gebhart/patrepeval huggingface dataset:
Sheared Flow Stabilization of them=1Kink Mode inZPinches (1995)

The effect of a sheared axial flow on the $m\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1$ kink instability in $Z$ pinches is studied numerically by reducing the linearized magnetohydrodynamic equations to a one-dimensional displacement equation. An equilibrium is used that is made marginally stable against the $m\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0$ sausage mode by tailoring its pressure profile. The principal result reveals that a sheared axial flow stabilizes the kink mode when the shear exceeds a threshold that is dependent on the location of the conducting wall. For the equilibria studied here the maximum threshold shear ( ${v}_{z}^{\ensuremath{'}}/{\mathrm{kV}}_{A}^{0}$) was about $0.1$.
Clinical and biologic activity of the farnesyltransferase inhibitor R115777 in adults with refractory and relapsed acute leukemias: a phase 1 clinical-laboratory correlative trial (2001)

R115777 is a nonpeptidomimetic enzyme-specific inhibitor of farnesyl protein transferase (FT) that was developed as a potential inhibitor of Ras protein signaling, with antitumor activity in preclinical models. This study was a phase 1 trial of orally administered R115777 in 35 adults with poor-risk acute leukemias. Cohorts of patients received R115777 at doses ranging from 100 mg twice daily (bid) to 1200 mg bid for up to 21 days. Dose-limiting toxicity occurred at 1200 mg bid, with central neurotoxicity evidenced by ataxia, confusion, and dysarthria. Non-dose-limiting toxicities included reversible nausea, renal insufficiency, polydipsia, paresthesias, and myelosuppression. R115777 inhibited FT activity at 300 mg bid and farnesylation of FT substrates lamin A and HDJ-2 at 600 mg bid. Extracellular signal-regulated kinase (ERK), an effector enzyme of Ras-mediated signaling, was detected in its phosphorylated (activated) form in 8 (36.4%) of 22 pretreatment marrows and became undetectable in 4 of those 8 after one cycle of treatment. Pharmacokinetics revealed a linear relationship between dose and maximum plasma concentration or area under the curve over 12 hours at all dose levels. Weekly marrow samples demonstrated that R115777 accumulated in bone marrow in a dose-dependent fashion, with large increases in marrow drug levels beginning at 600 mg bid and with sustained levels throughout drug administration. Clinical responses occurred in 10 (29%) of the 34 evaluable patients, including 2 complete remissions. Genomic analyses failed to detect N-ras gene mutations in any of the 35 leukemias. The results of this first clinical trial of a signal transduction inhibitor in patients with acute leukemias suggest that inhibitors of FT may have important clinical antileukemic activity. (Blood. 2001;97:3361-3369)
IL‐15 and IL‐16 overexpression in cutaneous T‐cell lymphomas: stage‐dependent increase in mycosis fungoides progression (2000)

Cytokines are of major importance for the pathogenesis of cutaneous T-cell lymphomas (CTCL). Recent data suggested that IL-15 and IL-16 are survival/growth factors for the malignant T cells in these entities. To investigate the expression of IL-15 and IL-16 in mycosis fungoides (MF) and CD30+ pleomorphic T-cell lymphoma in vivo, we established a competitive RT-PCR technique. Analyzing skin biopsies from CTCL patients at different stages in comparison to psoriatic and healthy skin, we found IL-15 and IL-16 mRNA overexpression in both CTCL entities. Remarkably, there was some evidence for a stage-dependent increase during MF progression. We found only slight overexpression in early stage MF, when only few tumor cells are detectable within the infiltrates, whereas marked overexpression was found in more advanced lesions, which are characterized by a higher density of malignant cells. These results suggested that CTCL cells themselves might produce the cytokines. To further elucidate this hypothesis, two CTCL cell lines were analyzed but gave conflicting results. Therefore, the cellular origin of the IL-15 and IL-16 overexpression in CTCL remains unclear. Considering the significant overexpression of IL-15 and IL-16 and their biological capacities it is likely that these cytokines contribute to the tumor development. So, they might be involved in growth and skin homing of CTCL cells.
Microgliosis and Impaired Cognition (1998)

