gebhart/patrepeval huggingface dataset:
Effect of a conjugate pneumococcal vaccine on the occurrence of respiratory infections and antibiotic use in day-care center attendees (2001)

The reduction of respiratory problems, including those not traditionally considered of pneumococcal origin and the ensuing lowered antibiotic use in day-care center attendees by pneumococcal conjugate vaccination suggest a broader benefit from the vaccine than preventing invasive disease only.
Biliary lipids and cholesterol gallstone disease (2008)

Biliary lipids are a family of four dissimilar molecular species consisting of a mixture of bile salts (substituted cholanoic acids), phospholipids, mostly (>96%) diacylphosphatidylcholines, unesterified cholesterol, and bilirubin conjugates known trivially as lipopigments. The primary pathophysiological defect in cholesterol gallstone disease is hypersecretion of hepatic cholesterol into bile with less frequent hyposecretion of bile salts and/or phospholipids. Several other gallbladder abnormalities contribute and include hypomotility, immune-mediated inflammation, hypersecretion of gelling mucins, and accelerated phase transitions; there is also reduced intestinal motility that augments "secondary" bile salt synthesis by the anaerobic microflora. Cholesterol nucleation is initiated when unilamellar vesicles of cholesterol plus biliary phospholipids fuse to form multilamellar vesicles. From these "plate-like" cholesterol monohydrate crystals, the building blocks of macroscopic stones are nucleated heterogeneously by mucin gel. Multiple Lith gene loci have been identified in inbred mice, paving the way for discovery of an ever-increasing number of LITH genes in humans. Because of the frequency of the metabolic syndrome today, insulin resistance and LITH genes all interact with a number of environmental cholelithogenic factors to cause the gallstone phenotype. This review summarizes current concepts of the physical-chemical state of biliary lipids in health and in lithogenic bile and outlines the molecular, genetic, hepatic, and cholecystic factors that underlie the pathogenesis of cholesterol gallstones.
Correlation of WNT/β-catenin pathway activation with immune exclusion across most human cancers. (2016)

3004 Background: The presence of intra-tumoral CD8+T cells has been associated with clinical benefit to immunotherapy and patients can be categorized based on the presence or absence of a T cell-inflamed tumor microenvironment. Molecular mechanisms underpinning the absence of a T cell response are beginning to be understood with identification of the WNT/β-catenin pathway playing a major role in melanoma. Methods: Gene expression data from TCGA was segregated using a T cell-inflamed gene expression signature to identify patient samples by immune phenotype. Within the subset of each tumor histology lacking the T cell signature, exomic sequencing data was interrogated for mutations and pathway analysis was performed to identify gene expression changes predicted to activate the β-catenin signaling pathway. Immunohistochemistry was performed on human primary and metastatic specimens of multiple tumor histologies to correlate the presence of nuclear β-catenin with the lack of a T cell infiltrate. Results: Predicted activating mutations in CTNNB1 or inactivating mutations in Axin1, Axin2, APC1, APC2 were observed within 13 tumor histologies ranging in frequency of 9% (esophageal) to 67% (colon) of tumor specific samples. Pathway analysis identified 12 further histologies harboring increased expression of β-catenin pathway elements such as WNT ligands. Only 3 tumors (pancreatic, thyroid, paraganlioma) showed no activation correlating with absence of immune signatures. Immunohistochemistry demonstrated inverse correlations between β-catenin and CD8+T cells. Conclusions: WNT/β-catenin pathway signaling correlates with T cell exclusion and is activated in most human solid tumors. Clinical development of β-catenin pathway inhibitors that combine with immunotherapies should be prioritized. Pathway activation by mutation Pathway activation by increased expression Colon Kidney – clear cell Melanoma (metastatic) Mesothelioma Glioma – low grade Head and Neck Testicular Gastric Lung – Squamous Breast Sarcoma Ovarian Lung – Adenocarcinoma Cervical Uveal Melanoma Bladder Hepatocellular Adrenocortical Kidney – Papillary Uterine Uterine Sarcoma Prostate Kidney – Chromophobe Glioblastoma
Topical and transdermal delivery of antisense oligonucleotides. (2001)

