Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic Characterization of ORF2 and ORF3 Proteins of Hepatitis E Virus (HEV)

To evaluate the antigenic properties of Hepatitis E Virus (HEV) Open Reading Frame 2 and 3 (ORF2 and ORF3) codified proteins, we expressed different portions of ORF2 and the entire ORF3 in E. coli, a truncated ORF2, was also expressed in baculovirus. A panel of 37 monoclonal antibodies (MAbs) was raised against ORF2 (1–660 amino acids) and MAbs were mapped and characterized using the ORF2 expressed portions. Selected HEV positive and negative swine sera were used to evaluate ORF2 and ORF3 antigens’ immunogenicity. The MAbs were clustered in six groups identifying six antigenic regions along the ORF2. Only MAbs binding to the sixth ORF2 antigenic region (394–608 aa) were found to compete with HEV positive sera and efficiently catch the recombinant antigen expressed in baculovirus. The ORF2 portion from 394–608 aa demonstrated to include most immunogenic epitopes with 85% of HEV positive swine sera reacting against the region from 461–544 aa. Only 5% of the selected HEV sera reacted against the ORF3 antigen.
Subcellular Genomics: Pervasive within-mitochondrion SNV heteroplasmy revealed by single mitochondrion sequencing

Jacqueline Morris1,4, Young-Ji Na2,4, Hua Zhu1, Jae-Hee Lee1, Hoa Giang2, Alexandra V. Ulyanova3, Gordon H. Baltuch3, Steven Brem3, H. Isaac Chen3, David K. Kung3, Timothy H. Lucas3, Donald M. O’Rourke3, John A. Wolf3, M. Sean Grady3, Jai-Yoon Sul1, Junhyong Kim2,5, and James Eberwine1,5,6 1Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Step-down infusions of Gd-DTPA yield greater contrast-enhanced magnetic resonance images of acute stroke than bolus injections

A rat model of transient suture occlusion of one middle cerebral artery (MCA) was used to create an unilateral reperfused cerebral ischemic infarct with blood-brain barrier (BBB) opening. Opening of the BBB was visualized and quantitated by magnetic resonance (MR) contrast enhancement with a Look-Locker T 1 -weighted sequence either following an i.v. bolus injection (n=7) or during a step-down infusion (n=7) of gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA). Blood levels of Gd-DTPA after either input were monitored via changes in sagittal sinus relaxation rate. Blood-to-brain influx constants (K i ) were calculated by Patlak plots. On the basis of the MRI parameters and lesion size, the ischemic injury was determined to be similar in the two groups. The bolus injection input produced a sharp rise in blood levels of Gd-DTPA that declined quickly, whereas the step-down infusion led to a sharp rise that was maintained relatively constant for the period of imaging. Visual contrast enhancement and signal-to-noise ratios (S/N) were better with the step-down method (S/N=1.8) than with bolus injection (S/N=1.3). The K i values were not significantly different between the two groups ( p >0.05) and were around 0.005 ml g − 1 min − 1 . The major reason for the better imaging of BBB opening by the step-down infusion was the higher amounts of Gd-DTPA in plasma and tissue during most of the experimental period. These results suggest that step-down MR contrast agent (MRCA) administration schedule may be advantageous for detection and delineation of acute BBB injury than the usually employed bolus injections.
Implementation of Trust reputation System (TRS) for E-commerce Applications using Data Mining

- With rapidly increasing use of internet sites mainly shopping is one of popular among all other sites . To keep it growing and stable one factor is important that is 'trust' hence aiming at designing a reputation system which will play crucial role in building trust. We aimed at designing TRS system which will give assurance to customers to keep trust on internet sites. TRS algorithm will not only calculate trust degree of user but also the score of the product with accuracy.
Tissue Fractionation Studies

Cathepsin and other intracellular acid hydrolases have long been suspected of playing an important role in the aseptic autolysis and necrosis of tissues, but no satisfactory explanation has yet been given oftheir relative lack of activity in intact cells, nor of the processes responsible for their activation in dying or dead cells (see, for instance, the review by Bradley, 1938). As pointed out before (de Duve & Berthet, 1954), the finding that these enzymes are segregated within particles which are impermeable to their respective substrates (lysosomes; see de Duve, Pressman, Gianetto, Wattiaux & Appelmans 1955) provides an obvious answer to the first question. This, however, implies as a necessary corollary and answer to the second question that the rupture of the particles in 8itU and consequent release of their enzymic content must be an early step in the chain of processes leading to the autolytic breakdown of tissue constituents. The experiments described in this paper were designed to test this hypothesis on a simple and reproducible material, namely on liver tissue entirely deprived of blood supply. Rat liver proved particularly suitable for this kind of study, since the hilum of one lobe can easily be ligated without injuring the remainder ofthe tissue, which may thus serve as an internal control. The results obtained indicate that lysosomes do indeed suffer a rapid disintegration or increase in fragility in necrotizing liver. The results have been previously reported briefly (Beaufay & de Duve, 1957).
Arabidopsis weep mutants exhibit narrow root angles

