gebhart/patrepeval huggingface dataset:
Quantitative confirmation of testosterone and epitestosterone in human urine by LC/Q‐ToF mass spectrometry for doping control (2008)

Testosterone (T) is the primary male sex hormone. In addition to the development of secondary sex characteristics, testosterone has anabolic effects including increases in muscle size and strength and increases in lean body mass, making it an attractive candidate to enhance athletic performance. In the case of exogenous administration of testosterone, the ratio of testosterone to its isomer, epitestosterone (E), is elevated. WADA has set a standard for T/E ratios of 4.0 as indicative of possible exogenous testosterone administration. Typically, a sample that screens for a T/E ratio above that threshold is then subjected to quantitative confirmation by GC/MS. This methodology, however, can limited due to sensitivity issues as well as a limited number of qualifying ions that can be used for unambiguous identification. We have developed a confirmation method which uses liquid/liquid extraction, followed by room temperature Girard P derivatization, and analysis using LC/MS-ToF. We observe a number of advantages over conventional GC/MS analysis. Analysis time is decreased. Sensitivity is increased, resulting in limits of detection of 2 and 0.5 ng/ml for testosterone and epitestosterone, respectively. The number of diagnostic qualifier ions is also increased allowing more confident identification of the analytes. Finally, while this method has been developed on a QToF instrument, it should be easily transferable to any tandem LC/MS/MS system.
Efficient Synthesis of Enantiomerically Pure 2-Acylaziridines:  Facile Syntheses of N-Boc-safingol, N-Boc-d-erythro-sphinganine, and N-Boc-spisulosine from a Common Intermediate (2003)

Various enantiomerically pure 2-acylaziridines were prepared efficiently from the corresponding aziridine-2-carboxylate via Weinreb's amide and the subsequent treatment of organometallic compounds. The carbonyl group of those 2-acylaziridines was stereoselectively reduced by NaBH4in the presence of ZnCl2 to give erythro-1,2-amino alcohols with high diastereoselectivities and chemical yields. Using this methodology, we prepared (1R,2S)-N-Boc-norephedrine 5, N-Boc-safingol 8, N-Boc-D-erythro-sphinganine 9, and N-Boc-spisulosine 10 in high yields.
Introduction to metallic nanoparticles (2010)

Metallic nanoparticles have fascinated scientist for over a century and are now heavily utilized in biomedical sciences and engineering. They are a focus of interest because of their huge potential in nanotechnology. Today these materials can be synthesized and modified with various chemical functional groups which allow them to be conjugated with antibodies, ligands, and drugs of interest and thus opening a wide range of potential applications in biotechnology, magnetic separation, and preconcentration of target analytes, targeted drug delivery, and vehicles for gene and drug delivery and more importantly diagnostic imaging. Moreover, various imaging modalities have been developed over the period of time such as MRI, CT, PET, ultrasound, SERS, and optical imaging as an aid to image various disease states. These imaging modalities differ in both techniques and instrumentation and more importantly require a contrast agent with unique physiochemical properties. This led to the invention of various nanoparticulated contrast agent such as magnetic nanoparticles (Fe(3)O(4)), gold, and silver nanoparticles for their application in these imaging modalities. In addition, to use various imaging techniques in tandem newer multifunctional nanoshells and nanocages have been developed. Thus in this review article, we aim to provide an introduction to magnetic nanoparticles (Fe(3)O(4)), gold nanoparticles, nanoshells and nanocages, and silver nanoparticles followed by their synthesis, physiochemical properties, and citing some recent applications in the diagnostic imaging and therapy of cancer.
Detection of All Single-Base Mismatches in Solution by Chemiluminescence (1996)

