gebhart/patrepeval huggingface dataset:
Myogenic tone and reactivity: definitions based on muscle physiology. (1989)

This paper suggests definitions of myogenic tone and reactivity in blood vessels on the basis of general muscle physiology and discusses some aspects of the cellular mechanisms involved. Tone is defined as a sustained state of contraction in a muscle. The word says nothing about the exact cellular events except that it is an active process in the contractile proteins. Myogenic implies that the stimulus for the tone originates in the muscle itself without involving nerves, hormones or specific autacoids. When working with isolated vascular smooth muscle we conclude that it has myogenic tone if we can demonstrate contractile force in standard physiological salt solution without the addition of vasoconstrictor agents or abnormal ion concentrations. Tone can occur in any type of muscle, principally through two different patterns of cellular activity: (1) The individual cells or motor units all contract in a tonic way, either by graded depolarization and contracture or by frequent action potentials and fused tetanus; and (2) the muscle as a whole shows tone as an integrated result of asynchronous phasic contractions in its separate units. These principles are discussed below in relation to vascular tone in various parts of the circulation. Myogenic reactivity in a blood vessel is defined as the ability of the vascular smooth muscle to contract in response to stretch or to an increase in transmural pressure. Many different components of the cellular machinery of the smooth muscle may respond to the applied force but the present discussion is concerned with excitation of the cell membrane by stretch (mechano-electrical coupling).(ABSTRACT TRUNCATED AT 250 WORDS)
Genomic Sequencing and Methylation Analysis by Ligation Mediated PCR (1989)

Genomic sequencing permits studies of in vivo DNA methylation and protein-DNA interactions, but its use has been limited because of the complexity of the mammalian genome. A newly developed genomic sequencing procedure in which a ligation mediated polymerase chain reaction (PCR) is used generates high quality, reproducible sequence ladders starting with only 1 microgram of uncloned mammalian DNA per reaction. Different sequence ladders can be created simultaneously by inclusion of multiple primers and visualized separately by rehybridization. Relatively little radioactivity is needed for hybridization and exposure times are short. Methylation patterns in genomic DNA are readily detectable; for example, 17 CpG dinucleotides in the 5' region of human X-linked PGK-1 (phosphoglycerate kinase 1) were found to be methylated on an inactive human X chromosome, but unmethylated on an active X chromosome.
In vitro Activity of Azithromycin in Combination with Amikacin, Ceftazidime, Ciprofloxacin or Imipenem against Clinical Isolates of <i>Acinetobacter baumannii</i> (2003)

The in vitro activity of the two-drug combinations of azithromycin with amikacin, ceftazidime, ciprofloxacin or imipenem against five clonally unrelated strains of Acinobacter baumannii were evaluated. Synergy studies were performed by the checkerboard microtiter method. The fractional inhibitory concentration (FIC) index was calculated for each drug combination. None of the four combinations tested was antagonistic. The combination of azithromycin and ceftazidime was synergistic (FIC index <or=0.5) for one strain and partially synergistic (FIC index 0.75) for another strain. An additive effect (FIC index = 1) was observed for the combinations of azithromycin with imipenem (two strains) or ceftazidime (one strain). The activities of the other combinations were indifferent (FIC index range from 1.5 to 2.5). It is concluded that azithromycin combined with ceftazidime has moderate synergistic activity against some multiresistant A. baumannii.
Towards Semi-supervised Transcription of Handwritten Historical Weather Reports (2012)

This paper addresses the automatic transcription of handwritten documents with a regular tabular structure. A method for extracting machine printed tables from images is proposed, using very little prior knowledge about the document layout. The detected table serves as query for retrieving and fitting a structural template, which is then used to extract handwritten text fields. A semi-supervised learning approach is applied to this fields, aiming at minimizing the human labeling effort for recognizer training. The effectiveness of the proposed approach is demonstrated experimentally on a set of historical weather reports. Compared to using all labels, competitive recognition performance is achieved by labeling only a small fraction of the data, keeping the required human effort very low.
Expression of a Glutamate Decarboxylase Homologue Is Required for Normal Oxidative Stress Tolerance in Saccharomyces cerevisiae (2001)

