gebhart/patrepeval huggingface dataset:
Fast Algorithms for Shortest Paths in Planar Graphs, with Applications (1987)

Graph decomposition and data structures techniques are presented that exploit the structure of planar graphs to yield faster algorithms for a number of shortest path and related problems. Improved algorithms are presented for the single source problem, the all pairs problem, the problem of finding a minimum cut in an undirected graph, and testing the feasibility of a multicommodity flow when all sources and sinks are on the same face. The algorithm for the single source takes $O(n\sqrt {\log n} )$ time in an n-vertex graph, an improvement from $O(n\log n)$. The algorithm for all pairs takes $O(n^2 )$ time, an improvement from $O(n^2 \log n)$. The algorithm for minimum cut takes $O(n\log n)$ time, an improvement from $O(n(\log n)^2 )$. As a consequence, an algorithm for maximum flow is similarly improved.
High-Throughput, Sensitive, and Accurate Multiplex PCR-Microsphere Flow Cytometry System for Large-Scale Comprehensive Detection of Respiratory Viruses (2007)

Human respiratory viruses are a diverse group of pathogens composed of hundreds of virus strains, and this presents a major challenge for diagnostic laboratories. To efficiently detect numerous viruses in a large epidemiologic study, we developed a fast, multitarget, sensitive, and specific assay named the Respiratory MultiCode-PLx Assay (RMA). The RMA utilizes improved multiplex PCR chemistry (EraGen MultiCode-PLx technology) coupled with high-throughput microsphere flow cytometry (Luminex). Eighteen sets of virus-specific multiplex PCR primers were developed based on the conserved sequences of all available respiratory-virus sequences for eight distinct groups: human rhinovirus (HRV), respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus (InfV), metapneumovirus, adenovirus (Ad), coronavirus, and enterovirus. Each primer set detected 20 cDNA copies of the intended target per sample and had no reaction with 60,000 copies of human genomic DNA. The accuracy and sensitivity of the RMA for detecting respiratory viruses in human samples were tested with two sets of clinical specimens. First, 101 nasal-wash specimens that were positive for HRV, RSV, InfV, PIV, or Ad by traditional techniques were reanalyzed by RMA, and all target viruses were detected with an overall sensitivity of 94% and specificity of 99%. Second, 103 nasal-wash samples from 5-year-old children with asthma and respiratory symptoms were analyzed; RMA detected viruses in 74 specimens (71.8%) compared to only 24 (23.3%) by traditional culture and immunofluorescent-staining techniques. These results show that RMA is an accurate, sensitive, and practical test for respiratory-virus infections.
Gemcitabine and platinum combinations in pancreatic cancer (2002)

Progress in the treatment of pancreatic cancer in the past several decades has been very modest. Several new agents with activity against this disease have been identified. Of these, gemcitabine appears to be the most promising when used in combination with other drugs. Gemcitabine and cisplatin combinations have been tested in several studies. The major toxicity reported to occur with the gemcitabine-cisplatin combination is myelosuppression, which is greater than that encountered with single-agent gemcitabine. However, episodes of neutropenic fever or spontaneous bleeding are reported to be very infrequent. Pilot Phase II studies combining gemcitabine with cisplatin have shown improved outcomes in objective response rates and survival; however, these findings must be confirmed in larger randomized studies.
Global disparities in the epilepsy treatment gap: a systematic review (2009)

There is dramatic global disparity in the care for epilepsy between high- and low- income countries, and between rural and urban settings. Our understanding of the factors affecting the treatment gap is limited; future investigations should explore other potential explanations of the gap.
The application of digital signal processing to transmitter linearisation (2003)

A description is given of three prototype transmitters, using digital signal processing in different ways to achieve linear RF amplification. The Cartesian feedback technique, the adaptive predistortion technique, and the LINC (linear amplification with nonlinear components) technique, are all shown to provide a good degree of intermodulation product suppression (>50 dB), with the LINC amplifier approach potentially the most power-efficient (>70%). Both the LINC and predistortion systems can operate in a wideband mode. The Cartesian approach, because of the inherent feedback control system, is limited to a bandwidth of about 10% of the operating frequency. The implementation costs are considerably reduced over conventional analog realizations of such systems for all three techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of interleukin 1β-converting enzyme-mediated apoptosis of mammalian cells by baculovirus IAP (1996)