A rapid in-solution method for the detection of all 12 single-base mismatches is described. The technique is based on the hybridization protection assay (HPA) format that utilizes oligonucleotide probes labeled with a highly chemiluminescent acridinium ester (AE). Hydrolysis by weak base renders AE permanently non-chemiluminescent. When an AE-labeled probe hybridizes to an exactly complementary target, AE is protected from hydrolysis relative to the unhybridized conformation. Single-base mutations in the duplex adjacent to the site of AE attachment disrupt this protection resulting in rapid AE hydrolysis and loss of chemiluminescence. The discrimination effect was seen in both DNA and RNA. Studies of Tm values revealed that this effect is not due to a decrease in the overall stability of the duplex, suggesting the AE is responding to local structural changes in the double helix induced by mismatches. Using this principle all 12 single mismatches were clearly discriminated from the corresponding matched sequences. The assay is homogeneous, simple, sensitive, applicable to both amplified and non-amplified targets, and is completed in 30-60 min. An example showing discrimination between wild-type and mutant sequences corresponding to the reverse transcriptase coding region of HIV-1 is given.
Role of heparin and heparinlike molecules in thrombosis and atherosclerosis. (1985)

Antithrombin is a protease inhibitor that neutralizes the activity of the serine proteases of the coagulation cascade, such as factors IXa, Xa, XIa, XIIa, and thrombin by forming a 1:1 stoichiometric complex between enzyme and inhibitor via a reactive site (arginine)-active center (serine interaction). Heparin binds to lysyl residues on antithrombin and accelerates the rate of complex formation. Studies of the binding parameters and kinetic characteristics of the heparin-antithrombin-hemostatic enzyme interactions have revealed that binding of heparin to antithrombin is responsible for a approximately 1000-fold acceleration of the thrombin-antithrombin or factor IXa-antithrombin and factor Xa-antithrombin interactions (allosteric effect). The reactions between free thrombin or free factor IXa and heparin provide an additional 4- to 15-fold enhancement in the rate of these processes (approximation effect) and account for 1-2% of the total rate of enhancement. It has been shown that commercial heparin is composed of anticoagulantly active and anticoagulantly inactive species. The anticoagulantly active mucopolysaccharide contains a unique antithrombin-binding site. Anticoagulantly inactive heparin does not possess this structure and does not bind to the protease inhibitor. Anticoagulantly active heparin also contains a critical region required for the acceleration of the various enzyme-inhibitor interactions. The two different domains of the heparin molecule interact with separate areas of antithrombin and induce distinct conformational transitions within the protease inhibitor. Anticoagulantly active heparinlike molecules (most likely a heparan sulfate with an appropriate sequence for anticoagulant activity) are found on the luminal surface of the endothelium. This heparinlike substance appears to alter the conformation of antithrombin in a manner virtually identical to that of commercial heparin. Both anticoagulantly active heparin and inactive heparin are able to suppress smooth muscle cell proliferation in vitro and in vivo and can reverse the effects of mitogenic factors such as platelet-derived growth factor. Furthermore, it has been shown that bovine aortic endothelial cells produce heparinlike molecules with growth inhibitory potency.
A phase I study of T101-ricin A chain immunotoxin in refractory chronic lymphocytic leukemia. (1988)

Four patients with chronic lymphocytic leukemia refractory to alkylating agents were treated with T101-ricin A chain immunotoxin (T101-RTA) as part of a phase I study. Over a 4-week period, each patient received eight intravenous infusions of 3 mg/m2 T101-RTA over 1 h. All infusions were well tolerated. Patients had mild fevers but no other systemic toxicities. In vivo binding of T101-RTA was detected by FACS analysis using anti-mouse Ig-FITC or anti-A chain-FITC antibody conjugates. Saturation of circulating leukemic cell-associated target antigen was achieved in three of the patients. Available CD5 sites per cell dropped precipitously at the completion of infusions in all four patients, returning to within 30% of baseline by 24 h. Pharmacokinetic studies revealed rapid clearance of T101-RTA, with wide interpatient variability in peak serum levels (the highest levels in those patients who saturated their circulating CD5 antigen with immunotoxin). Although no patient developed detectable levels of antimurine antibodies, one patient did have a rising titer of anti-ricin A chain antibody associated with declining peak serum levels of immunotoxin. All patients had a rapid fall in WBC count of less than 24-h duration after each T101-RTA infusion, most likely secondary to the antibody portion of immunotoxin. No sustained benefit could be demonstrated in any patient, possibly because in the absence of an enhancing agent the leukemic cells of all four patients were resistent to T101-RTA at concentrations up to 2,000 ng/ml in vitro.
Mechanisms of Hepatocyte Growth Factor Stimulation of Keratinocyte Metalloproteinase Production (1996)

