gebhart/patrepeval huggingface dataset:
EUV (13.5-nm) light generation using a dense plasma focus device (1999)

A dense plasma focus (DPF) device has been investigated as a source for EUV lithography. Initial characterizations have been made of a prototype DPF employing an all-solid-state pulse power drive. Using the results from a vacuum grating spectrometer combined with measurements with a silicon photo diode, it has been found that substantial amounts of radiation within the reflectance band of Mo/Si mirrors can be generated using the 13.5 nm emission line of doubly ionized Lithium. This prototype DPF converts 25J of stored electrical energy per pulse into approximately 0.76J of in- band 13.5nm radiation emitted into 4(pi) steradians. The pulse repetition rate performance of this device has been investigated up to its DC power supply limit of 200Hz. No significant reduction in EUV output was found up to this repetition rate. At 200Hz, the measured pulse-to-pulse energy stability was (sigma) equals 6 percent and no drop out pulses were observed. The electrical circuit and operation of this prototype DPF device is presented along with a description of several future modifications intended to improve stability and efficiency.
780 nm low power diode laser irradiation stimulates proliferation of keratinocyte cultures: Involvement of reactive oxygen species (1998)

The results indicate that 780 nm low power diode laser irradiation enhanced keratinocytes proliferation in vitro, with an apparent involvement of ROS in this response, and comparably, might be used to promote their proliferation in vivo to enhance wound healing.
Soluble Donor DNA and Islet Injury After Transplantation (2011)

These findings represent the first direct testing of allograft injury in humans undergoing islet cell transplantation. Injury to donor islets very soon after transplantation may represent an important barrier to achieving insulin independence other than adaptive immune responses targeting allografts at later times. In addition, soluble donor DNA merits further development as a quantifiable biomarker to evaluate new interventions aimed at mitigating immediate islet injury.
Crystal Structure Formation of CH3NH3PbI3-xClx Perovskite (2016)

Inorganic-organic hydride perovskites bring the hope for fabricating low-cost and large-scale solar cells. At the beginning of the research, two open questions were raised: the hysteresis effect and the role of chloride. The presence of chloride significantly improves the crystallization and charge transfer property of the perovskite. However, though the long held debate over of the existence of chloride in the perovskite seems to have now come to a conclusion, no prior work has been carried out focusing on the role of chloride on the electronic performance and the crystallization of the perovskite. Furthermore, current reports on the crystal structure of the perovskite are rather confusing. This article analyzes the role of chloride in CH₃NH₃PbI<sub>3-x</sub>Cl<sub>x</sub> on the crystal orientation and provides a new explanation about the (110)-oriented growth of CH₃NH₃PbI₃ and CH₃NH₃PbI<sub>3-x</sub>Cl<sub>x</sub>.
Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter (1999)

The promoters of the mar/sox/rob regulon of Escherichia coli contain a binding site (marbox) for the homologous transcriptional activators MarA, SoxS and Rob. In spite of data from footprinting studies, the marbox has not been precisely defined because of its degeneracy and asymmetry and seemingly variable location with respect to the -10 and -35 hexamers for RNA polymerase (RNP) binding. Here, we use DNA retardation studies and hybrid promoters to identify optimally binding 20 bp minimal marboxes from a number of promoters. This has yielded a more defined marbox consensus sequence (AYnGCACnnWnnRYYAAAYn) and has led to the demonstration that some marboxes are inverted relative to others. Using transcriptional fusions to lacZ, we have found that only one marbox orientation is functional at a given location. Moreover, the functional orientation is determined by marbox location: marboxes that are 15 or more basepairs upstream of the -35 hexamer are oriented opposite those closer to the -35 hexamer. Marbox orientation and the spacing between marbox and signals for RNP binding are critical for transcriptional activation, presumably to align MarA with RNP.
Novel immunomodulatory proteins generated via directed evolution of variant IgSF domains (2017)

