gebhart/patrepeval huggingface dataset:
Piscine myocarditis virus (PMCV) in wild Atlantic salmon Salmo salar (2012)

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of sea-farmed Atlantic salmon Salmo salar L., but CMS-like lesions have also been found in wild Atlantic salmon. In 2010 a double-stranded RNA virus of the Totiviridae family, provisionally named piscine myocarditis virus (PMCV), was described as the causative agent of CMS. In the present paper we report the first detection of PMCV in wild Atlantic salmon. The study is based on screening of 797 wild Atlantic salmon by real-time RT-PCR. The samples were collected from 35 different rivers along the coast of Norway, and all individuals included in the study were classified as wild, based on visual appearance and scale reading. Two samples tested positive during PCR analysis, and the results were confirmed by sequencing.
Molecular and cellular mechanisms of sulfur mustard-induced lesions of human skin (1992)

formation in human skin are proposed.This thesis also contains a chapter on the application of a cultured skin equivalent to promote the healing of extended or slowly improving skin defects.Experiments with this cultured skin equivalent can be considered as a "spin off' of the development of In vitro models of human skin for dermatotoxic research.In chapter 9 the successful treatment of venous leg ulcers with these skin grafts, composed of a dermal and an epidermal component, is reported. REFERENCES
The Electrochemical Behavior of Bunte Salts (1997)

Abstract A comparative cyclic voltammetric study of the Bunte salts adsorption and oxidation of the electrode reaction products on gold and platinum electrodes was performed. These were irreversibly adsorbed on both metals, and were oxidized to disulfides (on gold in basic solution) and in the anodic range of platinum electrode potentials to form water soluble sulfates. Also Bunte salts were oxidized directly from the bulk of solution. Platinum was found to show stronger (than gold) electrocatalytic properties to adsorb and oxidize the electrode reaction products of Bunte salts
GEF-H1 Couples Nocodazole-induced Microtubule Disassembly to Cell Contractility via RhoA (2008)

The RhoA GTPase plays a vital role in assembly of contractile actin-myosin filaments (stress fibers) and of associated focal adhesion complexes of adherent monolayer cells in culture. GEF-H1 is a microtubule-associated guanine nucleotide exchange factor that activates RhoA upon release from microtubules. The overexpression of GEF-H1 deficient in microtubule binding or treatment of HeLa cells with nocodazole to induce microtubule depolymerization results in Rho-dependent actin stress fiber formation and contractile cell morphology. However, whether GEF-H1 is required and sufficient to mediate nocodazole-induced contractility remains unclear. We establish here that siRNA-mediated depletion of GEF-H1 in HeLa cells prevents nocodazole-induced cell contraction. Furthermore, the nocodazole-induced activation of RhoA and Rho-associated kinase (ROCK) that mediates phosphorylation of myosin regulatory light chain (MLC) is impaired in GEF-H1-depleted cells. Conversely, RhoA activation and contractility are rescued by reintroduction of siRNA-resistant GEF-H1. Our studies reveal a critical role for a GEF-H1/RhoA/ROCK/MLC signaling pathway in mediating nocodazole-induced cell contractility.
Incorporating Point of Interconnect within the Australian National Broadband Network (2011)

The number of Point Of Interconnects (PoI) is a critical factor in the proposed Australian National Broadband Network (NBN) because there is a relationship to the Capital and Operational Expenditure. Initially a centralized model with 14 P0Is in 7 major cities was proposed and after a critical evaluation of the mode the Australian Competition and Consumer Commission proposed a decentralized option with more than 200 PoI. The two models are still being debated by the many stakeholders such as the Federal Government, service providers, backhaul access providers and the general public through the media. One of the NBN objectives is to promote innovative value added services to customers through enhanced competition amongst all service providers. The problem is to find the optimal number of PoI and their locations whilst minimizing cost and maintaining objectives. An analysis is provided in this paper of two potential traffic aggregation techniques: centralized and decentralized PoI models. A proof of concept model used to compare the two models is presented. Video streaming, Voice over Internet Protocol and File Transfer Protocol applications are used as broadband traffic and Weighted Fair Queuing was taken as the quality of service scheme.
Onset of Dielectric Breakdown in Silicon Oxynitride Thin Films (2006)

