Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete mitochondrial genome of the hydrothermal vent stalked barnacle Vulcanolepas fijiensis (Cirripedia, Scalpelliforms, Eolepadidae)

Abstract The family Eolepadidae is the only stalked barnacle in hydrothermal vent regions. Here, we determined the mitogenome of the eolepadid Vulcanolepas fijiensis. The mitogenome was 17,374 bp long, with 76.6% AT content. Its protein-coding gene organization was identical to that of the deep-sea scalpellid Arcoscalpellum epeeum. On the mitogenomic tree, two scalpellomorphan families (Eolepadidae and Scalpellidae) were monophyletic while the other scalpellomorphan family Pollicipedidae did not form the monophyletic group with them. Further mitogenomic analysis of undetermined taxa in hydrothermal vents is required to deepen our understanding of their phylogenetic relationships.
The complete chloroplast genome sequence of Polypodiodes amoena (Polypodiaceae), an important medical fern

Abstract Polypodiodes amoena is an important medical fern of Polypodiaceae. Its complete chloroplast genome is obtained through Illumina sequencing, which is 152,067 bp in length with a large single copy (LSC) region (81,187 bp), a small single copy (SSC) region (21,590 bp), and two inverted repeats (IRa and IRb) regions (24,645 bp). The genome encodes 130 genes, including 88 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. ML phylogenetic analysis reveals that P. amoena is clustered with polypodiaceous ferns.
Effects of Individualized Treadmill Endurance Training on Oxidative Stress in Skeletal Muscles of Transgenic Sickle Mice

Oxidative stress is a key feature in the pathophysiology of sickle cell disease. Endurance training has been shown to reduce oxidative stress in the heart and the liver of sickle mice. However, the effects of endurance training on skeletal muscles, which are major producers of reactive oxygen species during exercise, are currently unknown. The aim of this study was to evaluate the effect of sickle genotype on prooxidant/antioxidant response to individualized endurance training in skeletal muscles of sickle mice. Healthy and homozygous Townes sickle mice were divided into trained or sedentary groups. Maximal aerobic speed and V̇O2 peak were determined using an incremental test on a treadmill. Trained mice ran at 40% to 60% of maximal aerobic speed, 1 h/day, 5 days/week for 8 weeks. Oxidative stress markers, prooxidant/antioxidant response, and citrate synthase enzyme activities were assessed in the gastrocnemius, in the plantaris, and in the soleus muscles. Maximal aerobic speed and V̇O2 peak were significantly reduced in sickle compared to healthy mice (-57% and -17%; p < 0.001). NADPH oxidase, superoxide dismutase, and catalase activities significantly increased after training in the gastrocnemius of sickle mice only. A similar trend was observed for citrate synthase activity in sickle mice (p = 0.06). In this study, we showed an adaptive response to individualized endurance training on the prooxidant/antioxidant balance in the gastrocnemius, but neither in the plantaris nor in the soleus of trained sickle mice, suggesting an effect of sickle genotype on skeletal muscle response to endurance treadmill training.
Inferring Latent Disease-lncRNA Associations by Faster Matrix Completion on a Heterogeneous Network

Current studies have shown that long non-coding RNAs (lncRNAs) play a crucial role in a variety of fundamental biological processes related to complex human diseases. The prediction of latent disease-lncRNA associations can help to understand the pathogenesis of complex human diseases at the level of lncRNA, which also contributes to the detection of disease biomarkers, and the diagnosis, treatment, prognosis and prevention of disease. Nevertheless, it is still a challenging and urgent task to accurately identify latent disease-lncRNA association. Discovering latent links on the basis of biological experiments is time-consuming and wasteful, necessitating the development of computational prediction models. In this study, a computational prediction model has been remodeled as a matrix completion framework of the recommendation system by completing the unknown items in the rating matrix. A novel method named faster randomized matrix completion for latent disease-lncRNA association prediction (FRMCLDA) has been proposed by virtue of improved randomized partial SVD (rSVD-BKI) on a heterogeneous bilayer network. First, the correlated data source and experimentally validated information of diseases and lncRNAs are integrated to construct a heterogeneous bilayer network. Next, the integrated heterogeneous bilayer network can be formalized as a comprehensive adjacency matrix which includes lncRNA similarity matrix, disease similarity matrix, and disease-lncRNA association matrix where the uncertain disease-lncRNA associations are referred to as blank items. Then, a matrix approximate to the original adjacency matrix has been designed with predicted scores to retrieve the blank items. The construction of the approximate matrix could be equivalently resolved by the nuclear norm minimization. Finally, a faster singular value thresholding algorithm with a randomized partial SVD combing a new sub-space reuse technique has been utilized to complete the adjacency matrix. The results of leave-one-out cross-validation (LOOCV) experiments and 5-fold cross-validation (5-fold CV) experiments on three different benchmark databases have confirmed the availability and adaptability of FRMCLDA in inferring latent relationships of disease-lncRNA pairs, and in inferring lncRNAs correlated with novel diseases without any prior interaction information. Additionally, case studies have shown that FRMCLDA is able to effectively predict latent lncRNAs correlated with three widespread malignancies: prostate cancer, colon cancer, and gastric cancer.
The Human G Protein-Coupled ATP Receptor P2Y11 Is Associated With IL-10 Driven Macrophage Differentiation

