gebhart/patrepeval huggingface dataset:
Structural implications for the role of the N terminus in the ‘superactivation’ of collagenases (1994)

For the collagenases PMNL-CL and FIB-CL, the presence of the N-terminal Phe79 correlates with an increase in proteolytic activity. We have determined the X-ray crystal structure of the recombinant Phe79-Gly242 catalytic domain of human neutrophil collagenase (PMNL-CL, MMP-8) using the recently solved model of the Met80-Gly242 form for phasing and subsequently refined it to a final crystallographic R-factor of 18.0% at 2.5 A resolution. The PMNL-CL catalytic domain is a spherical molecule with a flat active site cleft separating a smaller C-terminal subdomain from a bigger N-terminal domain, that harbours two zinc ions, namely a 'structural' and a 'catalytic' zinc, and two calcium ions. The N-terminal segment prior to Pro86, which is disordered in the Met80-Gly242 form, packs against a concave hydrophobic surface made by the C-terminal helix. The N-terminal Phe79 ammonium group makes a salt link with the side chain carboxylate group of the strictly conserved Asp232. Stabilization of the catalytic site might be conferred via strong hydrogen bonds made by the adjacent, likewise strictly conserved Asp233 with the characteristic 'Met-turn', which forms the base of the active site residues.
Nominaties Nationale Renovatie Prijs 1999 (1999)

Jaren achtereen winnen naoorlogse projecten de Nationale Renovatie Prijs (NPR) in de categorie woningbouw renovatie en dan is er ineens een duidelijke trendbreuk. Alsof de jury een maatschappelijk getinte boodschap wil overbrengen: schenk meer aandacht aan met sloop bedreigde vooroorlogse wijken. Uit het grote aantal inzendingen in vier categorieën koos de jury dit jaar in totaal dertien nominaties. Geen verbazing wekt dat daar, in de categorie Utiliteitsbouw Overige, de Witte Dame in Eindhoven bij zit. De nieuwe categorie wordt nu al een succes genoemd.
Preparation and characterization of soy protein plastics plasticized with waterborne polyurethane (2004)

Abstract Utilizing anionic waterborne polyurethane (WPU) as a plasticizer, for the first time, we prepared new soy protein isolate (SPI) plastics. The WPU was prepared by using the emulsion‐extending‐chain method, and mixed with soy protein in aqueous dispersion. The mixture was cast, cured, pickled and hot‐pressed to form SPI plastics plasticized with WPU. The plastics sheets were characterized by infrared spectroscopy, scanning electron microscopy, ultraviolet spectrophotometry and wide‐angle X‐ray diffraction, and their properties were measured by using dynamic mechanical analysis, differential scanning calorimetry and tensile testing. The results revealed that SPI plastics plasticized with WPU possess good mechanical properties, such as a tensile strength (σ b ) of 7–19 MPa, water resistance (σ b(wet) /σ b(dry) = 0.4–0.5), optical transmittance and thermal stability, because of the good miscibility and strong interaction between WPU and SPI. With an increase of WPU content from 20 to 50 wt%, the elongation at break (ε b ) value of the sheets increased from 50 up to 150 %, and is much higher than that of the pure SPI sheet. WPU as a plasticizer can play an important role in improving the properties of SPI plastics. Copyright © 2004 Society of Chemical Industry
Continuous Glucose Monitoring by Means of Fiber-Based, Mid-Infrared Laser Spectroscopy (2006)

The application of mid-infrared laser spectroscopy to the reagent-free quantification of the concentration of glucose was investigated using cryogenically cooled lead salt lasers or, alternatively, quantum cascade lasers operating at room temperature. The concentration of glucose in aqueous solutions was quantified by means of fiber-based attenuated total reflection (ATR) spectroscopy (fiber-optical evanescent field analysis, FEFA) as well as fiber-based transmission spectroscopy. Both methods have the potential to be utilized by small fiber sensors, which can be inserted into the subcutaneous tissue in order to continuously measure the local concentration of glucose. In our in vitro experiments, noise-equivalent concentrations as low as 10 mg/dL were achieved. The mid-term stability of the measurement schemes was investigated by means of Allan variance analysis. Based on the research presented in this manuscript, an all-room-temperature measurement scheme using quantum cascade lasers, miniaturized fiber-optic sensors, and pyroelectric detectors appears well suited for the continuous monitoring of glucose concentrations at physiological levels.
Multicenter study of radiosensitizing gemcitabine combined with fractionated radioimmunotherapy for repeated treatment cycles in advanced pancreatic cancer (2009)