The action of gamma-aminobutyrate (GABA) as an intercellular signaling molecule has been intensively studied, but the role of this amino acid metabolite in intracellular metabolism is poorly understood. In this work, we identify a Saccharomyces cerevisiae homologue of the GABA-producing enzyme glutamate decarboxylase (GAD) that is required for normal oxidative stress tolerance. A high copy number plasmid bearing the glutamate decarboxylase gene (GAD1) increases resistance to two different oxidants, H(2)O(2) and diamide, in cells that contain an intact glutamate catabolic pathway. Structural similarity of the S. cerevisiae GAD to previously studied plant enzymes was demonstrated by the cross-reaction of the yeast enzyme to a antiserum directed against the plant GAD. The yeast GAD also bound to calmodulin as did the plant enzyme, suggesting a conservation of calcium regulation of this protein. Loss of either gene encoding the downstream steps in the conversion of glutamate to succinate reduced oxidative stress tolerance in normal cells and was epistatic to high copy number GAD1. The gene encoding succinate semialdehyde dehydrogenase (UGA5) was identified and found to be induced by H(2)O(2) exposure. Together, these data strongly suggest that increases in activity of the glutamate catabolic pathway can act to buffer redox changes in the cell.
The Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase (1997)

The function of UreC, the product of a 1,335-bp-long open reading frame upstream from the urease structural genes (ureAB) of Helicobacter pylori, was investigated. We present data showing that the ureC gene product is a phosphoglucosamine mutase. D. Mengin-Lecreulx and J. van Heijenoort (J. Biol. Chem. 271:32-39, 1996) observed that UreC is similar (43% identity) to the GlmM protein of Escherichia coli. Those authors showed that GlmM is a phosphoglucosamine mutase catalyzing interconversion of glucosamine-6-phosphate into glucosamine-1-phosphate, which is subsequently transformed into UDP-N-acetylglucosamine. The latter product is one of the main cytoplasmic precursors of cell wall peptidoglycan and outer membrane lipopolysaccharides. The present paper reports that, like its E. coli homolog glmM, the H. pylori ureC gene is essential for cell growth. It was known that growth of a lethal conditional glmM mutant of E. coli at a nonpermissive temperature can be restored in the presence of the ureC gene. We showed that complete complementation of the glmM mutant can be obtained with a plasmid overproducing UreC. The peptidoglycan content and the specific phosphoglucosamine mutase activity of such a complemented strain were measured; these results demonstrated that the ureC gene product functions as a phosphoglucosamine mutase. Homologs of the UreC and GlmM proteins were identified in Haemophilus influenzae, Mycobacterium leprae, Clostridium perfringens, Synechocystis sp. strain PCC6803, and Methanococcus jannaschii. Significant conservation of the amino acid sequence of these proteins in such diverse organisms suggests a very ancient common ancestor for the genes and defines a consensus motif for the phosphoglucosamine mutase active site. We propose renaming the H. pylori ureC gene the glmM gene.
The small heat shock protein HSP27 is not an independent prognostic marker in axillary lymph node-negative breast cancer patients. (1996)

Heat shock protein 27 (hsp27) belongs to the family of heat shock proteins and is thought to be involved in thermotolerance, cell proliferation, drug resistance, and chaperone processes. The aim of this study was to investigate whether hsp27 levels are correlated with clinical outcome in axillary lymph node-negative breast cancer patients. We describe a Western blot study measuring hsp27 levels in 425 patients and an immunohistochemistry (IHC) study analyzing 788 patients. Results obtained by both methods were concordant. Univariate survival analysis was performed considering hsp27 either as an optimally dichotomized variable or as a continuous variable. Additional data include age at biopsy, tumor size, estrogen receptor (ER) and progesterone receptor status, tumor ploidy and percentage of cells in S phase, and adjuvant therapy. hsp27 levels correlated positively with ER status (P = 0.0001 in Western blot and IHC study), progesterone receptor status (P = 0.0001 in Western blot and IHC study), and aneuploidy (Western blot study, P = 0.0012; IHC study, P = 0.0004) but not with tumor size (Western blot study, P = 0.69; IHC, P = 0.53) or S phase (Western blot study, P = 0.19; IHC study, P = 0.38). Overall, there was no relationship between hsp27 expression and disease-free survival (Western blot study, P = 0.70/0.54; IHC, P = 0.47/0.30) or overall survival (Western blot study, P = 0.16/0.15; IHC, P = 0.46/0.78). Exploratory subset analyses defined by ER status and use of adjuvant treatment indicated that in ER+/untreated patients, high hsp27 levels correlated modestly with shorter disease-free survival (Western blot, P = 0.04/0.04; IHC, P = 0.11/0. 03). hsp27 is not a useful prognostic marker for the clinic in axillary lymph node-negative patients. However, the finding of modest prognostic value of hsp27 in the subgroup of ER+/untreated patients raises new questions about the biological function of hsp27 in breast cancer.
Independence of Protein Kinase C-δ Activity from Activation Loop Phosphorylation (2006)

