gebhart/patrepeval huggingface dataset:
Identification of p54nrb and the 14-3-3 Protein HS1 as TNF-α-Inducible Genes Related to Cell Cycle Control and Apoptosis in Human Arterial Endothelial Cells (2005)

TNF-alpha plays a pivotal role in inflammation processes which are mainly regulated by endothelial cells. While TNF-alpha induces apoptosis of several cell types like tumor cells, endothelial cells are resistant to TNFa mediated cell death. The cytotoxic effects of TNF-alpha on most cells are only evident if RNA or protein synthesis is inhibited, suggesting that de novo RNA or protein synthesis protect cells from TNF-alpha cytotoxicity, presumably by NF-kappaB mediated induction of protective genes. However, the cytoprotective genes involved in NF-kappaB dependent endothelial cell survival have not been sufficiently identified. In the present study, the suppression subtractive hybridization (SSH) method was employed to identify rarely transcribed TNF-alpha inducible genes in human arterial endothelial cells related to cell survival and cell cycle. The TNF-alpha-induced expression of the RNA binding protein p54(nrb) and the 14-3-3 protein HS1 as shown here for the first time may contribute to the TNF-alpha mediated cell protection of endothelial cells. These genes have been shown to play pivotal roles in cell survival and cell cycle control in different experimental settings. The concerted expression of these genes together with other genes related to cell protection and cell cycle like DnaJ, p21(cip1) and the ubiquitin activating enzyme E1 demonstrates the identification of new genes in the context of TNF-alpha induced gene expression patterns mediating the prosurvival effect of TNF-alpha in endothelial cells.
Next Generation Memory Interfaces (2015)

The DDR4 standard allows for memory to be accessed at twice the data rate of its preceding standard, DDR3 while simultaneously reducing the total power consumption and increasing the memory density. In this project a physical layer (PHY) interface for the DDR4 subsystem has been conceptualized, and designed. As memory devices eternally seek to be faster, denser and extremely low power consuming systems, the PHY interface will get us another step further in this quest. In this report, the challenges and circuit techniques associated with the design of this high data-rate interface have been discussed along with the main differentiating factors between DDR4 and its predecessor, DDR3. The design process and results for the receiver front-end of the physical layer are among the major focus points of this report.
PI3-kinase/Akt modulates vascular smooth muscle tone via cAMP signaling pathways (2001)

Phosphatidylinositol 3-kinase (PI3-kinase) activates protein kinase B (also known as Akt), which phosphorylates and activates a cyclic nucleotide phosphodiesterase 3B. Increases in cyclic nucleotide concentrations inhibit agonist-induced contraction of vascular smooth muscle. Thus we hypothesized that the PI3-kinase/Akt pathway may regulate vascular smooth muscle tone. In unstimulated, intact bovine carotid artery smooth muscle, the basal phosphorylation of Akt was higher than that in cultured smooth muscle cells. The phosphorylation of Akt decreases in a time-dependent manner when incubated with the PI3-kinase inhibitor, LY-294002. Agonist (serotonin)-, phorbol ester (phorbol 12,13-dibutyrate; PDBu)-, and depolarization (KCl)-induced contractions of vascular smooth muscles were all inhibited in a dose-dependent fashion by LY-294002. However, LY-294002 did not inhibit serotonin- or PDBu-induced increases in myosin light chain phosphorylation or total O(2) consumption, suggesting that inhibition of contraction was not mediated by reversal or inhibition of the pathways that lead to smooth muscle activation and contraction. Treatment of vascular smooth muscle with LY-294002 increased the activity of cAMP-dependent protein kinase and increased the phosphorylation of the cAMP-dependent protein kinase substrate heat shock protein 20 (HSP20). These data suggest that activation of the PI3-kinase/Akt pathway in unstimulated smooth muscle may modulate vascular smooth muscle tone (allow agonist-induced contraction) through inhibition of the cyclic nucleotide/HSP20 pathway and suggest that cyclic nucleotide-dependent inhibition of contraction is dissociated from the myosin light chain contractile regulatory pathways.
MLL–ELL fusion gene in two infants with acute monoblastic leukemia and myeloid sarcoma (2011)

