gebhart/patrepeval huggingface dataset:
Thickness-dependent structure and properties of SnS2thin films prepared by atomic layer deposition (2017)

Tin disulfide (SnS2) thin films were deposited by a thermal atomic layer deposition (ALD) method at low temperatures. The physical, chemical, and electrical characteristics of SnS2 were investigated as a function of the film thickness. SnS2 exhibited a (001) hexagonal plane peak at 14.9° in the X-ray diffraction (XRD) results and an A1g peak at 311 cm−1 in the Raman spectra. These results demonstrate that SnS2 thin films grown at 150 °C showed a crystalline phase at film thicknesses above 11.2 nm. The crystallinity of the SnS2 thin films was evaluated by a transmission electron microscope (TEM). The X-ray photoelectron spectroscopy (XPS) analysis revealed that SnS2 consisted of Sn4+ and S2− valence states. Both the optical band gap and the transmittance of SnS2 decreased as the film thickness increased. The band gap of SnS2 decreased from 3.0 to 2.4 eV and the transmittance decreased from 85 to 32% at a wavelength of 400 nm. In addition, the resistivity of the thin film SnS2 decreased from 1011 to 106 Ω·cm as the film thickness increased.
The Ebola virus VP35 protein functions as a type I IFN antagonist (2000)

An assay has been developed that allows the identification of molecules that function as type I IFN antagonists. Using this assay, we have identified an Ebola virus-encoded inhibitor of the type I IFN response, the Ebola virus VP35 protein. The assay relies on the properties of an influenza virus mutant, influenza delNS1 virus, which lacks the NS1 ORF and, therefore, does not produce the NS1 protein. When cells are infected with influenza delNS1 virus, large amounts of type I IFN are produced. As a consequence, influenza delNS1 virus replicates poorly. However, high-efficiency transient transfection of a plasmid encoding a protein that interferes with type I IFN-induced antiviral functions, such as the influenza A virus NS1 protein or the herpes simplex virus protein ICP34.5, rescues growth of influenza delNS1 virus. When plasmids expressing individual Ebola virus proteins were transfected into Madin Darby canine kidney cells, the Ebola virus VP35 protein enhanced influenza delNS1 virus growth more than 100-fold. VP35 subsequently was shown to block double-stranded RNA- and virus-mediated induction of an IFN-stimulated response element reporter gene and to block double-stranded RNA- and virus-mediated induction of the IFN-beta promoter. The Ebola virus VP35 therefore is likely to inhibit induction of type I IFN in Ebola virus-infected cells and may be an important determinant of Ebola virus virulence in vivo.
Diabetic Vascular Complications: Pathophysiology, Biochemical Basis and Potential Therapeutic Strategy (2005)

Diabetic vascular complication is a leading cause of end-stage renal failure, acquired blindness, a variety of neuropathies and accelerated atherosclerosis, which could account for disabilities and high mortality rates in patients with diabetes. Recent large prospective clinical studies have shown that intensive glucose control reduces effectively microvascular complications among patients with diabetes, and insulin resistance and postprandial hyperglycemia seem to be involved in diabetic macrovascular complications. Chronic hyperglycemia is a major initiator of diabetic vascular complications. Indeed, high glucose, via various mechanisms such as increased production of advanced glycation end products, activation of protein kinase C, stimulation of the polyol pathway and enhanced reactive oxygen species generation, regulates vascular inflammation, altered gene expression of growth factors and cytokines, and platelet and macrophage activation, thus playing a central role in the development and progression of diabetic vascular complications. This article summarizes the molecular mechanisms of diabetic vascular complications and the potential therapeutic interventions that may prevent these disorders even in the presence of hyperglycemia, control of which is often difficult with current therapeutic options.
Characterization of a Gene Cluster Involved in 4-Chlorocatechol Degradation byPseudomonas reinekeiMT1 (2009)

