gebhart/patrepeval huggingface dataset:
Hydroxamate-based metalloprotease inhibitor blocks shedding of L-selectin adhesion molecule from leukocytes: functional consequences for neutrophil aggregation (1996)

L-selectin is an adhesion molecule that mediates the recruitment of neutrophils to inflammatory sites and initiates the migration of lymphocytes into the peripheral lymph nodes. In response to cell activation, L-selectin is shed from the cell surface, and altered levels of functional soluble L-selectin are detected in the plasma of patients suffering from numerous inflammatory diseases as well as AIDS. The mechanism that regulates L-selectin shedding is poorly understood. Here we show that a hydroxamate-based metalloprotease inhibitor, N-(D,L-[2-(hydroxyaminocarbonyl)- methyl]-4-methylpentano)-L-3-(tert-butyl)-alanyl-L-alanine, 2-aminoethyl amide, which blocks leukocyte TNF, TNF receptor, and IL-6 receptor release, also inhibits L-selectin shedding from neutrophils, eosinophils, and lymphocytes. Moreover, we show that such inhibition of L-selectin shedding profoundly affects neutrophil aggregation and permits reaggregation in the presence of a heterologous stimulus.
Screened surface waves and some possible applications (1965)

A pure surface wave requires, in principle, unbounded space outside the supporting surface, thus permitting the field in the transverse plane to decay, without obstruction, to zero at an infinite distance from the surface. Such a wave cannot therefore be contained within a screen, unless the bounding surface matches precisely the field impedance at the point of its location. A surface of this kind must have capacitive reactance and a small negative resistance, which implies a subsidiary generator. A second surface wave, supported on the inside of the screen, can be set up to satisfy the boundary conditions, and the paper discusses arrangements that should meet the requirements, enabling full or partial screening to be achieved. Moreover it appears that the dual surface wave proposed may have a lower attenuation in a straight guide than the corresponding TEM mode.
A Putative Role for Psoriasin in Breast Tumor Progression (2005)

Psoriasin (S100A7) was identifi;ed as a gene highly expressed in psoriatic keratinocytes and highly and more frequently expressed in ductal carcinoma in situ (DCIS) than in invasive breast carcinomas (IBC), suggesting a potential role in tumor progression. Psoriasin expression is associated with poor prognostic factors in both DCIS and IBC. Several putative functions have been proposed for psoriasin in various disease types, but none of these can fully explain its involvement in breast tumor progression. Here, we show that down-regulation of endogenous psoriasin expression via stable short hairpin RNAs in a human IBC cell line (MDA-MB-468) increases cell migration and invasion without influencing cell proliferation and survival in vitro but inhibits tumor growth in vivo. These seemingly paradoxical results are potentially explained by the dramatic up-regulation and down-regulation of matrix metalloproteinase-13 and vascular endothelial growth factor (VEGF), respectively, observed in cells with decreased psoriasin levels compared with controls. Correlating with this, high psoriasin expression in human IBC is associated with increased angiogenesis and worse clinical outcome, and psoriasin mRNA levels are coordinately regulated with VEGF and other genes related to hypoxia and mitochondrial reactive oxygen species (ROS). Based on these results, we propose that psoriasin may play a role in breast tumor progression by promoting angiogenesis and enhancing the selection for cells that overcome its anti-invasive function. This hypothesis may explain why psoriasin expression is highest in high-grade and/or estrogen receptor-negative tumors, as these are associated with increased hypoxia and ROS, a setting in which the angiogenic effects of psoriasin are most important.
Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression. (1987)

The coding sequences of genes in the yeast Saccharomyces cerevisiae show a preference for 25 of the 61 possible coding triplets. The degree of this biased codon usage in each gene is positively correlated to its expression level. Highly expressed genes use these 25 major codons almost exclusively. As an experimental approach to studying biased codon usage and its possible role in modulating gene expression, systematic codon replacements were carried out in the highly expressed PGK1 gene. The expression of phosphoglycerate kinase (PGK) was studied both on a high-copy-number plasmid and as a single copy gene integrated into the chromosome. Replacing an increasing number (up to 39% of all codons) of major codons with synonymous minor ones at the 5' end of the coding sequence caused a dramatic decline of the expression level. The PGK protein levels dropped 10-fold. The steady-state mRNA levels also declined, but to a lesser extent (threefold). Our data indicate that this reduction in mRNA levels was due to destabilization caused by impaired translation elongation at the minor codons. By preventing translation of the PGK mRNAs by the introduction of a stop codon 3' and adjacent to the start codon, the steady-state mRNA levels decreased dramatically. We conclude that efficient mRNA translation is required for maintaining mRNA stability in S. cerevisiae. These findings have important implications for the study of the expression of heterologous genes in yeast cells.
Design and analysis of DNA strand displacement devices using probabilistic model checking (2012)

Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DNA strand displacement (DSD) programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker prism, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs.
Porcine Stentless Bioprostheses: Prevention of Aortic Wall Calcification by Dye‐Mediated Photo‐Oxidation (2003)

Photo-oxidation of a porcine stentless valve prevents calcification not only in the cusps but also in the aortic wall portion.
Fibronectin (1983)

Fibronectin, a glycoprotein, is present in plasma and extracellular matrix and is responsible for cellular adhesion. With the use of affinity chromatography, we purified plasma fibronectin from two patients with trophic corneal ulcer and persistent epithelial defect after conventional therapy was ineffective. Reepithelialization began three days after initiation of treatment with autologous purified fibronectin eyedrops, and the epithelial defects disappeared completely within three weeks. No recurrence was observed after treatment ended. By modifying the original chromatographic procedure, we were able to obtain purified fibronectin in two hours, which allowed us to treat outpatients as well as inpatients.
Open reading frame 5 of porcine reproductive and respiratory syndrome virus as a cause of virus-induced apoptosis (1996)

The gene product of open reading frame 5 (p25) of porcine reproductive and respiratory syndrome (PRRS) virus has been expressed by coinfection of culture cells with vaccinia virus expressing the T7 RNA polymerase and a recombinant vaccinia virus encoding the open reading frame 5 gene under the T7 promoter and the encephalomyocarditis virus internal ribosome entry site. In spite of the reported efficiency of the expression system, very poor accumulation of p25 protein was observed and a strong cytotoxicity was produced in the doubly infected cells. This cell toxicity was shown to occur by induction of apoptosis, as indicated by nucleosome ladder formation, chromatin condensation, and rRNA degradation. Apoptosis induction was also observed after infection of cultured cells with an adapted PRRS virus strain and after infection of swine macrophage cells with a PRRS virus field strain. Contrary to the observations made for other cases of virus-induced apoptosis, we could not prevent p25 protein-induced apoptosis by using a cell line permanently expressing Bcl-2 protein.
Ultraprecise studies of the thermal expansion coefficient of diamond using backscattering x-ray diffraction (2011)

The linear thermal expansion coefficient of diamond crystals of type IIa and type Ia was measured in the temperature range from 10 to 295 K. Neither negative thermal expansion nor any substantial difference in the thermal expansion coefficient in crystals of the different types were observed. An empirical expression was obtained that approximates the temperature dependence of the thermal expansion coefficient of diamond. The ${T}^{3}$ temperature dependence of a Debye solid holds below $\ensuremath{\approx}$100 K with an accuracy of $\ensuremath{\approx}$${10}^{\ensuremath{-}8} {\mathrm{K}}^{\ensuremath{-}1}$. A slight increase in the value of the lattice parameter was found for the Ia-type crystal, which suggests lattice dilatation by nitrogen impurity. The measurements were performed using Bragg diffraction in backscattering from diamond crystals of highly monochromatic 23.7 keV x rays with the recently demonstrated high relative accuracy of $1.2\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}8}$ in the determination of the lattice parameter [S. Stoupin and Yu. Shvyd'ko, Phys. Rev. Lett. 104, 085901 (2010)].
Omega-3 Fatty Acid Supplementation in Advanced Kidney Disease (2010)

Long-chain polyunsaturated omega-3 fatty acids (n-3 PUFA), which are obtained primarily from dietary sources such as coldwater fish, have diverse and potent mediating effects on the immune, inflammatory, and metabolic pathways, signal transduction, and cell membrane physiology. N-3 PUFA are increasingly being studied for their clinical benefits in a variety of medical conditions, some of which are relevant to individuals with advanced chronic kidney disease (CKD). These include, among others, renoprotection in IgA nephropathy, cardioprotective effects via a variety of mechanisms including blood pressure and triglyceride reduction, maintenance of dialysis access patency, sparing of inflammation-associated muscle loss, and even mortality. However, further confirmatory work needs to be performed before establishing formal intake recommendations and dosing goals for advanced CKD patients. In the meantime, the current American Heart Association n-3 PUFA intake guidelines can be applied to CKD patients, especially given n-3 PUFA's potential benefits and negligible risk profile. Over time, it will be incumbent upon the nephrology community to more clearly define the utility and optimal dosing of n-3 PUFA in CKD patients with advanced disease via randomized clinical trials.
Subblock-Based Motion Derivation and Inter Prediction Refinement in the Versatile Video Coding Standard (2021)

