Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of human fecal and serum parvo-like viruses

Parvovirus-like particles found in the sera of two blood donors had the size and appearance on electron microscopy of a virus (B19) found in the serum of a blood donor by Cossart et al. (1975), and those of a virus found in the feces of a normal subject. Antibody to these viruses was detected by immune electron microscopy and immunoelectro-osmophoresis in the sera of 50 children aged 10 to 15 years. Of these, 36% had antibody to the fecal virus, 36% had antibody to B19, and 54% had antibody to the two other serum viruses. The results of these tests suggest that serologically the three serum viruses were similar to one another, but that the fecal virus was distinct. The two blood donors had nonspecific symptoms at the time of viremia. Both donors had developed immunoglobulin M antibody to the virus when tested 3.5 and 4.5 weeks later, but no viruses were detected in the feces or urine.
Ventral hippocampus mediates inter-trial responding in signaled active avoidance

The hippocampus has a central role in regulating contextual processes in memory. We have shown that pharmacological inactivation of ventral hippocampus (VH) attenuates the context-dependence of signaled active avoidance (SAA) in rats. Here, we explore whether the VH mediates intertrial responses (ITRs), which are putative unreinforced avoidance responses that occur between trials. First, we examined whether VH inactivation would affect ITRs. Male rats underwent SAA training and subsequently received intra-VH infusions of saline or muscimol before retrieval tests in the training context. Rats that received muscimol performed significantly fewer ITRs, but equivalent avoidance responses, compared to controls. Next, we asked whether chemogenetic VH activation would increase ITR vigor. In male and female rats expressing excitatory (hM3Dq) DREADDs, systemic CNO administration produced a robust ITR increase that was not due to nonspecific locomotor effects. Then, we examined whether chemogenetic VH activation potentiated ITRs in an alternate (non-training) test context and found it did. Finally, to determine if context-US associations mediate ITRs, we exposed rats to the training context for three days after SAA training to extinguish the context. Rats submitted to context extinction did not show a reliable decrease in ITRs during a retrieval test, suggesting that context-US associations are not responsible for ITRs. Collectively, these results reveal an important role for the VH in context-dependent ITRs during SAA. Further work is required to explore the neural circuits and associative basis for these responses, which may be underlie pathological avoidance that occurs in humans after threat has passed.
Understanding the mechanisms and limitations of immune control of HIV

Summary: A large number of experimental studies have been performed over the past decade in an attempt to develop a vaccine for human immunodeficiency virus (HIV). These studies have used a variety of approaches aimed at stimulating both antibody‐mediated and cell‐mediated immunity. Many of these experiments have been performed in macaque models of HIV. Analysis and modeling of the results of these studies provide the opportunity to investigate the mechanisms and limitations of viral control by humoral and cell‐mediated immunity. These studies suggest that CD8+ T cells do ‘too little too late’ to prevent the establishment of viral infection and latency. By contrast, passively administered antibody acts extremely early to reduce the initial inoculum and slow viral growth. In both cases, reduction in peak viral load appears crucial to the maintenance of CD4+ T cells in acute infection and for effective long‐term viral control. The insights gained from studies of simian human immunodeficiency virus infection have important implications for HIV vaccination. However, important questions remain as to whether differences in pathogenesis in HIV will lead to different ‘rules of engagement’ for immune control of virus.
Grapevine Shiraz Disease-associated viruses lead to significant yield losses by altering transcription of genes related to defence responses and photosynthesis

Grapevine Shiraz disease (SD), which is associated with Grapevine Virus A (GVA), is one of the highly destructive diseases affecting Australian and South African vineyards. However, virtually nothing is known about the transcriptional modifications in grapevine phloem tissues induced by SD as well as its impact on vine physiology, yield and fruit composition. In this study, we assessed the physiological parameters of SD-infected Vitis vinifera L. cv. Shiraz vines grown in a commercial vineyard in South Australia over two growing seasons. Viruses present in symptomatic SD-affected and asymptomatic vines were investigated using serological (ELISA) and molecular tests (PCR and Illumina next generation sequencing). SD did not alter plant water status over the growing season, however significantly decreased canopy size, leaf gas exchange, chlorophyll fluorescence, and yield. Differential gene expression analysis revealed significantly higher expression of genes associated with systemic acquired resistance (SAR) and downregulation of defence- and photosynthesis-related genes in phloem tissues of SD vines. This is the first comprehensive report of the physiological and transcriptomic responses of grapevine to SD.
Function estimation via wavelet shrinkage for long-memory data

