gebhart/patrepeval huggingface dataset:
Making It Easy to Do It Right (2001)

At the turn of the last century, William Osler, Harvey Cushing, and other clinical leaders restructured hospital organization, established scientific research as the foundation for clinical practice, formalized clinical education, and set and enforced high ethical and personal standards of performance among physicians and nurses. Their era marked a turning point in health care delivery. Prior to 1900, seeking a physician's help for a serious illness did little to change the course of the disease,1 but since that time life expectancy in the United States has almost doubled. A child born in the United States in 1998 can expect to . . .
High-performance multi-functional reverse osmosis membranes obtained by carbon nanotube·polyamide nanocomposite (2015)

Clean water obtained by desalinating sea water or by purifying wastewater, constitutes a major technological objective in the so-called water century. In this work, a high-performance reverse osmosis (RO) composite thin membrane using multi-walled carbon nanotubes (MWCNT) and aromatic polyamide (PA), was successfully prepared by interfacial polymerization. The effect of MWCNT on the chlorine resistance, antifouling and desalination performances of the nanocomposite membranes were studied. We found that a suitable amount of MWCNT in PA, 15.5 wt.%, not only improves the membrane performance in terms of flow and antifouling, but also inhibits the chlorine degradation on these membranes. Therefore, the present results clearly establish a solid foundation towards more efficient large-scale water desalination and other water treatment processes.
Ligands for the β-Glucan Receptor, Dectin-1, Assigned Using “Designer” Microarrays of Oligosaccharide Probes (Neoglycolipids) Generated from Glucan Polysaccharides (2005)

Dectin-1 is a C-type lectin-like receptor on leukocytes that mediates phagocytosis and inflammatory mediator production in innate immunity to fungal pathogens. Dectin-1 lacks residues involved in calcium ligation that mediates carbohydrate-binding by classical C-type lectins; nevertheless, it binds zymosan, a particulate beta-glucan-rich extract of Saccharomyces cerevisiae, and binding is inhibited by polysaccharides rich in beta1,3- or both beta1,3- and beta1,6-linked glucose. The oligosaccharide ligands on glucans recognized by Dectin-1 have not yet been delineated precisely. It is also not known whether Dectin-1 can interact with other types of carbohydrates. We have investigated this, since Dectin-1 shows glucan-independent binding to a subset of T-lymphocytes and is involved in triggering their proliferation. Here we assign oligosaccharide ligands for Dectin-1 using the neoglycolipid-based oligosaccharide microarray technology, a unique approach for constructing microarrays of lipid-linked oligosaccharide probes from desired sources. We generate "designer" microarrays from three glucan polysaccharides, a neutral soluble glucan isolated from S. cerevisiae and two bacterial glucans, curdlan from Alcaligenes faecalis and pustulan from Umbilicaria papullosa, and use these in conjunction with 187 diverse, sequence-defined, predominantly mammalian-type, oligosaccharide probes. Among these, Dectin-1 binding is detected exclusively to 1,3-linked glucose oligomers, the minimum length required for detectable binding being a 10- or 11-mer. Thus, the ligands assigned so far are exogenous rather than endogenous. We further show that Dectin-1 ligands, 11-13 gluco-oligomers, in clustered form (displayed on liposomes), mimic the macromolecular beta-glucans and compete with zymosan binding and triggering of tumor necrosis factor-alpha secretion by a Dectin-1-expressing macrophage cell line.
An Overview of the Analysis of Next Generation Sequencing Data (2011)

Next generation sequencing is a common and versatile tool for biological and medical research. We describe the basic steps for analyzing next generation sequencing data, including quality checking and mapping to a reference genome. We also explain the further data analysis for three common applications of next generation sequencing: variant detection, RNA-seq, and ChIP-seq.
Pathway for D-galactonate catabolism in nonpathogenic mycobacteria (1981)

D-Galactonate is catabolized in saprophytic mycobacteria to give pyruvate and glyceraldehyde-3-phosphate by a pathway that involves the sequential reactions of galactonate dehydratase, 2-keto-3-deoxy-galactonate kinase, and 6-phospho-2-keto-3-deoxy-galactonate aldolase.
HP Hyperplex(R) clustering technology (1999)

