gebhart/patrepeval huggingface dataset:
Regulation of ribosomal protein genes: An ordered anarchy (2020)

Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome-producing program and the second is a gene-specific feature responsible for fine-tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre-mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine-tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under: Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation.
The purinergic P2Y14 receptor links hepatocyte death to hepatic stellate cell activation and fibrogenesis in the liver (2022)

Fibrosis contributes to ~45% of deaths in western countries. In chronic liver disease, fibrosis is a major factor determining outcomes, but efficient antifibrotic therapies are lacking. Although platelet-derived growth factor and transforming growth factor-β constitute key fibrogenic mediators, they do not account for the well-established link between cell death and fibrosis in the liver. Here, we hypothesized that damage-associated molecular patterns (DAMPs) may link epithelial cell death to fibrogenesis in the injured liver. DAMP receptor screening identified purinergic receptor P2Y14 among several candidates as highly enriched in hepatic stellate cells (HSCs), the main fibrogenic cell type of the liver. Conversely, P2Y14 ligands uridine 5'-diphosphate (UDP)-glucose and UDP-galactose were enriched in hepatocytes and were released upon different modes of cell death. Accordingly, ligand-receptor interaction analysis that combined proteomic and single-cell RNA sequencing data revealed P2Y14 ligands and P2Y14 receptor as a link between dying cells and HSCs, respectively. Treatment with P2Y14 ligands or coculture with dying hepatocytes promoted HSC activation in a P2Y14-dependent manner. P2Y14 ligands activated extracellular signal-regulated kinase (ERK) and Yes-associated protein (YAP) signaling in HSCs, resulting in ERK-dependent HSC activation. Global and HSC-selective P2Y14 deficiency attenuated liver fibrosis in multiple mouse models of liver injury. Functional expression of P2Y14 was confirmed in healthy and diseased human liver and human HSCs. In conclusion, P2Y14 ligands and their receptor constitute a profibrogenic DAMP pathway that directly links cell death to fibrogenesis.
Reevaluating the Capability of Taq DNA Polymerase: Long PCR Amplification (2007)

We tested the ability of Taq DNA polymerase (Taq) to amplify long DNA fragments and showed that, if the conditions were set properly, Taq could successfully perform the "long PCR" up to 24 kb. The conditions include: (1) longer primers, (2) a 2-step cycling, and (3) a "long buffer." We propose that the most important requirements are the survival rate of Taq at high temperatures and that of the primers against the 5' to 3' exonuclease activity of Taq.
A Locking Compliant Device Inspired by the Anatomy of the Spine (2008)

A device reminiscent of the mammalian spine has been designed and built with the ability to lock each individual joint in a string of ball joints. The assembly may be controlled in a manner similar to other hyper-redundant robots, with the added advantage of locking in a straight or axial position. Locking is achieved by orienting two mating collars in a singular configuration that forces compression against neighboring collars and prohibits bending or rotation. Locking is desirable for added strength in supporting objects, as well as for stabilization and power efficiency when bending is not necessary. The split locking mechanism represents a biologically inspired structure with added strength and stability for use in robotics.
Journal Of The Nepal Medical Association (2003)

ACCOUNT OF THE SECOND ALL NEPAL MEDICAL CONFERENCE KATHMANDU BRANCH NEWS BIRATNAGAR BRANCH NEWS BIRGUNJ BRANCH NEWS RAJBIRAJ BRANCH NEWS NEPALGUNJ LIST OF THE MEMBERS OF NEPAL MEDICAL ASSOCIATION
Glycerol as a sustainable solvent for green chemistry (2010)

Glycerol, an organic waste generated by the biodiesel industry, has been recently proposed as a valuable green solvent. This review summarizes the advantages, disadvantages and potential uses of glycerol as a green solvent for catalysis, organic synthesis, separations and materials chemistry. In particular, through selected examples we show here that glycerol may combine the advantages of water (low toxicity, low price, large availability, renewability) and ionic liquids (high boiling point, low vapour pressure, low solubility in scCO2). More generally, all these reported works contribute to increase the portfolio of available green solvents and afford innovative solutions to the substitution of the conventionally used volatile organic solvents.
Minimum Cost Data Aggregation with Localized Processing for Statistical Inference (2008)

The problem of minimum cost in-network fusion of measurements, collected from distributed sensors via multihop routing is considered. A designated fusion center performs an optimal statistical-inference test on the correlated measurements, drawn from a Markov random field. Conditioned on the delivery of a sufficient statistic for inference to the fusion center, the structure of optimal routing and fusion is shown to be a Steiner tree on a transformed graph. This Steiner-tree reduction preserves the approximation ratio, which implies that any Sterner- tree approximation can be employed for minimum cost fusion with the same approximation ratio. The proposed fusion scheme involves routing packets of two types viz., raw measurements sent for local processing, and aggregates obtained on combining these processed values. The performance of heuristics for minimum cost fusion are evaluated through theory and simulations, showing a significant saving in routing costs, when compared to routing all the raw measurements to the fusion center.
Genetic characterization of the vaccinia virus DNA polymerase: identification of point mutations conferring altered drug sensitivities and reduced fidelity (1991)

