gebhart/patrepeval huggingface dataset:
Changes in secreted and cell associated proteoglycan synthesis during conversion of myoblasts to osteoblasts in response to bone morphogenetic protein‐2: Role of decorin in cell response to BMP‐2 (2005)

Proteoglycans have been identified within the extracellular matrices (ECM) of bone and are known to play a role in ECM assembly, mineralization, and bone formation. Bone morphogenetic protein-2 (BMP-2) specifically converts the differentiation pathway of C2C12 myoblasts into that of osteoblast lineage cells. Microarray analyses of the mouse myoblast cell line C2C12 and its differentiation into osteoblastic cells in response to BMP-2 have suggested the up-regulation of several proteoglycan species, although there is a lack of biochemical evidence for this response. In this study we have biochemically analyzed and characterized the proteoglycan populations that are induced in C2C12 cells upon osteoblastic differentiation produced by BMP-2. An important and specific increase in the synthesis of secreted decorin was observed in BMP-2-treated cells, as compared to untreated myoblasts and myoblasts induced to differentiate into myotubes. Decorin was seen to contain larger glycosaminoglycan (GAG) chains in induced than in non-induced cells. BMP-2 also produced an augment in the synthesis of different heparan sulfate proteoglycans such syndecan-2, - 3, glypican, and perlecan in detergent-soluble and non-soluble cellular fractions. We also examined whether the evident changes induced by BMP-2 in secreted decorin could have a functional role. BMP-2 signaling dependent as well as induction of alkaline phosphatase (ALP) activity was diminished in decorin null myoblasts compared to wild type myoblats although cell surface level of BPM-2 receptors was unchanged. These results are the first biochemical evidence and analysis for the effect of BMP-2 on the synthesis of proteoglycan during osteogenic conversion of myoblasts and suggest a role for decorin in cell response to BMP-2.
Rapid thermal oxidation of thin nitride dielectrics deposited on rapid thermal nitrided polycrystalline silicon (1992)

This letter compares the effects of two different oxidation techniques, i.e., rapid thermal and conventional wet (steam) oxidations, on the dielectric breakdown and charge trapping characteristics of thin Si3N4 films deposited on rapid thermally nitrided polycrystalline silicon. Results show that, in addition to the low thermal budget, rapid-thermal-oxidized Si3N4 shows superior time-dependent dielectric breakdown characteristics in terms of reduced defect densities and improved film intrinsic properties. Compared to wet-oxidized dielectrics, suppressed charge trapping is observed for rapid-thermal-oxidized Si3N4 stacked dielectrics.
Matrix metalloproteinases and tissue inhibitors of metalloproteinases in human fetal testis and ovary (2001)

Matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP) are major regulators of tissue remodelling of the extracellular matrix (ECM) and may also be involved in the control of growth factor availability. We have investigated their production and localization in the developing human gonad during mid-gestation using zymographic techniques and immunohistochemistry. The secretion of MMP-2, MMP-9 and all four TIMP was demonstrated from both testis and ovary, with the predominant gelatinase produced by both being MMP-2. In the testis, MMP-1, MMP-2, MMP-9 and all TIMP family members were localized to the interstitium and to varying degrees within the tubules. MMP-9 and TIMP-4 were abundant in both Sertoli cells and gonocytes and MMP-1 and TIMP-1 were localized in particular to Sertoli cells. In the ovary, all TIMP and MMP-1, MMP-2 and MMP-9 were localized to the oogonium/oocyte cytoplasm with varying intensities and MMP-1, TIMP-2 and TIMP-3 were also detected in the ovarian stroma. This study demonstrates that MMP-1, MMP-2, MMP-9 and all TIMP family members are secreted by the developing ovary and testis and are localized to specific cell and tissue sites. MMP and TIMP are likely to play a role in ECM remodelling during gonadal development and also in the cell and matrix interactions that control a range of cellular functions.
Degradation Mechanism and Life Prediction of Lithium-Ion Batteries (2006)