In this article we study function estimation via wavelet shrinkage for data with long-range dependence. We propose a fractional Gaussian noise model to approximate nonparametric regression with long-range dependence and establish asymptotics for minimax risks. Because of long-range dependence, the minimax risk and the minimax linear risk converge to 0 at rates that differ from those for data with independence or short-range dependence. Wavelet estimates with best selection of resolution leveldependent threshold achieve minimax rates over a wide range of spaces. Cross-validation for dependent data is proposed to select the optimal threshold. The wavelet estimates significantly outperform linear estimates. The key to proving the asymptotic results is a wavelet]vaguelette decomposition which decorrelates fractional Gaussian noise. Such wavelet]vaguelette decomposition is also very useful in fractal signal processing.
DNA methylation shows footprints of altitude selection in the clonal plant species Fragaria vesca

Climate change poses a significant threat to plant species, potentially pushing them beyond their adaptive capacities. Epigenetic modifications, such as DNA methylation, have emerged as a key candidate mechanism enabling plants to quickly adapt to environmental changes by generating locally adapted phenotypes. These phenotypic changes can be even inherited across multiple generations, thus potentially becoming targets of natural selection. However, whether natural selection can act on these epialleles has hardly been tested directly. Addressing this knowledge gap is crucial as population survival may heavily rely on DNA methylation, especially in scenarios with restricted genetic diversity, such as within clonal plant populations. Here, we employed population genomics approaches on seven natural populations of the clonal species wild strawberry (Fragaria vesca) distributed across an altitudinal range to investigate the presence of epigenetic sites under altitude-driven selection. Our genomic, epigenomic, and transcriptomic analyses found a wide intra- and inter-population epigenetic diversity despite a considerably low genetic diversity. We identified heritable epialleles exhibiting signs of positive selection related to altitude, i.e. reduced intrapopulation epigenetic diversity and increased epigenetic divergence between low and high altitude. These altitude-selected epigenetic loci overlapped with genes involved in biological processes such as DNA repair, molecular recognition, regulation of gene expression, and chromatin structure. Interestingly, some of these epialleles were independent of genetic variation, suggesting they may have arisen stochastically or in response to environmental variation. These findings suggest that heritable epigenetic variation could help clonal species quickly adapt to environmental challenges as those related to varying altitudes and/or temperatures. Significance statement The eventuality of epigenetic marks being inherited has led the scientific community to rethink evolution and adaptation, debating whether epigenetic information could be considered as the “fifth base”. However, direct evidence supporting that epigenetic marks are under evolutionary processes such as natural selection remain scarce. To address this knowledge gap, we screened natural populations of wild strawberries and searched for footprints of altitudinal selection on epi-alleles. We found loci matching the criteria for epigenetic selection, i.e. reduced epigenetic diversity in populations, increased epigenetic divergence between populations of different altitudes and transmission to the (clonal) progeny. Some of these selected epi-alleles were not associated with any genetic variant, suggesting that epigenetic marks are another layer of substrate for selection to act.
Multiplexed SNP Typing of Ancient DNA Clarifies the Origin of Andaman mtDNA Haplogroups amongst South Asian Tribal Populations

The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups ∼30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity.
A T6SS in the coral pathogen Vibrio coralliilyticus secretes an arsenal of anti-eukaryotic effectors and contributes to virulence

Vibrio coralliilyticus (Vcor) is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased Vcor pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in Vcor. We identified two omnipresent T6SSs that are activated at temperatures in which Vcor becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of three Vcor strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least nine novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to Vcor’s virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors. Author Summary Coral reefs are diverse ecosystems providing habitats for various fish, invertebrates, and microorganisms. Climate change, leading to rising ocean water temperatures, correlates with coral bleaching and mass mortality events. An implicated causal agent of coral disease outbreaks is the marine bacterium Vibrio coralliilyticus. Here, we found that two toxin injection systems present in all Vibrio coralliilyticus strains are regulated by temperature; we revealed the toxins that they secrete and their function in competition against rival bacteria and in the intoxication of an animal host. Our findings implicate these systems as previously unappreciated contributors to Vibrio coralliilyticus virulence, illuminating possible targets to treat or prevent coral infection.
Exploring structural diversity across the protein universe with The Encyclopedia of Domains

