Miracle-dz/UniFAR-FTUs huggingface dataset:
The yeast claudin Dcv1 is important for demarcating the front domain of pheromone-responding yeast cells

Cell polarization in response to chemical gradients is important in development and homeostasis across eukaryota. Chemosensing cells orient toward or away from gradient sources by polarizing along a front-rear axis. Using the chemotropic mating response of the budding yeast S. cerevisiae as a model of environmentally-induced cell polarization, we found that Dcv1, a claudin homolog, is a determinant of front-rear polarity. Although Dcv1 localized uniformly on the plasma membrane (PM)† of vegetative cells, it was confined to the rear of cells responding to pheromone, away from the pheromone receptor and mating projection. Deletion of DCV1 conferred mislocalization of sensory, polarity, and trafficking proteins, as well as the PM lipids ergosterol, phosphatidylinositol-4,5-bisphosphate (PIP2), and phosphatidylserine (PS). These phenotypes correlated with defects in pheromone-gradient tracking and cell fusion. We propose that the novel claudin-like and rear-domain protein, Dcv1, demarcates the mating-specific front domain primarily by restricting PM lipid distribution. Consistent with this hypothesis, a mutation that blocks ergosterol biosynthesis partially phenocopies dcv1Δ. Summary statement The yeast claudin Dcv1 facilitates the proper localization of plasma membrane lipids and proteins that are required for front-rear polarity, efficient chemotropism, and cell fusion.
A benchmark of Hi-C scaffolders using reference genomes and de novo assemblies

Background Studying a new species using high-throughput sequencing requires a high-quality reference genome. However, assembling chromosome length sequences remains challenging. Recent advances in chromatin conformation capture (Hi-C) have provided a new approach to scaffolding genome assemblies, and the last ten years have seen a proliferation of such methods. However, to our knowledge no comprehensive benchmarking of Hi-C scaffolders has been conducted to date. Results Through a literature review we identified the most popular Hi-C scaffolders – Lachesis, HiRise, 3d-dna, SALSA, and AllHiC. We tested their ability to scaffold four well studied genomes – S. cerevisiae, L. tarentolae, A. thaliana, and H. sapiens. Scaffolders were tasked with both scaffolding fragmented versions of the reference genome as well as de novo assemblies derived from long read datasets. We found that all scaffolders can exceed 80% accuracy under ideal circumstances but that their performance quickly deteriorates under more challenging conditions. Surprisingly, many scaffolders also showed poor performance on the best assemblies, where contigs are near chromosome length. Overall, we found that HiRise and Lachesis offer the best performance on average across all conditions. Conclusions We compare the performance of five Hi-C scaffolders using multiple reference species under both ideal and real-life conditions, thereby illuminating their strengths and weaknesses.
Deep learning can predict multi-omic biomarkers from routine pathology images: A systematic large-scale study

We assessed the pan-cancer predictability of multi-omic biomarkers from haematoxylin and eosin (H&E)-stained whole slide images (WSI) using deep learning (DL) throughout a systematic study. A total of 13,443 DL models predicting 4,481 multi-omic biomarkers across 32 cancer types were trained and validated. The investigated biomarkers included a broad range of genetic, transcriptomic, proteomic, and metabolic alterations, as well as established markers relevant for prognosis, molecular subtypes and clinical outcomes. Overall, we found that DL can predict multi-omic biomarkers directly from routine histology images across solid cancer types, with 50% of the models performing at an area under the curve (AUC) of more than 0.633 (with 25% of the models having an AUC larger than 0.711). A wide range of biomarkers were detectable from routine histology images across all investigated cancer types, with a mean AUC of at least 0.62 in almost all malignancies. Strikingly, we observed that biomarker predictability was mostly consistent and not dependent on sample size and class ratio, suggesting a degree of true predictability inherent in histomorphology. Together, the results of our study show the potential of DL to predict a multitude of biomarkers across the omics spectrum using only routine slides. This paves the way for accelerating diagnosis and developing more precise treatments for cancer patients.
Design and Behavior of Precast, Prestressed Girders Made Continuous â An Analytical and Experimental Study

