gebhart/patrepeval huggingface dataset:
IL-1 antagonism reduces hyperglycemia and tissue inflammation in the type 2 diabetic GK rat (2009)

Recent studies suggest an inflammatory process, characterized by local cytokine/chemokine production and immune cell infiltration, regulates islet dysfunction and insulin resistance in type 2 diabetes. However, the factor initiating this inflammatory response is not known. Here, we characterized tissue inflammation in the type 2 diabetic GK rat with a focus on the pancreatic islet and investigated a role for IL-1. GK rat islets, previously characterized by increased macrophage infiltration, displayed increased expression of several inflammatory markers including IL-1beta. In the periphery, increased expression of IL-1beta was observed primarily in the liver. Specific blockade of IL-1 activity by the IL-1 receptor antagonist (IL-1Ra) reduced the release of inflammatory cytokines/chemokines from GK islets in vitro and from mouse islets exposed to metabolic stress. Islets from mice deficient in IL-1beta or MyD88 challenged with glucose and palmitate in vitro also produced significantly less IL-6 and chemokines. In vivo, treatment of GK rats with IL-1Ra decreased hyperglycemia, reduced the proinsulin/insulin ratio, and improved insulin sensitivity. In addition, islet-derived proinflammatory cytokines/chemokines (IL-1beta, IL-6, TNFalpha, KC, MCP-1, and MIP-1alpha) and islet CD68(+), MHC II(+), and CD53(+) immune cell infiltration were reduced by IL-1Ra treatment. Treated GK rats also exhibited fewer markers of inflammation in the liver. We conclude that elevated islet IL-1beta activity in the GK rat promotes cytokine and chemokine expression, leading to the recruitment of innate immune cells. Rather than being directly cytotoxic, IL-1beta may drive tissue inflammation that impacts on both beta cell functional mass and insulin sensitivity in type 2 diabetes.
Attitude Sensing Using a GPS Antenna on a Turntable: Experimental Tests (2004)

ABSTRACT: A prototype of a new attitude sensor, one that uses a single GPS antenna mounted on a rotating turntable, is developed, and the accuracy of this system is evaluated using real data. The goal of this study is to experimentally validate this new concept. The new attitude sensor measures attitude by using the sinusoidal phase modulation of the GPS carrier signal that is caused by turntable rotation. The main components of the prototype are a turntable, a GPS antenna mounted off-axis on the turntable, an angle encoder, a GPS bit-grabber card, and a software receiver. Data from this system are processed using three alternative attitude estimation algorithms. The new sensor system has been demonstrated to work in practice, and its peak attitude error is between 0.4 and 1.9 deg for a 15 cm antenna mounting radius and a rotation rate of 1000 rpm.
Poly(ADP-ribose) polymerase-1 is a survival factor for radiation-exposed intestinal epithelial stem cells in vivo (2003)

Poly(ADP-ribose) polymerase-1 (PARP-1) is a key enzyme mediating the cellular response to DNA strand breaks. It plays a critical role in genomic stability and survival of proliferating cells in culture undergoing DNA damage. Intestinal epithelium is the most proliferative tissue in the mammalian body and its stem cells show extreme sensitivity to low-level genotoxic stress. We investigated the role of PARP-1 in the in vivo damage response of intestinal stem cells in crypts of PARP-1-/- and control mice following whole-body gamma-irradiation (1 Gy). In the PARP-1-/- mice there was a significant delay during the first 6 h in the transient p53 accumulation in stem cells whereas an increased number of cells were positive for p21(CIP1/WAF1). Either no or only marginal differences were noted in MDM2 expression, apoptosis, induction of or recovery from mitotic blockage, or inhibition of DNA synthesis. We further observed a dose-dependent reduction in crypt survival measured at 4 days post-irradiation in control mice, and this crypt-killing effect was significantly potentiated in PARP-1-/- mice. Our results thus establish that PARP-1 acts as a survival factor for intestinal stem cells in vivo and suggest a functional link with early p53 and p21(CIP1/WAF1) responses.
HLA-C and HIV-1: friends or foes? (2012)

