gebhart/patrepeval huggingface dataset:
The Demethylase JMJD2C Localizes to H3K4me3-Positive Transcription Start Sites and Is Dispensable for Embryonic Development (2014)

The histone demethylase JMJD2C, also known as KDM4C/GASC1, has activity against methylated H3K9 and H3K36 and is amplified and/or overexpressed in human cancers. By the generation of Jmjd2c knockout mice, we demonstrate that loss of Jmjd2c is compatible with cellular proliferation, embryonic stem cell (ESC) self-renewal, and embryonic development. Moreover, we report that JMJD2C localizes to H3K4me3-positive transcription start sites in both primary cells and in the human carcinoma KYSE150 cell line containing an amplification of the JMJD2C locus. Binding is dependent on the double Tudor domain of JMJD2C, which recognizes H3K4me3 but not H4K20me2/me3 in vitro, showing a binding specificity different from that of the double Tudor domains of JMJD2A and JMJD2B. Depletion of JMJD2C in KYSE150 cells has a modest effect on H3K9me3 and H3K36me3 levels but impairs proliferation and leads to deregulated expression of a subset of target genes involved in cell cycle progression. Taking these findings together, we show that JMJD2C is targeted to H3K4me3-positive transcription start sites, where it can contribute to transcriptional regulation, and report that the putative oncogene JMJD2C generally is not required for cellular proliferation or embryonic development.
Mesothelin Is Overexpressed in Pancreaticobiliary Adenocarcinomas but Not in Normal Pancreas and Chronic Pancreatitis (2005)

Mesothelin, a cell surface glycoprotein present on normal mesothelial cells, has been reported to be expressed in pancreatic adenocarcinomas. We conducted this study to fully characterize mesothelin expression in surgically resected, formalin-fixed, paraffin-embedded tissue specimens of 18 pancreatic adenocarcinomas, 9 adenocarcinomas of the ampulla of Vater, 12 adenocarcinomas of the common bile duct, and 17 cases of chronic pancreatitis. Mesothelin immunostaining was performed using the antimesothelin monoclonal antibody 5B2. All 18 cases (100%) of pancreatic adenocarcinomas showed mesothelin expression, as did 8 (89%) of 9 cases of ampullar adenocarcinoma and all 12 cases (100%) of common bile duct adenocarcinoma. In all cases of pancreaticobiliary adenocarcinoma, the adjacent normal pancreas did not stain for mesothelin. Of 17 specimens of chronic pancreatitis, 16 were negative for mesothelin expression, and 1 case showed weak mesothelin staining of fewer than 5% of normal pancreatic ducts. Our results demonstrated mesothelin expression in the majority of pancreaticobiliary adenocarcinomas and no expression in normal pancreatic tissues and in chronic pancreatitis.
The Effect of Doppler Flow Screening Studies and Elective Revisions on Dialysis Access Failure (1992)

A retrospective study was undertaken to see if screening ultrasounds and elective surgical revision could decrease access failure. Two hundred fifty-three accesses [177 gortex grafts, 76 arteriovenous (AV) fistulas] were studied with duplex imaging. Patients were subdivided by access type, flow, percent stenosis, and whether they were surgically revised. Data was examined to determine access failure within 6 months. Ten of 76 fistulas clotted (13.1%), while 53 of 177 grafts clotted (29.9%) (p = 0.005). In Gortex grafts, stenosis (p < 0.05) and decreased flow (p = 0.005) correlated with clotting. In unrevised grafts with flow < or = 801 ml/min, 13 of 14 (92.8%) clotted, whereas of those with flow > or = 1603 ml/min only, 10 of 38 (26.3%) clotted (chi-square = 24.74; p < 0.0001). Only 1 of 18 (5.6%) revised grafts with flow < or = 1300 ml/min clotted, while 29 of 69 (42%) unrevised grafts clotted (p = 0.004). We were unable to demonstrate decreased clotting in fistulae with revisions. In conclusion, screening duplex scanning was able to select groups with a higher risk of access failure over the subsequent 6 months. Elective revision with correction of areas of stenosis in grafts with flows < or = 1300 ml/min significantly decreased the incidence of clotting.
Newer insights into renal regulation of water homeostasis. (2008)