Efficient representation and coding of fine-granular motion information is one of the key research areas for exploiting inter-frame correlation in video coding. Representative techniques towards this direction are affine motion compensation (AMC), decoder-side motion vector refinement (DMVR), and subblock-based temporal motion vector prediction (SbTMVP). Fine-granular motion information is derived at subblock level for all the three coding tools. In addition, the obtained inter prediction can be further refined by two optical flow-based coding tools, the bi-directional optical flow (BDOF) for bi-directional inter prediction and the prediction refinement with optical flow (PROF) exclusively used in combination with AMC. The aforementioned five coding tools have been extensively studied and finally adopted in the Versatile Video Coding (VVC) standard. This paper presents technical details of each tool and highlights the design elements with the consideration of typical hardware implementations. Following the common test conditions defined by Joint Video Experts Team (JVET) for the development of VVC, 5.7% bitrate reduction on average is achieved by the five tools. For test sequences characterized by large and complex motion, up to 13.4% bitrate reduction is observed. Additionally, visual quality improvement is demonstrated and analyzed.
Angiotensin-converting-enzyme 2 inhibits liver fibrosis in mice # (2009)

ACE2 is a key negative regulator of the RAS and functions to limit fibrosis through the degradation of Ang II and the formation of Ang(1-7). Whereas loss of ACE2 activity worsens liver fibrosis in chronic liver injury models, administration of recombinant ACE2 shows therapeutic potential.
The Mitochondrial Amidoxime Reducing Component (mARC) Is Involved in Detoxification of N-Hydroxylated Base Analogues (2012)

The "mitochondrial Amidoxime Reducing Component" (mARC) is the newly discovered fourth molybdenum enzyme in mammals. All hitherto analyzed mammals express two mARC proteins, referred to as mARC1 and mARC2. Together with their electron transport proteins cytochrome b(5) and NADH cytochrome b(5) reductase, they form a three-component enzyme system and catalyze the reduction of N-hydroxylated prodrugs. Here, we demonstrate the reductive detoxification of toxic and mutagenic N-hydroxylated nucleobases and their corresponding nucleosides by the mammalian mARC-containing enzyme system. The N-reductive activity was found in all tested tissues with the highest detectable conversion rates in liver, kidney, thyroid, and pancreas. According to the presumed localization, the N-reductive activity is most pronounced in enriched mitochondrial fractions. In vitro assays with the respective recombinant three-component enzyme system show that both mARC isoforms are able to reduce N-hydroxylated base analogues, with mARC1 representing the more efficient isoform. On the basis of the high specific activities with N-hydroxylated base analogues relative to other N-hydroxylated substrates, our data suggest that mARC proteins might be involved in protecting cellular DNA from misincorporation of toxic N-hydroxylated base analogues during replication by converting them to the correct purine or pyrimidine bases, respectively.
New Lipophilic Derivatives of AZT and d4T 5′-Phosphonates (2003)

5'-Aminocarbonylphosphonyl and aminocarbonylmethylphosphonyl diesters of AZT and d4T were synthesized as potential anti-HIV agents.
Changes in the Expression of Many Ets Family Transcription Factors and of Potential Target Genes in Normal Mammary Tissue and Tumors (2004)

Interfering with Ets transcription factor function reverses multiple aspects of the transformed phenotype of mouse or human tumor cells. However, the unknown number of individual Ets factors expressed in any cellular context and the similar DNA binding specificities of Ets family members complicates the identification of those that mediate transformation. By utilizing quantitative PCR assays for 25 mouse Ets factors, we analyzed the expression of essentially the entire Ets family in normal mammary tissue, mammary-related cell lines, and mammary tumors. In normal mammary tissue, 24 Ets factors were expressed. Even clonal derived cell lines expressed 14-20 Ets members. The most abundant Ets factor mRNAs measured in normal mammary tissue were Elk4, Elf1, and Ets2. Subtractive analysis of mammary tissue identified which Ets factors were predominantly expressed in the myeloid/lymphoid or epithelial cell compartments. Comparison of Ets factor expression in normal mammary tissue and mammary tumors identified significantly elevated expression of Pse/PDEF, Ese2/Elf5, Ese3/Ehf, TEL/Etv6, and Elf2/NERF in mammary tumors and confirmed previously reported alterations in expression of Ese1/Elf3 and the PEA3 subfamily. Expression of 13 Ets target genes, implicated in various aspects of tumor progression, was also analyzed. Altered expression of particular Ets target genes was significantly correlated with particular Ets factors (e.g. maspin and Ese2), suggesting specific in vivo regulatory roles. Together, this comprehensive analysis revealed unexpectedly diverse Ets family gene expression, characterized novel Ets factor changes in mammary tumors, and implicated specific Ets factors in the regulation of multiple genes involved in mammary tumor progression.
Beyond body mass index (2001)