Peach ( Prunus persica ) trees with a mutation in the weep gene exhibit a weeping branch phenotype. In contrast, Arabidopsis ( Arabidopsis thaliana ) weep mutants do not have a shoot architecture phenotype. A recent report revealed that barley ( Hordeum vulgare ) and wheat ( Triticum aestivum ) with mutations in EGT2, a WEEP homolog, have steeper root angles than standard varieties. We investigated the root architecture of three Arabidopsis weep mutant lines. All three lines exhibited steeper root angles and a smaller convex hull area, indicating that the total area explored by the root system is reduced. These results reveal WEEP is important for regulating lateral root angles in a dicot.
Metformin Use and Mortality in Women with Ovarian Cancer: An Updated Meta-Analysis

Background Previous observational studies and meta-analysis suggested a possible association between metformin use and reduced mortality in women with ovarian cancer (OC). However, clinical factors that may influence the relationship remain poorly evaluated. We performed an updated meta-analysis to systematically evaluate the above association and to observe the potential influences of study characteristics on the association. Methods Relevant studies reporting the association between metformin use and mortality in women with OC in the multivariate adjusted model were identified by search of electronic databases that included PubMed, Embase, and Web of Science. The random-effects model was adopted to combine the results. Results Nine studies including 10030 women with OC were included. Overall, metformin use was independently associated with reduced overall mortality (hazard ratio (HR): 0.72, 95% confidence interval (CI): 0.55–0.93, P=0.01; I2 = 62%). Consistent results were observed for studies comparing metformin users with nondiabetic women and studies comparing metformin users with diabetic women who did not use metformin (P for subgroup analysis = 0.70). Further subgroup analyses showed consistent results in studies with metformin use before or after the diagnosis of OC, with or without adjustment of body mass index (BMI) and with or without adjustment of concurrent medications (P for subgroup analyses all >0.10). Conclusion Metformin use is associated with reduced mortality in women with OC, which may be independent of the diabetic status of the controls, timing of metformin use, or adjustment of BMI and concurrent medications. Clinical trials are needed to validate the potential benefits of metformin on survival of OC.
Semen Quality and Time-to-Pregnancy, the LIFE Study

Germaine M. Buck Louis, Ph.D.1, Rajeshwari Sundaram, Ph.D.1, Enrique F. Schisterman, Ph.D.1, Anne Sweeney, Ph.D.2, Courtney D. Lynch, Ph.D.3, Sungduk Kim, Ph.D.1, José M. Maisog, M.D., M.S.1, Robert Gore-Langton, Ph.D.4, Michael L. Eisenberg, M.D.5, and Zhen Chen, Ph.D.1 1Division of Epidemiology, Statistics and Prevention Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development; 6100 Executive Blvd., Room 7B03, Rockville, MD 20852 2Texas A & M Health Science Center, School of Rural Public Health, College Station, Texas 3Department of Obstetrics & Gynecology, College of Medicine, The Ohio State University, Columbus, Ohio 4The EMMES Corporation, Rockville, Maryland 20852 5Department of Urology, Stanford University, Palo Alto, California
Identification and characterization of a novel repressor site in the human tumor necrosis factor o gene

In human monocytic cell lines, tumor necrosis factor a (TNFa) expression is induced by phorbol myristate acetate (PMA). We have identified positive and negative cis-acting elements in the TNFx promoter by deletion analysis. Here we present the initial characterization of the repressor element. The repressor element was shown to function in either orientation and at various distances upstream from the positive element of the TNFa promoter. The TNFa repressor site (TRS) has been localized to a 25 bp region between base pairs - 254 and - 230 in the promoter. This region contains a 10 bp sequence with homology to the binding site of the activator protein AP-2. Mutation of the 6 C's of this 10 bp AP-2-like site abolish TRS repressor function. However, this AP-2-like site is not a binding site for AP-2 protein based on gel retardation analysis. In addition, a well-characterized AP-2 binding site placed upstream of the positive element of the TNFa gene did not cause repression. Therefore, this repression is very likely mediated by a novel protein(s) which interacts with the AP-2 consensus site in the TRS.
IRF5 and IRF5 Disease-Risk Variants Increase Glycolysis and Human M1 polarization By Regulating Proximal Signaling and Akt2 Activation