Apoptosis can be a potent weapon against viral infection and consequently has selected for viruses carrying antiapoptosis genes. Two baculovirus proteins, IAP and p35, can prevent insect cells from dying in response to infection. p35, which interferes with members of the Ced-3 family of cysteine proteases, can also function in mammalian cells. We investigated the ability of IAP from Orgyia pseudotsugata nuclear polyhedrosis virus to prevent death of mammalian cells. IAP was transiently expressed in mammalian cells and its ability to block cell death caused by expression of interleukin-1 beta converting enzyme (ICE), FADD, or the ICE homologues ICH-1 and ICE-Lap3, was investigated. IAP strongly inhibited ICE- and ICH-1-induced cell death but protected only partially against death by overexpression of FADD and not at all against death due to enforced ICE-Lap3 expression. These results demonstrate that a baculoviral IAP protein can functionally interact with conserved components of the apoptosis machinery in mammalian cells.
Isolation of a Monoclonal Antibody That Targets the Alpha-2 Helix of gp120 and Represents the Initial Autologous Neutralizing-Antibody Response in an HIV-1 Subtype C-Infected Individual (2011)

The C3-V4 region is a major target of autologous neutralizing antibodies in HIV-1 subtype C infection. We previously identified a Center for AIDS Program of Research in South Africa (CAPRISA) participant, CAP88, who developed a potent neutralizing-antibody response within 3 months of infection that targeted an epitope in the C3 region of the HIV-1 envelope (P. L. Moore et al., PLoS Pathog. 5:e1000598, 2009). Here we showed that these type-specific antibodies could be adsorbed using recombinant gp120 from the transmitted/founder virus from CAP88 but not by gp120 made from other isolates. Furthermore, this activity could be depleted using a chimeric gp120 protein that contained only the C3 region from the CAP88 viral envelope engrafted onto the unrelated CAP63 viral envelope (called 63-88C3). On the basis of this, a differential sorting of memory B cells was performed using gp120s made from 63-88C3 and CAP63 labeled with different fluorochromes as positive and negative probes, respectively. This strategy resulted in the isolation of a highly specific monoclonal antibody (MAb), called CAP88-CH06, that neutralized the CAP88 transmitted/founder virus and viruses from acute infection but was unable to neutralize CAP88 viruses isolated at 6 and 12 months postinfection. The latter viruses contained 2 amino acid changes in the alpha-2 helix of C3 that mediated escape from this MAb. One of these changes involved the introduction of an N-linked glycan at position 339 that occluded the epitope, while the other mutation (either E343K or E350K) was a charge change. Our data validate the use of differential sorting to isolate a MAb targeting a specific epitope in the envelope glycoprotein and provided insights into the mechanisms of autologous neutralization escape.
CYCLOSPORINE DOSE REDUCTION BY KETOCONAZOLE ADMINISTRATION IN RENAL TRANSPLANT RECIPIENTS (1991)

Cyclosporine metabolism occurs in the liver via hepatic cytochrome P-450 microsomal enzymes. Ketoconazole, an imidazole derivative, has been shown to inhibit the cytochrome P-450 enzyme system. Thirty-six renal transplant recipients receiving cyclosporine as part of a triple immunosuppressive drug regimen were started on 200 mg/day of oral ketoconazole. The dose of cyclosporine was reduced by 70% at the start of ketoconazole; this dose reduction was based on our previous experience with concomitant cyclosporine-ketoconazole therapy. Ketoconazole was started in patients who had been on cyclosporine for between 10 days and 74 months. The mean cyclosporine dose was 420 mg/day (5.9 mg/kg/day) before starting ketoconazole and 66 mg/day (0.9 mg/kg/day) one year after the addition of ketoconazole; this represents a cyclosporine dose reduction of 84.7% (P less than 0.0001). The mean trough whole-blood cyclosporine concentrations measured by HPLC, were 130 ng/mL preketoconazole and 149 ng/mL after 1 year of combination therapy. Mean serum creatinine and BUN levels were unchanged before and during ketoconazole administration, and no changes in liver function tests were noted. Cyclosporine pharmacokinetics were performed before and after at least three weeks of ketoconazole. Hourly whole-blood samples were measured by HPLC (parent cyclosporine only) and TDX (parent + metabolites). Combination therapy resulted in decreases in the maximum blood concentration and the steady-state volume of distribution divided by the fractional absorption, and increases in mean residence time and the parent-to-parent plus metabolite ratio (calculated by dividing the HPLC by the TDX value). The addition of ketoconazole to cyclosporine-treated patients resulted in a significant inhibition of cyclosporine metabolism and decrease in the dosage. There was minimal nephrotoxicity, and only four rejection episodes occurred on combined therapy. The concomitant administration of the two drugs was well tolerated, and there was no deleterious effect on the immunosuppressive activity of cyclosporine. This drug interaction provides a significant reduction in the costs associated with organ transplantation.
Use of multiattribute transforms to predict log properties from seismic data (2001)