4620 Background: In a phase I study, a single dose of 90 Y-labeled anti-mucin humanized antibody, hPAM4 ( 90 Y-hPAM4), led to several transient reductions or stabilization of lesions in advanced pancreatic cancer, with bone marrow toxicity limiting the maximum tolerated dose to 20 mCi/m 2 . Preclinical studies showed gemcitabine enhanced radioimmunotherapy, so a phase Ib study was undertaken to evaluate repeated treatment cycles of 90 Y-hPAM4 plus gemcitabine. Methods: Patients (pts) with previously untreated, locally advanced or metastatic, pancreatic cancer were treated in 4-week cycles (200 mg/m 2 gemcitabine once-weekly; 111 In-hPAM4 the 1 st wk for imaging, biodistribution, and dosimetry; 90 Y-hPAM4 once-weekly the last 3 wks), which could be repeated in the absence of progression or unacceptable toxicity. The 90 Y-dose was escalated by patient cohort following a 3+3 design, with tumor responses assessed by CT and FDG/PET imaging, and by CA19.9 serum levels. Results: Eight pts (3F/5M, 56–72 years old, 7 with metastatic disease) have now been treated at the first 2 dose levels (6.5 and 9.0 mCi/m 2 90 Y-hPAM4 x 3) with hematologic toxicity all transient Grade 1–2 (NCI CTC v3). 111 In-hPAM4 imaging showed normal biodistribution, evidence of tumor targeting and acceptable dosimetry estimates to normal organs per treatment cycle. Two pts had tumor responses to initial treatment with significant decreases in FDG metabolic activity on PET imaging, regression of lesion sizes on CT, and CA19.9 decreases. Both pts continue in excellent performance status now at 9 and 11 months after study entry, after receiving a total of 3 and 4 treatment cycles, respectively, without additional toxicity. A 3 rd pt with a stable response by PET and CT 4 weeks after initial treatment and decreases in CA19.9 levels is now undergoing a 2 nd treatment cycle. Four other pts had early progression of disease by or before post-treatment week-4 evaluation, and the remaining pt is still being evaluated. Conclusions: Dose escalation is continuing after fractionated radioimmunotherapy with 90 Y-hPAM4 plus low-dose gemcitabine demonstrated therapeutic activity at the first two 90 Y dose levels, with minimal hematologic toxicity, even after 4 treatment cycles. [Table: see text]
Protein microarrays: Molecular profiling technologies for clinical specimens (2003)

Proteomics, the study of protein function within biologic systems, will further our understanding of cancer pathogenesis. Coupled with transcript profiling, proteomics can herald the advent of molecular therapy tailored to the individual patient's neoplasm. Protein microarrays, one emerging class of proteomic technologies, have broad applications for discovery and quantitative analysis. This technology is uniquely suited to gather information about the post-translational modifications of proteins reflecting the activity state of signal pathways and networks. Protein microarrays now make it feasible to conduct signal network profiling within cellular samples. Nevertheless, to be successful, design and use of protein microarrays must take into consideration enormous analytical challenges. A subclass of protein microarrays, Reverse Phase Arrays, created to meet these challenges, has been optimized for use with tissue specimens, and is now in use for the analysis of biopsy samples for clinical trial research.
UniRef: comprehensive and non-redundant UniProt reference clusters (2007)

Supplementary data are available at Bioinformatics online.
Epicardial Mapping: How to Measure Local Activation? (1990)

(1) Maximal amplitude of the bipolar electrogram coincided with maximal negative slope of the unipolar electrogram; (2) Using onset of the bipolar electrogram, timing and location of earliest epicardial activation may be misinterpreted.
Incidence and Prognosis of Resistant Hypertension in Hypertensive Patients (2012)

Among patients with incident hypertension in whom treatment was begun, 1 in 50 patients developed resistant hypertension. Patients with resistant hypertension had an increased risk of cardiovascular events, which supports the need for greater efforts toward improving hypertension outcomes in this population.
Multimodal information seeking dialogues on the world wide web (1999)