Antisense oligonucleotides have great potential as therapeutic agents. As a result, a variety of chemistries have been developed to improve the efficacy of these molecules without compromising their specificity. Because the skin is such a large organ with extensive accessibility, it is a natural target for drug delivery. It is, however, an effective barrier, so physical and chemical methods to improve drug penetration have been developed. These enhancement techniques can be combined with modified oligonucleotide chemistries to provide sufficient levels of antisense activity either within the skin or systemically. This review will describe in vitro and in vivo experiments that demonstrate the potential of antisense oligonucleotides to treat both dermal and systemic disorders.
Comparative Molecular Dynamics Studies of Wild-Type and Oxidized Forms of Full-Length Alzheimer Amyloid β-Peptides Aβ(1−40) and Aβ(1−42) (2008)

In this study, all-atom 50 ns molecular dynamics simulations are performed on the full-length amyloid beta (Abeta) monomers (WT-Abeta(1-40) and WT-Abeta(1-42)) and their oxidized forms (Met35(O)-Abeta(1-40) and Met35(O)-Abeta(1-42)) in aqueous solution. The effects of the oxidation state of Met35 and the presence of dipeptide (Ile41-Ala42) on the secondary structures of the three distinct regions (the central hydrophobic core region 17-21 (LVFFA), the loop 23-28 (DVGSNK), and the second hydrophobic domain 29-35 (GAIIGLM)) of all monomers have been analyzed in detail, and results are compared with the available experimental information. Our simulations indicate that the WT-Abeta(1-40) monomer adopts an overall beta-hairpin-like structure, which is promoted by the turn region (24-27). This turn region is stabilized through salt-bridge formation between the Asp23 and Lys28 residues. In contrast, the overall structure of the oxidized (Met35(O)-Abeta(1-40)) monomer can be divided into three well-defined bend regions separated by coil segments. These structural differences may be critical for the measured decrease in the rate of aggregation of Met35(O)-Abeta(1-40) peptide. In the WT-Abeta(1-42) monomer, in comparison to the WT-Abeta(1-40), the Asp23-Lys28 salt bridge is absent, and consequently, the turn in the middle (24-27) region has a smaller curvature. The observed difference in the aggregation rates of these two peptides may be related to the opening of the turn (24-27) stabilized by the Asp23-Lys28 salt bridge. For WT-Abeta(1-42), in the absence of this salt bridge, the unfolding and aggregation events may be more favorable than for WT-Abeta(1-40).
High-fidelity qubit measurement with a microwave-photon counter (2014)

High-fidelity, efficient quantum nondemolition readout of quantum bits is integral to the goal of quantum computation. As superconducting circuits approach the requirements of scalable, universal fault tolerance, qubit readout must also meet the demand of simplicity to scale with growing system size. Here we propose a fast, high-fidelity, scalable measurement scheme based on the state-selective ring-up of a cavity followed by photodetection with the recently introduced Josephson photomultiplier (JPM), a current-biased Josephson junction. This scheme maps qubit state information to the binary digital output of the JPM, circumventing the need for room-temperature heterodyne detection and offering the possibility of a cryogenic interface to superconducting digital control circuitry. Numerics show that measurement contrast in excess of 95% is achievable in a measurement time of 140 ns. We discuss perspectives to scale this scheme to enable readout of multiple qubit channels with a single JPM.
Isolation of serum amyloid P-component (protein SAP) in the mouse. (1979)

Serum amyloid P-component (protein SAP) was associated from mouse serum and ascitic fluids by calcium-dependent affinity chromatography on Sepharose 4B (Pharmacia) followed by gel filtration on Ultrogel AcA44 (LKB) in the presence of EDTA. It was homogenous on gradient polyacrylamide gel and sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis, and induced a monospecific antiserum in the rabbit. The related protein, C-reactive protein (CRP) was present in only trace amounts not exceeding 2 mug/ml of serum even during acute phase reactions. It was isolated by calcium-dependent affinity chromatography on insolubilized pneumococcal C-polysaccharide. The availability of these isolated mouse proteins and their respective antisera will facilitate investigation of their function.
Direct visualization at the single-cell level of siRNA electrotransfer into cancer cells (2011)