The major histocompatibility complex class I protein HLA-C plays a crucial role as a molecule capable of sending inhibitory signals to both natural killer (NK) cells and cytotoxic T lymphocytes (CTL) via binding to killer cell Ig-like receptors (KIR). Recently HLA-C has been recognized as a key molecule in the immune control of HIV-1. Expression of HLA-C is modulated by a microRNA binding site. HLA-C alleles that bear substitutions in the microRNA binding site are more expressed at the cell surface and associated with the control of HIV-1 viral load, suggesting a role of HLA-C in the presentation of antigenic peptides to CTLs. This review highlights the role of HLA-C in association with HIV-1 viral load, but also addresses the contradiction of the association between high cell surface expression of an inhibitory molecule and strong cell-mediated immunity. To explore additional mechanisms of control of HIV-1 replication by HLA-C, we address specific features of the molecule, like its tendency to be expressed as open conformer upon cell activation, which endows it with a unique capacity to associate with other cell surface molecules as well as with HIV-1 proteins.
Isolation & characterization of tumour angiogenesis factor from solid tumours & body fluids from cancer patients. (1989)

Tumour angiogenesis factor (TAF) was isolated from malignant solid tumours (10) and from pleural and peritoneal fluids (10) collected from cancer patients. Normal tissues and body fluids from individuals with no clinical history of cancer did not show any detectable levels of TAF. Also, no angiogenic activity was detectable in the benign tumour samples studied (2). The TAFs isolated were all ribonucleoproteins. Molecular weight determination by SDS-PAGE (9%) of the TAFs isolated by DEAE cellulose chromatography of tumour extracts showed them to be 18,000 dalton (D) ribonucleoproteins, while the TAFs isolated by immunoaffinity chromatography (using immobilized anti-TAF IgG) of solid tumour extracts and body fluids had a molecular weight of 38,000 D. The TAFs isolated by both the methods were found to be angiogenic by the chick chorioallantoic membrane and the mouse intradermal assays. Immunoaffinity chromatography could be used for the one-step purification of TAF from solid tumour extracts as well as from body fluids.
Flat-field-grating demultiplexer for WDM (1996)

A concave grating etched into a planar waveguide can be used to demultiplex signals from a wavelength division multiplexed telecommunication system. After the effective index of the waveguide is specified, a grating can be designed so that each channel receives light of desired wavelength. In the manufacturing process, the effective index of the waveguides may differ slightly from the specified value. The error will cause the wavelength of light entering each channel to shift. A design is presented here that has an input focal curve that is flat and oriented along the edge of the device. During the packaging process, the position of the input fibre along the input focal plane can be adjusted to compensate for the shift caused by an error in the effective index of the waveguide. This offers an alternative to thermal tuning and brings reasonable performance specifications of the demultiplexer within fabrication capability.
Staphylococcus aureus Protein A Mediates Invasion across Airway Epithelial Cells through Activation of RhoA GTPase Signaling and Proteolytic Activity (2011)

Staphyococcus aureus and especially the epidemic methicillin-resistant S. aureus strains cause severe necrotizing pneumonia. The mechanisms whereby these organisms invade across the mucosal epithelial barrier to initiate invasive infection are not well understood. Protein A (SpA), a highly conserved and abundant surface protein of S. aureus, activates TNF receptor 1 and EGF receptor (EGFR) signaling cascades that can perturb the cytoskeleton. We demonstrate that wild-type S. aureus, but not spa mutants, invade across polarized airway epithelial cell monolayers via the paracellular junctions. SpA stimulated a RhoA/ROCK/MLC cascade, resulting in the contraction of the cytoskeleton. SpA(+) but not SpA(-) mutants stimulated activation of EGFR and along with subsequent calpain activity cleaved the membrane-spanning junctional proteins occludin and E-cadherin, facilitating staphylococcal transmigration through the cell-cell junctions. Treatment of polarized human airway epithelial monolayers with inhibitors of ROCK, EGFR, MAPKs, or calpain prevented staphylococcal penetration through the monolayers. In vivo, blocking calpain activity impeded bacterial invasion into the lung parenchyma. Thus, S. aureus exploits multiple receptors available on the airway mucosal surface to facilitate invasion across epithelial barriers.
Probabilistic CMOS (PCMOS) in the Nanoelectronics Regime (2007)

