were statistically analyzed by proteomic analysis; of these, SAA4 was significantly validated in individual enzyme-linked immunosorbent assays. Moreover, SAA4 was significantly upregulated in RA patients (n = 40, 66.43 ± 12.97 ng/mL) compared with normal controls (n = 40, 4.79 ± 0.95 ng/mL) and had a higher area under the curve than C-reactive protein. Thus, we identified SAA4 as a protein that was positively correlated with RF and RA. SAA4 may represent a novel prescreening marker for the diagnosis of RA.
Parallelizing Workload Execution in Embedded and High-Performance Heterogeneous Systems

In this paper, we introduce a software-defined framework that enables the parallel utilization of all the programmable processing resources available in heterogeneous system-on-chip (SoC) including FPGA-based hardware accelerators and programmable CPUs. Two platforms with different architectures are considered, and a single C/C++ source code is used in both of them for the CPU and FPGA resources. Instead of simply using the hardware accelerator to offload a task from the CPU, we propose a scheduler that dynamically distributes the tasks among all the resources to fully exploit all computing devices while minimizing load unbalance. The multi-architecture study compares an ARMV7 and ARMV8 implementation with different number and type of CPU cores and also different FPGA micro-architecture and size. We measure that both platforms benefit from having the CPU cores assist FPGA execution at the same level of energy requirements.
A Heterogeneous Distributed Virtual Geographic Environment - Potential Application in Spatiotemporal Behavior Experiments

Due to their strong immersion and real-time interactivity, helmet-mounted virtual reality (VR) devices are becoming increasingly popular. Based on these devices, an immersive virtual geographic environment (VGE) provides a promising method for research into crowd behavior in an emergency. However, the current cheaper helmet-mounted VR devices are not popular enough, and will continue to coexist with personal computer (PC)-based systems for a long time. Therefore, a heterogeneous distributed virtual geographic environment (HDVGE) could be a feasible solution to the heterogeneous problems caused by various types of clients, and support the implementation of spatiotemporal crowd behavior experiments with large numbers of concurrent participants. In this study, we developed an HDVGE framework, and put forward a set of design principles to define the similarities between the real world and the VGE. We discussed the HDVGE architecture, and proposed an abstract interaction layer, a protocol-based interaction algorithm, and an adjusted dead reckoning algorithm to solve the heterogeneous distributed problems. We then implemented an HDVGE prototype system focusing on subway fire evacuation experiments. Two types of clients are considered in the system: PC, and all-in-one VR. Finally, we evaluated the performances of the prototype system and the key algorithms. The results showed that in a low-latency local area network (LAN) environment, the prototype system can smoothly support 90 concurrent users consisting of PC and all-in-one VR clients. HDVGE provides a feasible solution for studying not only spatiotemporal crowd behaviors in normal conditions, but also evacuation behaviors in emergency conditions such as fires and earthquakes. HDVGE could also serve as a new means of obtaining observational data about individual and group behavior in support of human geography research.
Uterine influences on conceptus development in fertility-classified animals

Significance Successful pregnancy establishment requires synchronous interactions of the conceptus with the endometrium of the uterus. This study of pregnancy outcome after assisted reproduction in fertility-classified cattle determined how the uterine environment impacts and programs conceptus survival and development. The study found that ripple effects of dysregulated conceptus–endometrial interactions elicit postelongation pregnancy loss in subfertile animals during the implantation period. This research enhances our understanding of the mechanisms that lead to pregnancy loss in both natural and assisted reproduction and has wide implications for improving pregnancy success in domestic animals and humans. A major unresolved issue is how the uterus influences infertility and subfertility in cattle. Serial embryo transfer was previously used to classify heifers as high-fertile (HF), subfertile (SF), or infertile (IF). To assess pregnancy loss, two in vivo-produced embryos were transferred into HF, SF, and IF heifers on day 7, and pregnancy outcome was assessed on day 17. Pregnancy rate was substantially higher in HF (71%) and SF (90%) than IF (20%) heifers. Elongating conceptuses were about twofold longer in HF than SF heifers. Transcriptional profiling detected relatively few differences in the endometrium of nonpregnant HF, SF, and IF heifers. In contrast, there was a substantial difference in the transcriptome response of the endometrium to pregnancy between HF and SF heifers. Considerable deficiencies in pregnancy-dependent biological pathways associated with extracellular matrix structure and organization as well as cell adhesion were found in the endometrium of SF animals. Distinct gene expression differences were also observed in conceptuses from HF and SF animals, with many of the genes decreased in SF conceptuses known to be embryonic lethal in mice due to defects in embryo and/or placental development. Analyses of biological pathways, key players, and ligand–receptor interactions based on transcriptome data divulged substantial evidence for dysregulation of conceptus–endometrial interactions in SF animals. These results support the ideas that the uterus impacts conceptus survival and programs conceptus development, and ripple effects of dysregulated conceptus–endometrial interactions elicit loss of the postelongation conceptus in SF cattle during the implantation period of pregnancy.
Nitrite‐oxidizing activity responds to nitrite accumulation in soil

