gebhart/patrepeval huggingface dataset:
Out‐of‐pocket expenses and their burden in patients with rheumatoid arthritis (2009)

The out-of-pocket burden is substantial, particularly in those <65 years of age. Out-of-pocket expenses exert their severity predominantly on those with the most severe RA who have the least ability to pay. Household income is the primary determinant of out-of-pocket burden, followed by RA severity, and type of health insurance.
Matrix metalloproteinases and their inhibitors in connective tissue remodeling (1991)

Matrix metalloproteinases are an important group of zinc enzymes responsible for degradation of the extracellular matrix components such as collagen and proteoglycans in normal embryogenesis and remodeling and in many disease processes such as arthritis, cancer, periodontitis, and osteoporosis. A matrixin family is defined, comprising at least seven members that range in size from Mr 28,000 to 92,000 and are related in gene sequence to collagenase. All family members are secreted as zymogens that lose peptides of about 10,000 daltons upon activation. Latency is due to a conserved cysteine that binds to zinc at the active center. Latency is overcome by physical (chaotropic agents), chemical (HOCl, mercurials), and enzymatic (trypsin, plasmin) treatments that separate the cysteine residue from the zinc. Expression of the metalloproteinases is switched on by a variety of agents acting through regulatory elements of the gene, particularly the AP-1 binding site. A family of protein inhibitors of Mr 28,500 or less binds strongly and stoichiometrically in noncovalent fashion to inhibit members of the family. The serum protein alpha 2-macroglobulin and relatives are also strongly inhibitory.
Genetic organization and expression of citrate permease in lactic acid bacteria. (2004)

Citrate is present in many natural substrates, such as milk, vegetables and fruits, and its metabolism by lactic acid bacteria (LAB) plays an important role in food fermentation. The industrial importance of LAB stems mainly from their ability to convert carbohydrates into lactic acid and, in some species, like Lactococcus lactis and Leuconostoc mesenteroides, to produce C4 flavor compounds (diacetyl, acetoin) through citrate metabolism. Three types of genetic organization and gene locations, involving citrate metabolism, have been found in LAB. Citrate uptake is mediated by a citrate permease, which leads to a membrane potential upon electrogenic exchange of divalent citrate and monovalent lactate. The internal citrate is cleaved into acetate and oxaloacetate by a citrate lyase, and oxaloacetate is decarboxylated into pyruvate by an oxaloacetate decarboxylase, yielding a pH gradient through the consumption of scalar protons.
Irreversible inhibition of rat glutathione S-transferase 1-1 by quinones and their glutathione conjugates (1991)

The irreversible inhibition of the rat glutathione S-transferase (GST) isoenzyme 1-1 by a series of halogenated 1,4-benzoquinones and their GSH conjugates was studied quantitatively by analysing the time course of enzyme inactivation. With increasing numbers of chlorine substituents, the rate of inhibition greatly increased. Incorporation of a GSH moiety in all cases increased the rate of inactivation compared with the non-substituted compound, and this was due to the increased affinity of the inhibitor for the active site. The ratio between the rates of inhibition for a given quinone with and without GSH substituent was largest for the three dichlorobenzoquinones, with the 2,6-isomer showing a 41-fold increase in rate of inhibition upon conjugation with GSH. The time courses of inhibition could be fitted either to a bi-exponential function (for the GSH conjugates and the higher chlorinated quinones) or to a mono-exponential function (all other quinones). It is concluded that the second component describes the affinity part of the reaction. GST 1-1 possesses two cysteine residues, with modification of one of these, probably located in the vicinity of the active site, having a major impact on the enzyme activity. Compounds with affinity towards the active site preferentially react with this residue. Nonspecific quinones react equally with both cysteine residues. This was confirmed by the observation that complete inactivation of GST 1-1 by 2,5-dichlorobenzoquinone was achieved only after modification of two residues, whereas the corresponding GSH conjugate already completely inhibited the enzyme after modification of one residue. Chemicals/CAS: benzoquinone, 106-51-4; Benzoquinones; Cysteine, 52-90-4; Glutathione Transferase, EC 2.5.1.18; Glutathione, 70-18-8; Halogens; Isoenzymes; Quinones
Social spaces, casual interactions, meaningful exchanges: 'information ground' characteristics based on the college student experience (2006)