Motivated by the necessity to consider probabilistic approaches to future designs, the main objective of this thesis was to develop and characterize energy efficient probabilistic CMOS (PCMOS) circuits that can be used to implement low energy computing platforms. The simplest circuit characterized was a PCMOS inverter (switch). An analytical model relating the energy consumption per switching (E) of this switch to its probability of correctness, p was derived. This characterization can also be used to evaluate the energy and performance savings that are achieved by PCMOS switch based computing platforms. The characterization of a PCMOS inverter was also extended to larger circuits whose probabilistic behavior was analyzed by first developing probability models of primitive gates, which were then input to a graph-based model to find the probabilities of larger circuits. The analysis of larger probabilistic circuits provides a basis for analyzing probabilistic behaviors due to noise in future technologies, and can be used in probabilistic design and synthesis methods to improve circuit reliability. Another important design criterion is the speed of a PCMOS circuit. The trade-offs between the energy, speed, and p of PCMOS circuits were also analyzed. Based on this study, various methods were proposed to optimize energy delay product (EDP) and p under given constraints on p, performance, and EDP. The sensitivity of the analysis with respect to variations in temperature, supply voltage, and threshold voltage was also considered.
Hydraulic Fracture Geometry: Fracture Containment in Layered Formations (1982)

Abstract One of the main problems in hydraulic fracturing technology is the prediction of fracture height. In particular, the question of what constitutes a barrier to vertical fracture propagation is crucial to the success of field operations. An analysis of hydraulic fracture containment effects has been performed. The main conclusion is that in most cases the fracture will penetrate into the layers adjoining the pay zone, the depth of penetration being determined by the differences in stiffness and in horizontal in-situ stress between the pay zone and the adjoining layers. For the case of a stiffness contrast, an estimate of the penetration depth is given.
Design of a vibrotactile display via a rigid surface (2010)

This paper describes the analysis, optimized redesign and evaluation of a high fidelity vibrotactile interface integrated in a rigid surface. The main application of the embodiment described here is vibrotactile display of virtual ground surface material properties for immersive environments, although the design principles are general. The device consists of a light, composite plate mounted on an elastic suspension, with integrated force sensors. It is actuated by a single voice coil motor. The structural dynamics of the device were optimized, within constraints imposed by the requirements of user interaction, and corrected via digital inverse filtering, in order to enable accurate simulation of virtual ground materials. Measurements of the resulting display demonstrate that it is capable of accurately reproducing forces of more than 40 N across a usable frequency band from 50 Hz to 750 Hz.
Total Ionizing Dose Effects Mitigation Strategy for Nanoscaled FDSOI Technologies (2014)

We propose a TID effect hardening strategy for nanoscaled ultra-thin BOX and body SOI technologies. Experiments performed on NMOS and PMOS transistors demonstrate that TID effects can be mitigated by applying a dynamic back-bias technique. These data are used to calibrate the back-bias that has to be applied on UTSOI transistors to efficiently mitigate TID-induced effects. Elementary circuit cells made of inverters are then modeled using dedicated mixed TCAD calculations in order to validate the proof of concept of this hardening strategy at circuit level. Finally, results obtained on Ultra-Thin BOX devices typical of future FDSOI technologies show that the proposed hardening strategy efficiency increases with BOX thinning and then with technology downscaling.
Biochemical and Antibiotic Susceptibility Studies of H <sub>2</sub> S-Negative <i>Citrobacter</i> (1974)