Abstract The immunoglobulin superfamily (IgSF) is a large, diverse family of proteins expressed on immune cells that have been extensively targeted for treatment of cancers and autoimmune diseases. Most of the therapeutic strategies targeting this family have focused on high affinity antibodies that bind a single receptor. Moreover, wild-type IgSF receptors typically exhibit low affinities for their counter-structures, limiting their utility in therapeutic modulation of immune responses. We have developed a novel variant Ig domain (vIgD™) platform using directed evolution and yeast display to affinity mature human IgSF extracellular domains. In this platform, libraries of mutagenized IgSF domains were selected for enhanced or altered affinity to specific recombinant proteins. Fc fusion proteins incorporating these evolved immunomodulatory IgSF domains were then tested in vitro for their ability to either agonize or antagonize T cell responses. Multiple novel vIgD™ fusion proteins have been generated that significantly attenuate T cell activation in vitro as assessed by proliferation and cytokine production. Lead molecules also exhibited in vivo efficacy in the human PBMC-NSG™ GVHD mouse model. Efficacy in vitro and in vivo was superior to wild-type IgSF domains due to the induced alterations in affinity for cognate ligand and through specifically directed changes in their ability to bind additional counter-structures. Our results demonstrate that vIgDs™ can be developed to acquire unique biochemical properties that significantly enhance therapeutic utility as immunomodulatory agents. This vIgD™ therapeutic platform has broad potential to enhance the activity of biologics in treatment of both autoimmune disease and cancer.
Altering dimerization specificity by changes in surface electrostatics (2001)

Arc repressor forms a homodimer in which the subunits intertwine to create a single globular domain. To obtain Arc sequences that fold preferentially as heterodimers, variants with surface patches of excess positive or negative charge were designed. Several but not all oppositely charged sequence pairs showed preferential heterodimer formation. In the most successful design pair, alpha helix B of one subunit contained glutamic acids at positions 43, 46, 47, 48, and 50, whereas the other subunit contained lysines or arginines at these positions. A continuum electrostatic model captures many features of the experimental results and suggests that the most successful designs include elements of both positive and negative design.
Nonthermal decontamination of biological media by atmospheric-pressure plasmas: review, analysis, and prospects (2002)

Although the use of an electrical discharge to disinfect water was suggested and applied more than a hundred years ago, basic and applied research on the interaction of plasmas with biological media was extensively carried out only relatively recently. In this context, a review of various works on the germicidal effects of atmospheric pressure, "cold" plasmas, is presented. The nonequilibrium discharge devices discussed in this review, which have been used in biological applications by various investigators, are the corona discharge, the diffuse dielectric-barrier discharge, the resistive barrier discharge, and the atmospheric-pressure plasma jet. Analysis of the inactivation kinetics for various bacteria seeded in (or on) various media and exposed to the plasma generated by these devices, showed that three types of survivor curves exist, depending on the type of micro-organism, the type of medium, and the type of exposure (direct versus remote). Insights into the roles of UV radiation, active species, and charged particles has led to the conclusion that chemically reactive species, such as free radicals, play the most important role in the inactivation process. In addition, recent results suggesting that biomanipulation of the cells of micro-organisms with nonequilibrium plasmas is possible are highlighted.
MAGE-A Antigens and Cancer Immunotherapy (2017)

MAGE-A antigens are expressed in a variety of cancers of diverse histological origin and germinal cells. Due to their relatively high tumor specificity, they represent attractive targets for active specific and adoptive cancer immunotherapies. Here, we (i) review past and ongoing clinical studies targeting these antigens, (ii) analyze advantages and disadvantages of different therapeutic approaches, and (iii) discuss possible improvements in MAGE-A-specific immunotherapies.
Expression of IL-8, TNF-alpha and IFN-gamma m-RNA in ulcerative colitis, particularly in patients with inactive phase. (1995)

The expression of IL-8, TNF-alpha and IFN-gamma m-RNA increased even in inactive UC, suggesting that these three cytokines play an important role in the pathogenesis of repeated inflammation of UC.
Avaliação da prevalência do diabetes e da hiperglicemia de estresse no infarto agudo do miocárdio (2008)

The elevated DM and stress hyperglycemia prevalence observed in our study indicates that glycemic alterations is one of the most important risk factors for IAM.
Recurrent 16p11.2 microdeletions in autism (2007)