Activation loop phosphorylation plays critical regulatory roles for many kinases. Unlike other protein kinase Cs (PKC), PKC-delta does not require phosphorylation of its activation loop (Thr-507) for in vitro activity. We investigated the structural basis for this unusual capacity and its relevance to PKC-delta function in intact cells. Mutational analysis demonstrated that activity without Thr-507 phosphorylation depends on 20 residues N-terminal to the kinase domain and a pair of phenylalanines (Phe-500/Phe-527) unique to PKC-delta in/near the activation loop. Molecular modeling demonstrated that these elements stabilize the activation loop by forming a hydrophobic chain of interactions from the C-lobe to activation loop to N-terminal (helical) extension. In cells PKC-delta mediates both apoptosis and transcription regulation. We found that the T507A mutant of the PKC-delta kinase domain resembled the corresponding wild type in mediating apoptosis in transfected HEK293T cells. But the T507A mutant was completely defective in AP-1 and NF-kappaB reporter assays. A novel assay in which the kinase domain of PKC-delta and its substrate (a fusion protein of PKC substrate peptide with green fluorescent protein) were co-targeted to lipid rafts revealed a major substrate-selective defect of the T507A mutant in phosphorylating the substrate in cells. In vitro analysis showed strong product inhibition on the T507A mutant with particular substrates whose characteristics suggest it contributes to the substrate selective defect of the PKC-delta T507A mutant in cells. Thus, activation loop phosphorylation of PKC-delta may regulate its function in cells in a novel way.
Cardiac Resynchronization and Implantable Cardioverter Defibrillator Therapy: Preliminary Results from the InSync Implantable Cardioverter Defibrillator Italian Registry (2003)

The aim of this study was to evaluate ventricular arrhythmias occurring in recipients of the InSync ICD for the primary and secondary prevention of sudden death. The InSync ICD was implanted in 142 patients (128 men; mean age 65 +/- 10 years) with heart failure (mean NYHA functional Class 3.0 +/- 0.7) and wide QRS (mean 159 +/- 33 ms). The underlying etiology was ischemic in 55%, idiopathic in 33%, and valvular or hypertensive cardiomyopathy in 12% of patients. The numbers of arrhythmic episodes/100 patient-months was computed with their 95% CI, assuming a Poisson distribution. Implants were performed in 48 (34%) patients who did not have an ACC/AHA guidelines Class I indication for ICD therapy. A total of 104 patients were compliant for follow-up visits. During a 9-month median (range 0.1-24) follow-up of 104 compliant patients, 19 experienced a total of 94 ventricular arrhythmias, all successfully interrupted or self-terminated, with a median number of two separate episodes, corresponding to a rate of 10 episodes/100 person-month (95% CI 8-12). A rate of 12 episodes/100 person-months (95% CI 10-15) was measured in the subgroup of patients with ACC/AHA class I indications, versus two episodes/100 person-months (95% CI 1-5) in the remainder of the population. Among 12 deaths, 9 were due to heart failure, 1 to a non-cardiovascular cause, and 2 to unknown causes. The implantation of ICD in heart failure patients has been prominently extended to primary prevention. Patients without standard ICD indications experienced life-threatening arrhythmic events. The impact of ICD combined with cardiac resynchronization therapy on arrhythmic profile, mortality, and costs in this subgroup of patients need to be more precisely studied, with a particular focus on the various types of underlying heart disease.
Influenza immunization with trehalose-stabilized virus-like particle vaccine using microneedles (2010)

