Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual and combined effects of feeding Fusarium moniliforme culture material, containing known levels of fumonisin B1, and aflatoxin B1 in the young turkey poult.

The individual and combined effects of fumonisin B1 (FB1) and aflatoxin B1 (AF) were evaluated using a 2 x 2 factorial with treatments of 0 and 75 mg FB1/kg feed and 0 and 200 micrograms AF/kg feed. Each of the four diets was fed to eight pen replicates of six poults from Day 1 to 21. Body weight gain was reduced (P < .05) by AF and the FB1-AF combination. Poults fed AF or the FB1-AF combination were less efficient (P < .05) in converting feed to gain. Fumonisin B1 increased (P < .05) liver weights whereas AF and the FB1-AF combination increased (P < .05) spleen weights. The AF and the FB1-AF combination decreased (P < .05) serum concentrations of albumin, total protein, and cholesterol. Fumonisin B1 and the FB1-AF combination increased (P < .05) serum sphinganine:sphingosine (SA:SO) ratios. Treatment-associated lesions were observed only in the liver. Hepatocellular hyperplasia and biliary hyperplasia were seen in poults fed 75 mg FB1/kg and 200 micrograms AF/kg, respectively. The combination of FB1 and AF caused an increased primary immune response to sheep red blood cells. However, the phytohemagglutinin delayed hypersensitivity response was not affected by dietary treatment. These data indicate that FB1 and AF, alone and in combination, can adversely affect poult performance and health at these dietary concentrations.
T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable

Significance Success or failure of CD8+ T cell responses dictates whether an infected patient can control HIV durably. HIV-specific CD8+ T cells from HIV controllers and chronic progressors were shown to differ in their antiviral function. Here, we investigated whether HIV-specific T cell receptors (TCRs) can explain functional differences in CD8+ T cells from patients with differential immunologic control. Through in vitro, in vivo, and in silico studies, we found that HIV-specific TCRs were functionally equivalent. These results suggest that the factors that modulate the CD8+ T cell response to HIV are independent of their TCRs. HIV controllers (HCs) are individuals who can naturally control HIV infection, partially due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis that superior function of CD8+ T cells from HCs is encoded by their T cell receptors (TCRs). We compared the functional properties of immunodominant HIV-specific TCRs obtained from HLA-B*2705 HCs and chronic progressors (CPs) following expression in primary T cells. T cells transduced with TCRs from HCs and CPs showed equivalent induction of epitope-specific cytotoxicity, cytokine secretion, and antigen-binding properties. Transduced T cells comparably, albeit modestly, also suppressed HIV infection in vitro and in humanized mice. We also performed extensive molecular dynamics simulations that provided a structural basis for similarities in cytotoxicity and epitope cross-reactivity. These results demonstrate that the differential abilities of HIV-specific CD8+ T cells from HCs and CPs are not genetically encoded in the TCRs alone and must depend on additional factors.
Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance

Dengue is an infection of increasing global importance, yet uncertainty remains regarding critical aspects of its virology, immunology and epidemiology. One unanswered question is how infection is controlled and cleared during a dengue infection. Antibody is thought to play a role, but little past work has examined the kinetics of both virus and antibody during natural infections. We present data on multiple virus and antibody titres measurements recorded sequentially during infection from 53 Vietnamese dengue patients. We fit mechanistic mathematical models of the dynamics of viral replication and the host immune response to these data. These models fit the data well. The model with antibody removing virus fits the data best, but with a role suggested for ADCC or other infected cell clearance mechanisms. Our analysis therefore shows that the observed viral and antibody kinetics are consistent with antibody playing a key role in controlling viral replication. This work gives quantitative insight into the relationship between antibody levels and the efficiency of viral clearance. It will inform the future development of mechanistic models of how vaccines and antivirals might modify the course of natural dengue infection.
Supplement to the paper Identification of and correction for publication bias

This appendix contains proofs and supplementary results for the paper “Identification of and correction for publication bias. ” Section A collects proofs for the results stated in the main text. Section B discusses several details and extensions of the applications, including accounting for estimation error in p(·), identification with sign-normalized data, conditioning on covariates, and a range of robustness checks. Section C contains further empirical results, including moments and results for our GMM approaches which leave the distribution of true effects unrestricted, and empirical results for the Camerer et al. (2018) and Croke et al. (2016) applications. Finally, Section D gathers additional theoretical results on topics including the extension of our identification results to cases where publication probabilities depend on Σ and Ω, the interpretation of meta-regression coefficients in the presence of selectivity, the extension of our inference results to multivariate settings, the effect of selection on Bayesian inference, and optimal selection in a stylized model.
Sperm Quality and Testicular Histomorphometry of Wistar Rats Supplemented with Extract and Fractions of Fruit of Tribulus terrestris L.

