julilili42/papers huggingface dataset:
What Should I Eat and Why? The Environmental, Genetic, and Behavioral Determinants of Food Choice: Summary from a Pennington Scientific Symposium
2020-06-10

This review details the proceedings of a Pennington Biomedical scientific symposium titled, “What Should I Eat and Why? The Environmental, Genetic, and Behavioral Determinants of Food Choice.” The symposium was designed to review the literature about energy homeostasis, particularly related to food choice and feeding behaviors, from psychology to physiology. This review discusses the intrinsic determinants of food choice, including biological mechanisms (genetics), peripheral and central signals, brain correlates, and the potential role of the microbiome. This review also address the extrinsic determinants (environment) of food choice within our physical and social environments. Finally, this review reports the current treatment practices for the clinical management of eating‐induced overweight and obesity. An improved understanding of these determinants will inform best practices for the clinical treatment and prevention of obesity. Strategies paired with systemic shifts in our public health policies and changes in our “obesogenic” environment will be most effective at attenuating the obesity epidemic.
Phylogenomics ofMycobacterium africanumreveals a new lineage and a complex evolutionary history
2020-06-10

Abstract Human tuberculosis is caused by members of the Mycobacterium tuberculosis Complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto as well as two lineages (L5 and L6) traditionally referred to as M. africanum . Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known on their genomic diversity, phylogeography and evolution. Here, we analyzed the genomes of 365 L5 and 326 L6 strains, plus five related genomes that had not been classified into any of the known MTBC lineages, isolated from patients from 21 African countries. Our population genomic and phylogeographical analyses show that the unclassified genomes belonged to a new group that we propose to name MTBC Lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure, genetic diversity and association with drug resistance. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of tuberculosis in Africa and globally.
A novel missense variant in MYO3A is associated with autosomal dominant high‐frequency hearing loss in a German family
2020-06-10

Abstract Background MYO3A , encoding the myosin IIIA protein, is associated with autosomal recessive and autosomal dominant nonsyndromic hearing loss. To date, only two missense variants located in the motor‐head domain of MYO3A have been described in autosomal dominant families with progressive, mild‐to‐profound sensorineural hearing loss. These variants alter the ATPase activity of myosin IIIA. Methods Exome sequencing of a proband from a three‐generation German family with prelingual, moderate‐to‐profound, high‐frequency hearing loss was performed. Segregation analysis confirmed a dominant inheritance pattern. Regression analysis of mean hearing level thresholds per individual and ear was performed at high‐, mid‐, and low‐frequencies. Results A novel heterozygous missense variant c.716T&gt;C, p.(Leu239Pro) in the kinase domain of MYO3A was identified that is predicted in silico as disease causing. High‐frequency, progressive hearing loss was identified. Conclusion Correlation analysis of pure‐tone hearing thresholds revealed progressive hearing loss, especially in the high‐frequencies. In the present study, we report the first dominant likely pathogenic variant in MYO3A in a European family and further support MYO3A as an autosomal dominant hearing loss gene.
A cross-population study of sexual dimorphism in the bony labyrinth
2020-06-10

Abstract Previous research found sexual dimorphism in the bony labyrinth of a Greek population sample (Osipov et al. 2013). This study intends to investigate the nature of this structure’s sexual dimorphism across populations of diverse geographic origin and to identify the effect of inter-population variation on the accuracy of determining sex using the bony labyrinth. Three population samples of known sex were analyzed originating from Europe ( n = 30), Africa ( n = 38), and North America ( n = 30). The discriminant function developed in Osipov et al. (2013) was applied, and new function equations for sex estimation were developed. In addition, we used principal component analyses for investigating population differences, while bivariate tests were used to compare across population samples, sexes, and anatomical sides. A significant level of sexual dimorphism was found in all population samples, being driven by both size and shape differences. Discriminant functions for sex estimation were developed for all three population samples combined (71.4% accuracy) as well as separately (70–80% accuracy). The German sample was the least sexually dimorphic, whereas the North American sample exhibited the greatest sexual dimorphism. The size and shape of the bony labyrinth also significantly differed across population samples. The bony labyrinth is found to be sexually dimorphic across distinct population groups. Due to significant differences across our population samples, the accuracy of the previously proposed method for sex determination (Osipov et al., 2013) was relatively low. For this purpose, this study presented new functions, whose accuracy was tested in three distinct population samples.
Use of Real-Time Functional Magnetic Resonance Imaging-Based Neurofeedback to Downregulate Insular Cortex in Nicotine-Addicted Smokers
2020-06-10