We have developed the Halpin system to implement our multimodal conversational model for information retrieval. This dialogue-oriented interface allows the access to a digital library database, on the internet, in a natural language way, and gives its oral responses via usual browsers. The results of the first experiments show that the Halpin system provides some interesting dialogues (in particular with the beginners), according to the user's goals and skills, that leads to information retrieval success, while searches with the original user interface (traditional web form) failed.
Detection of protein–protein interactions in plants using bimolecular fluorescence complementation (2004)

Protein function is often mediated via formation of stable or transient complexes. Here we report the determination of protein-protein interactions in plants using bimolecular fluorescence complementation (BiFC). The yellow fluorescent protein (YFP) was split into two non-overlapping N-terminal (YN) and C-terminal (YC) fragments. Each fragment was cloned in-frame to a gene of interest, enabling expression of fusion proteins. To demonstrate the feasibility of BiFC in plants, two pairs of interacting proteins were utilized: (i) the alpha and beta subunits of the Arabidopsis protein farnesyltransferase (PFT), and (ii) the polycomb proteins, FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) and MEDEA (MEA). Members of each protein pair were transiently co-expressed in leaf epidermal cells of Nicotiana benthamiana or Arabidopsis. Reconstitution of a fluorescing YFP chromophore occurred only when the inquest proteins interacted. No fluorescence was detected following co-expression of free non-fused YN and YC or non-interacting protein pairs. Yellow fluorescence was detected in the cytoplasm of cells that expressed PFT alpha and beta subunits, or in nuclei and cytoplasm of cells that expressed FIE and MEA. In vivo measurements of fluorescence spectra emitted from reconstituted YFPs were identical to that of a non-split YFP, confirming reconstitution of the chromophore. Expression of the inquest proteins was verified by immunoblot analysis using monoclonal antibodies directed against tags within the hybrid proteins. In addition, protein interactions were confirmed by immunoprecipitations. These results demonstrate that plant BiFC is a simple, reliable and relatively fast method for determining protein-protein interactions in plants.
Regulation of Flowering in Arabidopsis by anFLCHomologue (2001)

The Arabidopsis FLC gene encodes a MADS domain protein that acts as a repressor of flowering. Late-flowering vernalization-responsive ecotypes and mutants have high steady-state levels of FLC transcript, which decrease during the promotion of flowering by vernalization. Therefore, FLC has a central role in regulating the response to vernalization. We have isolated an Arabidopsis gene, MAF1, which encodes a protein that is closely related to FLC. Overexpression studies demonstrate that MAF1 produces comparable effects to FLC, and likely has a similar function in the regulation of flowering. In contrast to FLC, however, MAF1 expression shows a less clear correlation with the vernalization response. In addition, MAF1 overexpression does not influence FLC transcript levels. Thus, MAF1 likely acts downstream or independently of FLC transcription. We further report identification of a cluster of four additional FLC-like genes in the Arabidopsis genome.
Synthetic Peptide Immunoassay Distinguishes HIV Type 1 and HIV Type 2 Infections (1987)

Efforts to solve the epidemiologic puzzle of AIDS in Africa are complicated by the presence of multiple human retroviruses. Simple serologic tests that unambiguously distinguish among infections by these retroviruses are essential. To that end, a partially conserved immunoreactive epitope was identified in the transmembrane glycoproteins of human immunodeficiency viruses (HIV) types 1 and 2. Synthetic peptides derived from these conserved domains were used in sensitive and specific immunoassays that detect antibodies in sera from patients infected with HIV-1 or HIV-2. By making single amino acid substitutions in the HIV-1 peptide, it was possible to demonstrate HIV-1 strain-specific antibody responses to this epitope. Such custom-designed peptides synthesized from this domain are likely to detect newly discovered HIV types, define infection with specific HIV strains, and allow detection of group-common antibodies.
Renewed interest in a difficult disease: Clostridium difficile infections – epidemiology and current treatment strategies (2008)