ABSTRACT The factors influencing how soil nitrite (NO2−)‐ and ammonia (NH3)‐oxidizing activities remain coupled are unknown. A short‐term study (<48 h) was conducted to examine the dynamics of NO2−‐oxidizing activity and the accumulation of NO2− in three Oregon soils stimulated by the addition of 1 mM NH4+ in soil slurry. Nitrite initially accumulated in all three soils; its subsequent decline or slowing of the accumulation of the NO2− pool by 24 h was accompanied by an increase in the size of the nitrate (NO3−) pool, indicating a change in NO2− oxidation kinetics. Bacterial protein synthesis inhibitors prevented the NO2− pool decline, resulting in a larger accumulation in all three soils. Although no significant increases in NO2−‐oxidizing bacteria nxrA (Nitrobacter) and nxrB (Nitrospira) gene abundances were detected over the time course, maximum NO2− consumption rates increased 2‐fold in the treatment without antibiotics compared to no change with antibiotics. No changes were observed in the apparent half saturation constant (Km) values for NO2− consumption. This study demonstrates phenotypic flexibility among soil NO2− oxidizers, which can undergo protein synthesis‐dependent increases in NO2− consumption rates to match NH3 oxidation rates and recouple nitrification.
A Novel Organosilicon Source for Low Temperature Plasma Deposition of Silicon Nitride‐like Thin Films

This paper deals with the deposition of silicon nitride-like films at low temperatures using radio frequency inductively coupled plasmas fed with bis(dimethylamino)- dimethylsilane (BDMADMS) and argon (Ar). The effect of input power and BDMADMS-to-Ar ratio on the chemical composition of the deposited films has been investigated by means of Fourier transform infrared absorption spectroscopy (FT-IRAS) and X-ray photoelectron spectroscopy (XPS) analysis. The results indicate that at high input power and low monomer-to-Ar ratio, low carbon and high nitrogen content films, stable and with a refractive index of 1.87, can be obtained. Under the same experimental conditions, high carbon content silicon carbonitride coatings have been deposited from hexamethyldisilazane and Ar fed discharges.
Complex ISNMF: A Phase-Aware Model for Monaural Audio Source Separation

This paper introduces a phase-aware probabilistic model for audio source separation. Classical source models in the short-time Fourier transform domain use circularly-symmetric Gaussian or Poisson random variables. This is equivalent to assuming that the phase of each source is uniformly distributed, which is not suitable for exploiting the underlying structure of the phase. Drawing on preliminary works, we introduce here a Bayesian anisotropic Gaussian source model in which the phase is no longer uniform. Such a model permits us to favor a phase value that originates from a signal model through a Markov chain prior structure. The variance of the latent variables are structured with nonnegative matrix factorization (NMF). The resulting model is called complex Itakura–Saito NMF (ISNMF) since it generalizes the ISNMF model to the case of nonisotropic variables. It combines the advantages of ISNMF, which uses a distortion measure adapted to audio and yields a set of estimates which preserve the overall energy of the mixture, and of complex NMF, which enables one to account for some phase constraints. We derive a generalized expectation-maximization algorithm to estimate the model parameters. Experiments conducted on a musical source separation task in a semiinformed setting show that the proposed approach outperforms state-of-the-art phase-aware separation techniques.
Raising Backyard Poultry in Rural Bangladesh: Financial and Nutritional Benefits, but Persistent Risky Practices