Myeloid sarcoma (MS) is a rare condition characterized by the occurrence of one or more tumor masses. It consists of immature myeloid cells presenting at an extramedullary site. MS is isolated or m...
Multiplexing regulated traffic streams: design and performance (2002)

The main network solutions for supporting QoS rely on traffic policing (conditioning, shaping). In particular, for IP networks the IETF has developed Intserv (individual flows regulated) and Diffserv (only aggregates regulated). The regulator proposed could be based on the (dual) leaky-bucket mechanism. This explains the interest in network element performance (loss, delay) for leaky-bucket regulated traffic. This paper describes a novel approach to the above problem. Explicitly using the correlation structure of the sources' traffic, we derive approximations for both small and large buffers. Importantly, for small (large) buffers the short-term (long-term) correlations are dominant. The large buffer result decomposes the traffic stream in a stream of constant rate and a periodic impulse stream, allowing direct application of the Brownian bridge approximation. Combining the small and large buffer results by a concave majorization, we propose a simple, fast and accurate technique to statistically multiplex homogeneous regulated sources. To address heterogeneous inputs, we present similarly efficient techniques to evaluate the performance of multiple classes of traffic, each with distinct characteristics and QoS requirements. These techniques, applicable under more general conditions, are based on optimal resource (bandwidth and buffer) partitioning. They can also be directly applied to set GPS (generalized processor sharing) weights and buffer thresholds in a shared resource system.
Application of a multivariate technique to Raman spectra for quantification of body chemicals (1995)

Raman spectroscopy is a highly specific technique for the identification of molecules by way of the associated characteristic spectra. The aim of this feasibility study is to assess the combination of the multivariate calibration technique of Partial Least-Squares with Raman spectroscopy for the estimation of glucose, lactic acid, and urea concentrations in the presence of each other in a water substrate. The instrument is a CCD-based Raman spectrometer utilizing the 514.5 nm argon laser line. The estimates for the analyte concentrations yielded a standard deviation of concentration residuals of 20.71 mg/dL for glucose, 12.92 mg/dL for lactic acid, and 19.07 mg/dL for urea.
Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing (2008)

If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in order to improve the outcomes of patients. This survey will also foster the pioneering and development of new molecular diagnostic tools, which can be used to identify the community compositions of chronic wound pathogenic biofilms and other medical biofilm infections.
The Chemistry of Sulfur Tetrafluoride. II. The Fluorination of Organic Carbonyl Compounds1 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Chemistry of Sulfur Tetrafluoride. II. The Fluorination of Organic Carbonyl Compounds1W. R. Hasek, W. C. Smith, and V. A. EngelhardtCite this: J. Am. Chem. Soc. 1960, 82, 3, 543–551Publication Date (Print):February 1, 1960Publication History Published online1 May 2002Published inissue 1 February 1960https://pubs.acs.org/doi/10.1021/ja01488a012https://doi.org/10.1021/ja01488a012research-articleACS PublicationsRequest reuse permissionsArticle Views2599Altmetric-Citations283LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Tracheobronchomalacia and excessive dynamic airway collapse (2006)

Tracheobronchomalacia and excessive dynamic airway collapse are two separate forms of dynamic central airway obstruction that may or may not coexist. These entities are increasingly recognized as asthma and COPD imitators. The understanding of these disease processes, however, has been compromised over the years because of uncertainties regarding their definitions, pathogenesis and aetiology. To date, there is no standardized classification, diagnosis or management algorithm. In this article we comprehensively review the aetiology, morphopathology, physiology, diagnosis and treatment of these entities.
Advances in small animal mesentery models for in vivo flow cytometry, dynamic microscopy, and drug screening (2007)