Morbidity and mortality due to seasonal and pandemic influenza could be reduced by simpler vaccination methods that enable improved vaccination coverage. In this study, solid metal microneedles coated with influenza virus-like particle (VLP) vaccine were inserted into skin for intradermal immunization. Microneedles were applied to the skin by hand and designed for simple administration with little or no training. Inclusion of trehalose in the coating formulation significantly increased vaccine stability during coating by maintaining hemagglutination activity. Mice vaccinated with stabilized microneedles developed strong antibody responses comparable to conventional intramuscular vaccination and were fully protected against subsequent viral challenge. Whereas, coating microneedles with a coating solution lacking trehalose led to only partial protection against lethal viral challenge. Therefore, our results show that microneedles coated with trehalose-stabilized VLP vaccine can be a promising tool for improving influenza vaccination.
Kinetic and thermodynamic characterization of the R17 coat protein-ribonucleic acid interaction (1983)

A filter retention assay is used to examine the kinetic and equilibrium properties of the interaction between phage R17 coat protein and its 21-nucleotide RNA binding site. The kinetics of the reaction are consistent with the equilibrium association constant and indicate a diffusion-controlled reaction. The temperature dependence of Ka gives delta H = -19 kcal/mol. This large favorable delta H is partially offset by a delta S = -30 cal mol-1 deg-1 to give a delta G = -11 kcal/mol at 2 degrees C in 0.19 M salt. The binding reaction has a pH optimum centered around pH 8.5, but pH has no effect on delta H. While the interaction is insensitive to the type of monovalent cation, the affinity decreases with the lyotropic series among monovalent anions. The ionic strength dependence of Ka reveals that ionic contacts contribute to the interaction. Most of the binding free energy, however, is a result of nonelectrostatic interactions.
Paradox of Richness: A Cognitive Model of Media Choice (2005)

Researchers have long studied the effects of social presence and media richness on media choice and the effects of media use. This focus on social presence and social psychological theories has led to valuable research on communication. However, little research (either empirical or theoretical) has been done to understand the ways in which media choices influence the cognitive processes that underlie communication. In this paper, we present a cognitive-based view of media choice and media use, based on dual process theories of cognition, which argue that in order for individuals to systematically process messages, they must be motivated to process the message and have the ability to process it. We argue that the use of rich media high in social presence induces increased motivation but decreases the ability to process information, while the use of lean media low in social presence induces decreased motivation but increases the ability to process information. The paradox of richness lies in its duality of impact: from a cognitive perspective, rich media high in social presence simultaneously acts to both improve and impair performance.
Characteristics of Uptake of Cefroxadine by Rabbit Small Intestinal Brush Border Membrane Vesicles. (1996)

Characteristics of transport of an oral aminocephalosporin, cefroxadine, in rabbit small intestinal brush border membrane vesicles were examined. Uptake rate of cefroxadine was saturable in the presence of an inward H+ gradient, and kinetic parameters were similar to those of cephradine. However, the uptake rate was almost linear with the concentration in the absence of an inward H+ gradient up to 5 mM. Overshoot phenomenon was observed in the presence of an inward H+ gradient at 37 degrees C, but it disappeared with decrease of temperature. The Arrhenius plot of uptake rate constant showed a break point at approximately 30 degrees C. Cefroxadine uptake was optimum in the vicinity of pH 5.5 at 37 degrees C, but the dependence on extravesicular pH disappeared at 15 degrees C. The uptake of cefroxadine in the presence of an inward H+ gradient was markedly inhibited by other aminocephalosporins such as cephalexin, but the inhibition was only slight in the absence of an inward H+ gradient. Alkyl alcohols such as n-hexyl alcohol also inhibited H(+)-coupled uptake of cefroxadine at the concentration range at which the alcohols increased the membrane fluidity, and overshoot phenomenon diminished, suggesting that H(+)-coupled transport of cefroxadine is sensitive to the alcohol-induced increase in membrane fluidity. On the other hand, the alcohols rather stimulated its uptake in the absence of an H+ gradient.
Towards an Understanding and Control of Nucleation, Growth, Habit, Dissolution, and Structure of Crystals Using “Tailor-Made” Auxiliaries (1999)

