gebhart/patrepeval huggingface dataset:
Molecular cloning and amino acid sequence of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase from flavobacterium meningosepticum. (1990)

A 3,000-base pair EcoRI fragment containing the Flavobacterium meningosepticum gene for peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase was cloned into the Bluescript plasmid vector and expressed in Escherichia coli. The gene consists of an open reading frame of 1,062 base pairs coding for a 354-amino acid protein; the first 40 amino acids are presumed to be the natural secretory signal sequence, with the remaining 314 amino acids (34,779 Da) representing the catalytically active protein. The deduced amino acid sequence was verified independently by direct microsequencing of over 94% of the pure protein (Flavobacterium peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase) as tryptic and cyanogen bromide peptides. Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase was not secreted by E. coli; molecular weight analysis of the partially purified recombinant enzyme suggested incomplete processing of the putative leader sequence.
New approaches for the repairs of memories with redundancy by row/column deletion for yield enhancement (1990)

Two approaches for the repair of large random access memory (RAM) devices in which redundant rows and columns are added as spares are presented. These devices, referred to as redundant RAMs, are repaired to achieve acceptable yield at manufacturing and production times. The first approach, the faulty line covering technique, is a refinement of the fault-driven approach. This approach finds the optimal repair solution within a smaller number of iterations than the fault-driven algorithm. The second approach exploits a heuristic criterion in the generation of the repair solution. This heuristic criterion permits a fast repair. The criterion is based on the calculation of efficient coefficients for the rows and columns of the memory. Simulation results are presented. Comparison of the proposed heuristic approaches with the fully exhaustive approach shows that repair can be accomplished in most cases. A considerable reduction in processing and complexity (number of records generated in the repair process for finding the optimal repair solution) is accomplished.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anti-inflammatory ω-3 endocannabinoid epoxides (2017)

Clinical studies suggest that diets rich in ω-3 polyunsaturated fatty acids (PUFAs) provide beneficial anti-inflammatory effects, in part through their conversion to bioactive metabolites. Here we report on the endogenous production of a previously unknown class of ω-3 PUFA-derived lipid metabolites that originate from the crosstalk between endocannabinoid and cytochrome P450 (CYP) epoxygenase metabolic pathways. The ω-3 endocannabinoid epoxides are derived from docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) to form epoxyeicosatetraenoic acid-ethanolamide (EEQ-EA) and epoxydocosapentaenoic acid-ethanolamide (EDP-EA), respectively. Both EEQ-EAs and EDP-EAs are endogenously present in rat brain and peripheral organs as determined via targeted lipidomics methods. These metabolites were directly produced by direct epoxygenation of the ω-3 endocannabinoids, docosahexanoyl ethanolamide (DHEA) and eicosapentaenoyl ethanolamide (EPEA) by activated BV-2 microglial cells, and by human CYP2J2. Neuroinflammation studies revealed that the terminal epoxides 17,18-EEQ-EA and 19,20-EDP-EA dose-dependently abated proinflammatory IL-6 cytokines while increasing anti-inflammatory IL-10 cytokines, in part through cannabinoid receptor-2 activation. Furthermore the ω-3 endocannabinoid epoxides 17,18-EEQ-EA and 19,20-EDP-EA exerted antiangiogenic effects in human microvascular endothelial cells (HMVEC) and vasodilatory actions on bovine coronary arteries and reciprocally regulated platelet aggregation in washed human platelets. Taken together, the ω-3 endocannabinoid epoxides' physiological effects are mediated through both endocannabinoid and epoxyeicosanoid signaling pathways. In summary, the ω-3 endocannabinoid epoxides are found at concentrations comparable to those of other endocannabinoids and are expected to play critical roles during inflammation in vivo; thus their identification may aid in the development of therapeutics for neuroinflammatory and cerebrovascular diseases.
A subpopulation of Mac-1 (CD11b/CD18) molecules mediates neutrophil adhesion to ICAM-1 and fibrinogen. (1993)