The regulation of high osmolality is an important driving force for water reabsorption and urinary concentration--the key functions of the kidney for maintaining optimum body fluid volume. New evidence shows that transcription factor tonicity responsive enhancer binding protein (TonEBP) and calcineurin-nuclear factor of activated T cells through cross-talk enhance Aquaporin 2 (AQP2) expression. AQP2 is the predominant vasopressin regulated water channel of the kidney collecting duct and is essential for urinary concentration. The serine/threonine phosphatase calcineurin is an important signaling molecule involved in kidney development and function. One potential target of calcineurin action is the water channel AQP2. The nuclear factor of activated T cells (NFAT) family has recently been expanded by the discovery of a new member, NFAT 5, or Ton EBP. Ton EBP is the only known mammalian transcription factor that regulates gene expression in response to hypertonicity. This review examines the importance of AQP2, calcineurin, NFATc and TonEBP in the renal regulation of water homeostasis.
New Strategies in Myelodysplastic Syndromes: Application of Molecular Diagnostics to Clinical Practice (2013)

An increasingly complete compendium of recurrently mutated genes in myelodysplastic syndromes (MDS) has been defined, and the application of massively parallel sequencing to identify mutations in clinical practice now promises to improve the care of patients with this disease. More than 25 recurrent MDS-associated somatic mutations have been identified, involving biologic pathways as diverse as chromatin remodeling and pre-mRNA splicing. Several of these mutations have been shown to have prognostic implications that are independent of existing risk stratification systems based on clinical and pathologic parameters. Application of these recent discoveries to diagnosis, prognosis, risk stratification, and treatment selection for patients with MDS has the potential to improve patient outcomes. Here, we review recent advances in MDS and discuss potential applications of these discoveries to clinical practice.
Expression of fibrinogen receptors during activation and subsequent desensitization of human platelets by epinephrine (1986)

Epinephrine causes platelet aggregation and secretion by interacting with alpha 2-adrenergic receptors on the platelet surface. Platelet aggregation requires the binding of fibrinogen to a specific receptor on the membrane glycoprotein IIb-IIIa complex. Although the IIb-IIIa complex is identifiable on the surface of resting platelets, the fibrinogen receptor is expressed only after platelet activation. The current studies were designed to examine the effect of occupancy of platelet alpha 2-adrenergic receptors by epinephrine on the expression of fibrinogen receptors and on the aggregation of platelets. The ability of epinephrine to induce the expression of fibrinogen receptors was studied under two different conditions: acute stimulation (less than 1 min) and prolonged stimulation (50 to 90 min), the latter of which is associated with a reduction or "desensitization" of the platelet aggregation response. Expression of the fibrinogen receptor was monitored with 125I-fibrinogen as well as with 125I-PAC-1 (PAC-1), a monoclonal antibody that binds to the glycoprotein IIb-IIIa complex only after platelets are activated. Epinephrine caused an immediate increase in PAC-1 and fibrinogen binding that was dependent on occupancy of the alpha 2-receptor by epinephrine and on the presence of extracellular free Ca (KCa = 30 mumol/L). By itself, 1 mmol/L Mg was unable to support induction of the fibrinogen receptor by epinephrine. However, it did decrease the Ca requirement by about two orders of magnitude. Prolonged stimulation of unstirred platelets by epinephrine led to a 70% decrease in the aggregation response when the platelets were subsequently stirred. Despite their decreased aggregation response, desensitized platelets bound PAC-1 and fibrinogen normally, indicating that the loss of aggregation was not due simply to a decrease in fibrinogen receptor expression. Although desensitization was not affected by pretreatment of the platelets with aspirin, it was partially prevented when extracellular Ca was chelated by EDTA during the long incubation with epinephrine. These studies demonstrate that once platelet alpha 2-adrenergic receptors are occupied by epinephrine, extracellular Ca is involved in initiating the aggregation response by supporting the induction of the fibrinogen receptor and the binding of fibrinogen. Furthermore. Ca-dependent reactions subsequent to fibrinogen binding may be necessary for maximal platelet aggregation and are impaired when platelets become desensitized to epinephrine.
Nerve Growth Factor Stimulation of the Ras-Guanine Nucleotide Exchange Factor and GAP Activities (1992)

