gebhart/patrepeval huggingface dataset:
Understanding and Using the Medical Subject Headings (MeSH) Vocabulary to Perform Literature Searches (1994)

The United States National Library of Medicine's (NLM) MEDLINE database is the largest and most widely used medical bibliographic database. MEDLINE is manually indexed with NLM's Medical Subject Headings (MeSH) vocabulary. Using MeSH, a searcher can potentially create powerful and unambiguous MEDLINE queries. This article reviews the structure and use of MeSH, directed toward the nonexpert, and outlines how MeSH may help resolve a number of common difficulties encountered when searching MEDLINE. The increasing importance of the MEDLINE database as an information resource and the trend toward individuals performing their own bibliographic searches makes it crucial that health care professionals become familiar with MeSH.
Development of Class IIa Bacteriocins as Therapeutic Agents (2011)

Class IIa bacteriocins have been primarily explored as natural food preservatives, but there is much interest in exploring the application of these peptides as therapeutic antimicrobial agents. Bacteriocins of this class possess antimicrobial activity against several important human pathogens. Therefore, the therapeutic development of these bacteriocins will be reviewed. Biological and chemical modifications to both stabilize and increase the potency of bacteriocins are discussed, as well as the optimization of their production and purification. The suitability of bacteriocins as pharmaceuticals is explored through determinations of cytotoxicity, effects on the natural microbiota, and in vivo efficacy in mouse models. Recent results suggest that class IIa bacteriocins show promise as a class of therapeutic agents.
Cloning and expression of the cDNA encoding mouse neutrophil gelatinase: demonstration of coordinate secondary granule protein gene expression during terminal neutrophil maturation (1993)

The 92-kD form of human type IV collagenase (gelatinase) is a member of the matrix metalloproteinase family. It is restricted in its expression to the granulocytic lineage of white blood cells. Within neutrophils it resides in secondary granules, which are markers of terminal myeloid differentiation. We have isolated and sequenced the cDNA encoding the murine counterpart to the human 92-kD metalloproteinase from a macrophage cDNA library. The human and murine genes are highly homologous and exist in an identical form in neutrophils and monocyte- macrophages in both species. Two polyadenylation signals are present in the murine 3′ untranslated sequence, accounting for equal expression of two messenger RNAs. We have shown that expression of gelatinase mRNA is controlled in a coordinate fashion together with lactoferrin, also a component of neutrophil secondary granules, and that this control occurs at the level of transcription. This is the first definitive demonstration of coordinate transcriptional regulation of secondary granule protein gene expression, a feature of normal myelopoiesis that is deranged in leukemogenesis.
dunce, a mutant of Drosophila deficient in learning. (1976)

Normal Drosophilia learn to avoid an odorant associated with electric shock. An X-linked mutant, dunce, has been isolated that fails to display this learning in spite of being able to sense the odorant and electric shock and showing essentially normal behavior in other respects.
Relocation of the Iliac Artery Bifurcation to Facilitate Endoluminal Treatment of Abdominal Aortic Aneurysms (1999)

Relocation of the iliac artery bifurcation appears to be a good alternative to preserve pelvic arterial flow in selected candidates for endoluminal AAA repair.
A Systematic Review of Newer Pharmacotherapies for Depression in Adults: Evidence Report Summary: Clinical Guideline, Part 2 (2000)

Newer antidepressants are clearly effective in treating depressive disorders in diverse settings. Because of similar efficacy, both newer and older antidepressants should be considered when making treatment decisions. Better information is urgently needed on the efficacy of newer antidepressants in patients with nonmajor depression and in special populations, including adolescents.
Synthesis of Thieno[2,3-d]pyrimidin-2-ylmethanamine Combinatorial Library with Four Diversity Points (2007)

The parallel solution-phase synthesis of more than 230 substituted thieno[2,3-d]pyrimidin-2-ylmethanamines has been accomplished. This strategy is based on the cyclization of 2-aminothiophen-3-carboxylates with chloroacetonitrile to construct the thieno[2,3-d]pyrimidine core with two diversity points. Derivatization of the active chlorine and functionalization of C-4 position of the pyrimidine ring allow the introduction of other diversity points. The products containing ester groups at the 6-position of the thieno[2,3-d]pyrimidine were used in amide synthesis. Simple manual techniques for parallel reactions, coupled with simple purification procedures, gave highly pure final products. The scope and limitations of the approach are discussed.
Circadian Rest-Activity Disturbances in Seasonal Affective Disorder (1997)