Using animal mesentery with intravital optical microscopy is a well-established experimental model for studying blood and lymph microcirculation in vivo. Recent advances in cell biology and optical techniques provide the basis for extending this model for new applications, which should generate significantly improved experimental data. This review summarizes the achievements in this specific area, including in vivo label-free blood and lymph photothermal flow cytometry, super-sensitive fluorescence image cytometry, light scattering and speckle flow cytometry, microvessel dynamic microscopy, infrared (IR) angiography, and high-speed imaging of individual cells in fast flow. The capabilities of these techniques, using the rat mesentery model, were demonstrated in various studies; e.g., real-time quantitative detection of circulating and migrating individual blood and cancer cells, studies on vascular dynamics with a focus on lymphatics under normal conditions and under different interventions (e.g. lasers, drugs, nicotine), assessment of lymphatic disturbances from experimental lymphedema, monitoring cell traffic between blood and lymph systems, and high-speed imaging of cell transient deformability in flow. In particular, the obtained results demonstrated that individual cell transportation in living organisms depends on cell type (e.g., normal blood or leukemic cells), the cellos functional state (e.g., live, apoptotic, or necrotic), and the functional status of the organism. Possible future applications, including in vivo early diagnosis and prevention of disease, monitoring immune response and apoptosis, chemo- and radio-sensitivity tests, and drug screening, are also discussed.
Suppression of Insulin Aggregation by Heparin (2008)

The aggregation of insulin near its isoelectric point and at low ionic strength was suppressed in the presence of heparin. To understand this effect, we used turbidimetry and stopped-flow to study the pH- and ionic strength ( I)-dependence of the aggregation of heparin-free insulin. The results supported the role of interprotein electrostatic interactions, contrary to the commonly held view that such forces are minimized at pH = pI. Electrostatic modeling of insulin (DelPhi) revealed that attractive interactions arise from the marked charge anisotropy of insulin near pI. We show how screening of the interprotein attractions by added salt lead to maximum aggregation near I = 0.01 M, corresponding to a Debye length nearly equal to the diameter of the insulin dimer, consistent with a dipole-like protein charge distribution. This analysis is also consistent with suppression of aggregation by heparin, a strong polyanion that by binding to the positive domain of one protein, inhibits its interaction with the negative domain of another.
Efficient Planar Perovskite Solar Cells Based on 1.8 eV Band Gap CH3NH3PbI2Br Nanosheets via Thermal Decomposition (2014)

Hybrid organometallic halide perovskite CH3NH3PbI2Br (or MAPbI2Br) nanosheets with a 1.8 eV band gap were prepared via a thermal decomposition process from a precursor containing PbI2, MABr, and MACl. The planar solar cell based on the compact layer of MAPbI2Br nanosheets exhibited 10% efficiency and a single-wavelength conversion efficiency of up to 86%. The crystal phase, optical absorption, film morphology, and thermogravimetric analysis studies indicate that the thermal decomposition process strongly depends on the composition of precursors. We find that MACl functions as a glue or soft template to control the initial formation of a solid solution with the main MAPbI2Br precursor components (i.e., PbI2 and MABr). The subsequent thermal decomposition process controls the morphology/surface coverage of perovskite films on the planar substrate and strongly affects the device characteristics.
Molecular Analysis of Chromosome Aberrations In Situ Hybridization (2003)

In situ hybridization provides a means of analyzing chromosomal aberrations in a very direct way. Nucleic acid probes are hybridized to chromosomal preparations, and the site of specific hybridization is detectable by various procedures. Although in the 1970s and 1980s isotopic detection was the preferred technique, new developments in the protocols of nonisotopic in situ hybridization resulted in an increasing popularity of this procedure since the late 1980s. This development is owing to the distinct advantages of nonradioactive in situ hybridization techniques, such as increased speed of the procedure, higher signal resolution, and most of all the potential to combine several nonisotopic techniques to delineate a number of chromosomal target regions simultaneously. These developments have been discussed in more detail elsewhere (see, e.g., refs. 1–3).
Cholesterol Depletion of Caveolae Causes Hyperactivation of Extracellular Signal-related Kinase (ERK) (1998)