After being considered a manageable pathogen for decades, C. difficile recently caused large outbreaks of severe disease. Refocused research is determining patients who are at risk for CDI, what methods are more effective in diagnosing CDI and what new treatments may be effective. This article reviews the recent findings in the literature regarding this difficult and challenging pathogen.
Hierarchical Attention Transfer Network for Cross-Domain Sentiment Classification (2018)

Cross-domain sentiment classification aims to leverage useful information in a source domain to help do sentiment classification in a target domain that has no or little supervised information. Existing cross-domain sentiment classification methods cannot automatically capture non-pivots, i.e., the domain-specific sentiment words, and pivots, i.e., the domain-shared sentiment words, simultaneously. In order to solve this problem, we propose a Hierarchical Attention Transfer Network (HATN) for cross-domain sentiment classification. The proposed HATN provides a hierarchical attention transfer mechanism which can transfer attentions for emotions across domains by automatically capturing pivots and non-pivots. Besides, the hierarchy of the attention mechanism mirrors the hierarchical structure of documents, which can help locate the pivots and non-pivots better. The proposed HATN consists of two hierarchical attention networks, with one named P-net aiming to find the pivots and the other named NP-net aligning the non-pivots by using the pivots as a bridge. Specifically, P-net firstly conducts individual attention learning to provide positive and negative pivots for NP-net. Then, P-net and NP-net conduct joint attention learning such that the HATN can simultaneously capture pivots and non-pivots and realize transferring attentions for emotions across domains. Experiments on the Amazon review dataset demonstrate the effectiveness of HATN.
A New 1T DRAM Cell With Enhanced Floating Body Ef (2006)

Recently the semiconductor industry tends to develop a smaller volume device and system with lower power consumption, lower leakage current, and high speed performance. SOI technology has many unique characteristics, which is one of the most promising methods to the direction. As the semiconductor memory is concerned, the 1T-DRAM cell realized by the concept of floating body effect in a PD-SOI nMOSFET can allow the DRAM cell to be scaled down in depth with less area occupied. In this paper, we propose a new structure of 1T-DRAM cell, which has bottom buried oxide with the sidewall block oxide around its body, which can suppress the leakage current between the S/D and the body of the cell. In addition it can also improve the programming window of the 1T-DRAM cell more than 39% by utilizing its own structural characteristic
Prognostic impact of urokinase, urokinase receptor, and type 1 plasminogen activator inhibitor in squamous and large cell lung cancer tissue. (1994)

We have studied the prognostic value of urokinase-type plasminogen activator (uPA), uPA receptor (uPAR), and type 1 plasminogen activator inhibitor (PAI-1) in tumor extracts from 84 patients with squamous cell lung carcinoma and 38 patients with large cell lung carcinoma, measuring each molecule with sandwich enzyme-linked immunosorbent assays. High uPAR levels were significantly associated with short overall survival in patients with squamous cell lung carcinomas when the median value was used as a cutoff point (P = 0.038), while no statistically significant prognostic impact of uPA and PAI-1 levels was found in this group of patients. The combination of high uPAR and high PAI-1 levels did, however, have a particular significant association with short overall survival (P = 0.008). None of the 3 components was found to have a statistically significant prognostic impact in the group of 38 large cell lung cancer patients. There was a positive correlation between uPAR and PAI-1 levels in both groups and between uPA and uPAR levels in the large cell carcinoma patients. In a multivariate analysis, high uPAR was found to be an independent prognostic variable in squamous cell carcinoma patients, with a relative risk of 2.1 (95% confidence interval, 1.1-4.0) and tumor size the only other significant prognostic parameter. These data suggest that uPAR is an important prognostic factor in squamous cell lung carcinoma. In addition to the potential direct clinical usefulness, this information could be helpful in understanding the biology of this disease and developing new therapeutic approaches.
Psychedelics in the treatment of unipolar mood disorders: a systematic review (2016)