Summary Interferon regulatory factor 5 (IRF5) regulates inflammatory M1 macrophage polarization, and disease-associated IRF5 genetic variants regulate pattern-recognition-receptor (PRR)-induced cytokines. PRR-stimulated macrophages and M1 macrophages exhibit enhanced glycolysis, a central mediator of inflammation. We find that IRF5 is needed for PRR-enhanced glycolysis in human macrophages and in mice in vivo. Upon stimulation of the PRR nucleotide binding oligomerization domain containing 2 (NOD2) in human macrophages, IRF5 binds RIP2, IRAK1 and TRAF6. IRF5, in turn, is required for optimal Akt2 activation, which increases expression of glycolytic pathway genes and HIF1A, as well as pro-inflammatory cytokines and M1 polarization. Furthermore, pro-inflammatory cytokines and glycolytic pathways co-regulate each other. demonstrate increased IRF5 expression and increased PRR-induced Akt2 activation, glycolysis, pro-inflammatory cytokines and M1 polarization relative to GG/CC carrier macrophages. Our findings identify that IRF5 disease-associated polymorphisms regulate diverse immunological and metabolic outcomes and provide further insight into mechanisms contributing to the increasingly recognized important role for glycolysis in inflammation. was incubated with pre-cleared lysates at 4°C overnight. Immunoprecipitates were run on 10% SDS-PAGE gels and transferred to PVDF membrane (Bio-Rad, Hercules, CA). IRF5 serine phosphorylation was examined by incubation with an anti-phospho-(Ser) R/KXXpSXP motif antibody (E2, Cell Signaling Technology). Signal was detected by secondary anti-rabbit or anti-mouse IgG DyLight 680 and DyLight 800 antibodies (Thermo Fisher Scientific) with the Odyssey Imager (Li-COR Biosciences, Lincoln, NE). Densitometry was performed using Image J software (NIH).
FXYD 7 is a brain-speci ® c regulator of Na , K-ATPase a 1 ± b isozymes

Recently, corticosteroid hormone-induced factor (CHIF) and the g -subunit, two members of the FXYD family of small proteins, have been identiﬁed as regulators of renal Na,K-ATPase. In this study, we have investigated the tissue distribution and the structural and functional properties of FXYD7, another family member which has not yet been characterized. type bearing N-terminal, post-transla-tionally added modiﬁcations on threonine residues, probably O -glycosylations that are important for in can interact with Na,K-ATPase a 1– b 1, a 2– b 1 and a 3– b 1 but not with a – b 2 it + afﬁnity of a 1– b 1 and a 2– but not of These data suggest that FXYD7 is a novel, tissue- and isoform-speciﬁc Na,K-ATPase regulator which could play an important role in
Inhibition of β -Catenin Signaling in Articular Chondrocytes Results in Articular Cartilage Destruction

Objective— Osteoarthritis is a degenerative joint disease whose molecular mechanism is currently unknown. Wnt/ β -catenin signaling has been demonstrated to play a critical role in the development and function of articular chondrocytes. To determine the role of β -catenin signaling in articular chondrocyte function, we generated Col2a1-ICAT –transgenic mice to inhibit β -catenin signaling in chondrocytes. Methods— The expression of the ICAT transgene was determined by immunostaining and Western blot analysis. Histologic analyses were performed to determine changes in articular cartilage structure and morphology. Cell apoptosis was determined by TUNEL staining and the immunostaining of cleaved caspase 3 and poly(ADP-ribose) polymerase (PARP) proteins. Expression of Bcl-2, Bcl-x L , and Bax proteins and caspase 9 and caspase 3/7 activities were examined in primary sternal MMP-13 expression was also reduced (data not shown). These results suggest that articular In summary, in this study we provide novel evidence that selective inhibition of β -catenin signaling in articular chondrocytes causes articular cartilage destruction in Col2a1-ICAT – transgenic mice. The findings not only suggest that increased cell apoptosis may contribute to completely inhibited. d and e , To further demonstrate FLAG-ICAT transgene expression in vitro, we performed Western blot ( d ) and immunostaining ( e ) assays using primary sternal chondrocytes derived from 3-day-old Col2a1-ICAT –transgenic mice and their WT littermates. Western blot and immunostaining data showed that FLAG-ICAT was detected only in chondrocytes derived from Col2a1-ICAT –transgenic mice and not in those from their WT littermates. f , The expression of β -catenin signaling downstream genes, Tcf3, Tcf4 , and Lef , was examined by reverse transcriptase–polymerase chain reaction assays. The mRNA expression of Tcf3, Tcf4 , and Lef was reduced in chondrocytes derived from Col2a1-ICAT – transgenic mice. (Original magnification × 10 in a ; × 20 in b and e .) DAPI = 4 ′ , 6-diamidino-2-phenylindole.
CRITICAL ROLE OF LARGE CONDUCTANCE VOLTAGE- AND CALCIUM-ACTIVATED POTASSIUM CHANNELS IN LEPTIN-INDUCED NEUROPROTECTION OF N-METHYL-D-ASPARTATE-EXPOSED CORTICAL NEURONS

