Miracle-dz/UniFAR-FTUs huggingface dataset:
Viruses are a dominant driver of protein adaptation in mammals

Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of proteins is unknown. Here, we analyze adaptation in ~1,300 virus-interacting proteins manually curated from a set of 9,900 proteins conserved across mammals. We show that viruses (i) use the more evolutionarily constrained proteins from the cellular functions they hijack and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. Our results demonstrate that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.
Candida tropicalis affects the virulence profile of Candida albicans: an in vitro and in vivo study

Candida albicans and Candida tropicalis are commensal microorganisms occurring in the oral cavity of approximately 50%-70% of healthy individuals. However, these microbes can become pathogenic through changes in the environment or weakened host immune system. Thus, the aim of this investigation was to evaluate the interaction between species of the genus Candida in the biofilm formation, filamentation, gene expression and virulence in Galleria mellonella. Coincubation of C. albicans with C. tropicalis cells after 48 h resulted in significant reduction of biofilm formation by decreasing viable cell counts, metabolic activity and hyphal growth. The C. albicans genes (BCR1, CPH1, EFG1, UME6, HWP1, ALS3, SAP5 and PLB2) were quantified by quantitative real-time polymerase chain reaction and most of genes were downregulated. Regarding in vivo assay, the groups that the larvae received C. albicans and C. tropicalis had a significant survival increase compared to the control group of C. albicans (P = 0.0001) in agreement with the in vitro results. In conclusion, C. tropicalis colonization was associated with a decrease in the growth of C. albicans, suggesting an antagonistic relation between these two species. Therefore, C. tropicalis by reducing C. albicans virulence profile may limit the ability of this pathogenic fungus to cause infection.
Mining stackoverflow for program repair

In recent years, automatic program repair has been a hot research topic in the software engineering community, and many approaches have been proposed. Although these approaches produce promising results, some researchers criticize that existing approaches are still limited in their repair capability, due to their limited repair templates. Indeed, it is quite difficult to design effective repair templates. An award-wining paper analyzes thousands of manual bug fixes, but summarizes only ten repair templates. Although more bugs are thus repaired, recent studies show such repair templates are still insufficient. We notice that programmers often refer to Stack Overflow, when they repair bugs. With years of accumulation, Stack Overflow has millions of posts that are potentially useful to repair many bugs. The observation motives our work towards mining repair templates from Stack Overflow. In this paper, we propose a novel approach, called SOFix, that extracts code samples from Stack Overflow, and mines repair patterns from extracted code samples. Based on our mined repair patterns, we derived 13 repair templates. We implemented these repair templates in SOFix, and conducted evaluations on the widely used benchmark, Defects4J. Our results show that SOFix repaired 23 bugs, which are more than existing approaches. After comparing repaired bugs and templates, we find that SOFix repaired more bugs, since it has more repair templates. In addition, our results also reveal the urgent need for better fault localization techniques.
Expression of the Osmotically Responsive Cationic Channel TRPV4 in the Endolymphatic Sac

The immunohistochemical expression pattern and the physiological role of transient receptor potential vanilloid (TRPV) 4 in the endolymphatic sac were investigated. TRPV4 was expressed predominantly in the apical membrane of mitochondria-rich cells, and cell volume regulation by TRPV4 was observed in a tissue culture of the rat endolymphatic sac. TRPV4 was also present in the endolymphatic sacs of patients with vestibular schwannoma and with Ménière’s disease. TRPV4 is assumed to play a role as an osmoreceptor in cell and fluid volume regulation in the human endolymphatic sac.
Covalent association of beta-1,3-glucan with beta-1,6-glucosylated mannoproteins in cell walls of Candida albicans

