gebhart/patrepeval huggingface dataset:
Thioredoxin-dependent regulatory networks in chloroplasts under fluctuating light conditions (2014)

Plants have adopted a number of mechanisms to restore redox homeostasis in the chloroplast under fluctuating light conditions in nature. Chloroplast thioredoxin systems are crucial components of this redox network, mediating environmental signals to chloroplast proteins. In the reduced state, thioredoxins control the structure and function of proteins by reducing disulfide bridges in the redox active site of a protein. Subsequently, an oxidized thioredoxin is reduced by a thioredoxin reductase, the two enzymes together forming a thioredoxin system. Plant chloroplasts have versatile thioredoxin systems, including two reductases dependent on ferredoxin and NADPH as reducing power, respectively, several types of thioredoxins, and the system to deliver thiol redox signals to the thylakoid membrane and lumen. Light controls the activity of chloroplast thioredoxin systems in two ways. First, light reactions activate the thioredoxin systems via donation of electrons to oxidized ferredoxin and NADP(+), and second, light induces production of reactive oxygen species in chloroplasts which deactivate the components of the thiol redox network. The diversity and partial redundancy of chloroplast thioredoxin systems enable chloroplast metabolism to rapidly respond to ever-changing environmental conditions and to raise plant fitness in natural growth conditions.
Design techniques for low-power multi-GS/s analog-to-digital converters (2013)

The HIVEP gene family encodes for very large sequence-specific DNA binding proteins containing multiple zinc fingers. Three mammalian paralogous genes have been identified, HIVEP1, -2 and -3, as well as the closely related Drosophila gene, Schnurri. These genes have been found to directly participate in the transcriptional regulation of a variety of genes. Mammalian HIVEP members have been implicated in signaling by TNF-alpha and in the positive selection of thymocytes, while Schnurri has been shown to be an essential component of the TGF-beta signaling pathway. In this study, we describe the isolation of Xenopus HIVEP1, as well as partial cDNAs of HIVEP2 and -3. Analysis of the temporal and spatial expression of the XHIVEP transcripts during early embryogenesis revealed ubiquitous expression of the transcripts. Assays using Xenopus oocytes mapped XHIVEP1 domains that are responsible for nuclear export and import activity. The DNA binding specificity of XHIVEP was characterized using a PCR-mediated selection and gel mobility shift assays.
Restoration of Large Bone Defects Using a Hard-Setting, Injectable Putty Containing Demineralized Bone Particles Compared to Cancellous Autograft Bone (2003)

An injectable, hard-setting, calcium sulfate-based putty containing demineralized bone matrix particles (AlloMatrix II, Wright Medical Technology, Inc, Arlington, Tenn) was compared to autogenous cancellous bone graft to evaluate healing in a canine model. Area fraction of new bone, modulus of elasticity, and compressive strength of new bone were evaluated, as was radiographic and histologic healing. Bilateral defects were created in the proximal humeri, and each defect was implanted with either the putty or autogenous bone according to a randomized schedule. Dogs were euthanized at 6, 13, and 26 weeks. The area fraction, modulus of elasticity, and compressive strength of newly formed bone was not significantly different between the putty and autogenous bone at 6, 13, or 26 weeks. The putty had excellent handling characteristics, was biocompatible, and was as effective as autograft bone in achieving near complete bony restoration of a large, critical-sized defect.
Heat Flux Measurement (2013)

Abstract Owing to the importance of energy in modern society, heat transfer (the movement of thermal energy) has become a crucial factor in many engineering systems. Measurements of heat transfer are therefore important, but remain a challenge to accomplish with accuracy. Various commercial heat flux gages and research methods are available to measure heat transfer in a wide range of applications. This chapter explores how to accurately and reliably measure heat flux (heat transfer per area) with these techniques in practical situations.
Force-directed scheduling for the behavioral synthesis of ASICs (1989)