Body mass index (BMI) is the cornerstone of the current classification system for obesity and its advantages are widely exploited across disciplines ranging from international surveillance to individual patient assessment. However, like all anthropometric measurements, it is only a surrogate measure of body fatness. Obesity is defined as an excess accumulation of body fat, and it is the amount of this excess fat that correlates with ill-health. We propose therefore that much greater attention should be paid to the development of databases and standards based on the direct measurement of body fat in populations, rather than on surrogate measures. In support of this argument we illustrate a wide range of conditions in which surrogate anthropometric measures (especially BMI) provide misleading information about body fat content. These include: infancy and childhood; ageing; racial differences; athletes; military and civil forces personnel; weight loss with and without exercise; physical training; and special clinical circumstances. We argue that BMI continues to serve well for many purposes, but that the time is now right to initiate a gradual evolution beyond BMI towards standards based on actual measurements of body fat mass.
Sirt5 Is a NAD-Dependent Protein Lysine Demalonylase and Desuccinylase (2011)

Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.
Novel mutations in African American patients with glycogen storage disease type II (1999)

The infantile form of GSD II (an inherited deficiency of the lysosomal enzyme, acid alpha-glucosidase, Pompe disease) is a severe and invariably fatal disease characterized by a rapidly progressive generalized hypotonia, hepatomegaly, and cardiomegaly. We have recently demonstrated that African American patients share a common nonsense R854X mutation in exon 18 (Becker et al., 1998). Two other mutations, D645E and M519V, have been identified in individual African American patients (Hermans et al., 1993a; Huie et al., 1994a). We describe here three novel mutations in this population group: a missense W481R in exon 10, a deletion of a T1441 in exon 10, and a splicing defect at the 5' donor site of intron 8 (IVS g+la) . The splicing defect is shared by two unrelated patients and it is linked to intragenic polymorphic sites identical to those found in patients bearing the common R854X mutation.
Carrier-mediated transport and enzymatic hydrolysis of the endogenous cannabinoid 2-arachidonylglycerol (2000)

The human astrocytoma cell line CCF-STTGI accumulates [3H]2-AG through an Na(+)- and energy-independent process, with a Km of 0.7 +/- 0.1 microM. Non-radioactive 2-AG, anandamide or the anandamide transport inhibitor 4-hydroxyphenyl arachidonamide inhibit [3H]2-AG uptake with half-maximal inhibitory concentrations (IC50) of 5.5 +/- 1.0 microM, 4.2 +/- 0.3 microM and 1.8 = 0.1 microM, respectively. A variety of lipid transport substrates and inhibitors interfere with neither [3H]2-AG nor [3H]anandamide uptake. These results suggest that 2-AG and anandamide are internalized in astrocytoma cells through a common carrier-mediated mechanism. After incubation with [3H]2-AG, radioactivity is recovered in phospholipids, monoacylglycerols (unmetabolized [3H]2-AG), free fatty acids ([3H]arachidonate) and, to a minor extent, diacylglycerols and triacylglycerols. Arachidonic acid (100 microM) and triacsin C (10 microM), an acyl-CoA synthetase inhibitor, prevent incorporation of [3H]arachidonic acid in phospholipids and significantly reduce [3H]2-AG transport. Thus, the driving force for 2-AG internalization may derive from the hydrolysis of 2-AG to arachidonate and the subsequent incorporation of this fatty acid into phospholipids.
Continuous Dual Oximetry in Surgical Critical Care (1992)

Continuous dual oximetry combines pulse and venous oximetry to provide real-time information about oxygen utilization and pulmonary function. The authors undertook this study to examine the accuracy, utility, and limitations of the technique in surgical critical care. Twelve critically ill patients underwent placement of a modified pulmonary artery catheter and a pulse oximeter, both connected to an on-line computer. Paired blood gas and oximeter measurements were recorded every 4 to 6 hours, with a minimum of six sets per patient. Blood-gas-derived shunt fraction correlated well with oximeter-derived ventilation-perfusion index (r = 0.78, p less than 0.01). Further, the continuous oxygen extraction ratio (O2EI) and mixed venous oxygen saturation (SpvO2) correlated with the oxygen utilization coefficient (O2EI:r = 0.6, p less than 0.01; SpvO2, r = 0.76, p less than 0.01). Computer modeling of ventilation-perfusion index found limitations in accuracy that occur at high arterial oxygen saturations and when pulse oximetry errors are present. The authors conclude that (1) Continuous dual oximetry offers a significant advantage over routine blood gas analysis for monitoring cardiopulmonary parameters in critically ill patients because of its real-time display; (2) Oximeter-derived determinations parallel traditional parameters; and (3) The most significant technical limitations occur primarily at high arterial saturations and with pulse oximetry errors.