Miracle-dz/UniFAR-FTUs huggingface dataset:
A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified bodywall layer in ascus-bearing cheilostomes) and asked if its presence has any bearing on the diversification rates of cheilostomes.
Identifying a GSK3-TRARG1 signaling axis reveals BCL9L as a novel regulator of GLUT4 trafficking

Trafficking regulator of GLUT4-1, TRARG1, positively regulates insulin-stimulated GLUT4 trafficking and insulin sensitivity. However, the mechanism(s) by which this occurs remain(s) unclear. Using biochemical and mass spectrometry analyses we found that TRARG1 is dephosphorylated in response to insulin in a PI3K/Akt-dependent manner and is a novel substrate for GSK3. Priming phosphorylation of mouse TRARG1 at serine 84 allows for GSK3-directed phosphorylation at serines 72, 76 and 80. A similar pattern of phosphorylation was observed in human TRARG1, suggesting that our findings are translatable to human TRARG1. Pharmacological inhibition of GSK3 increased cell surface GLUT4 in cells stimulated with a submaximal insulin dose, and this was impaired following Trarg1 knockdown, suggesting that TRARG1 acts as a GSK3-mediated regulator in GLUT4 trafficking. TRARG1 dephosphorylation in response to insulin or GSK3 inhibition regulated its protein-protein interactions, decreasing the interaction between TRARG1 and BCL9L, JAGN1, PYGO2 and HSD17B12. Knock-down of Bcl9l promoted GLUT4 translocation to the plasma membrane. These data place TRARG1 within the insulin signaling network and provide insights into how TRARG1 regulates GLUT4 trafficking in adipocytes.
Family matters: The genomes of conserved bacterial symbionts provide insight into specialized metabolic relationships with their sponge host

Sponges have evolved complex associations with conserved bacteria symbionts that contribute to the fitness of the host. Sponges of the family, Latrunculiidae, produce a diverse array of cytotoxic pyrroloiminoquinone alkaloids and their microbiomes are dominated by a conserved spirochete and betaproteobacterium. We investigated the microbiome of Tsitsikamma favus, a latrunculid species that produces predominantly tsitsikammamines. A total of 50 Metagenome-Assembled-Genomes (MAGs) were recovered from the four metagenomes, including representatives of the conserved spirochete and betaproteobacterium symbionts. We predict that the Sp02-3, one of two spirochetes unique to latrunculid species, is likely an anaerobic symbiont that produces vitamin B6. Dysbiosis of the spirochete population correlates with the chemistry associated with distinct sponge chemotypes, implying a role in pyrroloiminoquinone production. The betaproteobacteria symbiont belongs to the newly defined Tethybacterales order and likely aids in the removal of nitrate. There is also evidence to suggest that the two symbionts may work in tandem to remove sulfate from the sponge. Additionally, we analyzed seventeen Tethybacterales genomes and identified a third family within the order. The phylogeny of Tethybacterales is incongruent with that of the sponge hosts suggesting that the association of Tethybacterales and their sponge hosts likely occurred multiple times over their evolutionary history.
Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

Pathogen sensing via pattern recognition receptors triggers massive reprogramming of macro-phage gene expression. While the signaling cascades and transcription factors that activate these responses are well-known, the role of post-transcriptional RNA processing in modulating innate immune gene expression remains understudied. Recent phosphoproteomics analyses revealed that members of the SR and hnRNP families of splicing regulatory proteins are dynamically post-translationally modified in infected macrophages. To begin to test if these splicing factors play a privileged role in controlling the innate immune transcriptome, we analyzed steady state gene expression and alternatively spliced isoform production in ten SR/hnRNP knockdown RAW 264.7 macrophage cell lines following infection with the bacterial pathogen Salmonella enterica serovar Typhimurium (Salmonella). We identified thousands of transcripts whose abundance was increased or decreased by SR/hnRNP knockdown in macrophages. We observed that different SR/hnRNPs control the expression of distinct gene regulons in uninfected and Salmonella-infected macrophages, with several key innate immune genes (Nos2, Mx1, Il1a) relying on multiple SR/hnRNPs to maintain proper induction and/or repression. Knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for a number of key immune sensors and signaling molecules and many of these splicing changes were again, distinct in uninfected and Salmonella-infected macrophages. Finally, after observing a surprising degree of similarity between the DEGs and DIUs in hnRNP K and U knockdown macrophages, we found that these cells are better able to restrict vesicular stomatitis virus replication than control cells, supporting a role for these hnRNPs in controlling infection outcomes in macrophages ex vivo. Based on these findings, we conclude that many innate immune genes have evolved to rely on one or more splicing regulatory factors to ensure the proper timing and magnitude of their induction, bolstering a model wherein pre-mRNA splicing is a critical regulatory node in the innate immune response.
On a wing and a prayer: limitations and gaps in global bat wing morphology trait data

