Miracle-dz/UniFAR-FTUs huggingface dataset:
Coarse-grained molecular simulations of the binding of the SARS-CoV-2 spike protein RBD to the ACE2 receptor

Since it was first observed, the COVID-19 pandemic has created a global emergency for national health systems due to millions of confirmed cases and hundreds of thousands of deaths. At a molecular level, the bottleneck for the infection is the binding of the receptor binding domain (RBD) of the viral spike protein to ACE2, an enzyme exposed on human cell membranes. Several experimental structures of the ACE2:RBD complex have been made available, however they offer only a static description of the arrangements of the molecules in either the free or bound states. In order to gain a dynamic description of the binding process that is key to infection, we use molecular simulations with a coarse grained model of the RBD and ACE2. We find that binding occurs in an all-or-none way, without intermediates, and that even in the bound state, the RBD exhibits a considerably dynamic behaviour. From short equilibrium simulations started in the unbound state we provide snapshots that result in a tentative mechanism of binding. Our findings may be important for the development of drug discovery strategies that target the RBD.
Incorporating Genome Annotation Into Genomic Prediction for Carcass Traits in Chinese Simmental Beef Cattle

Various methods have been proposed for genomic prediction (GP) in livestock. These methods have mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits in Chinese Simmental beef cattle, we incorporated the genome annotation information into GP. Single nucleotide polymorphisms (SNPs) were annotated to five genomic classes: intergenic, gene, exon, protein coding sequences, and 3′/5′ untranslated region. Haploblocks were constructed for all markers and these five genomic classes by defining a biologically functional unit, and haplotype effects were modeled in both numerical dosage and categorical coding strategies. The first-order epistatic effects among SNPs and haplotypes were modeled using a categorical epistasis model. For all makers, the extension from the SNP-based model to a haplotype-based model improved the accuracy by 5.4–9.8% for carcass weight (CW), live weight (LW), and striploin (SI). For the five genomic classes using the haplotype-based prediction model, the incorporation of gene class information into the model improved the accuracies by an average of 1.4, 2.1, and 1.3% for CW, LW, and SI, respectively, compared with their corresponding results for all markers. Including the first-order epistatic effects into the prediction models improved the accuracies in some traits and genomic classes. Therefore, for traits with moderate-to-high heritability, incorporating genome annotation information of gene class into haplotype-based prediction models could be considered as a promising tool for GP in Chinese Simmental beef cattle, and modeling epistasis in prediction can further increase the accuracy to some degree.
Sex allocation, inbreeding, and measures of population differentiation in hermaphroditic metapopulations

Selection in inbreeding populations is expected to favour female-biased sex ratios in dioecious or gonochoristic species as a result of local mate competition, a prediction that finds strong support in populations in which females have control of the proportion of their sons versus daughters. Local mate competition due to inbreeding should also promote female-biased sex allocation in hermaphrodites, with reduced emphasis on the production of sperm or pollen relative to eggs, ovules or seeds. While inbreeding can be the direct result of the mating system in local populations, it can also result from demographic causes such as population turnover in metapopulations with frequent local extinction and recolonization. This effect of the turnover of demes has previously been analysed under the ‘haystack model’ for species with separate sexes. Here, we use quantitative genetic simulations to ask how population turnover affects the evolution of sex allocation in hermaphroditic metapopulations, and we assess the extent to which different genetic measures of inbreeding and population differentiation, especially FST and Jost’s D, predict the equilibrium sex allocation. We find that population turnover may dramatically enhance the female bias of hermaphroditic metapopulations, particularly where the inter-deme migration rate is low, even where local inbreeding, measured by FIS, is low or absent. In such situations, FST is a good predictor of the equilibrium sex allocation, and much better than Jost’s D. Our study extends predictions for sex allocation in subdivided populations that might experience population turnover to hermaphroditic species, and draws attention in general to the power of Wright’s hierarchical inbreeding statistics to predict the sex allocation in metapopulations at equilibrium.
A Three-Wave Longitudinal Study of Moderated Mediation Between High-Performance Work Systems and Employee Job Satisfaction: The Role of Relational Coordination and Peer Justice Climate