Unipolar mood disorders, including major depressive disorder and persistent depressive disorder (dysthymia), confer high rates of disability and mortality and a very high socioeconomic burden. Current treatment is suboptimal in most cases and there is little of note in the pharmaceutical development pipeline. The psychedelic drugs, including lysergic acid diethylamide and psilocybin, were used extensively in the treatment of mood disorders, and other psychiatric conditions, before their prohibition in the late 1960s. They are relatively safe when used in medically controlled environments, with no reported risk of dependence. Here, we present a systematic review of published clinical treatment studies using psychedelics in patients with broadly defined UMD, and consider their place in psychiatry. Whilst all of the included studies have methodological shortcomings, of 423 individuals in 19 studies, 335 (79.2%) showed clinician-judged improvement after treatment with psychedelics. A recently completed pilot study in the UK favours the use of psilocybin with psychological support in treatment resistant depressive disorder. The evidence overall strongly suggests that psychedelics should be re-examined in modern clinical trials for their use in unipolar mood disorders and other non-psychotic mental health conditions.
Glycosylation Motifs That Direct Arabinogalactan Addition to Arabinogalactan-Proteins (2003)

Hydroxyproline (Hyp)-rich glycoproteins (HRGPs) participate in all aspects of plant growth and development. HRGPs are generally highly O-glycosylated through the Hyp residues, which means carbohydrates help define the interactive molecular surface and, hence, HRGP function. The Hyp contiguity hypothesis predicts that contiguous Hyp residues are sites of HRGP arabinosylation, whereas clustered noncontiguous Hyp residues are sites of galactosylation, giving rise to the arabinogalactan heteropolysaccharides that characterize the arabinogalactan-proteins. Early tests of the hypothesis using synthetic genes encoding only clustered noncontiguous Hyp in the sequence (serine [Ser]-Hyp-Ser-Hyp)(n) or contiguous Hyp in the series (Ser-Hyp-Hyp)(n) and (Ser-Hyp-Hyp-Hyp-Hyp)(n) confirmed that arabinogalactan polysaccharide was added only to noncontiguous Hyp, whereas arabinosylation occurred on contiguous Hyp. Here, we extended our tests of the codes that direct arabinogalactan polysaccharide addition to Hyp by building genes encoding the repetitive sequences (alanine [Ala]-proline [Pro]-Ala-Pro)(n), (threonine [Thr]-Pro-Thr-Pro)(n), and (valine [Val]-Pro-Val-Pro)(n), and expressing them in tobacco (Nicotiana tabacum) Bright-Yellow 2 cells as fusion proteins with green fluorescent protein. All of the Pro residues in the (Ala-Pro-Ala-Pro)(n) fusion protein were hydroxylated and consistent with the hypothesis that every Hyp residue was glycosylated with arabinogalactan polysaccharide. In contrast, 20% to 30% of Pro residues remained non-hydroxylated in the (Thr-Pro-Thr-Pro)(n), and (Val-Pro-Val-Pro)(n) fusion proteins. Furthermore, although 50% to 60% of the Hyp residues were glycosylated with arabinogalactan polysaccharide, some remained non-glycosylated or were arabinosylated. These results suggest that the amino acid side chains of flanking residues influence the extent of Pro hydroxylation and Hyp glycosylation and may explain why isolated noncontiguous Hyp in extensins do not acquire an arabinogalactan polysaccharide but are arabinosylated or remain non-glycosylated.
Biotransformation in Review: Applications in Ocular Disease and Drug Design (1996)

The purpose of this paper is to review the biochemical processes of systemic biotransformation and describe their relevance to ocular disease and drug metabolism. The diverse nature of the biochemical pathways, commonly found in enzyme metabolism, is discussed. The occurrence of these processes in the eye has significance in that the products of metabolism may accumulate locally and exert deterimental effects, presumably by altering the cellular structure and/or function of crucial visual elements. The manipulation of these metabolic pathways within the eye has ramifications in the development of novel drug design for both ocular disease treatment and, perhaps more importantly, disease prevention.
Laser Therapy for Pain of Rheumatoid Arthritis (1987)

Human subjects received transcutaneous irradiation on the skin overlying peripheral nerves with a low-power helium–neon laser (1 MW, 632.5 nm, 20 Hz) for 20 s to each site. This treatment was accompanied by irradiation of the skin overlying painful joints for 4–8 min according to a predetermined protocol. Control group (n = 34) received treatment by an apparatus that looked identical to the laser apparatus but emitted no radiation. Laser or placebo therapy was repeated 3 times a week for 10 weeks. Subjects in the experimental group exhibited a highly significant reduction in pain intensity. Low-power laser may represent an adjunct in the management of the pain of rheumatoid arthritis.