gebhart/patrepeval huggingface dataset:
Pneumonia Caused by Methicillin‐ResistantStaphylococcus aureus (2008)

A recent increase in staphylococcal infections caused by methicillin-resistant Staphylococcus aureus (MRSA), combined with frequent, prolonged ventilatory support of an aging, often chronically ill population, has resulted in a large increase in cases of MRSA pneumonia in the health care setting. In addition, community-acquired MRSA pneumonia has become more prevalent. This type of pneumonia historically affects younger patients, follows infection with influenza virus, and is often severe, requiring hospitalization and causing the death of a significant proportion of those affected. Ultimately, hospital-acquired MRSA and community-acquired MRSA are important causes of pneumonia and present diagnostic and therapeutic challenges. Rapid institution of appropriate antibiotic therapy, including linezolid as an alternative to vancomycin, is crucial. Respiratory infection-control measures and de-escalation of initial broad-spectrum antibiotic regimens to avoid emergence of resistant organisms are also important. This article reviews the clinical features of, diagnosis of, and therapies for MRSA pneumonia.
Typing of Enterococcus species by DNA restriction fragment analysis (1992)

Enterococci are a frequent cause of hospital-acquired infection, being associated with urinary tract infections, wound sepsis, bacteremia, and endocarditis. The source of infection is usually thought to be endogenous, but some evidence points to cross-infection between patients. A better understanding of the epidemiology of enterococci has been limited by the lack of a good discriminatory typing system. This report describes the application of two DNA-based typing methods to Enterococcus faecalis and Enterococcus faecium: comparison of restriction fragments from total DNA by conventional electrophoresis and comparison of restriction fragments hybridizing to an rRNA gene probe (ribotyping). Comparison of restriction fragments (from SstI digestion) by conventional electrophoresis was simple and highly discriminatory. The results of analysis of blood culture isolates and of repeat isolates from individual patients are reported. Ribotyping (with BscI digestion) was more applicable at the level of species discrimination.
Wireless Communications in the 21st Century (2002)

Bringing together the best recent articles from the foremost IEEE publications, this book features contributions from leading communications experts, who discuss current and future developments in wireless technology. Major topics covered include wireless standards, radio channel propagation, modulations and coding issues pertinent to the physical layer, spatial and temporal signal processing, IM 2000 radio systems, new packet radio systems, and wireless ATM.
Predicting Initial Claims for Unemployment Benefits (2009)

One of the strongest leading indicators of economic activity is the number of people who file for unemployment benefits. Macroeconomists Robert Gordon and James Hamilton have recently examined the historical evidence. According to Hamilton's summary: ... in each of the last six recessions, the recovery began within 8 weeks of the peak in new unemployment claims.In an earlier blog post, we suggested that Google Trends/Search Insights data could be useful in short term predictions of economic variables. Given the importance of initial claims as a macroeconomic predictor, we thought it would be useful to try to forecast this economic metric. The initial claims data is available from the Department of Labor, while the Google Trends data for relevant categories is available here.We applied the methodology outlined in our earlier paper, building a model to forecast initial claims using the past values of the time series, and then added the Google Trends variables to see how much they improved the forecast. We found a 15.74% reduction in mean absolute error for one-week ahead out, of sample forecasts. Most economists would consider this to be a significant boost. Details of our analysis may be found in this paper. The bottom line is that initial claims have been generally declining from their peak and that, so far at least, the Google query data is forecasting further short term declines. It would be good news indeed if this particular Google trend continues.
Manipulating Charges and Excitons within a Single‐Host System to Accomplish Efficiency/CRI/Color‐Stability Trade‐off for High‐Performance OWLEDs (2009)

To reveal superior efficiency/CRI/color-stability trade-off for OWLED fabrications, a single-host concept is proposed in which the primary-color emitters are rationally arranged to render two types (R–G–B and RG–B) of OWLEDs with ultrahigh electroluminescence performance. Comprehensive experimental and theoretical evidence reveal that careful management of charges and excitons is the key to the realization of such high performances. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Effectiveness of Essential Oils and Their Combinations with Aluminum Starch Octenylsuccinate on Potato Storage Pathogens (2013)