There is growing evidence that immune responses within the CNS help to determine the course and severity of neurological diseases (1). Microglia, mononuclear phagocytes endogenous to the CNS, are the principal immune cells of the brain. Although normally found in a quiescent state, microglia are activated by a variety of disease-associated signals to release cytokines and cytotoxins. These factors, in turn, promote wound healing or, alternatively, induce neuron injury. Groups of reactive microglia are found scattered throughout the brain following infection by human immunodeficiency virus-1 (HIV-1) or clustered about senile plaques found in Alzheimer's disease (AD) (Fig. 1; refs. 2 and 3). We propose that chronic reactive microgliosis destroys neurons and contributes to loss of cognitive function. Blockade of activated microglia may slow cognitive deterioration occurring with inflammatory dementia.KeywordsAcquire Immune Deficiency SyndromeMononuclear PhagocyteQuinolinic AcidImpaired CognitionReactive MicrogliaThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
DNA manipulation, sorting, and mapping in nanofluidic systems (2010)

Fluidic systems with nanometre length scales enable sensitive analysis of DNA molecules. Nanofluidic systems have been used to probe conformational, dynamic, and entropic properties of DNA molecules, to rapidly sort DNA molecules based on length dependent interactions with their confining environment, and for determining the spatial location of genetic information along long DNA molecules. In this critical review, recent experiments utilizing fluidic systems comprised of nanochannels, nanoslits, nanopores, and zero-mode waveguides for DNA analysis are reviewed (161 references).
The influenza virus NS1 protein is a poly(A)-binding protein that inhibits nuclear export of mRNAs containing poly(A) (1994)

The influenza virus NS1 protein inhibits the nuclear export of a spliced viral mRNA, NS2 mRNA (F. V. Alonso-Caplen, M. E. Nemeroff, Y. Qiu, and R. M. Krug, Genes Dev. 6:255-267, 1992). To identify the sequence in NS2 mRNA that is recognized by the NS1 protein, we developed a gel shift assay for the formation of specific RNA-protein complexes. With this assay, it was established that the NS1 protein binds to the poly(A) sequence at the 3' end of NS2 mRNA and of other mRNAs. In addition, the NS1 protein was shown to bind to poly(A) itself. This specificity was also observed in vivo. The NS1 protein inhibited the nuclear export of every poly(A)-containing mRNA that was tested. In contrast, the NS1 protein failed to inhibit the nuclear export of an mRNA whose 3' end was generated by cleavage without subsequent addition of poly(A). Addition of poly(A) to this mRNA enabled the NS1 protein to inhibit mRNA export. The implications of these results for the role of the NS1 protein during virus infection are discussed.
Surface Modification of Stainless Steel-304 Electrode. 2. An Experimental Comparative Study of Electrochemically, Hydrothermally and Chemically Modified Oxide Films (1999)

Stainless steel-304 was modified electrochemically by potentiostatic and potentiodynamic methods (triangular and square-wave potential-time programs) in 1 mol dm(-3) NaOH solution, hydrothermally in 1 mol dm(-3) NaOH at 200 degrees C, and chemically in 0.5 mol dm(-3) K2Cr2O7 solution. Oxide films were characterized voltammetrically by the charge of Fe(OH)(2)/FeOOH surface electrochemical reaction. The stability of the oxide films was measured in 0.5 mol dm(-3) H2SO4 by anodic potentiodynamic polarization and by open-circuit potential-time measurements. The hydrothermally grown oxide film was most stable. The most efficient oxide growth was achieved by the use of square-wave type of modification. The oxide modified by this procedure exhibited lower stability than the oxide grown by triangular potential-time program, which was much more stable due to the uncompleted reduction of chromium oxide. The importance of careful control of experimental conditions, where a small change in surface treatment could lead to a significant change in corrosion behaviour, is pointed out.
Affinity labeling of NADP+-specific isocitrate dehydrogenase by a new fluorescent nucleotide analog, 2-[(4-bromo-2,3-dioxobutyl)thio]-1,N6-ethenoadenosine 2',5'-bisphosphate (1985)

