Miracle-dz/UniFAR-FTUs huggingface dataset:
You Want it Sweeter: How Glycosylation Affects Plant Response to Oxidative Stress

Oxidative stress is a cellular threat which puts at risk the productivity of most of crops valorized by humankind in terms of food, feed, biomaterial, or bioenergy. It is therefore of crucial importance to understand the mechanisms by which plants mitigate the deleterious effects of oxidizing agents. Glycosylation of antioxidant molecules and phytohormones modifies their chemical properties as well as their cellular and histological repartition. This review emphasizes the mechanisms and the outcomes of this conjugation reaction on plant ability to face growing conditions favoring oxidative stress, in mirror with the activity of deglycosylating enzymes. Pioneer evidence bridging flavonoid, glycosylation, and redox homeostasis paved the way for numerous functional analyses of UDP-glycosyltransferases (UGTs), such as the identification of their substrates and their role to circumvent oxidative stress resulting from various environmental challenges. (De)glycosylation appears as a simple chemical reaction regulating the biosynthesis and/or the activity of a myriad of specialized metabolites partaking in response to pathogen and abiotic stresses. This outcome underlies the possibility to valorize UGTs potential to upgrade plant adaptation and fitness in a rising context of sub-optimal growing conditions subsequent to climate change.
A simple linear relationship between resource availability and microbial community diversity

Microbial community diversity is pivotal for the functioning of our planet, but its drivers are still unclear, in particular the role of resource number and identity. To fill this gap, we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found a remarkable diversity in single resources but a linear one-by-one increase in the number of species with the number of additional resources. We show, both experimentally and theoretically, that both these observations could originate from generalist and specialist taxa interacting in a modular fashion within the community. Since generalists and specialists are ubiquitous in natural microbiomes, our results might apply to a variety of different ecological settings, providing a framework to predict how community diversity responds to changes in resource availability. One Sentence Summary While many species coexist in single resources, community diversity only increases one-by-one as more resources are added.
Cardiac cell type–specific gene regulatory programs and disease risk association

A human heart cell type–specific cis-regulatory element atlas reveals gene regulatory mechanisms of cardiovascular diseases. Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease–associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type–specific gene regulation in human hearts during health and disease.
RNA sequence and structure determinants of Pol III transcriptional termination in human cells

The precise mechanism of transcription termination of the eukaryotic RNA polymerase III (Pol III) has been a subject of considerable debate. Although previous studies have clearly shown that at the end of RNA transcripts, tracts comprised of multiple uracils are required for Pol III termination, whether upstream RNA secondary structure in the nascent transcript is necessary for robust transcriptional termination is still subject to debate. We sought to address this directly through the development of an in cellulo Pol III transcription termination assay using a synthetic biology approach. Specifically, we utilized the recently developed Tornado expression system and a stabilized Corn RNA aptamer to create a Pol III-transcribed RNA that produces a detectable fluorescent signal when transcribed in human cells. To study the effects of RNA sequence and structure on Pol III termination, we systematically varied the sequence context upstream of the aptamer and identified sequence characteristics that enhance or diminish termination. We found that in the absence of predicted secondary structure, only poly-U tracts longer than then the average length found in the human genome (4–5 nucleotides), efficiently terminate Pol III transcription. We found that shorter poly-U tracts could induce termination when placed in proximity to secondary structural elements, while secondary structure by itself was not sufficient to induce termination. These findings demonstrate a key role for sequence and structural elements within Pol III-transcribed nascent RNA for efficient transcription termination, and demonstrate a generalizable assay for characterizing Pol III transcription in human cells.
Convergent evolution of increased urine concentrating ability in desert mammals

One of the most celebrated textbook examples of physiological adaptations to desert environments is the unique ability that desert mammals have to produce hyperosmotic urine. Commonly perceived as an adaptation mainly observed in small rodents, the extent to which urine concentrating ability has independently evolved in distinct lineages, including medium-sized and large desert mammals, has not previously been assessed using modern phylogenetic approaches. Here, we explicitly test the general hypothesis that desert-dwelling mammals have evolved increased ability to concentrate urine compared to non-desert species, controlling for body mass and other covariates. Phylogenetic generalized least-squares models show that the mean aridity index of a species distribution range largely predicts its urine concentrating ability, even when accounting for body mass differences and phylogenetic correlations. In contrast, we find much weaker correlations between mass-adjusted basal metabolic rate and environmental variables.
Topographic gradients define the projection patterns of the claustrum core and shell in mice

