gebhart/patrepeval huggingface dataset:
Trehalose-recycling ABC transporter LpqY-SugA-SugB-SugC is essential for virulence of <i>Mycobacterium tuberculosis</i> (2010)

Mycobacterium tuberculosis (Mtb) is an exclusively human pathogen that proliferates within phagosomes of host phagocytes. Host lipids are believed to provide the major carbon and energy sources for Mtb, with only limited availability of carbohydrates. There is an apparent paradox because five putative carbohydrate uptake permeases are present in Mtb, but there are essentially no host carbohydrates inside phagosomes. Nevertheless, carbohydrate transporters have been implicated in Mtb pathogenesis, suggesting that acquisition of host sugars is important during some stages of infection. Here we show, however, that the LpqY-SugA-SugB-SugC ATP-binding cassette transporter is highly specific for uptake of the disaccharide trehalose, a sugar not present in mammals, thus refuting a role in nutrient acquisition from the host. Trehalose release is known to occur as a byproduct of the biosynthesis of the mycolic acid cell envelope by Mtb's antigen 85 complex. The antigen 85 complex constitutes a group of extracellular mycolyl transferases, which transfer the lipid moiety of the glycolipid trehalose monomycolate (TMM) to arabinogalactan or another molecule of TMM, yielding trehalose dimycolate. These reactions also lead to the concomitant extracellular release of the trehalose moiety of TMM. We found that the LpqY-SugA-SugB-SugC ATP-binding cassette transporter is a recycling system mediating the retrograde transport of released trehalose. Perturbations in trehalose recycling strongly impaired virulence of Mtb. This study reveals an unexpected accessory component involved in the formation of the mycolic acid cell envelope in mycobacteria and provides a previously unknown role for sugar transporters in bacterial pathogenesis.
The role of nuclear lamin B1 in cell proliferation and senescence (2011)

Nuclear lamin B1 (LB1) is a major structural component of the nucleus that appears to be involved in the regulation of many nuclear functions. The results of this study demonstrate that LB1 expression in WI-38 cells decreases during cellular senescence. Premature senescence induced by oncogenic Ras also decreases LB1 expression through a retinoblastoma protein (pRb)-dependent mechanism. Silencing the expression of LB1 slows cell proliferation and induces premature senescence in WI-38 cells. The effects of LB1 silencing on proliferation require the activation of p53, but not pRb. However, the induction of premature senescence requires both p53 and pRb. The proliferation defects induced by silencing LB1 are accompanied by a p53-dependent reduction in mitochondrial reactive oxygen species (ROS), which can be rescued by growth under hypoxic conditions. In contrast to the effects of LB1 silencing, overexpression of LB1 increases the proliferation rate and delays the onset of senescence of WI-38 cells. This overexpression eventually leads to cell cycle arrest at the G1/S boundary. These results demonstrate the importance of LB1 in regulating the proliferation and senescence of human diploid cells through a ROS signaling pathway.
Expression of Megsin mRNA, a Novel Mesangium-Predominant Gene, in the Renal Tissues of Various Glomerular Diseases (1999)

Mesangial cells play an important role in maintaining a structure and function of the glomerulus and in the pathogenesis of glomerular diseases. Recently, we discovered a new mesangium-predominant gene termed "megsin." Megsin is a novel protein that belongs to the serine protease inhibitor (serpin) superfamily. To elucidate the pathophysiologic role of megsin in the kidney, the expression and localization of megsin mRNA in renal tissues of patients with IgA nephropathy (IgA-N), diabetic nephropathy (DN), minimal change nephrotic syndrome (MCNS), membranous nephropathy (MN), and normal human kidney (NHK) was evaluated by in situ hybridization using digoxigenin-labeled oligonucleotide. Individual cells positive for megsin mRNA were observed only in glomeruli in all renal tissues. Their localization coincided with those of mesangial cells. The percentage of positive cells for megsin mRNA in total glomerular cells was significantly greater in IgA-N than in MCNS, MN, and NHK. It was also significantly greater in DN than in MCNS and NHK. In IgA-N, the percentage of megsin mRNA-positive cells was greater in tissues from those with mesangial cell proliferation and slightly mesangial matrix expansion (periodic acid-Schiff-positive area in the total glomerulus area, <30%; cell number in mesangial matrix area, >30; assessed in cross-sections through their vascular poles) than in tissues from those with severe mesangial matrix expansion (periodic acid-Schiff-positive area in total glomerulus area, >30%; cell number in mesangial matrix area, <30). In conclusion, megsin mRNA was predominantly expressed in glomerular mesangial cells in all renal tissues. The expression of megsin mRNA was upregulated in IgA-N and DN, both of which are diseases accompanied with mesangial cell proliferation and/or mesangial matrix expansion. These data suggest a link of megsin expression to the pathogenesis of IgA-N and DN, two major causes of end-stage renal failure.
Disassembly and Classification for Recovery of EOL Products (2003)