Patients with SAD have circadian rest-activity rhythms that are significantly phase delayed and more poorly entrained to the 24-hour day.
[Impact of instantaneous uniformity of SonoVue microbubbles on binding characteristics of a new contrast agent targeted to choriocarcinoma cells in vitro]. (2008)

The binding capacity of the targeted SonoVue microbubbles to JARs is related to instantaneous uniformity of the microbubble, which is determined by the shaking method before preparation. Improving instantaneous uniformity of SonoVue microbubbles may increase the binding rate and stability of targeted microbubbles to JARs, thus to improve the image of JARs.
[Preoperative phase of limited normovolemic hemodilution]. (1983)

In 35 cases, the attempt is made to present hemodilution as an appropriate means of hepatitis prophylaxis and blood sparing in patients having to undergo selective orthopedic or oral surgery. Especially in hospitals which cannot afford the expensive methods of autotransfusion, this method which is easy to perform from the technical and practical point of view offers a possibility of markedly reducing the transfusion rate of whole blood. Taking into account possible contraindications, this method is to be considered in all patients undergoing selective surgery where the general condition of the patient is sufficient and a blood loss of 1000-1500 ml is not exceeded.
Ribosomal Protein L17, RpL17, is an Inhibitor of Vascular Smooth Muscle Growth and Carotid Intima Formation (2012)

RpL17 acts as a vascular smooth muscle cell growth inhibitor (akin to a tumor suppressor) and represents a potential therapeutic target to limit carotid intima-media thickening.
Laser Generation of Excitons and Fluorescence in Anthracene Crystals (1965)

Experimental and theoretical studies are reported of the short-lived and delayed fluorescence of anthracene single crystals, excited by single- and double-photon absorption. A giant-pulse ruby laser provides the primary source of radiation of 14 400 cm−1 (up to 1027 photons/cm2·sec) and is also used to generate second-harmonic radiation from ADP, as well as stimulated Raman radiation of 12 800 and 17 500 cm−1 from liquid oxygen. The time dependence of the fluorescence intensity is studied as a function of laser intensity, crystal temperature and excitation wavelength. The very intense fast fluorescence with a half-life of 30 nsec at 300°K, characteristic of singlet exciton decay, and the relatively weak delayed fluorescence which involves intermediate triplet states, are separated using sectored disks. It is concluded that the triplet state at 14 750 cm−1 can be populated (i) by direct absorption of laser photons involving an activation energy of 350 cm−1; (ii) via two-photon absorption, presumably leading to a vibrationally excited state of the 1B2u exciton, followed by intersystem crossing; (iii) via one-photon (second-harmonic) excitation from levels≥700 cm−1 into the singlet absorption band, followed by conversion of the singlet exciton into a triplet pair. The latter process is suggested by the observed activation energy of 700 cm−1. In agreement with these interpretations, the delayed fluorescence intensity is found to vary with the second to fourth power of the laser intensity depending on the experimental conditions. Also, light of 17 500 cm−1 leads exclusively to Process (i), light of 12 800 cm−1 exclusively to (ii). Triplet lifetimes from 2–17 msec are obtained, depending on crystal purity, which indicates that unimolecular triplet decay is an extrinsic, radiationless process. A singlet—triplet intersystem crossing rate constant of about 3×10−5 sec−1 is estimated. The triplet—triplet annihilation rate constant is found to be about 5×10−11 cm3 sec−1. This value considered together with the triplet-pair creation process suggests a triplet exchange rate ≳ 1013 sec−1 and a triplet diffusion constant ≳o5×10−4cm2/sec.
Trafficking of G Protein–Coupled Receptors (2006)

G protein-coupled receptors (GPCRs) play an integral role in the signal transduction of an enormous array of biological phenomena, thereby serving to modulate at a molecular level almost all components of human biology. This role is nowhere more evident than in cardiovascular biology, where GPCRs regulate such core measures of cardiovascular function as heart rate, contractility, and vascular tone. GPCR/ligand interaction initiates signal transduction cascades, and requires the presence of the receptor at the plasma membrane. Plasma membrane localization is in turn a function of the delivery of a receptor to and removal from the cell surface, a concept defined most broadly as receptor trafficking. This review illuminates our current view of GPCR trafficking, particularly within the cardiovascular system, as well as highlights the recent and provocative finding that components of the GPCR trafficking machinery can facilitate GPCR signaling independent of G protein activation.
Directional control of lamellipodia extension by constraining cell shape and orienting cell tractional forces (2002)