Abstract We describe a new method for predicting well-log properties from seismic data. The analysis data consist of a series of target logs from wells which tie a 3-D seismic volume. The target logs theoretically may be of any type; however, the greatest success to date has been in predicting porosity logs. From the 3-D seismic volume a series of sample-based attributes is calculated. The objective is to derive a multiattribute transform, which is a linear or nonlinear transform between a subset of the attributes and the target log values. The selected subset is determined by a process of forward stepwise regression, which derives increasingly larger subsets of attributes. An extension of conventional crossplotting involves the use of a convolutional operator to resolve frequency differences between the target logs and the seismic data. In the linear mode, the transform consists of a series of weights derived by least-squares minimization. In the nonlinear mode, a neural network is trained, using the selected attributes as inputs. Two types of neural networks have been evaluated: the multilayer feedforward network (MLFN) and the probabilistic neural network (PNN). Because of its mathematical simplicity, the PNN appears to be the network of choice. To estimate the reliability of the derived multiattribute transform, crossvalidation is used. In this process, each well is systematically removed from the training set, and the transform is rederived from the remaining wells. The prediction error for the hidden well is then calculated. The validation error, which is the average error for all hidden wells, is used as a measure of the likely prediction error when the transform is applied to the seismic volume. The method is applied to two real data sets. In each case, we see a continuous improvement in predictive power as we progress from single-attribute regression to linear multiattribute prediction to neural network prediction. This improvement is evident not only on the training data but, more importantly, on the validation data. In addition, the neural network shows a significant improvement in resolution over that from linear regression.
N-Methyl-d-aspartate receptor antagonism decreases motility and inflammatory activation in the early phase of acute experimental colitis in the rat (2009)

These data demonstrate a potential modulatory mechanism of NMDA-R in altered colonic motility in TNBS colitis. Inhibition of the enteric NMDA-Rs may provide a therapeutic option via which to influence intestinal hypermotility, microcirculatory changes and inflammatory activation simultaneously.
Negative pressure wound therapy (2007)

iabetic foot disease is a major global burden. Foot ulcers frequently develop complications and become chronic, representing a considerable challenge as these are typically very difficult to treat. New therapies are needed to address these wounds and there is an increasing focus on negative pressure wound therapy (NPWT). This technique has been shown to accelerate wound healing and although its costs are significant, there is also evidence to show that it compares favourably with more conventional alternatives. However, most studies to date have been small, and larger trials are needed before NPWT becomes more routine. In the meantime, the procedure may be most suitable for large, chronic, heavily exuding wounds that do not respond to established therapies.
Multiple Ca2+-Calmodulin-dependent Protein Kinase Kinases from Rat Brain (1996)

