gebhart/patrepeval huggingface dataset:
The IBM Blue Gene/Q Interconnection Fabric (2011)

This article describes the IBM Blue Gene/Q interconnection network and message unit. Blue Gene/Q is the third generation in the IBM Blue Gene line of massively parallel supercomputers and can be scaled to 20 petaflops and beyond. For better application scalability and performance, Blue Gene/Q has new routing algorithms and techniques to parallelize the injection and reception of packets in the network interface.
MEASURING SHORT‐TERM RATES OF MILK SYNTHESIS IN BREAST‐FEEDING MOTHERS (1989)

A Moire contouring method was used to measure changes in the volume of the breast between infant feeds. A tungsten-halogen light source obliquely illuminated the breast through a moving Moire grid to produce contour shadows on the breast. Photographs of the Moire topographs were analysed to obtain three-dimensional co-ordinates of transverse sections through the breast. The cross-sectional areas were calculated using the trapezoidal rule and volumes were calculated by multiplying these areas by their vertical separation. The precision of the method was found to be dependent on the subject repositioning accurately. With careful control over subject posture and position the relative standard deviation was 1.8%, but without careful repositioning the relative standard deviation was 10%. The Moire topography method was accurate; the mean difference between changes in the volume of the breast after breast feeding as measured by the Moire topography method and test weighing was 0.34 +/- 7.26 ml (n = 21). For two women, the rate of increase in the volume of the right breast was found to range from 13 to 40 ml/h.
Secretion of phosphomannosyl-deficient arylsulphatase A and cathepsin D from isolated human macrophages (2002)

The transfer of macrophage-secreted arylsulphatase A (ASA) to enzyme-deficient brain cells is part of the therapeutic concept of bone marrow transplantation in lysosomal storage diseases. Here we have investigated this transfer in vitro. The uptake of (125)I-labelled recombinant human ASA purified from ASA-overexpressing mouse embryonic fibroblasts deficient for mannose 6-phosphate (M6P) receptors in a mouse ASA-deficient astroglial cell line was completely inhibited by M6P. In contrast, when ASA-deficient astroglial cells were incubated with secretions of [(35)S]methionine-labelled human macrophages or mouse microglia, containing various lysosomal enzymes, neither ASA nor cathepsin D (CTSD) were detected in acceptor cells. Co-culturing of metabolically labelled macrophages with ASA-deficient glial cells did not result in an M6P-dependent transfer of ASA or CTSD between these two cell types. In secretions of [(33)P]phosphate-labelled macrophages no or weakly phosphorylated ASA and CTSD precursor polypeptides were found, whereas both intracellular and secreted ASA from ASA-overexpressing baby hamster kidney cells displayed (33)P-labelled M6P residues. Finally, the uptake of CTSD from secretions of [(35)S]methionine-labelled macrophages in rat hepatocytes was M6P-independent. These data indicated that lysosomal enzymes secreted by human macrophages or a mouse microglial cell line cannot be endocytosed by brain cells due to the failure to equip newly synthesized lysosomal enzymes with the M6P recognition marker efficiently. The data suggest that other mechanisms than the proposed M6P-dependent secretion/recapture of lysosomal enzymes might be responsible for therapeutic effects of bone marrow transplantation in the brain.
The TSC1 gene product, hamartin, negatively regulates cell proliferation (2000)

Tuberous sclerosis is an autosomal dominant hereditary disease caused by mutations in either the TSC1 or the TSC2 tumor suppressor gene. The TSC1 gene on chromosome 9q34 encodes a 130 kDa protein named hamartin, and the TSC2 gene on chromosome 16p13.3 codes for tuberin, a 200 kDa protein. Here we show that expression of hamartin, assayed by immunoblot analyses, is high in G(0)-arrested cells and hamartin is expressed throughout the entire ongoing cell cycle. An interaction of hamartin and tuberin can be detected in every phase of the cell cycle. Ectopic expression of high levels of hamartin attenuates cellular proliferation. We provide evidence that this effect could depend on a coiled-coil region earlier proposed to be involved in binding of hamartin to tuberin. Further investigations revealed that hamartin affects cell proliferation via deregulation of G(1) phase. Our data have a clear impact on understanding the role of hamartin during development of this disease.
Structure and genetics ofShigellaO antigens (2008)