HP HyperPlex(R) is a clustering technology that leverages HP platforms, mass storage and interconnect products to provide customers with mission-critical high availability and increased processing capacity. A HyperPlex cluster consists of two or more symmetric multiprocessing (SMP) nodes, an interconnect, mass storage options, and a centrally-managed operating environment. Further, HyperPlex solutions lower costs by consolidating resources and increasing users' productivity. This paper describes the technologies for each of these components, the features and benefits of Hewlett-Packard's HyperPlex implementation, and the software that complements these technologies.
Fed-batch Process for Pyruvate Production by Recombinant Escherichia coli YYC202 strain (2003)

Fed-batch fermentation was applied to the production of pyruvate by using a recombinant Escherichia coli YYC202 strain. This strain is completely blocked in its ability to convert pyruvate into acetyl-CoA or acetate, resulting in acetate auxotrophy during growth in glucose minimal medium. By controlling acetate and glucose feed rate, a series of lab-scale fed-batch experiments were performed at pH 7 and 37 °C. CO2 production rate (CTR) was used for on-line regulation of the acetate feed rate. The correlation between CTR and acetate consumption rate (ACR) was determined experimentally. At optimal process conditions a final pyruvate concentration higher than 62 g/L, a space-time yield of up to 42 g/L/d and pyruvate/glucose molar yield of 1.11 mol/mol were achieved. Experimental evidence was gathered that pyruvate export is active.
Rapid Antibiotic Susceptibility Testing of Uropathogenic E. coli by Tracking Submicron Scale Motion of Single Bacterial Cells (2017)

To combat antibiotic resistance, a rapid antibiotic susceptibility testing (AST) technology that can identify resistant infections at disease onset is required. Current clinical AST technologies take 1-3 days, which is often too slow for accurate treatment. Here we demonstrate a rapid AST method by tracking sub-μm scale bacterial motion with an optical imaging and tracking technique. We apply the method to clinically relevant bacterial pathogens, Escherichia coli O157: H7 and uropathogenic E. coli (UPEC) loosely tethered to a glass surface. By analyzing dose-dependent sub-μm motion changes in a population of bacterial cells, we obtain the minimum bactericidal concentration within 2 h using human urine samples spiked with UPEC. We validate the AST method using the standard culture-based AST methods. In addition to population studies, the method allows single cell analysis, which can identify subpopulations of resistance strains within a sample.
Fluid biopsy for circulating tumor cell identification in patients with early-and late-stage non-small cell lung cancer: a glimpse into lung cancer biology (2012)

Circulating tumor cell (CTC) counts are an established prognostic marker in metastatic prostate, breast and colorectal cancer, and recent data suggest a similar role in late stage non-small cell lung cancer (NSCLC). However, due to sensitivity constraints in current enrichment-based CTC detection technologies, there are few published data about CTC prevalence rates and morphologic heterogeneity in early-stage NSCLC, or the correlation of CTCs with disease progression and their usability for clinical staging. We investigated CTC counts, morphology and aggregation in early stage, locally advanced and metastatic NSCLC patients by using a fluid-phase biopsy approach that identifies CTCs without relying on surface-receptor-based enrichment and presents them in sufficiently high definition (HD) to satisfy diagnostic pathology image quality requirements. HD-CTCs were analyzed in blood samples from 78 chemotherapy-naïve NSCLC patients. 73% of the total population had a positive HD-CTC count (>0 CTC in 1 mL of blood) with a median of 4.4 HD-CTCs mL⁻¹ (range 0-515.6) and a mean of 44.7 (±95.2) HD-CTCs mL⁻¹. No significant difference in the medians of HD-CTC counts was detected between stage IV (n = 31, range 0-178.2), stage III (n = 34, range 0-515.6) and stages I/II (n = 13, range 0-442.3). Furthermore, HD-CTCs exhibited a uniformity in terms of molecular and physical characteristics such as fluorescent cytokeratin intensity, nuclear size, frequency of apoptosis and aggregate formation across the spectrum of staging. Our results demonstrate that despite stringent morphologic inclusion criteria for the definition of HD-CTCs, the HD-CTC assay shows high sensitivity in the detection and characterization of both early- and late-stage lung cancer CTCs. Extensive studies are warranted to investigate the prognostic value of CTC profiling in early-stage lung cancer. This finding has implications for the design of extensive studies examining screening, therapy and surveillance in lung cancer patients.
The network video terminal (1996)