<br><b>Introduction.</b> In the late 1990s Fisher (writing as Pettigrew) proposed information grounds to describe social settings in which people share everyday information while attending to a focal activity. <br><b>Method.</b> This study was conducted at a major research university, home to 45,000 students. Data were collected by seventy-two Master of Library and Information Science (MLIS) students as part of an information behaviour class. Trained in interviewing techniques, each MLIS student interviewed ten students in public places, including the campus and the university commercial district. The survey, comprising twenty-seven primarily open-ended questions, was conducted from October 14-21, 2004. Data were collected from 729 college students and entered, along with extensive field notes, into an in-house Web form. <br><b>Analysis.</b> Qualitative and quantitative analyses were supplemented by mini-reports prepared by the student researchers along with full-team debriefings. <br><b>Results.</b> Using a 'people, place, information-related trichotomy', characteristics are discussed in terms of how they can be manipulated to optimize information flow in social settings. <br><b>Conclusion.</b> . By understanding better the characteristics of information grounds and the interactions among these characteristics, we may be able to develop social spaces in support of information flow and human interaction. Our college student and other studies suggest that information grounds play an intrinsic role in facilitating communication among people and that by building an in-depth typology, beginning with basic categorical characteristics, we may develop new methods for facilitating information exchange.
Dose perturbations from implanted helical gold markers in proton therapy of prostate cancer (2009)

Implanted gold fiducial markers are widely used in radiation therapy to improve targeting accuracy. Recent investigations have revealed that metallic fiducial markers can cause severe perturbations in dose distributions for proton therapy, suggesting smaller markers should be considered. The objective of this study was to estimate the dosimetric impact of small gold markers in patients receiving proton therapy for prostate cancer. Small, medium, and large helical wire markers with lengths of 10 mm and helix diameters of 0.35 mm, 0.75 mm, and 1.15 mm, respectively, were implanted in an anthropomorphic phantom. Radiographic visibility was confirmed using a kilovoltage x-ray imaging system, and dose perturbations were predicted from Monte Carlo simulations and confirmed by measurements. Monte Carlo simulations indicated that size of dose perturbation depended on marker size, orientation, and distance from the beam's end of range. Specifically, the perturbation of proton dose for the lateral-opposed-pair treatment technique was 31% for large markers and 23% for medium markers in a typical oblique orientation. Results for perpendicular and parallel orientations were respectively lower and higher. Consequently, these markers are not well suited for use in patients receiving proton therapy for prostate cancer. Dose perturbation was not observed for the small markers, but these markers were deemed too fragile for transrectal implantation in the prostate.
SEVERE SEPSIS AND SEPTIC SHOCK: The Role of Gram-Negative Bacteremia (2006)

Abstract Although Gram-negative bacteria have often been implicated in the pathogenesis of severe sepsis and septic shock, how they trigger these often lethal syndromes is uncertain. In particular, the role played by blood-borne bacteria is controversial. This review considers two alternatives. In the first, circulating Gram-negative bacteria induce toxic reactions directly within the vasculature; in the second, the major inflammatory stimulus occurs in local extravascular sites of infection and circulating bacteria contribute little to inducing toxic responses. Evidence for each alternative is found in the literature. Bacteremia and severe sepsis are not so closely linked that the most striking cases can be a model for the rest. Intravascular and extravascular triggers may warrant different approaches to prevention and therapy.
Expression and significance of heat shock protein 70 and glucose-regulated protein 94 in human esophageal carcinoma (2004)

HSP70 and grp94 express differently in cell plasma and nuclei. The expression intensity of HSP70 is related to the differentiation of esophageal carcinoma.
Linux in an Embedded Communications Gateway (1998)

This article describes a communications gateway system, why Linux was chosen for the implementation and why Linux is an excellent choice for similar gateways
On the target specificity of plasminogen activator inhibitor 1: the role of heparin, vitronectin, and the reactive site (1991)

Plasminogen activator inhibitor 1 (PAI-1) is the fast-acting inhibitor of both tissue-type and urokinase-type plasminogen activators (t-PA, u-PA) and is an essential regulatory protein of the fibrinolytic system. In the presence of either the protein vitronectin or the glycosaminoglycan heparin, PAI-1 is also an efficient inhibitor of thrombin. To assess whether these cofactors turn PAI-1 into a general protease inhibitor or whether their influence is restricted to thrombin, the second-order association rate constants between PAI-1 and the human plasma proteases t-PA, u-PA, plasmin, thrombin, Factor Xa (FXa), and Factor XIIa (FXIIa) in the absence and in the presence of either vitronectin or heparin are determined. In addition, the role of the PAI-1 reactive site P3 to P3' residues for the specificity of inhibition was studied by using PAI-1 reactive site mutants. Our results show that: (1) Heparin exclusively increases the rate of inhibition of thrombin by PAI-1, whereas in the presence of heparin the rate of inhibition of the other proteases is not altered; (2) Vitronectin is an obligatory cofactor for the inhibition of thrombin by PAI-1. In addition, vitronectin moderately increases the rate of inhibition by PAI-1 of u-PA and of plasmin, but does not alter the rate of inhibition of t-PA, FXa, or FXIIa; (3) Apart from the important role of the P1 residue, no consensus can be presented on the nature of other residues within the P3 to P3' region with regard to target protease specificity.
DELIMINATE—a fast and efficient method for loss-less compression of genomic sequences (2012)