We report that a subpopulation (10%) of the Mac-1 (CD1 1b/CD18) molecules on activated neutrophils mediates adhesion to ICAM-1 and fibrinogen. We describe a novel mAb (CBRM1/5) that binds to an activation-specific neoepitope on a subset of Mac-1 molecules on neutrophils and monocytes after stimulation with chemoattractants or phorobol esters but does not recognize Mac-1 on resting myeloid cells. CBRM1/5 immunoprecipitates a subpopulation of Mac-1 molecules from detergent lysates of neutrophils, binds to immunoaffinity-purified Mac-1, and localizes to the I domain on the alpha chain of Mac-1. Because CBRM1/5 recognizes a fraction of Mac-1 on activated neutrophils, but still blocks Mac-1-dependent adhesion to fibrinogen and ICAM-1, we suggest that only a small subset of Mac-1 molecules is competent to mediate adhesion.
Riociguat (BAY 63–2521) and Warfarin: A Pharmacodynamic and Pharmacokinetic Interaction Study (2010)

Riociguat (BAY 63-2521) and warfarin are likely to be used concomitantly to treat pulmonary hypertension. The aim of this double-blind, crossover, clinical pharmacological study in 30 healthy volunteers was to investigate potential pharmacodynamic and pharmacokinetic interactions between the 2 drugs. Healthy volunteers took 2.5 mg of oral riociguat or matching placebo 3 times daily for 10 days. A single oral dose of warfarin sodium (25 mg) was given 21 days before the study and on the seventh day of riociguat/placebo treatment. Twenty-one participants valid for safety analysis reported 89 treatment-emergent adverse events, all of mild or moderate severity. No serious adverse events occurred. The most frequently reported treatment-emergent adverse events considered to be drug-related were dyspepsia, headache, flatulence, nausea, and vomiting. Twenty-two participants were valid for pharmacodynamic/pharmaco-kinetic analysis. Riociguat (2.5 mg 3 times daily) had no pharmacodynamic interaction with warfarin. Steady-state plasma levels of riociguat did not affect prothrombin time, factor VII clotting activity, or the pharmacokinetics of warfarin. The single dose of warfarin led to a slight decrease (16%) in maximum concentration of riociguat in plasma, which is not likely to be clinically relevant. Clinical studies will confirm the finding here that combined use of riociguat with warfarin will not require dose adaptation.
Regulation of toxinogenesis in Corynebacterium diphtheriae. I. Mutations in bacteriophage beta that alter the effects of iron on toxin production (1981)

Diphtherial toxin is produced in maximal yields by Corynebacterium diphtheriae (C7(beta tox+) only when iron is present in growth-limiting amounts. Toxin production is markedly decreased under high-iron conditions. We studied the role of the bacteriophage beta genome in this apparent regulation of toxin production by iron. Using a passive immune hemolysis assay to detect toxin antigen production in individual plaques, we identified rare phage mutants that were toxinogenic in high-iron medium. Lysogenic derivatives of C. diphtheriae C7 harboring such phage mutants were constructed. The lysogens were compared with wild-type strain C7(beta) for their ability to produce toxin in deferrated liquid medium containing varying amounts of added iron. Quantitative tests for extracellular toxin were performed by competitive-binding radioimmunoassays. We identified phenotypically distinct mutant strains that produced slightly, moderately, or greatly increased yields of toxin antigen under high-iron conditions. The toxin produced by the mutant lysogens was biologically active and immunochemically indistinguishable from wild-type toxin. Complementation experiments demonstrated that the phage mutation designated tox-201 had a cis-dominant effect on the expression of the toxin structural gene of phage beta. The characteristics of the tox-201 mutation suggest that it defines a regulatory locus of phage beta that is involved in control of toxinogenesis by iron in C. diphtheriae.
Salivary analysis in oral cancer patients (2006)

The increase in ROS and RNS may have been the event that led to the consumption and reduction of salivary antioxidant systems, thus explaining the oxidative damage to the DNA and proteins, and possibly the promotion of OSCC. The oxidized proteins and DNA found in the saliva of the cancer patients seems to be the first demonstration of a direct link between salivary free radicals, antioxidants, and OSCC. This may be important for better understanding the pathogenesis of the disease and may contribute to its diagnosis and treatment.
Tn 5706 , a Transposon-Like Element from Pasteurella multocida Mediating Tetracycline Resistance (1998)