It has been more than a decade since the first functional magnetic resonance imaging (fMRI)-based neurofeedback approach was successfully implemented. Since then, various studies have demonstrated that participants can learn to voluntarily control a circumscribed brain region. Consequently, real-time fMRI (rtfMRI) provided a novel opportunity to study modifications of behavior due to manipulation of brain activity. Hence, reports of rtfMRI applications to train self-regulation of brain activity and the concomitant modifications in behavioral and clinical conditions such as neurological and psychiatric disorders [e.g., schizophrenia, obsessive compulsive Disorder (OCD), stroke] have rapidly increased. Neuroimaging studies in addiction research have shown that the anterior cingulate cortex, orbitofrontal cortex, and insular cortex are activated during the presentation of drug-associated cues. Also, activity in both left and right insular cortices have been shown to be highly correlated with drug urges when participants are exposed to craving-eliciting cues. Hence, the bilateral insula is of particular importance in researching drug urges and addiction due to its role in the representation of bodily (interoceptive) states. This study explores the use of rtfMRI neurofeedback for the reduction in blood oxygen-level dependent (BOLD) activity in bilateral insular cortices of nicotine-addicted participants. The study also tests if there are neurofeedback training-associated modifications in the implicit attitudes of participants towards nicotine-craving cues and explicit-craving behavior.
Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe
2020-06-10

Summary Sexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15 th century, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a previously unknown diversity of Treponema pallidum in historical Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws and bejel. These findings imply a more complex pattern of geographical prevalence and etiology of early treponemal epidemics than previously understood.
Individual Differences in Visual Attention: A Short, Reliable, Open Source, and Multilingual Test of Multiple Object Tracking in PsychoPy
2020-06-10

Individual differences in attentional abilities provide an interesting approach in studying visual attention as well as the relation of attention to other psychometric measures. However, recent research has demonstrated that many tasks from experimental research are not suitable for individual differences research as they fail to capture these differences reliably. Here, we provide a test for individual differences in visual attention which relies on the multiple object tracking task (MOT). This test captures individual differences reliably in 6-15 minutes. Within the task the participants have to maintain a set of targets (among identical distractors) across an interval of object motion. It captures the efficiency of attentional deployment. Importantly, this test was explicitly designed and tested for reliability under conditions that match those of most laboratory research (restricted sample of students, approximately n = 50). The test is free to use and runs fully under open source software. In order to facilitate the application of the test, we have translated it into 16 common languages (Chinese, Danish, Dutch, English, Finnish, French, German, Italian, Japanese, Norwegian, Polish, Portuguese, Russian, Spanish, Swedish, Turkish). The test can be downloaded at https://osf.io/qy6nb/. We hope that this MOT test supports researchers whose field of study requires capturing individual differences in visual attention reliably.
Statistical Analysis of Bistatic Radar Ground Clutter for Different German Rural Environments
2020-06-10

This article presents the statistical analysis of bistatic radar rural ground clutter for different terrain types under low grazing angles. Compared to most state-of-the-art analysis, we present country-specific clutter analysis for subgroups of rural environments rather than for the rural environment as a whole. Therefore, the rural environment analysis is divided into four dominant subgroup terrain types, namely fields with low vegetation, fields with high vegetation, plantations of small trees and forest environments representing a typical rural German environment. We will present the results for both the summer and the winter vegetation. Therefore, bistatic measurement campaigns have been carried out during the summer 2019 and the winter of 2019/20 in the aforementioned four different rural terrain types. The measurements were performed in the radar relevant X-band at a center frequency of 8.85 GHz and over a bandwidth of 100 MHz according to available transmit permission. The distinction of the rural terrain into different subgroups enables a more precise and accurate clutter analysis and modeling of the statistical properties as will be shown in the presented results. The statistical properties are derived from the calculated clutter amplitudes probability density functions and corresponding cumulative distribution functions for each of the four terrain types and the corresponding season. The data basis for the clutter analysis are the processed range-Doppler maps from the bistatic radar measurements. According to the authors’ current knowledge, a similar investigation based on real bistatic radar measurement data with the division into terrain subgroups has not yet been carried out and published for a German rural environment.
Beyond olfactory cortex – severity of post-traumatic olfactory loss is associated with response to odors in frontal-parietal-insular networks
2020-06-10

