gebhart/patrepeval huggingface dataset:
Alvimopan, a Novel, Peripherally Acting μ Opioid Antagonist (2004)

Alvimopan accelerated GI recovery and time to hospital discharge order written compared with placebo in patients undergoing laparotomy and was well tolerated.
Effects of soil type and farm management on soil ecological functional genes and microbial activities (2010)

Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.
Oligohis‐tags: mechanisms of binding to Ni2+‐NTA surfaces (2009)

Since immobilized metal ion affinity chromatography (IMAC) was first reported, several modifications have been developed. Among them, Ni(2+) immobilized by chelation with nitrilotriacetic acid (NTA) bound to a solid support has become the most common method for the purification of proteins carrying either a C- or N-terminal histidine (His) tag. Despite its broad application in protein purification, only little is known about the binding properties of the His-tag, and therefore almost no thermodynamic and kinetic data are available. In this study, we investigated the binding mechanism of His-tags to Ni(2+)-NTA. Different series of oligohistidines and mixed oligohistidines/oligoalanines were synthesized using automated solid-phase peptide synthesis (SPPS). Binding to Ni(2+)-NTA was analyzed both qualitatively and quantitatively with surface plasmon resonance (SPR) using commercially available NTA sensor chips from Biacore. The hexahistidine tag shows an apparent equilibrium dissociation constant (K(D)) of 14 +/- 1 nM and thus the highest affinity of the peptides synthesized in this study. Furthermore, we could demonstrate that two His separated by either one or four residues are the preferred binding motifs within hexahis tag. Finally, elongation of these referred motifs decreased affinity, probably due to increased entropy costs upon binding.
Solvent-Free Condensation of Pyrrole and Pentafluorobenzaldehyde:  A Novel Synthetic Pathway to Corrole and Oligopyrromethenes (1999)

The solvent-free condensation of pyrrole and pentafluorobenzaldehyde (and to a lesser extent other electron-poor aldehydes as well) leads to a variety of products, of which three have been isolated and fully characterized. The two main products (11% each) are an open-chain pentapyrrole and corrole, a tetrapyrrolic macrocycle.
Loss-of-Function Analysis Suggests ThatOmi/HtrA2Is Not an Essential Component of thepink1/parkinPathwayIn Vivo (2008)

Recently, a mutation in the mitochondrial protease Omi/HtrA2, G399S, was found in sporadic Parkinson's disease (PD) patients, leading to the designation of Omi/HtrA2 as PD locus 13 (PARK13). G399S reportedly results in reduced Omi protease activity. In vitro studies have suggested that Omi/HtrA2 acts downstream of PINK1, mutations in which mediate recessive forms of PD. We, as well as other, have previously shown that the Drosophila homologs of the familial PD genes, PINK1 (PARK6) and PARKIN (PARK2), function in a common genetic pathway to regulate mitochondrial integrity and dynamics. Whether Omi/HtrA2 regulates mitochondrial integrity and whether it acts downstream of PINK1 in vivo remain to be explored. Here, we show that Omi/HtrA2 null mutants in Drosophila, in contrast to pink1 or parkin null mutants, do not show mitochondrial morphological defects. Extensive genetic interaction studies do not provide support for models in which Omi/HtrA2 functions in the same genetic pathway as pink1, or carries out partially redundant functions with pink1, at least with respect to regulation of mitochondrial integrity and dynamics. Furthermore, Omi/HtrA2 G399S retains significant, if not full, function of Omi/HtrA2, compared with expression of protease-compromised versions of the protein. In light of recent findings showing that G399S can be found at comparable frequencies in PD patients and healthy controls, we do not favor a hypothesis in which Omi/HtrA2 plays an essential role in PD pathogenesis, at least with respect to regulation of mitochondrial integrity in the pink1/parkin pathway.
Negative Role of Colony-Stimulating Factor-1 in Macrophage, T Cell, and B Cell Mediated Autoimmune Disease in MRL-Fas lpr Mice (2004)

