gebhart/patrepeval huggingface dataset:
Cathepsin B, plasminogenactivator-inhibitor (PAI-1) and plasminogenactivator-receptor (uPAR) are prognostic factors for patients with non-small cell lung cancer. (2005)

To evaluate the possible role of cysteine proteases and serine proteases, as well as their respective inhibitors and receptors, as new prognostic factors in NSCLC, we examined, for the first time, 10 biological parameters related to three proteolytic systems within a homogeneous collective of 147 cases of NSCLC. Activities (cath B(AT), cath B(A7.5)) and protein levels of cath B(C), cath L(C), uPA, PAI-1, uPAR [measured by three different assays uPAR (ADI), uPAR (HD13), uPAR (IIIF10)] and TF were measured in homogenates of lung tumour tissue and corresponding non-malignant lung parenchyma. Total cath B activity (cath B(AT)) and enzymatic activity of the fraction of cath B, which is stable and active at pH 7.5 (cath B(A7.5)), were determined by a fluorogenic assay using synthetic substrate Z-Arg-Arg-AMC. The concentrations of cath B(C), cath L(C), uPA, PAI-1, uPAR and TF were determined by ELISAs. uPAR was determined using three different ELISA formats. The median levels of cath B(AT) (5.1-fold), cath B(A7.5) (2.5-fold), cath B(C), (8.5-fold), cath L(C) (6.6-fold), uPA (6.5-fold), PAI-1 (4.2-fold), uPAR (ADI) (2.2-fold), uPAR (HD13) (4.0-fold) and uPAR (IIIF10) (2.6-fold) were higher in tumour tissue compared to the lung parenchyma. Cath B(AT), cath B(A7.5) and cath B(C) in primary tumours correlated with lymph node metastases. Regarding histologies, the concentration of PAI-1 seems to be associated with the histological cell types of NSCLC. We found the highest values of PAI-1 in large cell carcinoma > SCC, AC > carcinoid and lowest values in metastases of primary tumours of other organs. Only PAI-1 was significantly increased in poorly-differentiated cells (G3) compared to well- and moderately- differentiated cells (G1/G2). PAI-1 significantly correlated with cath B(AT) and cath B(A7.5) with uPAR (ADI), uPAR (HD13), uPAR (IIIF10) with uPA, and only weakly with TF, but not with cath B(C) and cath L(C). Significant correlations with overall survival in the total population of NSCLC patients were observed in univariate analysis for cath B(AT), cath B(C), PAI-1, uPAR (ADI), uPAR (HD13), and uPAR (IIIF10). Cath L(C) was not significantly associated with poor prognosis. Regarding the histological tumour type, only in patients with squamous cell carcinomas did cath B(A7.5) and PAI-1 remain significant prognostic factors. In multivariate survival analysis only two proteolytic factors, PAI-1 and uPAR (III101F), stayed significant. In conclusion, among 10 biological parameters evaluated within the same cohort of patients, only PAI-1, uPAR (ADI), uPAR (HD13), uPAR (IIIF10), cath B(AT) and cath B(C) are prognostic factors for overall survival of NSCLC patients. Moreover, PAI-1 and uPAR (IIIF10) add independent prognostic information with regard to established clinical and histomorphological factors in NSCLC.
How Now, Brown Fat? (2008)

Brown adipose tissue is, surprisingly, more related to skeletal muscle than to white adipose tissue.
Use of Atomic Force Microscopy for the Study of Surface Acid−Base Properties of Carboxylic Acid-Terminated Self-Assembled Monolayers (1997)

Atomic force microscopy was used to measure the forces between a silica probe and a carboxylic acid-terminated self-assembled monolayer (SAM) on a gold substrate in the presence of KCl electrolyte solutions of different pH. Silica−silica interaction force measurements were conducted at different pH values to determine the silica probe surface electrostatic potentials under these conditions. The interaction between two silica surfaces is repulsive and can be accurately predicted (except at short distances) by the Derjaguin−Landau−Verwey−Overbeek theory. The interaction between silica and clean gold surfaces exhibits an attractive interaction at neutral pH. The interaction between a silica probe and carboxylic acid-terminated SAM-covered gold substrate was a strong function of the pH value of the electrolyte. The surface electrostatic potentials of the surface-confined monolayers of carboxylic acid were obtained by theoretical fits of the force data to solutions of the complete nonlinear Poisson−Boltzmann equation, with the knowledge of silica probe surface potentials, at different solution pH values. The surface titration curve was obtained by correlating the surface potentials to the different electrolyte pH values. A theoretical fit to the titration curve provides the surface pKa and an explanation for the broadening of the titration curve.
Pressure-induced skin lesions in pigs: reperfusion injury and the effects of vitamin E (2000)