In the present study, the neuroprotective effects of the adipokine leptin, and the molecular mechanism involved, have been studied in rat and mice cortical neurons exposed to N-methyl-D-Aspartate (NMDA) in vitro . In rat cortical neurons, leptin elicited neuroprotective effects against NMDA-induced cell death which were concentration-dependent (10–100 ng/ml) and largest when the adipokine was preincubated for 2 hours before the neurotoxic stimulus. In both rat and mouse cortical neurons, leptin-induced neuroprotection was fully antagonized by Paxilline (Pax, 0.01–1 μM) and Iberiotoxin (Ibtx, 1–100 nM), two blockers of Ca 2+ - and voltage-activated K + channels (Slo1 BK channels), with EC 50 s (38±10 nM and 5±2 nM for Pax and Ibtx, respectively) close to those reported for Pax- and Ibtx-induced BK channel blockade; the BK channel opener NS1619 (1–30 μM) induced a concentration-dependent protection against NMDA-induced excitotoxicity. Moreover, cortical neurons from mice lacking one or both alleles coding for Slo1 BK channel pore-forming subunits were insensitive to leptin-induced neuroprotection. Finally, leptin exposure dose-dependently (10–100 ng/ml) increased intracellular Ca 2+ levels in rat cortical neurons. In conclusion, our results suggest that Slo1 BK channel activation following increases in intracellular Ca 2+ levels is a critical step for leptin-induced neuroprotection in NMDA-exposed cortical neurons in vitro , thus highlighting leptin-based intervention via BK channel activation as a potential strategy to counteract neurodegenerative diseases. the the neuroprotective of BK channel activation by and the underlying molecular mechanism(s), have assessed in cortical exposed to the ionotropic glutamate receptor agonist N-methyl-D-Aspartate (NMDA), a classical excitotoxic insult. The results obtained indicate that leptin is endowed with significant neuroprotective effects in both rat and mouse cortical neurons exposed to NMDA; the pharmacological blockade of BK channels, or the lack of one ( Slo 1 +/− mice) or both ( Slo 1 −/− mice) Slo 1 alleles fully counteracted leptin-mediated neuroprotection. Furthermore, intracellular Ca 2+ concentration ([Ca 2+ ] i ) in mouse neurons revealed that acute leptin (10–100 ng/ml) application prompted an oscillatory behavior in [Ca 2+ ] i . These results reveal that the activation of BK channels is an obligatory step for leptin-induced neuroprotection, highlighting leptin-based intervention via BK channel activation as a potential strategy to treat neurodegenerative diseases.
Low testosterone is associated with frailty, muscle wasting and physical dysfunction among men receiving hemodialysis: a longitudinal analysis