We determined that 85 microM aphidicolin was sufficient to block macroscopic plaque formation by vaccinia virus and to cause a 10(4)-fold reduction in viral yield from a wild-type infection. A chemically mutagenized viral stock was passaged sequentially in the presence of drug, and plaque-purified viral stocks resistant to aphidicolin were isolated and characterized. By use of a marker rescue protocol, the lesion in each mutant was found to map within the same 500-bp fragment within the DNA polymerase gene. All of the mutants were found to contain a single nucleotide change in the same codon. In nine of these mutants, the alanine residue at position 498 was changed to a threonine, whereas a 10th mutant sustained a valine substitution at this position. Congenic viral strains which carried the Aphr lesion in an unmutagenized wild-type background were isolated. The Thr and Val mutations were found to confer equivalent levels of drug resistance. In the presence of drug, viral yields were 25% of control levels, and the levels of viral DNA synthesized were 30 to 50% of those seen in control infections. The two mutations also conferred an equivalent hypersensitivity to the cytosine analog 1-beta-D-arabinofuranosylcytosine (araC); strains carrying the Thr mutation were moderately hypersensitive to the pyrophosphate analog phosphonoacetic acid and the adenosine analog araA, whereas the Val mutation conferred acute hypersensitivity to these inhibitors. The Val mutation also conferred a mutator phenotype, leading to a 20- to 40-fold increase in the frequency of spontaneous mutations within the viral stock.
Nature of Driving Force for Protein Folding -- A Result From Analyzing the Statistical Potential (1995)

In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a $20\times 20$ matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we find that the MJ matrix can be accurately reconstructed from its first two principal component vectors as $M_{ij}=C_0+C_1(q_i+q_j)+C_2 q_i q_j$, with constant $C$'s, and 20 $q$ values associated with the 20 amino acids. This regularity is due to hydrophobic interactions and a force of demixing, the latter obeying Hildebrand's solubility theory of simple liquids.
Mining Performance Regression Testing Repositories for Automated Performance Analysis (2010)

Performance regression testing detects performance regressions in a system under load. Such regressions refer to situations where software performance degrades compared to previous releases, although the new version behaves correctly. In current practice, performance analysts must manually analyze performance regression testing data to uncover performance regressions. This process is both time-consuming and error-prone due to the large volume of metrics collected, the absence of formal performance objectives and the subjectivity of individual performance analysts. In this paper, we present an automated approach to detect potential performance regressions in a performance regression test. Our approach compares new test results against correlations pre-computed performance metrics extracted from performance regression testing repositories. Case studies show that our approach scales well to large industrial systems, and detects performance problems that are often overlooked by performance analysts.
On the design of user pairing algorithms in full duplexing wireless cellular networks (2014)

In this paper, we consider a full duplexing (FD) wireless cellular network where a central base station (BS) works in the FD mode while the downlink (DL) and uplink (UL) users work in the time division duplexing (TDD) mode. Since this FD system induces the inter-user interference from UL user to DL user, the main challenge for maximizing the system performances is user pairing that makes a pair of DL user and UL user to use the same radio resource simultaneously. We formulate two optimization problems for user pairing to maximize the cell throughput or minimize the outage probability, and then propose two suboptimal user pairing algorithms with low complexity. The first algorithm is designed in a way where the DL user with a better signal quality has a higher priority to choose its UL user for the throughput maximization. On the contrary, the second algorithm gives the DL user with a worse signal quality a higher priority to choose its UL user for the outage minimization. Simulation results show that the FD system using the proposed user pairing algorithms achieves the optimal performances and significantly outperforms the conventional TDD system in terms of the cell throughput and the outage probability.
Generation of bi-allelic MYBPC3 truncating mutant and isogenic control from an iPSC line of a patient with hypertrophic cardiomyopathy (2021)

MYBPC3 is the most frequently affected gene in hypertrophic cardiomyopathy (HCM), which is an autosomal-dominant cardiac disease caused by mutations in sarcomeric proteins. Bi-allelic truncating MYBPC3 mutations are associated with severe forms of neonatal cardiomyopathy. We reprogrammed skin fibroblasts from a HCM patient carrying a heterozygous MYBPC3 truncating mutation into human induced pluripotent stem cells (iPSC) and used CRISPR/Cas9 to generate bi-allelic MYBPC3 truncating mutation and isogenic control hiPSC lines. All lines expressed pluripotency markers, had normal karyotype and differentiated into endoderm, ectoderm and cardiomyocytes in vitro. This set of three lines provides a useful tool to study HCM pathomechanisms.
The prediction of pressure difference in a downcomer pipe during a depressurization process (1984)