Supplementary data are available at Bioinformatics online.
Wound healing essentials: Let there be oxygen (2009)

The state of wound oxygenation is a key determinant of healing outcomes. From a diagnostic standpoint, measurements of wound oxygenation are commonly used to guide treatment planning such as amputation decision. In preventive applications, optimizing wound perfusion and providing supplemental O(2) in the perioperative period reduces the incidence of postoperative infections. Correction of wound pO(2) may, by itself, trigger some healing responses. Importantly, approaches to correct wound pO(2) favorably influence outcomes of other therapies such as responsiveness to growth factors and acceptance of grafts. Chronic ischemic wounds are essentially hypoxic. Primarily based on the tumor literature, hypoxia is generally viewed as being angiogenic. This is true with the condition that hypoxia be acute and mild to modest in magnitude. Extreme near-anoxic hypoxia, as commonly noted in problem wounds, is not compatible with tissue repair. Adequate wound tissue oxygenation is required but may not be sufficient to favorably influence healing outcomes. Success in wound care may be improved by a personalized health care approach. The key lies in our ability to specifically identify the key limitations of a given wound and in developing a multifaceted strategy to specifically address those limitations. In considering approaches to oxygenate the wound tissue it is important to recognize that both too little as well as too much may impede the healing process. Oxygen dosing based on the specific need of a wound therefore seems prudent. Therapeutic approaches targeting the oxygen sensing and redox signaling pathways are promising.
Controlling the Microstructure of Solution-Processable Small Molecules in Thin-Film Transistors through Substrate Chemistry (2011)

Solution-processable small molecules have tremendous potential in macroelectronics applications by providing both high charge carrier mobility and low cost processing. Fluorinated 5,11-bis(triethylsilylethynl) anthradithiophene enables high performance thin film transistors due, in part, to a self-patterning process where crystals grow from chemically tailored contacts and bridge the transistor channel. This paper outlines a detailed microstructural study that identifies the crystallization mechanisms of the self-patterning. Two crystal habits are observed: we find that crystals on chemically modified electrodes predominantly form (001) oriented platelets while untreated surfaces form a fine mixture of (001) and (111) oriented crystals. For (001) oriented platelets, the (010) fast growth face lies in the plane of the film and allows extended growth from platelets nucleated on the electrode into the transistor channel. The in-plane charge carrier mobility of the (001) platelets is high; for short channel lengths, crystal growth fronts from adjacent electrodes bridge the channel gap, resulting in the excellent device performance. On untreated surfaces between devices, the low charge carrier mobility, finely mixed state provides self-isolation for stable device operation.
Many roads, one destination for T cell progenitors (2005)

The thymus manufactures new T cells throughout life but contains no self-renewing potential. Instead, replenishment depends on recruitment of bone marrow-derived progenitors that circulate in the blood. Attempts to identify thymic-homing progenitors, and to assess the degree to which they are precommitted to the T cell lineage, have led to complex and sometimes conflicting results. As described here, this probably reflects the existence of multiple distinct types of T cell lineage progenitors as well as differences in individual experimental approaches.
The Influence of Hormones and Pharmaceutical Agents on DHEA and DHEA‐S Concentrations: A Review of Clinical Studies (2002)

Low endogenous levels of dehydroepiandrosterone (DHEA) and/or its sulfoconjugated derivative DHEA-S have been associated with diseases such as lupus, cancer, and diabetes. Circulating concentrations of DHEA and DHEA-S resulting from endogenous production or hormone supplementation may also be relevant in psychiatric illness. Drugs may significantly increase or decrease circulating concentrations of these adrenal androgens by various mechanisms. Some agents, such as dexamethasone, affect the HPA axis by inhibiting ACTH and therefore decrease DHEA and DHEA-S concentrations. Central nervous system agents, including carbamazepine and phenytoin, induce the P450 enzymes that metabolize DHEA and DHEA-S and therefore decrease circulating concentrations of these hormones. Danazol alters the ratio between DHEA and DHEA-S by inhibiting sulfatase. As research moves forward to better understand the relationships of these adrenal androgens with health and disease, it is essential that studies be designed to control for the influence of administered pharmaceuticals on DHEA and DHEA-S.
Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli (1994)