Inflammation in the kidney and other tissues (lung, and salivary and lacrimal glands) is characteristic of MRL-Fas(lpr) mice with features of lupus. Macrophages (Mphi) are prominent in these tissues. Given that 1) Mphi survival, recruitment, proliferation, and activation during inflammation is dependent on CSF-1, 2) Mphi mediate renal resident cell apoptosis, and 3) CSF-1 is up-regulated in MRL-Fas(lpr) mice before, and during nephritis, we hypothesized that CSF-1-deficient MRL-Fas(lpr) mice would be protected from Mphi-mediated nephritis, and the systemic illness. To test this hypothesis, we compared CSF-1-deficient MRL-Fas(lpr) with wild-type strains. Renal pathology is suppressed and function improved in CSF-1-deficient MRL-Fas(lpr) mice. There are far fewer intrarenal Mphi and T cells in CSF-1-deficient MRL-Fas(lpr) vs wild-type kidneys. This leukocytic reduction results from suppressed infiltration, and intrarenal proliferation, but not enhanced apoptosis. The CSF-1-deficient MRL-Fas(lpr) kidneys remain preserved as indicated by greatly reduced indices of injury (nephritogenic cytokines, tubular apoptosis, and proliferation). The renal protective mechanism in CSF-1-deficient mice is not limited to reduced intrarenal leukocytes; circulating Igs and autoantibodies, and renal Ig deposits are decreased. This may result from enhanced B cell apoptosis and fewer B cells in CSF-1-deficient MRL-Fas(lpr) mice. Furthermore, the systemic illness including, skin, lung, and lacrimal and salivary glands pathology, lymphadenopathy, and splenomegaly are dramatically suppressed in CSF-1-deficient MRL-Fas(lpr) as compared with wild-type mice. These results indicate that CSF-1 is an attractive therapeutic target to combat Mphi-, T cell-, and B cell-mediated autoimmune lupus.
Preparation of chemically ‘mutated’ aprotinin homologues by semisynthesis (1988)

The semisynthesis of homologues of aprotinin (BPTI) is described. The P1 amino acid residue of these homologues was substituted by other amino acids using peptide synthetic methods. The reactive-site-modified inhibitor (with the Lys15-Ala16 peptide bond hydrolyzed) was used as starting material. All carboxyl groups of the modified inhibitor were esterified with methanol, then the Lys15 methyl ester group was hydrolyzed selectively. Afterwards, Lys15 itself was split off. A new amino acid residue was incorporated by using water-soluble carbodiimide combined with an acylation catalyst. tert-Butyl-ester-protected amino acids were used for reinsertion. The method was tested by re-insertion of Lys15 to reconstitute the original inhibitor. Thirteen BPTI homologues with coded (Lys, Glu, Gly, Ala, Val, Ile, Leu) or uncoded amino acids (Abu, Ape, aIle, Ahx, tLeu, Neo) in position 15 were synthesized and the specificity of the inhibitors investigated. Amongst these, [Val15]BPTI was shown to be an excellent inhibitor for human polymorphonuclear leukocyte elastase having a complex dissociation constant of 0.11 nM. This inhibitor showed no detectable affinity to bovine pancreatic trypsin.
Limiting efficiencies of ideal single and multiple energy gap terrestrial solar cells (1980)

The maximum efficiencies of ideal solar cells are calculated for both single and multiple energy gap cells using a standard air mass 1.5 terrestrial solar spectrum. The calculations of efficiency are made by a simple graphical method, which clearly exhibits the contributions of the various intrinsic losses. The maximum efficiency, at a concentration of 1 sun, is 31%. At a concentration of 1000 suns with the cell at 300 K, the maximum efficiencies are 37, 50, 56, and 72% for cells with 1, 2, 3, and 36 energy gaps, respectively. The value of 72% is less than the limit of 93% imposed by thermodynamics for the conversion of direct solar radiation into work. Ideal multiple energy gap solar cells fall below the thermodynamic limit because of emission of light from the forward-biased p-n junctions. The light is radiated at all angles and causes an entropy increase as well as an energy loss.
Raman Imaging (2012)

The past decade has seen an enormous increase in the number and breadth of imaging techniques developed for analysis in many industries, including pharmaceuticals, food, and especially biomedicine. Rather than accept single-dimensional forms of information, users now demand multidimensional assessment of samples. High specificity and the need for little or no sample preparation make Raman imaging a highly attractive analytical technique and provide motivation for continuing advances in its supporting technology and utilization. This review discusses the current tools employed in Raman imaging, the recent advances, and the major applications in this ever-growing analytical field.
Gene-Environment Interaction Signatures by Quantitative mRNA Profiling in Exfoliated Buccal Mucosal Cells (2004)