The claustrum is densely connected to the cortex and participates in brain functions such as attention and sleep. Although some studies have reported the widely divergent organization of claustrum projections, others describe parallel claustrocortical connections to different cortical regions. Therefore, the details underlying how claustrum neurons broadcast information to cortical networks remain incompletely understood. Using multicolor retrograde tracing we determined the density, topography, and co-projection pattern of fourteen claustrocortical pathways, in mice. We spatially registered these pathways to a common coordinate space and found that the claustrocortical system is topographically organized as a series of overlapping spatial modules, continuously distributed across the dorsoventral claustrum axis. The claustrum core projects predominantly to frontal-midline cortical regions, whereas the dorsal and ventral shell project to the cortical motor system and temporal lobe, respectively. Anatomically connected cortical regions receive common input from a subset of claustrum neurons shared by neighboring modules, whereas spatially separated regions of cortex are innervated by different claustrum modules. Therefore, each output module exhibits a unique position within the claustrum and overlaps substantially with other modules projecting to functionally related cortical regions. Claustrum inhibitory cells containing parvalbumin, somatostatin, and neuropeptide Y also show unique topographical distributions, suggesting different output modules are controlled by distinct inhibitory circuit motifs. The topographic organization of excitatory and inhibitory cell types may enable parallel claustrum outputs to independently coordinate distinct cortical networks.
PanACoTA: a modular tool for massive microbial comparative genomics

The study of the gene repertoires of microbial species, their pangenomes, has become a key topic of study in microbial evolution and genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanACoTA (https://github.com/gem-pasteur/PanACoTA), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate, and then build their pangenome, several variants of core genomes, their alignments, and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. The software is built in Python3 and includes features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions.
ISSR Analysis of Ten Breeding Lines of Pyropia yezoensis

Inter Simple Sequence Repeat (ISSR)-PCR was used to analyze the genetic variation and germplasm identification of ten different breeding lines of Pyropia yezoensis. 14 polymorphic and specifical primers were screened and optimized. From the generated ISSR products by these primers, 97.1% of the DNA bands amplified were polymorphic. These primers could be used as molecular genetic markers to discriminate and evaluate the ten lines. A number of peculiarity amplified bands of primer 826 were applied to establish the ISSR code patterns of the P. yezoensis ten lines.
Updating the Free Radical Theory of Aging

The free radical theory of aging, one of the nine suggested hallmarks of aging (López-Otín et al., 2016), implicates the gradual accumulation of oxidative cellular damage as a fundamental driver of cellular aging (Harman, 1956; Miquel et al., 1980). This theory has evolved over time to emphasize the role of free radical induced mitochondrial DNA (mtDNA) mutations and the accumulation of mtDNA deletions (Miquel et al., 1980; Cortopassi et al., 1992; Michikawa et al., 1999). Given the proximity of mtDNA to the electron transport chain, a primary producer of free radicals, it postulates that the mutations would promote mitochondrial dysfunction and concomitantly increase free radical production in a positive feedback loop. The observation of oxidative damage in the form of 7,8-dihydro-8-oxo-deoxyguanosine (8-oxodG) DNA oxidative lesions accumulating with age has been a cornerstone of the free radical theory of aging (Fraga et al., 1990).
Structure and Dynamic of Global Population Migration Network

People are the most important factors of economy and the primary carriers of social culture. Cross-border migration brings economic and cultural impacts to the origin and destination and is also a key to reflect the international relations of related countries. In fact, the migration relationships of countries are complex andmultilateral, but most traditional migrationmodels are bilateral. Network theories could provide a better description of global migration to show the structure and statistical characteristics more clearly. Based on the estimated migration data and disparity filter algorithm, the networks describing the global multilateral migration relationships have been extracted among 200 countries over fifty years. +e results show that the global migration networks during 1960–2015 exhibit a clustering and disassortative feature, implying globalized and multipolarized changes of migration during these years. +e networks were embed into a Poincaré disk, yielding a typical and hierarchical “coreperiphery” structure, which is associated with angular density distribution, and has been used to describe the “multicentering” trend since 1990s. Analysis on correlation and evolution of communities indicates the stability of most communities, yet some structural changes still exist since 1990s, which reflect that the important historical events are contributable to regional and even global migration patterns.
Peptidoglycan synthesis in Escherichia coli from a PBP1b perspective