Over the past fifty years, many states have recognized the benefits of making precast, prestressed multi-girder bridges continuous by connecting the girders with a continuity diaphragm. Although there is widespread agreement on the benefits of continuous construction, there has not been as much agreement on either the methods used for design of these systems or the details used for the continuity connections. To aid designers in choosing the most appropriate method, an analytical and experimental study was undertaken at Virginia Tech. Analyses were done to compare the differences in the predicted continuity moments for different design methods and assumptions over a range of commonly used systems of Precast Concrete Bulb Tee (PCBT) girders and cast-in-place slabs. The results of the analyses were used to develop three continuity connection details for testing during the experimental study. Three different continuity connections were tested using full depth PCBT 45 in. deep girders made continuous with a 6 ft wide slab. The bottom of the ends of the girders were made continuous with the continuity connection by extending prestressing strands for one test and extending 180 degree bent bars for the other test. Both connections adequately resisted service, cyclic, and ultimate loads. But, the test with the extended bars remained stiffer during cyclic loading and is recommended for use. A third test was performed on a system using only a slab cast across the top of the girders. Two primary cracks formed above the ends of the girders at the joint during service testing, after which no significant increase in damage took place. Results from the analytical study indicate that the predicted positive thermal restraint moments may be significant, similar in magnitude to the actual positive cracking moment capacities. Results from the experimental study indicate that restraint moments develop early due to thermal expansion of the deck during curing and subsequent differential shrinkage; however, the magnitudes of the early age restraint moments are much less than conventional analyses predict.
Survey of Feasible Numerical Approaches to Analyse the Behaviour of a Composite Skin Panel During a Water Impact

Water impacts are likely to have tragic consequences for the passengers of helicopters. Most of the passive safety devices developed for helicopter crashworthiness are designed for ground impact. When impacting a solid or a soft surface, impact loads are rather different and therefore energy absorption devices developed for ground impact are not effective during a water impact. In order to collect reliable data for numerical model validation, water impact drop tests were carried out: a Carbon Fiber Reinforced Plastic panel, similar to modern aircraft skin panels, was mounted on a specific test device and tested. Impact decelerations and deformations of the panels were measured. Afterwards, numerical models of the tests were created. Finite element and meshless approaches were used to model the water region. Eventually, a close experimentalnumerical correlation was obtained for each model in terms of impact dynamics, decelerations and deformations. The main features of the event and the differences between the four numerical approaches were discussed. Guidelines for further investigations were also drawn.
Development of laser measuring system to measure radial displacement of triaxial specimens based on high precision PSD

A new laser measuring system was developed to measure the radial displacement of triaxial specimens based on high precision PSD.In this system,direct measurement for the displacement of soil specimens with multi-points and non-contact method was carried out,which could measure change of diameters in several different positions at different time,meanwhile,a high precision of 0.009 mm could be reached through using the technique of laser photoelectricity measurement and the principle of optical rigonometry during triaxial tests.Using this system,it could be likely to study stress and strain property of triaxial specimens in accordance with the actual condition.In addition,the main factors which would affect the precision and error of measurement were analyzed,and the precision of this system was validated through the measured results of the diameter of standard specimens.
Evaluation de l'influence de l'inclinaison des modules photovoltaïques sur la production d'énergie d'un système hybride

Résumé Afin de maximiser la production d’électricité d’une installation photovoltaïque, il convient d’orienter les modules de façon optimale afin de capter un maximum du rayonnement solaire. En effet, la direction du soleil est importante. L’objectif de ce travail consiste à évaluer l’intérêt énergétique (le gain) de la correction d’angle d’inclinaison des modules photovoltaïques orientés plein sud dans un système énergétique hybride photovoltaïque / groupe électrogène.
Prenatal exposure to multiple organochlorine compounds and childhood body mass index