The RNA interference-mediated gene silencing approach is promising for therapies based on the targeted inhibition of disease-relevant genes. Electropermeabilization is one of the nonviral methods successfully used to transfer siRNA into living cells in vitro and in vivo. Although this approach is effective in the field of gene silencing by RNA interference, very little is known about the basic processes supporting siRNA transfer. In this study, we investigated, by direct visualization at the single-cell level, the delivery of Alexa Fluor 546-labeled siRNA into murine melanoma cells stably expressing the enhanced green fluorescent protein (EGFP) as a target gene. The electrotransfer of siRNA was quantified by time lapse fluorescence microscopy and was correlated with the silencing of egfp expression. A direct transfer into the cell cytoplasm of the negatively charged siRNA was observed across the plasma membrane exclusively on the side facing the cathode. When added after electropulsation, the siRNA was inefficient for gene silencing because it did not penetrate the cells. Therefore, we report that an electric field acts on both the permeabilization of the cell plasma membrane and on the electrophoretic drag of the negatively charged siRNA molecules from the bulk phase into the cytoplasm. The transfer kinetics of siRNA are compatible with the creation of nanopores, which are described with the technique of synthetic nanopores. The mechanism involved was clearly specific for the physico-chemical properties of the electrotransferred molecule and was different from that observed with small molecules or plasmid DNA.
Cloning and Characterization of the cDNA for Human Airway Trypsin-like Protease (1998)

Previously we isolated a trypsin-like enzyme designated human airway trypsin-like protease from the sputum of patients with chronic airway diseases. This paper describes the cDNA cloning, characterization of the primary protein structure deduced from the cDNA, and gene expression of this enzyme in various human tissues. We obtained an entire 1517-base pair sequence of cDNA with an open reading frame encoding a polypeptide with 418-amino acid residues. The polypeptide consisted of a 232-residue catalytic region and a 186-residue noncatalytic region with a hydrophobic putative transmembrane domain near the NH2 terminus. The polypeptide was suggested to be a type II integral membrane protein in which the COOH-terminal catalytic region is extracellular. Therefore, this protein is thought to be synthesized as a membrane-bound precursor and to mature to a soluble and active protease by limited proteolysis. It showed 29-38% identity in the sequence of the catalytic region with human hepsin, enteropeptidase, acrosin, and mast cell tryptase. The noncatalytic region had little similarity to other known proteins. In Northern blot analysis a transcript of 1.9 kilobases was detectable most prominently in the trachea among 17 human tissues examined.
Thiol–isocyanate “click” reactions: rapid development of functional polymeric surfaces (2010)

Functional, micropatterned and multicomponent polymer brush surfaces can be rapidly fabricated via base-catalyzed thiol–isocyanate “click” reactions.
Process Mining Online Assessment Data (2009)

Traditional data mining techniques have been extensively applied to find interesting patterns, build descriptive and predictive models from large volumes of data accumulated through the use of different information systems. The results of data mining can be used for getting a better understanding of the underlying educational processes, for generating recommendations and advice to students, for improving management of learning objects, etc. However, most of the traditional data mining techniques focus on data dependencies or simple patterns and do not provide a visual representation of the complete educational\n(assessment) process ready to be analyzed. To allow for these types of analysis\n(in which the process plays the central role), a new line of data-mining research, called process mining, has been initiated. Process mining focuses on the development of a set of intelligent tools and techniques aimed at extracting process-related knowledge from event logs recorded by an information system. In this paper we demonstrate the applicability of process mining, and the ProM framework in particular, to educational data mining context. We analyze assessment data from recently organized online multiple choice tests and demonstrate the use of process discovery, conformance checking and\nperformance analysis techniques.
Smart Technologies with Wireless Sensor Networks (2015)

In recent years, the studies in inter-devices communication (M2 M) which is considered to be the Internet, ecosystem of the objects have accelerated in line with the developments in mobile communication technologies. This way, development of systems making human lives easier in smart environment, smart agriculture, smart grid fields with monitoring purposes which can be considered among M2 M implementations is now possible. These systems can be developed with sensor node platform which can detect and communicate. Wireless Sensor Networks (WSN) consists of these sensor nodes containing simple processors, low power consuming antennas and various detectors. As the sensor networks do not require wired communication infrastructure, they can easily and inexpensively be formed with no harm to the environment. The sensor nodes have the ability to store and process data locally thanks to the software and hardware structure they have. The fact that they can get in contact with each other enables them to collaborate in performing complicated tasks along with exchanging information. As the communication means have low power consumption, it ensures that the life of the sensor nodes is long. The fact, too, that the nodes are programmable after being placed in the medium provides greater advantages. Because of the low cost and flexibility in use, the wireless sensor nodes are convenient to be used in many industrial and environmental applications. In this study, -how to develop smart environment, smart agriculture, smart grid with WSN- is analyzed.
Laboratory and in vitro Evaluation of Inbred and F2 Populations of Brown Midrib Mutants of Zea mays L.1 (1972)