The 4,378-bp putative tetracycline resistance transposon Tn5706 of Pasteurella multocida consists of an internal tet(H)-tetR resistance gene region which is flanked by almost identical insertion elements, IS1596 and IS1597. Two reading frames for proteins of 70 and 228 amino acids were detected in each of these insertion sequence elements. The 228-amino-acid protein revealed homology to transposase proteins of gram-positive bacteria.
Ecological Study of Purple Nonsulfer Bacteria (PNSB) in Yangzonghai Lake (2004)

For obtaining the information of microbial ecology in deep plateau lake,statistical analysis was applied in PNSB abundance in Yangzonghai Lake in 2002 by statistical software.The horizontal locations,depth and sampling-time are the main three factors influencing the amount of PNSB.Other factors,such as dissolved oxygen,temperature,secchi transparency,COD and chlorophyll-a content are also make effect.The correlations between the factors (eg.chlorophyll-a and secchi transparency) were studied and the linear regression equations were obtained.
You Only Look Once: Unified, Real-Time Object Detection (2016)

We present YOLO, a new approach to object detection. Prior work on object detection repurposes classifiers to perform detection. Instead, we frame object detection as a regression problem to spatially separated bounding boxes and associated class probabilities. A single neural network predicts bounding boxes and class probabilities directly from full images in one evaluation. Since the whole detection pipeline is a single network, it can be optimized end-to-end directly on detection performance. Our unified architecture is extremely fast. Our base YOLO model processes images in real-time at 45 frames per second. A smaller version of the network, Fast YOLO, processes an astounding 155 frames per second while still achieving double the mAP of other real-time detectors. Compared to state-of-the-art detection systems, YOLO makes more localization errors but is less likely to predict false positives on background. Finally, YOLO learns very general representations of objects. It outperforms other detection methods, including DPM and R-CNN, when generalizing from natural images to other domains like artwork.
Cancer-Associated Fibroblasts Drive the Progression of Metastasis through both Paracrine and Mechanical Pressure on Cancer Tissue (2012)

Neoplastic cells recruit fibroblasts through various growth factors and cytokines. These "cancer-associated fibroblasts" (CAF) actively interact with neoplastic cells and form a myofibroblastic microenvironment that promotes cancer growth and survival and supports malignancy. Several products of their paracrine signaling repertoire have been recognized as tumor growth and metastasis regulators. However, tumor-promoting cell signaling is not the only reason that makes CAFs key components of the "tumor microenvironment," as CAFs affect both the architecture and growth mechanics of the developing tumor. CAFs participate in the remodeling of peritumoral stroma, which is a prerequisite of neoplastic cell invasion, expansion, and metastasis. CAFs are not present peritumorally as individual cells but they act orchestrated to fully deploy a desmoplastic program, characterized by "syncytial" (or collective) configuration and altered cell adhesion properties. Such myofibroblastic cohorts are reminiscent of those encountered in wound-healing processes. The view of "cancer as a wound that does not heal" led to useful comparisons between wound healing and tumorigenesis and expanded our knowledge of the role of CAF cohorts in cancer. In this integrative model of cancer invasion and metastasis, we propose that the CAF-supported microenvironment has a dual tumor-promoting role. Not only does it provide essential signals for cancer cell dedifferentiation, proliferation, and survival but it also facilitates cancer cell local invasion and metastatic phenomena.
CXCR‐4, a chemokine receptor, is overexpressed in and required for proliferation of glioblastoma tumor cells (1998)

