Miracle-dz/UniFAR-FTUs huggingface dataset:
Reticulate Evolutionary History of a Western Palaearctic Bat Complex Explained by Multiple mtDNA Introgressions in Secondary Contacts

Aim There is increasing evidence showing that species within various taxonomic groups have reticulate evolutionary histories with several cases of introgression events. Investigating the phylogeography of species complexes can provide insight about the introgressions, when and where these hybridizations occurred. In this study, we investigate the biogeography of a widely distributed Western Palaearctic bat species complex, namely Myotis nattereri sensu lato. This complex exhibits high genetic diversity and in its western distribution range is composed of deeply diverged genetical lineages. However, little is known about the genetic structure of the eastern populations. We also infer the conservation and taxonomical implications of the identified genetic divergences. Location Western Palaearctic Methods We analyzed 175 specimens collected from 67 locations and sequenced one mitochondrial and four nuclear DNA markers, and combined these with the available Gen-Bank sequences. We used haplotype networks, PCA, t-SNE, and Bayesian clustering algorithms to investigate the population structure and Bayesian trees to infer the phylogenetic relationship of the lineages. Main conclusions We identified deeply divergent genetical lineages. In some cases, nuclear and mitochondrial markers were discordant, which we interpret are caused by hybridization between lineages. We identified three such introgression events. Our findings suggest that the M. nattereri complex has a reticulate evolutionary history with multiple cases of hybridizations between some of the identified lineages. We also suggest a revision in the taxonomy of this species group, with two possible new taxa: M. hoveli and M. tschuliensis.
The effect of aerobic training and vitamin D supplements on the neurocognitive functions of elderly women with sleep disorders

ABSTRACT Purpose The age-related physical and mental disorders in the elderly are issues that endure social and economic costs. The aim of the present study was to examine the effect of aerobic training and vitamin D supplements on the neurocognitive functions of elderly women with sleep disorders. Methods A quasi-experimental with a pre/post-test study design was used, where 36 aged women 60–70 years old were randomly divided into four groups: aerobic training (ATG), vitamin D (VDG), aerobic training + vitamin D (ATDG) and control (CG). The aerobic exercise protocol was performed for eight weeks with three sessions a week for 50 min. Pittsburgh Sleep Quality Scale was used to evaluate the sleep status profile of participants. The reaction speed, selective attention and information processing were measures of the neurocognitive functions before and after the training period. Results The information processing increased significantly from pre- to post-training by 18.0% in the ATDG, 15.7% in the VDG, and 13.2% in the ATG (p < 0.001). Also, selective attention increased significantly from pre- to post-training by 16.2% in the ATDG, 12.2% in the VDG, and 11.9% in the ATG (p < 0.001). The quality of sleep score was reduced from pre- to post-training by 42.3% in the ATDG, 19.1% in the VDG, and 35.6% in the ATG (p < 0.001). However, no difference was observed in the CG (p > 0.05). The reaction time was reduced significantly from pre- to post-training by 8.6% in the ATDG (p < 0.01). However, no significant difference was observed in the CG, the VDG and the ATG (p < 0.05). Conclusion The present study showed that aerobic exercise plus vitamin D supplements improved the neurocognitive functions of elderly women.
The bat influenza H17N10 can be neutralized by broadly-neutralizing monoclonal antibodies and its neuraminidase can facilitate viral egress