The pathogenesis of the development of pressure ulcers is still unclear. The aim of this study was to investigate the role of ischaemia and reperfusion in pressure-induced tissue necrosis in the trochanteric region in pigs. Pressure application was achieved with a newly developed computer-controlled pressure device. Histological examination showed damage in the subcutis and muscle tissue comparable with inflammation, extending in a vascular pattern beyond the area of pressure application. Electron-microscopic studies revealed neutrophil adherence to the capillary endothelium, which showed signs of injury. These observations were manifest two hours after the cessation of pressure. Pre-treatment with 500 mg vitamin E per day resulted in significantly less tissue damage compared with untreated animals. Pressure alone caused a significant decrease in reduced glutathione and total glutathione, suggesting oxidative stress. After pressure release there was a significant increase in hydrogen peroxide concentration, suggesting a decreased antioxidant protection. After pre-treatment with vitamin E, however, there was no increase of hydrogen peroxide. It is concluded that the early signs of necrosis after pressure application are concordant with typical ischaemia-reperfusion damage and this can be prevented in part by treatment with vitamin E. Prophylactic administration of vitamin E may influence the occurrence of pressure ulcers in humans undergoing elective surgery.
Deletion of a C–terminal intrinsically disordered region of WRINKLED1 affects its stability and enhances oil accumulation in Arabidopsis (2015)

WRINKLED1 (WRI1) is a key transcription factor governing plant oil biosynthesis. We characterized three intrinsically disordered regions (IDRs) in Arabidopsis WRI1, and found that one C-terminal IDR of AtWRI1 (IDR3) affects the stability of AtWRI1. Analysis by bimolecular fluorescence complementation and yeast-two-hybrid assays indicated that the IDR3 domain does not determine WRI1 stability by interacting with BTB/POZ-MATH proteins connecting AtWRI1 with CULLIN3-based E3 ligases. Analysis of the WRI1 sequence revealed that a putative PEST motif (proteolytic signal) is located at the C-terminal region of AtWRI1(IDR) (3). We also show that a 91 amino acid domain at the C-terminus of AtWRI1 without the PEST motif is sufficient for transactivation. We found that removal of the PEST motif or mutations in putative phosphorylation sites increased the stability of AtWRI1, and led to increased oil biosynthesis when these constructs were transiently expressed in tobacco leaves. Oil content was also increased in the seeds of stable transgenic wri1-1 plants expressing AtWRI1 with mutations in the IDR3-PEST motif. Taken together, our data suggest that intrinsic disorder of AtWRI1(IDR3) may facilitate exposure of the PEST motif to protein kinases. Thus, phosphorylation of the PEST motif in the AtWRI1(IDR) (3) domain may affect AtWRI1-mediated plant oil biosynthesis. The results obtained here suggest a means to increase accumulation of oils in plant tissues through WRI1 engineering.
Auto-parallelizing stateful distributed streaming applications (2012)

Streaming applications transform possibly infinite streams of data and often have both high throughput and low latency requirements. They are comprised of operator graphs that produce and consume data tuples. The streaming programming model naturally exposes task and pipeline parallelism, enabling it to exploit parallel systems of all kinds, including large clusters. However, it does not naturally expose data parallelism, which must instead be extracted from streaming applications. This paper presents a compiler and runtime system that automatically extract data parallelism for distributed stream processing. Our approach guarantees safety, even in the presence of stateful, selective, and user-defined operators. When constructing parallel regions, the compiler ensures safety by considering an operator's selectivity, state, partitioning, and dependencies on other operators in the graph. The distributed runtime system ensures that tuples always exit parallel regions in the same order they would without data parallelism, using the most efficient strategy as identified by the compiler. Our experiments using 100 cores across 14 machines show linear scalability for standard parallel regions, and near linear scalability when tuples are shuffled across parallel regions.
Improving the reliability of commodity operating systems (2003)