The Escherichia coli K-12 alpA gene product, when overproduced from a multicopy plasmid, leads to suppression of the capsule overproduction and UV sensitivity phenotypes of cells mutant for the Lon ATP-dependent protease. This suppression has previously been shown to correlate with increased in vivo activity of a previously unknown energy-dependent proteolytic activity capable of degrading Lon substrates, the Alp protease. We show in an accompanying paper that alpA, which has homology to a short open reading frame in bacteriophage P4, acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants (J. E. Trempy, J. E. Kirby, and S. Gottesman, J. Bacteriol. 176:2061-2067). The sequence of slpA suggests that it encodes an integrase gene closely related to P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. AlpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. Excision is dependent on integration host factor as well as on SlpA. Prophage excision is necessary but not sufficient for full expression of the Alp protease. A second function (named AHA) allows full protease expression; this function can be provided by the kanamycin resistance element from Tn903 when the element is present on a multicopy plasmid. Excision and loss of the cryptic prophage apparently allow expression of the Alp protease by inactivating a small stable RNA (10Sa RNA) encoded by the ssrA gene. The precursor of this RNA has its 3' end within the cryptic prophage; the mature 3' end lies within the prophage attL site. Inactivation of ssrA by insertional mutagenesis is sufficient to allow expression of the suppressing Alp protease, even in the presence of the cryptic prophage. Therefore, 10Sa RNA acts as a negative regulator of protease synthesis or activity, and prophage excision must inactivate this inhibitory function of the RNA.
Guanylyl cyclase C: a molecular marker for staging and postoperative surveillance of patients with colorectal cancer (2005)

Staging patients with colorectal cancer defines their prognosis and therapeutic management. Unfortunately, histopathology, the current standard for staging, is relatively insensitive for detecting occult micrometastases and a significant fraction of patients are understaged and, consequently, undertreated. Similarly, current approaches to postoperative surveillance of patients with colorectal cancer detect disease recurrence at a point when interventions have little impact on survival. The detection of rare cells in tissue, for accurately staging patients, and in blood, for detecting disease recurrence, could be facilitated by employing sensitive and specific markers of disease. Guanylyl cyclase C (GCC), the receptor for the diarrheagenic bacterial heat-stable enterotoxin, is expressed selectively by cells derived from intestinal mucosa, including normal intestinal cells and colorectal tumor cells, but not by extragastrointestinal tissues and tumors. The nearly uniform expression of relatively high levels by metastatic colorectal tumors suggests that GCC may be a sensitive and specific molecular marker for metastatic colorectal cancer cells. Employing GCC reverse transcriptase PCR, occult colorectal cancer micrometastases were detected in lymph nodes that escaped detection by histopathology. Moreover, marker expression correlated with the risk of disease recurrence. Similarly, GCC reverse transcriptase PCR revealed the presence of tumor cells in blood of all patients examined with metastatic colorectal cancer and, in some studies, was associated with an increased risk of disease recurrence and mortality. These observations suggest that GCC reverse transcriptase PCR is a sensitive and specific technique for identifying tumor cells in extraintestinal sites and may be useful for staging and postoperative surveillance of patients with colorectal cancer.
Infection in chronic wounds: controversies in diagnosis and treatment. (1999)

Chronic wounds all have bacterial contamination, which will not impair healing. Wound contamination must be distinguished from wound colonization and infection. Bacterial infection in wounds depends on the number of organisms present, their virulence, and host resistance. The most important indicators of infection are both local and systemic host characteristics and a holistic assessment of the patient. Several specimen collection and culture techniques are available to measure bacterial burden in the chronic wound. Advantages and disadvantages of each one discussed along with a rational approach to systemic antibiotic therapy. The presence of foreign material such as skin grafts or skin substitutes may lower the bacterial burden that may impair healing from 1.0 x 10(6) colony-forming units to 1.0 x 10(5) or less. The benefits of wound debridement, wound irrigation, and local nonantibiotic modes of treatment have been proven but the use of topical antibiotics and antiseptics requires further assessment. More widespread use of multiple nonantibiotic modalities of treatment for infected chronic wounds and rational antibiotic prescribing should reduce the risk of future antimicrobial resistance such as MRSA.
THE ROLE OF THE MUCOID POLYSACCHARIDE (HYALURONIC ACID) IN THE VIRULENCE OF GROUP A HEMOLYTIC STREPTOCOCCI (1944)

1. A quantitative turbidimetric method for the estimation of hyaluronidase activity, based on the ability of the enzyme to decrease the capacity of the polysaccharide to precipitate acidified protein has been developed. Two units of hyaluronidase, by this method, are equivalent to one viscosity-reducing unit. 2. Hyaluronidase added to a phagocytic system containing defibrinated human blood, immune or non-immune, greatly increases the rate of phagocytosis of group A streptococci. Phagocytosis of Type I pneumococci is not affected by hyaluronidase under the same conditions. 3. The bactericidal activity of non-immune blood against group A streptococci is increased by hyaluronidase; the activity of immune blood is, however, somewhat inhibited by the enzyme. Killing of pneumococci is not affected by the presence of the enzyme. 4. Mice can be protected against group A streptococcal infection by frequent treatment with 200 turbidity-reducing units of hyaluronidase; the protective action of the enzyme is removed by heating at 60°C. for 1 hour. Mice infected with Type I pneumococcus and treated with hyaluronidase die somewhat sooner than the untreated controls.