Poultry is commonly raised by households in rural Bangladesh. In 2007, the Government of Bangladesh began a mass media campaign to disseminate 10 recommended precautions to prevent transmission of H5N1 from poultry to humans. This longitudinal study explored the contribution of backyard poultry on household economy and nutrition and compared poultry-raising practices to government recommendations. From 2009 to 2012, we enrolled a nationally representative sample of 2489 primary backyard poultry raisers from 115 rural villages selected by probability proportional to population size. Researchers interviewed the raisers to collect data on poultry-raising practices. They followed the raisers for 2-12 months to collect data on household income and nutrition from poultry. Income from backyard poultry flocks accounted for 2.8% of monthly household income. Return on annual investment (ROI) per flock was 480%. Yearly, median family consumption of eggs was one-fifth of the total produced eggs and three poultry from their own flock. Respondents' reported practices conflicted with government recommendations. Sixty per cent of raisers had never heard of avian influenza or 'bird flu'. Among the respondents, 85% handled sick poultry or poultry that died due to illness, and 49% slaughtered or defeathered sick poultry. In 37% of households, children touched poultry. Fifty-eight per cent never washed their hands with soap after handling poultry, while <1% covered their nose and mouth with a cloth when handling poultry. Only 3% reported poultry illness and deaths to local authorities. These reported practices did not improve during the study period. Raising backyard poultry in rural Bangladesh provides important income and nutrition with an excellent ROI. Government recommendations to reduce the risk of avian influenza transmission did not impact the behaviour of poultry producers. Further research should prioritize developing interventions that simultaneously reduce the risk of avian influenza transmission and increase productivity of backyard poultry.
Understanding Book Popularity on Goodreads

Goodreads has launched the Readers Choice Awards since 2009 where users are able to nominate/vote books of their choice, released in the given year. In this work, we question if the number of votes that a book would receive (aka the popularity of the book) can be predicted based on the characteristics of various entities on Goodreads. We are successful in predicting the popularity of the books with high prediction accuracy (correlation coefficient ~0.61) and low RMSE (~1.25). User engagement and author's prestige are found to be crucial factors for book popularity.
Detecting and Correcting for Label Shift with Black Box Predictors

Faced with distribution shift between training and test set, we wish to detect and quantify the shift, and to correct our classifiers without test set labels. Motivated by medical diagnosis, where diseases (targets), cause symptoms (observations), we focus on label shift, where the label marginal $p(y)$ changes but the conditional $p(x|y)$ does not. We propose Black Box Shift Estimation (BBSE) to estimate the test distribution $p(y)$. BBSE exploits arbitrary black box predictors to reduce dimensionality prior to shift correction. While better predictors give tighter estimates, BBSE works even when predictors are biased, inaccurate, or uncalibrated, so long as their confusion matrices are invertible. We prove BBSE's consistency, bound its error, and introduce a statistical test that uses BBSE to detect shift. We also leverage BBSE to correct classifiers. Experiments demonstrate accurate estimates and improved prediction, even on high-dimensional datasets of natural images
Physico-chemical characteristics of evaporating respiratory fluid droplets

The detailed physico-chemical characteristics of respiratory droplets in ambient air, where they are subject to evaporation, are poorly understood. Changes in the concentration and phase of major components in a droplet—salt (NaCl), protein (mucin) and surfactant (dipalmitoylphosphatidylcholine)—may affect the viability of any pathogens contained within it and thus may affect the efficiency of transmission of infectious disease by droplets and aerosols. The objective of this study is to investigate the effect of relative humidity (RH) on the physico-chemical characteristics of evaporating droplets of model respiratory fluids. We labelled these components in model respiratory fluids and observed evaporating droplets suspended on a superhydrophobic surface using optical and fluorescence microscopy. When exposed to continuously decreasing RH, droplets of different model respiratory fluids assumed different morphologies. Loss of water induced phase separation as well as indication of a decrease in pH. The presence of surfactant inhibited the rapid rehydration of the non-volatile components. An enveloped virus, ϕ6, that has been proposed as a surrogate for influenza virus appeared to be homogeneously distributed throughout the dried droplet. We hypothesize that the increasing acidity and salinity in evaporating respiratory droplets may affect the structure of the virus, although at low enough RH, crystallization of the droplet components may eliminate their harmful effects.
Effect of dietary linoleic acid on fatty acid composition of egg yolk, liver and adipose tissue.