Recovery of end-of-life (EOL) products is an environmentally and economically sound way to achieve many of the goals of sustainable development. Many product recovery systems are dependent upon destructive disassembly such as shredding, which undesirably causes a large volume of shredder dust and makes parts reuse impossible. Although non-destructive disassembly has been considered as an alternative for solving the problems, the classification of disassembled items has not been sufficiently investigated. In this paper, we propose a model that mathematically optimizes the disassembly and classification of EOL products. Based on the AND/OR graph that illustrates all possible disassembly sequences of a given product, we identify the physical properties that are considered as constraints in the model. As a result of the solution procedure, the recovery problem can be transformed into a mixed integer linear programming (MILP) model. We show an example that illustrates the concept of our model.
The Effect of Molecular Weight Distribution on the Inhibition Efficiency Performance of Polymeric Scale Inhibitors During Retention (2015)

Abstract Polymeric scale inhibitors (SI) used for downhole oilfield squeeze treatments must perform the dual role of inhibiting scale formation at low concentration levels (~2-20ppm) whilst giving acceptably long return curves at the wellbore; i.e. good [SI] vs. time or produced water volume behavior with [SI]&gt;MIC, Minimum Inhibitor Concentration). Both the inhibition efficiency (IE) and retention design aspects of polymeric SI treatments are thought to be functions of the molecular weight (Mw) of the polymeric species. However, this has not yet been fully demonstrated experimentally. In this paper, we studied three polymeric SI, viz. PPCA, SPPCA and PFC in some detail. This paper describes the effects of the molecular weight distribution (MWD) on the IE performance of the polymeric SI. Our findings reveal that the precipitated PPCA and SPPCA are more efficient at inhibiting barite than either the stock or supernatant. We demonstrate that this is due to the fact that the precipitate preferentially contains larger Mw species which have an increased IE. We believe that the ideas proposed in this work for PPCA precipitation and inhibition is generally applicable to all polymeric SIs. Thus, this work will help us to develop a model for polymer precipitation (and adsorption) which can be used for designing squeeze precipitation treatments for polymeric SIs.
Helical Membrane Protein Folding, Stability, and Evolution (2000)

Helical membrane protein folding and oligomerization can be usefully conceptualized as involving two energetically distinct stages-the formation and subsequent side-to-side association of independently stable transbilayer helices. The interactions of helices with the bilayer, with prosthetic groups, and with each other are examined in the context of recent evidence. We conclude that the two-stage concept remains useful as an approach to simplifying discussions of stability, as a framework for folding concepts, and as a basis for understanding membrane protein evolution.
Antigen presenting cells in situ: their identification and involvement in immunopathology. (1983)

Macrophages and other dendritic non-lymphoid cells have been shown to be functionally capable of presenting antigen to induce lymphocyte responses. These cells can now be studied in situ and distinguished, one from another, within normal tissues and sites of cellular infiltration. Analysis of the microenvironment within which these cells are found can be made with immunohistological methods using monoclonal antibodies (McAbs) and cytochemical techniques. In some cases McAbs are specific for particular types of antigen presenting cell. Using such reagents, evidence is accumulating that these cells may be intimately involved in the pathogenesis of immunoregulatory disorders. What is now required is a more definitive correlation between functional capacity and cell phenotype established with cells isolated from blood, and from normal and pathological tissues. If this is possible the immunopathologist may be able, not only to analyse complex microenvironments but also directly determine the interactions and mechanisms at play within the diseased tissues.
Plant Physiological Adaptations to the Massive Foreign Protein Synthesis Occurring in Recombinant Chloroplasts (2009)