Pseudomonas reinekei MT1 has previously been reported to degrade 4- and 5-chlorosalicylate by a pathway with 4-chlorocatechol, 3-chloromuconate, 4-chloromuconolactone, and maleylacetate as intermediates, and a gene cluster channeling various salicylates into an intradiol cleavage route has been reported. We now report that during growth on 5-chlorosalicylate, besides a novel (chloro)catechol 1,2-dioxygenase, C12O(ccaA), a novel (chloro)muconate cycloisomerase, MCI(ccaB), which showed features not yet reported, was induced. This cycloisomerase, which was practically inactive with muconate, evolved for the turnover of 3-substituted muconates and transforms 3-chloromuconate into equal amounts of cis-dienelactone and protoanemonin, suggesting that it is a functional intermediate between chloromuconate cycloisomerases and muconate cycloisomerases. The corresponding genes, ccaA (C12O(ccaA)) and ccaB (MCI(ccaB)), were located in a 5.1-kb genomic region clustered with genes encoding trans-dienelactone hydrolase (ccaC) and maleylacetate reductase (ccaD) and a putative regulatory gene, ccaR, homologous to regulators of the IclR-type family. Thus, this region includes genes sufficient to enable MT1 to transform 4-chlorocatechol to 3-oxoadipate. Phylogenetic analysis showed that C12O(ccaA) and MCI(ccaB) are only distantly related to previously described catechol 1,2-dioxygenases and muconate cycloisomerases. Kinetic analysis indicated that MCI(ccaB) and the previously identified C12O(salD), rather than C12O(ccaA), are crucial for 5-chlorosalicylate degradation. Thus, MT1 uses enzymes encoded by a completely novel gene cluster for degradation of chlorosalicylates, which, together with a gene cluster encoding enzymes for channeling salicylates into the ortho-cleavage pathway, form an effective pathway for 4- and 5-chlorosalicylate mineralization.
Linear lightwave networks: performance issues (1993)

An architecture for lightwave networks is presented based on establishing controllable, optically transparent paths among network users. The objective is to provide high bandwidth (GigaHertz) «clear channel» optical connections on demand to large user populations (tens of thousands) spread over large geographical areas (thousands of kilometers). The networks in question perform only linear operations on the optical signals (including optical amplification but excluding regeneration); hence the name «linear lightwave network» (LLN). Because they are controllable, and are based on arbitrary topologies they are capable of being reconfigured dynamically in response to changing load conditions or component failures. The LLN's operate in a wavelength division multiplexed mode
Protein structure by mechanical triangulation (2006)

Knowledge of protein structure is essential to understand protein function. High-resolution protein structure has so far been the domain of ensemble methods. Here, we develop a simple single-molecule technique to measure spatial position of selected residues within a folded and functional protein structure in solution. Construction and mechanical unfolding of cysteine-engineered polyproteins with controlled linkage topology allows measuring intramolecular distance with angstrom precision. We demonstrate the potential of this technique by determining the position of three residues in the structure of green fluorescent protein (GFP). Our results perfectly agree with the GFP crystal structure. Mechanical triangulation can find many applications where current bulk structural methods fail.
Parenteral Nutrition Ordering Processes (2012)

Parenteral nutrition (PN) is a complex prescription consisting of many components such as dextrose, amino acids, electrolytes, vitamins, trace elements, and/or intravenous fat emulsions. The ordering process is inconsistent and has led to PN errors. PN prescriptions require knowledge, education for prescribers, and standardized processes.
Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices (2015)

Activating mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) underlie the pathogenesis and chemoresistance of ∼ 30% of all human tumors, yet the development of high-affinity inhibitors that target the broad range of KRAS mutants remains a formidable challenge. Here, we report the development and validation of stabilized alpha helices of son of sevenless 1 (SAH-SOS1) as prototype therapeutics that directly inhibit wild-type and mutant forms of KRAS. SAH-SOS1 peptides bound in a sequence-specific manner to KRAS and its mutants, and dose-responsively blocked nucleotide association. Importantly, this functional binding activity correlated with SAH-SOS1 cytotoxicity in cancer cells expressing wild-type or mutant forms of KRAS. The mechanism of action of SAH-SOS1 peptides was demonstrated by sequence-specific down-regulation of the ERK-MAP kinase phosphosignaling cascade in KRAS-driven cancer cells and in a Drosophila melanogaster model of Ras85D(V12) activation. These studies provide evidence for the potential utility of SAH-SOS1 peptides in neutralizing oncogenic KRAS in human cancer.
Disulfide bonds between two envelope proteins of lactate dehydrogenase-elevating virus are essential for viral infectivity (1995)