Previously we showed that activation of Erk in quiescent cells occurs in the caveolae fraction isolated from fibroblasts. Since the structure and function of caveolae is sensitive to the amount of cholesterol in the membrane, it might be that a direct link exists between the concentration of membrane cholesterol and mitogen-activated protein (MAP) kinase activation. We acutely lowered the cholesterol level of the caveolae fraction by incubating Rat-1 cells in the presence of either cyclodextrin or progesterone. Cholesterol-depleted caveolae had a reduced amount of several key protein components of the MAP kinase complex, including Ras, Grb2, Erk2, and Src. Incubation of these cells in the presence of epidermal growth factor (EGF) caused a rapid loss of EGF receptor from the caveolae fraction, but the usual recruitment of c-Raf was markedly inhibited. Despite the reduced amount of c-Raf and Erk2 in the cholesterol-depleted caveolae fraction, EGF caused a hyperactivation of the remaining caveolae Erk isoenzymes. This was followed by an increase in the amount of active Erk in the cytoplasm. The increased amount of activated Erk produced under these conditions was linked to a 2-fold higher level of EGF-stimulated DNA synthesis. Even cholesterol depletion by itself stimulated Erk activation and DNA synthesis. These results suggest that the MAP kinase pathway can connect the cholesterol level of caveolae membrane to the control of cell division.
Reduction by Granulocyte Colony-Stimulating Factor of Fever and Neutropenia Induced by Chemotherapy in Patients with Small-Cell Lung Cancer (1991)

The use of G-CSF as an adjunct to chemotherapy in patients with small-cell cancer of the lung was well tolerated and led to reductions in the incidence of fever with neutropenia and culture-confirmed infections; in the incidence, duration, and severity of grade IV neutropenia; and in the total number of days of treatment with intravenous antibiotics and days of hospitalization.
When F-actin Becomes Too Much of a Good Thing (2006)

An excess of a protein that regulates actin assembly in white blood cells unexpectedly kills the cell by altering mitochondrial function.
Pre‐organization of the Core Structure of E‐Selectin Antagonists (2011)

A new class of N-acetyl-D-glucosamine (GlcNAc) mimics for E-selectin antagonists was designed and synthesized. The mimic consists of a cyclohexane ring substituted with alkyl substituents adjacent to the linking position of the fucose moiety. Incorporation into E-selectin antagonists led to the test compounds 8 and the 2'-benzoylated analogues 21, which exhibit affinities in the low micromolar range. By using saturation transfer difference (STD)-NMR it could be shown that the increase in affinity does not result from an additional hydrophobic contact of the alkyl substituent with the target protein E-selectin, but rather from a steric effect stabilizing the antagonist in its bioactive conformation. The loss of affinity found for antagonists 10 and 35 containing a methyl substituent in a remote position (and therefore unable to support to the stabilization of the core) further supports this hypothesis. Finally, when a GlcNAc mimetic containing two methyl substituents (52 and 53) was used, in which one methyl was positioned adjacent to the fucose linking position and the other was in a remote position, the affinity was regained.
Environmental Enrichment Rescues Protein Deficits in a Mouse Model of Huntington's Disease, Indicating a Possible Disease Mechanism (2004)

Huntington's disease (HD) is a devastating neurodegenerative disorder caused by a CAG repeat expansion encoding an extended polyglutamine tract in the huntingtin protein. Transgenic mice expressing a human huntingtin transgene containing an expanded CAG repeat (R6/1 model) develop a neurodegenerative disorder closely resembling human HD. Previous work demonstrated that environmental enrichment delays the onset of motor symptoms in this mouse model. We confirmed that at 5 months of age, enrichment ameliorates motor symptoms (assessed using the rotarod test) and prevents loss of body weight induced by the HD transgene. We further examined molecular consequences of enrichment by determining changes in protein levels in the neostriatum, hippocampus, and anterior cortex using quantitative Western blot analysis. Non-enriched HD mice have severe reductions in BDNF in the hippocampus and striatum at 5 months, which are entirely rescued by enrichment. BDNF levels are unaltered by HD in the anterior cortex, suggesting that enrichment might prevent HD-induced impairment of anterograde transport of this neurotrophin to the striatum. NGF is unaffected by HD. Non-enriched HD mice also exhibit deficits in dopamine and cAMP-regulated phosphoprotein (32 kDa) in striatum and anterior cortex. Environmental enrichment rescues the cortical but not the striatal deficit at 5 months. These results suggest that environmental enrichment benefits animals at early stages of the disease by rescuing protein deficits, possibly through rescuing transcription or protein transport problems.
Adaptive nonlinear control of systems containing a deadzone (2002)