Species’ life history traits have a wide variety of applications in ecological and conservation research, particularly when assessing threats. The development and growth of global species trait databases are critical for improving trait-based analyses; however, it is vital to understand the gaps and biases of available data. Bats are an extremely diverse and widely distributed mammalian order, with many species facing local declines and extinction. We conducted a literature review for bat wing morphology, specifically wing loading and aspect ratio, to identify issues with data reporting and ambiguity. We collected data on field methodology, trait terminology, and data reporting and quality. We found several issues regarding semantic ambiguity in trait definitions and data reporting. Globally we found that bat wing morphology trait coverage was low. Only six bat families had over 40% trait coverage, and of those none consisted of more than 11 total species. We found similar biases in trait coverage across IUCN Redlist categories with threatened species having lower coverage. Geographically, North America, Europe, and the Indomalayan regions showed higher overall trait coverage, while both the Afrotropical and Neotropical ecoregions showed poor trait coverage. The underlying biases and gaps with bat wing morphology data have implications for researchers conducting global trait-based assessments. Implementing imputation techniques may address missing data, but only for smaller regional subsets with substantial trait coverage. However, due to the low overall trait coverage, increasing species representation in the database should be prioritized. We suggest adopting an Ecological Trait Standard vocabulary to reduce semantic ambiguity in bat wing morphology traits to improve data compilation and clarity. Additionally, we advocate that researchers adopt an Open Science approach to facilitate the growth of a bat wing morphology trait database.
Genetic Fine-mapping with Dense Linkage Disequilibrium Blocks: genetics of nicotine dependence

Fine-mapping is an analytical step to perform causal prioritization of the polymorphic variants on a trait-associated genomic region observed from genome-wide association studies (GWAS). The prioritization of causal variants can be challenging due to the linkage disequilibrium (LD) patterns among hundreds to thousands of polymorphisms associated with a trait. We propose a novel ℓ0 graph norm shrinkage algorithm to select causal variants from dense LD blocks consisting of highly correlated SNPs that may not be proximal or contiguous. We extract dense LD blocks and perform regression shrinkage to calculate a prioritization score to select a parsimonious set of causal variants. Our approach is computationally efficient and allows performing fine-mapping on thousands of polymorphisms. We demonstrate its application using a large UK Biobank (UKBB) sample related to nicotine addiction. Our results suggest that polymorphic variances in both neighboring and distant variants can be consolidated into dense blocks of highly correlated loci. Simulations were used to evaluate and compare the performance of our method and existing fine-mapping algorithms. The results demonstrated that our method outperformed comparable fine-mapping methods with increased sensitivity and reduced false-positive error rate regarding causal variant selection. The application of this method to smoking severity trait in UKBB sample replicated previously reported loci and suggested the causal prioritization of genetic effects on nicotine dependency. Author summary Disentangling the complex linkage disequilibrium (LD) pattern and selecting the underlying causal variants have been a long-term challenge for genetic fine-mapping. We find that the LD pattern within GWAS loci is intrinsically organized in delicate graph topological structures, which can be effectively learned by our novel ℓ0 graph norm shrinkage algorithm. The extracted LD graph structure is critical for causal variant selection. Moreover, our method is less constrained by the width of GWAS loci and thus can fine-map a massive number of correlated SNPs.
Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset

Cynomolgus macaque ( Macaca fascicularis ) and common marmoset ( Callithrix jacchus ) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research. Measurement(s) sequence_assembly • genome • DNA Technology Type(s) sequence assembly process • DNA sequencing Sample Characteristic - Organism Macaca fascicularis • Callithrix jacchus Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare. 14665314
The structurally conserved TELR region on shelterin protein TPP1 is essential for telomerase processivity but not recruitment