Ninety-four strains of H(2)S-negative Citrobacter were biochemically characterized and their antibiograms were determined. The antibiograms demonstrated not only a difference from Enterobacter cloacae but also a difference within the Citrobacter group between the indole-negative and indole-positive strains. These differences were statistically significant and emphasize the importance of the indole reaction as an aid to speciation of the H(2)S-negative Citrobacter.
The Genome Sequence of the Malaria Mosquito <i>Anopheles gambiae</i> (2002)

Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
Four-channel polarization-insensitive optically transparent wavelength converter (1997)

Multichannel wavelength converters may be important components in the cross-connects in future wavelength-division multiplexed (WDM) transport networks. We demonstrate a multichannel, polarization-insensitive, optically transparent wavelength converter, based on four-wave mixing in two semiconductor optical amplifiers in a polarization-diversity arrangement. Bit-error-rate (BER) measurements with four input 2.5-Gb/s WDM channels, spaced by 2 nm, show penalties for wavelength conversion less than 2.6 dB at 10/sup -9/ BER. Changes in the state of polarization of the input signals cause the output power to change by less than 1.2 dB, and the corresponding power penalties change by less than 0.9 dB.
Greedy Virtual Coordinates for Geographic Routing (2007)

We present a new approach for generating virtual coordinates that produces usable coordinates quickly and improves the routing performance of existing geographic routing algorithms. Starting from a set of initial coordinates derived from a set of elected perimeter nodes, greedy embedding spring coordinates (GSpring) detects possible dead ends and uses a modified spring relaxation algorithm to incrementally adjust virtual coordinates to increase the convexity of voids in the virtual routing topology. This reduces the probability that packets will end up in dead ends during greedy forwarding. The coordinates derived by GSpring achieve routing stretch that is up to 50% lower than that for NoGeo, the best existing algorithm for deriving virtual Euclidean coordinates for geographic routing. For realistic network topologies with obstacles, GSpring coordinates achieves from between 10 to 15% better routing stretch than actual physical coordinates.
A new class of obesity genes encodes leukocyte adhesion receptors (1997)

Obesity is a complex disease, and multiple genes contribute to the trait. The description of five genes (ob, db, tub, Ay, and fat) responsible for distinct syndromes of spontaneous monogenic obesity in mice has advanced our knowledge of the genetics of obesity. However, many other genes involved in the expression of this disease remain to be determined. We report here the identification of an additional class of genes involved in the regulation of adipose tissue mass. These genes encode receptors mediating leukocyte adhesion. Mice deficient in intercellular adhesion molecule-1 became spontaneously obese in old age on normal mouse chow or at a young age when provided with a diet rich in fat. Mice deficient in the counterreceptor for intercellular adhesion molecule-1, the leukocyte integrin alphaMbeta2 (Mac-1), showed a similar obesity phenotype. Since all mice consumed approximately the same amount of food as controls, the leukocyte function appears to be in regulating lipid metabolism and/or energy expenditure. Our results indicate that (i) leukocytes play a role in preventing excess body fat deposition and (ii) defects in leukocyte adhesion receptors can result in obesity.
Transition radiation as an X-ray source (1983)

Transition radiation is considered as a source of X-rays in the spectral range of 800 eV-10 keV. Both theoretical and experimental results for this region of the spectrum are presented. Medium energy ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> < 100 MeV) and high-energy particle beams are used as sources for the production of transition radiation. The resonance effect, wherein there is in-phase addition between foil interfaces, is shown to be a method for bandwidth and frequency selection, and experimental results are presented. A favorable comparison is made to synchrotron radiation, and transition radiation is suggested as an X-ray source for lithography.
Comparing accuracy of satellite- and airborne remote sensing data in the retrieval of forest stand attributes (2002)