Background and Objectives Using the technique of differential hybridization of AtlasTM Human cDNA expression arrays, we previously reported the isolation of a G protein coupled receptor, CXCR-4, which is overexpressed in glioblastoma multiforme tumor tissue (GMTT) compared to normal brain tissue (NBT). Methods Using gene specific reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization, we studied its expression in a variety of brain and breast tumor tissue samples. To demonstrate the requirement of CXCR-4 in glioblastoma cell proliferation an antisense construct was overexpressed. Glioblastoma cells were also treated with antibodies against CXCR-4 and its ligand, SDFβ-1. Results Expression analysis indicated that CXCR-4 is overexpressed in 57% of the primary glioblastoma tissues and in 88% of the glioblastoma cell lines analyzed. Overexpression of CXCR-4 in glioblastoma cell lines enhanced their soft agar colony-forming capability. Expression of antisense CXCR-4 in glioblastoma cell lines caused neurite outgrowth and cellular differentiation. Treatment of glioblastoma cell lines with CXCR-4 and SDFβ-1 specific antibodies caused inhibition of glioblastoma cell proliferation. Conclusions On the basis of these results, we conclude that CXCR-4 gene is required for the proliferation of human glioblastoma tumors. J. Surg. Oncol. 1998;69:99–104. © 1998 Wiley-Liss, Inc.
Bottom-up Recognition and Parsing of the Human Body (2007)

Recognizing humans, estimating their pose and segmenting their body parts are key to high-level image understanding. Because humans are highly articulated, the range of deformations they undergo makes this task extremely challenging. Previous methods have focused largely on heuristics or pairwise part models in approaching this problem. We propose a bottom-up parsing of increasingly more complete partial body masks guided by a parse tree. At each level of the parsing process, we evaluate the partial body masks directly via shape matching with exemplars, without regard to how the parses are formed. The body is evaluated as a whole, not the sum of its constituent parses, unlike previous approaches. Multiple image segmentations are included at each of the levels of the parsing, to augment existing parses or to introduce ones. Our method yields both a pose estimate as well as a segmentation of the human. We demonstrate competitive results on this challenging task with relatively few training examples on a dataset of baseball players with wide pose variation. Our method is comparatively simple and could be easily extended to other objects.
Modulation of Survival Motor Neuron Pre-mRNA Splicing by Inhibition of Alternative 3′ Splice Site Pairing (2001)

Spinal muscular atrophy is caused by the loss of functional survival motor neuron (SMN1) alleles. A translationally silent nucleotide transition in the duplicated copy of the gene (SMN2) leads to exon 7 skipping and expression of a nonfunctional gene product. It has been suggested that differential SMN2 splicing is caused by the disruption of an exonic splicing enhancer. Here we show that the single nucleotide difference reduces the intrinsic strength of the 3' splice site of exon 7 2-fold, whereas the strength of the 5' splice site of the exon 7 is not affected. Thus, a decrease in splice site strength is magnified in the context of competing exons. These data suggest that lower levels of exon 7 definition not only reduce intron 6 removal but, more importantly, increase the efficiency of the competing exon 7 skipping pathway. Antisense oligonucleotides were tested to modulate exon 7 inclusion, which contains the authentic translation stop codon. Oligonucleotides directed toward the 3' splice site of exon 8 were shown to alter SMN2 splicing in favor of exon 7 inclusion. These results suggest that antisense oligonucleotides could be used as a therapeutic strategy to counteract the progression of SMA.
Basophil-bound IgE and serum IgE directed against Haemophilus influenzae and Streptococcus pneumoniae in patients with chronic bronchitis during acute exacerbations. (1996)

The investigation includes 12 patients hospitalized with acute exacerbations of chronic bronchitis (CB) and infected in the lower respiratory tract with Haemophilus influenzae (HI) or Streptococcus pneumoniae (SP). Eight patients were infected the HI, three with SP, and one patient with both species. Basophil-bound IgE and serum IgE directed against these species were examined using the patients' own bacterial isolates. All patients showed IgE-mediated histamine release when their peripheral leukocytes were incubated in vitro with the infecting species, indicating basophil-bound IgE directed against their own bacterium. No IgE-mediated response was obtained in the control group of 12 healthy individuals. Bacteria-specific IgE in serum was demonstrated by immunofluorescence assay and further verified by passive sensitization. There was a positive serum titre in seven of nine patients housing HI and in all SP-infected patients but not in the control group. No synchronism was found between a positive response in the histamine release test and the immunofluorescence assay by parallel testing during the test period. This may be due to a time delay between production of serum IgE and its fixation to the cell surface. The results indicate a potential for a bacteria-specific IgE-mediated immune response in CB. Thus, by triggering mediator release, bacteria may be involved in the pathogenesis of exacerbations in CB.
The ubiquitin proteasome system in neuropathology (2009)