The G protein-coupled P2Y11 receptor is known to sense extracellular ATP during inflammatory and immune responses. The dinucleotide NAD+ has also been proposed to be a P2Y11 receptor ligand but its role is less clear. Here, we have examined for the first time human P2Y11 receptor protein levels and show that the receptor was upregulated during polarization of M2 macrophages. IL-10 reinforced P2Y11 receptor expression during differentiation of M2c macrophages expressing CD163, CD16, and CD274 (PD-L1). Nutlin-3a mediated p53 stabilization further increased P2Y11 receptor, CD16, and PD-L1 expression. AMP-activated kinase (AMPK), which mediates anti-inflammatory effects of IL-10, and nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ salvage pathway, which is under the control of AMPK, were also required for P2Y11 receptor expression. The P2Y11 receptor agonist ATPγS and NAD+ could independently stimulate the production of IL-8 in M2 macrophages, however, only the ATPγS-induced response was mediated by P2Y11 receptor. Both in a recombinant system and in macrophages, P2Y11 receptor-driven IL-8 production predominantly depended on IkB kinase (IKK), and extracellular signal–regulated kinase (ERK). In conclusion, our data indicate that an AMPK-NAMPT-NAD+ signaling axis promotes P2Y11 receptor expression during M2 polarization of human macrophages in response to IL-10. PD-L1 expressing M2c macrophages that secrete the cancer-promoting chemokine IL-8 in response to P2Y11 receptor stimulation may represent an important target in checkpoint blockade immunotherapy.
Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential

Kuwait is a semi-arid region with harsh climatic conditions with poor available soil nutrient essential for the growth of plants. Kuwait’s ecosystem is relatively N-poor ecosystem when compared to the other ecosystems. Biological nitrogen fixation (BNF) is a spontaneous process in which diazotrophic bacteria fixes the atmospheric nitrogen directly in to the bionetwork. At present, there is limited information on free-living and root associated nitrogen-fixing bacteria, their potential to fix nitrogen to aid natural plant communities in the desert of Kuwait. In this study, free-living N2-fixing bacteria were enriched and isolated from the rhizospheric soil of three keystone native plant species of Kuwait; such as Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root associated bacteria were directly isolated from the root nodules of Vachellia pachyceras. In this study, a number of free-living and root associated dizotrophs were isolated from various rhizospheric soils of three native shrubs and root nodules from one tree species. The screened isolates were assessed for nitrogen-fixing ability and identified using Acetylene Reduction Assay (ARA) and 16s rRNA gene sequencing, respectively. Our study successfully identified all the 50 nitrogen-fixers isolated initially and out of that, 78% were confirmed as nitrogen-fixers using ARA. Among the identified nitrogen fixers, the genus Rhizobium is dominant in rhizospheric soil of Rhanterium epapposum, whereas Pseudomonas and Rhizobium are dominant in the rhizospheric soil of Farsetia aegyptia, and Haloxylon salicornicum respectively. The species Agrobacterium tumefaciens is found dominant in the root nodules of V. pachyceras. The current results indicate that plant species and their rhizospheric effects are important drivers for specificity of microbial diversity in arid soils. To our knowledge, this study is the first investigation of culture-based isolation, molecular identification, and evaluation of N2-fixing ability of diazotrophs from Kuwait desert environment.
Shaping Ethylene Response: The Role of EIN3/EIL1 Transcription Factors