Yeast and hyphal walls of Candida albicans were extracted with sodium dodecyl sulfate (SDS). Some of the extracted proteins reacted with a specific beta-1,6-glucan antiserum but not with a beta-1,3-glucan antiserum. They lost their beta-1,6-glucan epitope after treatment with ice-cold aqueous hydrofluoric acid, suggesting that beta-1,6-glucan was linked to the protein through a phosphodiester bridge. When yeast and hyphal walls extracted with SDS were subsequently extracted with a pure beta-1,3-glucanase, several mannoproteins that were recognized by both the beta-1,6-glucan antiserum and the beta-1,3-glucan antiserum were released. Both epitopes were sensitive to aqueous hydrofluoric acid treatment, suggesting that beta-1,3-glucan and beta-1,6-glucan are linked to proteins by phosphodiester linkages. The possible role of beta-glucans in the retention of cell wall proteins is discussed.
Dual Active Full Bridge Implementation on Typhoon HIL for G2V and V2G Applications

The Dual Active Full Bridge (DAFB) is one of the promising isolated DC/DC converter topologies that will play a significant role in the future integration of Electric Vehicle (EV) into Smart Grids (SGs). This is due to its inherent soft switching, bidirectional energy transfer capability and control simplicity. Thus, this paper provides a brief overview highlighting the advantages of the DAFB compared to other existing topologies in-light of Grid-2-Vehicle (G2V) and Vehicle-2-Grid (V2G) applications. It also emphasizes the implementation and testing of a 6 kW DAFB with Typhoon Hardware-In-the-Loop (HIL) device. The results show that the HIL implementation validates well the theoretical and simulation results.
Joule heating and MHD free convection flow along a vertical wavy surface with viscosity and thermal conductivity dependent on temperature

A numerical study is conducted to analyze the effect of Joule heating and MHD (magnetohydrodynamic) free convection flow and heat transfer along a uniformly heated vertical wavy surface with temperature dependent variable viscosity and thermal conductivity. The governing boundary layer equations with associated boundary conditions for phenomenon are converted to non-dimensional form using the appropriate transformations. The resulting nonlinear system of partial differential equations are mapped into the domain of a vertical flat plate and solved numerically by employing implicit finite difference method, known as the Keller-box scheme. The behavior of the fluid in the ranges of Joule heating parameter (0.02.0), viscosity parameter (0.020.0) and thermal conductivity parameter (0.0 10.0) are explained in details. It is found that the flow and temperature fields are strongly dependent on the above stated parameters for the ranges considered. The skin friction coefficient and the rate of heat transfer are also presented. The skin friction coefficient and the heat transfer for different values of Prandtl number Pr are compared with previously published work and are found to be in excellent agreement. DOI: http://dx.doi. org/10.3329/jname.v10i2. 11707
Predicting Prostate Cancer Recurrence After Radical Prostatectomy

Prostate cancer prognosis is variable, and management decisions involve balancing patients’ risks of recurrence and recurrence‐free death. Moreover, the roles of body mass index (BMI) and race in risk of recurrence are controversial [1,2]. To address these issues, we developed and cross‐validated RAPS (Risks After Prostate Surgery), a personal prediction model for biochemical recurrence (BCR) within 10 years of radical prostatectomy (RP) that includes BMI and race as possible predictors, and recurrence‐free death as a competing risk.
Unfolded Protein Response-regulated Drosophila Fic (dFic) Protein Reversibly AMPylates BiP Chaperone during Endoplasmic Reticulum Homeostasis*

Background: The Fic domain mediates AMPylation and is highly conserved in various species. Results: BiP is identified as a substrate of Fic, and its AMPylation state is modulated by ER stress. Conclusion: AMPylation of BiP presents a regulatory mechanism for cells to achieve ER homeostasis. Significance: BiP is the first known substrate for AMPylation by a eukaryotic Fic protein. Drosophila Fic (dFic) mediates AMPylation, a covalent attachment of adenosine monophosphate (AMP) from ATP to hydroxyl side chains of protein substrates. Here, we identified the endoplasmic reticulum (ER) chaperone BiP as a substrate for dFic and mapped the modification site to Thr-366 within the ATPase domain. The level of AMPylated BiP in Drosophila S2 cells is high during homeostasis, whereas the level of AMPylated BiP decreases upon the accumulation of misfolded proteins in the ER. Both dFic and BiP are transcriptionally activated upon ER stress, supporting the role of dFic in the unfolded protein response pathway. The inactive conformation of BiP is the preferred substrate for dFic, thus endorsing a model whereby AMPylation regulates the function of BiP as a chaperone, allowing acute activation of BiP by deAMPylation during an ER stress response. These findings not only present the first substrate of eukaryotic AMPylator but also provide a target for regulating the unfolded protein response, an emerging avenue for cancer therapy.
Effects of Design Factors of HDFS on I/O Performance

