Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral.

OBJECTIVES T-705, also known as favipiravir, is a small-molecule inhibitor that is currently in clinical development for the treatment of influenza virus infections. This molecule also inhibits the replication of a broad spectrum of other RNA viruses. The objective of this study was to investigate the antiviral effect of favipiravir on chikungunya virus (CHIKV) replication and to contribute to unravelling the molecular mechanism of action against this virus. METHODS The anti-CHIKV effect of favipiravir was examined in cell culture and in a mouse model of lethal infection. A five-step protocol was used to select for CHIKV variants with reduced susceptibility to favipiravir. The resistant phenotype was confirmed in cell culture and the whole genome was sequenced. The identified mutations were reverse-engineered into an infectious clone to confirm their impact on the antiviral efficacy of favipiravir. RESULTS Favipiravir inhibits the replication of laboratory strains and clinical isolates of CHIKV, as well as of a panel of other alphaviruses. Several favipiravir-resistant CHIKV variants were independently selected and all of them in particular acquired the unique K291R mutation in the RNA-dependent RNA polymerase (RdRp). Reverse-engineering of this K291R mutation into an infectious clone of CHIKV confirmed the link between the mutant genotype and the resistant phenotype. Interestingly, this particular lysine is also highly conserved in the RdRp of positive-stranded RNA viruses in general. CONCLUSIONS This study provides an important insight into the precise molecular mechanism by which favipiravir exerts its antiviral activity against (alpha)viruses, which may be of help in designing other potent broad-spectrum antivirals.
When the Mind Forms Fear: Embodied Fear Knowledge Potentiates Bodily Reactions to Fearful Stimuli

In the present study, the authors tested whether conceptual fear knowledge can (a) evoke bodily reactions and (b) enhance subsequent bodily reactions to fearful stimuli. Participants unscrambled neutral or fear sentences and subsequently viewed fearful and neutral pictures in combination with startle sounds. As predicted, the authors found embodied reactions (i.e., increased electrodermal and corrugator activity) while participants unscrambled fear sentences. Importantly, these embodied reactions occurred in the absence of a subjective fear experience. In addition, the authors found increased electrodermal activity while viewing fear pictures and a stronger startle modulation effect after fear concept activation. Finally, concerning electrodermal activity, the results demonstrated that the effect of concept activation on subsequent emotional responding was fully mediated by participants' embodied reactions. These findings extend recent research on emotion concepts by showing that embodied emotion knowledge potentiates subsequent emotional responding.
Alternative replication factor C protein, Elg1, maintains chromosome stability by regulating PCNA levels on chromatin

Proliferating cell nuclear antigen (PCNA) is loaded on chromatin upon initiation of the S phase and acts as a platform for a large number of proteins involved in chromosome duplication at the replication fork. As duplication is completed, PCNA dissociates from chromatin, and thus, chromatin‐bound PCNA levels are regulated during the cell cycle. Although the mechanism of PCNA loading has been extensively investigated, the unloading mechanism has remained unclear. Here, we show that Elg1, an alternative replication factor C protein, is required for the regulation of chromatin‐bound PCNA levels. When Elg1 was depleted by small interfering RNA, chromatin‐bound PCNA levels were extremely increased during the S phase. The number of PCNA foci, regions in the nucleus normally representing DNA replication sites, was increased and PCNA remained on chromatin after DNA replication. Various chromatin‐associated protein levels on chromatin were affected, and chromatin loop size was increased. During mitosis, cells with aberrant chromosomes and lagging chromosomes were frequently detected. Our findings suggest that Elg1 has an important role in maintaining chromosome integrity by regulating PCNA levels on chromatin, thereby acting as a PCNA unloading factor.
The frequency of hamstring stretches required to maintain knee extension range of motion following an initial six-week stretching programme