EIN3/EIL1 transcription factors are the key regulators of ethylene signaling that sustain a variety of plant responses to ethylene. Since ethylene regulates multiple aspects of plant development and stress responses, its signaling outcome needs proper modulation depending on the spatiotemporal and environmental conditions. In this review, we summarize recent advances on the molecular mechanisms that underlie EIN3/EIL1-directed ethylene signaling in Arabidopsis. We focus on the role of EIN3/EIL1 in tuning transcriptional regulation of ethylene response in time and space. Besides, we consider the role of EIN3/EIL1-independent regulation of ethylene signaling.
Baveno Criteria Safely Identify Patients With Compensated Advanced Chronic Liver Disease Who Can Avoid Variceal Screening Endoscopy: A Diagnostic Test Accuracy Meta-Analysis

Background: The Baveno VI Consensus Workshop defined criteria (liver stiffness measured by transient elastography <20 kPa and platelet count >150 × 109 cells/L) to identify those patients with compensated advanced chronic liver diseases (cACLD) who are unlikely to have varices needing treatment (VNTs) and can safely avoid variceal screening endoscopy. This meta-analysis aimed to quantify the safety and efficacy of these criteria in suspected cACLD with liver stiffness >10 kPa and in compensated chronic liver diseases (cCLD) irrespective of liver stiffness. Methods: A systematic search was conducted in nine databases for studies discussed cACLD or cCLD and tested Baveno criteria against variceal screening endoscopy. The main safety and efficacy endpoints were missed VNT rate and spared endoscopy rate (SER), respectively; calculated with the random effect model. Pooled sensitivity, specificity, and area under the curve (AUC) were calculated with the hierarchical summary receiver operating characteristic model. For all outcome measures, 95% confidence intervals were computed. Heterogeneity was tested with I2-statistics. Results: The search yielded 13 studies including 4,464 patients which reported on suspected cACLD. Pooled missed VNT rate was 0.3% (0.1–0.6%; I2 = 45.5%), pooled SER was 32.8% (24.8–41.4%; I2 = 97.0%). Sensitivity, specificity, and AUC of Baveno criteria were 97% (95–98%), 41% (27–57%), and 96% (94–97%), respectively. In the subgroups of cACLD from hepatitis C and B viruses, non-alcoholic fatty liver disease/steatohepatitis, or alcohol, missed VNT rates were 0.0% (0.0–0.3%), 1.2% (0.4–2.2%), 0.0% (0.0–1.3%), or 0.0% (0.0–0.4%), while SERs were 24.2% (20.5–28.1%), 24.9% (21.7–28.4%), 38.6% (10.9–70.8%), or 27.0% (16.9–38.4%), respectively. If we expanded the study population to cCLD, 27 studies included 7,534 patients. Missed VNT rate was 0.2% (0.1–0.5%; I2 = 39.8%) with a SER of 30.5% (25.2–36.2%; I2 = 96.1%) while Se, Sp, and AUC were 97% (93–99%), 35% (27–44%), and 80% (77–84%), respectively. Conclusions: The application of Baveno criteria significantly reduces the number of unnecessary variceal screening endoscopies while being safe: cACLD patients with liver stiffness <20 kPa and platelet count > 150 × 109 cells/L carry a very low chance (i.e., 0.3%) of having VNTs. The criteria preserve low missed VNT rate with lower diagnostic performance among cCLD patients.
RESTRICTIVE CHARACTER-BASED ADVERTISE INTERMEDIARY RECONSTRUCTION AND ITS PETITION TO DISTORT EMAIL

Inside a CIBPRE arrangement, a decent key breed mall digitize the machinery parameters of, and generates independent keys for users. To cautiously split files to numerous receivers, a shopkeeper can solid the files accepting the receivers’ identities and file-discussing surrounding. If next the exporter would like to talk about some files interested identical arrangement better new receivers, the exporter can authorize a re-file encryption key labeled employing the precondition about the executor, and the parameters to form the re-file encryption classified enter supplement to the inventive receivers of the files. Conditional, identity-based PRE-and announce PRE, hit planned advised for soft appeals. enables a dealer to sure a note to different receivers by indicating the receivers’ identities, and the shopkeeper can authorize a re-file encryption obey a lawyer on the side of remodel the early resolve text into a restoration to an original categorize of planned receivers. By CPRE, IPRE and BPRE, this study proposes a soft undeveloped common as arrange mental identity-based beam PRE-and illustrate its linguistic confidence. Furthermore, the re-file encryption key conceivably associated having a rule to avoid just the identical estimate texts perhaps re-encrypted, whichever enables the introductory shopkeeper to apply approach command of his distant compute texts innards a solid system. Finally, we show a bank card petition in us to sure muddle information technology structure benign over alive settle e-mail techniques just as Very Good Privacy obligation or identity-based file encryption.
Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta

Alzheimer’s disease (AD) is the most common neurodegenerative disease affecting the elderly worldwide. Mitochondrial dysfunction has been proposed as a key event in the etiology of AD. We have previously modeled amyloid-beta (Aβ)-induced mitochondrial dysfunction in a transgenic Caenorhabditis elegans strain by expressing human Aβ peptide specifically in neurons (GRU102). Here, we focus on a deeper analysis of these metabolic changes associated with Aβ-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics, biochemical studies and computational modeling, we identify alterations in Tricarboxylic Acid (TCA) cycle metabolism following even low-level Aβ expression. In particular, GRU102 show reduced activity of a rate-limiting TCA cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects are associated with elevation of protein carbonyl content specifically in mitochondria. Importantly, metabolic failure occurs before any significant increase in global protein aggregate is detectable. Treatment with an antidiabetes drug, Metformin, reverses Aβ-induced metabolic defects, reduces protein aggregation and normalizes the lifespan of GRU102. Our results point to metabolic dysfunction as an early and causative event in AD pathology and a promising target for intervention.
Cooption and Specialization of Endothelin Signaling Pathways Drove Elaboration of the Neural Crest in Early Vertebrates

The neural crest (NC) is a vertebrate-specific embryonic tissue that forms an array of clade-defining adult features. A key step in the formation of these diverse derivatives is the partitioning of NC cells into subpopulations with distinct migration routes and potencies1. The evolution of these developmental modules is poorly understood. Endothelin (Edn) signaling is unique to vertebrates, and performs various functions in different NC subpopulations2–5. To better understand the evolution of NC patterning, we used CRISPR/Cas9-driven mutagenesis to disrupt Edn receptors, ligands, and Dlx transcription factors in the sea lamprey, Petromyzon marinus. Lampreys and modern gnathostomes last shared a common ancestor 500 million years ago6. Thus, comparisons between the two groups can identify deeply conserved and divergent features of vertebrate development. Using Xenopus laevis to facilitate side-by-side analyses, we show here that lamprey and gnathostomes display fundamental differences in Edn signaling function. Unlike gnathostomes, both lamprey Ednrs cooperate during oropharyngeal skeleton development. Furthermore, neither paralog regulates hand transcription factors, which are required for mandible development in gnathostomes. We also identify conserved roles for Edn signaling in dlx gene regulation, pigment cell, and heart development. Together our results illustrate the stepwise neofunctionalization and specialization of this vertebrate-specific signaling pathway, and suggest key intermediate stages in the early evolution of the NC.
Polycystic Ovary Syndrome: Novel and Hub lncRNAs in the Insulin Resistance-Associated lncRNA–mRNA Network