Existing literature lacks studies that examine the indirect effect of high-performance work systems (HPWSs) on employee job satisfaction through employee–employee relations. Moreover, less is known about the boundary conditions of this indirect effect. This study sought to longitudinally examine the mediating role of a specific form of employee–employee relations—relational coordination—in the relationship between HPWS and job satisfaction. Data were collected in three waves from the employees of commercial banks (N = 322). Partial least squares structural equation modeling was used for data analysis. Results from multiple linear autoregressive longitudinal analysis indicate that HPWSs predict relational coordination, which in turn partially mediates the HPWS–job satisfaction relationship. Perceptions of peer justice climate provide boundary conditions for the aforementioned mediating effect. This study contributes to existing literature by explaining moderated-mediation mechanisms through which HPWSs predict employee job satisfaction. Managers can strengthen the effect of HPWS on employee–employee relations and subsequent effect on employee job satisfaction by promoting peer justice climate in organizations.
A PRELIMINARY REPORT ON THE ACOUSTIC COMMUNICATION IN URUGUAYAN CTENOMYS (RODENTIA, OCTODONTIDAE): BASIC SOUND TYPES

ABSTRACT Subterranean rodents are interesting organisms for communication studies because of their fossorial way of life. Acoustic communication in the South American genus Ctenomys has not yet been studied even though this species is geographically widespread. This paper represents a preliminary survey of Ctenomys vocalizations. Three types of vocal signals were identified: S-, C- and G-signals. Using field, laboratory and literature data, we provide interpretations on the possible functions of these signals. S-signals are harsh and low-pitched putative spatial localization signals that may also encode for sexual identification. C-signals are relatively high-pitched and narrow-banded FM vocalizations that are sexual signals used by females in a copulatory context. Finally, G-signals are harsh and patternless sounds that are aggressive signals used in direct encounters with con- or hetero- specific individuals.
Drift algal subsidies to sea urchins in low-productivity habitats

Highly productive kelp beds off the coast of Nova Scotia, Canada, export a large quantity of detrital material to adjacent low-productivity habitats. We used a combination of dietary tracers (fatty acids, stable isotopes, and gut contents) and gonad index to evaluate the importance and spatial extent of this energy subsidy to green sea urchins Strongylocentrotus droebachiensis offshore from kelp beds along 240 m transects perpendicular to the shore at 4 sites. Gut contents and δ13C values indicated the presence of kelp in the diets of sea urchins collected up to 240 m offshore from kelp beds. We observed a corresponding decrease in gonad index with distance from the kelp at all sites but one, where patches of live kelp offshore from the main kelp bed provided an additional food source. Sea urchins that fed on a large pool of detrital kelp at another site had ~15% larger gonads than sea urchins at other locations. δ15N values were more enriched for sea urchins at 160 and 240 m from the kelp bed, suggesting that these sea urchins consume more animal matter, which was also evident in their gut contents. Our findings suggest that drift kelp represents an important energy source for sea urchins in subtidal habitats on the scale of tens to hundreds of meters offshore from kelp beds and that this resource is increasingly patchy in space and time with distance from the kelp bed.
The Effect of Perceived Effort on Reward Valuation: Taking the Reward Positivity (RewP) to Dissonance Theory