Lithium-ion cells with 5-Ah capacity were fabricated using a spinel as a cathode active material, graphitized carbon as an anode active material, and 1 M as an electrolyte. In order to improve the calendar life of the cell, we investigated the degradation mechanism by measuring the thickness of the solid electrolyte interphase (SEI) on anode active material. The SEI thickness was measured by focused ion beam, scanning electron microscope, and X-ray photoelectron spectroscopy. The thickness of the SEI was initially , and after storage for 392 days at 25 and 40°C, the thickness was 0.15 and , respectively. The capacity decreased with increase in the thickness of SEI, because Li in the cell is consumed by forming SEI. The amount of Li consumption was estimated theoretically assuming that SEI is formed by a reaction between intercalated Li and the electrolyte in SEI on the negative carbon surface, and a diffusion of the electrolyte in the SEI is the rate-determining step of the reaction. The theoretical equation showed a good agreement with experimental capacity fade at 25, 40, and 60°C for the storing days up to 380 days. A voltage decrease of the cell after 1-s at 20 A of discharge current was measured to estimate roughly the increase of the cell internal resistance during storage. The increase of SEI resistance was estimated by the theoretical equation and compared with the experimental voltage drop data after 1-s discharge. However, the theoretical data was not in a good agreement with the experimental data. The reason is that the charge-transfer resistance on the anode also increases during storage. Another reason is the resistance change of the cathode during the storage.
Proactive re-optimization (2005)

Traditional query optimizers rely on the accuracy of estimated statistics to choose good execution plans. This design often leads to suboptimal plan choices for complex queries, since errors in estimates for intermediate subexpressions grow exponentially in the presence of skewed and correlated data distributions. Reoptimization is a promising technique to cope with such mistakes. Current re-optimizers first use a traditional optimizer to pick a plan, and then react to estimation errors and resulting suboptimalities detected in the plan during execution. The effectiveness of this approach is limited because traditional optimizers choose plans unaware of issues affecting reoptimization. We address this problem using proactive reoptimization, a new approach that incorporates three techniques: i) the uncertainty in estimates of statistics is computed in the form of bounding boxes around these estimates, ii) these bounding boxes are used to pick plans that are robust to deviations of actual values from their estimates, and iii) accurate measurements of statistics are collected quickly and efficiently during query execution. We present an extensive evaluation of these techniques using a prototype proactive re-optimizer named Rio. In our experiments Rio outperforms current re-optimizers by up to a factor of three.
<i>Escherichia coli</i> K‐12 genes essential for the synthesis of <i>c</i>‐type cytochromes and a third nitrate reductase located in the periplasm (1996)

The 'aeg46.5' operon was originally detected as an 'anaerobically expressed gene' located at minute 46.5 on the Escherichia coli linkage map. Subsequent results from the E. coli Genome Sequencing Project revealed that the 'aeg46.5' promoter was located in the centisome 49 (minute 47) region. Downstream from this promoter are 15 genes, seven of which are predicted to encode a periplasmic nitrate reductase and eight encode proteins homologous to proteins essential for cytochrome c assembly in other bacteria. All of these genes, together with the 'aeg46.5' promoter, have been subcloned on a 20kb EcoRI fragment from Kohara phage 19D1. Evidence is presented that, as predicted, the region includes structural genes for two c-type cytochromes of mass 16kDa and 24 kDa, which are transcribed from the previously described 'aeg46.5' promoter, and that the first seven genes encode a functional nitrate reductase. We, therefore, propose that they should be designated nap (nitrate reductase in the periplasm) genes. Plasmids encoding the entire 20kb region, or only the downstream eight genes, complemented five mutations resulting in total absence of all five known c-type cytochromes in E coli, providing biochemical evidence that these are ccm (for cytochrome c maturation) genes. The ccm region was transcribed both from the FNR-dependent, NarL- and NarP-regulated nap promoter (formerly the 'aeg46.5' promoter) and from constitutive or weakly regulated promoters apparently located within the downstream nap and ccm genes.
Imaging osteomyelitis with streptavidin and indium-111-labeled biotin. (1996)

The results of this preliminary clinical investigation suggest that a two-step protocol with unlabeled streptavidin and radiolabeled biotin may be an alternative for the detection of infection.
Inhibitors of ABC-type drug efflux pumps: an overview of the current patent situation (2004)