Stretching exercises are commonly prescribed in training and rehabilitation programmes. The purpose of this study was to determine the frequency of on-going hamstring stretching required to maintain knee extension range of motion (ROM) following an initial stretching programme. A test-retest randomised control trial was undertaken. Sixty-three healthy male participants were randomly assigned to two stretch groups and a control group. Active knee extension (AKE) stretches were performed five days a week for an initial six weeks. Stretch group 1 then reduced the frequency of stretching to three days per week, and stretch group 2, to one day per week, for a further six weeks. The control group did not stretch. Active knee extension ROM was measured at baseline, weeks six and 12. A significant improvement in AKE ROM was observed in stretch group 1 (17.5° SD 11.8°) and 2 (18.8° SD 7.1°) after the initial six weeks of stretching (p < 0.05). After six-weeks of on-going stretching group 1 maintained their improvement in ROM, whereas stretch group 2 lost ROM. The difference between stretching groups was significant (p < 0.05) and no change in ROM was observed in the control group. These results indicate that an on-going hamstring stretching programme with a frequency of three times a week is required to maintain the initial improvement in ROM. Reid DA, Kim J (2014) The frequency of hamstring stretches required to maintain knee extension range of motion following an initial six-week stretching programme New Zealand Journal of Physiotherapy 42(1): 22-27.
Pediatric Nursing Procedures

Thoroughly updated for its Second Edition, this pediatric procedures book provides the student and professional nurse with a quick reference to essential nursing procedures and standards for practice. Its format is easily adaptable to organizational policy and procedure manuals. Chapters are alphabetically presented by procedure and contain clinical guidelines for practice. Tables and charts summarize key diagnostic information or parameters.
The morphology and diagnosis of atrioventricular septal defects

Summary In this review, we discuss and describe those features which distinguish hearts with abnormal atrioventricular septation from the normal heart. The hearts, best described as atrioventricular septal defects, are unified by having a common atrioventricular junction guarded by a valve having five leaflets. The left component has three leaflets and cannot be interpreted in terms of a cleft in a normal mitral valve. The papillary muscles supporting this valve are also markedly dissimilar from the arrangement seen in normal hearts. The subaortic outflow tract is displaced superiorly compared to the normal heart, and is no longer wedged between the left valve and the septum. There is marked discrepancy in the inlet and outlet lengths of the ventricular mass, these dimensions being equal in hearts with normal atrioventricular septation. Although having the above features in common, atrioventricular septal defects show anatomic variations related to the arrangement of the bridging leaflets and their relationship to the septal structures. There may be a common valvar orifice or separate right and left orifices. The anatomic potential for shunting may be at atrial or ventricular levels, or both. Rarely, the septal structures may be intact. Other important features include ventricular dominance, the left ventricular outflow tract, and the disposition of the atrioventricular conduction tissues.
Mammalian target of rapamycin (mTOR) complex 2 regulates filamin A‐dependent focal adhesion dynamics and cell migration

The serine/threonine kinase mTOR forms two distinct complexes, mTORC1 and mTORC2, and controls a number of biological processes, including proliferation, survival and autophagy. Although the function of mTORC1 has been extensively studied, the mTORC2 signaling pathway largely remains to be elucidated. Here, we have shown that mTORC2 phosphorylates filamin A, an actin cross‐linking protein, at serine 2152 (S2152) both in vivo and in living cells. Treatment of HeLa cells with Torin1 (an mTORC1/mTORC2 inhibitor), but not rapamycin (an mTORC1 inhibitor), suppressed the phosphorylation of filamin A, which decreased the binding of filamin A with β7‐integrin cytoplasmic tail. Torin1 also inhibited focal adhesion formation and cell migration in A7 filamin A‐replete melanoma cells but not in M2 filamin A‐deficient cells, suggesting a pivotal role for mTORC2 in filamin A function. Finally, reduced focal adhesion formation in M2 cells was significantly rescued by expressing wild type but not S2152A nonphosphorylatable mutant of filamin A. Taken together, our results indicate that mTORC2 regulates filamin A‐dependent focal adhesions and cell migration.
Anillin‐related protein Mid1 regulates timely formation of the contractile ring in the fission yeast Schizosaccharomyces japonicus