The biological activity of Ras proteins is thought to be controlled by the guanine nucleotide exchange factor and the guanosine triphosphatase activating protein (GAP). Treatment of rat pheochromocytoma PC-12 cells with nerve growth factor (NGF) increased the amount of active Ras guanosine triphosphate complex and stimulated the activities of both the guanine nucleotide exchange factor and GAP. In PC-12 cells that overexpressed the tyrosine kinase encoded by the trk proto-oncogene (a component of the high-affinity NGF receptor), the NGF-induced activation of the regulatory proteins was potentiated. These results suggest that the NGF receptor system enhances the activities of both the guanine nucleotide exchange factor and GAP and that the activation of Ras might be controlled by the balance in activity between these two regulatory proteins.
Die If You Must: Brazilian Indians in the Twentieth Century (2005)

Book review of Die If You Must: Brazilian Indians in the Twentieth Century. John Hemming. London: Pan Macmillan, 2003. xxxiv + 855pp., illustrations, maps, bibliography, notes, references, index. ISBN:1-4050-0095-3.
Purified and sterilized magnetosomes from Magnetospirillum gryphiswaldense MSR-1 were not toxic to mouse fibroblasts in vitro (2007)

This study provides methods for evaluating the purity and safety of magnetosomes from M. gryphiswaldense. The magnetosomes have the potential to be used as novel drug or gene carriers for tumour therapy.
Detection of hematogenous micrometastasis in patients with prostate cancer. (1992)

The goal of this study was to determine if patients with stage D0-3 prostatic adenocarcinoma have detectable hematogenous micrometastasis. Polymerase chain reaction amplification of prostate-specific antigen mRNA, which is exclusively expressed by prostatic epithelial cells, was used to detect circulating prostatic cells. Peripheral venous blood was obtained from 17 control and 12 prostate cancer patients with stage D0-3 prostatic adenocarcinoma. Of the 12 cancer cases, four patients (stage D1-3) tested positive for prostate-specific antigen RNA, indicating the presence of circulating micrometastasis. The 17 negative controls all tested negative. Contrary to a long held hypothesis, these data point to the possibility that hematogenous metastasis may be a relatively early event in the natural history of human prostate cancer. These findings may have an important impact on our understanding and treatment of prostate cancer.
A New Multifunctional Tactile Sensor for Detection of Material Hardness (2011)

This paper proposes a new multifunctional tactile sensor for detection of material hardness. The proposed sensor is the semielliptic structure imitating the human finger and consists of several piezoelectric ceramic transducers arranged on the surface part and a parallel plate condenser on the upper side. Capacitance values are simultaneously measured by the front electrodes of piezoelectric ceramic transducers and the parallel plate condenser. They depend on material hardness, and their values exhibit different characteristics versus the hardness. Therefore, higher detection ability is provided from two types of capacitance values. In the experiment, three kinds of materials - aluminum, acrylic resin, and silicone rubbers with four grades of hardness - were prepared. The detection of hardness was demonstrated by two types of capacitance measurements: the front electrodes and the parallel plate condenser. The results indicated that the proposed tactile sensor was useful for detection of material hardness although there are some problems that must be clearly addressed.
Transfusion-Acquired Human Immunodeficiency Virus Infection Among Immunocompromised Persons (1986)

Transmission of the human immunodeficiency virus (HIV) was studied in a group of patients with cancer who received transfusion of blood components harvested from a single, asymptomatic, seropositive donor. Of ten living recipients, nine had antibodies to the virus in fresh or cryopreserved sera at a median of 384 days (range, 237 to 686) after transfusion. In three patients, an enzyme-linked immunosorbent assay was negative at the same time that Western blot and radioimmunoprecipitation techniques showed seropositivity. Cultures for HIV obtained at a median of 615 days (range, 322 to 714) after transfusion were positive in seven of nine seropositive recipients. Six seropositive recipients have developed immunologic and clinical sequelae of HIV infection at a median of 286 days (range, 56 to 745) after transfusion. The sera of the two patients without clinical sequelae neutralized HIV in an in-vitro assay, whereas the seven other seropositive patients lacked such neutralizing antibodies. Our study characterizes the clinical, serologic, virologic, and immunologic manifestations of HIV infection in immunocompromised persons.
A New Mechanism of Resistance of Human Immunodeficiency Virus Type 2 to Integrase Inhibitors: A 5-Amino-Acid Insertion in the Integrase C-Terminal Domain (2018)