Currently, a variety of the MBONE video tools provide video conferencing capabilities on different platforms and with a variety of compression algorithms. However most of these tools lack the ability to interact with other media agents that might be used during a conferencing session. Such interaction is required, for example, for achieving lip synchronisation between audio and video streams or for quality of service control. In this paper we present a new video tool, NEVIT. This tool provides the basic capabilities needed for video conferencing services such as video capturing, compression and decompression engines and multicasting and ATM network interfaces. To ease the interaction with other media agents, NEVIT incorporates a message handling facility to interact over a local conference bus with other media agents, a floor controller of the conference controller. Currently, we are working on adding lip synchronisation and quality-of-service control using this conference bus.
Analysis of 31 CFTR mutations by polymerase chain reaction/oligonucleotide ligation assay in a pilot screening of 4476 newborns for cystic fibrosis (1999)

PCR/OLA is a robust, accurate, user friendly method for cystic fibrosis screening of newborns using blood spots in a semiautomated way at a low cost per mutation (0.8 Euro).
Expression of CD175 (Tn), CD175s (sialosyl‐Tn) and CD176 (Thomsen‐Friedenreich antigen) on malignant human hematopoietic cells (2008)

The expression of the histo-blood group carbohydrate structures T-nouvelle (Tn, CD175), sialylated Tn (CD175s) and the Thomsen-Friedenreich disaccharide (TF, CD176) on human leukemia cell lines was analyzed by their reactivity with specific monoclonal antibodies in flow cytometry, immunohistology and immunoprecipitation. Expression of sialylated CD176 was evaluated by comparative immunostaining with anti-CD176 antibodies before and after sialidase treatment. While only few cell lines expressed unmasked CD176, sialylated CD176 was present on all hematopoietic cell lines and native lymphocytes examined. CD175 and CD175s are preferentially expressed on erythroblastic leukemia cell lines. CD175s expression in these cells is consistent with the transcription of the gene encoding the key enzyme alpha2,6-sialyltransferase (hST6GalNAc1). The staining intensity was reduced after methanol pretreatment of cells, indicating that these glycans are partially expressed as constituents of glycosphingolipids. Immunoprecipitation and subsequent Western blotting revealed a series of distinct high molecular glycoproteins as carriers for these carbohydrate antigens. CD34 was identified as major carrier of CD176 by immunoprecipitation and microsequencing on a KG-1 subline enriched for CD176 expression. Incubation of several CD176-positive cell lines with anti-CD176 antibodies induced apoptosis of these cells, an effect not observed with anti-CD175/CD175s antibodies. Since the presence of naturally occurring anti-CD176 antibodies may represent a mechanism of immunosurveillance against CD176-positive tumor cells, we propose that sialylation of surface-expressed CD176--among other functions--protects against apoptosis.
Does Uncoupling Protein 2 Expression Qualify as Marker of Disease Status in LRRK2 -Associated Parkinson's Disease? (2013)

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common known genetic cause of late-onset Parkinson's disease (PD). However, the penetrance of the disease is below 50% at 60 years of age. LRRK2 is associated with the mitochondrial membrane, and mutant forms impair the function of the organelle and autophagosome clearance in human cells, including induced pluripotent stem cell-derived neurons. Elevated expression of uncoupling proteins has been identified as the cause of mitochondrial depolarization in human fibroblasts with G2019S LRRK2. To identify factors that contribute to the penetrance of LRRK2 mutations, we studied respiratory chain function, markers of mitochondrial uncoupling, oxidative stress, and autophagy in fibroblasts from affected and unaffected carriers of the G2019S mutation. Independent of disease status, all mutation carriers showed reduced mitochondrial membrane potential, increased proton leakage, and more fragmented mitochondria. However, a significant increase in the expression of uncoupling protein 2 (UCP2) was only detected in affected individuals with the G2019S mutation in LRRK2. Since oxidative stress and autophagic markers were selectively increased in some of the PD patients, we hypothesize that UCP2 expression is upregulated in response to elevated reactive oxygen species generation in affected mutation carriers and that UCP2 mRNA levels might, therefore, serve as markers of disease status in LRRK2-associated PD.
Development of an embedded system for classification of EMG signals (2014)