Olfactory impairment after trauma is associated with changes in olfactory cortex, including decreased gray matter density and decreased response to odors. Much less is known about the role of other cortical areas in olfactory impairment. We used fMRI in a sample of 63 participants, consisting of 25 with post-traumatic functional anosmia, 16 with post-traumatic hyposmia, and 22 healthy controls with normosmia to investigate whole brain response to odors. Similar neural responses were observed across the groups to odor versus odorless stimuli in the primary olfactory areas in piriform cortex, whereas response in the frontal operculum and anterior insula (fO/al) increased with olfactory function (normosmia &gt; hyposmia &gt; functional anosmia). Unexpectedly, a negative association was observed between response and olfactory function in the mediodorsal thalamus (mdT), ventromedial prefrontal cortex (vmPFC) and posterior cingulate cortex (pCC). Finally, connectivity within a network consisting of vmPFC, fO, and pCC could be used to successfully classify participants as having functional anosmia or normosmia. We conclude that, at the neural level, olfactory impairment due to head trauma is best characterized by heightened responses and differential connectivity in higher-order areas beyond olfactory cortex. Significance Statement Olfactory impairment affects a quarter of the population, with subjective complaints usually confirmed with psychophysical measurements. Here, we demonstrate that the degree of olfactory impairment can also be categorized using neural responses to odors. Remarkably, regions with neural responses that were predictive usually showed an increase in response to odors with degree of impairment, rather than a reduction, as might be expected. Further, predictive cortical regions were not isolated to canonical olfactory areas.
Automated Detection of Fetal Brain Signals with Principal Component Analysis
2020-06-10

<pre>Detection of fetal brain signals in fetal magnetoencephalographic recordings is -- due to the low signal to noise ratio -- challenging for researchers in this field. Up to now, state of the art is a manual evaluation of the signal. To make the evaluation more reproducible and less time consuming, an approach using Principal Component Analysis is introduced. Locations of the channels of most importance for the first three principal components are taken into account and their possibility of resembling brain activity evaluated. Data with auditory stimulation are taken for this analysis and trigger averaged signals from the channels selected as brain activity (manually \\&amp; automatically) compared. Comparisons are done with regard to their average baseline activity, activity during a window of interest and timing and amplitude of their highest auditory event-related peak. The number of evaluable data sets showed to be lower for the automated compared to manual approach but auditory event-related peaks did not differ significantly in amplitude or timing and in both cases there was a significant activity change following the tone event. The given results and the advantage of reproducibility make this method a valid alternative. </pre>
Weathering, alteration and reconstructing Earth's oxygenation
2020-06-11

Deciphering the role—if any—that free oxygen levels played in controlling the timing and tempo of the radiation of complex life is one of the most fundamental questions in Earth and life sciences. Accurately reconstructing Earth's redox history is an essential part of tackling this question. Over the past few decades, there has been a proliferation of research employing geochemical redox proxies in an effort to tell the story of Earth's oxygenation. However, many of these studies, even those considering the same geochemical proxy systems, have led to conflicting interpretations of the timing and intensity of oxygenation events. There are two potential explanations for conflicting redox reconstructions: (i) that free oxygen levels were incredibly dynamic in both time and space or (ii) that collectively, as a community—including the authors of this article—we have frequently studied rocks affected by secondary weathering and alteration (particularly secondary oxidation) while neglecting to address the impact of this alteration on the generated data. There are now multiple case studies that have documented previously overlooked secondary alteration, resolving some of the conflicting constrains regarding redox evolution. Here, an analysis of a large shale geochemistry database reveals significant differences in cerium (Ce) anomalies, a common palaeoredox proxy, between outcrop and drill core samples. This inconsistency provides support for the idea that geochemical data from altered samples are frequently published in the peer-reviewed literature. As individuals and a geochemical community, most of us have been slow to appreciate how pervasive the problem is but there are examples of other communities that have faced and met the challenges raised by such quality control crises. Further evidence of the high potential for alteration of deep-time geochemical samples, and recognition of the manner in which this may lead to spurious results and palaeoenvironmental interpretations, indicate that sample archiving, in publicly accessible collections needs to become a prerequisite for publication of new palaeoredox data. Finally, the geochemical community need to think about ways to implement additional quality control measures to increase the fidelity of palaeoredox proxy work.
Definable Conditionals
2020-06-11