Disulfide bonds were found to link the nonglycosylated envelope protein VP-2/M (19 kDa), encoded by open reading frame 6, and the major envelope glycoprotein VP-3 (25 to 42 kDa), encoded by open reading frame 5, of lactate dehydrogenase-elevating virus (LDV). The two proteins comigrated in a complex of 45 to 55 kDa when the virion proteins were electrophoresed under nonreducing conditions but dissociated under reducing conditions. Furthermore, VP-2/M was quantitatively precipitated along with VP-3 in this complex by three neutralizing monoclonal antibodies to VP-3. The infectivity of LDV was rapidly and irreversibly lost during incubation with 5 to 10 mM dithiothreitol (> 99% in 6 h at room temperature), which is known to reduce disulfide bonds. LDV inactivation correlated with dissociation of VP-2/M and VP-3. The results suggest that disulfide bonds between VP-2/M and VP-3 are important for LDV infectivity. Hydrophobic moment analyses of the predicted proteins suggest that VP-2/M and VP-3 both possess three adjacent transmembrane segments and only very short ectodomains (10 and 32 amino acids, respectively) with one and two cysteines, respectively. Inactivation of LDV by dithiothreitol and dissociation of the two envelope proteins were not associated with alterations in LDV's density or sedimentation coefficient.
Imaging biological molecules with single molecule sensitivity using near-field scanning optical microscopy (1995)

We have developed a near-field scanning optical microscope with the sensitivity to detect single fluorescent molecules. Our microscope is based on scanning a sample under a tapered and metal coated fiber optic probe and has an illumination-aperture diameter as small as 100 nm. The microscope simultaneously acquires a shear force image with a height noise of {approximately} 1 nm. We have used this system to demonstrate the detection of single molecules of Rhodamine-6G on silica. In this paper, we explore the use of NSOM for investigations of biological molecules. We have prepared and imaged double-stranded DNA intercalated with thiazole orange homodimer (TOTO); single chromosomes stained with propidium iodide; and {beta}-phycoerythrin proteins on dry, borosilicate-glass surfaces. At very dilute coverages, isolated fluorescent spots are observed for the un-intercalated TOTO dye and for {beta}-phycoerythrin. These fluorescent spots exhibit-emission intensity fluctuations and abrupt bleaching transitions, similar to the intensity behavior observed previously for single Rhodamine 6G molecules on silica.
The Relationship Of Serum Testosterone To Erectile Function In Normal Aging Men (2002)

Erectile dysfunction showed a clear association with aging but no consistent correlation of total testosterone with erectile condition was identified.
Reduction of waveguide facet reflection in optical hybrid integrated circuit using saw-toothed angled facet (1995)

A saw-toothed facet structure is proposed to reduce the waveguide facet reflection in an optical hybrid integrated circuit. This structure was used to achieve the hybrid integration of a semiconductor laser amplifier (SLA) on a planar lightwave circuit (PLC) platform. Gain ripple for a flat facet was reduced from 3.6 dB to 0.6 dB by setting a facet angle of 35 degrees. The SLA insertion loss was 3.5 dB at 0 degrees and 4.0 dB at 35 degrees with an SLA injection current of 80 mA. Thus the sawtoothed facet is confirmed to reduce facet reflection effectively without significant insertion loss increase.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cleaning and polishing as key steps for Smart-cut(R) SOI process (2002)

Silicon on insulator technologies appear to be suitable for low power and low voltage electronics. SIMOX wafers have been considered as the best candidates to realize ULSI devices. An alternative route has been proposed by M. Bruel (1995-96) referred to as the Smart-cut process. This new process is versatile enough to fabricate SOI structures (Unibond wafers) with tuned silicon and oxide layer thicknesses. Good thickness homogeneity, low defect density, high surface quality and good electrical properties are now available in these SOI wafers. The authors show that most of these parameters depend, to some degree, on the cleaning step before wafer bonding or on the final chemical mechanical polishing process. As an example, surface roughness and defect densities are investigated by comparison with SIMOX wafer results.
Rodinia: A benchmark suite for heterogeneous computing (2009)