Our results confirm the potency of INSTI on HIV-2 clinical isolates with wild-type integrase. In addition, we identified a new resistance pathway, 231INS, selected in antiretroviral-experienced patients with multiresistant HIV-2 viruses. This highlights the need of close follow-up of those patients initiating an INSTI-based regimen.
A fast, highly reliable data compression chip and algorithm for storage systems (1996)

Data compression allows more efficient use of storage media and communication bandwidth, and standard compression offerings for tape storage have been well established since the late 1980s. Compression technology lowers the cost of storage without changing applications or data access methods. The desire to extend these cost/performance benefits to higher-data-rate media and broader media forms, such as DASD storage subsystems, motivated the design and development of the IBMLZ1 compression algorithm and its implementing technology. The IBMLZ1 compression algorithm was designed not only for robust and highly efficient compression, but also for extremely high reliability. Because compression removes redundancy in the source, the compressed data become extremely vulnerable to data corruption. Key design objectives for the IBMLZ1 development team were efficient hardware execution, efficient use of silicon technology, and minimum system-integration overhead. Through new observations of pattern matching, match-length distribution, and the use of graph vertex coloring for evaluating data flows, the IBMLZ1 compression algorithm and the chip family achieved the above objectives.
Plane Detection in Point Cloud Data (2010)

Plane detection is a prerequisite to a wide variety of vision tasks. RANdom SAmple Consensus (RANSAC) algorithm is widely used for plane detection in point cloud data. Minimum description length (MDL) principle is used to deal with several competing hypothesis. This paper presents a new approach to the plane detection by integrating RANSAC and MDL. The method could avoid detecting wrong planes due to the complex geometry of the 3D data. The paper tests the performance of proposed method on both synthetic and real data. 1.1
Function of oligosaccharide modification in glucocerebrosidase, a membrane‐associated lysosomal hydrolase (1990)

The nature and function of oligosaccharide modification in glucocerebrosidase, a membrane-associated lysosomal hydrolase, have been investigated in cultured human skin fibroblasts. Glucocerebrosidase is synthesised as a 62.5-kDa precursor with high-mannose-type oligosaccharide chains and an apparent native isoelectric point of 6.0-7.0. Subsequent processing of the oligosaccharide moieties to sialylated complex-type structures results in formation of 65-68-kDa forms of the enzyme with apparent native isoelectric points of 4.3-5.0. These forms are transported to lysosomes and subsequently modified by the sequential action of lysosomal exoglycosidases, finally resulting in a 59-kDa form with an isoelectric point near neutrality. The existence of oligosaccharide modification of the enzyme in the lysosomes is illustrated by the accumulation of different intermediate forms of glucocerebrosidase in mutant cell lines deficient in lysosomal exoglycosidases. The enzyme does not undergo proteolytic modification during maturation. The possible physiological relevance of the oligosaccharide modification of glucocerebrosidase in the lysosomes was investigated by studying the properties of the enzyme in fibroblasts deficient in lysosomal exoglycosidases, and also the properties of homogeneous pure glucocerebrosidase from placenta, modified in the oligosaccharide moieties by digestion in vitro with glycosidases. Modification of the oligosaccharide moieties of glucocerebrosidase had no significant effect on the catalytic activity of the enzyme as measured with either artificial or natural substrates in the presence of artificial or natural activators. There was also no effect of modification of the oligosaccharide chains on the intracellular stability of the enzyme or on its apparent hydrophobicity. We conclude that oligosaccharide modification of glucocerebrosidase in the lysosomes simply reflects further maturation of the enzyme in the lysosome and is of no importance to its function.
Quantitative Studies of Rod-Coccus Morphogenesis in a Temperature-sensitive Rod- Mutant of Bacillus subtilis (1980)