The diversity of subtypes within the Influenza A virus genus has recently expanded with the identification of H17N10 and H18N11 from bats. In order to further study the tropism and zoonotic potential of these viruses, we have successfully produced lentiviral pseudotypes bearing both haemagglutinin H17 and neuraminidase N10. These pseudotypes were shown to be efficiently neutralized by the broadly-neutralizing monoclonal antibodies CR9114 and FI6. Our studies also confirm previous reports that H17 does not use sialic acid as its cellular receptor, as pseudotypes bearing the H17 envelope glycoprotein are released into the cell supernatant in the absence of NA. However, we demonstrate that N10 facilitates heterosubtypic (H5 and H7) influenza HA-bearing pseudotype release in the absence of another source of NA, significantly increasing luciferase pseudotype production titres. Despite this, N10 shows no activity in the enzyme-linked lectin assay used for traditional sialidases. These findings suggest that this protein plays an important role in viral egress, but is perhaps involved in further accessory roles in the bat influenza lifecycle that are yet to be discovered. Thus we show the lentiviral pseudotype system is a useful research tool, and amenable for investigation of bat influenza tropism, restriction and sero-epidemiology, without the constraints or safety issues with producing a replication-competent virus, to which the human population is naïve. Significance statement Influenza virus is responsible for mortality and morbidity across the globe; human populations are constantly at risk of newly emerging strains from the aquatic bird reservoir which harbors most of the subtypes of influenza A (H1-H16). Recently identified subtypes (H17N10, H18N11) from bats have broadened the reservoir from which potential pandemic strains of influenza can emerge. To evaluate the potential for these novel subtypes to cross over into human populations, their ability to establish an infection, in addition to the extent of cross-reactive immunity established by human seasonal strains needs to be investigated. This study highlights a novel platform for the study of the bat H17 and N10 envelope glycoproteins, using a lentiviral pseudotype system. Following the generation of this pseudotype it was employed in cell entry and microneutralization assays. These showed that two well-characterised monoclonal antibodies (mAb) which target avian and human influenza subtypes will also neutralize H17. Furthermore the data presented in this study show a novel aspect of the N10 glycoprotein in its ability to facilitate the budding of pseudotypes bearing different influenza HAs.
Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin-, cellulose-and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7,500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.
The insect‐focused classification of fruit syndromes in tropical rain forests: An inter‐continental comparison

We propose a new classification of rain forest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit‐feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand), and Wanang (Papua New Guinea). The three plots differed widely in fruit syndrome composition. Plant species with fleshy, indehiscent fruits containing multiple seeds were important at all three sites. However, in Panama, a high proportion of species had dry fruits, while in New Guinea and Thailand, species with fleshy drupes and thin mesocarps were dominant. Species with dry, winged seeds that do not develop as capsules were important in Thailand, reflecting the local importance of Dipterocarpaceae. These differences can also determine differences among frugivorous insect communities. Fruit syndromes and colors were phylogenetically flexible traits at the scale studied, as only three of the eight seed syndromes, and one of the 10 colors, showed significant phylogenetic clustering at either genus or family levels. Plant phylogeny was, however, the most important factor explaining differences in overall fruit syndrome composition among individual plant families or genera across the three study sites.
Tutorial on Pattern Classification in Cell Recording

Summary In this chapter, we outline a procedure to decode information from multivariate neural data. We assume that neural recordings have been made from a number of trials in which different conditions were present, and our procedure produces an estimate of how accurately we can predict the labels of these conditions in a new set of data. We call this estimate of future prediction the “decoding/readout accuracy,” and based on this measure we can make inferences about what information is present in the population of neurons and on how this information is coded. The steps we cover to obtain a measure of decoding accuracy include: (1) designing an experiment, (2) formatting the neural data, (3) selecting a classifier to use, (4) applying cross-validation to random splits of the data, (5) evaluating decoding performance through different measures, and (6) testing the integrity of the decoding procedure and significance of the results. We also discuss additional topics, including how to examine questions about neural coding and how to evaluate whether the population is representing stimuli in an invariant/abstract way. Chapter 18 (Singer and Kreiman) discusses statistical classifiers in further detail. The ideas discussed here are applied in several chapters in this book including chapter 2 (Nirenberg), chapter 3 (Poort, Pooresmaeili, and Roelfsema), chapter 7 (Pasupathy and Brincat), chapter 10 (Hung and DiCarlo), chapter 21 (Panzeri and Ince), and chapter 22 (Berens, Logothetis, and Tolias). Chapter 20 discusses related concepts within the domain of functional imaging.
Compression Using Huffman Coding