This paper presents and characterizes Rodinia, a benchmark suite for heterogeneous computing. To help architects study emerging platforms such as GPUs (Graphics Processing Units), Rodinia includes applications and kernels which target multi-core CPU and GPU platforms. The choice of applications is inspired by Berkeley's dwarf taxonomy. Our characterization shows that the Rodinia benchmarks cover a wide range of parallel communication patterns, synchronization techniques and power consumption, and has led to some important architectural insight, such as the growing importance of memory-bandwidth limitations and the consequent importance of data layout.
Familial Lymphedema Praecox (1981)

Familial lymphedema should be classified in two categories depending on onset. Milroy's disease, or congenital hereditary lymphedema, is present from birth, painless, without tendency to ulcerate, and may have cholestasis or intestinal lymphangiectasia associated with it. Meige's disease, hereditary lymphedema praecox, is lymphedema with onset in the first or second decade, often presenting with inflammation, and may have a number of associated related anomalies including distichiasis, extradural cysts, vertebral anomalies, cerebrovascular malformation, yellow nails, and sensorineural hearing loss. Both types follow an autosomal dominant pattern. This paper presents a family of 39 persons in 5 generations with 13 affected persons having Meige's disease. The importance of recognizing this type of familial lymphedema is discussed.
Proteomic analysis for the assessment of diabetic renal damage in humans (2004)

Renal disease in patients with Type II diabetes is the leading cause of terminal renal failure and a major healthcare problem. Hence early identification of patients prone to develop this complication is important. Diabetic renal damage should be reflected by a change in urinary polypeptide excretion at a very early stage. To analyse these changes, we used an online combination of CE/MS (capillary electrophoresis coupled with MS), allowing fast and accurate evaluation of up to 2000 polypeptides in urine. Employing this technology, we have examined urine samples from 39 healthy individuals and from 112 patients with Type II diabetes mellitus and different degrees of albumin excretion rate. We established a ‘normal’ polypeptide pattern in the urine of healthy subjects. In patients with Type II diabetes and normal albumin excretion rate, the polypeptide pattern in urine differed significantly from normal, indicating a specific ‘diabetic’ pattern of polypeptide excretion. In patients with higher grade albuminuria, we were able to detect a polypeptide pattern indicative of ‘diabetic renal damage’. We also found this pattern in 35% of those patients who had low-grade albuminuria and in 4% of patients with normal albumin excretion. Moreover, we could identify several of the indicative polypeptides using MS/MS sequencing. We conclude that proteomic analysis with CE/MS permits fast and accurate identification and differentiation of polypeptide patterns in urine. Longitudinal studies should explore the potential of this powerful diagnostic tool for early detection of diabetic renal damage.
Effects of Acamprosate on Neuronal Receptors and Ion Channels Expressed inXenopusOocytes (2008)

Acamprosate does not significantly modulate the function of these receptors and ion channels at clinically relevant concentrations. Thus, the clinical effectiveness of acamprosate in the treatment of alcoholism is not likely due to direct effects on these receptors or ion channels.
Stability of the ATF2 Transcription Factor Is Regulated by Phosphorylation and Dephosphorylation (2000)

Trans-activation of the activating transcription factor-2 (ATF2) in response to cellular stress requires the N-terminal phosphorylation of ATF2 by stress-activated protein kinases (SAPK). In this study, we investigated the role of ATF2 phosphorylation in the maintenance of ATF2 stability. Activation of SAPK by forced expression of DeltaMEKK1 increased overall ATF2 ubiquitination, presumably because of the enhanced dimerization of ATF2. Treatment of DeltaMEKK1-expressing cells with okadaic acid led to the increase in N-terminal phosphorylation, protection from ubiquitination, and accumulation of exogenously expressed ATF2, indicating the role of protein phosphatases in balancing the effects of stress kinases. Analysis of ubiquitination and degradation of the constitutively dimerized ATF2 mutant (ATF2(Delta150-248)) showed that activation of JNK or p38 kinase renders ATF2 resistant to ubiquitination and degradation. This effect is mediated by JNK/p38-dependent phosphorylation of ATF2 at Thr-69 and Thr-71, because the phosphorylation-deficient mutant (ATF2(Delta150-248-T69A,T71A)) was not protected from ubiquitination and degradation by the activation of SAPK. Treatment of cells with okadaic acid elevated the tumor necrosis factor alpha-induced ATF2 level and the extent of its specific N-terminal phosphorylation. Cycloheximide, which activates SAPK, while inhibiting protein synthesis, stabilized endogenous ATF2. However, treatment of cells with the high dose of SB203580, which inhibits JNK and p38 kinase, resulted in efficient degradation of ATF2 in cells exposed to cycloheximide. This degradation was abrogated by co-treatment with the proteasome inhibitor MG132. Our findings suggest that N-terminal phosphorylation of ATF2 dimers protect ATF2 from ubiquitination and degradation. We propose the hypothesis that the balance between SAPK and protein phosphatases affects the duration and magnitude of ATF2 transcriptional output because of the effect on substrate recognition for ubiquitination and degradation.
Surface tension confined (STC) tracks for capillary-driven transport of low surface tension liquids (2012)