Abstract The purpose of this research was to determine the effect of brown midrib mutants on the lignin percentage and in vitro dry matter disappearance (IVDMD) of corn ( Zea mays L.) stover. F 2 populations of corn carrying the brown midrib mutants bm 1 , bm 2 , and bm 3 , were grown under field conditions and harvested at 35 and 55 days post‐silking. Plants harvested at 35 days post‐silking were separated into several parts. Samples were analyzed for structural composition and in vitro dry matter disappearance using detergent solution and rumen fermentation techniques, respectively. Stover, harvested 55 days postsilking, contained 8.15, 8.07, 4.96, and 8.81% acid detergent lignin for genotypes bm 1 , bm 2 , bm 3 , and F 2 normal, respectively. The IVDMD percentages were 49.3, 47.6, 56.3, and 46.2, respectively. At 35 days post‐silking, the lignin content was lower and the IVDMD higher in bm 3 than in the other genotypes for all plant parts except the kernel. The structural composition and IVDMD of normal corn was similar to that of a commercial hybrid included in the study. Mutant inbred lines (Tr background) of bm 1 , bm 3 , bm 2 , bm 3 , and bm 4 were also evaluated. Mutants bm 3 and bm 1 bm 3 were lowest in lignin and highest in IVDMD. In both the inbred and F 2 populations, structural components other than acid detergent lignin did not differ appreciable among the genotypes. Since lignin limits the digestion and utilization of fibrous feeds by ruminant animals, the possible use of brown midrib mutants for improving the nutritional quality of corn stover and silage appears promising. Mutant bm 3 appears to have the most potential for this purpose.
Civil Rights and Asian Americans (1997)

Asian American community composed of no less than 20 different ethnic groups is one of the most diverse and complex minority groups in the nation. This article examines the civil rights perspective on Asian Americans through a historical account of major Asian immigrant groups who have experienced and are confronting institutionalized discrimination and violence; and analyzes contemporary civil rights issues affecting Asian Americans in the areas of public and higher education, the work place, and voting rights.
Asymmetric reduction of cyclic imines with chiral sodium acyloxyborohydrides (1983)

Asymmetric reduction of prochiral cyclic imines with chiral sodium acyloxyborohydrides (5a–i), which are easily prepared by the reaction of NaBH4 with various N-acyl α-amino-acids, has been investigated. Of these new reducing agents, triacyloxyborohydrides (5c–f), derived from NaBH4(1 equiv.) and (S)-N-acylproline (3 equiv.), were found to reduce 3,4-dihydropapaverine (2) in tetrahydrofuran to (S)-norlaudanosine (3) hydrochloride in 60% optical yield. The N-benzyloxycarbonyl derivative (5c) could be isolated as a powder and characterized. The effect of solvents on this asymmetric reduction has been examined by the use of the isolated reagent (5c); halogenated alkane solvents such as CH2Cl2 or CHCl2CH3 gave a better optical yield of compound (3)(70% e.e.). The reagent (5c) also reduced other cyclic imines (6a–c) and (8) to the corresponding alkaloids (7a–c) and (9) in excellent optical yields (70–86% e.e.), providing an effective route to the asymmetric synthesis of these alkaloids. A possible reaction path for this reduction is also presented.
MRF Optimization via Dual Decomposition: Message-Passing Revisited (2007)

A new message-passing scheme for MRF optimization is proposed in this paper. This scheme inherits better theoretical properties than all other state-of-the-art message passing methods and in practice performs equally well/outperforms them. It is based on the very powerful technique of Dual Decomposition [1] and leads to an elegant and general framework for understanding/designing message-passing algorithms that can provide new insights into existing techniques. Promising experimental results and comparisons with the state of the art demonstrate the extreme theoretical and practical potentials of our approach.
Monolithic achromatic nulling interference coronagraph: design and performance (2009)