A general scheduling methodology is presented that can be integrated into specialized or general-purpose high-level synthesis systems. An initial version of the force-directed scheduling algorithm at the heart of this methodology was originally presented by the authors in 1987. The latest implementation of the logarithm introduced here reduces the number of functional units, storage units, and buses required by balancing the concurrency of operations assigned to them. The algorithm supports a comprehensive set of constraint types and scheduling modes. These include multicycle and chained operations; mutually exclusive operations; scheduling under fixed global timing constraints with minimization of functional unit costs, minimization of register costs, and minimization of global interconnect requirements; scheduling with local time constraints (on operation pairs); scheduling under fixed hardware resource constraints; functional pipelining; and structural pipeline (use of pipeline functional units). Examples from current literature, one of which was chosen as a benchmark for the 1988 High-Level Synthesis Workshop, are used to illustrate the effectiveness of the approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microbiota and Gut–Liver Axis (2013)

A specific bacterial gut microbiota profile with increased extraction of energy has recently been associated with obesity, which has been shown to be a transmissible phenotype by microbiota transplantation. At the same time, there is now increasing evidence that gut microbiota plays a role in the development of hepatic steatosis and its progression to nonalcoholic steatohepatitis. This review summarizes well known and unexpected interacting factors leading to obesity and its related hepatic diseases, including intestinal mucosal permeability and its regulation, gut microbiota and translocation of its biological products, and gut-associated lymphoid tissue. These intestinal factors dictate also the balance between tolerance and immune response, which are critical for most of the complications in near and far organs or systems. We review novel mechanisms involving the development of gut permeability and adipose tissue plasticity, for example, the cross-talk between the gut microbiota, lipopolysaccharide, high-fat diet, and the endocannabinoid system tone, which have not been fully explored. Interactions between gut microbiota and other factors (eg, inflammasome deficiency) also are reviewed as emerging but far from being completely elucidated mechanisms influencing the onset of obesity and nonalcoholic fatty liver disease.
Maintaining remission of ulcerative colitis with the probiotic <i>Escherichia coli</i> Nissle 1917 is as effective as with standard mesalazine (2004)

The probiotic drug E coli Nissle 1917 shows efficacy and safety in maintaining remission equivalent to the gold standard mesalazine in patients with ulcerative colitis. The effectiveness of probiotic treatment further underlines the pathogenetic significance of the enteric flora.
Migrating from ISODE/ROSE to DCE/RPC: A Common Interface and a Compiler (1996)

ROSE of the OSI Reference Model and the RPC paradigm are two major concepts in the area of distributed computing. ISODE and DCE RPC are implementations of these models. This paper is addressed towards distributed application programmers, who use the RO—notation of ASN.1 as specification language and want to develop RPC applications as well. We introduce an approach of a common interface, which consists of two parts: A common interface to the runtime environments of ISODE and DCE, and a transformation from a specification given in the RO—notation into DCE IDL. Using this interface we provide a migration path from an application based on ISODE to one based on DCE. The concept also enables newly developed applications to run in both environments, which increases the number of potential users substantially. Furthermore the specification of user specific data types and operations can be preserved in ASN.1, since the transformation into DCE IDL is generated by the compiler ro2idl.
Morphology and Dynamic Viscoelastic Behavior of Blends of Styrene-Butadiene Block Copolymers (1979)

Different block length distributions in styrene—butadiene block copolymers of the linear SBS or (SB)x "star" type and their mixtures can cause wide changes in domain morphology at constant overall monomer composition (75 wt % styrene). Block polymers of substantially uniform block length had the expected spherical, polystyrene-continuous morphology. Broadening the styrene block length distribution by blending polymers of different block lengths led to appearance of cylindrical and lamellar structures and, ultimately, to complex polybutadiene-continuous morphologies. Polymers and blends were characterized by electron microscopy and by their viscoelastic behavior. Correlations were established between morphology on one hand and anisotropy in the storage modulus and the height and position of the polybutadiene tan δ maximum on the other.
Gold nanoparticles inhibit activation of cancer-associated fibroblasts by disrupting communication from tumor and microenvironmental cells (2020)

Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment (TME) and an important contributor to cancer progression and therapeutic resistance. Regulation of CAF activation is a promising strategy to influence cancer outcomes. Here, we report that ovarian cancer cells (OCs) and TME cells promote the activation of ovarian CAFs, whereas gold nanoparticles (GNPs) of 20 nm in diameter inhibit the activation, as demonstrated by the changes in cell morphology, migration, and molecular markers. GNPs exert the effect by altering the levels of multiple fibroblast activation or inactivation proteins, such as TGF-β1, PDGF, uPA and TSP1, secreted by OCs and TME cells. Thus, GNPs represent a potential tool to help understand multicellular communications existing in the TME as well as devise strategies to disrupt the communication.
A 400MHz current starved ring oscillator with temperature and supply voltage insensitivity (2014)

A ring oscillator with temperature and supply voltage compensation is presented in this paper. In the proposed configuration, low drop-out regulator (LDO) is adapted to reject the influence of supply voltage variation on the output frequency of ring oscillator. Temperature sensor and voltage adder/subtractor are used to generate a bias voltage which can maintain a constant output frequency of ring oscillator with temperature variation. In addition, for the purpose of high stability, a high accuracy band-gap reference provides DC bias voltage for LDO, temperature sensor and voltage adder/subtractor. The proposed circuit configuration is realized in 0.35 μm CMOS technology and simulated with cadence tools. The simulation results show the temperature coefficient of output frequency is 57.5 ppm/°C in temperature range of -20 to 100°C and the variation of output frequency with supply voltage is ±0.07% in voltage rang of 3.2 to 4 V.
Evaluation of ZAP‐70 expression by flow cytometry in chronic lymphocytic leukemia: A multicentric international harmonization process (2006)

The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous with some patients requiring early therapy whereas others will not be treated for years. The evaluation of an individual CLL patient's prognosis remains a problematic issue. The presence or absence of somatic mutations in the IgVH genes is currently the gold-standard prognostic factor, but this technique is labor intensive and costly. Genomic studies uncovered that 70 kDa zeta-associated protein (ZAP-70) expression was associated with unmutated IgVH genes and ZAP-70 protein expression was proposed as a surrogate for somatic mutational status. Among the available techniques for ZAP-70 detection, flow cytometry is most preferable as it allows the simultaneous quantification of ZAP-70 protein expression levels in CLL cells and residual normal lymphocyte subsets. However, several factors introduce variability in the results reported from different laboratories; these factors include the anti-ZAP-70 antibody clone and conjugate, the staining procedure, the gating strategy, and the method of reporting the results. The need for standardization of the approach led to the organization of an international working group focused on harmonizing all aspects of the technique. During this workshop, a technical consensus was reached on the methods for cell permeabilization and immunophenotyping procedures. An assay was then designed that allowed comparison of two clones of anti-ZAP-70 antibody and the identification of the expression of this molecule in B, T, and NK cells identified in a four multicolor analysis. This procedure was applied to three stabilized blood samples, provided by the UK NEQAS group to all participating members of this study, in order to minimize variability caused by sample storage and shipment. Analysis was performed in 20 laboratories providing interpretable data from 14 centers. Various gating strategies were used and the ZAP-70 levels were expressed as percentage positive (POS) relative to isotype control or normal B-cells or normal T-cells; in addition the levels were reported as a ratio of expression in CLL cells relative to T-cells. The reported level of ZAP-70 expression varied greatly depending on the antibody and the method used to express the results. The CLL/T-cell ZAP-70 expression ratio showed a much lower interlaboratory variation than other reporting strategies and is recommended for multicenter studies. Stabilization results in decreased expression of CD19 making gating more difficult and therefore stabilized samples are not optimal for multicentric analysis of ZAP-70 expression. We assessed the variation of ZAP-70 expression levels in fresh cells according to storage time, which demonstrated that ZAP-70 is labile but sufficiently stable to allow comparison using fresh samples distributed between labs in Europe. These studies have demonstrated progress toward a consensus reporting procedure, and further work is underway to harmonize the preparation and analysis procedures.
Study of dye decolorization in an immobilized laccase enzyme‐reactor using online spectroscopy (2004)