Background: Prenatal exposure to organochlorine compounds (OCs) has been associated with increased childhood body mass index (BMI); however, only a few studies have focused on longitudinal BMI trajectories, and none of them used multiple exposure mixture approaches. Aim: To determine the association between in-utero exposure to eight OCs and childhood BMI measures (BMI and BMI z-score) at 4 years and their yearly change across 4–12 years of age in 279 Rhea child-mother dyads. Methods: We applied three approaches: (1) linear mixed-effect regressions (LMR) to associate individual compounds with BMI measures; (2) Bayesian weighted quantile sum regressions (BWQSR) to provide an overall OC mixture association with BMI measures; and (3)Bayesian varying coefficient kernel machine regressions (BVCKMR) to model nonlinear and nonadditive associations. Results: In the LMR, yearly change of BMI measures was consistently associated with a quartile increase in hexachlorobenzene (HCB) (estimate [95% Confidence or Credible interval] BMI: 0.10 [0.06, 0.14]; BMI z-score: 0.02 [0.01, 0.04]). BWQSR results showed that a quartile increase in mixture concentrations was associated with yearly increase of BMI measures (BMI: 0.10 [0.01, 0.18]; BMI z-score: 0.03 [0.003, 0.06]). In the BVCKMR, a quartile increase in dichlorodiphenyldichloroethylene concentrations was associated with higher BMI measures at 4 years (BMI: 0.33 [0.24, 0.43]; BMI z-score: 0.19 [0.15, 0.24]); whereas a quartile increase in HCB and polychlorinated biphenyls (PCB)-118 levels was positively associated with BMI measures yearly change (BMI: HCB:0.10 [0.07, 0.13], PCB-118:0.08 [0.04, 012]; BMI z-score: HCB:0.03 [0.02, 0.05], PCB-118:0.02 [0.002,04]). BVCKMR suggested that PCBs had nonlinear relationships with BMI measures, and HCB interacted with other compounds. Conclusions: All analyses consistently demonstrated detrimental associations between prenatal OC exposures and childhood BMI measures.
Bioactive Keratin and Fibroin Nanoparticles: An Overview of Their Preparation Strategies

In recent years, several studies have focused their attention on the preparation of biocompatible and biodegradable nanocarriers of potential interest in the biomedical field, ranging from drug delivery systems to imaging and diagnosis. In this regard, natural biomolecules—such as proteins—represent an attractive alternative to synthetic polymers or inorganic materials, thanks to their numerous advantages, such as biocompatibility, biodegradability, and low immunogenicity. Among the most interesting proteins, keratin extracted from wool and feathers, as well as fibroin extracted from Bombyx mori cocoons, possess all of the abovementioned features required for biomedical applications. In the present review, we therefore aim to give an overview of the most important and efficient methodologies for obtaining drug-loaded keratin and fibroin nanoparticles, and of their potential for biomedical applications.
Regions and Represses Class Switching to IgA Protein Late SV40 Factor Binds Ig Switch The Ubiquitously Expressed DNA-Binding

Ig heavy chain class switch recombination (CSR) determines the expression of Ig isotypes. The molecular mechanism of CSR and the factors regulating this process have remained elusive. Recombination occurs primarily within switch (S) regions, located upstream of each heavy chain gene (except C (cid:1) ). These repetitive sequences contain consensus DNA-binding sites for the DNA-binding protein late SV40 factor (LSF) (CP2/leader-binding protein-1c). In this study, we demonstrate by EMSA that puriﬁed rLSF, as well as LSF within B cell extracts, directly binds both S (cid:2) and S (cid:3) sequences. To determine whether LSF is involved in regulating CSR, two different LSF dominant negative variants were stably expressed in the mouse B cell line I.29 (cid:2) , which can be induced to switch from IgM to IgA. Overexpression of these dominant negative LSF proteins results in decreased levels of endogenous LSF DNA-binding activity and an increase in cells undergoing CSR. Thus, LSF represses class switching to IgA. In agreement, LSF DNA-binding activity was found to decrease in whole cell extracts from splenic B cells induced to undergo class switching. To elucidate the mechanism of CSR regulation by LSF, the interactions of LSF with proteins involved in chromatin modiﬁcation were tested in vitro. LSF interacts with both histone deacetylases and the corepressor Sin3A. We propose that LSF represses CSR by histone deacetylation of chromatin within S regions, thereby limiting accessibility to the switch recombination machinery. The Journal of Immunology, 2002, 168: 2847–2856. these we this class at
PMEPA1 Serves as a Prognostic Biomarker and Correlates with Immune Infiltrates in Cervical Cancer