Four major design factors of HDFS, the block size, the number of data nodes, the number of client processes and replication factor are investigated to find out the effects on the I/O performance of HDFS by performing experiments in a real physical HDFS infrastructure consisting of 64 Hadoop data nodes of Intel i9 based blades. The block size is observed to be optimal when it equals to about 1Gb or 128MB that is the amount of the data the hard disk drive device can effectively input and output for 1 second in most of today’s off-the-shelf computers. Sophisticated allocation strategy is required to determine the number of mappers and reducers as the number of data nodes increase because the overall performance is influenced in complicated manner by the number of raw data blocks of the job to be processed, the processing time of the blocks for each node and the overhead of shuffling. Experiments shows that Hadoop distributes the work properly that the number of clients does not have a significant impact as the number of clients increases. There is little delay in copying the replica because replication is done in pipelined manner although the network is overloaded.
Orbital Angular Momentum Antennas: Understanding Actual Possibilities Through the Aperture Antennas Theory

In this article, we propose a method based on the aperture antennas theory to understand the limitations of orbital angular momentum (OAM) antennas in far-field links. Additional insight is also given by analyzing the properties of the operators relating source and farfield distributions for a given order of the vortex and emphasizing additional drawbacks. The degrees-of-freedom (DoF) of the fields associated with the different orders of the vortices are also discussed.
Cbl E3 Ligase Mediates the Removal of Nectin-1 from the Surface of Herpes Simplex Virus 1-Infected Cells

ABSTRACT The Cbl E3 ligase has been linked to the down-modulation of surface signaling responses by inducing internalization of surface receptors. The adaptor protein CIN85 is a partner of Cbl that augments many of these interactions. Previously, an interaction was demonstrated between ICP0 and CIN85, which results in the removal of epidermal growth factor receptor (EGFR) from the surface of the infected cells with a concomitant attenuation of EGFR signaling. Here, we examined whether Cbl mediates the removal of the herpes simplex virus 1 (HSV-1) entry receptor Nectin-1 from the surface of infected cells. We found the following: (i) that Cbl, Nectin-1, and the viral glycoprotein D (gD) form a complex in infected cells; (ii) that during infection Nectin-1 is removed from the surface of the infected cells but is retained on the surface of cells that have been depleted of Cbl; and (iii) that in cells infected with a ΔICP0 mutant virus, Nectin-1 remained on the cell surface. Thus, Cbl is necessary but not sufficient for the removal of Nectin-1 from the cell surface. In addition, we observed that in Cbl-depleted cells there was enhanced entry after infection. These cells were susceptible to secondary infections by HSV-1. Viral entry in CIN85-depleted cells was only moderately enhanced compared to that in the Cbl-depleted cells, suggesting that the Cbl–Nectin-1 interaction is likely the key to the downregulation of surface Nectin-1. The removal of the HSV-1 entry receptor Nectin-1 from the surface of the infected cells may be part of the strategy of the virus to efficiently spread to uninfected cells. IMPORTANCE The Cbl E3 ligase suppresses surface signaling responses by inducing internalization of surface components. The targets of Cbl include such components as immune system receptors, growth factor receptors, adhesion, and cell-to-cell contact molecules. The immediate early protein ICP0 of herpes simplex virus 1 (HSV-1) interacts with CIN85, an adaptor protein that augments Cbl functions. The consequence of this interaction is the removal of the epidermal growth factor receptor (EGFR) from the surface of the infected cells with concomitant suppression of the EGF ligand signaling. The viral entry receptor Nectin-1 is also internalized during HSV-1 infection in a Cbl-dependent mechanism, and that increases the opportunity of the virus to spread to uninfected cells. The diversion of the Cbl/CIN85 endocytic machinery may be a strategy utilized by the virus to alter the cell surface pattern to prevent detrimental host responses.
Laboratory Evidence of Norwalk Virus Contamination on the Hands of Infected Individuals