S-carvone, L-menthone, peppermint and spearmint oils were tested in vitro against Fusarium coeruleum, F. sambucinum, F. avenaceum, F. oxysporum, Alternaria solani, Rhizoctonia solani, Helminthosporium solani, Phytophthora infestans (A1 and A2 mating types), Phytophthora erythroseptica, Phoma exigua and Pythium ultimum which are causal agents of major potato storage diseases. The majority of these pathogens were completely inhibited due to pure oils, although F. sambucinum, F. avenaceum, A. solani and P. exigua were not completely inhibited by one or more pure oils. Peppermint oil was the least effective among tested oils. However, R. solani, H. solani, P. erythroseptica, and P. infestans (A1 and A2 mating types) were completely inhibited for a period of 1-18 weeks by single treatments of all four pure oils. Effects of mixtures of aluminum starch octenylsuccinate (ASOS) and L-menthol or peppermint oil on F. sambucinum and R. solani were also tested in vitro for a period of over 5 weeks. Percent inhibition of F. sambucinum by single application of mixtures of ASOS and L-menthol or peppermint oil decreased over 11-13 days after treatment, while the mixtures at the same rates consistently inhibited the growth of R. solani for over 15 days. Mixtures of 10 g of ASOS and 4 g or 8 g doses of essential oils were the most effective in inhibiting pathogens growth for periods over 13 or 20 days, respectively. The antifungal effects of essential oils and their components against all tested pathogens suggest their potential use as alternative tools for controlling potato storage diseases.
Blind restoration method of scanning tunneling and atomic force microscopy images (1996)

In the nanometer resolution range, image formation in scanning tunneling microscopy and atomic force microscopy is essentially governed by the geometrical interaction between the specimen surface and the tip surface. This nonlinear process can be described by using the tools of mathematical morphology. In principle, if the tip shape is precisely known, an image restoration can be performed. In this article, the capabilities of a blind restoration procedure which needs neither a precise knowledge of the tip shape nor the use of a known test object are presented. The efficiency of the blind restoration is demonstrated on an experimental atomic force microscopy image of a DNA molecule obtained in the ‘‘tapping mode’’.
The hydrophobic surface of colipase influences lipase activity at an oil–water interface (1998)

The interaction of pancreatic triglyceride lipase and colipase at an oil-water interface is required for efficient digestion of dietary fats and provides a model system for the interaction of proteins at biological membranes. Colipase has two important surfaces, a hydrophilic surface that interacts with lipase and a hydrophobic surface that presumably interacts with substrate. To begin our investigations into the role of the hydrophobic surface in the function of colipase, we replaced three neighboring tyrosine residues at positions 55, 58, and 59 in the hydrophobic surface with aspartic acid. Two of the three residues, Tyr55 and Tyr59, influenced the activity of colipase. Introducing aspartic acid at either position decreased the activity with long-chain triglycerides, but not with a short-chain triglyceride. Decreased ability of the mutants to anchor lipase to long-chain triglycerides did not explain the altered activity of the mutants. A mutant containing aspartic acid at positions 55 and 59 had no activity with any substrate and did not anchor lipase to either short- or long-chain triglycerides. These results identify the two tyrosine residues that interact with substrate and suggest that the hydrophobicity of the surface containing these tyrosines influences colipase function and the substrate selectivity of pancreatic triglyceride lipase.
Subcellular localization of a sporulation membrane protein is achieved through a network of interactions along and across the septum (2005)