Data compression is also called as source coding. It is the process of encoding information using fewer bits than an uncoded representation is also making a use of specific encoding schemes. Compression is a technology for reducing the quantity of data used to represent any content without excessively reducing the quality of the picture. It also reduces the number of bits required to store and/or transmit digital media. Compression is a technique that makes storing easier for large amount of data. There are various techniques available for compression in my paper work , I have analyzed Huffman algorithm and compare it with other common compression techniques like Arithmetic, LZW and Run Length Encoding.
The Infectious Bronchitis Virus Coronavirus Envelope Protein Alters Golgi pH to Protect Spike Protein and Promote Release of Infectious Virus

Coronaviruses (CoVs) are important human pathogens with significant zoonotic potential. Progress has been made toward identifying potential vaccine candidates for highly pathogenic human CoVs, including use of attenuated viruses that lack the CoV envelope (E) protein or express E mutants. However, no approved vaccines or anti-viral therapeutics exist. CoVs assemble by budding into the lumen of the early Golgi prior to exocytosis. The small CoV E protein plays roles in assembly, virion release, and pathogenesis. CoV E has a single hydrophobic domain (HD), is targeted to Golgi membranes, and has cation channel activity in vitro. The E protein from the avian infectious bronchitis virus (IBV) has dramatic effects on the secretory system, which requires residues in the HD. Mutation of the HD of IBV E during infection results in impaired growth kinetics, impaired release of infectious virions, accumulation of IBV S protein on the plasma membrane when compared IBV WT infected cells, and aberrant cleavage of IBV S on the surface of virions. We previously reported the formation of two distinct oligomeric pools of IBV E in transfected and infected cells. Disruption of the secretory pathway by IBV E correlates with a form that is likely monomeric, suggesting that the effects on the secretory pathway are independent of E ion channel activity. Here, we present evidence suggesting that the monomeric form of IBV E correlates with a rise in the pH of the Golgi lumen. We demonstrate that infection with IBV induces neutralization of Golgi luminal pH, promoting a model in which IBV E alters the secretory pathway through interaction with host cells factors, protecting IBV spike protein (S) from premature cleavage and leading to the efficient release of infectious virus from the cells.
CWCNFS: a cluster NFS server with cooperative write mechanism

Cluster technology can organize many cheap computers to cluster, and obtain the high performance. The traditional cluster file systems can achieve high performance, but most of them require modifying the software of client. This requirement makes these systems lose flexibility and can not be widely applied. This paper provides a novel network file server (NFS) cluster server: CWCNFS, which uses cooperative write mechanism (CWM). CWM is a novel mechanism presented in this paper, which can improve the performance of synchronous write in cluster file system. CWCNFS has following features: (1) CWCNFS unitizes the advantage of cluster file system, and then can adequately use the network bandwidth and the storage capability; (2) CWCNFS applies cooperative write mechanism on the cluster file system, and can greatly improve the performance; (3) CWCNFS can give normal NFS access interface to clients and do not require any software modification of clients. In this paper, the architecture of CWCNFS and the design of CWM are presented. At last, we take some experiments to validate the performance of CWCNFS. The experiment results show that CWCNFS cannot only inherit the universality of NFS, but also can provide high performance NIPS Me service.
Excretion initiates walking in the cricket Gryllus bimaculatus

Feces contain information about the donor and potentially attracts both conspecifics and predators and parasites. The excretory system must be coordinated with other behaviors in insects. We found that crickets start walking forward following excretion of feces. Most intact crickets walked around the experimental arena, stopped at a particular site and raised up their body with a slight backward drift to excrete feces. After the feces dropped on the floor, the animal started walking with a random gait pattern away from the feces, and then changed the gait pattern to a tripod gait. Headless cricket also showed walking following excretion. In more than half of excretion events, headless crickets walked backward before excretion. The posture adopted during excretion was similar to that of intact crickets, and post-excretory forward walking was also observed. The occurrence rate of post-excretory walking was more than that of intact crickets. The gait pattern during forward walking was random and never transitioned to a tripod gait in the headless crickets. In animals whose abdominal nerve cords were cut, in any position, pre- or post-excretion walking was not shown in both intact and headless crickets, although they excreted feces. These results indicate that ascending signals from the terminal abdominal ganglion initiate leg movement through the neuronal circuits within thoracic ganglia, and that descending signals from the brain must regulate leg the motor circuit to express the appropriate walking gait.
Decoding voluntary movements and postural tremor based on thalamic LFPs for closed-loop stimulation for essential tremor

