Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Pan‐Specific B‐Cell Epitopes From Nucleocapsid Protein of Hantaviruses Causing Hantavirus Cardiopulmonary Syndrome

Hantaviruses are emerging viral pathogens that causes hantavirus cardiopulmonary syndrome (HCPS) in the Americas, a severe, sometimes fatal, respiratory disease in humans with a case fatality rate of ≥50%. IgM and IgG‐based serological detection methods are the most common approaches used for laboratory diagnosis of hantaviruses. Such emerging viral pathogens emphasizes the need for improved rapid diagnostic devices and vaccines incorporating pan‐specific epitopes of genotypes. We predicted linear B‐cell epitopes for hantaviruses that are specific to genotypes causing HCPS in humans using in silico prediction servers. We modeled the Andes and Sin Nombre hantavirus nucleocapsid protein to locate the identified epitopes. Based on the mean percent prediction probability score, epitope IMASKSVGS/TAEEKLKKKSAF was identified as the best candidate B‐cell epitope specific for hantaviruses causing HCPS. Promiscuous epitopes were identified in the C‐terminal of the protein. Our study for the first time has reported pan‐specific B‐cell epitopes for developing immunoassays in the detection of antibodies to hantaviruses causing HCPS. Identification of epitopes with pan‐specific recognition of all genotypes causing HCPS could be valuable for the development of immunodiagnositic tools toward pan‐detection of hantavirus antibodies in ELISA. J. Cell. Biochem. 118: 2320–2324, 2017. © 2017 Wiley Periodicals, Inc.
Auditor Industry Specialization and Evidence of Cost Efficiencies in Homogenous Industries

ABSTRACT: This study examines the audit pricing effects when auditors specialize in industries conducive to transferable audit processes. Our results indicate that industry specialists charge incrementally lower fees in industries with homogenous operations, and particularly in industries with both homogenous operations and complex accounting practices. Moreover, we discover that audit quality is no lower for clients audited by these specialists offering fee discounts, consistent with a conclusion that the reduction in fees indicates cost efficiencies rather than lower-quality audits. Further analysis indicates that the shared economies of scale only occur in a subsample of client firms with relatively high bargaining power. When considered in conjunction with prior research using a survivorship approach, our study provides evidence that certain industries lend themselves to specialization because auditors generate cost-based competitive advantages without compromising service quality. Data Availability:.
Comparative Studies on Thermal, Mechanical, and Flame Retardant Properties of PBT Nanocomposites via Different Oxidation State Phosphorus-Containing Agents Modified Amino-CNTs

High-performance poly(1,4-butylene terephthalate) (PBT) nanocomposites have been developed via the consideration of phosphorus-containing agents and amino-carbon nanotube (A-CNT). One-pot functionalization method has been adopted to prepare functionalized CNTs via the reaction between A-CNT and different oxidation state phosphorus-containing agents, including chlorodiphenylphosphine (DPP-Cl), diphenylphosphinic chloride (DPP(O)-Cl), and diphenyl phosphoryl chloride (DPP(O3)-Cl). These functionalized CNTs, DPP(Ox)-A-CNTs (x = 0, 1, 3), were, respectively, mixed with PBT to obtain the CNT-based polymer nanocomposites through a melt blending method. Scanning electron microscope observations demonstrated that DPP(Ox)-A-CNT nanoadditives were homogeneously distributed within PBT matrix compared to A-CNT. The incorporation of DPP(Ox)-A-CNT improved the thermal stability of PBT. Moreover, PBT/DPP(O3)-A-CNT showed the highest crystallization temperature and tensile strength, due to the superior dispersion and interfacial interactions between DPP(O3)-A-CNT and PBT. PBT/DPP(O)-A-CNT exhibited the best flame retardancy resulting from the excellent carbonization effect. The radicals generated from decomposed polymer were effectively trapped by DPP(O)-A-CNT, leading to the reduction of heat release rate, smoke production rate, carbon dioxide and carbon monoxide release during cone calorimeter tests.
Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

Significance The splicing of human pre-mRNAs is tightly controlled and regulated during the assembly of the spliceosome onto pre-mRNA introns. Recognition of regulatory RNA sequence motifs by splicing factors is an essential early step during spliceosome assembly. We combine single-pair FRET and NMR to show that the recognition of the 3′ splice site in pre-mRNA introns by the essential heterodimeric splicing factor U2 auxiliary factor (U2AF) involves conformational dynamics and population shifts of its RNA binding domains between open and closed conformations. Unexpectedly, the small subunit U2AF35 facilitates the recognition of weak splice sites by a population shift of the RNA binding domains of U2AF65 toward the open conformation. Notably, disease-linked mutations in U2AF65 do not affect RNA or U2AF35 binding. An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein–RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.
The Gαq/11 Proteins Contribute to T Lymphocyte Migration by Promoting Turnover of Integrin LFA-1 through Recycling

