gebhart/patrepeval huggingface dataset:
ASSESSMENT OF DAMAGE AND RECOVERY OF SINUSOIDAL ENDOTHELIAL CELL FUNCTION BY IN VIVO HYALURONIC ACID UPTAKE IN COLD-PRESERVED AND TRANSPLANTED RAT LIVERS (1996)

We sought to evaluate the significance of endogenous hyaluronic acid levels and in vivo uptake of exogenous hyaluronic acid as markers of liver endothelial cell damage and correlate these findings to graft survival/function in a rat orthotopic liver transplant model. Endogenous hyaluronic acid levels were measured after orthotopic liver transplantation performed with freshly explanted livers, with livers preserved for 30 hr, and after sham operation. Exogenous hyaluronic acid uptake was evaluated in six study groups: fresh liver grafts, livers preserved for 12 hr, 24 hr, 30 hr and 48 hr, and sham-operated livers. Endogenous hyaluronic acid levels fell after orthotopic liver transplantation with freshly harvested livers and after sham operation, but rose in animals transplanted with livers preserved for 30 hr (P<0.01 vs. sham operation). In the preserved group, there was no difference in endogenous hyaluronic acid levels between survivors and nonsurvivors. Uptake of exogenous hyaluronic acid was significantly lower after orthotopic liver transplant with grafts preserved for 12 hr than after sham operation or orthotopic liver transplant with nonpreserved livers (P<0.05). Hyaluronic acid uptake further deteriorated in the 24-, 30-, and 48-hr groups. No significant difference in hyaluronic acid elimination rate was found when results obtained from livers preserved for extended periods (>12 hr) were compared in survivors and nonsurvivors. Hyaluronic acid uptake was reevaluated in surviving animals after 2 weeks. Completely restored function was observed in all survivors, indicating recovery of endothelial cells. We conclude that endogenous hyaluronic acid levels and exogenous hyaluronic acid uptake are reliable markers of liver sinusoidal endothelial cell function and that normal or moderately compromised hyaluronic acid uptake is associated with good graft function. On the other hand, endothelial cell dysfunction suggested by poor hyaluronic acid elimination is not a completely reliable predictor of subsequent deterioration of graft function in rat liver transplantation.
28 Mechanisms of Transcriptional Control as Revealed by Studies of Human Transcription Factor Sp1 (1992)

OVERVIEW Specificity protein 1 (Sp1) is a promoter-selective transcription factor that binds DNA (GC boxes) and activates a wide range of vertebrate genes. Studies of Sp1 have revealed that combinations of regulatory proteins interact with promoter/enhancers and with each other to generate transcriptional specificity. The analysis of Sp1 function also provided evidence for the notion that distantly bound factors can mediate activation by direct protein:protein interactions with factors bound close to the initiation site. Studies of Sp1 have helped establish the concept that transcription factors are remarkably modular proteins with multiple structurally distinct functional domains responsible for DNA recognition (Zn fingers) and transcriptional activation (glutamine-rich domains). Recently, in vitro reconstitution experiments with Sp1 led to the discovery of coactivators, a novel class of transcription factors that are thought to mediate communication between site-specific regulatory factors and the general transcriptional machinery. INTRODUCTION By the late 1970s, many of the principles underlying the regulation of bacterial gene expression were firmly established. In particular, it was clear that much of this regulation occurred at the level of transcriptional initiation and involved the action of sigma factors and sequence-specific DNA-binding proteins (Miller and Reznikoff 1978; Rodriguez and Chamberlin 1982; for review, see McClure 1985). These proteins were found to interact with promoter elements close to the transcriptional start site and to modulate the activity of RNA polymerase. Furthermore, biochemical and genetic analyses were beginning to illuminate the mechanisms whereby these proteins could alter the rate of transcriptional initiation. At the same time, our understanding...
Polymer Electrolytes (2013)

