gebhart/patrepeval huggingface dataset:
Divalent cation regulation of the function of the leukocyte integrin LFA-1. (1992)

The integrin lymphocyte function-associated antigen-1 (LFA-1) expressed on T cells serves as a useful model for analysis of leukocyte integrin functional activity. We have assessed the role of divalent cations Mg2+, Ca2+, and Mn2+ in LFA-1 binding to ligand intercellular adhesion molecule-1 (ICAM-1) and induction of the divalent cation-dependent epitope recognized by mAb 24. Manganese strongly promoted both expression of the 24 epitope and T cell binding to ICAM-1 via LFA-1, suggesting that Mn2+ is able to directly alter the conformation of LFA-1 in a manner that favors ligand binding. Since Mn2+ also promotes functional activity of other integrins, parallels in mechanism of ligand binding may span the integrin family. In contrast, induction of 24 epitope expression by Mg2+ required removal of Ca2+ from T cell LFA-1 with EGTA. Furthermore, binding of mAb 24 to T cell LFA-1 in the presence of either Mn2+ or Mg2+ was found to be specifically inhibited by Ca2+, suggestive of a negative regulatory role for Ca2+ in the control of leukocyte integrin function. Analysis of T cell binding to ICAM-1 via LFA-1 in the presence of Mg2+ or Mn2+, confirmed that Ca2+ exerted inhibitory effects upon LFA-1 function. The implication of our findings is that Ca2+ bound with relatively high affinity to LFA-1 may serve to maintain an inactive state. Thus induction of function and 24 epitope expression may occur as a result of displacement of Ca2+ from leukocyte integrins or alternatively, such activators may be able to impose the required conformational change in the presence of bound Ca2+.
Pathology of Proliferative Haemorrhagic Enteropathy in Pigs (1979)

Examination of the small intestine of pigs with proliferative haemorrhagic enteropathy showed changes consistent with defects in vascular permeability. Early in the disease there were many eosinophils and distension of lacteals and intercellular spaces with proteinaceous material. Later the predominant features were red blood cells and exudate in tissue spaces. This was most severe and extensive at the tips of villi which were covered by a cast of cells and fibrinous exudate. Adenomatous intestinal mucosal cells contained organisms that were free within the apical cytoplasm and were morphologically identical with those seen in the related disease, porcine intestinal adenomatosis. Also these bacteria were seen free in the subepithelial mucosal area, in blood vessels and within membrane-bound vesicles in phagocytic cells in the mucosa and its blood vessels. Mast cells were prominent in some areas as were thrombosed vessels.
Fibroblast growth enhancing activity of tumor necrosis factor and its relationship to other polypeptide growth factors. (1986)

Tumor necrosis factor (TNF) is a monocyte-derived protein cytotoxic or cytostatic for some tumor cell lines. Here we show that highly purified E. coli-derived recombinant human TNF stimulated the growth of human FS-4 diploid fibroblasts. Stimulation of cell growth was demonstrable at a TNF concentration of 10 pg/ml (3 X 10(-13) M). Maximal stimulation was attained at TNF concentrations of 10 ng/ml (3 X 10(-10) M) or higher. Growth-stimulatory activity of TNF was inhibited by an mAb neutralizing the cytotoxic activity of TNF. Growth stimulation was not inhibited by another mAb specific for TNF, lacking neutralizing activity for the cytotoxic activity of TNF. Growth stimulation by TNF was more marked and more sustained in the presence of greater than or equal to 10% FCS than in medium with less than or equal to 5% FCS. Addition of TNF to confluent FS-4 cultures also produced a marked stimulation of cell growth in the presence of fresh FCS, while a much less marked stimulation was seen in the absence of FCS. Stimulation of confluent cultures by TNF in serum-free medium was enhanced by insulin, suggesting that insulin or insulin-like growth factor(s) in the serum can act synergistically with TNF in producing growth stimulation. While the growth-stimulatory effects of TNF and insulin were synergistic, the actions of TNF and epidermal growth factor (EGF) were less than additive, suggesting that TNF and EGF may activate identical or similar pathways. We conclude that stimulation of cell growth is probably a physiological function of TNF, and that the cytotoxic and cytostatic actions of TNF may be the result of an anomalous growth signal transduction in neoplastic cells lacking the constraints of normal growth control mechanisms.
Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation (1999)