Recent advances in developing remote sensing methods for forest inventory have suggested a good potential for the use of multi-source, multi-dimensional remote sensing data. This paper describes results of the retrieval of stem volume, basal area, and mean height utilizing the following remote sensing data: Landsat TM, SPOT Pan and XS, ERS-1/2 PRI and SLC, airborne data from imaging spectrometer AISA, radar-derived forest canopy profiles (obtained with HUTSCAT), and aerial photographs. Ground truth data consist of 40 spruce-dominated and mixed stands, which have been carefully measured using about 10 relascope sample plots in each stand. Multivariate data analysis techniques were applied. The results suggested that (1) radar-derived stand profiles seemed to be the most accurate data source for forest inventory, (2) combining ERS-1/2 coherence images with Landsat TM improved estimation accuracy, (3) Landsat TM was a more accurate data source than other satellite data (SPOT Pan and XS, ERS-1/2 intensity and coherence images), (4) principal component analysis was found to be a good technique with this dataset to derive predictor variables from AISA data (30 channels with high multicollinearity), (5) higher coherence was obtained for winter images than summer images due to snow-covered ground.
Automatic Diagnosis of Pulmonary Embolism Using an Attention-guided Framework: A Large-scale Study (2020)

Pulmonary Embolism (PE) is a life-threatening disorder associated with high mortality and morbidity. Prompt diagnosis and immediate initiation of therapeutic action is important. We explored a deep learning model to detect PE on volumetric contrast-enhanced chest CT scans using a 2-stage training strategy. First, a residual convolutional neural network (ResNet) was trained using annotated 2D images. In addition to the classification loss, an attention loss was added during training to help the network focus attention on PE. Next, a recurrent network was used to scan sequentially through the features provided by the pre-trained ResNet to detect PE. This combination allows the network to be trained using both a limited and sparse set of pixel-level annotated images and a large number of easily obtainable patient-level image-label pairs. We used 1,670 sparsely annotated studies and more than 10,000 labeled studies in our training. On a test set with 2,160 patient studies, the proposed method achieved an area under the ROC curve (AUC) of 0.812. The proposed framework is also able to provide localized attention maps that indicate possible PE lesions, which could potentially help radiologists accelerate the diagnostic process.
Genotype-phenotype correlations for EPM2A mutations in Lafora's progressive myoclonus epilepsy: exon 1 mutations associate with an early-onset cognitive deficit subphenotype (2002)

Mutations in the EPM2A gene encoding a dual-specificity phosphatase (laforin) cause an autosomal recessive fatal disorder called Lafora's disease (LD) classically described as an adolescent-onset stimulus-sensitive myoclonus, epilepsy and neurologic deterioration. Here we related mutations in EPM2A with phenotypes of 22 patients (14 families) and identified two subsyndromes: (i) classical LD with adolescent-onset stimulus-sensitive grand mal, absence and myoclonic seizures followed by dementia and neurologic deterioration, and associated mainly with mutations in exon 4 (P = 0.0007); (ii) atypical LD with childhood-onset dyslexia and learning disorder followed by epilepsy and neurologic deterioration, and associated mainly with mutations in exon 1 (P = 0.0015). To understand the two subsyndromes better, we investigated the effect of five missense mutations in the carbohydrate-binding domain (CBD-4; coded by exon 1) and three missense mutations in the dual phosphatase domain (DSPD; coded by exons 3 and 4) on laforin's intracellular localization in HeLa cells. Expression of three mutant proteins (T194I, G279S and Y294N) in DSPD formed ubiquitin-positive cytoplasmic aggregates, suggesting that they were folding mutants set for degradation. In contrast, none of the three CBD-4 mutants showed cytoplasmic clumping. However, CBD-4 mutants W32G and R108C targeted both cytoplasm and nucleus, suggesting that laforin had diminished its usual affinity for polysomes. Our data, thus, represent the first report of a novel childhood syndrome for LD. Our results also provide clues for distinct roles for the CBD-4 and DSP domains of laforin in the etiology of two subsyndromes of LD.