In the fission yeast Schizosaccharomyces pombe (Sp), Mid1/Dmf1 plays an important role in positioning the division site by inducing formation of the contractile ring (CR). Mid1, emanating from the nucleus located in the cell center, forms a dozen of nodes in the middle cell cortex ahead of mitosis, and actin filaments and myosin II accumulated at each node interact and assemble the CR in metaphase. Curiously, in another fission yeast S. japonicus (Sj), CR formation begins after nuclear segregation in late anaphase. Here, we investigated the role of S. japonicus Mid1 during mitosis to compare the molecular mechanisms that determine the cell division site in Schizosaccharomyces. Similar to Sp Mid1, Sj Mid1 often accumulated in the nucleus of interphase cells. Moreover, Sj Mid1 localized to cortical dots with myosin II in the future division site and formed a medial ring in mitotic cells. However, S. japonicus cells without Mid1 function still carried out symmetrical binary division. Therefore, the Mid1 dependency for positional control of the cell division site is possibly different between the two species. Meanwhile, we found that Sj Mid1 enhanced CR formation, in a manner possibly similar to that by Sp Mid1.
Targeting ID2 expression triggers a more differentiated phenotype and reduces aggressiveness in human salivary gland cancer cells

Inhibitors of DNA‐binding (ID) proteins are negative regulators of basic helix‐loop‐helix transcription factors and generally stimulate cell proliferation and inhibit differentiation. We previously determined that ID1 was highly expressed in aggressive salivary gland cancer (SGC) cells in culture. Here, we show that ID2 is also expressed in aggressive SGC cells. ID2 knockdown triggers important changes in cell behavior, that is, it significantly reduces the expression of N‐cadherin, vimentin and Snail, induces E‐cadherin expression and leads to a more differentiated phenotype exemplified by changes in cell shape. Moreover, ID2 knockdown almost completely suppresses invasion and the expression of matrix metalloproteinase 9. In conclusion, ID2 expression maintains an aggressive phenotype in SGC cells, and ID2 repression triggers a reduction in cell aggressiveness. ID2 therefore represents a potential therapeutic target during SGC progression. ID proteins are negative regulators of basic helix‐loop‐helix transcription factors and generally stimulate cell proliferation and inhibit differentiation. ID2 knockdown triggers important changes in cell behavior, that is, it significantly reduces the expression of N‐cadherin, vimentin and Snail, induces E‐cadherin expression and leads to a more differentiated phenotype exemplified by changes in cell shape. ID2 therefore represents a potential therapeutic target during SGC progression.
WGS accurately predicts antimicrobial resistance in Escherichia coli.

OBJECTIVES The objective of this study was to determine the effectiveness of WGS in identifying resistance genotypes of MDR Escherichia coli and whether these correlate with observed phenotypes. METHODS Seventy-six E. coli strains were isolated from farm cattle and measured for phenotypic resistance to 15 antimicrobials with the Sensititre(®) system. Isolates with resistance to at least four antimicrobials in three classes were selected for WGS using an Illumina MiSeq. Genotypic analysis was conducted with in-house Perl scripts using BLAST analysis to identify known genes and mutations associated with clinical resistance. RESULTS Over 30 resistance genes and a number of resistance mutations were identified among the E. coli isolates. Resistance genotypes correlated with 97.8% specificity and 99.6% sensitivity to the identified phenotypes. The majority of discordant results were attributable to the aminoglycoside streptomycin, whereas there was a perfect genotype-phenotype correlation for most antibiotic classes such as tetracyclines, quinolones and phenicols. WGS also revealed information about rare resistance mechanisms, such as structural mutations in chromosomal copies of ampC conferring third-generation cephalosporin resistance. CONCLUSIONS WGS can provide comprehensive resistance genotypes and is capable of accurately predicting resistance phenotypes, making it a valuable tool for surveillance. Moreover, the data presented here showing the ability to accurately predict resistance suggest that WGS may be used as a screening tool in selecting anti-infective therapy, especially as costs drop and methods improve.
Production of Recombinant Adeno‐Associated Viral Vectors and Use for In Vitro and In Vivo Administration