High frequency deep brain stimulation (DBS) targeting motor thalamus is an effective therapy for essential tremor (ET). However, conventional continuous stimulation may deliver unnecessary current to the brain since tremor mainly affects voluntary movements and sustained postures in ET. We recorded LFPs from the motor thalamus, surface electromyographic (EMG) signals and/or behavioural measurements in seven ET patients during temporary lead externalization after the first surgery for DBS when they performed different voluntary upper limb movements and in nine more patients during the surgery, when they were asked to lift their arms to trigger postural tremor. We show that both voluntary movements and postural tremor can be decoded based on features extracted from thalamic LFPs using a machine learning based binary classifier. This information can be used to close the loop for DBS so that stimulation could be delivered on demand, without the need for peripheral sensors or additional invasive electrodes.
Hypothesis: A plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage

The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host-range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host-range in the presence of R-M systems. The model makes two main predictions. First, that offspring of the first phage to gain a new methylation pattern by infecting a new host make up a disproportionate fraction of the subsequent specialist population, indicating that the plastically-produced phenotype is highly predictive of evolutionary outcome. Second, that the first phage gain this pattern is not always genetically distinct from other phages in the population. Taken together, these results suggest that plasticity could play a causal role on par with mutation during the evolution of phage host range. This uniquely tractable system could enable the first direct test of ‘plasticity first’ evolution.
A single-chip 1.8 GHz image reject RF receiver front-end with boot-strapped inductors

A fully integrated RF front-end for 1.8 GHz wireless receiver is presented. The circuit is based on a single-conversion heterodyne architecture with a band-pass low noise amplifier and an image-reject mixer. Bootstrapped inductors are used to realize the high quality factor inductors of the tunable LC active filters in the variable gain low noise amplifier. The front-end, which has been designed for a 50 GHz bipolar process, presents an overall image-rejection greater than 62 dB at 100 MHz of intermediate frequency. The main characteristics of this design are a gain of 17.3 dB, a bandwidth of 45 MHz, a linearity range up to -20 dBm, a power consumption of 120 mW, a low area on die and a low cost, since no external components in the RF and IF signal paths are needed.
Implementation of Optimal Investment Problem on a Linear Systolic Array

One of the main problems in operational research is the problem of optimal invest- ments. This paper describes a procedure for synthesis a linear systolic array that implements the algorithm for solvin a problem of optimal investments. The performances of the obtained array, including execution time, number of processing elements, speed-up and efficiency are then discussed.
Intraductal patient derived xenografts of estrogen receptor positive (ER+) breast cancer recapitulate the histopathological spectrum and metastatic potential of human lesions

Estrogen receptor α positive (ER+) or “luminal” breast cancers were notoriously difficult to establish as patient-derived xenografts (PDXs). We and others recently demonstrated that the microenvironment is critical for ER+ tumor cells; by grafting them into milk ducts >90% take rates are achieved and many features of the human disease are recapitulated. This intra-ductal (ID) approach holds promise for personalized medicine, yet human and murine stroma are organized differently and this and other species specificities may limit the value of this model. Here, we analyzed 21 ER+ ID-PDXs histopathologically. We find that ID-PDXs vary in extent and define four histopathological patterns: flat, lobular, in situ, and invasive, which occur in pure and combined forms. The ID-PDXs replicate earlier stages of tumor development than their clinical counterparts. Micrometastases are already detected when lesions appear in situ. Tumor extent, histopathological patterns, and metastatic load correlate with biological properties of their tumors of origin. Our findings add evidence to the validity of the intraductal model for in vivo studies of ER+ breast cancer and raise the intriguing possibility that tumor cell dissemination may occur earlier than currently thought. Conflict of interest statement: The authors declare no conflict of interest.