gebhart/patrepeval huggingface dataset:
Effect of Cytoplasmic Tail Truncations on the Activity of the M 2 Ion Channel of Influenza A Virus (1999)

The M(2) protein of influenza A virus forms a proton channel that is required for viral replication. The M(2) ion channel is a homotetramer and has a 24-residue N-terminal extracellular domain, a 19-residue transmembrane domain, and a 54-residue cytoplasmic tail. We show here that the N-terminal methionine residue is cleaved from the mature protein. Translational stop codons were introduced into the M(2) cDNA at residues 46, 52, 62, 72, 77, 82, 87, and 92. The deletion mutants were designated truncx, according to the amino acid position that was changed to a stop codon. We studied the role of the cytoplasmic tail by measuring the ion channel activity (the current sensitive to the M(2)-specific inhibitor amantadine) of the cytoplasmic tail truncation mutants expressed in oocytes of Xenopus laevis. When their conductance was measured over time, mutants trunc72, trunc77, and trunc92 behaved comparably to wild-type M(2) protein (a decrease of only 4% over 30 min). In contrast, conductance decreased by 28% for trunc82, 27% for trunc62, and 81% for trunc52 channels. Complete closure of the channel could be observed in some cells for trunc62 and trunc52 within 30 min. These data suggest that a role of the cytoplasmic tail region of the M(2) ion channel is to stabilize the pore against premature closure while the ectodomain is exposed to low pH.
New perspectives in the differentiation of bone-forming cells. (1992)

Bone formation comprises a complex but ordered sequence of events which involves the proliferation and differentiation of chondrogenic and osteoblastic precursor cells ultimately leading to the formation of a calcified extracellular matrix. This process can be observed in vivo but under these conditions is difficult to study at the molecular level. A number of in vitro models have been developed which recapitulate discrete elements of this process. Using these models, detailed information has been obtained regarding the differentiation of bone forming cells and the molecular biology of the mineralization process. It has been shown that, in vitro, osteoblastic precursor cells can form a mineralized matrix similar to that seen in vivo. This calcification process was shown to consist of three interdependent phases: proliferation, matrix maturation and mineralization. Each of these phases was characterized by the expression of particular genes. Osteoblast precursors have been cloned and consequently shown to be able to differentiate in vitro into a number of other mesenchymal cells, supporting the theory that osteoblasts are derived from multipotent mesenchymal cells. It is possible that markers derived from these models could be used in the future to extend our knowledge of bone formation in vivo.
The program dependence graph and its use in optimization (1987)

In this paper we present an intermediate program representation, called the program dependence graph ( PDG ), that makes explicit both the data and control dependences for each operation in a program. Data dependences have been used to represent only the relevant data flow relationships of a program. Control dependences are introduced to analogously represent only the essential control flow relationships of a program. Control dependences are derived from the usual control flow graph. Many traditional optimizations operate more efficiently on the PDG. Since dependences in the PDG connect computationally related parts of the program, a single walk of these dependences is sufficient to perform many optimizations. The PDG allows transformations such as vectorization, that previously required special treatment of control dependence, to be performed in a manner that is uniform for both control and data dependences. Program transformations that require interaction of the two dependence types can also be easily handled with our representation. As an example, an incremental approach to modifying data dependences resulting from branch deletion or loop unrolling is introduced. The PDG supports incremental optimization, permitting transformations to be triggered by one another and applied only to affected dependences.
Raman Microscopy of Human Embryonic Stem Cells Exposed to Heat and Cold Stress (2011)

