gebhart/patrepeval huggingface dataset:
An overview of nosocomial infections, including the role of the microbiology laboratory (1993)

An estimated 2 million patients develop nosocomial infections in the United States annually. The increasing number of antimicrobial agent-resistant pathogens and high-risk patients in hospitals are challenges to progress in preventing and controlling these infections. While Escherichia coli and Staphylococcus aureus remain the most common pathogens isolated overall from nosocomial infections, coagulase-negative staphylococci (CoNS), organisms previously considered contaminants in most cultures, are now the predominant pathogens in bloodstream infections. The growing number of antimicrobial agent-resistant organisms is troublesome, particularly vancomycin-resistant CoNS and Enterococcus spp. and Pseudomonas aeruginosa resistant to imipenem. The active involvement and cooperation of the microbiology laboratory are important to the infection control program, particularly in surveillance and the use of laboratory services for epidemiologic purposes. Surveillance is used to identify possible infection problems, monitor infection trends, and assess the quality of care in the hospital. It requires high-quality laboratory data that are timely and easily accessible.
Acrolein scavenging: a potential novel mechanism of attenuating oxidative stress following spinal cord injury (2009)

It has long been established that oxidative stress plays a critical role in the pathophysiology of spinal cord injury, and represents an important target of therapeutic intervention following the initial trauma. However, free radical scavengers have been largely ineffective in clinical trials, and as such a novel target to attenuate oxidative stress is highly warranted. In addition to free radicals, peroxidation of lipid membranes following spinal cord injury (SCI) produces reactive aldehydes such as acrolein. Acrolein is capable of depleting endogenous antioxidants such as glutathione, generating free radicals, promoting oxidative stress, and damaging proteins and DNA. Acrolein has a significantly longer half-life than the transient free radicals, and thus may represent a potentially better target of therapeutic intervention to attenuate oxidative stress. There is growing evidence, from our lab and others, to suggest that reactive aldehydes such as acrolein play a critical role in oxidative stress and SCI. The focus of this review is to summarize the cellular and biochemical mechanisms of acrolein-induced membrane damage, mitochondrial injury, oxidative stress, cell death, and functional loss. Evidence will also be presented to suggest that acrolein scavenging may be a novel means of therapeutic intervention to attenuate oxidative stress and improve recovery following traumatic SCI.
Hepsin, a Putative Membrane-associated Serine Protease, Activates Human Factor VII and Initiates a Pathway of Blood Coagulation on the Cell Surface Leading to Thrombin Formation (1995)

Previous studies have shown that hepsin is a putative membrane-associated serine protease that is required for cell growth (Torres-Rosado, A., O'Shea, K. S., Tsuji, A., Chou, S.-H., and Kurachi, K. (1993) Proc. Natl. Acad. Sci. U.S. A. 90, 7181 7185). In the present study, we have transfected baby hamster kidney (BHK) cells with a plasmid containing the cDNA for human hepsin and examined these cells for their ability to activate several blood coagulation factors including factors X, IX, VII, prothrombin, and protein C. Little, if any, proteolytic activation of factors X, IX, prothrombin, or protein C was observed when these clotting factors were incubated with hepsin-transfected cells. On the other hand, hepsin-transfected cells proteolytically activated significant concentrations of human factor VII in a time- and calcium-dependent manner, whereas essentially no activation of factor VII was observed in BHK cells transfected with plasmid lacking the cDNA for hepsin. The factor VII activating activity in the hepsin-transfected BHK cell line was confined exclusively to the total membrane fraction and was inhibited > 95% by antibody raised against a fusion protein consisting of maltose-binding protein and the extracellular domain of human hepsin. An active site factor VII mutant, S344A factor VII, was cleaved as readily as plasma-derived factor VII by hepsin-transfected cells, indicating that factor VII was not converted to factor VIIa autocatalytically on the cell surface. In contrast, an activation cleavage site factor VII mutant, R152E factor VII, was not cleaved by hepsin-transfected cells, suggesting that factor VII and S344A factor VII were activated on these cells by cleavage of the Arg152-Ile153 peptide bond. In the copresence of factor VII and factor X, hepsin-transfected BHK cells supported the formation of factor Xa. In addition, in the copresence of factor VII, factor X, and prothrombin, hepsin-transfected BHK cells supported the formation of thrombin. These results strongly suggest that membrane-associated hepsin converts zymogen factor VII to factor VIIa, which in turn, is capable of initiating a coagulation pathway on the cell surface that ultimately leads to thrombin formation.
Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. (2002)