Despite decades of research in extensible operating system technology, extensions such as device drivers remain a significant cause of system failures. In Windows XP, for example, drivers account for 85% of recently reported failures. This paper describes Nooks, a reliability subsystem that seeks to greatly enhance OS reliability by isolating the OS from driver failures. The Nooks approach is practical: rather than guaranteeing complete fault tolerance through a new (and incompatible) OS or driver architecture, our goal is to prevent the vast majority of driver-caused crashes with little or no change to existing driver and system code. To achieve this, Nooks isolates drivers within lightweight protection domains inside the kernel address space, where hardware and software prevent them from corrupting the kernel. Nooks also tracks a driver's use of kernel resources to hasten automatic clean-up during recovery.To prove the viability of our approach, we implemented Nooks in the Linux operating system and used it to fault-isolate several device drivers. Our results show that Nooks offers a substantial increase in the reliability of operating systems, catching and quickly recovering from many faults that would otherwise crash the system. In a series of 2000 fault-injection tests, Nooks recovered automatically from 99% of the faults that caused Linux to crash.While Nooks was designed for drivers, our techniques generalize to other kernel extensions, as well. We demonstrate this by isolating a kernel-mode file system and an in-kernel Internet service. Overall, because Nooks supports existing C-language extensions, runs on a commodity operating system and hardware, and enables automated recovery, it represents a substantial step beyond the specialized architectures and type-safe languages required by previous efforts directed at safe extensibility.
Multicopy suppression of the cdc24 budding defect in yeast by CDC42 and three newly identified genes including the ras-related gene RSR1. (1989)

Genes CDC24, CDC42, and CDC43 are required for the establishment of cell polarity and the localization of secretion in Saccharomyces cerevisiae; mutants defective in these genes fail to form buds and display isotropic expansion of the cell surface. To identify other genes that may be involved in these processes, we screened yeast genomic DNA libraries for heterologous genes that, when overexpressed from a plasmid, can suppress a temperature-sensitive cdc24 mutation. We identified four such genes. One of these proved to be CDC42, which has previously been shown to be a member of the rho (ras-homologous) family of genes, and a second is a newly identified ras-related gene that we named RSR1. RSR1 maps between CDC62 and ADE3 on the right arm of chromosome VII; its predicted product is approximately 50% identical to other proteins in the ras family. Deletion of RSR1 is nonlethal but disrupts the normal pattern of bud site selection. Although both CDC42 and RSR1 can suppress cdc24 and both appear to encode GTP-binding proteins, these genes do not themselves appear to be functionally interchangeable. However, one of the other genes that was isolated by virtue of its ability to suppress cdc24 can also suppress cdc42. This gene, named MSB1, maps between ADE9 and HIS3 on the right arm of chromosome XV.
Aire-Dependent Thymic Development of Tumor-Associated Regulatory T Cells (2013)

Despite considerable interest in the modulation of tumor-associated Foxp3(+) regulatory T cells (T(regs)) for therapeutic benefit, little is known about the developmental origins of these cells and the nature of the antigens that they recognize. We identified an endogenous population of antigen-specific T(regs) (termed MJ23 T(regs)) found recurrently enriched in the tumors of mice with oncogene-driven prostate cancer. MJ23 T(regs) were not reactive to a tumor-specific antigen but instead recognized a prostate-associated antigen that was present in tumor-free mice. MJ23 T(regs) underwent autoimmune regulator (Aire)-dependent thymic development in both male and female mice. Thus, Aire-mediated expression of peripheral tissue antigens drives the thymic development of a subset of organ-specific T(regs), which are likely coopted by tumors developing within the associated organ.
Ontology mapping for the interoperability problem in network management (2005)

Interoperability between different network management domains, heterogeneous devices, and various management systems is one of the main requirements for managing complex enterprise services. While substantial advances have been made in low-level device and data interoperability using common data formats and specifications such as simple network management protocol's (SNMP's) SMI and TMF's SID, various interoperability issues including semantic interoperability offer interesting research challenges. While semantic interoperability is a difficult problem in its own right, the semantic web that incorporates intelligent agents necessitates an interoperability solution requiring agents to communicate unambiguously and reason intelligently to perform cooperative management tasks. Agents need a formal representation of knowledge; an ontology is capable of modeling the rich semantics of the managed environment (and especially, relationships between managed entities) so that agents can act on them. This paper presents an ontology-driven approach for solving the semantic interoperability problem in the management of enterprise services, illustrated here with a router configuration management application.
Hepatitis B surface antigen seroclearance during chronic HBV infection (2010)