This review article covers applications in which polymer electrolytes are used: lithium batteries, fuel cells, and water desalination. The ideas of electrochemical potential, salt activity, and ion transport are presented in the context of these applications. Potential is defined, and we show how a cell potential measurement can be used to ascertain salt activity. The transport parameters needed to fully specify a binary electrolyte (salt + solvent) are presented. We define five fundamentally different types of homogeneous electrolytes: type I (classical liquid electrolytes), type II (gel electrolytes), type III (dry polymer electrolytes), type IV (dry single-ion-conducting polymer electrolytes), and type V (solvated single-ion-conducting polymer electrolytes). Typical values of transport parameters are provided for all types of electrolytes. Comparison among the values provides insight into the transport mechanisms occurring in polymer electrolytes. It is desirable to decouple the mechanical properties of polymer electrolyte membranes from the ionic conductivity. One way to accomplish this is through the development of microphase-separated polymers, wherein one of the microphases conducts ions while the other enhances the mechanical rigidity of the heterogeneous polymer electrolyte. We cover all three types of conducting polymer electrolyte phases (types III, IV, and V). We present a simple framework that relates the transport parameters of heterogeneous electrolytes to homogeneous analogs. We conclude by discussing electrochemical stability of electrolytes and the effects of water contamination because of their relevance to applications such as lithium ion batteries.
Coeliac disease: current approach and future prospects (2008)

Public anxiety over gluten has fuelled widespread demand for gluten-free food, yet coeliac disease remains significantly underdiagnosed and some confusion remains regarding optimal diagnostic practices. Small bowel histology is the gold standard for diagnosis. High-quality commercial enzyme-linked immunosorbent assays for transglutaminase immunoglobulin A and deamidated gliadin immunoglobulin A and G are sensitive tools for screening, but almost 10% of coeliac disease is seronegative and serological testing is unreliable in the very young, in people already following a gluten-reduced diet, and those using immunosuppressive medications. HLA DQA and DQB genotyping to show that alleles encoding HLA DQ2 and DQ8 are absent virtually excludes coeliac disease. Confirming histological remission reduces the risks of later complications, such as osteoporosis and cancer. Monitoring remission by serology is unreliable. Because gluten is an exogenous antigen and the small intestine is readily accessible, the immunopathogenesis of coeliac disease is better understood than other strongly major histocompatibility complex class II-associated diseases, such as type 1 diabetes mellitus. Therapeutic targets have been identified and drugs are under development to supplement or even replace gluten-free diet. With greater awareness and non-dietary therapeutics, diagnosis and treatment of coeliac disease will be increasingly prominent in medical practice.
Desmutagens and bio‐antimutagens – their modes of action (1987)

Abstract There are two ways of preventing induced cellular mutagenesis. In the first, mutagens are inactivated by ‘desmutagens’ before they can attack the DNA. In the second, ‘bio‐antimutagens’ interfere with cellular fixation processes working on damage in DNA. Examples of modes of action are shown for these inhibitors of induced mutations and implications for reducing genetic damage in man are discussed.
Fungal Endophytes of Grasses: A Defensive Mutualism between Plants and Fungi (1988)

Many grasses are infected by systemic fungal endophytes (family Clavicipitaceae, Ascomycetes) that produce pysiologically active alkaloids in the tissues of their hosts. Infection makes grasses toxic to domestic mammals and increases resistance to insect herbivores. Some grasses are sterilized by endophyte infection while remaining vegetatively vigorous; other infected grasses remain completely fertile. Experiments demonstrate that plant growth and seed production can be increased by infection. This symbiotic association may be a defensive mutualism in which the fungi defend their hosts against herbivory, thereby defending their own resources. Recent studies suggest that defensive mutualism of endophytes with grasses may be widespread.
Metabolism of agmatine in macrophages: modulation by lipopolysaccharide and inhibitory cytokines (1998)