The aim of this study was to assess the sperm quality and testicular histomorphometry of Wistar rats supplemented with extract and fractions of fruits of Tribulus terrestris L. The ethanolic extract was obtained by dynamic maceration of spray-dried fruit. This extract was fractionated by liquid-liquid partition, using increasing polarity solvents. Twenty male rats were separated in four groups, with five rats in each group. The control was supplemented with distilled water, while the others were daily given the ethanolic extract, hexanic or aqueous fraction soluble in methanol in a dose of 42 mg.kg-1.day-1 for 70 days. Sperm was obtained from the right epididymal tail for the analysis of motility, count, morphology and viability. The testicular weight of groups supplemented with ethanolic extract and aqueous fraction soluble in methanol was higher when compared to the control. The gonadosomatic index increased in the group supplemented with ethanolic extract. The nuclear, cytoplasmic and individual volume of Leydig cells increased in supplementation with hexanic and aqueous fractions soluble in methanol. It was concluded that the extract influenced the spermatogenesis, while hexanic and aqueous fractions soluble in methanol promoted the changes in the intertubular compartment. Therefore, Tribulus terrestris did not improve the sperm quality of the rats.
Phytate phosphorus content of feed ingredients derived from plants.

Abstract A portion of the phosphorus in feed ingredients of plant origin is present as the mineral salt of phytic acid. Phytate phosphorus is either unavailable to, or poorly utilized by, the chick. In addition, phytic acid chelates mineral elements, including calcium, and thereby reduces their availability in whole or part. However, the quantitative effect of phytic acid on the total dietary level of any element in a feed has been neglected. It is important, therefore, to know the phytic acid content of feeds in order that adequate amounts of essential elements may be supplied, particularly phosphorus and calcium. Common (1940), McCance and Widdowson (1944) and Mollgaard (1946) have reported the phytic acid content of various feed ingredients, but limited information is available for those currently used in the United States. This report lists phytate phosphorus content of many feed ingredients used in poultry rations. EXPERIMENTAL PROCEDURES AND RESULTS Feed ingredients .
Hessian-based Analysis of Large Batch Training and Robustness to Adversaries

Large batch size training of Neural Networks has been shown to incur accuracy loss when trained with the current methods. The exact underlying reasons for this are still not completely understood. Here, we study large batch size training through the lens of the Hessian operator and robust optimization. In particular, we perform a Hessian based study to analyze exactly how the landscape of the loss function changes when training with large batch size. We compute the true Hessian spectrum, without approximation, by back-propagating the second derivative. Extensive experiments on multiple networks show that saddle-points are not the cause for generalization gap of large batch size training, and the results consistently show that large batch converges to points with noticeably higher Hessian spectrum. Furthermore, we show that robust training allows one to favor flat areas, as points with large Hessian spectrum show poor robustness to adversarial perturbation. We further study this relationship, and provide empirical and theoretical proof that the inner loop for robust training is a saddle-free optimization problem \textit{almost everywhere}. We present detailed experiments with five different network architectures, including a residual network, tested on MNIST, CIFAR-10, and CIFAR-100 datasets. We have open sourced our method which can be accessed at [1].
Memory Fusion Network for Multi-view Sequential Learning

Multi-view sequential learning is a fundamental problem in machine learning dealing with multi-view sequences. In a multi-view sequence, there exists two forms of interactions between different views: view-specific interactions and cross-view interactions. In this paper, we present a new neural architecture for multi-view sequential learning called the Memory Fusion Network (MFN) that explicitly accounts for both interactions in a neural architecture and continuously models them through time. The first component of the MFN is called the System of LSTMs, where view-specific interactions are learned in isolation through assigning an LSTM function to each view. The cross-view interactions are then identified using a special attention mechanism called the Delta-memory Attention Network (DMAN) and summarized through time with a Multi-view Gated Memory. Through extensive experimentation, MFN is compared to various proposed approaches for multi-view sequential learning on multiple publicly available benchmark datasets. MFN outperforms all the multi-view approaches. Furthermore, MFN outperforms all current state-of-the-art models, setting new state-of-the-art results for all three multi-view datasets.
Polarization and Fake News