Adeno‐associated virus is a nonpathogenic human virus that has been developed into a gene‐delivery vector due to its high efficiency of infection for many different cell types and its ability to persist and lead to long‐term gene expression. This unit describes efficient methods to generate high‐titer, research‐grade, adenovirus‐free recombinant single‐stranded and self‐complementary adeno‐associated virus in various serotypes, along with methods to quantify the viral vectors. Two detailed methods are provided for viral vector injection into rat brain and for histological detection of transgene expression, including lacZ and GFP.
In vitro site‐specific recombination mediated by the tyrosine recombinase XerA of Thermoplasma acidophilum

In organisms with circular chromosomes, such as bacteria and archaea, an odd number of homologous recombination events can generate a chromosome dimer. Such chromosome dimers cannot be segregated unless they are converted to monomers before cell division. In Escherichia coli, dimer‐to‐monomer conversion is mediated by the paralogous XerC and XerD recombinases at a specific dif site in the replication termination region. Dimer resolution requires the highly conserved cell division protein/chromosome translocase FtsK, and this site‐specific chromosome resolution system is present or predicted in most bacteria. However, most archaea have only XerA, a homologue of the bacterial XerC/D proteins, but no homologues of FtsK. In addition, the molecular mechanism of XerA‐mediated chromosome resolution in archaea has been less thoroughly elucidated than those of the corresponding bacterial systems. In this study, we identified two XerA‐binding sites (dif1 and dif2) in the Thermoplasma acidophilum chromosome. In vitro site‐specific recombination assays showed that dif2, but not dif1, serves as a target site for XerA‐mediated chromosome resolution. Mutational analysis indicated that not only the core consensus sequence of dif2, but also its flanking regions play important roles in the recognition and recombination reactions mediated by XerA.
A Comparison of Service Quality in Teaching and Non-teaching Hospitals: The Gap Analysis

Introduction : Service quality is a judgment that the customer compares his/her expectations by this judgment, with the perception of the received services. The purpose of this study was to compare service quality in teaching hospitals with non-teaching hospitals in Kerman city. Methods : This cross-sectional study has been done on 166 hospitalized patients and the standard SERVQUAL questionnaire with an approved validity and reliability was used. Data analysis was performed using SPSS software version 19. Results : The results show that the service quality from the patients’ perception in non-teaching hospitals is more than the teaching hospitals (p=0.002). Most of the service quality gap is in the tangibility dimensions and also in providing amenities for patients and their companions. Conclusion : Teaching setting of the hospital typically can cause poor subjectivity in patients about the quality of services provided and it is recommended that authorities identify factors causing these kind of thinking and solve them. Also the negative scores indicate a need for improvement in all aspects, especially the tangibility dimensions having the maximum gap. Keywords : Patient Expectations, Service Quality, Teaching Hospital, SERVQUAL
Induction of erythropoietin gene expression in epithelial cells by chemicals identified in GATA inhibitor screenings

Erythropoietin (EPO) is a hormone that promotes proliferation, differentiation and survival of erythroid progenitors. EPO gene expression is regulated in a tissue‐specific and hypoxia‐inducible manner and is mainly restricted to renal EPO‐producing cells after birth. Chronic kidney disease (CKD) confers high risk for renal anemia due to lower EPO production from injured kidneys. In transgenic reporter lines of mice, disruption of a GATA‐binding motif within the Epo gene promoter‐proximal region restores constitutive reporter expression in epithelial cells. Here, mitoxantrone and its analogues, identified as GATA factor inhibitors through high‐throughput chemical library screenings, markedly induce EPO/Epo gene expression in epithelium‐derived cell lines and mice regardless of oxygen levels. In contrast, mitoxantrone interferes with hypoxia‐induced EPO gene expression in Hep3B cells. Cryptic promoters are created for the EPO/Epo gene expression in epithelial cells upon mitoxantrone treatment, and consequently, unique 5′‐untranslated regions are generated. The mitoxantrone‐induced aberrant transcripts contribute to the reporter protein production in epithelial cells that carry the reporter gene in the proper reading frame of mouse Epo gene. Thus, EPO production in uninjured adult epithelial cells may be a therapeutic approach for renal anemia in patients with CKD.
Online Video Game Addiction: Exploring a New Phenomenon