Genetically engineered chloroplasts have an extraordinary capacity to accumulate recombinant proteins. We have investigated in tobacco (Nicotiana tabacum) the possible consequences of such additional products on several parameters of plant development and composition. Plastid transformants were analyzed that express abundantly either bacterial enzymes, alkaline phosphatase (PhoA-S and PhoA-L) and 4-hydroxyphenyl pyruvate dioxygenase (HPPD), or a green fluorescent protein (GFP). In leaves, the HPPD and GFP recombinant proteins are the major polypeptides and accumulate to higher levels than Rubisco. Nevertheless, these engineered metabolic sinks do not cause a measurable difference in growth rate or photosynthetic parameters. The total amino acid content of transgenic leaves is also not significantly affected, showing that plant cells have a limited protein biosynthetic capacity. Recombinant products are made at the expense of resident proteins. Rubisco, which constitutes the major leaf amino acid store, is the most clearly and strongly down-regulated plant protein. This reduction is even more dramatic under conditions of limited nitrogen supply, whereas recombinant proteins accumulate to even higher relative levels. These changes are regulated posttranscriptionally since transcript levels of resident plastid genes are not affected. Our results show that plants are able to produce massive amounts of recombinant proteins in chloroplasts without profound metabolic perturbation and that Rubisco, acting as a nitrogen buffer, is a key player in maintaining homeostasis and limiting pleiotropic effects.
Blue-phase liquid crystal droplets (2015)

Blue phases of liquid crystals represent unique ordered states of matter in which arrays of defects are organized into striking patterns. Most studies of blue phases to date have focused on bulk properties. In this work, we present a systematic study of blue phases confined into spherical droplets. It is found that, in addition to the so-called blue phases I and II, several new morphologies arise under confinement, with a complexity that increases with the chirality of the medium and with a nature that can be altered by surface anchoring. Through a combination of simulations and experiments, it is also found that one can control the wavelength at which blue-phase droplets absorb light by manipulating either their size or the strength of the anchoring, thereby providing a liquid-state analog of nanoparticles, where dimensions are used to control absorbance or emission. The results presented in this work also suggest that there are conditions where confinement increases the range of stability of blue phases, thereby providing intriguing prospects for applications.
256-pixel CMOS-integrated thermoelectric infrared sensor array (2002)

This paper presents a micromachined 16/spl times/16 array of thermoelectric infrared sensors fabricated in a commercial CMOS IC process with subsequent bulk-micromachining on wafer-scale. Each pixel contains a integrated heater, which makes calibration and self-testing possible. Addressing circuity and four low-noise amplifiers are cointegrated with the array on a single chip with a size of 7.4/spl times/12 mm/sup 2/. A thermal imager based on the infrared sensor-array, operates in ambient air, without thermal stabilization or cooling. The thermoelectric sensor principle allows to measure DC radiation signals even without a radiation chopper. The temperature resolution achieved at 1 Hz framerate in 176 mK.
Insulin-stimulated tyrosine protein kinase. Characterization and relation to the insulin receptor. (1984)

Utilizing histone phosphorylation as the basis for a quantitative assay, the insulin-stimulated protein kinase in human placenta has been characterized. The kinase copurifies through wheat germ agglutinin-Sepharose and DEAE-cellulose in constant ratio to the insulin binding function. Both activities are bound to the same extent on insulin-Sepharose, and the immobilized kinase, after extensive washing, exhibits activity versus histone, which closely approaches that of the insulin-stimulated, solubilized kinase. In addition, the bound kinase retains the ability to phosphorylate the Mr = 95,000 subunit of the bead-bound receptor. Elution of the beads with sodium dodecyl sulfate yields on electrophoresis two major peptides of Mr = 130,000 and 95,000. Thus, insulin binding and insulin-stimulated histone kinase copurify in a constant stoichiometric ratio in close physical relation and are likely functional expressions of the same molecule. After the DEAE step, the insulin-stimulated kinase phosphorylates histone subfraction 2b exclusively on tyrosine residues. Insulin increases the Vmax for H2b by 3-5-fold and increases the rate of the histone phosphorylation in direct correspondence to the steady state level of specifically bound insulin. ATP is the preferred phosphate donor. The reaction is supported by either Mn2+ or Mg2+. At [ATP] less than 0.5 mM, insulin-stimulated kinase is substantially higher with Mn2+ as the sole divalent cation, as compared to Mg2+. At [ATP] greater than or equal to 0.5 mM, the rates observed with Mn2+ have plateaued, whereas the rates in the presence of Mg2+ show a continued increase such that maximal activity is seen with Mg2+ and 2-3 mM ATP. Under these conditions, the estimated turnover number of the kinase ranges between 30 and 100 pmol of 32P transferred per min/pmol of insulin bound. Thus, the tyrosine kinase activity of the insulin receptor is quantitatively comparable to that estimated for several serine protein kinases and is unlikely to reflect the side reaction of another enzymatic function.
Optimal Expected-Time Algorithms for Closest Point Problems (1980)