The ubiquitin proteasome system (UPS) orchestrates the turnover of innumerable cellular proteins. In the process of ubiquitination the small protein ubiquitin is attached to a target protein by a peptide bond. The ubiquitinated target protein is subsequently shuttled to a protease complex known as the 26S proteasome and subjected to degradative proteolysis. The UPS facilitates the turnover of proteins in several settings. It targets oxidized, mutant or misfolded proteins for general proteolytic destruction, and allows for the tightly controlled and specific destruction of proteins involved in development and differentiation, cell cycle progression, circadian rhythms, apoptosis, and other biological processes. In neuropathology, alteration of the UPS, or mutations in UPS target proteins may result in signaling abnormalities leading to the initiation or progression of tumors such as astrocytomas, hemangioblastomas, craniopharyngiomas, pituitary adenomas, and medulloblastomas. Dysregulation of the UPS may also contribute to tumor progression by perturbation of DNA replication and mitotic control mechanisms, leading to genomic instability. In neurodegenerative diseases caused by the expression of mutant proteins, the cellular accumulation of these proteins may overload the UPS, indirectly contributing to the disease process, e.g., sporadic Parkinsonism and prion diseases. In other cases, mutation of UPS components may directly cause pathological accumulation of proteins, e.g., autosomal recessive Parkinsonism and spinocerebellar ataxias. Defects or dysfunction of the UPS may also underlie cognitive disorders such as Angelman syndrome, Rett syndrome and autism, and muscle and nerve diseases, e.g., inclusion body myopathy and giant axon neuropathy. This paper describes the basic biochemical mechanisms comprising the UPS and reviews both its theoretical and proven involvement in neuropathological diseases. The potential for the UPS as a target of pharmacological therapy is also discussed.
A Journey with Platelet P-Selectin: The Molecular Basis of Granule Secretion, Signalling and Cell Adhesion (2001)

P-selectin is a transmembrane protein that resides within the alpha granule membrane of unstimulated platelets. The "extracellular" domains face into the lumen of the granule and the cytoplasmic tail extends into the platelet cytoplasm. Upon platelet stimulation, P-selectin is phosphorylated and translocated to the plasma membrane via a secretory pathway. P-selectin in the plasma membrane surface is exposed and serves as a cell adhesion receptor to interact with other cell receptors, including PSGL-1 and GPIb. P-selectin upregulates tissue factor in monocytes and leads to leukocyte accumulation in areas of vascular injury associated with thrombosis and inflammation.
A Cysteine-rich Adipose Tissue-specific Secretory Factor Inhibits Adipocyte Differentiation (2001)

A 12.5-kDa cysteine-rich adipose tissue-specific secretory factor (ADSF/resistin) is a novel secreted protein rich in serine and cysteine residues with a unique cysteine repeat motif of CX(12)CX(8)CXCX(3)CX(10)CXCXCX(9)CC. A single 0.8-kilobase mRNA coding for this protein was found in various murine white adipose tissues including inguinal and epididymal fats and also in brown adipose tissue but not in any other tissues examined. Two species of mRNAs with sizes of 1.4 and 0.8 kilobases were found in rat adipose tissue. Sequence analysis indicates that this is because of two polyadenylation signals, the proximal one with the sequence AATACA with a single base mismatch from murine AATAAA and the distal consensus sequence AATAAA. The mRNA level was markedly increased during 3T3-L1 and primary preadipocyte differentiation into adipocytes. Its expression in adipose tissue is under tight nutritional and hormonal regulation; the mRNA level was very low during fasting and increased 25-fold when fasted mice were refed a high carbohydrate diet. It was also very low in adipose tissue of streptozotocin-diabetes and increased 23-fold upon insulin administration. Upon treatment with the conditioned medium from COS cells transfected with the expression vector, conversion of 3T3-L1 cells to adipocytes was inhibited by 80%. The regulated expression pattern suggesting this factor as an adipose sensor for the nutritional state of the animals and the inhibitory effect on adipocyte differentiation implicate its function as a feedback regulator of adipogenesis.