Abstract not Available.
Bioluminescent Probes for Imaging Biology beyond the Culture Dish (2017)

Bioluminescence with luciferase-luciferin pairs is an attractive method for surveying cells in live tissues and whole organisms. Recent advances in luciferin chemistry and luciferase engineering are further expanding the scope of the technology. It is now possible to spy on cells in a variety of deep tissues and visualize multicellular interactions, feats that are enabling new questions to be asked and new ideas to be explored. This perspective piece highlights recent successes in bioluminescent probe development and their applications to imaging in live cells, tissues, and animals.
Detection of antibodies to a linear epitope on the major coat protein (L1) of human papillomavirus type‐16 (HPV‐16) in sera from patients with cervical intraepithelial neoplasia and children (1992)

Antibodies to the major (L1) coat protein of human papillomavirus type 16 (HPV-16) in sera from patients with cervical intra-epithelial neoplasia (CIN) have been investigated by means of recombinant proteins and synthetic peptides. When L1-HPV-16 fusion proteins were used in immunoblot assays, no antibody reactivity was found in sera from 52 patients with CIN or from 21 unrelated children. Amino-acid sequence analyses indicated that L1-HPV-16 amino acids 473 to 492 may contain an HPV-16 type-restricted epitope since the greatest diversity occurs in this region. In the ELISA, seropositivity to peptides 473 to 492 was more common among CIN patients whose biopsies contained HPV-16 DNA (91%, 21 of 23) than among their children (24%, 5 of 21; p less than 0.001) or other CIN patients with HPV-16 DNA-negative biopsies (66%, 19 of 29; p less than 0.05), but was unrelated to the severity of the CIN lesion. Antibodies to L1-HPV-16 peptide 473 to 492 among seropositive CIN patients cross-reacted with the analogous L1-HPV-33, but not with the L1-HPV-6b peptide, and were predominantly IgM. In contrast, antibodies which recognized a less variable region of L1-HPV-16 (amino acids 279 to 293) showed no association with HPV-16 DNA status. Seropositivity to the L1-HPV-6b (amino acids 473-492) was less frequent (33%) among CIN patients and unassociated with HPV-16 DNA status (p greater than 0.1); however 51% (37 of 72) of patients with genital warts had antibodies to this peptide.
Prospective, randomized controlled trial on<i>Lactobacillus rhamnosus</i>in infants with moderate to severe atopic dermatitis (2006)

Our results could not confirm LGG as an effective treatment of AD in infancy.
Partner Molecules of Accessory Protein Vpr of the Human Immunodeficiency Virus Type 1 (2004)

Vpr (Viral protein-R) of the Human Immunodeficiency Virus type-1 is a 14-kDa virion-associated protein, conserved in HIV-1, -2 and the Simian Immunodeficiency Virus (SIV). Vpr is incorporated into the virion, travels to the nucleus, and has multiple activities including promoter activation, cell cycle arrest at the G2/M transition and apoptosis induction. Through these activities, Vpr is thought to influence not only viral replication but also numerous host cell functions. These functions may be categorized in three groups depending on the domains of Vpr that support them: (1) functions mediated by the amino terminal portion of Vpr, like virion packaging; (2) functions mediated by the carboxyl terminal portion such as cell cycle arrest; and (3) functions that depend on central alpha-helical structures such as transcriptional activation, apoptosis and subcellular shuttling. Association of these activities to specific regions of the Vpr molecule appears to correlate to the host/viral molecules that interact with corresponding portion of Vpr. They include Gag, host transcription factors/coactivators such as SP1, the glucocorticoid receptor, p300/CREB-binding protein and TFIIB, apoptotic adenine nucleotide translocator, cyclophilin A and 14-3-3 proteins. The properties of Vpr molecule has made it difficult to assess its function and determine the true cellular interactors. Further studies on Vpr function are needed to fully assess the function of this important early regulatory molecule of HIV and other lentiviruses.
Bridging the programming gap between persistent and volatile memory using WrAP (2013)