Human embryonic stem cells (hESCs) have large nucleus-to-cytoplasm ratios and nucleic acid spectral bands are prominent in their characteristic Raman signatures. Under normal conditions, the major variations in these signatures are due to changes in glycogen content, but how these signatures vary in response to different external conditions is largely unknown. In this study we investigated the influences of temperature variations on hESC Raman signatures. At 32 °C, compared to the 37 °C control condition, cell proliferation rates were markedly reduced and glycogen Raman band intensities were elevated. In addition, at both temperatures, an inverse relationship between cell proliferation rates (i.e., onset of exponential growth phase vs. end of exponential phase) and glycogen Raman band intensities was observed. This relationship suggested a role for glycogen in the energy metabolism of hESC self-renewal. Protein and lipid spectral variations were small and co-varied with those of nucleic acids, suggesting that they were related to changes in cellular dimensions occurring during the cell cycle. When the temperature was elevated to 39 °C, increased glycogen band intensities, compared to controls, were also observed. In addition, spectral evidence of differentiation emerged that was supported by reduced SSEA-3 expression. Taken together, these results demonstrated that heat and cold stress had quite different effects on the characteristic Raman signatures of hESCs. Thus, Raman spectroscopy can be used to detect deviation from optimal culturing temperatures and therefore it could be of considerable value in the routine and noninvasive determination of hESC culture quality.
Optical trapping and binding (2013)

The phenomenon of light's momentum was first observed in the laboratory at the beginning of the twentieth century, and its potential for manipulating microscopic particles was demonstrated by Ashkin some 70 years later. Since that initial demonstration, and the seminal 1986 paper where a single-beam gradient-force trap was realized, optical trapping has been exploited as both a rich example of physical phenomena and a powerful tool for sensitive measurement. This review outlines the underlying theory of optical traps, and explores many of the physical observations that have been made in such systems. These phenomena include 'optical binding', where trapped objects interact with one another through the trapping light field. We also discuss a number of the applications of 'optical tweezers' across the physical and life sciences, as well as covering some of the issues involved in constructing and using such a tool.
Management of Intractable Sternal Wound Infections with Topical Negative Pressure Dressing (2005)

The advantages of applying TNP dressings in cases of intractable sternal wound infections include (1) protecting the underlying mediasternal structure from infection, (2) permitting delayed sternal closure to avoid cardiac compression induced compromised cardiopulmonary function, (3) possibility of repeated wound inspection and bedside debridement, (4) cost-effectiveness of wound care, and (5) providing an option to promote sternal wound secondary healing for patients in poor physical condition.
The Smart Box Application Model (2004)

This paper proposes the usage of a software framework, based on the Smart Box application model, for the development of applications or appliances of the Smart Box application domain. This class of ubiquitous computing applications can be described as automatic content monitoring applications using Auto-ID technologies such as Radio Frequency Identification (RFID). The Smart Box application model is based on the concepts of location and object to represent a kind of a box and the items and persons that are related to the box. States defined through conditions abstract from the content of the box and limit notification of the application to exceptional cases. Implementing the model and framework we could show that the model is adequate to describe the Smart Box application domain and that the framework decreases the development effort of Smart Box applications. 1.
Photopatterned liquid crystalline polymers for microactuators (2006)

We have investigated the properties of thermally-responsive, patterned liquid crystalline polymers as their dimensions are scaled to a size suitable for use in microelectromechanical systems. All samples were fabricated using surface alignment and photopatterning techniques that can be used to produce integrated devices anchored on a substrate. The thermomechanical properties of free-standing macroscopic samples with varying concentration of crosslinking molecules were investigated in order to optimize the thermal response of the material. It was found that samples containing 12% crosslinker were able to expand by up 19% when heated. The thermomechanical properties of surface-anchored films were also investigated, and it was found that by employing a polymerized cholesteric structure of the liquid crystalline units a thermal expansion of up to 11% could be achieved when the sample was heated to 200 °C. Patternability was demonstrated using a simple photopatterning process that was used to fabricate samples consisting of lines of cholesteric material on a bare substrate, or alternating regions of liquid crystalline polymer in the isotropic and cholesteric phases. Actuation of these films was also demonstrated.
An Operational Near-Infrared Fluorescence Imaging System Prototype for Large Animal Surgery (2003)