ABSTRACT Human norovirus (NoV) outbreak investigations suggest that the hands of infected individuals play an important role in NoV transmission. However, there is no experimental evidence documenting the likelihood and degree of NoV contamination on hands. As part of a clinical trial designed to evaluate the efficacy of high-pressure processing for Norwalk virus (NV) inactivation in oysters, 159 hand rinse samples were collected from 6 infected and 6 uninfected subjects. NV was concentrated from the samples by polyethylene glycol precipitation, followed by RNA extraction using an automated guanidinium isothiocyanate-silica method. NV RNA was detected and quantified using multiple NV-specific reverse transcription-quantitative PCR (RT-qPCR) assays. A total of 25.4% (18/71) of the hand rinse samples collected from 6 infected volunteers were presumptively positive for NV, with an average of 3.86 log10 genomic equivalent copies (GEC) per hand. Dot blot hybridization of PCR products obtained using a different primer set, and DNA sequencing of selected amplicons, provided further confirmation of the presence of NV in the hand rinses. NV contamination was also detected in two hand rinse samples obtained from one uninfected subject. These findings provide definitive evidence of NV contamination on the hands of infected subjects observed under controlled clinical research conditions. Such data support the need for better hand hygiene strategies to prevent NoV transmission.
Economic models for allocating resources in computer systems

With the advances in computer and networking technology thousands of heterogeneous com puters can be interconnected to provide a large collection of computing and communication resources These systems are used by a growing and increasingly heterogeneous set of users A macroscopic view of distributed computer systems reveals the complexity of the organi zation and management of the resources and services they provide This complexity arises from size e g no of systems no of users and heterogeneity in applications e g on line transaction processing multimedia intelligent information search and resources CPU memory bandwidth locks naming services The complexity of resource allocation is further increased by several factors First in many distributed systems the resources are in fact owned by multiple organizations Second the satisfaction of users and the performance of applications is determined by the simultane ous allocation of multiple resources A multimedia server application requires I O bandwidth to retrieve content CPU time to execute server logic and communication protocols and net working bandwidth to deliver the content to clients The performance of applications may also be altered by trading one resource for another For example the multimedia server ap plication may perform better by releasing memory and acquiring higher CPU priority This trade may result in smaller bu ers for I O and networking but improve the performance
Recombination, meiotic expression and human codon usage

Synonymous codon usage (SCU) varies widely among human genes. In particular, genes involved in different functional categories display a distinct codon usage, which was interpreted as evidence that SCU is adaptively constrained to optimize translation efficiency in distinct cellular states. We demonstrate here that SCU is not driven by constraints on tRNA abundance, but by large-scale variation in GC-content, caused by meiotic recombination, via the non-adaptive process of GC-biased gene conversion (gBGC). Expression in meiotic cells is associated with a strong decrease in recombination within genes. Differences in SCU among functional categories reflect differences in levels of meiotic transcription, which is linked to variation in recombination and therefore in gBGC. Overall, the gBGC model explains 70% of the variance in SCU among genes. We argue that the strong heterogeneity of SCU induced by gBGC in mammalian genomes precludes any optimization of the tRNA pool to the demand in codon usage.
The Effects of Prolonged Ethanol Exposure on the Mechanical Properties of Polyurethane and Silicone Catheters Used for Intravascular Access