Verification a l'aide de donnees experimentales de la validite de 2 methodes numeriques de resolution des equations de l'ecoulement diphasique transitoire monodimensionnel dans un ecoulement descendant en conduite verticale produit par depressurisation
Single-photon modulation spectrum (2014)

We present a robust method of single-photon modulation by directly modulating the single photons and observe its frequency spectrum. Compared with conventional photon counting technique, the single-photon modulation spectrum shows that the method could not only realize high-frequency modulation but also obtain higher signal-to-noise ratio. Moreover, the theoretical calculations show good agreement with the experimental results.
Flexor digitorum longus tendon transfer to the navicular: tendon-to-tendon repair is stronger compared with interference screw fixation (2018)

Minimal tendon displacement of less than 2 mm occurred during cyclic testing in both groups. The two premature failures and significantly reduced load to failure observed in the ISF group, however, indicate that the traditional TT technique is more robust. Regarding clinical relevance, this study suggests that early active range of motion and protected weight bearing may be safe following FDL tendon transfer for stage 2 tibialis posterior tendon dysfunction.
An Experimental Study on Structural Performance of Welded Built-up Square CFT Stub Columns (2008)

Welded built-up square tubes are manufactured by flare welding at the center of the column width for cold-formed L-shaped four-piece plates and improved composite effect of concrete and steel by vertical inner anchor. Also, the axial resistance of concrete is increased by the thinness of the steel column, and the composite effect of concrete and steel prevents the steel column from local buckling. In this study, we introduced a manufacturing method of built-up square column steel square concrete-filled tubular column with vertical inner anchor and superior structural performance of the square stub column verified by the structural test for 15 specimens with parameters of shape of tube (built-up square tube, general steel tube), width over thickness of the steel tube (B/t=50, 58, 67) and the strength of concrete (f'c=10MPa, 50MPa).
Breadth of humoral immune responses to the C-terminus of the circumsporozoite protein is associated with protective efficacy induced by the RTS,S malaria vaccine (2021)

The circumsporozoite protein (CSP) is the main surface antigen of malaria sporozoites, a prime vaccine target, and is known to have polymorphisms in the C-terminal region. Vaccines using a single allele may have lower efficacy against genotypic variants. Recent studies have found evidence suggesting the efficacy of the CSP-based RTS,S malaria vaccine may be limited against P. falciparum CSP alleles that diverge from the 3D7 vaccine allele, particularly in this polymorphic C-terminal region. In order to assess the breadth of the RTS,S-induced antibody responses against CSP C-terminal antigenic variants, we used a novel multiplex assay to measure reactivity of serum samples from a recent RTS,S study against C-terminal peptides from 3D7 and seven additional CSP alleles that broadly represent the genetic diversity found in circulating P. falciparum field isolates. We found that responses to the variants showed, on average, a ~ 30-fold reduction in reactivity relative to the vaccine-matched 3D7 allele. The extent of this reduction, ranging from 21 to 69-fold, correlated with the number of polymorphisms between the variants and 3D7. We calculated antibody breadth of each sample as the median relative reactivity to the seven CSP variants compared to 3D7. Surprisingly, protection from 3D7 challenge in the RTS,S study was associated with higher C-terminal antibody breadth. These findings suggest CSP C-terminal-specific avidity or fine-specificity may play a role in RTS,S-mediated protection and that breadth of C-terminal CSP-specific antibody responses may be a marker of protection.
P505 Real-world short-term effectiveness of ustekinumab in Crohn’s disease: Results from the ENEIDA Registry (2019)

Ustekinumab is a monoclonal antibody targeting interleukins 12 and 23. Its effectiveness in clinical practice has not yet been demonstrated. The aim of this study was to assess the real-world, short-term effectiveness of ustekinumab in medically refractory Crohn’s disease (CD) (CROHNUSK study). Multi-centre study of CD patients receiving ustekinumab after June 2017 (when it was approved in Spain) and at the recommend dose (a single iv infusion of 6 mg/kg followed by a sc injection of 90 mg at Week 8). The Harvey‐Bradshaw Index (HBI) was used to evaluate clinical remission (HBI score ≤4). Values for HBI, C-reactive protein (CRP), and faecal calprotectin (FC) were recorded at baseline and at Weeks 8 and 14. Demographic and clinical data, endoscopy at baseline when available, previous treatments, adverse events (AEs), and hospitalisations were documented. Possible predictors of clinical remission were examined. A total of 305 CD patients were analysed (Table 1). Characteristics of study population At baseline, 217 (72%) had an HBI score of >4 points. Of these, 101 (47%) and 126 (58%) achieved clinical remission at Weeks 8 and 14, respectively. Of the 109 patients who were on corticosteroids at baseline, 52 (48%) were in corticosteroid-free remission at Week 14. FC levels returned to normal (<250 µg/g) in 66 (22%) and 74 (24%) patients at Weeks 8 and 14, respectively. CRP returned to normal levels (<3 mg/l) in 122 (40%) and 106 (35%) patients at Week 8 and 14, respectively. HBI, FC, and CRP values over time are shown in Figure 1. HBI, FC, and CRP values over time. AEs were recorded in 12% of patients. A total of 40 patients (13%) were hospitalised, in 7 cases owing to AEs. Intolerance to the most recent anti-TNF agent and fewer previous anti-TNF agents were associated with clinical remission at Week 14. Endoscopic severity, but not previous vedolizumab treatment, was associated with poor response. This is the first study to show the real-world safety and effectiveness of ustekinumab in a large cohort of highly refractory CD patients.
Supplementary Table 2 from A Genome-Wide Scan Identifies Variants in <i>NFIB</i> Associated with Metastasis in Patients with Osteosarcoma (2023)