Advances in memory technology are promising the availability of byte-addressable persistent memory as an integral component of future computing platforms. This change has significant implications for software that has traditionally made a sharp distinction between durable and volatile storage. In this paper we describe a software-hardware architecture, WrAP, for persistent memory that provides atomicity and durability while simultaneously ensuring that fast paths through the cache, DRAM, and persistent memory layers are not slowed down by burdensome buffering or double-copying requirements. Trace-driven simulation of transactional data structures indicate the potential for significant performance gains using the WrAP approach.
One-electron reduction potentials of substituted nitroimidazoles measured by pulse radiolysis (1976)

The differences between the one-electron reduction potentials at pH 7 (E17) of a quinone couple (Q/Q–), and seventeen nitroimidazole couples (S/S–) were estimated for S = substituted 2-, 4-, and 5-nitroimidazoles, by measuring the equilibrium constant Kc of the reaction S–+ Q ⇌ S + Q–. The radical-ions S– and Q– were generated by pulse radiolysis, and their concentrations measured spectrophotometrically after the equilibrium was attained (typically 1–50 µs after the pulse). Estimated values of E17(S/S–) range from –243 mV for S = 5-formyl-1-methyl-2-nitroimidazole; –398 mV for 1-(2-hydroxyethyl)-2-nitroimidazole; –486 mV for 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole to ⩽–527 mV for 4-nitroimidazole (all ± 10 mV). In the absence of other factors, 2-nitroimidazoles have more positive E17 values than the 5-nitro-analogues, and 4-nitroimidazoles are still weaker oxidants. Substitution with electron-withdrawing groups in the side chain can increase E17 by amounts greater than the difference between 2- and 5-nitroimidazoles. These values are based on E17(Q/Q–)=–244 ± 7 mV for duroquinone, and –375 ± 8 mV for 9,10-anthraquinone-2-sulphonate. These reference potentials were determined by measuring Kc for one-electron transfer equilibria between the quinones and 1,1′-dibenzyl-4,4′-bipyridylium ion (BV2+), assuming E17(BV2+/BV+)=–354 ± 6 mV. The usefulness of viologens as redox indicators in this type of study is discussed.
Androgen receptor CAG repeat lengths in prostate cancer: correlation with age of onset. (1996)

The androgen receptor (AR) is a structurally conserved member of the nuclear receptor superfamily. The amino-terminal domain is required for transcriptional activation and contains a region of polyglutamine encoded by CAG trinucleotide repeats. In humans, the number of CAG repeats is polymorphic; the average number is 22 in Caucasian males. Expansion of CAG repeats in the AR has clinical implications for human disease. As androgen influences prostate cancer growth, polymorphisms in CAG repeat length may affect the clinical course of patients with prostate cancer. To test for an association between clinical parameters of human prostate cancer and CAG repeat length, we analyzed normal lymphocyte DNA from 109 patients. The CAG region of the AR was amplified by the PCR. Reaction products were then amplified using end-labeled internal primers, cut at the internal PstI site and assayed on sequencing gels using a sequence ladder as a size standard. Sequence analysis of several samples validated this method for measurement of CAG repeat number. The median age of patients was 63 yr (range, 42-83), with 104 Caucasian, 2 African American, 1 Asian, and 2 other racial origin. The median repeat length was 25 for patients with stage A, 22 for patients with stage B, 22 for patients with stage C, and 23 for patients presenting with stage D disease. A significant correlation between CAG repeat length and age at onset was observed, whereas correlations with stage, level of prostate-specific antigen at diagnosis, and time to prostate-specific antigen relapse were not significant. Shorter CAG repeat lengths may be associated with the development of prostate cancer in men at a younger age. These data suggest that CAG repeat length can affect the risk of developing prostate cancer.
Optical trapping of nonspherical particles in the T-matrix formalism (2007)