Geometric closest potnt problems deal with the proxLmity relationships in k-dimensional point sets. Examples of closest point problems include building minimum spanning trees, nearest neighbor searching, and triangulation constructmn Shamos and Hoey In this paper we extend thmr work by giving optimal expected.trine algorithms for solving a number of closest point problems in k-space, including nearest neighbor searching, finding all nearest neighbors, and computing planar minimum spanning trees. In addition to establishing theoretical bounds, the algorithms in this paper can be implemented to solve practical problems very efficiently.
List of Theses in Foreign Missions and Related Subjects Accepted during the Academic Year 1955–1956 (1956)

The compiler wishes to express deep gratitude to the professors of missions in 59 schools and seminaries for the reports which have made possible the compilation of the following list of dissertations and theses. No theses were written in 25 of the schools from which reports were received. The annotations following the theses are by the professors who reported them. Neither compiler nor editor has examined these theses or passed judgment upon them. The professors making the reports have indicated that each particular thesis is related to foreign missions or, in a few instances, to home missions. It is assumed that such is the case where no annotation has been given. Inquiries concerning a title should be addressed to the school concerned and not to the Missionary Research Library, An index to the theses will be found on paga 9.
Interval-velocity studies in the Southern North Sea (1990)

Interval velocities have been derived from a dense grid of non-exclusive seismic data in the Southern Gas Basin of the North Sea. The analysis of around 8000 velocity spectra has enabled detailed interval velocity maps to be drawn down to Top Zechstein level. A comparison of the seismically derived velocities with known well-derived velocities indicates that in most circumstances the "Dix" interval velocities are a good approximation to the well velocities - particularly for the Tertiary and Upper Cretaceous Chalk intervals. Consequently, the interval velocity maps so derived are useful for the purposes of depth conversion. In addition , these maps reveal interesting trends and anomalies many of which can be interpreted as having distinct geological causes. This poster paper concentrates on the interpretation of velocity anomalies in the Upper Cretaceous Chalk.
Elevated Levels of Interleukin-18 Predict the Development of Type 2 Diabetes (2005)

We investigated prospectively the association between serum levels of interleukin (IL)-18 and the risk of type 2 diabetes in a case-cohort study conducted in middle-aged men and women who represented 7,936 participants of the three MONItoring of trends and determinants in CArdiovascular disease (MONICA)/Cooperative Research in the Region of Augsburg (KORA) surveys. Levels of IL-18 were measured in stored samples of 527 case subjects with incident type 2 diabetes and 1,698 noncase subjects. Elevated levels of IL-18 were associated with a significantly increased risk of type 2 diabetes after adjustment for age, sex, survey, BMI, systolic blood pressure, ratio of total cholesterol to HDL cholesterol, physical activity, alcohol intake, smoking status, and parental history of diabetes. Hazard ratios and 95% confidence intervals comparing quartile extremes were 1.73 (1.25-2.40). Further adjustment for C-reactive protein and IL-6 had no impact on the observed associations. However, the risk of developing type 2 diabetes was highest among subjects with elevated levels of both IL-18 and CRP or IL-18 and IL-6, respectively. In conclusion, elevated levels of IL-18 are associated with a considerably increased risk of type 2 diabetes. This association is independent of a generalized proinflammatory state, but subjects with elevated levels of several inflammatory markers seem to be particularly prone to develop type 2 diabetes.
Morphologic precursors of ovarian epithelial tumors. (1993)