Matrix metalloproteinases participate in normal physiologic processes; however, their overproduction has been associated with connective tissue destruction in a variety of pathological states. Migrating basal keratinocytes transiently express collagenase-1 during normal cutaneous reepithelialization. However, the overexpression of both collagenase-1 and stromelysin-1 has been associated with the pathogenesis of chronic nonhealing ulcers. Aberrant expression of metalloproteinases in inflammation is mediated, at least in part, by soluble factors. Since hepatocyte growth factor/scatter factor (HGF/SF) has been reported to promote keratinocyte migration and proliferation, key events in wound repair, and since HGF/SF is produced by dermal fibroblasts and its c-Met receptor is expressed by basal keratinocytes in wounded skin, we have studied the effects of HGF/SF upon keratinocyte metalloproteinase expression. We have found that HGF/SF can stimulate keratinocyte collagenase-1 and stromelysin-1 production in a dose-dependent and matrix-dependent manner. Expression of 92-kDa gelatinase was not affected by HGF/SF. We determined that HGF/SF regulation of collagenase-1 expression is transcriptionally mediated and requires tyrosine kinase and protein kinase C activaties. HGF/NK1, a naturally occurring, truncated form of HGF/SF, also stimulates collagenase-1 production, but much less efficiently than does the parent molecule. However, HGF/NK2, another HGF/SF splice variant, as well as heparin, potently inhibit HGF/SF-induced collagenase-1 synthesis. These results indicate that HGF/SF and its naturally occurring splice variants have diverse biological effects on keratinocytes and suggest an additional mechanism whereby HGF/SF may regulate keratinocyte function during wound repair.
Tunneling conductance and local density of states in tight-binding junctions (2011)

We study the relationship between the differential conductance and the local density of states in tight-binding tunnel junctions where the junction geometry can be varied between the point-contact and the planar-contact limits. The conductances are found to differ significantly in these two limiting cases. We also examine how the matrix element influences the tunneling characteristics and produces contrast in a simple model of scanning tunneling microscope (STM). Some implications regarding the interpretation of STM spectroscopic data in the cuprates are discussed. The calculations are carried out within the real-space Keldysh formalism.
Anti-Inflammatory and Anti-Nociceptive Activities of Methanol Extract from Aerial Part of Phlomis younghusbandii Mukerjee (2014)

This study was designed to investigate the anti-inflammatory and anti-nociceptive activity of the methanol extract from the aerial part of Phlomis younghusbandii (MEAP) and to explore the possible related mechanisms. Anti-inflammatory effects of MEAP were evaluated by using the ear edema test induced by dimethylbenzene and vascular permeability test induced by acetic acid. Anti-nociceptive activities of MEAP were evaluated by the chemical nociception in models of acetic acid-induced writhing and formalin-induced hind paw licking, and by the thermal nociception in hot plate tests. Mechanisms of MEAP activities also were explored by evaluating expression levels of TNF-α, IL-6 and iNOS induced by LPS using real-time fluorogenic PCR and expression of COX-2 using Western blotting and an open-field test. The results indicated that the MEAP administered orally could significantly decrease ear edema induced by dimethylbenzene and increase vascular permeability induced by acetic acid. Additionally, the nociceptions induced by acetic acid and formalin were significantly inhibited. The anti-nociceptive effect could not be decreased by naloxone in the formalin test, and MEAP did not affect the normal autonomic activities of mice. Expression levels of pro-inflammatory cytokines (TNF-α, IL-6, iNOS) induced by LPS were decreased obviously by treatment with MEAP. Furthermore, COX-2 expression in the spinal dorsal horns of the pain model mice induced by formalin was significantly down-regulated by MEAP. In conclusion, MEAP has significant anti-inflammatory and antinociceptive activities, and the mechanisms may be related to the down-regulated expression of TNF-α, IL-6, iNOS and COX-2.
Antimicrobial Use and Resistance in Animals (2002)