Agmatine is an amine derived from the decarboxylation of arginine by arginine decarboxylase (ADC) and metabolized to putrescine by agmatinase. While prevalent in bacteria and plants, agmatine and its metabolic enzymes have been recently identified in mammalian tissues. In the present study we sought to determine: (a) whether macrophages (cell line RAW 264.7) express ADC and agmatinase, and (b) if the enzymes are regulated by lipopolysaccharide (LPS), and/or by the inhibitory cytokines transforming growth factor-beta (TGF-beta), interleukin-10 (IL-10) and interleukin-4 (IL-4). LPS induced a dose-dependent stimulation of agmatinase, while it decreased ADC, the effect in both cases being maximum at 20 h. As expected, LPS dose-dependently stimulated the inducible nitric oxide synthase activity (iNOS). A strong correlation was observed between the effects of LPS on the agmatine-related enzymes and iNOS. By contrast, exposure to IL-10 and TGF-beta caused a reduction in ADC and agmatinase, whereas IL-4 was ineffective on ADC, but reverted the LPS-induced increase of agmatinase. We conclude that the agmatine pathway may be an alternative metabolic route for arginine in macrophages, suggesting a regulatory role of agmatine during inflammation.
The DARPA internet protocol suite (1985)

THE MILITARY requirement for computer communications between heterogeneous computers on heterogeneous networks has driven the development of a standard suite of protocols to permit such communications to take place in a robust and flexible manner. These protocols support an architecture consisting of multiple packet switched networks interconnected by gateways. The DARPA experimental internet system consists of satellite, terrestrial, radio, and local networks, all interconnected through a system of gateways and a set of common protocols.
Integrated thermal stabilization of a microring modulator (2013)

A defect-enhanced silicon photodiode and heater are integrated with and used to thermally stabilize a microring modulator. These optoelectronic components are interfaced with external control circuitry to create a closed-looped feedback system for thermally stabilizing the microring modulator. The thermal stabilization system enables the microring modulator to provide error-free 5-Gb/s modulation while being subjected to thermal fluctuations that would normally render it inoperable.
DNA Methylation and Cancer (2004)

DNA methylation is an important regulator of gene transcription, and its role in carcinogenesis has been a topic of considerable interest in the last few years. Alterations in DNA methylation are common in a variety of tumors as well as in development. Of all epigenetic modifications, hypermethylation, which represses transcription of the promoter regions of tumor suppressor genes leading to gene silencing, has been most extensively studied. However, global hypomethylation has also been recognized as a cause of oncogenesis. New information concerning the mechanism of methylation and its control has led to the discovery of many regulatory proteins and enzymes. The contribution of dietary folate and methylene terahydrofolate reductase polymorphisms to methylation patterns in normal and cancer tissues is under intense investigation. As methylation occurs early and can be detected in body fluids, it may be of potential use in early detection of tumors and for determining the prognosis. Because DNA methylation is reversible, drugs like 5'-azacytidine, decitabine, and histone deacetylase inhibitors are being used to treat a variety of tumors. Novel demethylating agents such as antisense DNA methyl transferase and small interference RNA are being developed, making the field of DNA methylation wider and more exciting.
Portable checkpointing and recovery (2002)

This paper presents a checkpointing scheme that was implemented in a parallel library that runs on top of CHIMP/MPI. The main goals of the checkpointing mechanism are portability and efficiency. It runs on every platform supported by MPI in a machine-independent way. The scheme allows the migration of checkpoints and offers a flexible recovery mechanism based on data-reconfiguration. Some performance results will be presented at the end of the paper together with some techniques that can be used to increase the efficiency of the checkpointing mechanism.
Synthese von 7‐unsubstituierten 7H‐Pyrrolo[2,3‐d]‐pyrimidinen (1986)

Abstract Die Titelverbindungen 4 werden durch N‐7‐Dealkylierung der 2‐Furanylmethyl‐, 2‐Thiophenylmethyl‐, oder 1‐Phenylethyl‐Gruppe aus den Derivaten 2a – g und 10a – j mit Polyphosphoräure erhalten. Im Gegensatz zur 2‐Furanylmethyl‐Gruppe lassen sich die 2‐Thiophenylmethyl‐ und 1‐Phenylethyl‐Gruppen unabhängig von der Substitution am Heterobicyclus entfernen.
Optimization of Process Conditions for Preparing an Iron-polysaccharide Complex by Response Surface Methodology (2011)