The present research was designed to test whether the subjective experience of more effort related to more reward valuation as measured by a neural response. This prediction was derived from the theory of cognitive dissonance and its effort justification paradigm. Young adult participants (n = 82) engaged in multiple trails of a low or high effort task that resulted in a loss or reward on each trial. Neural responses to the reward (loss) cue were measured using EEG so that the event-related potential known as the Reward Positivity (RewP) could be assessed. Results revealed no significant differences between low and high effort conditions on the RewP. However, within the high effort condition, a more subjective experience of effort was associated with a larger RewP. This research extends past research on the effort justification paradigm of cognitive dissonance theory by suggesting that effort justification is associated with an implicit measure of reward valuation. It, therefore, challenges recent perspectives on dissonance processes that posit that these evaluative changes should only occur on explicit but not implicit measures.
Early-Life Interpersonal and Affective Risk Factors for Pathological Gaming

Internet gaming is among the most popular entertainment options, worldwide; however, a considerable proportion of gamers show symptoms of pathological gaming. Internet gaming disorder (IGD) has been proposed to describe a behavioral addiction, which shares many similarities, both physical and psychological, with substance use disorder. Environmental factors, such as interpersonal and relationship dynamics during childhood and adolescence, have been suggested to modulate the onset and trajectories of IGD. However, studies exploring the contributions of dysfunctional family environments to the development of IGD remain limited. This minireview aims to offer an overview of the current knowledge regarding the impacts of early-life interpersonal and relationship dynamics on the development of IGD and to provide a snapshot of the current state of the literature in this field. Specifically, it underlines the modulatory role of early-life relational factors such as a) family function, b) parent-child relationships, c) childhood maltreatment, and d) bullying and cyberbullying on the development of IGD. Consistent with this evidence, therapeutic interventions that aim to “restructure” the emotional ties and familiar dynamics that are known to be associated with dysfunctional behaviors and feelings, and likely promote pathological gaming, are recognized as the most successful clinical therapeutic approaches for IGD.
100 Years of poultry genetics

The beginning of the 21st century is an appropriate time to review a century of poultry genetics, because it is one hundred years since Mendel's pioneering work was rediscovered and became part of the mainstream of science. Although, in my opinion, Mendel enjoyed more than a fair share of luck in reaching his conclusions, he nevertheless laid a foundation on which students of poultry, and many other species, were able to build a vast body of literature. Mendel's choice of the height of pea plants, in retrospect, was not a wise one. Here is a trait that is basically quantitative, and yet he was able to describe it, and reach his conclusions, in qualitative terms!
College-Age Millennials' Preferences for Food Supplied by Urban Agriculture

Millennials are the largest generation, yet. As a result, their preferences are critical when it comes to evaluating success of urban agriculture. Using two online choice experiments, this paper investigates the preferences and willingness to pay of college student millennials for unprocessed (fresh) or processed (typically come in a container) food products sold at urban farms. We also examine whether competing points of sale and other attributes, such as organic, affect preferences, and willingness to pay for urban farm food. We find that, on average, college-age millennials are willing to pay a premium for local food. However, they are not willing to pay premiums for local food that is sold at farmers markets, and discount it when it is purchased directly from an urban farm. Our findings suggest that, if the goal is to increase the sales of urban farm food, targeted promotions are needed. Urban farms have to show the value from purchasing products through their channels to college-age millennials or seek the means to supply their food through grocery stores.
Bilingual Language Experience Shapes Resting-State Brain Rhythms

An increasing body of research has investigated how bilingual language experience changes brain structure and function, including changes to task-free, or “resting-state” brain connectivity. Such findings provide important evidence about how the brain continues to be shaped by different language experiences throughout the lifespan. The neural effects of bilingual language experience can provide evidence about the additional processing demands placed on the linguistic and/or executive systems by dual-language use. While considerable research has used MRI to examine where these changes occur, such methods cannot reveal the temporal dynamics of functioning brain networks at rest. The current study used data from task-free EEGS to disentangle how the linguistic and cognitive demands of bilingual language use impact brain functioning. Data analyzed from 106 bilinguals and 91 monolinguals revealed that bilinguals had greater alpha power, and significantly greater and broader coherence in the alpha and beta frequency ranges than monolinguals. Follow-up analyses showed that higher alpha was related to language control: more second-language use, higher native-language proficiency, and earlier age of second-language acquisition. Bilateral beta power was related to native-language proficiency, whereas theta was related to native-language proficiency only in left-hemisphere electrodes. The results contribute to our understanding of how the linguistic and cognitive requirements of dual-language use shape intrinsic brain activity, and what the broader implications for information processing may be.
Efficacy, Safety, and Tolerability of Theta-Burst Stimulation in Mixed Depression: Design, Rationale, and Objectives of a Randomized, Double-Blinded, Sham-Controlled Trial