Fibroblast activation protein (FAP) is a type II integral membrane glycoprotein belonging to the serine protease family. Human FAP is selectively expressed by tumor stromal fibroblasts in epithelial carcinomas, but not by epithelial carcinoma cells, normal fibroblasts, or other normal tissues. FAP has been shown to have both in vitro dipeptidyl peptidase and collagenase activity, but its biological function in the tumor microenvironment is unknown. The modeled structure of murine FAP consists of a short cytoplasmic tail, a single hydrophobic transmembrane region, and a large extracellular domain. A seven-bladed beta-propeller domain is situated on top of the catalytic triad and may serve as a "gate" to selectively filter protein access to the catalytic site. HEK293 cells transfected to constitutively express murine FAP, when xenografted into scid mice, were 2-4 times more likely to develop s.c. tumors and showed a 10-40-fold enhancement of tumor growth compared with mock-transfected HEK293 cells. Rabbits immunized with recombinant murine FAP developed polyclonal anti-FAP antibodies that significantly inhibited murine FAP dipeptidyl peptidase activity in vitro. HT-29 xenografts treated with these inhibitory anti-FAP antisera exhibited attenuated growth compared with tumors treated with preimmunization rabbit antisera. These data demonstrate the ability of FAP to potentiate tumor growth in an animal model. Moreover, tumor growth is attenuated by antibodies that inhibit the proteolytic activity of FAP. These findings suggest a possible therapeutic role for functional inhibition of FAP activity.
Transfer of Pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and Description of Burkholderia vandii sp. nov. (1994)

Plant-associated bacteria were characterized and are discussed in relation to authentic members of the genus Pseudomonas sensu stricto. Bacteria belonging to Pseudomonas rRNA group II are separated clearly from members of the genus Pseudomonas sensu stricto (Pseudomonas fluorescens rRNA group) on the basis of plant association characteristics, chemotaxonomic characteristics, DNA-DNA hybridization data, rRNA-DNA hybridization data, and the sequences of 5S and 16S rRNAs. The transfer of Pseudomonas cepacia, Pseudomonas mallei, Pseudomonas pseudomallei, Pseudomonas caryophylli, Pseudomonas gladioli, Pseudomonas pickettii, and Pseudomonas solanacearum to the new genus Burkholderia is supported; we also propose that Pseudomonas plantarii and Pseudomonas glumae should be transferred to the genus Burkholderia. Isolate VA-1316T (T = type strain) was distinguished from Burkholderia species on the basis of physiological characteristics and DNA-DNA hybridization data. A new species, Burkholderia vandii sp. nov. is proposed for this organism; the type strain of B. vandii is VA-1316 (= JCM 7957).
Simvastatin Protects against the Development of Endometriosis in a Nude Mouse Model (2009)

Simvastatin exerted a potent inhibitory effect on the development of endometriosis in the nude mouse. Mechanisms of action of simvastatin may include inhibition of MMP-3. The present findings may lead to the development of novel treatments of endometriosis involving statins.
Pharmacological inhibition of HSP90 and ras activity as a new strategy in the treatment of HNSCC (2012)

Advanced head and neck squamous cell cancer (HNSCC) is currently treated with taxane-based chemotherapy. We have previously shown that docetaxel (DTX) induces a ras-dependent survival signal that can be antagonized by farnesyl transferase inhibitors (FTI) such as tipifarnib (TIP). Here we show that the synergistic TIP/DTX combination determines synergistic apoptotic conditions but, at the same time, it modulates the expression of the components of the multichaperone complex that is, in turn, involved in the regulation of the stability of members of the ras-mediated pathway. Therefore, we have stably transfected HNSCC KB and Hep-2 cells with a plasmid encoding for HSP90. The expression of the protein was increased in both transfected cell lines but its activation status was increased in Hep-2 clones and decreased in KB clones. On the basis of these results, we have treated both parental and HSP90-transfected cells with a HSP90 inhibitor geldanamycin (GA). We have found that the antiproliferative activity of GA is dependent upon the activation status of HSP90 and that it is strongly synergistic when added in combination with TIP but not with DTX in cells overexpressing HSP90 and even more in cells with increased HSP90 activity. These data were paralleled by the decreased expression and activity of the components belonging to the ras→mediated signal transduction pathway. The present results suggest that multichaperone complex activation could be a resistance mechanism to the anti-proliferative and apoptotic effects induced by TIP and that the combination of FTIs such as TIP with GA could be a suitable therapeutic strategy in the treatment of HSP90-overexpressing HNSCC.
Humanin: A Novel Therapeutic Target in Prostate Cancer (2007)

