Miracle-dz/UniFAR-FTUs huggingface dataset:
“Escalibur”—A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes

The revolution in genomics has enabled large‐scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant‐calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome‐wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb. edu.au/bioscience/escalibur (version 0.3‐beta) and is essentially applicable to any prokaryote or eukaryote.
Dietary fats and their sources in association with the risk of bladder cancer: A pooled analysis of 11 prospective cohort studies

The effects of fat intake from different dietary sources on bladder cancer (BC) risk remains unidentified. Therefore, the present study aimed to investigate the association between fat intakes and BC risk by merging world data on this topic. Data from 11 cohort studies in the BLadder cancer Epidemiology and Nutritional Determinants (BLEND) study, provided sufficient information on fat intake for a total of 2731 BC cases and 544 452 noncases, which yielded 5 400 168 person‐years of follow‐up. Hazard ratios (HRs), with corresponding 95% confidence intervals (CIs), were estimated using Cox‐regression models stratified on cohort. Analyses were adjusted for total energy intake in kilocalories, gender, smoking status (model‐1) and additionally for sugar and sugar products, beers, wine, dressing and plant‐based and fruits intakes (model‐2). Among women, an inverse association was observed between mono‐unsaturated fatty acids (MUFAs) and BC risk (HR comparing the highest with the lowest tertile: 0.73, 95% CI: 0.58‐0.93, P‐trend = .01). Overall, this preventative effect of MUFAs on BC risk was only observed for the nonmuscle invasive bladder cancer (NMIBC) subtype (HR: 0.69, 95% CI: 0.53‐0.91, P‐trend = .004). Among men, a higher intake of total cholesterol was associated with an increased BC risk (HR: 1.37, 95% CI: 1.16‐1.61, P‐trend = .01). No other significant associations were observed. This large prospective study adds new insights into the role of fat and oils in BC carcinogenesis, showing an inverse association between consumption of MUFAs and the development of BC among women and a direct association between higher intakes of dietary cholesterol and BC risk among men.
Comparison of genetically modified insect-resistant maize and non-transgenic maize revealed changes in soil metabolomes but not in rhizosphere bacterial community

ABSTRACT The deliberate introduction of the beneficial gene in crop plants through transgenic technology can provide enormous agricultural and economic benefits. However, the impact of commercialization of these crops on the ecosystem particularly on belowground soil biodiversity is still uncertain. Here, we examined and compared the effects of a non-transgenic maize cultivar and an insect-resistant transgenic maize cultivar genetically engineered with cry1Ah gene from Bacillus thuringiensis, on the rhizosphere bacterial community using 16S rDNA amplicon sequencing and soil metabolome profile using UPLC/MS analysis at six different growth stages. We found no significant differences in bacterial community composition and diversity at all growth stages between the two cultivars. The analysis of bacterial beta-diversity showed an evident difference in community structure attributed to plant different growth stages but not to the plant type. In contrast, the soil metabolic profile of transgenic maize differed from that of the non-transgenic plant at some growth stages, and most of the altered metabolites were usually related to the metabolism but not to the plant-microbe interaction related pathways. These results suggest that genetic modification with the cry1Ah gene-altered maize soil metabolism but had no obvious effect on the rhizosphere bacterial community.
PSCAD based modeling and simulation on grid-connected wind power

A complete dynamic model for variable speed wind turbines(VSWT) is presented and the model includes wind speed,wind-turbine and pitch control and generator.Based on the models,a simulation example of VSWT is developed by using PSCAD.Then taking ramp change of wind speed as example,the dynamic characteristics of a VSWT which has capacity of 2 000 kW are simulated.The results show VSWT has good running characteristics as well as show the influence factors on the stable run of similar wind turbines.
LegalVis: Exploring and Inferring Precedent Citations in Legal Documents