Hepatitis B surface antigen (HBsAg) seroclearance in chronic HBV infection occurs at an annual incidence of 1-2%. The long-term outcome after HBsAg seroclearance is excellent if there is no pre-existing cirrhosis or viral superinfection. For this reason, HBsAg seroclearance has attracted recent interest in both long-term studies of the natural history of HBV infection and in patients receiving antiviral therapy. Here, we review a diverse range of studies investigating spontaneous HBsAg seroclearance in varied groups of patients and consider the many predictive factors - of both viral and host origin - for seroclearance. Studies to assess the effects of antiviral therapy, and in particular interferon treatment, are also discussed together with virological, biochemical and histological profiles following HBsAg seroclearance and the long-term outcomes.
Electron Transfer of Carotenoids Imbedded in MCM-41 and Ti−MCM-41:  EPR, ENDOR, and UV−Vis Studies (2002)

Electron transfer (ET) reactions of carotenoids (Car), β-carotene (I), canthaxanthin (II), and 7‘-apo-7‘,7‘-dicyano-β-carotene (III) imbedded in MCM-41 and Ti−MCM-41 were studied as a function of oxidation potential. The ET efficiency in MCM-41 was highest for the carotenoid with the lowest oxidation potential. The presence of Ti4+ in the framework of MCM-41 enhanced the ET efficiency of all carotenoids, but the enhancement did not depend on oxidation potential. The enhancement depends on whether complexes are formed between carotenoids and Ti4+. Complexes were formed with I and III but not with II. The presence of Ti4+ results in a large blue shift of the maximum absorption wavelength due to changes in the carotenoid conformation.
Characterisation of Schlemm's canal cross-sectional area (2014)

Subjectively located SC CSA measurements produce high estimates of SC CSA. SC assessed by measuring five random locations estimate CSA was similar to the gold standard estimate.
.sigma. Ligands with Subnanomolar Affinity and Preference for the .sigma.2 Binding Site. 2. Spiro-Joined Benzofuran, Isobenzofuran, and Benzopyran Piperidines (1995)

Spiro[isobenzofuran-1(3H),4'-piperidines] and the corresponding benzofuran and benzopyran derivatives have been synthesized and evaluated as sigma ligands. The compounds are related to Lu 28-179 (1'-[4-[1-(4-fluorophenyl)-1H-indol-3-yl]-1- butyl]spiro[isobenzofuran-1(3H),4'-piperidine]) that has been demonstrated to be a selective sigma 2 ligand with affinity in the subnanomolar range. The object of the study was to determine the structural factors governing sigma 1/sigma 2 affinity and selectivity within this class of compounds. The N-substituent in spiro[isobenzofuran-1(3H),4'-piperidines] is highly important, both for affinity and selectivity. Spiropiperidines with no or small N-substituents (H, Me, Et) exert very low affinity for both sigma 1 and sigma 2 binding sites (IC50(sigma 1, sigma 2) > 100 nM), whereas medium-sized substituents (e.g., Pr, Bu, Ph(CH2)2) result in potent, but unselective compounds (IC50(sigma 1, sigma 2) = 2-5 nM). Increasing the chain length and the lipophilicity of the N-substituent result in compounds in which high affinity for sigma 2 binding sites is retained and with selectivity for sigma 2 vs sigma 1 binding sites (e.g., 4-cyclohexyl-1-butyl: IC50-(sigma 1) = 1.5 nM, IC50(sigma 2) = 0.07 nM). Introduction of substituents in the benzene ring of the spiro[isobenzofuran-1(3H),4'-piperidine] ring system of Lu 28-179 mainly affects affinity for sigma 1 binding sites. Compounds with substituents (F, CF3) in the 4- or 7-position of the isobenzofuran display high affinity for sigma 2 binding sites (IC50(sigma 2) = 0.5-2 nM) and very low affinity for sigma 1 binding sites (IC50(sigma 1) > 100 nM). Compounds with substituents (F, CF3, Me) in the 5- or 6-position of the isobenzofuran exert increased affinity for sigma 1 binding sites (IC50(sigma 1) = 5-30 nM, IC50(sigma 2) = 0.3-7 nM), thus rendering unselective compounds. Exchanging the isobenzofuran moiety of Lu 28-179 with thioisobenzofuran, benzofuran, or benzopyran also has a pronounced effect on both affinity and selectivity for sigma binding sites. The position of the oxygen atom and the position of the spiroconnection with the 4-position of the piperidine ring were varied, and only compounds in which both the benzene ring and the heteroatom are attached directly to the piperidine ring retain high affinity and selectivity for sigma 2 binding sites (e.g., 3,4-dihydro-1'-[4-[1-(4-fluorophenyl)-1H-indol-3-yl]-1- butyl]spiro[1H-2-benzopyran-1,4'-piperidine]: IC50(sigma 1) = 53 nM, IC50(sigma 2) = 0.9 nM).(ABSTRACT TRUNCATED AT 400 WORDS)
Screening model for nanowire surface-charge sensors in liquid (2007)