The role of Gαi proteins coupled to chemokine receptors in directed migration of immune cells is well understood. In this study we show that the separate class of Gαq/11 proteins is required for the underlying ability of T cells to migrate both randomly and in a directed chemokine-dependent manner. Interfering with Gαq or Gα11 using dominant negative cDNA constructs or siRNA for Gαq causes accumulation of LFA-1 adhesions and stalled migration. Gαq/11 has an impact on LFA-1 expression at plasma membrane level and also on its internalization. Additionally Gαq co-localizes with LFA-1- and EEA1-expressing intracellular vesicles and partially with Rap1- but not Rab11-expressing vesicles. However the influence of Gαq is not confined to the vesicles that express it, as its reduction alters intracellular trafficking of other vesicles involved in recycling. In summary vesicle-associated Gαq/11 is required for the turnover of LFA-1 adhesion that is necessary for migration. These G proteins participate directly in the initial phase of recycling and this has an impact on later stages of the endo-exocytic pathway.
New approaches to conversion hysteria

Patients with hysterical conversion, now called conversion disorder by the main US psychiatric glossary,1 often present with striking neurological symptoms such as weakness, paralysis, sensory disorders, or memory loss, in the absence of any pathology that could be responsible. Most patients will be referred to a neurologist or psychiatrist after consulting their family doctor. As many as 4% of those attending neurology outpatient clinics in the United Kingdom have been estimated to have conversion disorders.2 Similar rates have been reported for both in and outpatient clinics in other European countries. Empirical research on hysterical conversion has lagged behind theoretical speculation. Recent advances in functional imaging (positron emission tomography scanning) and cognitive neuropsychology have, however, made the field more amenable to investigation.3 Key clinical and theoretical problems remain over case definition and differential diagnosis, the psychological mechanisms underlying conversion hysteria, and how patients are best managed. Despite attempts over the past century to abolish and reinstate the condition by using different labels, conversion hysteria continues to attract controversy. …
CGRP attenuates hyperoxia-induced oxidative stress-related injury to alveolar epithelial type II cells via the activation of the Sonic hedgehog pathway.

The aim of this study was to examine the effect of calcitonin gene-related peptide (CGRP) on primary alveolar epithelial type II (AECII) cells and expression of Sonic hedgehog (SHH) signaling pathway components following exposure to hyperoxia. The AECII cells were isolated and purified from premature rats and exposed to air (21% oxygen), air + CGRP, hyperoxia (95% oxygen) or hyperoxia + CGRP. The production of intracellular reactive oxygen species (ROS) was determined using the 2',7'-dichlorofluorescin diacetate molecular probe. The levels of malondialdehyde (MDA) and superoxide dismutase (SOD) in the culture supernatant were detected by spectrophotometry. The apoptosis of AECII cells was assayed by flow cytometry, and the mRNA and protein expression levels of Shh and Ptc1 in the AECII cells were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), western blot analysis and immunofluorescence, respectively. The cellular pathological changes partly improved and apoptosis was markedly decreased upon treatment with CGRP under hyperoxic conditions. The levels of ROS in the hyperoxia + CGRP group were significantly lower than thoe in the hyperoxia group. In addition, the hyperoxia-induced increase in MDA levels and the decrease in SOD activity in the culture supernatant of the AECII cells were attenuated by CGRP. Compared with the cells exposed to air, hyperoxia markedly inhibited the mRNA and protein expression levels of Shh and Ptc1 in the AECII cells; however, this inhibition was partly attenuated by treatment with CGRP. On the whole, our data suggest that CGRP can partly protect AECII cells from hyperoxia-induced injury, and the upregulation of CGRP may be a potential therapeutic approach with which to combat hyperoxia-induced lung injury, which may be associated with the activation of the SHH signaling pathway.
INFLUENCE OF AMENDMENTS ON PHOSPHOGYPSUM CHEMICAL CHARACTERISTICS AND BERMUDAGRASS GROWTH