Food animals in the United States are often exposed to antimicrobials to treat and prevent infectious disease or to promote growth. Many of these antimicrobials are identical to or closely resemble drugs used in humans. Precise figures for the quantity of antimicrobials used in animals are not publicly available in the United States, and estimates vary widely. Antimicrobial resistance has emerged in zoonotic enteropathogens (e.g., Salmonella spp., Campylobacter spp.), commensal bacteria (e.g., Escherichia coli, enterococci), and bacterial pathogens of animals (e.g., Pasteurella, Actinobacillus spp.), but the prevalence of resistance varies. Antimicrobial resistance emerges from the use of antimicrobials in animals and the subsequent transfer of resistance genes and bacteria among animals and animal products and the environment. To slow the development of resistance, some countries have restricted antimicrobial use in feed, and some groups advocate similar measures in the United States. Alternatives to growth-promoting and prophylactic uses of antimicrobials in agriculture include improved management practices, wider use of vaccines, and introduction of probiotics. Monitoring programs, prudent use guidelines, and educational campaigns provide approaches to minimize the further development of antimicrobial resistance.
Skeletal muscle stem cells (2003)

Satellite cells are myogenic stem cells responsible for the post-natal growth, repair and maintenance of skeletal muscle. This review focuses on the basic biology of the satellite cell with emphasis on its role in muscle repair and parallels between embryonic myogenesis and muscle regeneration. Recent advances have altered the long-standing view of the satellite cell as a committed myogenic stem cell derived directly from the fetal myoblast. The experimental basis for this evolving perspective will be highlighted as will the relationship between the satellite cell and other newly discovered muscle stem cell populations. Finally, advances and prospects for cell-based therapies for muscular dystrophies will be addressed.
Bipolar installed CMOS technology without any process step increase for high speed cache SRAM (2002)

Double-polysilicon self-aligned bipolar transistor was installed to the CMOS process without any process step increase. The collector region and n-well were fabricated simultaneously by ion implantation. Gate self-aligned contact technique for 6T memory cell was applied for bipolar emitter contact. Obtained bipolar transistor characteristics were sufficient for current-sense amplifier use, which can realize low cost and high performance L2 cache SRAM.
Amino acid sequence of human plasma galactoglycoprotein: identity with the extracellular region of CD43 (sialophorin). (1992)

The amino acid sequence of galactoglycoprotein purified from human plasma was elucidated to 75% completeness by using chemical degradation of peptides and glycopeptides derived from digests of the protein with seven specific proteases. This sequence represents a polypeptide chain of approximately 220 amino acid residues including a high content of serine, threonine, alanine, and proline with one N-linked and multiple O-linked glycans. Comparison of peptide sequences from the native galactoglycoprotein and the deglycosylated derivative demonstrated the locations of 25 sites of O-glycosylation and three serine sites that are not glycosylated. The homogeneous N terminus was established as serine. C-terminal analysis revealed multiple C-terminal residues, suggesting that galactoglycoprotein molecules are of varying lengths. A search of a protein data base revealed that the galactoglycoprotein polypeptide is identical to the N-terminal (extracellular) polypeptide region of the blood-cell surface molecule CD43 (sialophorin, leukosialin). Further support of the relatedness of these molecules was obtained by immunoprecipitation of 125I-labeled galactoglycoprotein by monoclonal anti-CD43 antibodies. The composition and properties of the molecules together with the known structure of the gene encoding CD43 suggest that galactoprotein is derived by proteolytic cleavage from transmembrane "hexasaccharide CD43," known to be expressed on neutrophils, activated T lymphocytes, and platelets.
Growth hormone in male infertility (2011)

Growth hormone (GH) is expressed in a variety of tissues, including the testes, and has autocrine and paracrine functions as well. This, along with other factors, exerts autocrine and paracrine control over spermatogenesis. GH, used as an adjuvant therapy, induces spermatogenesis in non-responder patients with hypogonadotropic hypogonadism, who are not responding to gonadotropin or pulsatile luteinizing hormone (LH) therapy. GH has an important physiological role to play in spermatogenesis and male fertility.
Design of integrated radiation detectors with a-Si photodiodes on ceramic scintillators for use in X-ray computed tomography (1990)