The conductance change of nanowire field-effect transistors is considered a highly sensitive probe for surface charge. However, Debye screening of relevant physiological liquid environments challenge device performance due to competing screening from the ionic liquid and nanowire charge carriers. The authors discuss this effect within Thomas-Fermi and Debye-Hückel theory and derive analytical results for cylindrical wires which can be used to estimate the sensitivity of nanowire surface-charge sensors. They study the interplay between the nanowire radius, the Thomas-Fermi and Debye screening lengths, and the length of the functionalization molecules. The analytical results are compared to finite-element calculations on a realistic geometry.
Control of magnesium corrosion and biocompatibility with biomimetic coatings (2010)

The use of magnesium and its alloys as biodegradable metallic implant materials requires that their corrosion behavior can be controlled. We tailored the Mg release kinetics and cell adhesion properties of commercially pure Mg by chemical surface treatments in simulated body fluid, in Dulbecco's Modified Eagle's cell culture medium in the presence or absence of fetal bovine serum (FBS), or in 100% FBS. HeLa cells were cultured for 24 h on these Mg surfaces to characterize their biocompatibility. Cell density on all treated surfaces was significantly increased compared with a polished Mg surface, where almost no cells survived. This low biocompatibility of pure Mg was not caused by the high Mg ion release with concentrations of up to 300 mg/L in the cell culture medium after 24 h, as cells grown on a glass substrate showed no adverse reactions to high Mg ion concentrations. Rather, the most critical factor for cell adhesion was a sufficiently reduced initial dissolution rate of the surface. A comparison among all surface treatments showed that an incubation of the Mg samples in cell culture medium gave the lowest dissolution rate and resulted in the best cell adhesion and spreading behavior.
Demand Response in Electricity Markets: An Overview (2007)

This paper presents an overview of demand response (DR) in electricity market. The definition and a classification of demand response will be presented. Different potential benefits as well as cost components of demand response will be presented. The most common indices used for demand response evaluation are highlighted. Moreover, some utilities experiences with different demand response programs will be presented.
Power harvesting from microwave oven electromagnetic leakage (2013)

In this paper, we considered the possibility of using electricity harvested from the microwave field leaked from commercial microwave ovens. Our experimental results showed that the leakage received by a dipole antenna was about 0 dBm (1 mW) at a point 5 cm in front of the door. A rectenna consisting of a dipole antenna and charge pump can convert the leaked microwave energy into a DC current. When a microwave oven is operated for 2 min, 9.98 mJ of energy was harvested. We demonstrated that this energy is sufficient for powering a digital cooking timer to count down for 3 min and beep for 2.5 s. The operation of other kitchen devices was also demonstrated.
Compositional dependence of phase separation in InGaN layers (2004)

Phase separation in InGaN layers grown by metalorganic chemical vapor deposition on GaN epilayers was investigated using transmission electron microscopy. Layer thicknesses of 220 and 660nm were deposited with InN fractions ranging from 3% to 34%. At InN contents of 3%, plan-view TEM images show a homogeneous microstructure and selected area diffraction (SAD) patterns exhibit no evidence of satellite spots. InN contents of 12% result in a speckled contrast. Satellites close to the fundamental spots belonging to the wurtzite structure are present in SAD patterns and they are indicative of composition modulations lying in the (0001) growth plane. No satellites are observed along the [0001] direction, implying that phase separation is two-dimensional in nature. Samples containing InN fractions of between 22% and 28% have microstructures exhibiting much stronger contrast variations. Satellite spots in SAD patterns are further spaced from the fundamental reflections. This trend continues on increasing InN content to 34%. In addition, cross-sectional TEM images show an absence of contrast from InGaN layers with InN contents above 12%, in the vicinity of the InGaN∕GaN interface, indicating that coherency strain inhibits phase separation. Arguments are developed to rationalize these observations.