Near-infrared (NIR) fluorescence imaging has the potential to revolutionize human cancer surgery by providing sensitive, specific, and real-time intraoperative visualization of normal and disease processes. We have previously introduced the concept of a low-cost, safe, and easy-to-use NIR fluorescence imaging system that permits the surgeon to "see" surgical anatomy and NIR fluorescence simultaneously, non-invasively, with high spatial resolution, in real-time, and without moving parts. In this study, we present an operational prototype designed specifically for use during large animal surgery. Such a system serves as a foundation for future clinical studies. We discuss technical considerations, and provide details of the implementation of subsystems related to excitation light, light collection, computer, and software. Using the prototype, and the clinically available NIR fluorophore indocyanine green, we demonstrate vascular imaging in 35 kg pigs. Cancer-specific applications of this imaging system include image-guided cancer resection with real-time assessment of surgical margins, image-guided sentinel lymph node mapping, intraoperative mapping of tumor and normal vasculature, image-guided avoidance of critical structures such as nerves, and intraoperative detection of occult metastases in the surgical field. Taken together, this study describes an optical imaging system engineered for eventual translation to the clinic.
A Serum Response Factor-Dependent Transcriptional Regulatory Program Identifies Distinct Smooth Muscle Cell Sublineages (1997)

The SM22alpha promoter has been used as a model system to define the molecular mechanisms that regulate smooth muscle cell (SMC) specific gene expression during mammalian development. The SM22alpha gene is expressed exclusively in vascular and visceral SMCs during postnatal development and is transiently expressed in the heart and somites during embryogenesis. Analysis of the SM22alpha promoter in transgenic mice revealed that 280 bp of 5' flanking sequence is sufficient to restrict expression of the lacZ reporter gene to arterial SMCs and the myotomal component of the somites. DNase I footprint and electrophoretic mobility shift analyses revealed that the SM22alpha promoter contains six nuclear protein binding sites (designated smooth muscle elements [SMEs] -1 to -6, respectively), two of which bind serum response factor (SRF) (SME-1 and SME-4). Mutational analyses demonstrated that a two-nucleotide substitution that selectively eliminates SRF binding to SME-4 decreases SM22alpha promoter activity in arterial SMCs by approximately 90%. Moreover, mutations that abolish binding of SRF to SME-1 and SME-4 or mutations that eliminate each SME-3 binding activity totally abolished SM22alpha promoter activity in the arterial SMCs and somites of transgenic mice. Finally, we have shown that a multimerized copy of SME-4 (bp -190 to -110) when linked to the minimal SM22alpha promoter (bp -90 to +41) is necessary and sufficient to direct high-level transcription in an SMC lineage-restricted fashion. Taken together, these data demonstrate that distinct transcriptional regulatory programs control SM22alpha gene expression in arterial versus visceral SMCs. Moreover, these data are consistent with a model in which combinatorial interactions between SRF and other transcription factors that bind to SME-4 (and that bind directly to SRF) activate transcription of the SM22alpha gene in arterial SMCs.
Experimental mononeuropathy reduces the antinociceptive effects of morphine: implications for common intracellular mechanisms involved in morphine tolerance and neuropathic pain (1995)

Recent evidence suggests that hyperalgesia and morphine tolerance, two seemingly unrelated phenomena, have in common certain neural substrates such as activation of the N-methyl-D-aspartate (NMDA) receptor and the subsequent intracellular activation of protein kinase C and nitric oxide. Should common cellular elements be involved in hyperalgesia and morphine tolerance, these cellular and intracellular commonalities might be expected to result in interactions between these two phenomena. Indeed, our previous studies have shown that thermal hyperalgesia develops when animals are made tolerant to the antinociceptive effects of morphine. In this study, we examined the hypothesis that reduction of morphine antinociception occurs following unilateral ligation of the rats's sciatic nerve, a procedure which produces symptoms of a neuropathic pain syndrome including thermal hyperalgesia. When tested using the paw-withdrawal test on day 8 (D8) after either nerve ligation or sham operation, a single intrathecal treatment with 10 micrograms morphine sulfate (30 min after administration) produced significant antinociception in sham-operated rats but not in nerve-injured ones. These results also were obtained when thermal hyperalgesia was reversed in nerve-injured rats by the non-competitive NMDA receptor antagonist MK-801. Consistently, 8 days after sciatic nerve ligation but not after a sham operation, an approximately 6-fold rightward shift occurred in the morphine antinociceptive dose-response curve. This rightward shift of the morphine antinociceptive dose-response curve did not occur at 24 h after either nerve ligation or sham operation. In addition, once daily treatment with 10 nmol MK-801 from D2 to D7 after nerve ligation prevented both the development of thermal hyperalgesia and the rightward shift of the morphine antinociceptive dose-response curve on D8. The results indicate that the antinociceptive effects of morphine are reduced in nerve-injured rats in the absence of daily exposure to morphine and that the NMDA receptor activation may have a critical role in mechanisms of this phenomenon. These data provide further evidence indicating that interactions do occur between neural mechanisms underlying thermal hyperalgesia and morphine tolerance.
Glycosylation at the Fab portion of myeloma immunoglobulin G and increased fucosylated biantennary sugar chains: structural analysis by high-performance liquid chromatography and antibody-lectin enzyme immunoassay using Lens culinaris agglutinin. (1991)