Decolorization of textile dyes by a laccase from Trametes modesta immobilized on gamma-aluminum oxide pellets was studied. An enzyme reactor was equipped with various UV/Vis spectroscopic sensors allowing the continuous online monitoring of the decolorization reactions. Decolorization of the dye solutions was followed via an immersion transmission probe. Adsorption processes were observed using diffuse reflectance measurements of the solid carrier material. Generally, immobilization of the laccase does not seem to sterically affect dye decolorization. A range of commercial textile dyes was screened for decolorization and it was found that the application of this enzymatic remediation system is not limited to a certain structural group of dyes. Anthrachinonic dyes (Lanaset Blue 2R, Terasil Pink 2GLA), some azo dyes, Indigo Carmine, and the triphenylmethane dye Crystal Violet were efficiently decolorized. However, the laccase displayed pronounced substrate specificities when a range of structurally related model azodyes was subjected to the biotransformation. Azodyes containing hydroxy groups in ortho or para position relative to the azo bond were preferentially oxidized. The reactor performance was studied more closely using Indigo Carmine.
Mutations in Phosphoinositide Metabolizing Enzymes and Human Disease (2009)

Phosphoinositides are implicated in the regulation of a wide variety of cellular functions. Their importance in cellular and organismal physiology is underscored by the growing number of human diseases linked to perturbation of kinases and phosphatases that catalyze interconversion from one phosphoinositide to another. Many such enzymes are attractive targets for therapeutic interventions. Here, we review diseases linked to inheritable or somatic mutations of these enzymes.
Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, <i>Pyrococcus furiosus</i> (2012)

The anaerobic archaeon Pyrococcus furiosus grows by fermenting carbohydrates producing H(2), CO(2), and acetate. We show here that it is surprisingly tolerant to oxygen, growing well in the presence of 8% (vol/vol) O(2). Although cell growth and acetate production were not significantly affected by O(2), H(2) production was reduced by 50% (using 8% O(2)). The amount of H(2) produced decreased in a linear manner with increasing concentrations of O(2) over the range 2-12% (vol/vol), and for each mole of O(2) consumed, the amount of H(2) produced decreased by approximately 2 mol. The recycling of H(2) by the two cytoplasmic hydrogenases appeared not to play a role in O(2) resistance because a mutant strain lacking both enzymes was not more sensitive to O(2) than the parent strain. Decreased H(2) production was also not due to inactivation of the H(2)-producing, ferredoxin-dependent membrane-bound hydrogenase because its activity was unaffected by O(2) exposure. Electrons from carbohydrate oxidation must therefore be diverted to relieve O(2) stress at the level of reduced ferredoxin before H(2) production. Deletion strains lacking superoxide reductase (SOR) and putative flavodiiron protein A showed increased sensitivity to O(2), indicating that these enzymes play primary roles in resisting O(2). However, a mutant strain lacking the proposed electron donor to SOR, rubredoxin, was unaffected in response to O(2). Hence, electrons from sugar oxidation normally used to produce H(2) are diverted to O(2) detoxification by SOR and putative flavodiiron protein A, but the electron flow pathway from ferredoxin does not necessarily involve rubredoxin.|
The ROSE data manager: using object technology to support interactive engineering applications (1989)

The relational object system for engineering (ROSE) is an experimental database system for interactive engineering applications. The ROSE system and the way it uses object technology are described. The system has an open architecture which allows new tools to be added easily. Several tools are described, including an inheritance manager, version control system, and user interface manager. These tools enhance the ROSE system and broaden its application to other types of data-management problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Large scale detection of IDN domain name masquerading (2018)