This article describes a methodology to create high-level algorithms, such as artificial neural networks and other pattern recognition techniques to be implemented in embedded systems. A system was developed on a DSP (Digital Signal Processor), for identification and classification of EMG signals; for this purpose the Code Composer Studio software V3.3 and Matlab package were coupled for programming the TMS320F28335 card. The aim of this study was to create a model of an artificial neural network from a previous pre-processing to be implemented on an embedded hardware with the respective network. A typical MLP (Multilayer Perceptron) Network was developed from a pre-processed data set, which were obtained through the acquisition of EMG signals. The data were validated with the discrimination technique as Principal Components Analysis (PCA), which was useful to determine the repeatability and selectivity of the measuring system. Through this application it was possible to improve the processing speed, portability and response of EMG device, which opens a wide range of possibilities for this methodology to be applied in different sectors (e.g, industry, health, etc.) and mainly as a signal classification system.
Block Vector Prediction for Intra Block Copying in HEVC Screen Content Coding (2015)

In screen content video, the spatial correlation among pixels shows different characteristics as compared to natural content video. Intra-picture motion compensation (or intra block copy in HEVC) plays a key role in reducing the bit rate of representing high resolution video with contents such as text and graphics. The efficiency of intra block copy is highly related to the accuracy of block vector prediction. In this paper, several block vector prediction methods are proposed to improve the performance of intra block copy technology in HEVC screen content coding extension. Simulation results show that an average bit rate reduction of 8.0% can be achieved for typical 1080p text and graphics sequences in all intra configuration, when compared to the standard's test model SCM-1.0. As a result, some of the proposed methods have been adopted into the standard working draft and reference software.
Human antigen-presenting cells respond differently to gut-derived probiotic bacteria but mediate similar strain-dependent NK and T cell activation (2007)

The intestinal microbiota is essential for homeostasis of the local and systemic immune system, and particularly strains of lactic acid bacteria and Escherichia coli have been shown to have balancing effects on inflammatory conditions such as allergy and inflammatory bowel disease. However, in vitro assessment of the immunomodulatory effects of distinct strains may depend strongly on the cell type used as a model. To select the most appropriate model for screening of beneficial bacteria in human cells, the response to strains of intestinal bacteria of three types of antigen-presenting cells (APC) was compared; blood myeloid dendritic cells (DC), monocyte-derived DC and monocytes, and the effector response of natural killer cells and naïve T cells was characterized. Maturation induced by gut-derived bacteria differed between APC, with blood DC and monocytes responding with the production of IL-6 and tumour necrosis factor-alpha to bacteria, which elicited mainly IL-10 in monocyte-derived DC. In contrast, comparable IFN-gamma production patterns were found in both natural killer cells and T cells induced by all bacteria-matured APC. An inhibitory effect of certain strains on this IFN-gamma production was also mediated by all types of APC. The most potent responses were induced by monocyte-derived DC, which thus constitute a sensitive screening model.
Network security and storage security: symmetries and symmetry-breaking (2003)

It has been hypothesized that storage security and network security are essentially the same, at least insofar as mapping solutions from one domain in a straightforward manner to the other We discuss similarities and differences that shed some doubt on the propriety of equaling the two. While there are many ways to apply methods from one domain to another, there are fundamental differences between data at rest and data in motion. Storage is often an endpoint as well as a link and it requires different treatment under such circumstances.
Abstract 2834: Anti-DLL4 treatment inhibits melanoma tumor growth, recurrence, metastases, and reduces frequency of cancer stem cells in a clinically relevant tumor model in NOD/SCID mice (2011)