This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.
In Vivo Induction of the Interferon-Stimulated Protein 2′5′Oligoadenylate Synthetase in Tumor and Peripheral Blood Cells During IFN-α Treatment of Metastatic Melanoma (1998)

Interferon-alpha (IFN-alpha) therapy induces a response in a proportion of patients with metastatic melanoma. However, the mechanism of the antitumor action and reason(s) for resistance to IFN therapy are not known. To investigate whether lack of clinical response may be due to resistance of the melanoma cells to IFN-alpha or to an inability of IFN-alpha to reach the tumor cells during treatment, we investigated the in vivo and in vitro susceptibility of primary tumor cells obtained through fine needle aspiration biopsies and peripheral blood mononuclear cells (PBMC) to the induction of the IFN-induced enzyme 2'5'-oligoadenylate synthetase (2'5'OAS) during initiation of IFN-alpha therapy in 10 patients with metastatic melanoma. None of the patients showed an objective response to IFN-alpha treatment. The melanoma cells from 2 of the 10 patients were resistant to IFN-induced enhancement of 2'5'OAS in vitro. This correlated well with the in vivo induction of 2'5'OAS in the malignant cells, as no in vivo induction was seen in the 2 patients whose malignant cells were resistant in vitro, whereas tumor cells from 7 of 8 of the remaining patients showed enhancement also in vivo. This study shows that it is possible to monitor the cellular susceptibility of tumor cells to IFN-alpha in vivo and that melanoma cells from a small percentage of patients are resistant to the cellular effects of IFN-alpha. Furthermore, the absence of a clinical response to IFN-alpha therapy in the majority of melanoma patients can be explained neither by impaired cellular susceptibility to IFN nor by an inability of IFN-alpha to reach the tumor.
Obtainment of the polarizing and retardation parameters of a non-depolarizing optical system from the polar decomposition of its Mueller matrix (1986)

Les proprietes de polarisation et de retard sont donnees par les parametres du polariseur partiel elliptique equivalent et du retardateur elliptique equivalent qui forme un systeme optique equivalent
The evolving field of imaging mass spectrometry and its impact on future biological research (2011)

Within the past decade, imaging mass spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution and current state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research.
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks (2008)

Our approach to abstract classification shows that a simple linear model, using relatively few features, can generalize and uncover the conceptual nature of protein-protein interactions from the bibliome. Because the novel approach is based on a rather lightweight linear model, it can easily be ported and applied to similar problems. In full-text problems, the expansion of word features with word proximity networks is shown to be useful, although the need for some improvements is discussed.
Susceptibility to Exacerbation in Chronic Obstructive Pulmonary Disease (2010)

Although exacerbations become more frequent and more severe as COPD progresses, the rate at which they occur appears to reflect an independent susceptibility phenotype. This has implications for the targeting of exacerbation-prevention strategies across the spectrum of disease severity. (Funded by GlaxoSmithKline; ClinicalTrials.gov number, NCT00292552.)
Multiresolution feature-based image registration (2000)

Image registration is the fundamental task used to match two or more partially overlapping images and stitch these images into one panoramic image comprising the whole scene. To register two images, the coordinate transformation between a pair of images must be found. In this paper, a multiresolution feature-based method is developed to efficiently estimate an eight-parametric projective transformation model between pairs of images. The proposed method has been tested and work well on many images of static scene taken with a hand-held digital still camera.
Cofactor‐Assisted Self‐Cleavage in DNA Libraries with a 3′–5′‐Phosphoramidate Bond (1997)

Catalytic activity in combinatorial DNA libraries is demonstrated for a cofactor-assisted self-cleavage reaction. In vitro selection allowed the isolation of one dominating sequence from a sequence library containing 72 randomized nucleotide positions. The selected sequence undergoes self-cleavage of an internal 3′–5′ phosphoramidate bond by intramolecular catalysis in the presence of the trimer pCGG (see drawing on the right).
Synthesis and receptor affinities of some conformationally restricted analogs of the dopamine D1 selective ligand (5R)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3-benzazepin-7-ol (1989)