Users’ polarization and confirmation bias play a key role in misinformation spreading on online social media. Our aim is to use this information to determine in advance potential targets for hoaxes and fake news. In this article, we introduce a framework for promptly identifying polarizing content on social media and, thus, “predicting” future fake news topics. We validate the performances of the proposed methodology on a massive Italian Facebook dataset, showing that we are able to identify topics that are susceptible to misinformation with 77% accuracy. Moreover, such information may be embedded as a new feature in an additional classifier able to recognize fake news with 91% accuracy. The novelty of our approach consists in taking into account a series of characteristics related to users’ behavior on online social media such as Facebook, making a first, important step towards the mitigation of misinformation phenomena by supporting the identification of potential misinformation targets and thus the design of tailored counter-narratives.
Targeting Heterogeneous Findings in Neuronal Oscillations in Tinnitus: Analyzing MEG Novices and Mental Health Comorbidities

Tinnitus is a prevalent phenomenon and bothersome for people affected by it. Its occurrence and maintenance have a clear neuroscientific tie and one aspect are differences in the neuronal oscillatory pattern, especially in auditory cortical areas. As studies in this field come to different results, the aim of this study was to analyze a large number of participants to achieve more stable results. Furthermore, we expanded our analysis to two variables of potential influence, namely being a novice to neuroscientific measurements and the exclusion of psychological comorbidities. Oscillatory brain activity of 88 subjects (46 with a chronic tinnitus percept, 42 without) measured in resting state by MEG was investigated. In the analysis based on the whole group, in sensor space increased activity in the delta frequency band was found in tinnitus patients. Analyzing the subgroup of novices, a significant difference in the theta band emerged additionally to the delta band difference (sensor space). Localizing the origin of the activity, we found a difference in theta and gamma band for the auditory regions for the whole group and the same significant difference in the subgroup of novices. However, no differences in oscillatory activity were observed between tinnitus and control groups once subjects with mental health comorbidity were excluded. Against the background of previous studies, the study at hand underlines the fragility of the results in the field of neuronal cortical oscillations in tinnitus. It supports the body of research arguing for low frequency oscillations and gamma band activity as markers associated with tinnitus.
Efficient Optimization for Rank-Based Loss Functions

The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.
The Transcriptome of Type I Murine Astrocytes under Interferon-Gamma Exposure and Remyelination Stimulus

Astrocytes are considered to be an important contributor to central nervous system (CNS) disorders, particularly multiple sclerosis. The transcriptome of these cells is greatly affected by cytokines released by lymphocytes, penetrating the blood–brain barrier—in particular, the classical pro-inflammatory cytokine interferon-gamma (IFNγ). We report here the transcriptomal profiling of astrocytes treated using IFNγ and benztropine, a putative remyelinization agent. Our findings indicate that the expression of genes involved in antigen processing and presentation in astrocytes are significantly upregulated upon IFNγ exposure, emphasizing the critical role of this cytokine in the redirection of immune response towards self-antigens. Data reported herein support previous observations that the IFNγ-induced JAK-STAT signaling pathway may be regarded as a valuable target for pharmaceutical interventions.
Efficient Bias-Span-Constrained Exploration-Exploitation in Reinforcement Learning

We introduce SCAL, an algorithm designed to perform efficient exploration-exploitation in any unknown weakly-communicating Markov decision process (MDP) for which an upper bound $c$ on the span of the optimal bias function is known. For an MDP with $S$ states, $A$ actions and $\Gamma \leq S$ possible next states, we prove a regret bound of $\widetilde{O}(c\sqrt{\Gamma SAT})$, which significantly improves over existing algorithms (e.g., UCRL and PSRL), whose regret scales linearly with the MDP diameter $D$. In fact, the optimal bias span is finite and often much smaller than $D$ (e.g., $D=\infty$ in non-communicating MDPs). A similar result was originally derived by Bartlett and Tewari (2009) for REGAL.C, for which no tractable algorithm is available. In this paper, we relax the optimization problem at the core of REGAL.C, we carefully analyze its properties, and we provide the first computationally efficient algorithm to solve it. Finally, we report numerical simulations supporting our theoretical findings and showing how SCAL significantly outperforms UCRL in MDPs with large diameter and small span.
Is adjustment disorder unidimensional or multidimensional? Implications for ICD‐11