Abstract : Humanin is a recently discovered potent survival peptide encoded by the 16S mitochondrial RNA. We cloned humanin as an insulin-like growth factor binding protein-3 (IGFBP-3) antagonist, and others identified it as a Bax antagonist. We hypothesize that humanin is an important prostate cancer regulator and that it may have a role as a diagnostic or prognostic marker in this disease. We proposed to characterize the role of humanin as a regulator of cell survival, growth, and signalling in prostate cancer in vitro, to define its interactions with IGF related molecules including IGFBP-3. We also proposed to identify alterations in humanin levels in sera and tissues of men with prostate cancer using a serum bank and a CaP tissue array. Our data so far indicates that humanin is present in prostate and seminal plasma, and is increased in prostate cancer specimens and its presence is a poor prognostic factor for disease free survival. As findings indicate that humanin levels are related to outcome in CaP, using humanin assays as a potential prognostic tool in patients with prostate cancer could improve treatment decisions in the future.
Oligo(thiophénylènes‐1,4) α,ω‐difonctionnalisés, 3. Oligomères α,ω‐diaminés et copolyamides qui en dérivent (1983)

Abstract Polyamides 7a and 7b were prepared from α‐(4‐aminophenyl)‐ω‐aminopoly(thio‐1,4‐phenylene)s (3a) by reaction with 1,12‐dodecanedioic acid (6) , tribloc copolymers 9 from 3a and 11 aminoundecanoic acid (8) , and multibloc copolymers 10 from 3a, 6 , and 8 . The properties of these copolymers were studied by DSC and compared with those of N, N '‐lauroyl derivatives of 3a as model compounds. Phase separations were observed with products containing at least four phenylene units in the thiophenylene blocs. However, the T g was found to increase with increasing number of phenylene units.
Modulation of P2X7 nucleotide receptor expression by pro- and anti-inflammatory stimuli in THP-1 monocytes (1998)

Regulation of P2X7 receptor expression is of interest because activation of this receptor by extracellular ATP triggers maturation and release of the pro-inflammatory cytokine interleukin-1 beta (IL-1 beta) in monocytes and macrophages. We report that interferon-gamma (IFN-gamma) and tumor necrosis factor alpha (TNF-alpha) synergistically induce P2X7R mRNA and functional responses in the human THP-1 monocytic cell line. Induction was dose dependent, with maximal functional activity requiring 1000 units/mL IFN-gamma and 10 ng/mL TNF-alpha and incubations of 36-72 h. The up-regulation of P2X7R function by lipopolysaccharide (LPS)/IFN-gamma and TNF-alpha/IFN-gamma was markedly attenuated by coincubation with prostaglandin E2 or the cell permeant cyclic AMP analog dibutryl cAMP (Bt2cAMP). Bt2cAMP did not significantly alter P2X7 function in HEK-293 cells stably transfected with the human P2X7 cDNA, indicating that Bt2cAMP does not exert a generalized effect on P2X7R synthesis or downstream signal transduction. These studies demonstrate that elevated cAMP negatively modulates P2X7R expression.
Functional Cellulose Beads: Preparation, Characterization, and Applications (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFunctional Cellulose Beads: Preparation, Characterization, and ApplicationsMartin Gericke, Jani Trygg, and Pedro Fardim*View Author Information Laboratory of Fibre and Cellulose Technology, Åbo Akademi, Porthansgatan 3, FI-20500 Turku, Finland, Members of the European Polysaccharide Network of Excellence (EPNOE)*E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 7, 4812–4836Publication Date (Web):March 29, 2013Publication History Received15 June 2012Published online29 March 2013Published inissue 10 July 2013https://pubs.acs.org/doi/10.1021/cr300242jhttps://doi.org/10.1021/cr300242jreview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views13808Altmetric-Citations239LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Carbohydrates,Cellulose,Colloids,Reaction products,Solvents Get e-Alerts
Liquid Extraction Surface Analysis Mass Spectrometry Coupled with Field Asymmetric Waveform Ion Mobility Spectrometry for Analysis of Intact Proteins from Biological Substrates (2015)

Previously we have shown that liquid extraction surface analysis (LESA) mass spectrometry is suitable for the analysis of intact proteins from a range of biological substrates. Here we show that LESA mass spectrometry may be coupled with high field asymmetric waveform ion mobility spectrometry (FAIMS) for top-down protein analysis directly from thin tissue sections (mouse liver, mouse brain) and from bacterial colonies (Escherichia coli) growing on agar. Incorporation of FAIMS results in significant improvements in signal-to-noise and reduced analysis time. Abundant protein signals are observed in single scan mass spectra. In addition, FAIMS enables gas-phase separation of molecular classes, for example, lipids and proteins, enabling improved analysis of both sets of species from a single LESA extraction.
Metal–Organic Frameworks as Efficient Materials for Drug Delivery (2006)

Fill 'em up: The metal carboxylates MIL-100 and MIL-101 act as porous matrices (see picture; MIL=Materials of Institut Lavoisier) for drug-delivery systems using Ibuprofen as a model substrate. Very large amounts of the drug could be incorporated, up to an unprecedented capacity of 1.4 g of drug per gram of porous solid for MIL-101, and the total release of Ibuprofen was achieved under physiological conditions in 3 (MIL-100) and 6 days (MIL-101). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z601878_s.pdf or from the author. 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.
Reproducibility of signal transmissions in the ocean (1965)