An integrated radiation detector with a-Si photodiodes on ceramic scintillators is designed for use in X-ray computed tomography. The output signal is estimated using Monte Carlo simulation. Results show that this detector has higher sensitivity than a c-Si photodiode/scintillator detector when a transparent layer between the scintillator and the thin film semiconductor is optimized. The noise characteristic is also considered when an integrated detector is coupled with an operational amplifier. Good agreement is shown between predicted and measured parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical free-space multichannel switches composed of liquid-crystal light-modulator arrays and birefringent crystals (1998)

Transparent optical multichannel switches composed of liquid-crystal light modulator arrays and polarization beam routers composed of birefringent crystals are reported. For suppressing diffraction loss and stabilizing loss property, lens waveguide arrays are established in the switch body by inserting Fresnel lenslet arrays. The highly improved loss and crosstalk properties of the switch are confirmed.
A Cystic Fibrosis Transmembrane Conductance Regulator Splice Variant With Partial Penetrance Associated With Variable Cystic Fibrosis Presentations (1997)

Some patients express various features of cystic fibrosis (CF) even though essential characteristics of the disease might be absent. Such patients may suffer from respiratory disease without pancreatic insufficiency and normal sweat chloride levels. Others may present as male infertility because of congenital bilateral aplasia of the vas deferens (CBAVD) with no other signs of CF. The 5T allele, a DNA variant in a noncoding region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene that reduces the level of the normal CFTR transcripts, was found in increased frequency among male patients with CBAVD. The purpose of this study was to investigate the possibility that the 5T allele is associated with dysfunction of organs other than the male reproductive system, leading to CF or atypical CF. Analysis of the 5T allele was performed on 148 subjects (29 with CF, 61 with atypical CF, and 58 with CBAVD) carrying 232 chromosomes with unidentified CFTR mutations, and on 142 non-CF chromosomes from healthy subjects of Ashkenazi origin. The frequency of the 5T allele among chromosomes from patients of Jewish Ashkenazi origin with CF and atypical CF (six of 33; 18%) was significantly higher than the frequency in the normal Ashkenazi population (eight of 142; 6%; p = 0.03). Analysis of the clinical presentation of the five patients with CF and the 12 patients with atypical CF carrying the 5T allele indicated that most patients suffered from respiratory disease presenting as asthma like symptoms, nasal polyposis, chronic sinusitis, chronic bronchitis, or bronchiectasis. Six patients had pancreatic insufficiency, two with meconium ileus. Sweat Cl- levels ranged from normal to elevated. Of the six male patients with respiratory disease who were old enough to be evaluated for fertility status, five were fertile and one had pancreatic insufficiency. Among male patients with CBAVD, 41% suffered from respiratory symptoms. Thus, the 5T allele is a variant with partial penetrance causing disease with an extreme variability of clinical presentation: from normal healthy fertile subjects or male patients with CBAVD to those with atypical or typical clinical phenotype of CF.
Mixed T Helper Cell Signatures In Chronic Rhinosinusitis with and without Polyps (2014)

T cell cytokine patterns in healthy and inflamed sinonasal mucosa revealed that Th2 cells (IL-4 and IL-5 producing cells) are significantly increased in CRSwNP mucosal inflammation. Exposure to SEB stimulates Tr1 cells that may contribute to the Th2 bias in CRSwNP.
Resonant and notch behavior in intracranial pressure dynamics (2009)

This transfer function behavior is characteristic of a resonant notch system. This may represent a component of the intracranial Windkessel mechanism, which protects the microvasculature from arterial pulsatility. The impairment of this resonant notch system may play a role in the altered pulse pressure in conditions such as hydrocephalus and traumatic brain swelling. New models of intracranial dynamics are needed for understanding the frequency-sensitive behavior elucidated in these studies and could open a path for development of new therapies that are geared toward addressing the pulsation dysfunction in pathological conditions, such as hydrocephalus and traumatic brain injury, affecting ICP and flow dynamics.