A new reactive fluorescent adenine nucleotide analogue has been synthesized and characterized: 2-[(4-bromo-2,3-dioxobutyl)thio]-1,N6-ethenoadenosine 2',5'-bisphosphate (BDB-T epsilon ADP). This compound reacts irreversibly with NADP+-specific isocitrate dehydrogenase. Biphasic kinetics of inactivation are observed that can be described in terms of a fast initial phase of inactivation resulting in partially active enzyme of 8-10% residual activity, followed by a slower phase leading to total inactivation. NADPH protects completely against the fast phase of the reaction, indicating that modification occurs at the coenzyme binding site, whereas isocitrate with MnSO4 protects totally against the slow phase of reaction. The inactivation rate constants for both phases exhibit nonlinear dependence on BDB-T epsilon ADP concentration, consistent with the formation of a reversible complex with the enzyme prior to irreversible modification. Covalent incorporation of BDB-T epsilon ADP is limited and specific; only 0.99 mol of reagent/mol of subunit is incorporated when the enzyme is 98% inactivated in the absence of ligands. A maximum incorporation of 0.5 mol of reagent/mol of subunit is obtained in the presence of isocitrate and MnSO4, while incorporation in the presence of NADPH equals the difference between the incorporation in the absence of ligands and that measured in the presence of isocitrate and MnSO4. It appears that 0.5 mol of reagent/mol of subunit is responsible for the fast phase of inactivation and the remaining incorporation causes the slow phase. Under all conditions used in this study, isocitrate dehydrogenase has been shown to exist as a dimer by analytical ultracentrifugation and by cross-linking with dimethyl suberimidate followed by analysis on polyacrylamide gels in the presence of sodium dodecyl sulfate. It is proposed that, in the fast phase of inactivation, 2-[(4-bromo-2,3-dioxobutyl)thio]-1,N6-ethenoadenosine 2',5'-bisphosphate reacts at the coenzyme binding site of one subunit of dimeric isocitrate dehydrogenase, causing complete inactivation of the modified subunit and substantial inactivation of the other subunit. This new reagent is likely to have general applicability as an affinity label for other NADP+ binding enzymes.
A three-dimensional culture system for the growth of hematopoietic cells. (1990)

A physiological three-dimensional culture system was developed for the growth of human bone marrow. Bone marrow stromal cells were established on a nylon filtration screen template, suspended in liquid medium and grown to 70% confluence, and inoculated with hematopoietic cells. An intricate microenvironment is established to support hematopoiesis, which proceeds in a three-dimensional orientation. Analysis of the adherent zone of these cultures with flow cytometry and progenitor cell assays reveals multilineage hematologic expression and active proliferation of immature cells for the 12 week experimental period. Similar results were obtained with rat bone marrow cultures using this methodology. The suspended nylon mesh system is novel in that it supports the growth of several hematologic lineages concurrently. This system may lend itself to the growth of purged or untreated bone marrow for transplantation.
Extracellular matrix alters PDGF regulation of fibroblast integrins. (1996)

Extracellular matrix (ECM) and growth factors are potent regulators of cell phenotype. These biological mediators of cellular responses are potentially interactive and as such could drive cells through progressive phenotypes to create new tissue as in morphogenesis and wound repair. In fact, ECM composition changes during tissue formation accompanied by alterations in cell growth and migration. How alterations in the ECM regulate cell activities is poorly defined. To address this question in wound repair, we cultured normal human dermal skin fibroblasts in relaxed collagen gels, fibronectin-rich cultures or stressed fibrin gels, and stressed collagen gels to model normal dermis, early wound provisional matrix, and late granulation tissue, respectively. Integrin subunits, alpha 2, alpha 3, and alpha 5, that define receptor specificity for collagen and provisional matrix, respectively, were measured at mRNA steady-state level before and after stimulation with platelet-derived growth factor-BB (PDGF-BB), a potent mitogen and chemoattractant for fibroblasts. Fibronectin-rich cultures and fibrin gels supported PDGF-BB induction of alpha 3 and alpha 5 mRNA. In contrast, both stressed and relaxed collagen attenuated these responses while promoting maximal alpha 2 mRNA expression. Posttranscriptional regulation was an important mechanism in this differential response. Together PDGF-BB and collagen gels promoted alpha 2, but not alpha 3 and alpha 5, mRNA stability. Conversely, when fibroblasts were in fibronectin-rich cultures, PDGF-BB promoted alpha 3 and alpha 5, but not alpha 2, mRNA stability. We suggest that ECM alterations during wound healing or any new tissue formation cause cells to respond differently to repeated growth factor stimuli. An ordered progression of cell phenotypes results, ultimately consummating tissue repair or morphogenesis.
Principles for Valid Histopathologic Scoring in Research (2013)