Abstract The variably strict analysis of conditionals does not only largely dominate the philosophical literature, since its invention by Stalnaker and Lewis, it also found its way into linguistics and psychology. Yet, the shortcomings of Lewis–Stalnaker’s account initiated a plethora of modifications, such as non-vacuist conditionals, presuppositional indicatives, perfect conditionals, or other conditional constructions, for example: reason relations, difference-making conditionals, counterfactual dependency, or probabilistic relevance. Many of these new connectives can be treated as strengthened or weakened conditionals. They are definable conditionals . This article develops a technique to infer the logic for such definable conditionals from the known logic of the underlying defining conditional. The technique is applied to central examples. The results show that a large part of the zoo of conditionals arises from a basic conditional—a constant nucleus of the different contextual and conceptual variations of variably strict conditionals.
Prompt tau neutrinos at the LHC
2020-06-11

We investigate tau neutrinos from heavy flavor hadrons that can be explored at a high rapidity LHC experiment. A large number of tau neutrinos can be produced in collision at the LHC in the very forward region, where its main source is mesons since the weak boson contribution is negligible. Abundant production of tau neutrinos will allow the precise study of tau neutrino charged current interactions to test lepton universality. In addition, it will provide the opportunity to probe the mixing between sterile neutrinos and tau neutrinos. We evaluate the fluxes and the event rates of the prompt tau neutrinos as well as the theoretical uncertainty using fits to the experimental data for charm meson production. Also, we describe the sterile neutrino masses and mixing angles that can be constrained by tau neutrinos from the LHC.
EuBIC 2020 Developer's Meeting keynote recordings
2020-06-11

The EuBIC Developers’ Meeting is organized each second year by the European Bioinformatics Community (EuBIC), an initiative of the European Proteomics Association (EuPA) for user-oriented bioinformatics. This meeting is aimed at bringing together computer scientists and developers in the field of proteomics bioinformatics to discuss and work together in an open and constructive spirit. The program is split between keynote lectures and multiple hackathon sessions where the participants develop bioinformatics tools and resources addressing outstanding needs in the proteomics bioinformatics and user community. The 2020 EuBIC Developers’ Meeting was held from January 13th – 17th 2020 in Nyborg, Denmark. All bioinformaticians were invited to join this second EuBIC Developers’ Meeting. All keynotes, including the introduction to computational mass spectrometry, were recorded and are freely available here and on YouTube: www.youtube.com/playlist?list=PL_6fafgzU1nHd13qqjm3uNvyHh62JpPcB. More info: https://eubic-ms.org/events/2020-developers-meeting/.
Bridging the Gap between Autonomous and Predetermined Paradigms: The Role of Sampling in Evaluative Learning
2020-06-11

&lt;p&gt;While most evaluative learning paradigms remove participants’ autonomy over the information they receive, other research traditions have demonstrated that information sampling has an important role in learning. We investigate the impact of information sampling on a central evaluative learning paradigm: evaluative conditioning. We compare a traditional evaluative conditioning paradigm with a paradigm in which participants have autonomy over the stimulus pairings they receive. Participants in the high-autonomy condition show a strong preference for positively paired CSs. Nevertheless, we obtained evaluative conditioning effects in all conditions. High-autonomy participants, but not their low-autonomy counterparts, also show effects of the sampling decision on evaluations. Specifically, sampled stimuli become more positive, whereas ignored stimuli become more negative over the learning phase. Thus, the present research provides a cornerstone for integrating several research traditions within and beyond the evaluative learning literature, providing a foundation for new insights and more comprehensive theories of learning.&lt;/p&gt;
Bridging the Gap between Autonomous and Predetermined Paradigms: The Role of Sampling in Evaluative Learning
2020-06-11

While most evaluative learning paradigms remove participants’ autonomy over the information they receive, other research traditions have demonstrated that information sampling has an important role in learning. We investigate the impact of information sampling on a central evaluative learning paradigm: evaluative conditioning. We compare a traditional evaluative conditioning paradigm with a paradigm in which participants have autonomy over the stimulus pairings they receive. Participants in the high-autonomy condition show a strong preference for positively paired CSs. Nevertheless, the strength of evaluative conditioning effects was independent of autonomy. Moreover, high-autonomy participants, but not their low-autonomy counterparts, demonstrate a relationship between sampling frequency and evaluations, in line with the interpretation that sampled stimuli become more positive, whereas ignored stimuli become more negative over the course of the learning phase. The present research provides a cornerstone for integrating several research traditions within and beyond the evaluative learning literature, providing a foundation for new insights and more comprehensive theories of evaluative learning.