Significance Telomerase directs the synthesis of new telomeric repeats at chromosome ends, enabling cells to overcome the end replication problem and to continue to divide. The shelterin protein TPP1 interacts with telomerase, promoting both telomerase recruitment and processivity (the addition of multiple telomeric repeats after a single substrate binding event). Here, we identify separation-of-function mutants of TPP1 that eliminate telomerase processivity but leave the telomerase recruitment function intact. When introduced into human cells in a homozygous manner, these mutations can induce critical telomere shortening and cellular senescence. Our observations therefore demonstrate that TPP1 stimulation of telomerase processivity is a key regulatory step in vivo for telomerase-mediated extension of telomeres and continued cell proliferation. The shelterin protein TPP1 is involved in both recruiting telomerase and stimulating telomerase processivity in human cells. Assessing the in vivo significance of the latter role of TPP1 has been difficult, because TPP1 mutations that perturb telomerase function tend to abolish both telomerase recruitment and processivity. The Saccharomyces cerevisiae telomerase-associated Est3 protein adopts a protein fold similar to the N-terminal region of TPP1. Interestingly, a previous structure-guided mutagenesis study of Est3 revealed a TELR surface region that regulates telomerase function via an unknown mechanism without affecting the interaction between Est3 and telomerase [T. Rao et al., Proc. Natl. Acad. Sci. U.S.A. 111, 214–218 (2014)]. Here, we show that mutations within the structurally conserved TELR region on human TPP1 impaired telomerase processivity while leaving telomerase recruitment unperturbed, hence uncoupling the two roles of TPP1 in regulating telomerase. Telomeres in cell lines containing homozygous TELR mutations progressively shortened to a critical length that caused cellular senescence, despite the presence of abundant telomerase in these cells. Our findings not only demonstrate that telomerase processivity can be regulated by TPP1 in a process separable from its role in recruiting telomerase, but also establish that the in vivo stimulation of telomerase processivity by TPP1 is critical for telomere length homeostasis and long-term viability of human cells.
Superpixel-Based Minimum Noise Fraction Feature Extraction for Classification of Hyperspectral Images

In this paper, a novel feature extraction technique called SuperMNF is proposed, which is an extension of the minimum noise fraction (MNF) transformation. In SuperMNF, each superpixel has its own transformation matrix and MNF transformation is performed on each superpixel individually. The basic idea behind the SuperMNF is that each superpixel contains its specific signal and noise covariance matrices which are different from the adjacent superpixels. The extracted features, owning spatial-spectral content and provided in the lower dimension, are classified by maximum likelihood classifier and support vector machines. Experiments that are conducted on two real hyperspectral images, named Indian Pines and Pavia University, demonstrate the efficiency of SuperMNF since it yielded more promising results than some other feature extraction methods (MNF, PCA, SuperPCA, KPCA, and MMP).
Understanding Echo Chambers and Filter Bubbles: The Impact of Social Media on Diversification and Partisan Shifts in News Consumption

Echo chambers and filter bubbles are potent metaphors that encapsulate widespread public fear that the use of social media may limit the information that users encounter or consume online. Specifically, the concern is that social media algorithms combined with tendencies to interact with like-minded others both limits users’ exposure to diverse viewpoints and encourages the adoption of more extreme ideological positions. Yet empirical evidence about how social media shapes information consumption is inconclusive. We articulate how characteristics of platform algorithms and users’ online social networks may combine to shape user behavior. We bring greater conceptual clarity to this phenomenon by expanding beyond discussion of a binary presence or absence of echo chambers and filter bubbles to a richer set of outcomes incorporating changes in both diversity and slant of users’ information sources. Using a data set with over four years of web browsing history for a representative panel of nearly 200,000 U.S. adults, we analyzed how individuals’ social media usage was associated with changes in the information sources they chose to consume. We find differentiated impacts on news consumption by platform. Increased use of Facebook was associated with increased information source diversity and a shift toward more partisan sites in news consumption; increased use of Reddit with increased diversity and a shift toward more moderate sites; and increased use of Twitter with little to no change in either. Our results demonstrate the value of adopting a nuanced multidimensional view of how social media use may shape information consumption.
ANDI @ CONcreTEXT: Predicting Concreteness in Context for English and Italian using Distributional Models and Behavioural Norms (short paper)

In this paper we describe our participation in the CONcreTEXT task of EVALITA 2020, which involved predicting subjective ratings of concreteness for words presented in context. Our approach, which ranked first in both the English and Italian subtasks, relies on a combination of context-dependent and context-independent distributional models, together with behavioural norms. We show that good results can be obtained for Italian, by first automatically translating the Italian stimuli into English, and then using existing resources for both Italian and English.
Who influences employees’ dark side: A multi-foci meta-analysis of counterproductive workplace behaviors