Abstract Metastatic burden at the time of diagnosis is often the cause of death in patients suffering from malignant melanoma. More predictive in vivo animal tumor models are needed to elucidate both the efficacy and mechanism of activity for newly developed anti-cancer therapeutic agents. We have developed an orthotopic melanoma model in NOD/SCID mice with intradermal implant of human melanoma cells that are derived directly from human cancer patient specimens. These tumors retain much of the original human cancer heterogeneity, phenotype, and the ability to form metastases in the lungs, lymph nodes, liver, intestines, and brain _ recapitulating the metastatic invasiveness seen in the clinic. We have developed antibodies against the human and the murine Delta-like Notch ligand DLL4, which target both tumor cells and vasculature, and reduce the frequency of cancer stem cells (CSCs) in human tumors implanted into NOD/SCID mice (Hoey et al., Cell Stem Cell 5:1680177, 2009). In our studies with a human melanoma model, we evaluated the anti-tumor and anti-metastatic activities of anti-DLL4 and found a significant inhibition of both primary tumor and metastases in the lungs, liver, intestine and brain. Moreover, in combination with the standard-of-care Paclitaxel, anti-DLL4 treatment caused a greater reduction of tumor growth than either agent alone and an increase in apoptosis of tumor cells compared to control antibody or paclitaxel alone These data were consistent with the results from the limiting dilution assay experiments that demonstrated a significant reduction of tumor initiating cells by the anti-DLL4 alone (1:15) and a further decrease in combination with paclitaxel (1:33) compared to the control antibody (1:5), but no effect by paclitaxel (1:5). In other studies aimed to examine tumor recurrence after excision of the primary tumors, treatment with anti-DLL4, alone and with paclitaxel, prevented recurrence of the primary tumors. In contrast, paclitaxel alone increased the frequency of tumor relapse when compared to the control and other treatments. In addition, anti-DLL4 alone inhibited metastases to lungs, lymph nodes, liver, brain and intestines and this effect was further enhanced by the combination with paclitaxel in the liver and intestines. The results from these studies demonstrate for the first time a significant inhibition of tumor recurrence and metastases in human melanoma by anti-DLL4 and establish a link between reduction of CSC frequency and the concurrent inhibition of metastases. Therefore our findings reveal great potential of our anti-DLL4 antibody as an effective anti-cancer therapy for melanoma patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2834. doi:10.1158/1538-7445.AM2011-2834
Register-based study of the incidence, comorbidities and demographics of obsessive-compulsive disorder in specialist healthcare (2017)

These findings suggest that incidence of treated OCD in specialist healthcare has increased. The reason may be increased awareness and rate of referrals but a true increase cannot be ruled out. Further research on risk factors of OCD is warranted.
Inhibition of procollagen C‐proteinase reduces scar hypertrophy in a rabbit model of cutaneous scarring (2006)

Hypertrophic scarring, which results from excessive collagen deposition at sites of dermal wound repair, can be functionally and cosmetically debilitating to the surgical patient. Pharmacological regulation of collagen synthesis and deposition is a direct approach to the control of scar tissue formation. One of the key steps in collagen stabilization is the cleavage of the C-terminal propeptide from the precursor molecule to form collagen fibrils, a reaction catalyzed by procollagen C-proteinase (PCP). We tested the ability of a PCP inhibitor to reduce hypertrophic scar formation in a rabbit ear model. After the placement of four, 7-mm dermal wounds on each ear, New Zealand white rabbits received PCP inhibitor subcutaneously in the left ear at four time points postwounding: days 7, 9, 11, 13 (early treatment; n=20 wounds) or days 11, 13, 15, 17 (late treatment; n=20 wounds). The right ear of each animal served as a control (vehicle alone). Wounds were harvested on postoperative day 28 and scar hypertrophy quantified by measurement of the scar elevation index. Early treatment of wounds with PCP inhibitor did not reduce scar formation compared with controls (p>0.05). However, late treatment resulted in a statistically significant reduction in the scar elevation index (p<0.01). Our results point not only to the potential use of PCP inhibitors to mitigate hypertrophic scarring but also to the temporal importance of drug delivery for antiscarring therapy.