The synthesis of a structurally novel series of 6,6a,7,8,9,13b-hexahydro-5H-benzo[d]naphtho[2,1-b]azepines (2), conformationally restricted analogues of the dopamine D1 antagonist (5R)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3-benzazepin -7-ol (SCH 23390, 1c), is described. Affinity for D1 receptors was determined by competition for rat striatal binding sites labeled by [3H]SCH 23390; affinity for D2 receptors was similarly determined by competition experiments using [3H]spiperone. Compounds in this series having the B/C-trans ring junction (2b and related analogues), where the D ring is unequivocally fixed in an equatorial orientation, possess considerably more D1 receptor affinity and selectivity vs the D2 receptor than the conformationally mobile cis stereoisomers (2a), thus leading to the conclusion that axial substituents at the 4- or 5-positions of the benzazepine nucleus are detrimental to D1 receptor affinity. Resolution and X-ray analysis demonstrated that D1 receptor affinity was preferentially associated with the (-)-6aS,13bR enantiomer of 2b.
How azide inhibits ATP hydrolysis by the F-ATPases (2006)

In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
The structures ofEscherichia coliO-polysaccharide antigens (2006)

Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/.
Large-Scale Offshore Wind Power in the United States: Assessment of Opportunities and Barriers (2010)

This paper assesses the potential for U.S. offshore wind to meet the energy needs of many coastal and Great Lakes states.
Identification of semaphorin E gene expression in metastatic human lung adenocarcinoma cells by mRNA differential display (1999)

Our results point to the relevance of semaphorin E in metastatic spread of human lung adenocarcinoma cells.
The Dose-Dependent Reduction in Blood Pressure Through Administration of Magnesium A Double Blind Placebo Controlled Cross-Over Study (1993)

Seventeen patients with a diastolic blood pressure over 90 mm Hg were recruited from a running health screening program to participate in a double blind cross-over study of magnesium supplementation (15 mmol Mg2+/day (Emgesan, Kabi Pharmacia) for 3 weeks, followed by 30 mmol Mg2+/day for another 3 weeks, finishing with 40 mmol Mg2+/day for a final 3 weeks). A significant decrease in the mean systolic blood pressure was recorded from 154.0 +/- 10.7 mm Hg to 146.1 +/- 16.9 mm Hg (P = .031) while the mean diastolic blood pressure decreased from 100.2 +/- 4.2 mm Hg to 92.0 +/- 6.6 mm Hg (P = .0001).
A factor X-activating cysteine protease from malignant tissue. (1981)

A proteolytic procoagulant has been identified in extracts of human and animal tumors and in cultured malignant cells. It directly activated Factor X but its similarity to other Factor S-activating serine proteases was not clear. This study describes work done to determine whether this enzyme, cancer procoagulant, is a serine or cysteine protease. Purified cancer procoagulant from rabbit V2 carcinoma was bound to a p-chloromercurialbenzoate-agarose affinity column and was eluted with dithiothreitol. The initiation of recalcified, citrated plasma coagulation activity by cancer procoagulant was inhibited by 5 mM diisopropylfluorophosphate, 1 mM phenylmethylsulfonylfluoride, 0.1 mM HgCl2, and 1 mM iodoacetamide. Activity was restored in the diisopropylfluorophosphate-, phenylmethylsulfonylfluoride-, and HgCl2-inhibited samples by 5 mM dithiothreitol; iodoacetamide inhibition was irreversible. Russell's viper venom, a control Factor X-activating serine protease, was not inhibited by either 0.1 mM HgCl2 or 1 mM iodoacetamide. The direct activation of Factor X by cancer procoagulant in a two-stage assay was inhibited by diisopropylfluorophosphate and iodoacetamide. Diisopropylfluorophosphate inhibits serine proteases, and an undefined impurity in most commercial preparations inhibits cysteine proteases. Hydrolysis of diisopropylfluorophosphate with CuSO4 and imidazole virtually eliminated inhibition of thrombin, but cancer procoagulant inhibition remained complete, suggesting that cancer procoagulant was inhibited by the undefined impurity. These results suggest that cancer procoagulant is a cysteine endopeptidase, which distinguishes it from other coagulation factors including tissue factor. This and other data suggest that neoplastic cells produce this unique cysteine protease which may initiate blood coagulation.
Artecoll: A Long-Lasting Injectable Wrinkle Filler Material: Report of a Controlled, Randomized, Multicenter Clinical Trial of 251 Subjects (2004)