The AlphaFold Protein Structure Database (AFDB) contains full-length predictions of the three-dimensional structures of almost every protein in UniProt. Because protein function is closely linked to structure, the AFDB is poised to revolutionise our understanding of biology, evolution and more. Protein structures are composed of domains, independently folding units that can be found in multiple structural contexts and functional roles. The AFDB’s potential remains untapped due to the difficulty of characterising 200 million structures. Here we present The Encyclopedia of Domains or TED, which combines state-of-the-art deep learning-based domain parsing and structure comparison algorithms to segment and classify domains across the whole AFDB. TED describes over 370 million domains, over 100 million more than detectable by sequence-based methods. Nearly 80% of TED domains share similarities to known superfamilies in CATH, greatly expanding the set of known protein structural domains. We uncover over 10,000 previously unseen structural interactions between superfamilies, expand domain coverage to over 1 million taxa, and unveil thousands of architectures and folds across the unexplored continuum of protein fold space. We expect TED to be a valuable resource that provides a functional interface to the AFDB, empowering it to be useful for a multitude of downstream analyses.
Trade and human capital as determinants of growth

Do openness to trade and higher levels of human capital growth promote faster growth? To answer that question we use a panel of countries to investigate the role of human capital and two measures of openness in determining both the level of income and its growth rate. We argue that focusing on the levels of income by estimating a production function will give misleading estimates if there are unobserved differences in the underlying growth of technical efficiency across countries that are correlated with the explanatory variables. Using a growth rate equation, where we allow for country fixed effects and for possible endogeneity of explanatory variables, we show that both measures of openness, one the Sachs-Warner measure which reflects policy, and one from the PENN World Tables, the share of trade in GDP, give similar results. We argue that openness has a highly significant and large effect on the underlying rate of growth of productivity, while human capital does not.
Video observations of nearshore bar behaviour . Part 2 : alongshore non-uniform variability

A considerable portion of the variability in nearshore sandbars is related to changes in the plan shape of quasirhythmic alongshore non-uniform features, such as rip channels and crescentic shapes. These changes may include changes in their alongshore length, cross-shore amplitude and alongshore position. Here, we use complex empirical orthogonal eigenfunction analysis to quantify these changes from a 3.4-year data set of almost daily time-exposure images of the double-barred coast at Noordwijk (Netherlands). The observed alongshore non-uniform features had alongshore lengths between 380 and approximately 3000 m and lifetimes in the order of months, considerably longer than the characteristic time scale of individual wave events. Transitions from one feature to another were mostly gradual, resulting from an alongshore differential growth in amplitude. Abrupt transitions, that is, the existing features disappeared entirely and were subsequently replaced by different features, were barely observed and did not always take place during high-energy wave events. The amplitude of the non-uniform features varied between 0 and 30 m on a weekly to monthly scale, unrelated to variations in the wave height. In addition, the features migrated back and forth along the shore with typical rates of Oð10 m=dayÞ on weekly scales with the rates increasing with an increase in the alongshore component of the wave power. On the whole our observations suggest that alongshore non-uniform sandbar variability is governed by free behaviour rather than by the direct forcing of the prevailing wave conditions. r 2003 Elsevier Science Ltd. All rights reserved.
Effects on the particle verb alternation across English dialects

This paper examines regional and grammatical effects on the English particle verb alternation. We report on a judgment experiment and a Twitter corpus study designed to address Hughes et al.’s (2005) claim that the continuous order is favored in Scotland while the discontinuous order is favored in Southern England. The results from both the acceptability judgment study and the Twitter corpus revealed no support for a North-South difference across UK dialects, but instead show a trans-Atlantic difference: respondents from the UK and Ireland favored discontinuous orders while US and Canadian participants favored continuous orders. Based on a preliminary analysis of historical corpus data, we speculate that this difference reflects change toward an innovative discontinuous order that has proceeded more quickly in Old World dialects than in North America. Other effects tested in the judgment study were the information-structural factor of object givenness, which did not prove significant, and the prosodic factor of object weight, which had the anticipated negative effect on the discontinuous order while also showing an unexpected positive effect on the continuous order.
A Generalized Framework for the Calcium Control Hypothesis Describes Weight-Dependent Synaptic Plasticity