Emerging studies have demonstrated that Prostate transmembrane protein androgen induced 1 (PMEPA1) plays crucial roles in the carcinogenesis of many developing human tumors. However, the clinical significance of PMEPA1 expression in cervical cancer (CC) and its contribution to cancer immunity have not been investigated. In this study, we identified PMEPA1 as a survival-related gene in CC based on TCGA datasets. Univariate and multivariate analysis showed that PMEPA1 expression was an independent predictor for overall survival in CC patients. We could observe a strong negative correlation between PMEPA1 expression and PMEPA1 methylation. Two CpG sites of PMEPA1 were associated with overall survival, and one CpG site of PMEPA1 was associated with progression-free survival. The low level of PMEPA1 methylation was associated with advanced clinical stage of CC patients. KEGG assays revealed the genes associated with PMEPA1 expression were mainly enriched in several tumor-related pathways. Increased PMEPA1 expressions were observed to be positively related to high immune infiltration levels in several immune cells. Finally, the pan-cancer assays revealed that PMEPA1 expression was associated with the overall survival of UVM, PAAD, LUSC, BLCA, CESC, and LUAD. Taken together, PMEPA1 is a prognosis-related biomarker for multiple cancer types, especially CC. PMEPA1 is involved in tumor immunity, suggesting PMEPA1 may be a potential immunotherapeutic target in CC.
Human Dendritic and B Cells Receptor RDC1 and Its Putative Ligand in Expression and Regulation of the Orphan

Based on phylogenetic analysis and chromosomal mapping, the orphan receptor RDC1 was proposed to be a chemokine receptor. In this study we examined the expression of RDC1 on leukocytes by measuring mRNA levels and receptor expression using a new speciﬁc mAb. Both mRNA and protein levels were high in monocytes and B cells, relatively low on immature dendritic cells (DC), and up-regulated during ﬁnal stages of maturation. Strikingly, in mature plasmacytoid DC the mRNA was up-regulated, but did not correlate with protein surface expression. We indeed report that CpG-activated plasmacytoid DC produce a putative ligand for RDC1, which selectively down-regulates RDC1, but not CXCR4 on primary human B cells. RDC1 expression was found to be tightly regulated during B cell development and differentiation. In blood-derived switch memory B cells, the expression of RDC1 appeared to correlate with the ability to differentiate into plasma cells upon activation, suggesting that RDC1 is a marker for memory B cells, which are competent to become Ab-secreting cells. The Journal of Immunology, 2006, 176: 2197–2207. deﬁned ability
A microtubule-dynein tethering complex regulates the axonemal A microtubule-dynein tethering complex regulates the axonemal inner dynein f (I1) inner dynein f (I1)

Motility of cilia/flagella is generated by a coordinated activity of thousands of dyneins. Inner dynein arms (IDAs) are particularly important for the formation of ciliary/flagel-lar waveforms, but the molecular mechanism of IDA regulation is poorly understood. Here we show using cryoelectron tomography and biochemical analyses of Chlamydomonas flagella that a conserved protein FAP44 forms a complex that tethers IDA f (I1 dynein) head domains to the A-tubule of the axonemal outer doublet microtubule. In wild-type flagella, IDA f showed little nucleotide-dependent movement except for a tilt in the f β head perpendicular to the microtubule-sliding direction. In the absence of the tether complex, however, addition of ATP and vanadate caused a large conformational change in the IDA f head domains, suggesting that the movement of IDA f is mechanically restricted by the tether complex. Motility defects in flagella missing the tether demonstrates the importance of the IDA f -tether interaction in the regulation of ciliary/flagellar beating.
Securing Data in IOT Using Cryptography and Steganography Techniques