Introduction Mixed-specifier mood disorders are probably a different subgroup in terms of response to treatment, socio-demographic parameters, course, and family history. Here we describe the rationale and design of a clinical trial aimed to test the efficacy, safety, and tolerability of a non-pharmacological treatment known as theta-burst stimulation (TBS) for treating the mixed depressive episodes of both bipolar (I or II), and unipolar depression. Methods The study is designed as a randomized, sham-controlled, double-blinded clinical trial evaluating TBS for the treatment of moderate or severe major depressive episodes with mixed features of patients receiving at least one first or second-line pharmacological treatment for depressive episodes without adequate response. Ninety adult (18 to 65 years old) patients will be enrolled and submitted to 6-week (comprising 5 consecutive days a week sessions for the first 3 weeks and then 2 days a week for a further 3 week) of inhibitory followed by excitatory TBS in dorsolateral prefrontal cortex. Participants will be assessed using clinical and neuropsychological tests before and after the intervention. The primary outcome is change in Montgomery–Åsberg Depression Scale (MADRS) score over time and across groups. Cognitive parameters will also be assessed with neuropsychological tests. Results The clinical results will provide evidence about TBS as an adjunctive treatment for mixed depression treatment and neuropsychological parameters will contribute toward an improved understanding the effects of TBS in cognition. Conclusion Our results could introduce a novel therapeutic technique for mixed depressive episodes of both bipolar and unipolar disorders. Clinical Trial Registration www.ClinicalTrials. gov, identifier NCT04123301; date of registration: 10/10/2019; URL: https://clinicaltrials.gov/ct2/show/NCT04123301? term=NCT04123301&rank=1.
The non-typeable Haemophilus influenzae major adhesin Hia is a dual function lectin that binds to human-specific respiratory tract sialic acid glycan receptors

NTHi is a human-adapted pathogen that colonises the human respiratory tract. Strains of NTHi express multiple adhesins, however there is a unique, mutually exclusive relationship between the major adhesins Hia and HMW1/2. Approximately 25% of NTHi strains express Hia, a phase-variable autotransporter protein, and which has a critical role in colonisation of the host nasopharynx. The remaining 75% of strains express HMW1/2. Previous work has shown that the HMW1 and HMW2 proteins mediate binding to 2,3- and 2,6-linked sialic acid glycans found in the human respiratory tract. Here we show that that the high affinity binding domain of Hia, binding domain 1 (BD1) is responsible for binding to α2,6-sialyllactosamine glycans. BD1 is highly specific for glycans that incorporate the form of sialic acid expressed by humans, N-acetylneuraminic acid (Neu5Ac). We further show that Hia has lower affinity binding activity for 2,3-linked sialic acid and that this binding activity is mediated via a distinct domain. Thus, Hia with its dual binding activities functionally mimics the combined activities of the HMW1 and 2 adhesins. In addition, we show that Hia has a role in biofilm formation by strains of NTHi that express the adhesin. Knowledge of the binding affinity of a major NTHi adhesin, and putative vaccine candidate, will direct and inform development of future vaccines and therapeutic strategies for this important pathogen. Importance Host-adapted bacterial pathogens like NTHi have evolved specific mechanisms to colonize their restricted host niche. Relatively few of the adhesins expressed by NTHi have been characterized as regards their binding affinity at the molecular level. In this work we show that the major NTHi adhesin, Hia, preferentially binds to Neu5Ac-α2,6-sialyllactosamine, the form of sialic acid expressed in humans. The receptors targeted by Hia in the human airway mirror those targeted by influenza A virus and indicates the broad importance of sialic acid glycans as receptors for airway pathogens.
Song sparrows do not discriminate between their own song and stranger song