An antibody-lectin enzyme immunoassay technique which had been developed for the analysis of sugar chains of alpha-fetoprotein (N. Kinoshita et al., Clin. Chim. Acta, 179: 143-152, 1989) was used for analysis of sugar chains of myeloma immunoglobulin G (IgG). The IgG sugar chains of four of nine patients with myeloma were found to be highly reactive to Lens culinaris agglutinin as compared with those of six normal controls and 177 patients without myeloma. This reflected a high L. culinaris agglutinin/concanavalin A ratio. The IgGs of these patients were found to have highly sialylated, fucosylated, and bisected biantennary sugar chains at Fab portions as judged by the lectin-blotting technique as well as by high-performance liquid chromatography analysis. These results indicate that some of the myeloma IgG proteins undergo unusual glycosylation processes.
Striatal Enriched Phosphatase 61 Dephosphorylates Fyn at Phosphotyrosine 420 (2002)

A family of protein tyrosine phosphatases enriched within the central nervous system called striatal enriched phosphatase (STEP) has been implicated in the regulation of the N-methyl-d-aspartate receptor. STEP(61), a membrane-associated isoform located in the postsynaptic densities (PSDs) of striatal neurons, contains two transmembrane domains, two proline-rich domains, and a kinase-interacting motif. This study demonstrates that STEP(61) associates with Fyn, a member of the Src family kinases that is also enriched in PSDs. By using human embryonic kidney 293 cells for co-transfection, we determined that a substrate-trapping variant (STEP(61) CS) binds to Fyn but not to other members of the Src family present in PSDs. In a complementary experiment, myc-tagged Fyn immunoprecipitates STEP(61) CS. STEP(61) binds to Fyn through one of its proline-rich domains and the kinase-interacting motif domain, whereas Fyn binds to STEP(61) through its Src homology 2 domain and the unique N-terminal domain. STEP(61) CS pulls down Fyn when the Tyr(420) site is phosphorylated. In vitro, wild-type STEP(61) dephosphorylates Fyn at Tyr(420) but not at Tyr(531). These results suggest that STEP regulates the activity of Fyn by specifically dephosphorylating the regulatory Tyr(420) and may be one mechanism by which Fyn activity is decreased within PSDs.
STUDIES ON Vi ANTIGEN (1961)

Journal Article STUDIES ON Vi ANTIGEN: ROLE OF ACETYL IN ANTIGENIC ACTIVITY Get access MAURICE LANDY, MAURICE LANDY Search for other works by this author on: Oxford Academic PubMed Google Scholar ARTHUR G. JOHNSON, ARTHUR G. JOHNSON Search for other works by this author on: Oxford Academic PubMed Google Scholar MARION E. WEBSTER MARION E. WEBSTER Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 73, Issue 1, January 1961, Pages 55–65, https://doi.org/10.1093/oxfordjournals.aje.a120165 Published: 01 January 1961 Article history Received: 12 August 1960 Published: 01 January 1961
Multiple Versus Single Antipsychotic Agents for Hospitalized Psychiatric Patients: Case-Control Study of Risks Versus Benefits (2004)

Short-term treatment with multiple antipsychotics was associated with major increases in drug exposure, adverse events, and time in the hospital but with no apparent gain in clinical benefit. These findings require further testing in controlled prospective studies.
Production, Distribution, and Kinetic Properties of Inulinase in Continuous Cultures of Kluyveromyces marxianus CBS 6556 (1988)