We adopt a multi-foci perspective to provide a theory-driven quantitative review of employee counterproductive workplace behaviors (CWBs) by meta-analyzing the relationships between CWB and four groups of antecedents. Specifically, CWB antecedents stemming from four sources—supervisors, organization, coworkers, and private life—were included to investigate differences in their relationships with employee CWB. Based on the Conservation of Resources Theory, we argue that favorable and unfavorable correlates relate to employee CWB to different degrees. The meta-analysis included 181 field studies with 223 independent samples. Results indicated that unfavorable antecedents correlate more strongly with CWB than favorable antecedents. We also found that supervisor- and organization-related antecedents have stronger relationships with CWB than those from the two other groups. Implications include a deeper understanding of which situational factors relate the most—or least—to CWB which can help better address CWB in the workplace.
Short title: The paraquat-tolerance mechanism in transgenic rice

45 Paraquat is an important bipyridine herbicide by acting on the photosynthetic system 46 of the plants and generating reactive oxygen species leading to cell death, whereas the 47 mechanism of the paraquat resistance remains to be explored. In this study, a putative 48 paraquat-resistant gene EiKCS from goosegrass (Eleusine indica L.) was isolated and 49 overexpressed in a transgenic rice (Oryza sativa L.). This transgenic rice (KCSox) 50 was treated by exogenous spermidine and paraquat and then was analyzed by 51 qualitative and quantitative proteomics. Overexpressing of EiKCS enhanced paraquat 52 tolerance in KCSox by the accumulation of endogenous polyamines whose dominant 53 presences of polyamines benzoylation derivatizations in rice were C18H20N2O2, 54 C28H31N3O3, and C38H42N4O4. The mechanism underlying the improving tolerance 55 enhanced antioxidant capacity of ROS systems and light-harvesting in photosynthesis 56 in KCSox rice leaves to reducing paraquat toxicity. The protein β-Ketoacyl-CoA 57 Synthase (EiKCS) encoded by the EiKCS gene promoted the synthesis and 58 metabolism of proteins of the polyamine pathway. Three cofactors CERs were 59 identified and positively correlated with the function of EiKCS on very-long-chain 60 fatty acids (VLCFAs) biosynthesis via promoting the polyamine pathway and 61 inhibiting the links with the TCA pathway and fatty acid pathway to responding to the 62 paraquat tolerance in the KCSox rice, which also caused the prolongation of the 63 overproduction of spermine and a transient increase of intracellular malondialdehyde 64 (MDA). These results expanded the polyamines pathway manipulated in cereals using 65 genetic engineering to clarify the mechanism of paraquat-tolerance. 66 67
Green HRM: A Sustainable Approach Adopted By Green Banks

Article History Published Online: 02 June 2018 Currently, our environment is deteriorating as a result of remorseless human activities leading to global warming and changes in worldwide weather patterns. Environmental protection has become the most pressing matter of the moment. To strengthen the call for environmental protection, various green standards have been established which aims at mitigating corporate practices that are not eco-friendly. Subsequently, a fast growing corporate trend of integrating green practices into HR can be seen. Corporations have taken a green turn while focusing on the “go green” concept to find a fine balance between their pursuit of profits and environmental protection. The banking sector has also taken various green initiatives in recent years in order to adopt the “go green” concept. Their objective is to conduct all banking operations in an efficient manner by taking care of earth‟s ecosystems with minimal environmental impact. The paper largely focuses on various green components which can be incorporated into basic HR practices and attempts to highlight the present position of Green HRM practices implemented in selected green banks through systematic review of collected literature. Finally, it helps in understanding the role of HR professionals in achieving green goals of the organisation.
DFT: B3LYP/ LANL2DZ Study for the Removal of Fe, Ni, Cu, As, Cd and Pb with Chitosan

Human activities are responsible for the existence of heavy metals in the environment. The accumulation of these metals in the environment causes several risks, such as toxicological, mutagenic, and carcinogenic effects. Chitosan (Cs) based materials have been explored its competitive efficacy in heavy metals removal from contaminated water. In this study, an attempt is presented to develop a natural, reliable, and cost-effective biopolymer structure of Cs with a high ability to entrap some heavy metals, which can be found in polluted water. The correlation between Cs-heavy metals and its stability was studied by density functional theory (DFT) using B3LYP together with the basis set LANL2DZ. The observed results revealed that the bandgap energy values for Cs, CsFe, Cs-Ni, Cs-Cu, Cs-As, CsCd and Cs-Pb were 2.571, 0.6147, 0.7176, 0.3396, 0.6648, 1.5007 and 0.4128 eV, respectively. The later showed that Cs structure has high selectivity and binding affinity to Cu and Pb hydrated metals, respectively rather than Fe, Ni, As and Cd. The examined correlation between Cu and Pb with Cs revealed that Cs could be applied for sensing and removing of Cu and Pb from wastewater.