Surface tension confined (STC) open tracks for pumpless transport of low-surface tension liquids (e.g., acetone, ethanol, hexadecane) on microfluidic chips are fabricated using a large-area, wet-processing technique. Wettable, paraffin-wax, submillimeter-wide tracks are applied by a fountain-pen procedure on superoleophobic, fluoroacrylic-carbon nanofiber (CNF) composite coatings. The fabricated anisotropic wetting patterns confine the low-surface-tension liquids onto the flow tracks, driving them with meniscus velocities up to 3.1 cm s(-1). Scaling arguments and Washburn's equation provide estimates of the liquid velocities measured in the STC tracks. These tracks are also shown to act as rails for directional sliding control of mm-sized water droplets. The present facile top-down patterned wettability approach can be extended to deposit micrometer-wide tracks, which bear promise for pumpless handling of low-surface tension liquids (e.g., aqueous solutions containing alcohols or surfactants) in lab-on-a-chip type applications or in low power, high-throughput bio-microfluidics for health care applications.
Solvent‐Enabled Nonenyzmatic Sugar Production from Biomass for Chemical and Biological Upgrading (2015)

We recently reported a nonenzymatic biomass deconstruction process for producing carbohydrates using homogeneous mixtures of γ-valerolactone (GVL) and water as a solvent. A key step in this process is the separation of the GVL from the aqueous phase, enabling GVL recycling and the production of a concentrated aqueous carbohydrate solution. In this study, we demonstrate that phenolic solvents-sec-butylphenol, nonylphenol, and lignin-derived propyl guaiacol-are effective at separating GVL from the aqueous phase using only small amounts of solvent (0.5 g per g of the original water, GVL, and sugar hydrolysate). Furthermore, using nonylphenol, we produced a hydrolysate that supported robust growth and high yields of ethanol (0.49 g EtOH per g glucose) at an industrially relevant concentration (50.8 g L(-1) EtOH). These results suggest that using phenolic solvents could be an interesting solution for separating and/or detoxifying aqueous carbohydrate solutions produced using GVL-based biomass deconstruction processes.
Identification of Proteins by Matrix-Assisted Laser DesorptiorVlonization Mass Spectrometry Using Peptide and Fragment Ion Masses (2003)

Methods for the identification of proteins have advanced dramatically this decade through the introduction of mass spectrometric techniques and instrumentation sensitive enough to be applicable to biological systems (1). The two mass spectrometric techniques that have provided these advantages are electrospray-ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) (see Chapters 52 , 54 , and 55 ).
Human urinary megakaryocyte colony‐stimulating factor in thrombopoietic disorders (1986)

The level of urinary Meg-CSF activity in patients with various thrombopoietic disorders was studied. Five out of eight patients with idiopathic thrombocytopenic purpura had megakaryocytic hyperplasia in the marrow and increased Meg-CSF activity in the urine. Urinary Meg-CSF activity in patients with polycythaemia vera and essential thrombocythaemia was normal. There was a significant inverse correlation between urinary Meg-CSF activity and peripheral blood platelet count but not bone marrow megakaryocyte mass. There was a significant increase of urinary Meg-CSF activity during the period of thrombocytopenia after chemotherapy in patients with acute leukaemia who were in complete remission. The timing of maximal Meg-CSF levels corresponded to the nadirs of platelet counts. These results support the concept that Meg-CSF may play a significant role in the regulation of megakaryopoiesis and/or thrombopoiesis in vivo.