From a screening of several Kluyveromyces strains, the yeast Kluyveromyces marxianus CBS 6556 was selected for a study of the parameters relevant to the commercial production of inulinase (EC 3.2.1.7). This yeast exhibited superior properties with respect to growth at elevated temperatures (40 to 45 degrees C), substrate specificity, and inulinase production. In sucrose-limited chemostat cultures growing on mineral medium, the amount of enzyme decreased from 52 U mg of cell dry weight at D = 0.1 h to 2 U mg of cell dry weight at D = 0.8 h. Experiments with nitrogen-limited cultures further confirmed that synthesis of the enzyme is negatively controlled by the residual sugar concentration in the culture. High enzyme activities were observed during growth on nonsugar substrates, indicating that synthesis of the enzyme is a result of a derepression/repression mechanism. A substantial part of the inulinase produced by K. marxianus was associated with the cell wall. The enzyme could be released from the cell wall via a simple chemical treatment of cells. Results are presented on the effect of cultivation conditions on the distribution of the enzyme. Inulinase was active with sucrose, raffinose, stachyose, and inulin as substrates and exhibited an S/I ratio (relative activities with sucrose and inulin) of 15 under standard assay conditions. The enzyme activity decreased with increasing chain length of the substrate.
A study of tremor in multiple sclerosis (2001)

One hundred patients with definite multiple sclerosis, who were randomly selected from a multiple sclerosis unit in London, were examined in order to study the prevalence, subtypes, clinical features and associated disability of tremor in this population. There were 35 males and 65 females with an average age of 47 years and an average disease duration of 18.8 years. The mean tremor duration was 13 years, with a median latency of 11 years from disease onset to appearance of tremor. Tremor was reported in 37 patients but was detected in 58. Tremor affected the arms (56%), legs (10%), head (9%) and trunk (7%). There were no examples of face, tongue or jaw tremor. All the patients had action tremor, either postural or kinetic (including intention). Rest, Holmes' ('rubral') and primary orthostatic tremors were not encountered. Tremor severity ranged from minimal in 27%, to mild in 16% and moderate or severe in 15% of cases. Tremor severity correlated with the degree of dysarthria, dysmetria and dysdiadochokinesia but not with grip strength. In order to determine the clinical characteristics of these tremors, the action tremors of the upper limbs were subclassified according to the predominant site and state of tremulous activity. Of the 50 patients with tremor in the right arm, 32% had distal postural tremor, 36% had distal postural and kinetic tremor, 16% had proximal postural and kinetic tremor; 4% had proximal and distal postural and kinetic tremor and 12% isolated intention tremor. Twenty-seven percent of the overall study population had tremor-related disability and 10% had incapacitating tremor. Patients with abnormal tremor (severity grade >1/10) were more likely than those without tremor to be wheelchair dependent and have a worse Expanded Disability Systems Score, but Barthel activities of daily living indices and cognitive scores were comparable in the two groups.
APOPTOSIS INDUCTION IN HUMAN PERIPHERAL BLOOD T LYMPHOCYTES BY HIGH-DOSE STEROID THERAPY (1997)

High-dose steroid pulse therapy is effective in transplant rejection and severe autoimmune diseases. Our goal was to identify the mechanism by which high-dose steroid exerts specific immunosuppressive actions. In this study, we investigated the in vivo effects of high-dose (1 g) methylprednisolone infusion on peripheral blood T lymphocyte apoptosis induction in 15 patients with severe autoimmune diseases. DNA fragmentation was detected in peripheral blood T cells isolated from these patients after 2 and 4 hr of steroid infusion. In contrast, T cells isolated from the same patients before or 8 or more hours after infusion did not show DNA fragmentation. DNA fragmentation was more significant in CD4+ than CD8+ T cells. The susceptibility of CD4+ T cells to apoptosis was associated with a lower expression of Bcl-2 in these cells compared with that on CD8+ T cells. To support the T-cell apoptosis induction by pulse therapy, peripheral blood T cells from normal subjects underwent DNA fragmentation after in vitro exposure to 2.5-10 microg/ml of methylprednisolone for 30 min. Our results indicate that induction of peripheral blood T-cell apoptosis is an important mechanism contributing to the immunosuppression observed after high-dose steroid therapy.