Phosphogypsum (PG) is primarily a calcium sulfate dihydrate (CaS04.2H20) byproduct of the production of phosphoric acid from phosphate ore. Approximately 5 mt of PG is produced per metric ton of phosphoric acid. Acidity and nutrient deficiencies are concerns that must be addressed for successful establishment of vegetation in PG. Therefore, a glasshouse study was conducted to determine the effects of dolomite, phosphatic clay (PC), and sewage sludge (SS) on PG chemical characteristics and bermudagrass (Cynodon daclylon [L.] Pers.) growth in PG. Phosphogypsum from an active stack, International Mineral Corp. (IMC-PG), and an old, inactive stack, Estech (ET-PG), was used. The pH and EC in water (2:1, V:W) were 2.78 and 4.16 dS/m for IMC-PG, and 4.82 and 2.29 dS/m for ET-PG. According to Mehlich-I extraction interpretations, both PG sources are classified as deficient in magnesium (Mg) and potassium (K) for optimum plant growth. Dolomite, ranging from 0.87 to 6.98 g/kg, PC from 21.7 to 174 g/kg, and SS from 4.35 to 17.4 g/kg were applied to IMC-PG. Similarly, dolomite at 0.22 to 1.74 g/kg, PC at 0.87 to 6.96 g/kg, and SS at 0.87 to 3.48 g/kg were applied to ET-PG. Each rate of amendment was increased successively by a factor of 2 to give 4 rates of dolomite and PC, respectively, and 3 rates of SS, and was mixed with the PG source and incubated for six months prior to this study. At the beginning of this study, ammonium nitrate (NH4N03), potassium-magnesium sulfate (K2S04-MgS04), and potassium sulfate (K2S04) fertilizers were selectively added to supply 50 mg/kg N, 20 mg/kg K, and 12 mg/kg Mg before sowing (0.14 g seeds/pot). Germination and growth occurred at pH 4.3 despite moderate salinity (15.6 dS/m), suggesting that attaining a desired pH is more critical than salinity for germination and growth. Phosphatic clays reduced salinity in recently decommissioned stacks that are generally higher in salts. The rates of amendments applied to ET-PG did not supply sufficient K for plant growth. Additionally, SS rates did not supply sufficient Mg. Dolomite, PC, and SS each have potential for use as nutrient sources and for raising pH. However, higher rates would be required to provide adequate nutrients in older, leached stacks and to increase pH in recently deactivated stacks. Additional
Pancreatic Islet Transplantation Using Vascularised Chambers Containing Nerve Growth Factor Ameliorates Hyperglycaemia in Diabetic Mice

Intraportal islet transplantation has shown initial promise for the treatment of type 1 diabetes. However, the portal vein site is associated with complications such as thrombosis and hepatic steatosis, leading to transplant failure. The aims of this study were to (1) test the feasibility of an alternative islet transplantation method that utilises a FDA-approved gelatin sponge as a novel islet carrier and (2) assess if exogenous addition of nerve growth factor (NGF) has any additional beneficial effects on graft performance in diabetic mice. Mice were rendered diabetic by a single intraperitoneal injection of streptozotocin. Five hundred syngeneic islets were seeded onto a Gelitaspon® disc in the presence or absence of NGF, and placed into a silicone chamber surrounding the femoral neurovascular pedicle. Islet function was assessed by weekly monitoring of blood glucose levels and an intraperitoneal glucose tolerance test performed at the end of the study. Chambers were harvested for further histological analysis. Four of five mice transplanted with islets seeded onto Gelitaspon with NGF showed a significant reduction in blood glucose levels by 4 weeks after transplantation, and demonstrated a response similar to non-diabetic mice when tested with an intraperitoneal glucose tolerance test. Chamber tissue from this group contained islets with insulin-producing β cells adjacent to the vascular pedicle. Islets seeded onto Gelitaspon with NGF and sited on femoral vessels using a tissue-engineering chamber offer an alternative method for islet transplantation in diabetic mice. This may have potential as a method for clinical islet transplantation.
Distinct Stages of Moment‐to‐Moment Processing in the Cinguloopercular and Frontoparietal Networks

Abstract Control of goal‐directed tasks is putatively carried out via the cinguloopercular (CO) and frontoparietal (FP) systems. However, it remains unclear whether these systems show dissociable moment‐to‐moment processing during distinct stages of a trial. Here, we characterize dynamics in the CO and FP networks in a meta‐analysis of 5 decision‐making tasks using fMRI, with a specialized “slow reveal” paradigm which allows us to measure the temporal characteristics of trial responses. We find that activations in left FP, right FP, and CO systems form separate clusters, pointing to distinct roles in decision‐making. Left FP shows early “accumulator‐like” responses, suggesting a role in pre‐decision processing. CO has a late onset and transient response linked to the decision event, suggesting a role in performance reporting. The majority of right FP regions show late onsets with prolonged responses, suggesting a role in post‐recognition processing. These findings expand upon past models, arguing that the CO and FP systems relate to distinct stages of processing within a trial. Furthermore, the findings provide evidence for a heterogeneous profile in the FP network, with left and right FP taking on specialized roles. This evidence informs our understanding of how distinct control networks may coordinate moment‐to‐moment components of complex actions.
Investigation on the Origin of Sperm DNA Fragmentation: Role of Apoptosis, Immaturity and Oxidative Stress