We have purified to near homogeneity from rat brain two Ca(2+)-calmodulin-dependent protein kinase I (CaM kinase I) activating kinases, termed here CaM kinase I kinase-alpha and CaM kinase I kinase-beta (CaMKIK alpha and CaMKIK beta, respectively). Both CaMKIK alpha and CaMKIK beta are also capable of activating CaM kinase IV. Activation of CaM kinase I and CaM kinase IV occurs via phosphorylation of an equivalent Thr residue within the "activation loop" region of both kinases, Thr-177 and Thr-196, respectively. The activities of CaMKIK alpha and CaMKIK beta are themselves strongly stimulated by the presence of Ca(2+)-CaM, and both appear to be capable of Ca(2+)-CaM-dependent autophosphorylation. Automated microsequence analysis of the purified enzymes established that CaMKIK alpha and -beta are the products of distinct genes. In addition to rat, homologous nucleic acids corresponding to these CaM kinase kinases are present in humans and the nematode, Caenorhabditis elegans. CaMKIK alpha and CaMKIK beta are thus representatives of a family of enzymes, which may function as key intermediaries in Ca(2+)-CaM-driven signal transduction cascades in a wide variety of eukaryotic organisms.
Optical interconnects in systems (2000)

Future enhancement of system performance will decreasingly rely on reduction in transistor dimensions. Rather, performance gains will increasingly come from improved hardware and software architectures and emerging technologies such as optical interconnects, which provide a new design space for system designers. It is possible that hybrid optoelectronic interconnects may revolutionize system implementation in the next decade.
Software radio FM broadcast receiver for audio indexing applications (2012)

Broadcast radio is a rich but underexploited source of multimedia content. To make this available to users, it will be indispensable to develop new types of navigators capable of searching the large quantities of information contained in the radio bands. The article introduces a prototype of a new software radio enabled broadcast media navigator implemented on an FPGA, which is able to demodulate simultaneously all channel in the FM band and perform audio indexing upon them, ultimately using a Graphics Processing Unit.
Role of Monocyte Chemoattractant Protein-1 in Cardiovascular Remodeling Induced by Chronic Blockade of Nitric Oxide Synthesis (2000)

These results suggest that MCP-1 is necessary for the development of medial thickening as well as monocyte recruitment. In contrast, the pathogenesis of fibrosis may involve other factors, such as TGF-beta(1).
Bio-inspired visual attention and object recognition (2007)

This paper describes a bio-inspired Visual Attention and Object Recognition System (VARS) that can (1) learn representations of objects that are invariant to scale, position and orientation; and (2) recognize and locate these objects in static and video imagery. The system uses modularized bio-inspired algorithms/techniques that can be applied towards finding salient objects in a scene, recognizing those objects, and prompting the user for additional information to facilitate interactive learning. These algorithms are based on models of human visual attention, search, recognition and learning. The implementation is highly modular, and the modules can be used as a complete system or independently. The underlying technologies were carefully researched in order to ensure they were robust, fast, and could be integrated into an interactive system. We evaluated our system's capabilities on the Caltech-101 and COIL-100 datasets, which are commonly used in machine vision, as well as on simulated scenes. Preliminary results are quite promising in that our system is able to process these datasets with good accuracy and low computational times.
A double-blind placebo-controlled trial of baclofen in the treatment of tinnitus. (1996)

Baclofen is no more effective than placebo in ameliorating tinnitus in adult patients.
Alterations in the Content and Composition of Glycosaminoglycans in Human Laryngeal Carcinoma (2002)

Glycosaminoglycans in normal and cancerous human laryngeal cartilage were isolated and characterized by means of enzyme susceptibility and high performance liquid chromatography. The known mammalian glycosaminoglycans were identified in all samples but their content and composition varied between normal and malignant samples. Chondroitin/dermatan sulphate was the major glycosaminoglycan in all cases, but its relative proportion was decreased in malignant samples. Its sulphation pattern showed that in normal samples it was sulphated mainly at the C6 position of galactosamine, whereas in malignant samples it was sulphated mainly at C4. Dermatan sulphate, expressed as a result of the different digestion of samples with chondroitinases, was present in very small amounts in normal samples (2.7% of total sulphated glycosaminoglycans) but increased in proportion up to 27.7% in malignant samples. The content of oversulphated chondroitin/dermatan was increased twofold in malignant samples. The content of heparan sulphate was increased almost fivefold in malignant samples as compared to normal ones. The content of hyaluronan was increased in malignant samples 3.5-fold, amounting to up to 11.4% of total glycosaminoglycans. These dramatic changes in the content and composition of glycosaminoglycans seemed to be characteristic of the tumour and independent of its status.
Bone marrow transplantation for sickle cell anemia. (1994)