Overexpression of drug efflux pumps is one of the main reasons for the development of multi-drug resistant tumours and bacterial and fungal infections. Inhibition of these pumps gives rise to a restoration of drug sensitivity and thus represents a versatile approach for overcoming multi-drug resistance. Although clinical trials were not as encouraging as expected, several compounds are currently undergoing Phase III clinical studies. This review gives an overview on the patent literature (from the year 2000 to mid 2003) on the field of inhibitors of drug efflux pumps.
<i>In Vivo</i> Pharmacokinetics/Pharmacodynamics of Colistin and Imipenem in Pseudomonas aeruginosa Biofilm Infection (2012)

Many Pseudomonas aeruginosa isolates from the airways of patients with cystic fibrosis (CF) are sensitive to antibiotics in susceptibility testing, but eradication of the infection is difficult. The main reason is the biofilm formation in the airways of patients with CF. The pharmacokinetics (PKs) and pharmacodynamics (PDs) of antimicrobials can reliably be used to predict whether antimicrobial regimens will achieve the maximum bactericidal effect against infections. Unfortunately, however, most PK/PD studies of antimicrobials have been done on planktonic cells and very few PK/PD studies have been done on biofilms, partly due to the lack of suitable models in vivo. In the present study, a biofilm lung infection model was developed to provide an objective and quantitative evaluation of the PK/PD profile of antimicrobials. Killing curves were set up to detect the antimicrobial kinetics on planktonic and biofilm P. aeruginosa cells in vivo. Colistin showed concentration-dependent killing, while imipenem showed time-dependent killing on both planktonic and biofilm P. aeruginosa cells in vivo. The parameter best correlated to the elimination of bacteria in lung by colistin was the area under the curve (AUC) versus MIC (AUC/MIC) for planktonic cells or the AUC versus minimal biofilm inhibitory concentration (MBIC; AUC/MBIC) for biofilm cells. The best-correlated parameter for imipenem was the time that the drug concentration was above the MIC for planktonic cells (T(MIC)) or time that the drug concentration was above the MBIC (T(MBIC)) for biofilm cells. However, the AUC/MIC of imipenem showed a better correlation with the efficacy of imipenem for biofilm infections (R(2) = 0.89) than planktonic cell infections (R(2) = 0.38). The postantibiotic effect (PAE) of colistin and imipenem was shorter in biofilm infections than planktonic cell infections in this model.
Pseudorandom encoding of complex-valued functions onto amplitude-coupled phase modulators (1998)

Pseudorandom encoding is a method of statistically approximating desired complex values with those values that are achievable with a given spatial light modulator. Originally developed for phase-only modulators, pseudorandom encoding is extended to modulators for which amplitude is a function of phase. This is accomplished by transforming the phase statistics to compensate for the amplitude coupling. Example encoding formulas are derived, evaluated, and compared with a noncompensating pseudorandom-encoding algorithm. Compensating algorithms encode a smaller area of the complex plane and can produce more noise than is possible for arbitrary pseudorandom algorithms. However, the encoding formulas have greatly simplified numerical implementations.
Acid adaptation induces cross-protection against environmental stresses in Salmonella typhimurium (1993)

The relationship of acid adaptation to tolerance of other environmental stresses was examined in Salmonella typhimurium. S. typhimurium was adapted to acid by exposing the cells to mildly acidic conditions (pH 5.8) for one to two cell doublings. Acid-adapted cells were found to have increased tolerance towards various stresses including heat, salt, an activated lactoperoxidase system, and the surface-active agents crystal violet and polymyxin B. Acid adaptation increased cell surface hydrophobicity. Specific outer membrane proteins were induced by acid adaptation, but the lipopolysaccharide component appeared to be unaltered. These results show that acid adaptation alters cellular resistance to a variety of environmental stresses. The mechanism of acid-induced cross-protection involved changes in cell surface properties in addition to the known enhancement of intracellular pH homeostasis.
Technology, development status, and routine application of Thermal Response Test (2007)