Summary During the process of spore formation in Bacillus subtilis many membrane proteins localize to the sporulation septum where they play key roles in morphogenesis and cell‐cell signalling. However, the mechanism by which these proteins are anchored at this site is not understood. In this report we have defined the localization requirements for the mother‐cell membrane protein SpoIVFA, which anchors a signalling complex in the septal membrane on the mother cell side. We have identified five proteins (SpoIID, SpoIIP, SpoIIM, BofA and SpoIIIAH) synthesized in the mother cell under the control of σ E and one protein (SpoIIQ) synthesized in the forespore under the control of σ F that are all required for the proper localization of SpoIVFA. Surprisingly, these proteins appear to have complementary and overlapping anchoring roles suggesting that SpoIVFA is localized in the septal membrane through a web of protein interactions. Furthermore, we demonstrate a direct biochemical interaction between the extracellular domains of two of the proteins required to anchor SpoIVFA: the forespore protein SpoIIQ and the mother‐cell protein SpoIIIAH. This result supports the idea that the web of interactions that anchors SpoIVFA is itself held in the septal membrane through a zipper‐like interaction across the sporulation septum. Importantly, our results suggest that a second mechanism independent of forespore proteins participates in anchoring SpoIVFA. Finally, we show that the dynamic localization of SpoIIQ in the forespore is impaired in the absence of SpoIVFA but not SpoIIIAH. Thus, a complex web of interactions among mother cell and forespore proteins is responsible for static and dynamic protein localization in both compartments of the sporangium. We envision that this proposed network is involved in anchoring other sporulation proteins in the septum and that protein networks with overlapping anchoring capacity is a feature of protein localization in all bacteria.
Stimulation of T cells by antigen-presenting cells is kinetically controlled by antigenic peptide binding to major histocompatibility complex class II molecules. (1995)

Activation of CD4+ T cells by antigenic peptide involves the interaction of major histocompatibility complex (MHC) class II-peptide complexes on the surface of antigen-presenting cells (APCs) with T-cell receptors. This report describes the kinetics of T-cell triggering by exogenous antigenic peptides in the presence of APCs. A rapid specific increase in extracellular acidification rate is observed within minutes upon exposure of A.E7 T cells (restricted for IEk and moth cytochrome c peptide containing residues 88-103) and 4R3.9 T cells (restricted for IAk and myelin basic protein peptide containing residues 1-14 [AcMBP-(1-14)]) to their cognate peptides in the presence of CH27 cells bearing both IAk and IEk MHC class II molecules. Pretreatment of cloned T cells, but not APCs, with herbimycin A resulted in complete inhibition of triggering events, indicating that the acidification response is mediated by T-cell second messenger pathways. This rapid assay for 4R3.9 T-cell stimulation showed increased T-cell triggering activity for AcMBP-(1-14)-A4 and MBP-(1-14)-M4 peptides compared to the native AcMBP-(1-14)-K4. By using the previously determined kinetic constants for MBP-(1-14)-A4 reactions with IAk, it is possible to show that at the lowest peptide concentrations the kinetics of T-cell triggering are limited by the kinetics of the peptide binding to MHC class II molecules.
Stereoselective Synthesis of 1,2-cis-N-Glycosides by the N-Bromosuccinimide Promoted Reaction of Thioglycosides with Silylated Pyrimidme Bases (1993)

Abstract The coupling of O-benzylated 1-thioglycosides, derived from d-glucose, d-mannose, d-ribose, d-xylose, and d-arabinose, with silylated pyrimidme bases by activation with N-bromosuccinimide uniformly afforded the corresponding 1,2-cis-N-glycosides with good selectivity.
Only site-directed antibodies reactive with the highly conserved src-homologous region of the v-abl protein neutralize kinase activity (1984)

Antisera specific for six regions of the v- abl protein were used to serologically characterize the Abelson murine leukemia virus tyrosine kinase. Chemically synthesized peptides corresponding to the predicted v- abl protein sequence and larger regions of the v- abl protein expressed as fusion proteins in bacteria were used as immunogens. The specificity of each antiserum was confirmed by immunoprecipitation analysis with defined deletion mutants of Abelson murine leukemia virus. Several of these v- abl -specific antisera display much higher titers and avidities than serum harvested from mice bearing Abelson murine leukemia virus-induced tumors, previously the only source of anti- abl -specific serum. Two antisera were found to block the in vitro autophosphorylation of the v- abl protein as well as its ability to phosphorylate a peptide substrate. Examination of the sites against which the kinase-blocking antisera were prepared revealed that both are in close proximity to the in vivo sites of tyrosine phosphorylation, which fall within the region of high homology with v-src and other tyrosine kinases. Antisera directed against other regions of v- abl did not inhibit kinase activity.
Cancer of the Pancreas: Are we Making Progress? A Review of Studies in the US Oncology Research Network (2008)