Although crystals and crystallization as a process play an important role in pure and applied science, our ability to design crystals with desired properties and our control over crystallization based on structural understanding are still limited. Indeed, our ignorance of the overall process of crystal growth is brought to the fore by comparison with the controlled crystal growth provided in biomineralization. Organisms can mold crystals of specific morphologies, sizes, and orientations in the form of composites of minerals and organic materials with characteristics vastly different from those of their inorganic counterparts (Löwenstam and Weiner 1989; Addadi and Weiner 1992; Mann 1993). Nevertheless, the technological advances in controlling the microstructure of inorganic materials on the subnanometer scale have led to tremendous success in the preparation of ceramics, synthetic layered microstructures, and semiconducting materials. Paradoxically, advances in the field of organic materials have not been as striking, although the techniques for the preparation of films such as Langmuir–Blodgett and self-assembled multilayers on solid support hold promise as pyroelectric, piezoelectric, and frequency doubling devices, etc. The thread that binds these diverse topics involves molecular interactions at interfaces.
Chemiluminescent assay of β-D-galactosidase based on indole luminescence (1998)

We developed a novel chemiluminescent assay of beta-D-galactosidase (beta-gal) based on the chemiluminescence of indole. 5-Bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-gal) was used as a substrate for beta-gal and also as a light emitter. X-gal was hydrolysed by beta-gal to liberate free indoxyl, followed by oxidation to indigo dye, and simultaneously produces hydrogen peroxide (H2O2). H2O2 reacts with the residual X-gal in the presence of horseradish peroxidase (HRP) to emit light. The measurable range of beta-gal obtained by this method was 6 x 10(-14) mol/L to 6 x 10(-11) mol/L; the detection limit was 3 amol/assay. This chemiluminescent assay could be applied to an enzyme immunoassay of thyroxine using beta-gal as the enzyme label.
Evolutionary Dynamics of the Glycan Shield of theHuman Immunodeficiency Virus Envelope during Natural Infection andImplications for Exposure of the 2G12Epitope (2004)

Elucidation of the kinetics of exposure of neutralizing epitopes on the envelope of human immunodeficiency virus type 1 (HIV-1) during the course of infection may provide key information about how HIV escapes the immune system or why its envelope is such a poor immunogen to induce broadly efficient neutralizing antibodies. We analyzed the kinetics of exposure of the epitopes corresponding to the broadly neutralizing human monoclonal antibodies immunoglobulin G1b12 (IgG1b12), 2G12, and 2F5 at the quasispecies level during infection. We studied the antigenicity and sequences of 94 full-length envelope clones present during primary infection and at least 4 years later in four HIV-1 clade B-infected patients. No or only minor exposure differences were observed for the 2F5 and IgG1b12 epitopes between the early and late clones. Conversely, the envelope glycoproteins of the HIV-1 quasispecies present during primary infection did not expose the 2G12 neutralizing epitope, unlike those present after several years in three of the four patients. Sequence analysis revealed major differences at potential N-linked glycosylation sites between early and late clones, particularly at positions known to be important for 2G12 binding. Our study, in natural mutants, confirms that the glycosylation sites N295, N332, and N392 are essential for 2G12 binding. This study demonstrates the relationship between the evolving "glycan shield " of HIV and the kinetics of exposure of the 2G12 epitope during the course of natural infection.
Changes associated with the development of resistance to imatinib (STI571) in two leukemia cell lines expressing p210 Bcr/Abl protein (2004)

BCR/ABL amplification with subsequent overexpression of Bcr/Abl protein, loss of apoptotic response, or point mutation of the ATP-binding site of BCR/ABL was associated alternatively with the acquisition of the resistant phenotype, supporting the notion that multiple mechanisms are involved in the induction of resistance to imatinib. The initial number of BCR/ABL copies itself was not related directly to the degree of resistance. The reversibility of the resistance may be complete, partial, or irreversible, depending on the mechanism(s) involved and the degree of resistance. Both cell lines serve as models for further elucidation of various aspects of imatinib-resistance mechanisms.