Cells of Bacillus subtilis RodB changed from rods to cocci when shifted from 20 to 42 degrees C in media containing no additional anions. Quantitative studies of surface growth, including cross-wall formation and pole construction, have been made from reconstructions obtained from central, longitudinal sections of cells. Measurements of surface area and volume were obtained by mathematical rotation of axial sections about their longitudinal axis. Surface markers, perhaps analogous to the wall bands of streptococci, have been used to distinguish septal from cylindrical wall. During the shape change, wall volume increased most rapidly, in relation to cell volume, at the division site. The average volume of wall distal to the septum also increased but the slopes of the lines relating distal wall volume to cell volume were the same at all stages of the shape change. The quantity of wall per distal pole gradually declined with increase of cell volume and as the cells became more coccus-like. Collectively, these features suggest that wall continues to be produced at sites of cylindrical extension but fails to become incorporated into the existing cylinder to maintain a constant diameter. Instead, wall material may be used to thicken the surface of distal poles, but the rate of addition may decline as the cells assume a coccal morphology. The change from rods to cocci may involve a progressive dependence on septal growth for surface expansion and a modification of the time at which the cross-wall is closed. Septal closure is progressively delayed as the organisms change into cocci, so that cross-wall separation precedes septal closure, as in streptococci.
Sialochemistry: A Diagnostic Tool? (1993)

Saliva has proven to be a discriminating element in forensic arenas, an effective indicator of acute diseases of salivary glands, and a promising probe for drug monitoring. With the advent of sensitive immunochemical assays, the compositional profile of human salivary secretions has been expanded considerably. Thus, the establishment of a range of "normal values" for a variety of "intrinsic" and "extrinsic" salivary components represented the initial step to use saliva as a diagnostic tool of oral health status. Unfortunately, numerous cross-sectional studies have shown a wide individual variation in the salivary composition of healthy populations, thus precluding its use as a diagnostic chair-side test for the screening of the most common chronic oral diseases (e.g., caries and periodontal disease). A possible explanation may arise from the wide functional versatility of salivary molecules. For instance, it has been recognized recently that in addition to its digestive properties, salivary amylase may modulate bacterial colonization, whereas histatins are not only antifungal but also bactericidal. Thus, low levels of already known antimicrobial salivary molecules (e.g., secretory IgA, lactoferrin, and lysozyme) could be compensated with higher concentrations of other molecules with antimicrobial activity, such as amylase and histatins. Consequently, for caries and periodontal diseases, longitudinal sialochemical studies may yield more insight than cross-sectional studies.
Comparative Proteome Analysis of Saccharomyces cerevisiae Grown in Chemostat Cultures Limited for Glucose or Ethanol (2004)

The use of chemostat culturing enables investigation of steady-state physiological characteristics and adaptations to nutrient-limited growth, while all other relevant growth conditions are kept constant. We examined and compared the proteomic response of wild-type Saccharomyces cerevisiae CEN.PK113-7D to growth in aerobic chemostat cultures limited for carbon sources being either glucose or ethanol. To obtain a global overview of changes in the proteome, we performed triplicate analyses using two-dimensional gel electrophoresis and identified proteins of interest using MS. Relative quantities of about 400 proteins were obtained and analyzed statistically to determine which protein steady-state expression levels changed significantly under glucose- or ethanol-limited conditions. Interestingly, only enzymes involved in central carbon metabolism showed a significant change in steady-state expression, whereas expression was only detected in one of both carbon source-limiting conditions for 15 of these enzymes. Side effects that were previously reported for batch cultivation conditions, such as responses to continuous variation of specific growth rate, to carbon-catabolite repression, and to accumulation of toxic substrates, were not observed. Moreover, by comparing our proteome data with corresponding mRNA data, we were able to unravel which processes in the central carbon metabolism were regulated at the level of the proteome, and which processes at the level of transcriptome. Importantly, we show here that the combined approach of chemostat cultivation and comprehensive proteome analysis allowed us to study the primary effect of single limiting conditions on the yeast proteome.
<title>Mask fabrication rules for proximity-corrected patterns</title> (1996)

Optical proximity correction (OPC) adds complex convolutions to mask pattern shapes which can stress mask-making capabilities. Because the `decorations'--jogs, serifs, assist features--created by proximity correction are approximations to `ideal' corrected shapes there are many variations of corrected mask shapes that provide the same result on the wafer. With an understanding of specific mask- making limitations it is possible to leverage this leeway to create more `mask friendly' patterns with OPC.
Multivesicular liposome (MVL) sustained delivery of a novel synthetic cationic GnRH antagonist for prostate cancer treatment (2011)

The data obtained from in-vivo study indicated that a sustained anticancer effect can be achieved over a 7-day period with subcutaneous administration of DepoLXT-101 in rats.