Histopathologic scoring is a tool by which semiquantitative data can be obtained from tissues. Initially, a thorough understanding of the experimental design, study objectives, and methods is required for the pathologist to appropriately examine tissues and develop lesion scoring approaches. Many principles go into the development of a scoring system such as tissue examination, lesion identification, scoring definitions, and consistency in interpretation. Masking (aka "blinding") of the pathologist to experimental groups is often necessary to constrain bias, and multiple mechanisms are available. Development of a tissue scoring system requires appreciation of the attributes and limitations of the data (eg, nominal, ordinal, interval, and ratio data) to be evaluated. Incidence, ordinal, and rank methods of tissue scoring are demonstrated along with key principles for statistical analyses and reporting. Validation of a scoring system occurs through 2 principal measures: (1) validation of repeatability and (2) validation of tissue pathobiology. Understanding key principles of tissue scoring can help in the development and/or optimization of scoring systems so as to consistently yield meaningful and valid scoring data.
A Convenient and General Iron-Catalyzed Hydrosilylation of Aldehydes (2007)

A general and highly chemoselective hydrosilylation of aldehydes using iron catalysts is reported. Fe(OAc)2 in the presence of tricyclohexylphosphine as ligand and polymethylhydrosiloxane (PMHS) as an economical hydride source forms an efficient catalyst system for the hydrosilylation of a variety of aldehydes. Aryl, heteroaryl, alkyl and alpha,beta-unsaturated aldehydes are successfully reduced to the corresponding primary alcohols. Broad substrate scope and high tolerance against several functional groups make the process synthetically useful.
T1/ST2 is preferentially expressed on murine Th2 cells, independent of interleukin 4, interleukin 5, and interleukin 10, and important for Th2 effector function (1998)

T helper (Th) cells can be categorized according to their cytokine expression. The differential induction of Th cells expressing Th1 and/or Th2 cytokines is key to the regulation of both protective and pathological immune responses. Cytokines are expressed transiently and there is a lack of stably expressed surface molecules, significant for functionally different types of Th cells. Such molecules are of utmost importance for the analysis and selective functional modulation of Th subsets and will provide new therapeutic strategies for the treatment of allergic or autoimmune diseases. To this end, we have identified potential target genes preferentially expressed in Th2 cells, expressing interleukin (IL)-4, IL-5, and/or IL-10, but not interferon-gamma. One such gene, T1/ST2, is expressed stably on both Th2 clones and Th2-polarized cells activated in vivo or in vitro. T1/ST2 expression is independent of induction by IL-4, IL-5, or IL-10. T1/ST2 plays a critical role in Th2 effector function. Administration of either a mAb against T1/ST2 or recombinant T1/ST2 fusion protein attenuates eosinophilic inflammation of the airways and suppresses IL-4 and IL-5 production in vivo following adoptive transfer of Th2 cells.
The effects of vasoactive intestinal peptide on neuromuscular transmission in the frog (1982)

1. The effects of vasoactive intestinal peptide (VIP) on cholinergic transmission were studied at the neuromuscular junction of the frog.2. Bath application of VIP (10(-8)-10(-7) M) produced a dose-dependent increase in quantal content of the end-plate potential (e.p.p.), while having no effect on quantal size or on resting membrane potential of the muscle fibres.3. The increases in e.p.p. amplitude observed at end-plates blocked with Mg(2+) or curare were comparable.4. VIP increased miniature end-plate potential frequency when the nerve terminal was depolarized with K(+). This effect was abolished by removing Ca(2+) from the bathing solution.5. Ionophoretic application of VIP to the end-plate also increased quantal content, while having no effect on quantal size or on the input resistance and resting membrane potential of the fibres.6. Some possible mechanisms for the action of VIP are discussed, and it is proposed that it may act on some step involved in depolarization-secretion coupling.
99mTc-labeled antimicrobial peptides for detection of bacterial and Candida albicans infections. (2001)