An essential and unique component of the bacterial cell envelope is the peptidoglycan layer. This layer, formed by glycan chains that are interlinked by peptide bridges, is essential for the maintenance of the specific cell shape of the bacterium, and protects it from rupture by osmotic pressure. Because this layer is so essential, easy accessible, on the outside of the bacterium, and we humans do not possess this structure, and hence its synthesis machinery, it has always been and still is an attractive target for antibacterial compounds. Since now a days more and more bacteria become resistant against the available antibiotics, it is of great importance to find new targets for the development of new classes of antibiotics. In this perspective, we focused on the cell division-specific bifunctional peptidoglycan synthase PBP1b of E. coli. By getting more insight in its interactions with and its regulation by (new) interacting proteins, the complex mechanism of peptidoglycan synthesis by PBP1b, and the regulation of this in space and time can be further clarified. This information can then be used for the rational development of new antibiotics. Site specific incorporation of an unnatural amino acid with cross-linking properties in PBP1b in vivo, is one strategy used to obtain information on the interaction profile of PBP1b. Using this technique, we found one new interacting protein, having a decreasing effect on the transpeptidase activity of PBP1b (CpoB), and we specified the interaction site of this, and an already known PBP1b regulator, FtsN, to be in a cleft between the UB2H and transpeptidase domain. Moreover, we also showed that a loop structure of the transpeptidase domain is an interaction hot spot which is also essential for proper functioning of this domain. We furthermore demonstrated the usefulness of a new immobilization strategy for SPR experiments, to allow measurements with fully active and correctly orientated proteins. This strategy should more reflect the in vivo situation, and prevent measurements of non-relevant interactions. Different fluorescently labeled substrate variants were also created, which can be used to analyze the activity of PBP1b, and other peptidoglycan synthases. These new variants allowed us to obtain results with a higher resolution and sensitivity. Finally, we describe an attempt to identify the part of PBP1b important for dimer formation. In vitro experiments have shown that dimerization increases the activity of PBP1b, however, the in vivo role of dimerization remains unclear. These results present new players in the vast amount of interactions in which PBP1b is involved, which reflects the complexity and importance of correct spatio-temporal regulation of peptidoglycan synthesis. Furthermore, the improvement of the assays to measure interaction kinetics and the activity of PBPs can be used in the ongoing research on bacterial cell wall synthesis, to find new targets for antibiotic development.
Impact of Compensation on Employee Performance

Compensation is the remuneration received by an employee in return for their contribution to the organization. It is an organized practice that involves balancing the work-employee relation by providing monetary and nonmonetary benefits to employees. Compensation includes payments such as bonuses, profit sharing, overtime pay, recognition rewards and sales commission. Compensation is an integral part of human resource management which helps in motivating the employees and improving organizational effectiveness. Direct Compensation is typically made up of salary payments and health benefits. The creation of salary ranges and pay scales for different positions within the company are the central responsibility of compensation management staff. Direct compensation that is in line with industry standards provides employees with the assurance that they are getting paid fairly. Indirect Compensation focuses on the personal motivations of each person to work. Although salary is important, people are most productive in jobs where they share the company's values and priorities. These benefits can include things like free staff development courses, subsidized day care, the opportunity for promotion or transfer within the company, public recognition, the ability to effect change in the workplace, and service to others. Employees should be managed properly and motivated by providing best remuneration and compensation as per the industry standards. The lucrative compensation will also serve the need for attracting and retaining the best employees. The impact of compensation and benefits on employee performance and organizational effectiveness depends on the existing compensation and performance management programs in the organization. Typically, most employees respond to increases in pay and benefits with a positive and more productive attitude. Sometimes, employees only notice rewards of a salary increase the day the increase is communicated to them, and the day they receive the first paycheck that includes the salary increase. In this Paper I would like to discuss the components and importance of compensation and I would like to emphasis more on the impact of compensation on employee performance in the organization.
SYLLABLE FREQUENCY EFFECTS IN ENGLISH