Artecoll, an injectable wrinkle filler composed of polymethylmethacrylate microspheres and bovine collagen, is widely available outside the United States. For domestic availability, a multicenter Investigational Device Exemption study was required by the U.S. Food and Drug Administration. This study consisted of 251 subjects at eight centers who received injections of Artecoll or the currently approved collagen dermal filler (control) in 1334 wrinkles of the glabella, nasolabial fold, radial upper lip lines, and corner-of-the-mouth lines. The treatments were randomized, and follow-up safety, efficacy, investigator success rating, and subject satisfaction rating data were collected at 1, 3, and 6 months. The safety data, measured as adverse events and immunoglobulin G serum levels, were low and similar for both groups. The efficacy data, measured by masked observers using a photographic facial fold assessment scale, demonstrated a combined significant improvement with Artecoll compared with collagen at 6 months (p < 0.001). At 6 months, the investigator success ratings and the subject satisfaction ratings for each of the four injections sites were superior for Artecoll (p < 0.001). In the Artecoll group, 12-month follow-up was obtained for 111 subjects (86.7 percent) and showed persistence of significant augmentation. Artecoll had fewer adverse events reported throughout the 12-month safety study period than the control group did in 6 months, although the difference was not statistically significant.
Predictive factors for prolonged survival in acquired immunodeficiency syndrome—associated progressive multifocal leukoencephalopathy (1998)

Progressive multifocal leukoencephalopathy (PML) complicating the acquired immunodeficiency syndrome (AIDS) is typically inexorably progressive with death usually occurring within 6 months of symptom onset. Occasional patients have been observed to survive longer than 1 year, often with remission of clinical features. In this study, we identify predictive factors for prolonged survival in patients with biopsy proven, AIDS-associated PML, by comparing 7 patients with survival exceeding 12 months from symptom onset with 45 patients with shorter survivals. PML was the presenting manifestation of AIDS in 5 (71.4%) of 7 long-term survivors compared with 8 (17.8%) of 45 short-term survivors. CD4 T-lymphocyte counts were substantially higher in the long-term survivors, with 3 (42.9%) of 7 having counts exceeding 300 cells/mm3 in comparison with only 1 (4.3%) of 23 short-term survivors. Contrast enhancement on radiographic imaging was observed in 3 (50%) of 6 long-term survivors in comparison with 4 (8.9%) of 45 short-term survivors. Neurological recovery and radiographic improvement were not observed in any short-term survivors but were seen in 5 (71.4%) long-term survivors. There was no association between treatment modalities and survival. Predictors of long-term survival in AIDS patients with PML include PML as the heralding manifestation of AIDS, high CD4 T-lymphocyte count at disease onset, lesion enhancement on computed tomographic scan or magnetic resonance imaging, and evidence of recovery of neurological function.
Glucokinase activators in diabetes management (2008)

Type 2 diabetes is a chronic metabolic disease that adversely affects both the quality and longevity of life. The disease is characterised by elevated blood glucose (hyperglycaemia) that is associated with microvascular complications and increased macrovascular risk. Existing oral agents, either alone or in combination, do not exhibit adequate or sustained glucose lowering efficacy in Type 2 diabetics. Consequently, there is an unmet medical need for improved antidiabetic agents which are both more effective at lowering glucose and which display sustained efficacy over a number of years. Such agents would allow present glycaemic treatment targets to be achieved with greater success. Glucokinase activators (GKAs) represent a novel class of glucose-lowering agents. Preclinical data supports the notion that these agents act to lower blood glucose through effects in both the liver and pancreas. It is predicted that this dual compartment mechanism of action of GKAs will translate to robust glucose lowering in diabetic patients. The potential benefits and risks associated with the pharmacological activation of glucokinase are evaluated. The status of GKAs in preclinical and clinical development is assessed are the future prospects of these agents.
Citrate-process pilot-plant operation at the Bunker Hill Company. Report of investigations (1979)

The prevalence of the metabolic syndrome among adults from the Nutritional Survey of the Canary Islands is high and similar to that observed in the USA (21.8%).
Tauons and Prions: Infamous Cousins? (2011)

The paradigm of Alzheimer's disease (AD) is one subject to frequent change: what was thought to be a rare form of pre-senile dementia was revealed as a wide-spread malady; where amyloid-β was deemed the sole causative agent for the better part of 20 years, tau protein was shown to play a crucial role in AD genesis. With the discovery of possible prion-like phenomena in this disease supposedly driven by cell-autonomous processes, an evaluation of the similarities and differences between tau-driven neurodegeneration and prion disease becomes necessary. In this article, we provide a comparison of the template agent genesis, filament assembly, as well as intra- and inter-individual spread of prions and tauons.