The Taq DNA polymerase is the most commonly used enzyme in DNA sequencing. However, all versions of Taq polymerase are deficient in two respects: (i) these enzymes incorporate each of the four dideoxynucleoside 5' triphosphates (ddNTPs) at widely different rates during sequencing (ddGTP, for example, is incorporated 10 times faster than the other three ddNTPs), and (ii) these enzymes show uneven band-intensity or peak-height patterns in radio-labeled or dye-labeled DNA sequence profiles, respectively. We have determined the crystal structures of all four ddNTP-trapped closed ternary complexes of the large fragment of the Taq DNA polymerase (Klentaq1). The ddGTP-trapped complex structure differs from the other three ternary complex structures by a large shift in the position of the side chain of residue 660 in the O helix, resulting in additional hydrogen bonds being formed between the guanidinium group of this residue and the base of ddGTP. When Arg-660 is mutated to Asp, Ser, Phe, Tyr, or Leu, the enzyme has a marked and selective reduction in ddGTP incorporation rate. As a result, the G track generated during DNA sequencing by these Taq polymerase variants does not terminate prematurely, and higher molecular-mass G bands are detected. Another property of these Taq polymerase variants is that the sequencing patterns produced by these enzymes are remarkably even in band-intensity and peak-height distribution, thus resulting in a significant improvement in the accuracy of DNA sequencing.
The role of oxidants and free radicals in reperfusion injury (2006)

While timely reperfusion of acute ischemic myocardium is essential for myocardial salvage, reperfusion results in a unique form of myocardial damage. Functional alterations occur, including depressed contractile function and decreased coronary flow as well as altered vascular reactivity. Both myocardial stunning and infarction are seen. Over the last two decades, it has become increasingly clear that oxidant and oxygen radical formation is greatly increased in the post-ischemic heart and serves as a critical central mechanism of post-ischemic injury. This oxidant formation is generated through a series of interacting pathways in cardiac myocytes and endothelial cells and triggers subsequent leukocyte chemotaxis and inflammation. Nitric oxide (NO) production and NO levels are also greatly increased in ischemic and post-ischemic myocardium, and this occurs through NO synthase (NOS)-dependent NO formation and NOS-independent nitrite reduction. Recently, it has been shown that the pathways of oxygen radical and NO generation interact and can modulate each other. Under conditions of oxidant stress, NOS can switch from NO to oxygen radical generation. Under ischemic conditions, xanthine oxidase can reduce nitrite to generate NO. NO and peroxynitrite can inhibit pathways of oxygen radical generation, and, in turn, oxidants can inhibit NO synthesis from NOS. Ischemic preconditioning markedly decreases NO and oxidant generation, and this appears to be an important mechanism contributing to preconditioning-induced myocardial protection.
Problem-Independent Approach to Multiprocessor Dependent Task Scheduling (2012)

Abstract This paper concerns Directed Acyclic Graph task scheduling on parallel executors. The problem is solved using two new implementations of Tabu Search and genetic algorithm presented in the paper. A new approach to solution coding is also introduced and implemented in both metaheuristics algorithms. Results given by the algorithms are compared to those generated by greedy LPT and SS-FF algorithms; and HAR algorithm. The analysis of the obtained results of multistage simulation experiments confirms the conclusion that the proposed and implemented algorithms are characterized by very good performance and characteristics.
Diversity and distribution of cholix toxin, a novel ADP‐ribosylating factor from Vibrio cholerae (2010)

Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47% of 83 non-O1, non-O139 strains and 16% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.
Developing assessment system for wireless capsule endoscopy videos based on event detection (2009)

Along with the advancing of technology in wireless and miniature camera, Wireless Capsule Endoscopy (WCE), the combination of both, enables a physician to diagnose patient's digestive system without actually perform a surgical procedure. Although WCE is a technical breakthrough that allows physicians to visualize the entire small bowel noninvasively, the video viewing time takes 1 - 2 hours. This is very time consuming for the gastroenterologist. Not only it sets a limit on the wide application of this technology but also it incurs considerable amount of cost. Therefore, it is important to automate such process so that the medical clinicians only focus on interested events. As an extension from our previous work that characterizes the motility of digestive tract in WCE videos, we propose a new assessment system for energy based events detection (EG-EBD) to classify the events in WCE videos. For the system, we first extract general features of a WCE video that can characterize the intestinal contractions in digestive organs. Then, the event boundaries are identified by using High Frequency Content (HFC) function. The segments are classified into WCE event by special features. In this system, we focus on entering duodenum, entering cecum, and active bleeding. This assessment system can be easily extended to discover more WCE events, such as detailed organ segmentation and more diseases, by using new special features. In addition, the system provides a score for every WCE image for each event. Using the event scores, the system helps a specialist to speedup the diagnosis process.
Concanavalin A causes an increase in sodium permeability and intracellular sodium content of pig lymphocytes (1983)