The theory of the trapping of nonspherical particles in the focal region of a high-numerical-aperture optical system is formulated in the framework of the transition matrix approach. Both the case of an unaberrated lens and the case of an aberrated one are considered. The theory is applied to single latex spheres of various sizes and, when the results are compared with the available experimental data, a fair agreement is attained. The theory is also applied to binary clusters of spheres of latex with a diameter of 220nm in various orientations. Although, in this case we have no experimental data to which our results can be compared, we get useful indications for the trapping of nonspherical particles. In particular, we find substantial agreement with recent results on the trapping of prolate spheroids in aberrated gaussian fields [S. H. Simpson and S. Hanna, J. Opt.Soc. Am. A 24, 430 (2007)].
The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs (2017)

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNA<sup>Lys</sup>(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.
Robust Separation of Reflection from Multiple Images (2014)

When one records a video/image sequence through a transparent medium (e.g. glass), the image is often a superposition of a transmitted layer (scene behind the medium) and a reflected layer. Recovering the two layers from such images seems to be a highly ill-posed problem since the number of unknowns to recover is twice as many as the given measurements. In this paper, we propose a robust method to separate these two layers from multiple images, which exploits the correlation of the transmitted layer across multiple images, and the sparsity and independence of the gradient fields of the two layers. A novel Augmented Lagrangian Multiplier based algorithm is designed to efficiently and effectively solve the decomposition problem. The experimental results on both simulated and real data demonstrate the superior performance of the proposed method over the state of the arts, in terms of accuracy and simplicity.
Thermophysical Properties of the Liquid Ga–In–Sn Eutectic Alloy (2014)

Among different Ga-based alloys the properties of the Ga–In–Sn eutectic alloy make it particularly suitable for many applications, in particular as it is liquid at room temperature. However, the experimental data on its thermophysical properties are rather discrepant. In this work, the electrical and thermal conductivity, thermoelectric power, viscosity, surface tension and density of the Ga–In–Sn eutectic have been investigated in the temperature range between the melting temperature and 700 K. The experimental results obtained are compared with the data available in the literature.
Construction of Spiro[pyrrolidine‐3,3′‐oxindoles] — Recent Applications to the Synthesis of Oxindole Alkaloids (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
CD122 blockade restores immunological tolerance in autoimmune type 1 diabetes via multiple mechanisms (2018)

Signaling through IL-2/IL-15Rβ (CD122) is essential for the differentiation and function of T cells and NK cells. A mAb against CD122 has been implicated to suppress autoimmune type 1 diabetes (T1D) development in animal models. However, the mechanisms remain poorly understood. We find that in vivo administration of an anti-CD122 mAb (CD122 blockade) restores immune tolerance in nonobese diabetic (NOD) mice via multiple mechanisms. First, CD122 blockade selectively ablates pathogenic NK cells and memory phenotype CD8+ T cells from pancreatic islets. In contrast, islet CD4+Foxp3+ Tregs are only mildly affected. Second, CD122 blockade suppresses IFN-γ production in islet immune cells. Third, CD122 blockade inhibits the conversion of islet Th17 cells into diabetogenic Th1 cells. Furthermore, a combination of anti-CD122 mAb and Treg-trophic cytokines (IL-2 or IL-33) enhances the abundance and function of islet Tregs. In summary, these data provide crucial mechanistic insights into CD122 blockade-mediated immunoregulation and support therapeutic benefits of this combinational treatment in T1D.
A reporter system for translational readthrough of stop codons in human cells (2012)

Agents to induce readthrough of premature termination codons (PTCs) are useful research tools and potential therapeutics. Reporters used to detect PTC readthrough are gene-specific and thus are not suited to for general assessment of readthrough activity or in cases where PTC-inactivated genes are unknown. Here we describe a GFP-based reporter construct pMHG-W57* which is capable of detecting dose-dependent drug-induced PTC readthrough both by fluorescence microscopy and flow cytometry. pMHG-W57* may be used as a general indicator of PTC readthrough in living cells and obviates the need for gene-specific recoding sequences in reporter constructs.
Blood group O protects against severe <i>Plasmodium falciparum</i> malaria through the mechanism of reduced rosetting (2007)