Abstract Background: Products containing alcohol are commonly used with intravascular devices at insertion, to remove lipids from occluded intravascular devices used during parenteral nutrition, and increasingly for the prevention and treatment of intravascular device-related bloodstream infection. The effects of alcohol on the integrity of intravascular devices remain unknown. Methods: Two types of widely used commercial peripherally inserted central catheters, one made of polyether-urethane and one made of silicone, were exposed to a 70% etha-nol lock solution for up to 10 weeks. Mechanical testing was performed to identify force-at-break, stress, strain, modulus of elasticity, modulus of toughness, and wall area of ethanol-exposed and control catheters. Results: No significant differences between exposed and unexposed catheters were identified for any of the mechanical parameters tested except for a marginal reduction in the modulus of elasticity for both polyetherurethane and silicone catheters and minor increases in the wall area of polyetherurethane catheters. Conclusions: These data indicate that exposure to a 70% ethanol lock solution does not appreciably alter the integrity of selected commercial polyetherurethane and silicone catheters. Given the greatly expanded use of alcoholic solutions with intravascular devices of all types, we believe that manufacturers would be well advised to subject their catheters and other intravascular devices to formal testing of the type employed in this study.
Callus induction, in vitro shoot regeneration and hairy root formation by the assessment of various plant growth regulators in tomato (Solanum lycopersicum Mill.).

In vitro morphogenesis is greatly influenced by plant growth regulators (PGRs). The effect of different plant growth regulators was assessed on callus induction, in vitro shoot regeneration and hairy root formation in tomato. The maximum callus induction frequency was recorded culturing hypocotyls, while in vitro shoot regeneration frequency was significantly higher when leaf discs were used as explants. The highest callus induction frequency (67.48%) was recorded in cv. Rio Grande followed by Roma (62%) and Moneymaker (58.23%) on MS basal media along with 2.0 mg/l IAA and 2.5 mg/l BAP. Similarly, the highest in vitro shoot regeneration frequency (69.6 and 65.3%) was recorded in Rio Grande and Roma on MS media fortified with 0.1 mg/l IAA, 1.0 mg/l ZEA and 2.0 mg/l BAP, while in case of Moneymaker, the highest in vitro shoot regeneration frequency (67.3%) was obtained on MS media enriched with 0.1 mg/l IAA and 3.0 mg/l BAP. The highest hairy root formation frequency (100, 91.72 and 93.74%) was achieved in cvs. Rio Grande, Moneymaker and Roma, respectively on MS media supplemented with 0.1 mg/l IAA, 2.0 mg/l ZEA and 2.0 mg/l BAP. These optimized procedures would be applicable to other genotypes of tomato for the development of cultivars tolerant to abiotic stresses developed via Agrobacterium mediated transformation system.
Simulating urban land-use changes at a large scale by integrating dynamic land parcel subdivision and vector-based cellular automata

ABSTRACT Cellular automata (CA) have been widely used to simulate complex urban development processes. Previous studies indicated that vector-based cellular automata (VCA) could be applied to simulate urban land-use changes at a realistic land parcel level. Because of the complexity of VCA, these studies were conducted at small scales or did not adequately consider the highly fragmented processes of urban development. This study aims to build an effective framework called dynamic land parcel subdivision (DLPS)-VCA to accurately simulate urban land-use change processes at the land parcel level. We introduce this model in urban land-use change simulations to reasonably divide land parcels and introduce a random forest algorithm (RFA) model to explore the transition rules of urban land-use changes. Finally, we simulate the land-use changes in Shenzhen between 2009 and 2014 via the proposed DLPS-VCA model. Compared to the advanced Patch-CA and RFA-VCA models, the DLPS-VCA model achieves the highest simulation accuracy (Figure-of-Merit = 0.232), which is 32.57% and 18.97% higher respectively, and is most similar to the actual land-use scenario (similarity = 94.73%) at the pattern level. These results indicate that the DLPS-VCA model can both accurately split the land during urban land-use changes and significantly simulate urban expansion and urban land-use changes at a fine scale. Furthermore, the land-use change rules that are based on DPLS-VCA mining and the simulation results of several future urban development scenarios can act as guides for future urban planning policy formulation.