99mTc-labeled antimicrobial peptides UBI 29-41, UBI 18-35, UBI 31-38, hLF 1-11, and defensins accumulate significantly in tissues infected with gram-positive and gram-negative bacteria and C. albicans. Significantly lower (P < 0.01) accumulation of these peptides occurs in sterile inflamed tissues. These data indicate that the peptides preferentially tag microorganisms at the site of infection, which is in agreement with their preferential binding to the microorganisms in vitro and in vivo. 99mTc-labeled ciprofloxacin does not distinguish between infections and sterile inflammatory lesions, which implies that its specificity for the detection of bacterial infections is not warranted.
Microscopic theory of elastico-mechanoluminescent smart materials (2014)

The concepts of piezoelectric field dependence of the detrapping probability and lifetime of charge carriers in traps are developed. The charge carriers in traps become unstable after a particular piezoelectric field whereby more number of charge carriers are detrapped with increasing piezoelectric field. The detrapped electrons tunnel to the energy level of the hole-captured activator ions lying adjacent to the conduction band or tunnel to conduction band. Subsequently, luminescence is induced by the electron-hole recombination. Using these concepts microscopic theory of elastico-mechanoluminescent smart materials is explored. Present study may be useful in tailoring intense elastico-mechanoluminescent materials needed for different applications.
<title>Dark-field Scheimpflug imaging for surface inspection</title> (1997)

Automated Visual Surface Inspection is an important task in industrial quality control and there are a plethora of optical systems with imaging or scanning configurations at work in industry. Surface Inspection on ceramic tiles however, is a task that is still performed manually by most manufacturing companies. The main reason that the Ceramic Tile industry has not yet fully automated its inspection procedures is that the particular surfaces are produced in an extremely wide range of surface textures, colours, dimensions and patterns. Visual surface inspection systems can normally handle a limited range of surface textures. The system described here detects defects such as dents and scratches, using Dark Field Illumination'. The defects are detected by imaging deflected and scattered light respectively. Dark Field Illumination is a technique that in principle can only be used with specular surfaces. In order to cope with the tile surfaces that are not always specular (surface roughnesses ranging from O.O8tm to 1.5am), grazing incidence illumination is used to increase the ratio of specular versus diffuse reflection2. The surfaces are imaged on a Line Scan Camera, which is placed at a large angle relative to the surface normal. This can be up to 23° away from the specular direction; for separation angles wider than that the signal from scratches is too weak to be useful for an industrial application. In the resultant images, the surfaces show dark, while defects show bright. Illumination and imaging take place in a plane that is perpendicular to the direction of motion of the conveyor belt. The imaging is oblique, and the image plane forms an angle with the lens plane. This angle is specified by the Scheimpflug imaging condition. Being able to tilt the camera relative to the lens, enables the use of the small depth of field from a wide aperture imaging lens (low F number). This increases the total light throughput of the system. The image is formed on a Line Scan Camera, thus limiting the perspective distortion due to oblique imaging to one direction. The surface flaws that can be detected with the presented configuration, are topographic (bumps, dents, inclusions) as well as digs and scratches. The two different types of defects are detected by imaging deflected and scattered light respectively, on two separate camera heads.
Expression pattern of Motch, a mouse homolog of Drosophila Notch, suggests an important role in early postimplantation mouse development (1992)

The Notch gene of Drosophila encodes a large transmembrane protein involved in cell-cell interactions and cell fate decisions in the Drosophila embryo. To determine if a gene homologous to Drosophila Notch plays a role in early mouse development, we screened a mouse embryo cDNA library with probes from the Xenopus Notch homolog, Xotch. A partial cDNA clone encoding the mouse Notch homolog, which we have termed Motch, was used to analyze expression of the Motch gene. Motch transcripts were detected in a wide variety of adult tissues, which included derivatives of all three germ layers. Differentiation of P19 embryonal carcinoma cells into neuronal cell types resulted in increased expression of Motch RNA. In the postimplantation mouse embryo Motch transcripts were first detected in mesoderm at 7.5 days post coitum (dpc). By 8.5 dpc, transcript levels were highest in presomitic mesoderm, mesenchyme and endothelial cells, while much lower levels were detected in neuroepithelium. In contrast, at 9.5 dpc, neuroepithelium was a major site of Motch expression. Transcripts were also abundant in cell types derived from neural crest. These data suggest that the Motch gene plays multiple roles in patterning and differentiation of the early postimplantation mouse embryo.