Malaria has been a major selective force on the human population, and several erythrocyte polymorphisms have evolved that confer resistance to severe malaria. Plasmodium falciparum rosetting, a parasite virulence phenotype associated with severe malaria, is reduced in blood group O erythrocytes compared with groups A, B, and AB, but the contribution of the ABO blood group system to protection against severe malaria has received little attention. We hypothesized that blood group O may confer resistance to severe falciparum malaria through the mechanism of reduced rosetting. In a matched case-control study of 567 Malian children, we found that group O was present in only 21% of severe malaria cases compared with 44-45% of uncomplicated malaria controls and healthy controls. Group O was associated with a 66% reduction in the odds of developing severe malaria compared with the non-O blood groups (odds ratio 0.34, 95% confidence interval 0.19-0.61, P < 0.0005, severe cases versus uncomplicated malaria controls). In the same sample set, P. falciparum rosetting was reduced in parasite isolates from group O children compared with isolates from the non-O blood groups (P = 0.003, Kruskal-Wallis test). Statistical analysis indicated a significant interaction between host ABO blood group and parasite rosette frequency that supports the hypothesis that the protective effect of group O operates through the mechanism of reduced P. falciparum rosetting. This work provides insights into malaria pathogenesis and suggests that the selective pressure imposed by malaria may contribute to the variable global distribution of ABO blood groups in the human population.
Kinetic and Regiospecific Interrogation of Covalent Intermediates in the Nonribosomal Peptide Synthesis of Yersiniabactin (2004)

For interrogation of enzyme-bound intermediates in nonribosomal peptide synthetases (NRPSs), mass spectrometry is used to read out the kinetics and substrate specificity of this medicinally important class of enzymes. The protein HMWP2 (230 kDa) catalyzes 11 chemical reactions, four of which could be resolved by fast quench approaches combined with mass spectrometry. The rate of complex intermediate accumulation at the PCP1 active site was observed to occur with a rate of 19 s(-1), with the rate of cysteine acylation faster than that of intermediate translocation. Use of alternative substrates for salicylic acid (at the ArCP carrier domain) and l-cysteine (at the PCP1 carrier domain) revealed a high penalty for omission of the salicyl alcohol. For some substrates, large discrepancies were found between prior adenylation assays and the current MS-based readouts. Indirect evidence for condensation via a thiolate attack (vs an amino group) was also accumulated. This is the first report to correlate the percent occupancy of multiple active sites in parallel with kinetic and structural resolution of intermediates and provides new evidence of interdomain and intermodule communication within thiotemplate assembly lines.
30,000 Feet Overview of Lifestyle Medicine (2023)

Chronic diseases account for the highest morbidity and mortality among adults and, increasingly, adolescents and young adults in the United States. This imposes great economic stress on the healthcare system. Chronic diseases can largely be attributed to several key harmful lifestyle behaviors, including poor diet, low physical activity, substance abuse, and stress, to mention just a few. Recent research demonstrates that sustained healthy lifestyle behaviors can not only prevent and treat but may even reverse many of these chronic diseases. The American College of Lifestyle Medicine (ACLM) defines Lifestyle Medicine (LM) as "the use of evidence-based lifestyle therapeutic intervention—including a whole-food, plant-predominant eating pattern, regular physical activity, restorative sleep, stress management, avoidance of risky substances, and positive social connection—as a primary modality, delivered by clinicians trained and certified in this specialty, to prevent, treat, and often reverse chronic disease.” ACLM has worked to establish and update LM core competencies over the last decade. Many training programs have adopted evidence-based LM didactic and clinical training across various health professions students to ensure trainees meet these competencies. We aim to provide a brief overview of LM, discuss the six pillars of LM: nutrition, physical activity, avoidance of risky substances, restorative sleep, stress reduction, and positive social connection, and discuss their significance in wellness from the patient’s and the physician’s perspectives.