Sperm DNA fragmentation (sDF) represents a threat to male fertility, human reproduction and the health of the offspring. The causes of sDF are still unclear, even if apoptosis, oxidative assault and defects in chromatin maturation are hypothesized. Using multicolor flow cytometry and sperm sorting, we challenged the three hypothesized mechanisms by simultaneously evaluating sDF and signs of oxidative damage (8-hydroxy, 2′-deoxyguanosine (8-OHdG) and malondialdehyde (MDA)), apoptosis (caspase activity and cleaved poly(ADP-ribose) polymerase (cPARP)) and sperm immaturity (creatine phosphokinase (CK) and excess of residual histones). Active caspases and c-PARP were concomitant with sDF in a high percentage of spermatozoa (82.6% ± 9.1% and 53.5% ± 16.4%, respectively). Excess of residual histones was significantly higher in DNA-fragmented sperm versus sperm without DNA fragmentation (74.8% ± 17.5% and 37.3% ± 16.6%, respectively, p < 0.005), and largely concomitant with active caspases. Conversely, oxidative damage was scarcely concomitant with sDF in the total sperm population, at variance with live sperm, where 8-OHdG and MDA were clearly associated to sDF. In addition, most live cells with active caspase also showed 8-OHdG, suggesting activation of apoptotic pathways in oxidative-injured live cells. This is the first investigation on the origin of sDF directly evaluating the simultaneous presence of the signs of the hypothesized mechanisms with DNA breaks at the single cell level. The results indicate that the main pathway leading to sperm DNA breaks is a process of apoptosis, likely triggered by an impairment of chromatin maturation in the testis and by oxidative stress during the transit in the male genital tract. These findings are highly relevant for clinical studies on the effects of drugs on sDF and oxidative stress in infertile men and for the development of new therapeutic strategies.
Fuzzy Bio-Inspired Hybrid Techniques for Server Consolidation and Virtual Machine Placement in Cloud Environment

Abstract Cloud computing technology has transformed the information and communication technology industry by authorizing on-demand resource delivery to the cloud users. Datacenters are the major resource storage places from where the resources are disseminated to the requesters. When several requests are received by datacenters, the available resources are to be handled in an optimized way; otherwise the datacenters suffer from resource wastage. Virtualization is the technology that helps the cloud providers to handle several requests in an optimized way. In this regard, virtual machine placement, i.e., the process of mapping virtual machines to physical machines is considered to be the major research issue. In this paper, we propose to apply fuzzy hybrid bio-inspired meta-heuristic techniques for solving the virtual machine placement problem. The cuckoo search technique is hybridized with the fuzzy ant colony optimization and fuzzy firefly colony optimization technique. The experimental results obtained show competing performance of the proposed algorithms.
DNA Barcode Libraries Provide Insight into Continental Patterns of Avian Diversification

Background The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries. Methodology and Principal Findings Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity. Conclusions and Significance DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.
A Framework for Executive Function in the Late Elementary Years

Objective: Executive function (EF) is a commonly used but difficult to operationalize construct. In this study, we considered EF and related components as they are commonly presented in the neuropsychological literature, as well as the literatures of developmental, educational, and cognitive psychology. These components have not previously been examined simultaneously, particularly with this level of comprehensiveness, and/or at this age range or with this sample size. We expected that the EF components would be separate but related, and that a bifactor model would best represent the data relative to alternative models. Method: We assessed EF with 27 measures in a large sample (N = 846) of late elementary school-age children, many of whom were struggling in reading, and who were demographically diverse. We tested structural models of EF, from unitary models to methodological models, utilizing model-comparison factor analytic techniques. We examined both a common factor as well as a bifactor structure. Results: Initial models showed strong overlap among several latent EF variables. The final model was a bifactor model with a common EF, and five specific EF factors (working memory-span/manipulation and planning; working memory-updating; generative fluency, self-regulated learning; metacognition). Conclusions: Results speak to the commonality and potential separability of EF. These results are discussed in light of prevailing models of EF and how EF might be used for structure/description, prediction, and for identifying its mechanism for relevant outcomes.