Introducing Unicode characters to domain names enabled end users to register a domain name in different languages, i.e., Russian, Arabic or Chinese. This process is defined as Internationalized Domain Names (IDN). The Unicode standard contains a large number of characters and character sets. Some of those Unicode characters' sets may resemble some ASCII characters (this is commonly referred as "homoglyph") which are the basic building blocks for a domain name address. As such, an attacker could use the concept of homoglyph to spoof a domain name and lure an innocent user to visit a decoy domain instead of a legitimate one. IDN domain spoofing could be best detected at the end user side or by using a centralized monitoring solution. This research work is focusing on the different IDN spoofing attack types, and it proposes a new centralized monitoring system that can detect those attacks.
The higher alcohol synthesis over promoted Cu/ZnO catalysts (1983)

Abstract Alkali oxides added to methanol catalysts increase the formation of ethanol, n ‐propanol and isobutyl alcohol. This result has been known for many years, yet few quantitative studies have been reported in the literature. Data obtained on a commercial copper‐zinc oxide catalyst promoted with K 2 CO 3 are presented and compared with published work. The optimum promoter concentration was about 0.5% by weight. The H 2 to CO feed ratio was important in determining the higher alcohol selectivity. The rate of production of isobutyl alcohol varied as p p while for methanol, ethanol and n ‐propanol both exponents were positive and less than 1.6. Decreasing the hydrogen to carbon monoxide ratio from 2 to 0.5 more than doubled the isobutyl alcohol selectivity. Chain growth schemes predicting the higher alcohol selectivity are presented and estimates of the parameters are given.
Highly tunable and efficient diode pumped operation of Tm <sup>3+</sup> doped fibre lasers (1990)

The characteristics of a Tm3+ doped fibre laser pumped by a laser diode are reported. Operating at a wavelength of 1.94 μm, the laser had a threshold of 4.4 mW, a launched power slope efficiency of 17% and 1 mW output power. Measurements on the tuning range of Tm3+ are presented and lasing is found to be possible from 1.65–2.0 μm, the specific range depending on the fibre type. The largest range for a single laser was 300 nm.
Synthetic Modular Antibody Construction by Using the SpyTag/SpyCatcher Protein‐Ligase System (2017)

Efforts to engineer recombinant antibodies for specific diagnostic and therapy applications are time consuming and expensive, as each new recombinant antibody needs to be optimized for expression, stability, bio-distribution, and pharmacokinetics. We have developed a new way to construct recombinant antibody-like "devices" by using a bottom-up approach to build them from well-behaved discrete recombinant antibody domains or "parts". Studies on antibody structure and function have identified antibody constant and variable domains with specific functions that can be expressed in isolation. We used the SpyTag/SpyCatcher protein ligase to join these parts together, thereby creating devices with desired properties based on summed properties of parts and in configurations that cannot be obtained by using genetic engineering. This strategy will create optimized recombinant antibody devices at reduced costs and with shortened development times.
Escherichia coli mutants deficient in exonuclease VII (1977)

Mutants of Escherichia coli having reduced levels of exonuclease VII activity have been isolated by a mass screening procedure. Nine mutants, five of which are known to be of independent origin, were obtained and designated xse. The defects in these strains lie at two or more loci. One of these loci, xseA, lies in the interval between purG and purC; it is 93 to 97% co-transducible with guaA. The order of the genes in this region is purG-xseA guaA,B-purC. The available data do not allow xseA to be ordered with respect to guaA,B. Exonuclease VII purified from E. coli KLC3 xseA3 is more heat labile than exonuclease VII purified from the parent, E. coli PA610 xse+. Therefore, xseA is the structural gene for exonuclease VII. Mutants with defects in the xseA gene show increased sensitivity to nalidixic acid and have an abnormally high frequency of recombination (hyper-Rec phenotype) as measured by the procedure of Konrad and Lehlman (1974). The hyper-Rec character of xseA strains is approximately one-half that of the polAex1 mutant defective in the 5' leads to 3' hydrolytic activity of deoxyribonucleic acid polymerase I. The double mutant, polAex1 xseA7, is twice as hyper-Rec as the polAex1 mutant alone. The xseA- strains are slightly more sensitive to ultraviolet irradiation than the parent strain. Bacteriophages T7, fd, and lambdared grow normally in xseA- strains.