The synthetic process of an iron-polysaccharide complex drug substance was improved to make it more suitable for industrial scale production.The complex was synthesized by reacting FeCl 3 and syrup in basic solution followed by separation and purification by ethanol precipitation and low speed centrifugation.Process conditions were optimized using response surface methodology (RSM) based on the central composite design (CCD).A quadratic polynomial equation was developed, which indicated the effect of variables on the yield of the complex.The optimal conditions were 20 % Na 2 CO 3 aqueous solution 51.7 g, concentration of FeCl 3 6H 2 O w = 30.3% , and the temperature of the ferric hydroxide synthesis 6.5 C.Under these conditions, the experimental yield was 40.1 %, which was agreed closely with the predicted value (38.9 %).The results of scale-up experiments indicated that the optimized process conditions could also improve the yield at larger scales.
Non-contact mode excitation of small structures in air using ultrasound radiation force (2005)

With the advent of MEMS, modal analysis of small structures is increasingly important. However, conventional excitation techniques normally require contact, which may not be feasible for small objects. We present a non-contact method that uses interference of ultrasound frequencies in air to produce low-frequency excitation of structures. Objects studied included hard-drive HGA suspensions and MEMS devices. The vibration induced by the ultrasound radiation force was varied in a wide range from 0 Hz to 50 kHz. Object motion was detected using a laser vibrometer; measured frequencies agreed with expected values. Also demonstrated was the unique capability to selectively enhance or suppress modes independently. For example, the ratio of the vibrational amplitudes of the 175 Hz first-bending and 1.33 kHz torsional modes of a small cantilever could be changed from in excess of 10:1 to less than 1:10 by shifting the ultrasound modulation phase 90 degrees. Similar changes were obtained for a 3 mm square MEMS mirror in the ratios of vibration amplitude around its two separate axes. Torsional modes of a hard-drive suspension could be selectively enhanced by over a factor of two by moving the ultrasound focus point from near the center to near the edge of the suspension.
Immunodiagnosis of Ehrlichia canis Infection with Recombinant Proteins (2001)

Ehrlichia canis causes a potentially fatal rickettsial disease of dogs that requires rapid and accurate diagnosis in order to initiate appropriate therapy leading to a favorable prognosis. We recently reported the cloning of two immunoreactive E. canis proteins, P28 and P140, that were applicable for serodiagnosis of the disease. In the present study we cloned a new immunoreactive E. canis surface protein gene of 1,170 bp, which encodes a protein with a predicted molecular mass of 42.6 kDa (P43). The P43 gene was not detected in E. chaffeensis DNA by Southern blot, and antisera against recombinant P43 (rP43) did not react with E. chaffeensis as detected by indirect fluorescent antibody (IFA) assay. Forty-two dogs exhibiting signs and/or hematologic abnormalities associated with canine ehrlichiosis were tested by IFA assay and by recombinant Western immunoblot. Among the 22 samples that were IFA positive for E. canis, 100% reacted with rP43, 96% reacted with rP28, and 96% reacted with rP140. The specificity of the recombinant proteins compared to the IFAs was 96% for rP28, 88% for P43 and 63% for P140. The results of this study demonstrate that the rP43 and rP28 are sensitive and reliable serodiagnostic antigens for E. canis infections.
Modulated Supramolecular Assemblies Composed of Tripeptide Derivatives:  Formation of Micrometer-Scale Rods, Nanometer-Size Needles, and Regular Patterns with Molecular-Level Flatness from the Same Compound (2000)