Background. Despite the high prevalence of frailty among patients receiving hemodialysis, few preventable or treatable contributing causes have been identiﬁed. Hypogonadism is also common in this population and low serum testosterone concentrations share several clinical phenotypes with frailty. We hypothesized that low serum testosterone concentrations would be associated with frailty and several of its individual components. Methods. We used data from 440 men from A Cohort Study To Investigate the Value of Exercise in ESRD/Analysis Designed to Investigate the Paradox of Obesity and Survival in ESRD, a longitudinal study that recruited participants from 14 dialysis centers in Atlanta, GA and the San Francisco, CA Bay Area from 2009 to 2011. We assessed frailty using the Fried Frailty Phenotype. We examined the association between free testosterone (as a continuous and dichotomous variable) and frailty, individual frailty components, sarcopenia, lower extremity function and muscle mass estimation by creatinine and body impedance spectroscopy over 12months using generalized estimating equations. Results. The mean age was 56.1 6 14.2 years and 27% were white. A 50% lower concentration of free testosterone was associated with 1.40-fold higher odds of being frail [95% conﬁdence interval (CI) 1.05–1.53] and 1.40-fold higher odds of becoming frail over 12 months (95% CI 1.07–1.73). This association was mainly due to an association with two components of frailty: grip strength and gait speed. In addition, 50% lower free testosterone concentration was associated with a 1.55-fold higher odds of having sarcopenia (95% CI 1.09–2.02) and 1.72-fold higher odds for developing sarcopenia (95% CI 1.13–2.33) as well as with lower muscle mass and a decrease in muscle mass over 12months as estimated by serum creatinine and by bioelectrical impedance spectroscopy. Conclusion. Serum free testosterone concentration was associated with frailty, physical function, sarcopenia and muscle mass as well as with changes in these outcomes over 12 months. Testosterone replacement may be a feasible therapeutic target toward prevention of frailty, although clinical trials are needed to test this possibility. ABSTRACT Background. Abnormally high estimated glomerular ﬁltration rates (eGFRs) are associated with endothelial dysfunction and frailty. Previous studies have shown that low eGFR is associated with increased morbidity, but few reports address high eGFR. The purpose of this study is to evaluate the association of high eGFR with surgical outcomes in patients undergoing surgery for gastrointestinal malignancies. Methods. We identiﬁed patients who underwent elective surgery for gastrointestinal
E(cid:128)ect of 18 b -glycyrrhetinic acid on electromechanical coupling in the guinea-pig renal pelvis and ureter

1 We have tested the e(cid:128)ect of the gap junction inhibitor, 18 b -glycyrrhetinic acid (18 b GA) on electromechanical coupling in the guinea-pig renal pelvis and ureter by the sucrose gap technique. 2 In the ureter 18 b GA (3– 30 m M ) produced a concentration-dependent inhibition of the spike component of the action potential (AP) and reduced contraction evoked by electrical stimulation. 3 Neurokinin A (NKA) produced a slow depolarization with superimposed APs and phasic contractions of the ureter. 18 b GA (30 m M ) markedly inhibited the depolarization and APs evoked by NKA. However the contractile response was more sustained in the presence than in the absence of 18 b GA. At 100 m M , 18 b GA inhibited the mechanical responses to NKA. 4 KCl (80 m M ) produced APs and phasic contractions followed by sustained depolarization and tonic contraction. At 30 m M 18 b GA markedly inhibited the KCl-evoked APs and phasic contractions without a(cid:128)ecting the sustained responses. At 100 m M 18 b GA inhibited the tonic contraction to KCl. 5 In the renal pelvis 18 b GA (30 m M ) inhibited the amplitude of pacemaker potentials and accompanying contractions and induced the appearance of low-amplitude APs not associated with contraction. 6 We conclude that, up to 30 m M , the action of 18 b GA is consistent with an inhibition of cell-to- cell electrical coupling via gap junctions. The single-unit character of smooth muscles in the guinea-pig upper urinary tract is partly converted to a multi-unit pattern. At high concentrations 18 b GA possesses non speciﬁc e(cid:128)ects which limit its usefulness as a tool for studying the role of gap junctions in smooth muscles. British Journal of Pharmacology (2000) 129, 163 –169
AUDITORY FREQUENCY GENERALIZATION IN THE GOLDFISH (CARASSIUS AURATUS)1

Auditory frequency generalization in the goldfish was studied at five points within the best hearing range through the use of classical respiratory conditioning. Each experimental group received single-stimulus conditioning sessions at one of five stimulus frequencies (100, 200, 400, 800, and 1600 Hz), and were subsequently tested for generalization at eight neighboring frequencies. All stimuli were presented 30 db above absolute threshold. Sig- nificant generalization decrements were found for all subjects. For the subjects conditioned in the range between 100 and 800 Hz, a nearly complete failure to generalize was found at one octave above and below the training frequency. The subjects conditioned at 1600 Hz produced relatively more flat gradients between 900 and 2000 Hz. The widths of the gen- eralization gradients, expressed in Hz, increased as a power function of frequency with a slope greater than one.