Despite aggressive efforts to improve treatment for patients with pancreatic cancer, limited progress has been made. It is hoped that new studies being planned and conducted will improve outcomes for patients with this disease.
Quantification of p53 protein in tumor cell lines, breast tissue extracts and serum with time-resolved immunofluorometry. (1993)

We have developed a highly sensitive time-resolved immunofluorometric procedure for quantifying mutant or wild-type, human or murine, p53 protein. The method uses monoclonal PAb240 or PAb421 antibodies for capture and a polyclonal rabbit antibody for detection. The final immunocomplex is quantified with an alkaline phosphatase substrate which, when hydrolyzed by the enzyme, forms highly fluorescent long-lived complexes with Tb(3+)-EDTA. The detection limit is approximately 1 pg of protein per assay. The assay was applied for the quantification of p53 protein in lysates from 23 cell lines and overproducers of mutant protein were identified. Eight hundred cancer patients sera tested negative for the presence of p53. We have also applied the quantitative immunofluorometric procedure for measuring mutant p53 protein in breast tumor extracts specifically prepared for steroid hormone receptor analysis. Sixty-four out of the 264 extracts (24%) were positive for p53. Significant negative correlations between levels of p53 and steroid hormone receptors were found. The proposed analytical methodology simplifies the assessment of p53 status in tumor extracts, has many advantages over immunohistochemical techniques and is proposed as a method of choice for routine clinical use and other investigations involving p53.
Germanium on double-SOI photodetectors for 1550-nm operation (2004)

We have fabricated and characterized the first resonant cavity enhanced (RCE) germanium photodetectors on double silicon-on-insulator substrates (Ge/DSOI) for operation around the 1550 nm communication wavelength. The Ge layer is grown through a novel two-step UHV/CVD process, while the underlying double-SOI substrate is formed through an ion-cut process. Absorption measurements of an undoped Ge-on-Si (Ge/Si) structure reveal a red-shift of the Ge absorption edge in the NIR, due primarily to a strain-induced bandgap narrowing within the Ge film. By using the strained-Ge absorption coefficients extracted from the absorption measurements, in conjunction with the known properties of the DSOI substrate, we were able to design strained-Ge/DSOI photodetectors optimized for 1550 nm operation. We predict a quantum efficiency of 76% at 1550 nm for a Ge layer thickness of only 860 nm as a result of both strain-induced and resonant cavity enhancement, compared to 2.3% for the same unstrained Ge thickness in a single-pass configuration. We also estimate a transit-time limited bandwidth of 28 GHz. Although the fabricated Ge/DSOI photodetectors were not optimized for 1550 nm operation, we were able to demonstrate an over four-fold improvement in the quantum efficiency, compared to its single-pass counterpart.
The Selective SGLT2 Inhibitor Ipragliflozin Has a Therapeutic Effect on Nonalcoholic Steatohepatitis in Mice (2016)

Ipragliflozin improved the pathogenesis of NASH by reducing insulin resistance and lipotoxicity in NASH-model mice. Our results suggest that ipragliflozin has a therapeutic effect on NASH with T2DM.
Dendritic cells: biology of the skin (2009)

Allergic contact dermatitis results from a T-cell-mediated, delayed-type hypersensitivity immune response induced by allergens. Skin dendritic cells (DCs) play a central role in the initiation of allergic skin responses. Following encounter with an allergen, DCs become activated and undergo maturation and differentiate into immunostimulatory DCs and are able to present antigens effectively to T cells. The frequency of allergic skin disorders has increased in the past decades. Therefore, the identification of potential sensitizing chemicals is important for skin safety. Traditionally, predictive testing for allergenicity has been conducted in animal models. For regulatory reasons, animal use for sensitization testing of compounds for cosmetic purposes is shortly to be prohibited in Europe. Therefore, new non-animal-based test methods need to be developed. Several DC-based assays have been described to discriminate allergens from irritants. Unfortunately, current in vitro methods are not sufficiently resilient to identify allergens and therefore need refinement. Here, we review the immunobiology of skin DCs (Langerhans' cells and dermal dendritic cells) and their role in allergic and irritant contact dermatitis and then explore the possible use of DC-based models for discriminating between allergens and irritants.
Evaluation of the Platelet Mapping™ Assay on rotational thromboelastometry ROTEM® (2009)