To reduce the number of pending cases and conflicting rulings in the Brazilian Judiciary, the National Congress amended the Constitution, allowing the Brazilian Supreme Court (STF) to create binding precedents (BPs), i.e., a set of understandings that both Executive and lower Judiciary branches must follow. The STF’s justices frequently cite the 58 existing BPs in their decisions, and it is of primary relevance that judicial experts could identify and analyze such citations. To assist in this problem, we propose LegalVis, a web-based visual analytics system designed to support the analysis of legal documents that cite or could potentially cite a BP. We model the problem of identifying potential citations (i.e., non-explicit) as a classification problem. However, a simple score is not enough to explain the results; that is why we use an interpretability machine learning method to explain the reason behind each identified citation. For a compelling visual exploration of documents and BPs, LegalVis comprises three interactive visual components: the first presents an overview of the data showing temporal patterns, the second allows filtering and grouping relevant documents by topic, and the last one shows a document’s text aiming to interpret the model’s output by pointing out which paragraphs are likely to mention the BP, even if not explicitly specified. We evaluated our identification model and obtained an accuracy of 96%; we also made a quantitative and qualitative analysis of the results. The usefulness and effectiveness of LegalVis were evaluated through two usage scenarios and feedback from six domain experts.
The Effect of Endometrial Cell Culture on α3 and β1 integrin Genes and Protein Expression in Type 2 Diabetic Rats at The Time of Implantation

Objective Given the prevalence of fertility problems in couples and the defect in embryo implantation as well as the low success rate of assisted reproductive techniques, it is necessary to investigate the causes of this phenomenon. Type 2 diabetes mellitus (T2DM) is a metabolic disease with multiple effects on various organs as well as the endometrium. In this study, the effects of endometrial cell culture on the expression of α3 and β1 integrin genes and protein in type 2 diabetic rats were investigated. Materials and Methods In this experimental study, 35 female rats were divided into five groups: control, sham, diabetic, Pioglitazone-treated and Metformin-treated groups. First, rats were maintained in diabetic condition for 4 weeks. Then, treatment was performed for the next four weeks. Four weeks after induction of diabetes, rats were sacrificed at the time of embryo implantation. The uterus was removed. Endometrial cells were isolated and cultured for 7 days. Immunocytochemistry staining was used to confirm endometrial cells. Expression of α3 and β1 integrin genes was determined by real-time polymerase chain reaction (PCR) technique and the α3β1 protein content measured using Western blot both before and after endometrial cell culture. Results The expression level of α3 integrin gene in the Pioglitazone-treated group compared with metformin-treated group was significantly decreased (P<0.001). The same result was observed in β1 integrin gene expression (P=0.004). Also, the α3β1 protein level increased in all diabetic groups, but its reduction was significantly greater in pioglitazone- treated group (P=0.004). Conclusion T2DM altered the expression of α3 and β1 integrin genes and related proteins, which endometrial cell culture regulated this disorder. According to these results, may be the endometrial cell culture can reduce the adverse effects of diabetes on α3 and β1 integrin expression at the level of gene and protein, in endometrial cells.
Comparing impacts of meditation training in focused attention, open monitoring, and mindfulness‐based cognitive therapy on emotion reactivity and regulation: Neural and subjective evidence from a dismantling study

Abstract Commonly conducted mindfulness‐based trainings such as Mindfulness‐based Stress Reduction (MBSR) and Mindfulness‐based Cognitive Therapy (MBCT) highlight training in two key forms of meditation: focused attention (FA) and open monitoring (OM). Largely unknown is what each of these mindfulness practices contributes to emotional and other important training outcomes. This dismantling trial compared the effects of structurally equivalent trainings in MBCT, FA, and OM on neural and subjective markers of emotional reactivity and regulation among community adults, with the aim to better understand which forms of training represent active ingredients in mindfulness trainings. Participants with varying levels of depressive symptoms were randomized to one of the three trainings. Before and after each 8‐week training, N = 89 participants completed a modified version of the Emotional Reactivity and Regulation Task while electroencephalographic (EEG) and self‐reported emotional responses to negative, positive, and neutral photographic images were collected. Examination of EEG‐based frontal alpha band asymmetry during passive viewing (reactivity) and active regulation phases of the task showed that FA and MBCT trainings produced significant leftward hemispheric shifts in frontal alpha asymmetry, commonly associated with a shift toward approach‐based positive affect. Self‐reported emotional responses to negative images corroborated these results, suggesting salutary changes in both emotional reactivity and regulation. OM training had limited beneficial effects, restricted to the subjective outcomes. The findings suggest that MBCT may derive its greatest benefit from training in FA rather than OM. Discussion highlights the potential value of FA training for emotional health.
Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom

Spiders are the most abundant venomous predators in the world. Previous research related to spider venom has mostly relied on transcriptomes and proteomes, with only a few high‐quality genomes available. This is far from consistent with the species diversity of spiders. In this study, we constructed a high‐quality chromosome‐level genome assembly of Hylyphantes graminicola, which contained 13 chromosomes, with a genome length of 931.68 Mb and scaffold N50 of 77.07 Mb. Integrating genome, transcriptome, and proteome profiling, we identified a total of 59 coding genes among nine toxin gene families. Among them, Group 7 allergen (ALL7) protein was reported in spider venom for the first time. Its coding genes had a predicted signal peptide and maintained high expression levels in the venom, suggesting that ALL7 plays an important role in venom and maybe is a type of newly discovered venom toxin in the spider. By implementing comparative genomics, we found a similar gene number of main toxin gene families in spiders and the scorpion genome with conservative evolutionary rates, indicating that these toxin genes could be an ancient (~400 million years) and a conserved "basic toolkit" for spiders and scorpions to perform primary defence functions. Obtaining high‐quality chromosome‐level genomes from spiders not only facilitates venom research and toxin resource application, but also can improve comparative genomic analysis in other important traits, like the evolution of silk or behaviour.
p21 restricts influenza A virus by perturbing the viral polymerase complex and upregulating type I interferon signaling

Many cellular genes and networks induced in human lung epithelial cells infected with the influenza virus remain uncharacterized. Here, we find that p21 levels are elevated in response to influenza A virus (IAV) infection, which is independent of p53. Silencing, pharmacological inhibition or deletion of p21 promotes virus replication in vitro and in vivo, indicating that p21 is an influenza restriction factor. Mechanistically, p21 binds to the C-terminus of IAV polymerase subunit PA and competes with PB1 to limit IAV polymerase activity. Besides, p21 promotes IRF3 activation by blocking K48-linked ubiquitination degradation of HO-1 to enhance type I interferons expression. Furthermore, a synthetic p21 peptide (amino acids 36 to 43) significantly inhibits IAV replication in vitro and in vivo. Collectively, our findings reveal that p21 restricts IAV by perturbing the viral polymerase complex and activating the host innate immune response, which may aid the design of desperately needed new antiviral therapeutics.
Plasma p217+tau vs NAV4694 amyloid and MK6240 tau PET across the Alzheimer continuum.

INTRODUCTION: We evaluated a new Simoa plasma assay for phosphorylated tau at aa217 enhanced by additional ptau sites (p217+tau). METHODS: Plasma p217+tau levels were compared to 18F-NAV4694 amyloid-beta (A{beta} PET and 18F-MK6240 tau PET in 174 cognitively impaired (CI) and 223 cognitively unimpaired (CU) participants. RESULTS: Compared to A{beta}- CU, the plasma levels of p217+tau increased two-fold in A{beta}+ CU and 3.5-fold in A{beta}+ CI. In A{beta}- the p217+tau levels did not significantly differ between CU, MCI or dementia. P217+tau correlated with A{beta} centiloids {rho}=0.67 (CI 0.64; CU 0.45) and tau SUVRMT {rho}=0.63 (CI 0.69; CU 0.34). Area under curve (AUC) for AD vs A{beta}- CU was 0.94, for AD vs other dementia was 0.93, for A{beta}+ vs A{beta} PET was 0.89 and for tau+ vs tau- PET was 0.89. DISCUSSION: Plasma p217+tau levels elevate early in the AD continuum and correlate well with A{beta} and tau PET.
Latent Profiles of Social Reactions to Sexual Assault Disclosure Among Undergraduate Women

The types of social reactions that victims receive when they disclose experiences of sexual assault are important for post-trauma recovery. Using a person-centered analytic approach, we identified latent profiles based upon the nature of two types of negative (turning against and unsupportive acknowledgment) and two types of positive (emotional support and informational/tangible aid) reactions received by 300 undergraduate women who disclosed sexual assault. Analyses identified four latent profiles characterized by (a) moderate emotional support/low negative reactions, (b) moderate emotional support/moderate negative reactions, (c) high positive/some unsupportive acknowledgment reactions, and (d) moderate positive/high negative reactions. Differences between the profiles in sexual assault acknowledgment, self- and perpetrator-blame, and some assault-related characteristics (victim injury but not victim or perpetrator intoxication) were identified. Group comparisons revealed that the two profiles characterized by greater negative reactions reported greater posttraumatic stress, whereas the profile characterized by moderate support/moderate negative reactions reported greater depression. No differences were identified for hazardous alcohol use. Findings highlight the importance of addressing negative reactions to sexual assault disclosure as potential barriers to recovery. Colleges may benefit from programming targeted at disclosure recipients as part of violence prevention efforts. A broader societal shift is also imperative to eliminate stigmatization of victims. Additional online materials for this article are available on PWQ’s website at: http://journals.sagepub. com/doi/suppl/10.1177/03616843211038924.
PASSIVITY AND NONCOLLOCATION IN THE CONTROL OF FLEXIBLE STRUCTURES