Exfoliated cytologic specimens from mouth (buccal) epithelium may contain viable cells, permitting assay of gene expression for direct and noninvasive measurement of gene-environment interactions, such as for inhalation (e.g., tobacco smoke) exposures. We determined specific mRNA levels in exfoliated buccal cells collected by cytologic brush, using a recently developed RNA-specific real-time quantitative reverse transcription-PCR strategy. In a pilot study, metabolic activity of exfoliated buccal cells was verified by 3-[4,5-dimethylthiazol-2-yl]-2,5- diphenyltetrazolium assay in vitro. Transcriptional activity was observed, after timed in vivo exposure to mainstream tobacco smoke resulted in induction of CYP1B1 in serially collected buccal samples from the one subject examined. For a set of 11 subjects, mRNA expression of nine genes encoding carcinogen- and oxidant-metabolizing enzymes qualitatively detected in buccal cells was then shown to correlate with that in laser-microdissected lung from the same individuals (Chi2 = 52.91, P < 0.001). Finally, quantitative real-time reverse transcription-PCR assays for seven target gene (AhR, CYP1A1, CYP1B1, GSTM1, GSTM3, GSTP1, and GSTT1) and three reference gene [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin, and 36B4] transcripts were performed on buccal specimens from 42 subjects. In multivariate analyses, gender, tobacco smoke exposure, and other factors were associated with the level of expression of CYP1B1, GSTP1, and other transcripts on a gene-specific basis, but substantial interindividual variability in mRNA expression remained unexplained. Within the power limits of this pilot study, gene expression signature was not clearly predictive of lung cancer case or control status. This noninvasive and quantitative method may be incorporated into high-throughput human applications for probing gene-environment interactions associated with cancer.
Evaluation of a noninvasive continuous cardiac output monitoring system based on thoracic bioreactance (2007)

Noninvasive cardiac output (CO) measurement can be useful in many clinical settings where invasive monitoring is not desired. Bioimpedance (intrabeat measurement of changes in transthoracic voltage amplitude in response to an injected high-frequency current) has been explored for this purpose but is limited in some clinical settings because of inherently low signal-to-noise ratio. Since changes in fluid content also induce changes in thoracic capacitive and inductive properties, we tested whether a noninvasive CO measurement could be obtained through measurement of the relative phase shift of an injected current (i.e., bioreactance). We constructed a prototype device that applies a 75-kHz current and determines the relative phase shift (dPhi/dt) of the recorded transthoracic voltage. CO was related to the product of peak dPhi/dt, heart rate, and ventricular ejection time. The preclinical study was done in nine open-chest pigs put on right heart bypass so that CO could be varied at known values. This was followed by a feasibility study in 27 postoperative patients who had a Swan-Ganz catheter (SGC). The measurements of noninvasive CO measurement and cardiopulmonary bypass pump correlated to each other (r = 0.84) despite the large variation in CO and temperatures. Similarly, in patients, mean CO values were 5.18 and 5.17 l/min as measured by SGC and the noninvasive CO measurement system, respectively, and were highly correlated over the range of values studied (r = 0.90). Preclinical and clinical data demonstrate the feasibility of using blood flow-related phase shifts of transthoracic electric signals to perform noninvasive continuous CO monitoring.
Major biological obstacles for persistent cell-based regeneration of articular cartilage (2007)

Hyaline articular cartilage, the load-bearing tissue of the joint, has very limited repair and regeneration capacities. The lack of efficient treatment modalities for large chondral defects has motivated attempts to engineer cartilage constructs in vitro by combining cells, scaffold materials and environmental factors, including growth factors, signaling molecules, and physical influences. Despite promising experimental approaches, however, none of the current cartilage repair strategies has generated long lasting hyaline cartilage replacement tissue that meets the functional demands placed upon this tissue in vivo. The reasons for this are diverse and can ultimately result in matrix degradation, differentiation or integration insufficiencies, or loss of the transplanted cells and tissues. This article aims to systematically review the different causes that lead to these impairments, including the lack of appropriate differentiation factors, hypertrophy, senescence, apoptosis, necrosis, inflammation, and mechanical stress. The current conceptual basis of the major biological obstacles for persistent cell-based regeneration of articular cartilage is discussed, as well as future trends to overcome these limitations.
The use of lactoperoxidase for the bleaching of fluid whey (2012)