Over a period of thirty years, video games have evolved from Pac Man to photorealistic, massively populated, three-dimensional environments. Adolescents become involved with online virtual communities (tribes, guilds, groups) and play games on a daily basis with people they have never seen in ‘real’ life. Large online games provide a virtual environment in which they have fun and can freely experiment with different identities, speak other languages, and form new social connections at the same time. Nowadays, games have developed beyond simple concepts such as ‘eat-the-yellow-dots’ in Pac Man. Gaming now includes sophisticated persistent virtual worlds (World of Warcraft, Lord of the Rings Online, Guild Wars), competitive team-based online shooting games (Counterstrike, Team Fortress 2), and multiuser real-time strategy games (Starcraft 2, Warcraft 3). These changes are largely driven by the rapid developments in computing power and internet access, as well as by the declining costs of consumer electronics. As a result of increased availability, more people are playing games; however, some individuals seem to be playing more as well. A 2008 press release by the market research group NPD states that: “…of the 174 million gamers who personally play games on PC/Mac or video game systems, three percent are Extreme Gamers” (NPD, 2008). Extreme gamers play an average of 45 hours per week. A press release by the same firm two years later stated that this percentage had increased. In 2010 the NPD group reported that the group of extreme gamers had grown to four percent, emphasizing that “…extreme gamers spend two full days per week playing video games” (NPD, 2010).
Automated Three‐Chambered Social Approach Task for Mice

Autism is diagnosed by three major symptom categories: unusual reciprocal social interactions, impaired communication, and repetitive behaviors with restricted interests. Direct social approach in mice has strong face validity to simple social approach behaviors in humans, which are frequently impaired in autism. This unit presents a basic protocol for a standardized, high‐throughput social approach test for assaying mouse sociability. Our automated three‐chambered social approach task quantifies direct social approach behaviors when a subject mouse is presented with the choice of spending time with either a novel mouse or a novel object. Sociability is defined as the subject mouse spending more time in the chamber containing the novel target mouse than in the chamber containing the inanimate novel object. The Basic Protocol describes procedures for testing one subject at a time in a single apparatus. A Support Protocol addresses data collection. Curr. Protoc. Neurosci. 56:8.26. 1‐8.26. 16. © 2011 by John Wiley & Sons, Inc.
An Unsteady State Tracer Method for Characterizing Fractures in Bedrock Wells

Evaluating contaminants impacting wells in fractured crystalline rock requires knowledge of the individual fractures contributing water. This typically involves using a sequence of tools including downhole geophysics, flow meters, and straddle packers. In conjunction with each other these methods are expensive, time consuming, and can be logistically difficult to implement. This study demonstrates an unsteady state tracer method as a cost‐effective alternative for gathering fracture information in wells. The method entails introducing tracer dye throughout the well, inducing fracture flow into the well by conducting a slug test and then profiling the tracer concentration in the well to locate water contributing fractures where the dye has been diluted. By monitoring the development of the dilution zones within the wellbore with time, the transmissivity and the hydraulic head of the water contributing fractures can be determined. Ambient flow conditions and the contaminant concentration within the fractures can also be determined from the tracer dilution. This method was tested on a large physical model well and a bedrock well. The model well was used to test the theory underlying the method and to refine method logistics. The approach located the fracture and generated transmissivity values that were in excellent agreement with those calculated by slug testing. For the bedrock well tested, two major active fractures were located. Fracture location and ambient well conditions matched results from conventional methods. Estimates of transmissivity values by the tracer method were within an order of magnitude of those calculated using heat‐pulse flow meter data.