Collocation of actuation and sensing in flexible structures leads to the desirable input-output property of passivity which greatly simplifies the stabilization problem. However, many control problems of aerospace interest such as robotic manipulation and attitude control of tip-mounted payloads are noncollocated in nature. This paper examines the possibility of combining collocated and noncollocated outputs so as to achieve passivity. An appropriate combination is shown to depend on the interplay between collocated and noncollocated mass properties. Tracking problems are also studied and a controller with adaptive feedforward elements is introduced. An experimental study using a simple flexible apparatus with one rigid degree of freedom and two vibration modes is used to validate the analysis.
Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

Background Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Our results are evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate a core microbiome in Lake Hillier composed of multiple pigment-producer microbes, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia’s Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.
FAM21 is critical for TLR2/CLEC4E-mediated dendritic cell function against Candida albicans

FAM21 is essential for CD11c+ dendritic cell function to activate host immune response against C.albicans infection. FAM21 (family with sequence similarity 21) is a component of the Wiskott–Aldrich syndrome protein and SCAR homologue (WASH) protein complex that mediates actin polymerization at endosomal membranes to facilitate sorting of cargo-containing vesicles out of endosomes. To study the function of FAM21 in vivo, we generated conditional knockout (cKO) mice in the C57BL/6 background in which FAM21 was specifically knocked out of CD11c-positive dendritic cells. BMDCs from those mice displayed enlarged early endosomes, and altered cell migration and morphology relative to WT cells. FAM21-cKO cells were less competent in phagocytosis and protein antigen presentation in vitro, though peptide antigen presentation was not affected. More importantly, we identified the TLR2/CLEC4E signaling pathway as being down-regulated in FAM21-cKO BMDCs when challenged with its specific ligand Candida albicans. Moreover, FAM21-cKO mice were more susceptible to C. albicans infection than WT mice. Reconstitution of WT BMDCs in FAM21-cKO mice rescued them from lethal C. albicans infection. Thus, our study highlights the importance of FAM21 in a host immune response against a significant pathogen.
Multisensory integration of social signals by a pathway from the basal amygdala to the auditory cortex in maternal mice

Social encounters are inherently multimodal events, yet how and where social cues of distinct sensory modalities merge and interact in the brain is poorly understood. When their pups wander away from the nest, mother mice use a combination of vocal and olfactory signals emitted by the pups to locate and retrieve them. Previous work revealed the emergence of multisensory interactions in the auditory cortex (AC) of both dams and virgins who co-habitate with pups (‘surrogates’). Here we identify a neural pathway that integrates information about odors with responses to sound. We found that a scattered population of glutamatergic neurons in the basal amygdala (BA) projects to the AC and responds to odors, including the smell of pups. These neurons exhibit increased activity when the female is searching for pups that terminates upon contact. Finally, we show that selective optogenetic activation of BA-AC neurons modulates responses to pup calls, and that this modulation switches from predominantly suppressive to predominantly excitatory after maternal experience. This supports an underappreciated role for the amygdala in directly shaping sensory representations in an experience-dependent manner. We propose that the BA-AC pathway integrates olfaction and audition to facilitate maternal care, and speculate that it may carry valence information to the AC.
Mechanism of voltage gating in the voltage-sensing phosphatase Ci-VSP

The conformational changes in voltage-sensing domain (VSD) are driven by the transmembrane electric field acting on charges and countercharges. Yet, the overall energetics and detailed mechanism of this process are not fully understood. Here, we determined free energy and displacement charge landscapes, as well as major conformations corresponding to a complete functional gating cycle in the isolated voltage-sensing domain of the phosphatase Ci-VSP (Ci-VSD) comprising four transmembrane helices (segments S1-S4). Molecular dynamics simulations highlight the extent of S4 movements. In addition to the crystallographically determined activated ‘Up’ and resting ‘Down’ states, the simulations predict two novel Ci-VSD conformations: a deeper resting state (‘Down-minus’) and an extended activated (‘Up-plus’) state. These additional conformations were experimentally probed via systematic cysteine mutagenesis with metal-ion bridges and the engineering of proton conducting mutants at hyperpolarizing voltages. These results show that voltage activation involves sequentially populating these four states in a stepwise way, translating one arginine across the membrane electric field per step, transferring ~3 e0 charges.