— Although cryptography and steganography could be used to provide data security, each of them has a problem. Cryptography problem is that, the cipher text looks meaningless, so the attacker will interrupt the transmission or make more careful checks on the data from the sender to the receiver. Steganography problem is that once the presence of hidden information is revealed or even suspected, the message is become known. According to the work in this paper, a merged technique for data security has been proposed using Cryptography and Steganography techniques to improve the security of the information. Firstly, the Advanced Encryption Standard (AES) algorithm has been modified and used to encrypt the secret message. Secondly, the encrypted message has been hidden using method in [1]. Therefore, two levels of security have been provided using the proposed hybrid technique. In addition, the proposed technique provides high embedding capacity and high quality stego images.
and Inflammasome Activation Immune Complexes Inhibit IL-1 Secretion

IgG immune complexes have been shown to modify immune responses driven by APCs in either a pro- or anti-inﬂammatory di-rection depending upon the context of stimulation. However, the ability of immune complexes to modulate the inﬂammasome-dependent innate immune response is unknown. In this study, we show that IgG immune complexes suppress IL-1 a and IL-1 b secretion through inhibition of inﬂammasome activation. The mechanism by which this inhibition occurs is via immune complex ligation of activating Fc g Rs, resulting in prevention of both activation and assembly of the inﬂammasome complex in response to nucleotide-binding domain leucine-rich repeat (NLR) P3, NLRC4, or AIM2 agonists. In vivo, administration of Ag in the form of an immune complex during priming of the immune response inhibited resultant adaptive immune responses in an NLRP3-dependent model of allergic airway disease. Our data reveal an unexpected mechanism regulating CD4 + T cell differentiation, by which immune complexes suppress inﬂammasome activation and the generation of IL-1 a and IL-1 b from APCs, which are critical for the Ag-driven differentiation of CD4 + T cells. The Journal of Immunology , 2014, 193: 000–000.
Three-Input Single-Output Voltage-Mode Multifunction Filter with Electronic Controllability Based on Single Commercially Available IC

This paper presents a second-order voltage-mode filter with three inputs and single-output voltage using single commercially available IC, one resistor, and two capacitors. The used commercially available IC, called LT1228, is manufactured by Linear Technology Corporation. The proposed filter is based on parallel RLC circuit. The filter provides five output filter responses, namely, band-pass (BP), band-reject (BR), low-pass (LP), high-pass (HP), and all-pass (AP) functions. The selection of each filter response can be done without the requirement of active and passive component matching condition. Furthermore, the natural frequency and quality factor are electronically controlled. Besides, the nonideal case is also investigated. The output voltage node exhibits low impedance. The experimental results can validate the theoretical analyses.
E-Commerce and SME Performance: The Moderating Inﬂuence of Entrepreneurial Competencies

: This research aims to examine the mediating role of the use of the e-commerce and moderating inﬂuence of entrepreneurial competencies on the performance of small and medium enterprises (SMEs). The study data were collected via a structured questionnaire comprised of a seven-point Likert scale from practitioners serving at the top and middle-level positions in Pakistani SMEs. The Partial Least Squares Structural Equation Modelling (PLS-SEM) technique was applied on 250 useable returned questionnaires. The results showed that the association between the use of ecommerce and ﬁrm performance is positively signiﬁcant. Moreover, the use of e-commerce mediates the positive association between technological readiness, adoption cost, and ﬁrm performance. However, the moderating role of entrepreneurial competencies does not appear as signiﬁcant between the use of e-commerce and manufacturing SMEs’ performance. The present study is the ﬁrst to explore entrepreneurial competencies as a moderator between e-commerce adoption and ﬁrm performance. The empirical outcomes of this research provide useful theoretical and practical implications for the managers and practitioners to understand the underlying factors for the successful implementation of e-commerce in the SME sector to enhance ﬁrm performance.