Bone marrow transplantation is an effective therapeutic modality that should be considered in patients with severe SCA.
The Receptor Binding Domain of the New Middle East Respiratory Syndrome Coronavirus Maps to a 231-Residue Region in the Spike Protein That Efficiently Elicits Neutralizing Antibodies (2013)

The spike (S) protein of the recently emerged human Middle East respiratory syndrome coronavirus (MERS-CoV) mediates infection by binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we mapped the receptor binding domain in the S protein to a 231-amino-acid fragment (residues 358 to 588) by evaluating the interaction of spike truncation variants with receptor-expressing cells and soluble DPP4. Antibodies to this domain--much less so those to the preceding N-terminal region--efficiently neutralize MERS-CoV infection.
Consumption of Fish and Fish Oils and Decreased Risk of Stroke (2003)

Consumption of fish and fish oils was first associated with decreased risk of cardiovascular disease almost 50 years ago. Since then, a number of epidemiologic studies have evaluated whether their consumption is specifically associated with stroke. Ecologic/cross-sectional and case-control studies have generally shown an inverse association between consumption of fish and fish oils and stroke risk. Results from five prospective studies have been less consistent, with one showing no association, one showing a possible inverse association, and three demonstrating a significant inverse association. In the latest and largest of these, the Nurses Health Study, the relative risk of total stroke was lower, although not significantly so, among women who regularly ate fish than among those who did not. A significant decrease in the risk of thrombotic stroke (relative risk, 0.49; 95% confidence interval, 0.26-0.93) was observed among women who ate fish at least two times per week compared with women who ate fish less than once per month, after adjustment for age, smoking, and other cardiovascular risk factors; a nonsignificant decrease was observed among women in the highest quintile of long-chain omega-3 polyunsaturated fatty acid intake. No association was observed between consumption of fish or fish oil and hemorrhagic stroke. These data support the hypothesis that consumption of fish several times per week reduces the risk of thrombotic stroke but does not increase the risk of hemorrhagic stroke.
Inflammasomes: guardians of cytosolic sanctity (2008)

The innate immune system is critical in recognizing bacterial and viral infections to evoke a proper immune response. Certain members of the intracellular nucleotide-binding and oligomerization domain (NOD)-like receptor (NLR) family detect microbial components in the cytosol and trigger the assembly of large caspase-1-activating complexes termed inflammasomes. Autoproteolytic maturation of caspase-1 zymogens within these inflammasomes leads to maturation and secretion of the pro-inflammatory cytokines interleukin-1 beta (IL-1 beta) and IL-18. The NLR proteins ICE protease-activating factor (IPAF), NALP1b (NACHT domain-, leucine-rich repeat-, and PYD-containing protein 1b), and cryopyrin/NALP3 assemble caspase-1-activating inflammasomes in a stimulus-dependent manner. Bacterial flagellin is sensed by IPAF, whereas mouse NALP1b detects anthrax lethal toxin. Cryopyrin/NALP3 mediates caspase-1 activation in response to a wide variety of microbial components and in response to crystalline substances such as the endogenous danger signal uric acid. Genetic variations in Nalp1 and cryopyrin/Nalp3 are associated with autoinflammatory disorders and increased susceptibility to microbial infection. Further understanding of inflammasomes and their role in innate immunity should provide new insights into the mechanisms of host defense and the pathogenesis of autoimmune diseases.
Elevated basal and post-feed glucagon-like peptide 1 (GLP-1) concentrations in the neonatal period (2008)

Basal and post-feed amidated GLP-1 concentrations in neonates are grossly raised with the major fractions of circulating GLP-1 being (7-36) amide and (9-36) amide. Elevated GLP-1 concentrations in the newborn period may have a role in regulating maturation of enteroendocrine system and also of increasing pancreatic beta-cell mass and regeneration. The high levels of GLP-1 may be due to immaturity of the dipeptidyl peptidase IV and or lower glomerular filtration rate in the neonatal period. Further studies are required to understand the role of GLP-1 in the neonatal period.