Bird song is socially learned. During song learning, the bird’s hearing its own vocalization is important for normal development of song. Whether bird’s own song is represented and recognized as a special category in adult birds, however, is unclear. If birds respond differently to their own songs when these are played back to them, this would be evidence for auditory self-recognition. To test this possibility, we presented song sparrow males (Melospiza melodia) playbacks of their own songs or stranger songs and measured aggressive responses as well as type matching. We find no evidence of behavioral discrimination of bird’s own song relative to the (non-matching) stranger song. These findings cast doubt on an earlier proposal that song sparrows display auditory self-recognition and support the common assumption in playback experiments that bird’s own song is perceived as stranger song.
Dysregulated Mucosal Immunity and Associated Pathogeneses in Preterm Neonates

Many functions of the immune system are impaired in neonates, allowing vulnerability to serious bacterial, viral and fungal infections which would otherwise not be pathogenic to mature individuals. This vulnerability is exacerbated in compromised newborns such as premature neonates and those who have undergone surgery or who require care in an intensive care unit. Higher susceptibility of preterm neonates to infections is associated with delayed immune system maturation, with deficiencies present in both the innate and adaptive immune components. Here, we review recent insights into early life immunity, and highlight features associated with compromised newborns, given the challenges of studying neonatal immunity in compromised neonates due to the transient nature of this period of life, and logistical and ethical obstacles posed by undertaking studies newborns and infants. Finally, we highlight how the unique immunological characteristics of the premature host play key roles in the pathogenesis of diseases that are unique to this population, including necrotizing enterocolitis and the associated sequalae of lung and brain injury.
Classifying Autism Spectrum Disorder Using the Temporal Statistics of Resting-State Functional MRI Data With 3D Convolutional Neural Networks

Resting-state functional magnetic resonance imaging (rs-fMRI) data are 4-dimensional volumes (3-space + 1-time) that have been posited to reflect the underlying mechanisms of information exchange between brain regions, thus making it an attractive modality to develop diagnostic biomarkers of brain dysfunction. The enormous success of deep learning in computer vision has sparked recent interest in applying deep learning in neuroimaging. But the dimensionality of rs-fMRI data is too high (~20 M), making it difficult to meaningfully process the data in its raw form for deep learning experiments. It is currently not clear how the data should be engineered to optimally extract the time information, and whether combining different representations of time could provide better results. In this paper, we explored various transformations that retain the full spatial resolution by summarizing the temporal dimension of the rs-fMRI data, therefore making it possible to train a full three-dimensional convolutional neural network (3D-CNN) even on a moderately sized [~2,000 from Autism Brain Imaging Data Exchange (ABIDE)-I and II] data set. These transformations summarize the activity in each voxel of the rs-fMRI or that of the voxel and its neighbors to a single number. For each brain volume, we calculated regional homogeneity, the amplitude of low-frequency fluctuations, the fractional amplitude of low-frequency fluctuations, degree centrality, eigenvector centrality, local functional connectivity density, entropy, voxel-mirrored homotopic connectivity, and auto-correlation lag. We trained the 3D-CNN on a publically available autism dataset to classify the rs-fMRI images as being from individuals with autism spectrum disorder (ASD) or from healthy controls (CON) at an individual level. We attained results competitive on this task for a combined ABIDE-I and II datasets of ~66%. When all summary measures were combined the result was still only as good as that of the best single measure which was regional homogeneity (ReHo). In addition, we also applied the support vector machine (SVM) algorithm on the same dataset and achieved comparable results, suggesting that 3D-CNNs could not learn additional information from these temporal transformations that were more useful to differentiate ASD from CON.