1. The 3mV depolarization of pig lymphocytes observed within 2 1/2 min of treatment with concanavalin A [Felber & Brand (1983) Biochem. J. 210, 885-891] is dependent on the presence of high extracellular [Na+]. 2. The concanavalin A-induced changes in membrane potential at high and low extracellular [Na+] are quantitatively explained by an increase in the electrogenic permeability coefficient for Na+ (PNa). This rises from a negligible value in resting cells to around 4% of the permeability coefficient for K+ or Cl- in stimulated cells. 3. Concanavalin A induces a 4mM increase in the Na+ content of pig lymphocytes. This increase in intracellular [Na+] is not due solely to stimulation of electrogenic Na+ influx resulting from the rise in PNa. 4. Thus concanavalin A stimulates both an electrogenic pathway for Na+ influx, resulting in a small depolarization of the plasma membrane, and a non-electrogenic Na+ influx pathway, resulting in a rise in intracellular [Na+].
Cytomegalovirus infection enhances the immune response to influenza (2015)

Cytomegalovirus (CMV) is a β-herpesvirus present in a latent form in most people worldwide. In immunosuppressed individuals, CMV can reactivate and cause serious clinical complications, but the effect of the latent state on healthy people remains elusive. We undertook a systems approach to understand the differences between seropositive and negative subjects and measured hundreds of immune system components from blood samples including cytokines and chemokines, immune cell phenotyping, gene expression, ex vivo cell responses to cytokine stimuli, and the antibody response to seasonal influenza vaccination. As expected, we found decreased responses to vaccination and an overall down-regulation of immune components in aged individuals regardless of CMV status. In contrast, CMV-seropositive young adults exhibited enhanced antibody responses to influenza vaccination, increased CD8(+) T cell sensitivity, and elevated levels of circulating interferon-γ compared to seronegative individuals. Experiments with young mice infected with murine CMV also showed significant protection from an influenza virus challenge compared with uninfected animals, although this effect declined with time. These data show that CMV and its murine equivalent can have a beneficial effect on the immune response of young, healthy individuals, which may explain the ubiquity of CMV infection in humans and many other species.
Sesamin is a potent and specific inhibitor of Δ5 desaturase in polyunsaturated fatty acid biosynthesis (1991)

Incubation with sesame oil increases the mycelial dihomo-gamma-linolenic acid content of an arachidonic acid-producing fungus, Mortierella alpina, but decreases its arachidonic acid content [Shimizu, S., K. Akimoto, H. Kawashima, Y. Shinmen and H. Yamada (1989) J. Am. Oil Chem. Soc. 66, 237-241]. The factor causing these effects was isolated and identified to be (+)-sesamin. The results obtained in experiments with both a cell-free extract of the fungus and with rat liver microsomes demonstrated that (+)-sesamin specifically inhibits delta 5 desaturase at low concentrations, but does not inhibit delta 6, delta 9 and delta 12 desaturases. Kinetic analysis showed that (+)-sesamin is a noncompetitive inhibitor (Ki for rat liver delta 5 desaturase, 155 microM). (+)-Sesamolin, (+)-sesaminol and (+)-episesamin also inhibited only delta 5 desaturases of the fungus and liver. These results demonstrate that (+)-sesamin and related lignan compounds present in sesame seeds or its oil are specific inhibitors of delta 5 desaturase in polyunsaturated fatty acid biosynthesis in both microorganisms and animals.
Detecting individual memories through the neural decoding of memory states and past experience (2010)

A wealth of neuroscientific evidence indicates that our brains respond differently to previously encountered than to novel stimuli. There has been an upswell of interest in the prospect that functional MRI (fMRI), when coupled with multivariate data analysis techniques, might allow the presence or absence of individual memories to be detected from brain activity patterns. This could have profound implications for forensic investigations and legal proceedings, and thus the merits and limitations of such an approach are in critical need of empirical evaluation. We conducted two experiments to investigate whether neural signatures of recognition memory can be reliably decoded from fMRI data. In Exp. 1, participants were scanned while making explicit recognition judgments for studied and novel faces. Multivoxel pattern analysis (MVPA) revealed a robust ability to classify whether a given face was subjectively experienced as old or new, as well as whether recognition was accompanied by recollection, strong familiarity, or weak familiarity. Moreover, a participant's subjective mnemonic experiences could be reliably decoded even when the classifier was trained on the brain data from other individuals. In contrast, the ability to classify a face's objective old/new status, when holding subjective status constant, was severely limited. This important boundary condition was further evidenced in Exp. 2, which demonstrated that mnemonic decoding is poor when memory is indirectly (implicitly) probed. Thus, although subjective memory states can be decoded quite accurately under controlled experimental conditions, fMRI has uncertain utility for objectively detecting an individual's past experiences.
KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space (2013)

Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.
An Update on Vitamin D<sub>3</sub> Analogues in the Treatment of Psoriasis (1998)