Autism is a childhood neurodevelopmental disorder with a strong genetic component, yet the identification of autism susceptibility loci remains elusive. We investigated 180 autism probands and 372 control subjects by array comparative genomic hybridization (aCGH) using a 19K whole-genome tiling path bacterial artificial chromosome microarray to identify submicroscopic chromosomal rearrangements specific to autism. We discovered a recurrent 16p11.2 microdeletion in two probands with autism and none in controls. The deletion spans approximately 500-kb and is flanked by approximately 147-kb segmental duplications (SDs) that are >99% identical, a common characteristic of genomic disorders. We assessed the frequency of this new autism genomic disorder by screening an additional 532 probands and 465 controls by quantitative PCR and identified two more patients but no controls with the microdeletion, indicating a combined frequency of 0.6% (4/712 autism versus 0/837 controls; Fisher exact test P = 0.044). We confirmed all 16p11.2 deletions using fluorescence in situ hybridization, microsatellite analyses and aCGH, and mapped the approximate deletion breakpoints to the edges of the flanking SDs using a custom-designed high-density oligonucleotide microarray. Bioinformatic analysis localized 12 of the 25 genes within the microdeletion to nodes in one interaction network. We performed phenotype analyses and found no striking features that distinguish patients with the 16p11.2 microdeletion as a distinct autism subtype. Our work reports the first frequency, breakpoint, bioinformatic and phenotypic analyses of a de novo 16p11.2 microdeletion that represents one of the most common recurrent genomic disorders associated with autism to date.
Changes in ghrelin and ghrelin receptor expression according to feeding status (2003)

Ghrelin, a newly identified gut hormone, has been implicated in the regulation of food intake and energy homeostasis. This study was undertaken to investigate changes in expression levels of stomach ghrelin as well as of ghrelin receptor in the hypothalamus and pituitary glands according to feeding state. Stomach ghrelin mRNA levels were increased by 48 h fasting but decreased by re-feeding. The ghrelin receptor mRNA levels of 48h fasted rats were 8 times higher in the hypothalamus and 3 times higher in the anterior pituitary gland than levels in fed rats. In summary, not only stomach ghrelin, but also hypothalamic ghrelin receptor mRNA expression, increased during a fast. Such as enhanced ghrelin receptor expression could contribute to the amplification of ghrelin action in a negative-energy balance state.
Protecting Chemistry Inventions: The Double-Edged Sword of Being an Unpredictable Art (2015)

Recent decisions by the highest courts in the US in regard to written description and enablement as well as parallel restrictions previously established in Europe emphasize that applicants in the fields of chemistry/pharma/life sciences should strive to include as many examples, data, and guidance about how to extrapolate from the example(s) in the description. This holds in particular whenever a broad genus and/or functional features is/are to be protected. It is important to keep in mind that these data and this guidance must be disclosed in the application at the time of filing. Data collected at a later stage can only be used to further support data and evidence already present in the application as filed.
Localization during development of alternatively spliced forms of cytotactin mRNA by in situ hybridization. (1990)

Cytotactin, an extracellular glycoprotein found in neural and nonneural tissues, influences a variety of cellular phenomena, particularly cell adhesion and cell migration. Northern and Western blot analysis and in situ hybridization were used to determine localization of alternatively spliced forms of cytotactin in neural and nonneural tissues using a probe (CT) that detected all forms of cytotactin mRNA, and one (VbVc) that detected two of the differentially spliced repeats homologous to the type III repeats of fibronectin. In the brain, the levels of mRNA and protein increased from E8 through E15 and then gradually decreased until they were barely detectable by P3. Among the three cytotactin mRNAs (7.2, 6.6, and 6.4 kb) detected in the brain, the VbVc probe hybridized only to the 7.2-kb message. In isolated cerebella, the 220-kD polypeptide and 7.2-kb mRNA were the only cytotactin species present at hatching, indicating that the 220-kD polypeptide is encoded by the 7.2-kb message that contains the VbVc alternatively spliced insert. In situ hybridization showed cytotactin mRNA in glia and glial precursors in the ventricular zone throughout the central nervous system. In all regions of the nervous system, cytotactin mRNAs were more transient and more localized than the polypeptides. For example, in the radial glia, cytotactin mRNA was observed in the soma whereas the protein was present externally along the glial fibers. In the telencephalon, cytotactin mRNAs were found in a narrow band at the edge of a larger region in which the protein was wide-spread. Hybridization with the VbVc probe generally overlapped that of the CT probe in the spinal cord and cerebellum, consistent with the results of Northern blot analysis. In contrast, in the outermost tectal layers, differential hybridization was observed with the two probes. In nonneural tissues, hybridization with the CT probe, but not the VbVc probe, was detected in chondroblasts, tendinous tissues, and certain mesenchymal cells in the lung. In contrast, hybridization with both probes was observed in smooth muscle and lung epithelium. Both epithelium and mesenchyme expressed cytotactin mRNA in varying combinations: in the choroid plexus, only epithelial cells expressed cytotactin mRNA; in kidney, only mesenchymal cells; and in the lung, both of these cell types contained cytotactin mRNA. These spatiotemporal changes during development suggest that the synthesis of the various alternatively spliced cytotactin mRNAs is responsive to tissue-specific local signals and prompt a search for functional differences in the various molecular forms of the protein.
Mechanisms underlying PTEN regulation of vascular endothelial growth factor and angiogenesis (2002)