To design borehole heat exchangers (BHE) for Ground Source Heat Pumps (GSHP) or Underground Thermal Energy Storage (UTES), the knowledge of underground thermal properties is paramount. In small plants (residential houses), these parameters usually are estimated. However, for larger plants (commercial GSHP or UTES) the thermal conductivity should be measured on site. A useful tool to do so is a thermal response test, carried out on a BHE in a pilot borehole (later to be part of the borehole field). For a thermal response test, basically a defined heat load is put into the hole and the resulting temperature changes of the circulating fluid are measured. Since late 1990s, this technology became more and more popular, and today is used routinely in many countries for the design of larger plants with BHEs, allowing sizing of the boreholes based upon reliable underground data. The paper includes a short description of the basic concept and the theory behind the thermal response test, looks at the history of its development, and then refers the commercial experience of UBeG GbR with this technology.
Yeasts and bacterial biosurfactants as demulsifiers for petroleum derivative in seawater emulsions (2017)

Oil sludge or waste generated in transport, storage or refining forms highly stable mixtures due to the presence and additives with surfactant properties and water forming complex emulsions. Thus, demulsification is necessary to separate this residual oil from the aqueous phase for oil processing and water treatment/disposal. Most used chemical demulsifiers, although effective, are environmental contaminants and do not meet the desired levels of biodegradation. We investigated the application of microbial biosurfactants as potential natural demulsifiers of petroleum derivatives in water emulsions. Biosurfactants crude extracts, produced by yeasts (Candida guilliermondii, Candida lipolytica and Candida sphaerica) and bacteria (Pseudomonas aeruginosa, Pseudomonas cepacia and Bacillus sp.) grown in industrial residues, were tested for demulsification capacity in their crude and pure forms. The best results obtained were for bacterial biosurfactants, which were able to recover about 65% of the seawater emulsified with motor oil compared to 35-40% only for yeasts products. Biosurfactants were also tested with oil-in-water (O/W) and water-in-oil (W/O) kerosene model emulsions. No relationship between interfacial tension, cell hydrophobicity and demulsification ratios was observed with all the biosurfactants tested. Microscopic illustrations of the emulsions in the presence of the biosurfactants showed the aspects of the emulsion and demulsification process. The results obtained demonstrate the potential of these agents as demulsifiers in marine environments.
The Recruitment of AMP-activated Protein Kinase to Glycogen Is Regulated by Autophosphorylation (2015)

The mammalian AMP-activated protein kinase (AMPK) is an obligatory αβγ heterotrimeric complex carrying a carbohydrate-binding module (CBM) in the β-subunit (AMPKβ) capable of attaching AMPK to glycogen. Nonetheless, AMPK localizes at many different cellular compartments, implying the existence of mechanisms that prevent AMPK from glycogen binding. Cell-free carbohydrate binding assays revealed that AMPK autophosphorylation abolished its carbohydrate-binding capacity. X-ray structural data of the CBM displays the central positioning of threonine 148 within the binding pocket. Substitution of Thr-148 for a phospho-mimicking aspartate (T148D) prevents AMPK from binding to carbohydrate. Overexpression of isolated CBM or β1-containing AMPK in cellular models revealed that wild type (WT) localizes to glycogen particles, whereas T148D shows a diffuse pattern. Pharmacological AMPK activation and glycogen degradation by glucose deprivation but not forskolin enhanced cellular Thr-148 phosphorylation. Cellular glycogen content was higher if pharmacological AMPK activation was combined with overexpression of T148D mutant relative to WT AMPK. In summary, these data show that glycogen-binding capacity of AMPKβ is regulated by Thr-148 autophosphorylation with likely implications in the regulation of glycogen turnover. The findings further raise the possibility of regulated carbohydrate-binding function in a wider variety of CBM-containing proteins.
Identification and characterization of a pore-forming protein of human peripheral blood natural killer cells. (1986)