Abstract THE polyunsaturated fatty acids: linoleic, linolenic and arachidonic acids were first recognized by Burr and Burr (1930) to possess biopotency in curing or preventing the fat-deficiency produced by the rigid exclusion of fat from the diet. More recent studies using vegetable oil as the source of dietary linoleic acid have shown that linoleic acid was essential for optimum performance of laying hens. Improved egg weight and rate of egg production by hens after the addition of corn oil to both practical and semi-purified diets were shown by Jensen et al. (1958). It was later referred to as the unidentified factor necessary for maximum egg weight by Schutze et al. (1962). Further investigations (Shutze and Jensen, 1963; Menge et al., 1965), suggested that the linoleic acid in corn oil was essential for maximum egg production, egg weight, fertility and hatchability. It was concluded, however, by Harms and Waldroup (1963) and Blamberg…
Modulation by Polymyxin-B Hemoperfusion of Inflammatory Response Related to Severe Peritonitis

ABSTRACT Conflicting results have been reported on the influence of Polymyxin-B hemoperfusion treatment on systemic inflammation markers. The aim of the study was to assess in a randomized control trial the influence on plasma cytokine concentrations of Polymyxin-B hemoperfusion in septic shock due to peritonitis. A panel of 10 pro- or anti-inflammatory cytokines was measured in 213 patients with peritonitis-induced septic shock enrolled in the randomized trial ABDOMIX testing the impact of 2 Polymyxin-B hemoperfusion sessions with standard treatment. Gram-negative bacteria were identified in 69% of patients. In the overall population, baseline plasma cytokine concentrations were not different between the two groups. Circulating tumor necrosis factor-&agr;, interleukin (IL)-1&bgr;, IL-10, IL-6, and IL-1RA decreased significantly over time in both groups (P <0.0001 for all in controls, and P = 0.0002, 0.003, and <0.0001 in patients treated with Polymyxin-B hemoperfusion). IL-17A decreased significantly in patients treated with Polymyxin B hemoperfusion (P = 0.045) but not in controls. At the end of the second Polymyxin-B hemoperfusion session or at corresponding time in controls, plasma levels of cytokines did not differ between the two groups. Similar results were found in the subgroup of patients with gram-negative peritonitis who completed two Polymyxin-B hemoperfusion sessions. These results do not support a significant influence of Polymyxin-B hemoperfusion on circulating cytokines assessed except for IL-17A which clinical significance remains to be elucidated.
Comparing growth and condition in post release juvenile common pheasants on different diets.

ABSTRACT We studied juvenile common pheasants Phasianus colchicus in 10 large open-topped release pens in woodlands on a shooting estate in southern England in 1998. In six pens the pheasants were fed a pelleted high-protein feed from 6 to 16 wk of age; in the four other pens they were fed the diet from 6 to 10 wk and then wheat grain only from 10 to 16 wk. Natural plant and animal food was also available to the birds in and around the release pens. When a sample of previously tagged, numbered, and weighed birds was caught from each pen and reweighed at 16 wk of age, we noted that birds from pens that remained on the high-protein feed had gained more weight than those from pens in which the diet was switched to grain only (P < 0.05). Of approximately 500 tagged birds collected during shooting days between 5 and 15 wk later, differences in body mass gain between groups were still significant (P < 0.05). A subsample, 50 males and 50 females aged 22 to 24 wk, of tagged birds that were shot were kept for postmortem examination. From this smaller sample, the differences in body mass were not significant (P > 0.05). Breast muscle mass and tarsal length did not differ between treatments. However cloacal fat was higher in the birds fed a high-protein diet (P < 0.05), suggesting that the results relating to body mass were due to differences in fat accumulation. Most pheasants examined postmortem contained the gut nematode Heterakis gallinarum with an average burden of 118 +/- 14 worms per bird. Although the abundance of these worms was not related to diet, it was negatively correlated with body mass, breast muscle mass, and cloacal fat (P < 0.05).
Optimized Bacteria are Environmental Prediction Engines

Experimentalists observe phenotypic variability even in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log-growth rate, potentially aided by epigenetic (all inheritable nongenetic) markers that store information about past environments. Crucially, we assume a time delay between sensing and action, so that a past epigenetic marker is used to generate the present phenotypic variability. We show that, in a complex, memoryful environment, the maximal expected log-growth rate is linear in the instantaneous predictive information-the mutual information between a bacterium's epigenetic markers and future environmental states. Hence, under resource constraints, optimal epigenetic markers are causal states-the minimal sufficient statistics for prediction-or lossy approximations thereof. We propose new theoretical investigations into and new experiments on bacteria phenotypic bet-hedging in fluctuating complex environments.