Vitamin D3 analogues have revolutionized the topical treatment of psoriasis during the last decade. The mode of action of this ligand for the vitamin D3 receptor is via modulation of the transcription of genes with vitamin D3 response elements in their promoter region. Vitamin D3 analogues cause inhibition of various aspects of cutaneous inflammation and epidermal proliferation with enhancement of normal keratinization. In vivo, active vitamin D3 analogues proved to have a substantial antipsoriatic effect. Calcipotriol (50 micrograms/g in ointment or cream), tacalcitol (4 micrograms/g in ointment) and calcitriol (3 micrograms/g in ointment) have been shown to have an antipsoriatic effect in placebo-controlled studies. The most extensive body of information on comparative studies and on combination therapies is available for the analogue calcipotriol. So far, calcipotriol is available as a routine treatment in most countries, whereas tacalcitol has been registered in Japan and some European countries. From the available data in the literature we may conclude that calcipotriol is a first-line treatment for psoriasis and is advantageous in the combination with several other antipsoriatic treatments such as topical corticosteroids, PUVA, cyclosporin and acitretin. Tacalcitol 4 micrograms/g as a once-daily principle is effective in psoriasis. Comparative studies will indicate the position of the existing and new vitamin D3 analogues.
IL-12 regulates VEGF and MMPs in a murine breast cancer model (1998)

In a murine model of breast cancer, IL-12 therapy exerts potent anti-angiogenic effects which contribute to tumor regression. After 7 days of treatment, levels of tumor VEGF protein decline markedly and are undetectable at 14 days. This decline is accompanied by a fall in MMP-9 and, as the tumors regress, an increase in its natural inhibitor, TIMP-1. A cell line established from the primary tumor produced VEGF in vitro. IFN-gamma reduced tumor cell production of VEGF over a 24-hr period in vitro, suggesting that IL-12-induced IFN-gamma may be responsible for the decline in VEGF levels in vivo. There is also in vitro evidence that IL-12 regulates stromal cell interactions, leading to decreased MMP-9 and increased TIMP-1 production. Thus, we suggest that at least 2 mechanisms are involved in IL-12 regulation of angiogenesis, removing the pro-angiogenic stimulus and blocking the release and activity of MMPs.
Road Test Results of an I-C Engine Misfire Detection System (1993)

&lt;div class="htmlview paragraph"&gt;This paper presents results of experimental results of a misfire detection system for cars equipped with gasoline fueled engines and both manual and automatic transmissions. A brief overview of the theory of the method and discussion of instrumentation is also given. The performance of the method for cars operated on a chassis dynamometer and on various roads is presented.&lt;/div&gt;
Salivary Proteomics for Oral Cancer Biomarker Discovery (2008)

Patient-based saliva proteomics is a promising approach to searching for OSCC biomarkers. The discovery of these new targets may lead to a simple clinical tool for the noninvasive diagnosis of oral cancer. Long-term longitudinal studies with large populations of individuals with oral cancer and those who are at high risk of developing oral cancer are needed to validate these potential biomarkers.
McKeever Metallic Hemiarthroplasty of the Knee in Unicompartmental Degenerative Arthritis (1985)

Forty patients with forty-four unicorn- partmental McKeever metallic uncemented herniarthro- plasties were followed for five to thirteen years (average, eight years). Thirty-nine knees had a medial and five, a lateral arthroplasty. The age at surgery ranged from thirty-two to eighty-two years (average, sixty-seven years). At the final follow-up, 70 per cent of the knees were rated as good or excellent. Seventy-nine per cent of the knees in patients who were less than sixty-five years old at the time of surgery were in these categories. Six knees (14 per cent) had required revision to either a unicompartmental or a bicompartmental total knee replacement. The average preoperative and postopera- tive knee flexion did not change, but knees with initially poor motion improved. The average preoperative flexion contracture of 10 degrees improved postoperatively to 5
Electrochemical copolymerization of thiophene and aniline (1996)

In this study homopolymer, copolymer, and composites of aniline and thiophene were synthesized in nitrogen atmosphere by using TEATFB (Tetraethyl ammonium tetrafluoroborate) and Lithium perchlorate as supporting electrolytes. In order to analyze their structure and characteristics, IR spectrums of the samples were taken and thermogravimetric analysis (TGA) was applied. Also, the samples were photographed under scanning electron microscope (SEM) for microstructure analysis and their electrochemical properties were observed and conductivities were obtained by four probe method. Homopolymerization and copolymerization reactions were carried out in two different solvents viz. acetonitrile and benzonitrile in order to see the solvent effect on polymerization. However, changing the solvent was found to have no significant effect on the resulting properties. It was concluded that changing the supporting electrolyte caused a structural difference in the resulting homopolymer. It also affects the properties considerably. During the bilayer preparation changing the coating turn led to variations in the properties of the samples. When polythiophene (PT) was coated with polyaniline (PA), the resulting system was a composite. However, in coating PA with PT the system was identified to be a copolymer. © 1996 John Wiley & Sons, Inc.