Inactivation of the tumor suppressor gene PTEN and overexpression of VEGF are two of the most common events observed in high-grade malignant gliomas. The purpose of this study was to determine whether PTEN controls VEGF expression in gliomas under normoxic conditions. Transfer of PTEN to human glioma cells resulted in the transduction of a functional PTEN protein as evidenced by the upregulation of p27 and modification of the phosphorylation status of Akt. Under normoxic conditions, enzyme-linked immunosorbent assay and Northern blot analyses showed downregulation of VEGF in PTEN-treated cells. Moreover, conditioned media from PTEN-treated glioma cells significantly diminished the ability of endothelial cells to grow and migrate. Western blot assays demonstrated that, in a normoxic environment, PTEN downregulates HIF-1 alpha. Finally, promoter activity assays showed that the VEGF promoter region containing the HIF-1alpha binding site is necessary and sufficient for PTEN-mediated downregulation of VEGF. Experiments with PI3-K inhibitors and kinase assays suggested that PI3-K is mediating the effect of PTEN on VEGF, and not the p42/p48 or p38 MAP kinases. These results indicate that restoration of PTEN function in gliomas may induce therapeutic effect by downregulating VEGF. Furthermore, this close functional relationship between PTEN and VEGF suggests that a better understanding of the transduction signal regulated by PTEN might enhance the knowledge of the cause and physiology of vascular and inflammatory diseases.
Nanometer-scale mapping and single-molecule detection with color-coded nanoparticle probes (2008)

We report a method for single-molecule detection and biomolecular structural mapping based on dual-color imaging and automated colocalization of bioconjugated nanoparticle probes at nanometer precision. In comparison with organic dyes and fluorescent proteins, nanoparticle probes such as fluorescence energy-transfer nanobeads and quantum dots provide significant advantages in signal brightness, photostability, and multicolor-light emission. As a result, we have achieved routine two-color superresolution imaging and single-molecule detection with standard fluorescence microscopes and inexpensive digital color cameras. By using green and red nanoparticles to simultaneously recognize two binding sites on a single target, individual biomolecules such as nucleic acids are detected and identified without target amplification or probe/target separation. We also demonstrate that a powerful astrophysical method (originally developed to analyze crowded stellar fields) can be used for automated and rapid statistical analysis of nanoparticle colocalization signals. The ability to rapidly localize bright nanoparticle probes at nanometer precision has implications not only for ultrasensitive medical detection but also for structural mapping of molecular complexes in which individual components are tagged with color-coded nanoparticles.
Characterization of a human immunodeficiency virus neutralizing monoclonal antibody and mapping of the neutralizing epitope (1988)

A monoclonal antibody was produced to the exterior envelope glycoprotein (gp120) of the human T-cell lymphotropic virus (HTLV)-IIIB isolate of the human immunodeficiency virus (HIV). This antibody binds to gp120 of HTLV-IIIB and lymphadenopathy-associated virus type 1 (LAV-1) and to the surface of HTLV-IIIB- and LAV-1-infected cells, neutralizes infection by cell-free virus, and prevents fusion of virus-infected cells. In contrast, it does not bind, or weakly binds, the envelope of four heterologous HIV isolates and does not neutralize heterologous isolates HTLV-IIIRF and HTLV-IIIMN. The antibody-binding site was mapped to a 24-amino-acid segment, using recombinant and synthetic segments of HTLV-IIIB gp120. This site is within a segment of amino acid variability known to contain the major neutralizing epitopes (S. D. Putney, T. J. Matthews, W. G. Robey, D. L. Lynn, M. Robert-Guroff, W. T. Mueller, A. J. Langlois, J. Ghrayeb, S. R. Petteway, K. J. Weinhold, P. J. Fischinger, F. Wong-Staal, R. C. Gallo, and D. P. Bolognesi, Science 234:1392-1395, 1986). These results localize an epitope of HIV type-specific neutralization and suggest that neutralizing antibodies may be effective in controlling cell-associated, as well as cell-free, virus infection.
Recombinant Haplotypes Narrow the ARMS2/HTRA1 Association Signal for Age-Related Macular Degeneration (2016)