In this paper, we demonstrated that supramolecular structures of amphiphilic tripeptides can be effectively modulated by selecting the appropriate casting solvents. The tripeptide derivatives having an ammonium head and hydrophobic tails were dispersed in three kinds of solvents (nonpolar, medium nonpolar, and polar) followed by casting the solutions onto fleshly cleaved mica. The supramolecular structures in the cast films were observed using an atomic force microscope (AFM). The tripeptide derivative possessing the Ala-Ala-Glu sequence formed needles with nanometer-scale width, micrometer-scale rods, and patterns with molecular-level flatness by casting from H2O, CCl4, and CHCl3, respectively. Since the major driving forces of the assembly are significantly influenced by the polarity of the surrounding media, the assembling process can be altered depending on the nature of the solvents. In polar H2O, the hydrophobic interaction is dominant and the resulting assemblies are supported by hydrogen bonding. The strong hydrophobic interaction led to formation of a charged surface of unit structures and they were hardly fused upon solvent evaporation. As a result, thin needlelike structures remained in the cast film. In a nonpolar solvent such as CCl4, the assembly was driven by the insolubility of a polar part of the component and the hydrogen bonding, and solidification at the hydrophobic tails is induced only upon solvent evaporation. This two-step assembling process led to growth of the assembly, resulting in a larger structure. A medium nonpolar solvent, i.e., CHCl3 is not good for both interactions, thus resulting in a nonassembling structure in the solution. Therefore, assembly occurred only when the solvent was evaporated. This process gave a two-dimensional pattern with molecular-level flatness. By using the solvents with a wide range of polarities, a variety of assembling processes leads to successful modulation of the supramolecular structures.
Efficient Tagged Memory (2017)

We characterize the cache behavior of an in-memory tag table and demonstrate that an optimized implementation can typically achieve a near-zero memory traffic overhead. Both industry and academia have repeatedly demonstrated tagged memory as a key mechanism to enable enforcement of powerful security invariants, including capabilities, pointer integrity, watchpoints, and information-flow tracking. A single-bit tag shadowspace is the most commonly proposed requirement, as one bit is the minimum metadata needed to distinguish between an untyped data word and any number of new hardware-enforced types. We survey various tag shadowspace approaches and identify their common requirements and positive features of their implementations. To avoid non-standard memory widths, we identify the most practical implementation for tag storage to be an in-memory table managed next to the DRAM controller. We characterize the caching performance of such a tag table and demonstrate a DRAM traffic overhead below 5% for the vast majority of applications. We identify spatial locality on a page scale as the primary factor that enables surprisingly high table cache-ability. We then demonstrate tag-table compression for a set of common applications. A hierarchical structure with elegantly simple optimizations reduces DRAM traffic overhead to below 1% for most applications. These insights and optimizations pave the way for commercial applications making use of single-bit tags stored in commodity memory.
The Bacillus subtilis dacB gene, encoding penicillin-binding protein 5*, is part of a three-gene operon required for proper spore cortex synthesis and spore core dehydration (1995)

Studies of gene expression using fusions to lacZ demonstrated that the Bacillus subtilis dacB gene, encoding penicillin-binding protein 5*, is in an operon with two downstream genes, spmA and spmB. Mutations affecting any one of these three genes resulted in the production of spores with reduced heat resistance. The cortex peptidoglycan in dacB mutant spores had more peptide side chains, a higher degree of peptide cross-linking, and possibly less muramic acid lactam than that of wild-type spores. These cortex structure parameters were normal in spmA and spmB mutant spores, but these spores did not attain normal spore core dehydration. This defect in spore core dehydration was exaggerated by the additional loss of dacB expression. However, loss of dacB alone did not alter the spore core water content. Spores produced by spmA and spmB mutants germinated faster than did those of the wild type. Spores produced by dacB mutants germinated normally but were delayed in spore outgrowth. Electron microscopy revealed a drastically altered appearance of the cortex in dacB mutants and a minor alteration in an spmA mutant. Measurements of electron micrographs indicate that the ratio of the spore protoplast volume to the sporoplast (protoplast-plus-cortex) volume was increased in dacB and spmA mutants. These results are consistent with spore core water content being the major determinant of spore heat resistance. The idea that loosely cross-linked, flexible cortex peptidoglycan has a mechanical activity involved in achieving spore core dehydration is not consistent with normal core dehydration in spores lacking only dacB.