In preparation for ICD‐11, the adjustment disorder (AjD) diagnosis has undergone considerable revisions; however, the latent structure of AjD remains uncertain. It is unclear whether AjD is best represented as a unidimensional or multidimensional construct. This study performed a comprehensive assessment of the latent structure of AjD symptomatology and assessed its concurrent and discriminant validity. Individuals who experienced involuntary job loss (N = 333) completed a self‐report measure of AjD symptoms. Seven alternative models of AjD were tested using confirmatory factor analysis. General psychological distress, impairment in social functioning, occupational self‐efficacy, and sense of coherence were used as criterion variables for construct validity. In the confirmatory factor analysis, a bifactor solution with one dominant general AjD factor and 5 correlated group factors (preoccupation, failure‐to‐adapt, avoidance, affective reaction, and impulsivity) provided optimal fit. As expected, the AjD factor showed strong positive associations with general psychological distress and impairments in social functioning and moderately negative associations with occupational self‐efficacy and sense of coherence. With regard to unidimensionality or multidimensionality of AjD symptoms, the current results indicate the plausibility of a unidimensional conceptualization. Future research should focus on essential key characteristics and a reduction of symptoms for the AjD definition.
Out‐of‐hospital emergency care providers' work and challenges in a changing care environment

Acutely ill patients are often treated on site instead of being transported to hospital, so wide-ranging professional competence is required from staff. The aim of this study was to describe and produce new information about out-of-hospital emergency care providers' competence, skills and willingness to engage in self-development activities, and to uncover challenges experienced by care providers in the midst of changing work practices. A quantitative questionnaire was sent to out-of-hospital emergency care providers (N = 142, response rate 53%) of one Finnish hospital district. Data were analysed using spss for Windows 22 software. Almost all respondents found their work interesting and their ability to work independently sufficient. The majority found the work meaningful. Almost 20% felt that work was dominated by constant rush, and 40%, more than half of 25-year-olds but <10% of over 45-years-olds, found the work physically straining. The majority indicated that they had a sufficient theoretical-practical basis to perform their regular duties, and more than one-third felt that they had sufficient skills to deal with multiple patient or disaster situations. Over 20% stated that they were unsure about performing new or infrequent procedures. A number of factors experienced as challenging were revealed. The results provide a basis for improving care providers' initial and further training.
Bifidobacterium pseudocatenulatum CECT 7765 supplementation restores altered vascular function in an experimental model of obese mice

Aims. Bifidobacterium pseudocatenulatum CECT 7765 improves metabolic and immunological altered functions in high fat fed mice, however little is known about the effects of potential probiotics on vascular reactivity. The aim of the present study was to investigate the effects of a potential probiotic strain, Bifidobacterium pseudocatenulatum CECT 7765, on vascular response in obese mice. Methods. Aorta samples were obtained from mice, which were divided into three groups: a control group, receiving a standard diet; an obese group, receiving a high-fat diet; and an obese group receiving high-fat diet and a daily dose of B. pseudocatenulatum CECT 7765 by oral gavage. Aortic rings were suspended in organ baths for isometric recording of tension. mRNA expression of eNOS was evaluated by real-time polymerase chain reaction. Results. Contractions induced by KCl, noradrenaline and thromboxane analogue were 33%, 30% and 45% lower respectively in aortic rings from obese mice. Bifidobacteria administration reversed this effect. eNOS inhibition increased the response to noradrenaline in the three groups with a significant lower magnitude in aortic rings from obese mice receiving bifidobacteria supplement. Acetylcholine caused a greater vasodilation in aorta from obese group (46±3% for control and 69±4% for obese group; p<0.05) and bifidobacteria reversed it (57±5%). Response to sodium nitroprusside was displaced 2.9 times to the left in a parallel manner in obese group. Relaxation to sodium nitroprusside remained unchanged in the bifidobacteria fed group. There was about five-fold decreased mRNA expression of eNOS in aortic segments from the group receiving bifidobacteria. Conclusion. Bifidobacterium pseudocatenulatum CECT 7765 restores the obesity-induced altered vascular function mainly by reducing nitric oxide release.
Comparative effectiveness of primary tumor resection in patients with stage IV colon cancer

Although the safety of combination chemotherapy without primary tumor resection (PTR) in patients with stage IV colon cancer has been established, questions remain regarding a potential survival benefit with PTR. The objective of this study was to compare mortality rates in patients who had colon cancer with unresectable metastases who did and did not undergo PTR.