Rotational thromboelastometry ROTEM is available as point-of-care coagulation monitoring in an increasing number of European operating theatres and emergency rooms. The Platelet Mapping Assay has been described as a platelet aggregation assay for thromboelastography TEG. The aim of this experimental trial was to evaluate feasibility of the Platelet Mapping Assay on the ROTEM test system. Whole blood was drawn from 22 adult volunteers and patients with and without antiplatelet medication. Platelet aggregability was determined in three whole blood assays: the Platelet Mapping Assay using both activators arachidonic acid (AA) and adenosine diphosphate (ADP) on TEG, its adapted version on ROTEM, and the multiple electrode impedance aggregometer Multiplate. Percent aggregation inhibition results were plotted in a linear regression analysis and correlation was estimated. Sensitivity and specificity for detecting antiplatelet medication were determined. Overall correlations were statistically significant with an r(2) = 0.83 in AA-activated and an r(2) = 0.82 in ADP-activated Platelet Mapping Assay. AA-activated tests and the Multiplate analysis identified aspirin-inhibition in 86% and 100%, respectively. ADP-activated tests and the Multiplate analysis identified clopidogrel-inhibition in 67% and 89%, respectively. Specificity was low both in ROTEM and TEG. Differences in frequency distribution between the results obtained in ROTEM and TEG were not statistically significant. The Platelet Mapping Assay can be performed on the ROTEM. For the perioperative scenario, however, longer test duration and higher costs have to be considered compared to Multiplate analyses.
The Fourth Epidermal Growth Factor-like Domain of Thrombomodulin Interacts with the Basic Exosite of Protein C (2003)

Thrombomodulin (TM) functions as a cofactor to enhance the rate of protein C activation by thrombin approximately 1000-fold. The molecular mechanism by which TM improves the catalytic efficiency of thrombin toward protein C is not known. Molecular modeling of the protein C activation based on the crystal structure of thrombin in complex with the epidermal growth factor-like domains 4, 5, and 6 of TM (TM456) predicts that the binding of TM56 to exosite 1 of thrombin positions TM4 so that a negatively charged region on this domain juxtaposes a positively charged region of protein C. It has been hypothesized that electrostatic interactions between these oppositely charged residues of TM4 and protein C facilitate a proper docking of the substrate into the catalytic pocket of thrombin. To test this hypothesis, we have constructed several mutants of TM456 and protein C in which charges of the putative interacting residues on both TM4 (Asp/Glu) and protein C (Lys/Arg) have been reversed. Results of TM-dependent protein C activation studies by such a compensatory mutagenesis approach support the molecular model that TM4 interacts with the basic exosite of protein C.
ACE2, an activator of yeast metallothionein expression which is homologous to SWI5. (1991)

Transcription of the Saccharomyces cerevisiae metallothionein gene CUP1 is induced in response to high environmental levels of copper. Induction requires the ACE1 gene product, which binds to specific sites in the promoter region of the CUP1 gene. In this study, we found that deleting the entire coding sequence of the ACE1 gene resulted in a decrease in basal-level transcription of CUP1 to low but detectable levels and conferred a copper-sensitive phenotype to the cells. We have isolated a gene, designated ACE2, which when present on a high-copy-number plasmid suppresses the copper-sensitive phenotype of an ace1-deletion strain. The presence of multiple copies of the ACE2 gene enhanced expression of an unlinked CUP1-lacZ fusion integrated in the yeast genome and resulted in an increase in the steady-state levels of CUP1 mRNA in an ace1-deletion background. A large deletion of the coding region of the genomic copy of ACE2 resulted in a decrease in steady-state levels of CUP1 mRNA, indicating that ACE2 plays a role in regulating basal-level expression of CUP1. The ACE2 open reading frame encodes a polypeptide of 770 amino acids, with putative zinc finger structures near the carboxyl terminus. This protein is 37% identical to the SWI5 gene product, an activator of HO gene transcription in S. cerevisiae, suggesting that ACE2 and SWI5 may have functional similarities.