Polycystic ovary syndrome (PCOS) is a common metabolic and reproductive disorder with an increasing risk for type 2 diabetes. Insulin resistance is a common feature of women with PCOS, but the underlying molecular mechanism remains unclear. This study aimed to screen critical long non-coding RNAs (lncRNAs) that might play pivotal roles in insulin resistance, which could provide candidate biomarkers and potential therapeutic targets for PCOS. Gene expression profiles of the skeletal muscle in patients with PCOS accompanied by insulin resistance and healthy patients were obtained from the publicly available Gene Expression Omnibus (GEO) database. A global triple network including RNA-binding protein, mRNA, and lncRNAs was constructed based on the data from starBase. Then, we extracted an insulin resistance-associated lncRNA–mRNA network (IRLMN) by integrating the data from starBase and GEO. We also performed a weighted gene co-expression network analysis (WGCNA) on the differentially expressed genes between the women with and without PCOS, to identify hub lncRNAs. Additionally, the findings of key lncRNAs were examined in an independent GEO dataset. The expression level of lncRNA RP11-151A6.4 in ovarian granulosa cells was increased in patients with PCOS compared with that in control women. Levels were also increased in PCOS patients with higher BMI, hyperinsulinemia, and higher HOMA-IR values. As a result, RP11-151A6.4 was identified as a hub lncRNA based on IRLMN and WGCNA and was highly expressed in ovarian granulosa cells, skeletal muscle, and subcutaneous and omental adipose tissues of patients with insulin resistance. This study showed the differences between lncRNA and mRNA profiles from healthy women and women with PCOS and insulin resistance. Here, we demonstrated that RP11-151A6.4 might play a vital role in insulin resistance, androgen excess, and adipose dysfunction in patients with PCOS. Further study concerning RP11-151A6.4 could elucidate the underlying mechanisms of insulin resistance.
Genome Sequences of Two Cold-Adapted Cryobacterium Spp. SO1 and SO2 from Fildes Peninsula, Antarctica

Psychrophilic and psychrotrophic bacteria play important roles in nutrient cycling in cold environments. These bacteria are suitable as model organisms for studying coldadaptation, and sources of cold-active enzymes and metabolites for industrial applications. Here, we report the genome sequences of two Cryobacterium sp. strains SO1 and SO2. Genes coding major proteins related to coldor thermal-stress adaptations and those with industrial applications found in their genomes are described. Keyword: Fluctuation; Genomes; King George Island; 16S Rdna; Temperature
Examining the Impact of Propagating and Partitioning for Mutation Analysis of C Programs

Mutation analysis is a technique for assessing the quality of test suites by seeding artificial defects into a program. The application of this method is still limited as it places a high demand on computational resources. There are techniques called infection, propagation, and partitioning that leverage the information available at run-time to reduce the execution time of mutation analysis. Although the effectiveness of these techniques has been investigated for Java, it is not known how they behave on programs written in low-level languages such as C. This thesis makes contributions toward investigating the effectiveness and efficiency of infection, propagation, and partitioning optimizations for programs written in C. It also explores the impact of statically pruning redundant mutants on these optimizations. The analysis of five real-world applications, with 402,000 lines of code in total, suggests that while infection might have the same effectiveness in C and Java, propagation and partitioning could be more effective for C. Additionally, it shows that static pruning reduces the impact of infection, propagation, and partitioning by 5.51%, 7.29%, and 11.90% respectively.
Roadkill Distribution at the Wildland ‐ Urban Interface

The growing wildland ‐ urban interface is a frontier of human ‐ wildlife con ﬂ ict worldwide. Where natural and developed areas meet, there is potential for negative interactions between humans and wild animals, including wildlife ‐ vehicle collisions. Understanding the environmental and anthropogenic factors leading to these collisions can inform transportation and habitat planning, with an objective of reducing animal mortality and human costs. We investigated spatial, temporal, and species ‐ speci ﬁ c patterns of roadkill on Interstate ‐ 280 ( I ‐ 280 ) in California, USA, and examined the e ﬀ ects of land cover, fencing, lighting, and tra ﬃ c. The highway is situated just south of San Francisco, dividing a large wildlife refuge to the west from dense residential areas to the east, and therefore presents a major barrier to wildlife movement. Areas with a higher percentage of developed land east of I ‐ 280 and areas with more open space on the west side of I ‐ 280 were associated with an increase in overall roadkill, suggesting that hard boundaries at the wildland ‐ urban interface may be zones of high risk for dispersing animals. This pattern was especially strong for raccoons ( Procyon lotor ) and black ‐ tailed deer ( Odocoileus hemionus ) . The presence of lighting correlated with increased roadkill with the exception of coyote ( Canis latrans ) . Contrary to our expectations, we found weak evidence that fencing increases roadkill, perhaps because animals become trapped on roadways or because fencing is not su ﬃ cient to block access to the road by wildlife. Finally, we found strong evidence for roadkill seasonality, correlated with di ﬀ erences in movement and dispersal across life ‐ history stages. We highlight the value of citizen ‐ science datasets for monitoring human ‐ wildlife con ﬂ ict and suggest potential mitigation measures to reduce the negative e ﬀ ects of wildlife ‐ vehicle collisions for people and wildlife. © 2019 The Wildlife Society.