Abstract Age-related macular degeneration (AMD) is the leading cause of blindness in ageing societies, triggered by both environmental and genetic factors. The strongest genetic signal for AMD with odds ratios of up to 2.8 per adverse allele was found previously over a chromosomal region in 10q26 harboring two genes, ARMS2 and HTRA1, although with little knowledge as to which gene or genetic variation is functionally relevant to AMD pathology. In this study, we analyzed rare recombinant haplotypes in 16,144 AMD cases and 17,832 controls from the International AMD Genomics Consortium and identified variants in ARMS2 but not HTRA1 to exclusively carry the AMD risk with P-values between 1.0 × 10−773 and 6.7 × 10−5. This now allows prioritization of the gene of interest for subsequent functional studies.
Kink‐Block and Gauche‐Block Structures of Bimolecular Films (1976)

Abstract Layer silicates and some other layer compounds can take up organic compounds such as long‐chain alkanols and alkylammonium ions with formation of ordered bimolecular films. This system enables new ideas to be developed concerning the structure of monomolecular and bimolecular films: the films form reversible kink‐block and gauche‐block structures. Conclusions can be derived about the structure of the lipid layers in membranes.
A NAT Traversal Mechanism for Peer-To-Peer Networks (2008)

In this demo we present our approach for establishing a communication channel between hosts behind a NAT-based router. To do so, we developed a peer-to-peer based variant of the STUN protocol using so-called superpeers. Using this protocol we determine the used NAT types for the hosts and select a suitable NAT traversal technique dynamically.
Identification and HPLC Quantitation of the Sulfides and Dialk(en)yl Thiosulfinates in Commercial Garlic Products (1991)

The content of dialk(en)yl thiosulfinates, including allicin, and their degradation products has been determined by high performance liquid chromatography (HPLC), using the respective determined extinction coefficients, for a number of commercially available garlic products. Quantitation has been achieved for the thiosulfinates; diallyl, methyl allyl, and diethyl mono-, di-, tri-, tetra-, penta-, and hexasulfides; the vinyldithiins; and (E)- and (Z)-ajoene. The thiosulfinates were found to be released only from garlic cloves and garlic powder products. The vinyldithiins and ajoenes were found only in products containing garlic macerated in vegetable oil. The diallyl, methyl allyl, and dimethyl sulfide series were the exclusive constituents found in products containing the oil of steam-distilled garlic. Typical steam-distilled garlic oil products contained about the same amount of total sulfur compounds as total thiosulfinates released from freshly homogenized garlic cloves; however, oil-macerated products contained only 20% of that amount, while garlic powder products varied from 0 to 100%. Products containing garlic powder suspended in a a gel or garlic aged in aqueous alcohol did not contain detectable amounts of these non-ionic sulfur compounds. A comparison of several brands of each type of garlic product revealed a large range in content (4-fold for oil-macerates and 33-fold for steam-distilled garlic oils), indicating the importance of analysis before garlic products are used for clinical investigations or commercial distribution.
大洋甲烷水合物是一种“未勘探”的气资源 (1996)

水合物(也可按它们的化学种名字冰状甲烷笼形化合物来称呼)是一种冰状化合物,它们在非常低温的永冻地区和低温-高压体制的深大洋地区均保持稳定。在气水合物中烃类气(主要是甲烷)和流体在热动力学上是稳定的。那是由于氢结合在由水分子提供的结晶格内的缘故。结晶作用使得甲烷分子的体积要大大地小于它们作为气体或熔解在流体中的气的体积。每立方米的水合物拥有164立方米的天然气和0.8立方米的水。或许150立方米的天然气可以从1立方米的水合物中释放,因为水台物晶格内适合甲烷的一些分子品格位置没有占用,或充填着另外的天然气和碳氢化合物。