Directed cell migration is critical for tissue morphogenesis and wound healing, but the mechanism of directional control is poorly understood. Here we show that the direction in which cells extend their leading edge can be controlled by constraining cell shape using micrometer-sized extracellular matrix (ECM) islands. When cultured on square ECM islands in the presence of motility factors, cells preferentially extended lamellipodia, filopodia, and microspikes from their corners. Square cells reoriented their stress fibers and focal adhesions so that tractional forces were concentrated in these corner regions. When cell tension was dissipated, lamellipodia extension ceased. Mechanical interactions between cells and ECM that modulate cytoskeletal tension may therefore play a key role in the control of directional cell motility.
The application of numerical estimates of base calling accuracy to DNA sequencing projects (1995)

During DNA sequencing projects one of the most labour intensive and highly skilled tasks is to view the original trace descriptions of gels and to adjudicate between conflicting readings. Given the current methods of calculating a consensus, the majority of the time employed in viewing traces and editing readings is actually devoted to making the poorer data fit the good data. We propose new consensus calculation algorithms that employ numerical estimates of base calling accuracy and which when used in conjunction with an automatic detector of contradictory data should greatly reduce the time spent checking and editing readings and hence improve DNA sequencing productivity.
Human herpes virus 8 interleukin‐6 homologue triggers gp130 on neuronal and hematopoietic cells (2000)

Human herpes virus-8 (HHV8) encodes a cytokine named viral interleukin-6 (vIL-6) that shares 25% amino-acid identity with its human homologue. Human IL-6 is known to be a growth and differentiation factor of lymphatic cells and plays a potential role in the pathophysiology of various lymphoproliferative diseases. vIL-6 is expressed in HHV8-associated-diseases including Kaposi's sarcoma, Body-cavity-based-lymphoma and Castleman's disease, suggesting a pathogenetic involvement in the malignant growth of B-cell associated diseases and other malignant tumours. We expressed vIL-6 in Escherichia coli as a fusion protein with recombinant periplasmic maltose binding protein. After cleavage from the maltose binding protein moiety and purification, vIL-6 was shown to be correctly folded using circular dichroism spectroscopy. A rabbit antiserum was raised against the recombinant vIL-6 protein. vIL-6 turned out to be active on cells that expressed gp130 but no IL-6 receptor (IL-6-R) suggesting that, in contrast to human IL-6, vIL-6 stimulated gp130 directly. Accordingly, vIL-6 activity could be inhibited by a soluble gp130 Fc Fusion protein. vIL-6 was shown to induce neuronal differentiation of rat pheochromocytoma cells and to stimulate colony formation of human hematopoietic progenitor cells. Thus, vIL-6 exhibits biologic activity that has only been observed for the IL-6/soluble IL-6-R complex but not for IL-6 alone. These properties are important for the evaluation of the pathophysiological potential of vIL-6.
Computer-aided diagnosis: a neural-network-based approach to lung nodule detection (1998)

In this work, we have developed a computer-aided diagnosis system, based on a two-level artificial neural network (ANN) architecture. This was trained, tested, and evaluated specifically on the problem of detecting lung cancer nodules found on digitized chest radiographs. The first ANN performs the detection of suspicious regions in a low-resolution image. The input to the second ANN are the curvature peaks computed for all pixels in each suspicious region. This comes from the fact that small tumors possess and identifiable signature in curvature-peak feature space, where curvature is the local curvature of the image data when viewed as a relief map. The output of this network is thresholded at a chosen level of significance to give a positive detection. Tests are performed using 60 radiographs taken from routine clinic with 90 real nodules and 288 simulated nodules. We employed free-response receiver operating characteristics method with the mean number of false positives (FP's) and the sensitivity as performance indexes to evaluate all the simulation results. The combination of the two networks provide results of 89%-96% sensitivity and 5-7 FP's/image, depending on the size of the nodules.
Kinetics of Oxidation of Tyrosine and Dityrosine by Myeloperoxidase Compounds I and II (1995)