The hyperplastic and metaplastic changes of the surface epithelium and related inclusion cysts can be considered morphologic precursors of common epithelial tumors. Similar changes are found as a response to a hormonal ovarian or extraovarian stimulus, which may play an important role in ovarian carcinogenesis.
Characterization of Clostridium perfringens isolates obtained from 2010 to 2012 from chickens with necrotic enteritis in Korea (2015)

Clostridium perfringens produces diverse virulent toxins that cause necrotic enteritis in poultry, resulting in a great negative impact on the poultry industry. To study the characteristics of C. perfringens in chickens, we isolated 88 strains from chickens (1 strain per flock) with necrotic enteritis. The isolated bacterial strains were screened for toxin type and antimicrobial susceptibility. Necropsy of 17 chickens that died from necrotic enteritis revealed that their intestines were dilated with inflammatory exudates and characterized by mucosal necrosis. All the isolated strains were identified as toxin type A using multiplex PCR for toxin typing. We found that the rate of netB-positive strains isolated from dead chickens was significantly higher (8 of 17) than the rate among healthy chickens (2 of 50). We performed antimicrobial susceptibility test with 20 selected antimicrobial agents using the disk diffusion test and found that 30 tested strains were completely resistant to 5 antibiotics and partially resistant to 6 antibiotics whereas all the strains were susceptible to 9 antimicrobial agents. Using pulsed-field gel electrophoresis analysis, the 17 strains were divided into 13 genetic clusters showing high genetic diversity. In conclusion, C. perfringens strains isolated from Korean poultry showed a high resistance to antimicrobial drugs and high genetic diversity, suggesting that continuous monitoring is essential to prevent outbreaks of necrotic enteritis in chickens.
Digistain: a digital staining instrument for histopathology (2012)

We describe a new mid-infrared (mid-IR) imaging method specifically designed to augment the H + E tissue staining protocol. Images are taken with bespoke IR filters at wavelengths that enable chemical maps to be generated, corresponding to the cytoplasmic (amide) and nuclear (phosphodiester) components of unstained oesophageal tissue sections. A suitably calibrated combination of these generates false colour computer images that reproduce not only the tissue morphology, but also accurate and quantitative distributions of the nuclear-to-cytoplasmic ratio throughout the tissue section. This parameter is a well documented marker of malignancy, and because the images can be taken and interpreted by clinically trained personnel in a few seconds, we believe this new "digistain" approach makes spectroscopic mid-IR imaging techniques available for the first time as a practical, specific and sensitive augmentation to standard clinical cancer diagnosis methods.
Design Thinking (2016)

Abstract This chapter explores the dilemmas we face from our disaggregation of the world, reflected in public policies and economic incentives that encourage us to take apart the world in order to analyse, understand, and ultimately control it. Design represents a contrary process of reintegrating the broken relations, dysfunctions, and misconnections by synthesizing our knowledge about the world into greater wholes. This chapter examines a set of strategies designers use to reconnect the disjointed reality around us, with an example of how well-designed technology can help us all do the same.
The particle size effect of the spin-density wave in cubic γ-Fe precipitates in Cu (2004)

It is common knowledge that the magnetic structure of fcc Fe (γ-Fe) can be described by means of an incommensurate spin-density wave (SDW). Previous experimental data, however, were mostly obtained for γ-FeCo alloy precipitates in Cu in order to avoid the complexity of the structural phase transition. Since Fe is a fundamental element, reliable data on the SDW state for pure γ-Fe are highly desired. We present here neutron scattering data for the SDW in pure γ-Fe precipitates in Cu and discuss the particle size effect of the SDW.
Hand-held microwave direction-of-arrival finder based on varactor-tuned analog aerial beamforming (2002)

A newly developed prototype microwave direction-of-arrival (DOA) finder is presented. Varactor-loaded passive radiators around the main monopole radiator steer the beam in the full 360-degree azimuth angles. Unlike digital beamforming (DBF) approaches, only one RF receiver is needed for estimating the DOA. This simplicity provides sufficient light weight for hand-held portability, and low power consumption for 4-hour continuous battery operation.