Syllable frequency effects in production tasks are interpreted as evidence that speakers retrieve precompiled articulatory programs for high frequency syllables from a mental syllabary. They have not been found reliably in English, nor isolated to the phonetic encoding processes during which the syllabary is thought to be accessed. In this experiment, 48 participants produced matched highand novel/low-frequency syllables in a near-replication of Laganaro and Alario’s [(2006) On the locus of the syllable frequency effect in speech production. Journal of Memory and Language, 55(2), 198-196, http://dx.doi. org/10.1016/j.jml. 2006.05. 001] production conditions: immediate naming, naming following an unfilled delay, and naming after delay filled by concurrent articulation. Immediate naming was faster for high frequency syllables, demonstrating a robust syllable frequency effect in English. There was no high frequency advantage in either delayed naming condition, leaving open the question of whether syllable frequency effects arise during phonological or phonetic encoding.
Moderating role of self-efficacy in the link between work-family conflict and job satisfaction

Job satisfaction has continued to attract the attention of researchers because of its importance in human resources management. There has been much research linking work-family conflict to job satisfaction among teachers, but there has been little effort to study the moderating role of self-efficacy in this link in the Nigerian teachers. Leaning on the theoretical assumptions underlying the conservation of resources and job demandresources models linking work-family conflict and self-efficacy to job satisfaction, this cross-sectional survey investigated the moderating role of self-efficacy in work-family conflict and job satisfaction relations among female secondary school teachers in Enugu urban area of Enugu State, Nigeria. One hundred and seven (107) female teachers between the ages of 30 to 59 years were sampled using multi-stage sampling techniques. The 30-item Self-efficacy Scale, 20-item Minnesota Satisfaction Questionnaire and 32-item Work-family Conflict Scale were the measures for data collection. Results of moderated regression revealed that work-family conflict and self-efficacy did not equally predict job satisfaction. Specifically, work-to-family conflict and family-towork conflict jointly and independently did not correlate with job satisfaction while self-efficacy positively related with job satisfaction. Self-efficacy accounted for 4 % of the variance in job satisfaction among the teachers. There is need for policy makers in Nigeria such as the Nigeria Union of Teachers and Ministry of Education to consider self-efficacy in order to enhance job satisfaction of teachers.
Species composition and quantitative distribution of crabs in the northern continental shelf of South China Sea

The species composition and distribution status of crabs were evaluated based on the data of four seasonal fishery resources surveys in the northern continental shelf of South China Sea from 2006 to 2007.The results showed that there were 51 species belonging to 10 families and 24 genera in the area,most of which were tropical warm-water species belonging to South China-Southeast Asia subregion of Indian-western Pacific fauna.Depending on their adaptability,all crab species were categorized into three ecological groups: tropical euryhaline group,eurythermic euryhaline group,and tropical halophile group,with predominant tropical euryhaline species including Portunus argentatus,P.sanguinolentus,P.tweediei,Charybdis feriatus,Charybdis hongkongensis,Calappa philargius,and Charybdis miles,C.truncata,by Pinkas.The catching rate of the predominant species(2.99 kg/h)was around 81.69% in total catching rate of crab species(3.66 kg/h). The economic crab species Portunus sanguinolentus,P.trituberculatus,P.haanii,P.pelagicus,Charybdis feriatus,C.miles,and C.japonica belonging to Portunidae(2.37 kg/h) had the catching rate of around 64.75% of total catch rate(3.66 kg/h). The crabs were stocked at a density of 97.47 kg/km2,including the economic crabs at stocking density of 63.20 kg/km2.The maximal distribution area of the crabs were found in the transect D(125.60 kg/km2) and the minimal in the transect C(70.93 kg/km2). The maximal biomass of the crabs were observed in autumn(181.60 kg/km2) and the minimal in winter(50.13 kg/km2). The most aggregation of crabs species were mainly distributed in depths of 10-60 m with the peak(222.13 kg/km2) in depth of near 10 m,negative relation with the water depths.
The Impact of Linguistic Knowledge in Different Strategies to Learn Cross-Lingual Distributional Models

In recent years, with the emergence of neural networks and word embeddings, there has been a growing interest in working on cross-lingual distributional models learned from monolingual corpora to induce bilingual lexicons However, interest in these models existed prior to the emergence of deep learning. In this article, we will study the differences between the recent strategies, which are based on the alignment of models, as opposed to the old methods focused on the use of bilingual anchors aligning the text itself. We will also analyze the impact of including different levels of linguistic knowledge (e