The authors present an adaptive nonlinear controller for a plant containing a nonsmooth nonlinearity with unknown parameters in the span of the control (specifically, a deadzone). They develop a Lyapunov-based adaptation scheme which updates the parameters of the specific region of the deadzone in which the system is operating. They then employ some switching logic to turn on and off the adaptation as the state of the system proceeds from one region of the deadzone to another. A significant feature of the adaptive controller is the presence of set uncertainty. Thus, conceptually, adaptation is not only for unknown parameters, but also for the regions of the piecewise smooth nonlinearity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Demonstration of saturated high repetition rate tabletop soft x-ray lasers at wavelengths down to 13.2 nm (2005)

We have demonstrated gain-saturated operation of high repetition rate table-top soft x-ray lasers producing microwatt average powers at wavelengths ranging from 13.2 to 32.6 nm in transitions of Ni-like and Ne-like ions. Lasing was also observed for shorter wavelength transitions of the 4<i>d</i><sup>1</sup><i>S</i><sub>0</sub>&rarr;4<i>p</i><sup>1</sup><i>P</i><sub>1</sub> Ni-like isoelectronic sequence, with amplification approaching gain saturation in the 11.9 nm line of Ni-like Sn and progressively reduced gain for wavelengths as low as 10.9 nm in Ni-like Te. The results were obtained heating a pre-created plasma with a picosecond optical laser pulse with an energy of only 1 J impinging at optimized grazing angles of incidence for maximum pump energy deposition efficiency. This pumping geometry takes advantage of the refraction of the pump beam to increase the energy deposition efficiency of the pump beam into the gain region, making it possible to operate soft x-ray lasers in this wavelength range at significantly increased repetition rates. The results demonstrate the feasibility of producing high average powers of coherent radiation in the 100 eV spectral region for applications using a table-top source.
Adjustable, short focal length permanent-magnet quadrupole based electron beam final focus system (2005)

Advanced high-brightness beam applications such as inverse-Compton scattering (ICS) depend on achieving of ultrasmall spot sizes in high current beams. Modern injectors and compressors enable the production of high-brightness beams having needed short bunch lengths and small emittances. Along with these beam properties comes the need to produce tighter foci, using stronger, shorter focal length optics. An approach to creating such strong focusing systems using high-field, small-bore permanent-magnet quadrupoles (PMQs) is reported here. A final-focus system employing three PMQs, each composed of 16 neodymium iron boride sectors in a Halbach geometry has been installed in the PLEIADES ICS experiment. The field gradient in these PMQs is $560\text{ }\mathrm{T}/\mathrm{m}$, the highest ever reported in a magnetic optics system. As the magnets are of a fixed field strength, the focusing system is tuned by adjusting the position of the three magnets along the beam line axis, in analogy to familiar camera optics. This paper discusses the details of the focusing system, simulation, design, fabrication, and experimental procedure in creating ultrasmall beams at PLEIADES.
Gram Type-Specific Broad-Range PCR Amplification for Rapid Detection of 62 Pathogenic Bacteria (1999)

Broad-range PCR has proven to be useful for the detection of bacteria. A set of broad-range PCR primers directed against conserved regions in the 16S rRNA gene was designed to specifically amplify either gram-positive or gram-negative bacteria. The gram type-specific broad-range PCR correctly classified all 62 pathogenic species tested.