The oxidation of lipoproteins is considered to play a key role in atherogenesis, and tyrosyl radicals have been implicated in the oxidation reaction. Tyrosyl radicals are generated in a system containing myeloperoxidase, H2O2, and tyrosine, but details of this enzyme-catalyzed reaction have not been explored. We have performed transient spectral and kinetic measurements to study the oxidation of tyrosine by the myeloperoxidase intermediates, compounds I and II, using both sequential mixing and single-mixing stopped-flow techniques. The one-electron reduction of compound I to compound II by tyrosine has a second order rate constant of (7.7 +/- 0.1) x 10(5) M-1 s-1. Compound II is then reduced by tyrosine to native enzyme with a second order rate constant of (1.57 +/- 0.06) x 10(4) M-1 s-1. Our study further revealed that, compared with horseradish peroxidase, thyroid peroxidase, and lactoperoxidase, myeloperoxidase is the most efficient catalyst of tyrosine oxidation at physiological pH. The second order rate constant for the myeloperoxidase compound I reaction with tyrosine is comparable with that of its compound I reaction with chloride: (4.7 +/- 0.1) x 10(6) M-1 s-1. Thus, although chloride is considered the major myeloperoxidase substrate, tyrosine is able to compete effectively for compound I. Steady state inhibition studies demonstrate that chloride binds very weakly to the tyrosine binding site of the enzyme. Coupling of tyrosyl radicals yields dityrosine, a highly fluorescent stable compound that had been identified as a possible marker for lipoprotein oxidation. We present spectral and kinetic data showing that dityrosine is further oxidized by both myeloperoxidase compounds I and II. The second order rate constants we determined for dityrosine oxidation are (1.12 +/- 0.01) x 10(5) M-1 s-1 for compound I and (7.5 +/- 0.3) x 10(2) M-1 s-1 for compound II. Therefore, caution must be exercised when using dityrosine as a quantitative index of lipoprotein oxidation, particularly in the presence of myeloperoxidase and H2O2.
The determination of device noise parameters (1969)

A novel noise measurement technique is outlined which results in data that directly give the noise parameters of the test device when processed by a simple computer program.
Epidermal Growth Factor Receptor Expression in Human Lung Carcinomas Defined by a Monoclonal Antibody<xref ref-type="fn" rid="FN2">2</xref> (1987)

Acetone-fixed frozen tissue sections from 56 cases of human lung carcinoma were tested for reactivity by an indirect immunoperoxidase technique with a monoclonal antibody (MAb 528) specific for the external domain of the epidermal growth factor receptor (EGFR). MAb 528 reacted with all epidermoid (22/22) and large-cell (4/4) lung carcinomas evaluated. The antibody was also positive with a subset of lung adenocarcinomas (13/21) and did not react with small-cell lung cancers (SCLCs) (0/9). MAb 528 also stained normal bronchial epithelium identified within the tumor sections of 5 cases. Thus EGFR was expressed by all epidermoid and large-cell lung carcinomas examined, a subset of lung adenocarcinomas, and normal bronchial epithelium. EGFR expression was not identified in any of the SCLCs tested. These data imply that immunohistochemical detection of EGFR expression may find future application in distinguishing epidermoid, large-cell, and some adenocarcinomas of the lung from SCLCs.
A novel stationary wavelet denoising algorithm for array-based DNA Copy Number data (2007)

High-throughput microarrays have recently been developed to detect DNA Copy Number (DCN) aberrations. The resulting DCN data is often very noisy. Previous denoising methods proposed for DCN data assumed uniform spacing between adjacent probes, which is not true and can potentially result in erroneous output. To address this issue, we developed a novel stationary wavelet denoising scheme for DCN data. Empirical results on synthetic data showed that our method outperformed the best previous method by 4.612.7% in terms of the root mean squared error. Experiments on a real data set also confirmed the applicability of our method.
Apolipoprotein E Expression and Behavioral Toxicity of High Charge, High Energy (HZE) Particle Radiation (2002)

These studies show that apoE expression influences the behavioral toxicity of HZE particle radiation and suggest that apoE plays a role in the repair/recovery from radiation injury of the CNS. ApoE deficiency may exacerbate the previously reported effects of HZE particle radiation in accelerating the brain aging process.
Effects of Dietary Restriction and Antioxidants on Presbyacusis (2000)