We show here that human peripheral blood NK cells contain a pore-forming protein (PFP) with an Mr of 70,000-72,000 that assembles structural lesions (with an average internal diameter of 150-170 A) and forms functional channels. The PFP was isolated by affinity chromatography from human NK cells, using a specific anti-C9 antiserum as the immunoadsorbent. The NK cells were isolated from PBL by positive or negative selection by indirect rosetting using a panel of monoclonal antibodies directed against different NK and T cell surface antigens. PFP was identified in NK cells freshly isolated and isolated from cultured PBL, both stimulated with interleukin 2, but not in NK cell-depleted lymphocytes. In planar bilayers, the channels formed by the NK cell-derived PFP are highly voltage resistant, with most channels persisting in the open state once they have inserted into the bilayer. The unit conductances of these channels range 0.3-1 nS in 0.1 M NaCl. The channels show poor selectivity for monovalent and divalent ions. The PFP is also released from human NK cells stimulated with the calcium ionophore A23187, suggesting that this protein, like the one produced by murine CTL lines, may be similarly secreted during cell-mediated killing. Its identification in primary human NK cell cultures indicates that this protein may play an active role in NK cell-mediated killing.
[The molecular genetic mapping of cereal crops]. (2000)

The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes. Genetic mapping of cereal genomes, such as rye, wheat, maize and rice using common set of DNA-probes permitted to reveal considerable evolutionary conservation in gene organization and localization. This allows to use more effectively method of comparative mapping for fast localization and tagging of genes in genomes of less investigated species.
Power-scaling effects in dye lasers under high-power laser excitation (1978)

Eight laser dyes emitting in the spectral region from 550 to 915 nm were investigated to determine their power scalability under excitation by Q-switched frequency-doubled Nd : YAG lasers possessing up to 480 mJ pulse energy at 10 Hz pulse repetition frequency (PRF). Conversion efficiencies for some dyes begin to be limited at pump-power densities as low as 14 MW/cm2 due to excited-state absorption of the pumping radiation. The dependence on resonator length of dye spectral emission, conversion efficiency, and temporal modulation are reported. Divergence of the beam emerging from the dye laser was found to be adversely affected by measures taken to avoid output power saturation at high pump-power densities.
Robot Motion Planning on a Chip (2016)

We describe a process that constructs robot-specific circuitry for motion planning, capable of generating motion plans approximately three orders of magnitude faster than existing methods. Our method is based on building collision detection circuits for a probabilistic roadmap. Collision detection for the roadmap edges is completely parallelized, so that the time to determine which edges are in collision is independent of the number of edges. We demonstrate planning using a 6-degreeof-freedom robot arm in less than 1 millisecond.
Identification of CD8 <sup>+</sup> CD25 <sup>+</sup> Foxp3 <sup>+</sup> suppressive T cells in colorectal cancer tissue (2008)

We have identified a new regulatory T cell population (CD8(+)Foxp3(+)) in colorectal tumours. After isolation from cancer tissue these CD8(+)Foxp3(+) cells demonstrated strong immunosuppressive properties in vitro. These data suggest that these cells may contribute to tumoral immune escape and disease progression.
The application of supervisory control to deadlock avoidance in concurrent software (2008)

Ensuring deadlock-free execution of concurrent programs is a notoriously difficult problem, but an increasingly important one as multicore processors compel performance-conscious software developers to parallelize applications. We propose and validate a novel methodology for dynamically controlling the execution of concurrent software in order to provably avoid deadlocks. The methodology is based on supervisory control of discrete event systems modeled by Petri nets. Specifically, we synthesize feedback controllers for concurrent programs based on the theory of supervision based on place invariants and implement the controllers online to guarantee deadlock avoidance. We describe a full implementation of this methodology and report initial experimental results demonstrating its effectiveness and scalability.
Anomaly Detection and Fault Prognosis for Bearings (2016)

In this paper, a new bearing anomaly detection and fault prognosis method is proposed. The method detects bearing anomalies and then predicts its remaining useful life (RUL). To achieve these two goals, an autoregressive model, which is used to filter out fault-unrelated signals, is derived according to healthy bearing vibrational signals. A health index is developed to indicate bearing health conditions. Anomalies of bearings are detected by choosing an appropriate threshold with the aid of a Box-Cox transformation. A nonlinear model is built to track the bearings' degradation process and an extended Kalman filter is designed to model adaptation and RUL prediction. Finally, PRONOSTIA bearing data are used to demonstrate the effectiveness of the proposed method.