We present the design of the monolithic achromatic nulling interference coronagraph (MANIC), a nulling interferometer consisting of optically contacted prisms and a symmetric beam splitter. The optic is designed to enable the direct detection of nearby Jupiter-like exoplanets, and may be extended to enable Earth-like system detection. The monolithic nature of the optic improves on the current state-of-the-art in nulling interferometers by providing built-in alignment and stability, as well as a reduction in size and mass. These qualities make the MANIC extremely robust and simple to integrate, and an excellent candidate for space-based applications.
Relationship Between Standing Posture and Stability (1998)

Posture and stability had a low correlation. Subjects with bilateral vestibular hypofunction did not demonstrate a forward head or backward trunk lean, as has been reported anecdotally. Changing from standing with feet apart to feet together increased whole-body movement patterns to control standing stability.
Magnetic recording channel front-ends (1991)

Readback front-end electronics for both inductive and magnetic recording (MR) heads are investigated. For inductive front-ends, it is shown that the channel bandwidth is determined by the transfer of the induced head voltage to the front-end input terminals. The parameters limiting this bandwidth are calculated. A noise analysis shows that the signal-to-noise ratio can be optimized and gives the parameter values for which this happens. The effect of noise matching of the head to the front-end is demonstrated. For MR front-ends the principles of auto bias and relative resistance sensing are presented. Front-end configurations producing voltage biasing and current biasing are discussed. Two examples of signal conditioning in MR front-ends are given: an on-the-chip equalizer compensating the frequency roll-off introduced by the head cable inductance, and a signal-adaptive circuit for removing thermal asperities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Association of Kaposi's sarcoma-associated herpesvirus-positive primary effusion lymphoma with expression of the CD138/syndecan-1 antigen. (1997)

Primary effusion lymphoma (PEL) represents a novel B-cell non-Hodgkin's lymphoma (NHL) type associated with Kaposi's sarcoma-associated herpesvirus infection and typically growing as lymphomatous effusions in the body cavities. The precise B-cell subset from which PEL originates as well as the biologic mechanisms responsible for its peculiar growth pattern are unclear. In this study, we have analyzed PEL for the expression status of CD138/syndecan-1, a molecule selectively associated with late stages of B-cell differentiation and implicated in cell-to-cell and cell-to-extracellular matrix interactions. PEL patient samples (n = 7) and cell lines (n = 5) were investigated by multiple approaches, including immunocytochemistry, flow cytometry, RNA analysis, and Western blot studies. For comparison, lymphomatous effusions other than PEL (n = 13) and tissue-based NHL (n = 103) were also tested. Expression of CD138/syndecan-1 associates at high frequency with PEL (5 of 7 patient samples and 5 of 5 cell lines), whereas it is consistently absent among other lymphomatous effusions (n = 13). The CD138/syndecan-1 isoform expressed by PEL has an average molecular weight of 420 kD, which is substantially different from that of CD138/syndecan-1 molecules generally expressed by plasma cells. These data, along with previous immunophenotypic evidence, unequivocally define that PEL cells represent a preterminal stage of B-cell differentiation and may bear implications for the peculiar growth pattern of this lymphoma.
Sensor-Triggered, Rate-Variable Cardiac Pacing (1987)

Conventional implantable dual-chamber cardiac pacemakers adjust heart rate and maintain normal atrial and ventricular contraction by tracking "native" atrial electrical activity and pacing the ventricles after a predetermined programmable atrioventricular delay. However, in patients with symptomatic bradyarrhythmias, optimal function of "atrial-tracking" devices may be limited by concomitant sinoatrial disease. Provision of chronotropic response during physical exertion or emotional stress may be achieved by using physiologic sensors to alter pacing rate independently of atrial activity. Additional systems using sensor technologies are being developed. Future pacing systems will have dual-chamber pacing capability and may use several sensors coupled synergistically in order to take advantage of particular strengths of each. Physiologic sensor technology may be of diagnostic value in both antitachycardia devices and implantable cardioverter and defibrillator systems.