&lt;p&gt;Relationship of variables to metastasis at diagnosis in the discovery set.&lt;/p&gt;
Structural Control of Hybrid Colloidal Particle Surface by Plasma-etching Treatment (2016)

A reactive-ion etching system was used to control the surface of gold–polystyrene hybrid colloidal particles with an eccentric structure, and a function of the etched particles was demonstrated as ...
Explicit and implicit measures of expectancy and related alcohol cognitions: A meta-analytic comparison. (2010)

Implicit measures assess the influence of past experience on present behavior in the absence of respondents' awareness of that influence. Application of implicit measurement to expectancy and related alcohol cognition research has helped elucidate the links between alcohol-related experiences, the functioning of alcohol-related memory, and alcohol-related behavior. Despite these advances, a coherent picture of the role of implicit measurement has been difficult to achieve because of the diversity of implicit measures used. Two central questions have emerged: Do implicit measures assess a distinct aspect of the alcohol associative memory domain not accessible via explicit measurement; when compared with explicit measurement, do they offer unique prediction of alcohol consumption? To address these questions, the authors conducted a meta-analysis of studies using both implicit and explicit measures of alcohol expectancy and other types of alcohol-related cognition. Results indicate that implicit and explicit measures are weakly related, and although they predict some shared variance in drinking, each also contributes a unique component. Results are discussed in the context of the theoretical distinction made between the 2 types of measures.
Re: Successful Testicular Sperm Retrieval in Adolescents with Klinefelter Syndrome Treated with at Least 1 Year of Topical Testosterone and Aromatase Inhibitor (2014)

No AccessJournal of UrologyAdult Urology1 Jul 2014Re: Successful Testicular Sperm Retrieval in Adolescents with Klinefelter Syndrome Treated with at Least 1 Year of Topical Testosterone and Aromatase Inhibitor Craig NiederbergerMD Craig NiederbergerCraig Niederberger More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2014.04.060AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Successful Testicular Sperm Retrieval in Adolescents with Klinefelter Syndrome Treated with at Least 1 Year of Topical Testosterone and Aromatase Inhibitor." The Journal of Urology, 192(1), pp. 180–181 © 2014 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 192Issue 1July 2014Page: 180-181Supplementary Materials Advertisement Copyright & Permissions© 2014 by American Urological Association Education and Research, Inc.MetricsAuthor Information Craig Niederberger More articles by this author Expand All Advertisement PDF downloadLoading ...
Comprehensive overview of COVID-19-related respiratory failure: focus on cellular interactions (2022)

The pandemic outbreak of coronavirus disease 2019 (COVID-19) has created health challenges in all parts of the world. Understanding the entry mechanism of this virus into host cells is essential for effective treatment of COVID-19 disease. This virus can bind to various cell surface molecules or receptors, such as angiotensin-converting enzyme 2 (ACE2), to gain cell entry. Respiratory failure and pulmonary edema are the most important causes of mortality from COVID-19 infections. Cytokines, especially proinflammatory cytokines, are the main mediators of these complications. For normal respiratory function, a healthy air-blood barrier and sufficient blood flow to the lungs are required. In this review, we first discuss airway epithelial cells, airway stem cells, and the expression of COVID-19 receptors in the airway epithelium. Then, we discuss the suggested molecular mechanisms of endothelial dysfunction and blood vessel damage in COVID-19. Coagulopathy can be caused by platelet activation leading to clots, which restrict blood flow to the lungs and lead to respiratory failure. Finally, we present an overview of the effects of immune and non-immune cells and cytokines in COVID-19-related respiratory failure.
ChemInform Abstract: Enantioselective Allyltitanation. Application to the Synthesis of Lactone Units Related to Compactin and Mevinolin. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.