The brain modifies synaptic strengths to store new information via long-term potentiation (LTP) and long-term depression (LTD). Evidence has mounted that long-term plasticity is controlled via concentrations of calcium ([Ca2+]) in postsynaptic spines. Several mathematical models describe this phenomenon, including those of Shouval, Bear, and Cooper (SBC) (Shouval et al., 2002, 2010) and Graupner and Brunel (GB)(Graupner & Brunel, 2012). Here we suggest a generalized version of the SBC and GB models, based on a fixed point – learning rate (FPLR) framework, where the synaptic [Ca2+] specifies a fixed point toward which the synaptic weight approaches asymptotically at a [Ca2+]-dependent rate. The FPLR framework offers a straightforward phenomenological interpretation of calcium-based plasticity: the calcium concentration tells the synaptic weight where it is going and how fast it goes there. The FPLR framework can flexibly incorporate various experimental findings, including the existence of multiple regions of [Ca2+] where no plasticity occurs, or plasticity in cerebellar Purkinje cells, where the directionality of calcium-based synaptic changes is thought to be reversed relative to cortical and hippocampal neurons. We also suggest a modeling approach that captures the dependency of late-phase plasticity stabilization on protein synthesis. We demonstrate that due to the asymptotic, saturating nature of synaptic changes in the FPLR rule, the result of frequency- and spike-timing-dependent plasticity protocols are weight-dependent. Finally, we show how the FPLR framework can explain plateau potential-induced place field formation in hippocampal CA1 neurons, also known as behavioral time scale plasticity (BTSP).
Open Access Methodology Article Predicting Nucleosome Positioning Using a Duration Hidden Markov Model

Background: The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software tool for predicting nucleosome positioning can help understanding how a genome's nucleosome organization may facilitate genome function. Results: We present a duration Hidden Markov model for nucleosome positioning prediction by explicitly modeling the linker DNA length. The nucleosome and linker models trained from yeast data are re-scaled when making predictions for other species to adjust for differences in base composition. A software tool named NuPoP is developed in three formats for free download. Conclusions: Simulation studies show that modeling the linker length distribution and utilizing a base composition re-scaling method both improve the prediction of nucleosome positioning regarding sensitivity and false discovery rate. NuPoP provides a user-friendly software tool for predicting the nucleosome occupancy and the most probable nucleosome positioning map for genomic sequences of any size. When compared with two existing methods, NuPoP shows improved performance in sensitivity. Background Most eukaryotic genomic DNA is wrapped in nucleosomes, which occlude and strongly distort the wrapped DNA. Accumulating evidence shows that the DNA sequence itself is highly predictive of nucleosome positioning in vivo [1-7], and that nucleosome positioning is closely related to chromosome functions [1,8-11]. A fast software tool for predicting nucleosome positioning is highly desirable. Several statistical methods for nucleosome positioning prediction have been proposed in the literature. In [2] a method was proposed based on cross-correlation with a nucleosome DNA sequence signature. In [1] a Markov model was used together with consideration of steric exclusion and thermodynamic equilibrium. In [3], a support vector machine (SVM) was trained based on the differential k-mer usage between nucleosome and linker
Cervical Cancer in Africa

Cervical cancer is a relatively rare disease in countries that have instituted and maintained national screening programs, with call and recall of women at various intervals and built-in quality control with appropriate monitoring and evaluation. Unfortunately, this process has failed in most areas of the world where more than 80% of new cases of cervical cancer are diagnosed. Cervical cancer affects women in the prime of their lives causing premature and needless suffering and death in a critically important segment of the world's population, despite being one of the few cancers that can be prevented with simple testing. In the past 15 years innovative approaches to both primary and secondary prevention of cervical cancer have been subjected to a number of large scale, scientifically valid and applicable studies that have opened the way for new approaches. Treatment of cervical cancer in Africa is hampered by the lack of diagnostic and treatment facilities, lack of healthcare infrastructure and poor pathology services. Further, there is a significant brain drain of trained healthcare workers in Africa that exacerbates the problem. Cancer is becoming an increasingly important public health problem as more people live longer. It is time to develop programs for the prevention, early detection, treatment, and palliation of cancer sufferers in Africa. Cancer Epidemiol Biomarkers Prev; 21(9); 1434–8. ©2012 AACR.