Repeated transmissions of acoustical signals were made over a distance of 20 nm. One transmission was compared with succeeding transmissions with the matched signal technique. The experiments showed 10 average arrivals added coherently. The signal is matched for particular source and receiver positions. Displacement of the source or receiver from these positions reduces the coherent addition of arrivals. The sensitivity to small displacements also depends upon the signal bandwidth. These experiments were done at 400 c/s with a bandwidth of 100 c/s. A displacement of the source of about 0.1 nm decreased the peak of the coherently added arrivals to about 60 %.
Laser-induced periodic surface structure. I. Theory (1983)

We develop a theory for laser-induced periodic surface structure by associating each Fourier component of induced structure with the corresponding Fourier component of inhomogeneous energy deposition just beneath the surface. We assume that surface roughness, confined to a region of height much less than the wavelength of light, is responsible for the symmetry breaking leading to this inhomogeneous deposition; we find strong peaks in this deposition in Fourier space, which leads to predictions of induced fringe patterns with spacing and orientation dependent on the angle of incidence and polarization of the damaging beam. The nature of the generated electromagnetic field structures and their relation to the simple "surface-scattered wave" model for periodic surface damage are discussed. Our calculation, which is for arbitrary angle of incidence and polarization, applies a new approach to the electrodynamics of randomly rough surfaces, introducing a variational principle to deal with the longitudinal fields responsible for local field, or "depolarization," corrections. For a $p$-polarized damaging beam our results depend on shape and filling factors of the surface roughness, but for $s$-polarized light they are essentially independent of these generally unknown parameters; thus an unambiguous comparison of our theory with experiment is possible.
C3: Internet-Scale Control Plane for Video Quality Optimization (2018)

As Internet video goes mainstream, we see increasing user expectations for higher video quality and new global policy requirements for content providers. Inspired by the case for centralizing network-layer control, we present C3, a control system for optimizing Internet video delivery. The design of C3 addresses key challenges in ensuring scalability and tackling data plane heterogeneity. First, to ensure scalability and responsiveness, C3 introduces a novel split control plane architecture that can tolerate a small increase in model staleness for a dramatic increase in scalability. Second, C3 supports diverse client-side platforms via a minimal clientside sensing/actuation layer and offloads complex monitoring and control logic to the control plane. C3 has been operational for eight years, and today handles more than 100M sessions per day from 244 countries for 100+ content providers and has improved the video quality significantly. In doing so, C3 serves as a proof point of the viability of fine-grained centralized control for Internetscale applications. Our experiences reinforce the case for centralizing control with the continued emergence of new use case pulls (e.g., client diversity) and technology pushes (e.g., big data platforms).
Effects of Different Concentrations of Formalin on Paw Edema and Pain Behaviors in Rats (2002)

The aim of this study was to determine whether formalin reliably provokes a paw edema and pain behavior. The paw of male Sprague-Dawley rats were injected with 100 microliter of formalin with 2.5% (F2.5), 5% (F5), and 10% (F10) concentrations. Following the formalin (n=8) or saline (control, n=6) injection, the flinching or licking of the paw was recorded for the phase 1 response (0-5 min after injection) and phase 2 response (20-60 min). The formalin-induced paw edema was assessed by measuring the diameters of the injected paws at 4 hr after injection. As for flinching, phase 1 and 2 of all three groups showed higher frequency than those of the control group (p<0.05). As for licking, phase 1 cumulative time of the F2.5 and F10 groups, and phase 2 cumulative time of the F2.5 and F5 groups showed a longer duration than those in the control group (p<0.05). The diameters of the paw in the F10 group were significantly larger than those in the control group (p<0.05). Flinching behavior was more reliably expressed the biphasic response than licking response at all formalin concentrations. Peak of the licking was reached at 2.5% and that of flinching was reached at 5%, whereas the paw edema peaked at 10% concentration. This suggests that there may be some dissociation of nociception from the edema formation.
Pore size of agarose gels by atomic force microscopy (1997)

The pore size of agarose gel in water at different concentrations was directly measured using atomic force microscopy (AFM). The experiment was specially designed to work under aqueous conditions and allows direct observation of the "unperturbed" gel without invasive treatment. The pore size a as a function of gel concentration C shows a power law dependence a approximately C-gamma, where gamma lies between the prediction of the Ogston model for a random array of straight chains, 0.5, and the value predicted by De Gennes for a network of flexible chains, 0.75. We confirm that gels present a wide pore size distribution and show that it narrows as the concentration increases.