Intervention designed to reduce reactive oxygen metabolite damage appears to protect against age-related hearing loss specifically and aging in general. This is reflected by an overall reduction in mtDNA deletions. These data also suggest that the common aging deletion appears to be associated with presbyacusis, as demonstrated by an increased frequency of the mtDNA del4834 in the cochleae with the most significant hearing loss. Nutritional and pharmacological strategies may very well provide rational treatment options that would limit the age-associated increase in ROM generation, reduce mtDNA damage, and reduce the degree of hearing loss as the organism advances in age.
Probing Bacterial‐Toxin Inhibition with Synthetic Glycopolymers Prepared by Tandem Post‐Polymerization Modification: Role of Linker Length and Carbohydrate Density (2012)

Probing the depths: A tandem post-polymerization modification strategy was used to systematically probe the multivalent inhibition of a bacterial toxin as a function of linker length (see scheme), carbohydrate density, and glycopolymer chain length. Guided by structural-biology information, the binding-pocket depth of the toxin was probed and used as a means to specifically improve inhibition of the toxin by the glycopolymer.
Structure-based discovery of an inhibitor of Arf activation by Sec7 domains through targeting of protein–protein complexes (2007)

Small molecules that produce nonfunctional protein-protein complexes are an alternative to competitive inhibitors for the inhibition of protein functions. Here we target the activation of the small GTP-binding protein Arf1, a major regulator of membrane traffic, by the Sec7 catalytic domain of its guanine nucleotide exchange factor ARNO. The crystal structure of the Arf1-GDP/ARNO complex, which initiates the exchange reaction, was used to discover an inhibitor, LM11, using in silico screening of a flexible pocket near the Arf1/ARNO interface. Using fluorescence kinetics and anisotropy, NMR spectroscopy and mutagenesis, we show that LM11 acts following a noncompetitive mechanism in which the inhibitor targets both Arf1-GDP and the Arf1-GDP/ARNO complex and produces a nonfunctional Arf-GDP/ARNO complex whose affinity is similar to that of the native complex. In addition, LM11 recognizes features of both Arf and ARNO near the Arf/Sec7 interface, a characteristic reminiscent of the paradigm interfacial inhibitor Brefeldin A. We then show that LM11 is a cell-active inhibitor that impairs Arf-dependent trafficking structures at the Golgi. Furthermore, LM11 inhibits ARNO-dependent migration of Madin-Darby canine kidney (MDCK) cells, demonstrating that ARNO is a target of LM11 in cells. Remarkably, LM11 inhibits the activation of Arf1 but not Arf6 in vitro, pointing to a possible synergy between Arf1 and Arf6 activation by ARNO in cell migration. Our design method shows that flexible regions in protein-protein complexes provide drugable sites with the potential to develop novel tools for investigating and inhibiting signaling pathways.
Venlafaxine Pharmacobezoar Causing Intestinal Ischemia Requiring Emergent Hemicolectomy (2011)

Pharmacobezoars are an uncommon but potentially problematic manifestation of drug overdose. Diagnosed radiographically, endoscopically, intraoperatively, or postmortem, a bezoar is a mass of any form of unabsorbed material within the gastrointestinal tract. When they occur, they tend to form at anatomic strictures at any point between the esophagus and the rectum. They commonly occur in patients with prior abdominal surgery or altered GI motility. Besides obstructive and ischemic complications when impacted, pharmacobezoars can also cause prolonged toxicologic effects due to the retained drug mass.

Venlafaxine is a bicyclic phenylethylamine antidepressant that inhibits serotonin, norepinephrine, and dopamine reuptake in the CNS. Morbidity and mortality from venlafaxine overdose are typically from seizures and cardiovascular toxicity. We describe a novel case of massive overdose of extended-release (ER) venlafaxine leading to obstructive pharmacobezoar formation at the ileocecal junction, with consequent bowel ischemia and necrosis requiring emergent hemicolectomy.
Synthese von (‐)‐(R)‐4‐Hydroxy‐β‐ionon und (‐)‐(5 R, 6 S)‐5‐Hydroxy‐4,5‐dihydro‐α‐ionon aus (‐)‐(S)‐α‐Ionon (1980)

Synthesis of (‐)‐( R )‐4‐Hydroxy‐β‐ionone and (‐)‐(5 R , 6 S )‐5‐Hydroxy‐4,5‐dihydro‐α‐ionone aus (‐)‐( S )‐α‐Ionone The absolute configuration of the chiral 4‐hydroxy‐β‐ionones and 5‐hydroxy‐4,5‐dihydro‐α‐ionones has been determined by chemical connection with (‐)‐( S )‐α‐ionone i.e. by stereoselective epoxidation of the latter, followed by base catalyzed opening of the epoxide as well as by its hydride reduction.