Lactoperoxidase (LP) is the second most abundant enzyme in bovine milk and has been used in conjunction with hydrogen peroxide (H₂O₂) and thiocyanate (SCN⁻) to work as an antimicrobial in raw milk where pasteurization is not feasible. Thiocyanate is naturally present and the lactoperoxidase system purportedly can be used to bleach dairy products, such as whey, with the addition of very little H₂O₂ to the system. This study had 3 objectives: 1) to quantify the amount of H₂O₂ necessary for bleaching of fluid whey using the LP system, 2) to monitor LP activity from raw milk through manufacture of liquid whey, and 3) to compare the flavor of whey protein concentrate 80% (WPC80) bleached by the LP system to that bleached by traditional H₂O₂ bleaching. Cheddar cheese whey with annatto (15 mL of annatto/454 kg of milk, annatto with 3% wt/vol norbixin content) was manufactured using a standard Cheddar cheesemaking procedure. Various levels of H₂O₂ (5-100 mg/kg) were added to fluid whey to determine the optimum concentration of H₂O₂ for LP activity, which was measured using an established colorimetric method. In subsequent experiments, fat-separated whey was bleached for 1h with 250 mg of H₂O₂/kg (traditional) or 20 mg of H₂O₂/kg (LP system). The WPC80 was manufactured from whey bleached with 250 mg of H₂O₂/kg or 20mg of H₂O₂/kg. All samples were subjected to color analysis (Hunter color values and norbixin extraction) and proximate analysis (fat, protein, and moisture). Sensory and instrumental volatile analyses were conducted on WPC80. Optimal LP bleaching in fluid whey occurred with the addition of 20mg of H₂O₂/kg. Bleaching of fluid whey at either 35 or 50°C for 1 h with LP resulted in > 99% norbixin destruction compared with 32 or 47% destruction from bleaching with 250 mg of H₂O₂/kg, at 35 or 50°C for 1 h, respectively. Higher aroma intensity and increased lipid oxidation compounds were documented in WPC80 from bleached whey compared with WPC80 from unbleached whey. Monitoring of LP activity throughout cheese and whey manufacture showed that LP activity sharply decreased after 30 min of bleaching (17.01 ± 1.4 to < 1 U/mL), suggesting that sufficient bleaching takes place in a very short amount of time. Lactoperoxidase averaged 13.01 ± 0.7 U/mL in unpasteurized, fat-separated liquid whey and 138.6 ± 11.9 U/mL in concentrated retentate (11% solids). Lactoperoxidase may be a viable alternative for chemical whey bleaching.
Autologous stem cell transplantation for solid tumors in children (1997)

The dose-effect relationship in pediatric oncology conventional chemotherapy is emphasized. Rationales for the use of megatherapy protocols with stem cell support and associated procedures are given. It has been more than 15 years since this approach was used in neuroblastoma, and it has subsequently been applied to most of advanced, common childhood solid tumors. The ongoing use of new strategies for dose intensification with peripheral blood stem cell or autologous purged bone marrow rescue has raised expectations for cure. To date, results of megatherapy followed by autologous stem cell reinfusion are encouraging in metastatic neuroblastoma and Ewing's sarcoma, with an increase in event-free survival rates of about 30% as compared with that of conventional treatments. However, with the exception of metastatic neuroblastoma, there is still no proven role for this treatment strategy. Thus, there is still an urgent need for international collaboration to design randomized studies that could rapidly address the issue of these expensive and high-morbidity procedures in childhood cancer.
Theoretical Insights into the Mechanism for Thiol/Disulfide Exchange (2003)

The mechanism for thiol/disulfide exchange has been studied with high-level theoretical calculations. Free energies, transition structures, charge densities, and solvent effects along the reaction pathway have been determined for the first time. Mechanistic results agree with experimental data, and support the idea that the thiolate is the reacting species and that the reaction indeed proceeds through an uncomplicated S(N)2 transition state. The transition structures have the charge density evenly concentrated in the attacking and leaving sulfur atoms. The charge densities allow us to rationalize the solvent effects. As transition structures have the charge density more widely distributed than reactants, hydrophobic environments catalyze the reaction. The effect can be so dramatic that disulfide exchange inside the active site of ribonucleotide reductase is estimated to be catalyzed 10(3) times faster than the reaction in water. It was also found that attack by thiol is much faster than previously assumed, if mediated through water chains. Although the present results, as well as experimental data, still suggest that thiolate is the main reaction species, water-mediated thiol attack is almost kinetically competitive, and can eventually become competitive under specific experimental conditions.
A study on lipid production of the mixotrophic microalgae Phaeodactylum tricornutum on various carbon sources (2012)

This study is aimed to investigate the potential use of various carbon sources (glucose, starch, and acetate sodium) for culturing Phaeodactylum tricornutum with higher microalgae oil production in mixotrophic batch cultures. Results showed P. tricornutumcould grow mixotrophically with those organic substrate in a tested range from 0.5 to 5.0 g/l. Glucose and acetate sodium exerted significant promotion on growth of P. tricornutum, while starch did not exhibit this enhancement. The presence of carbon sources in medium could significantly increase the lipid content, especially with glucose. The maximum lipid productivities in mixotrophic cultures with glucose, starch and acetate in medium were 0.053, 0.023 and 0.020 g/lÂ·day, respectively. These values were respectively 4.6-, 2.0-, and 1.7-fold of those obtained in the corresponding photoautotrophic control cultures. For the composition of fatty acids in microalgae oil, there was no significant sensitivity to the variation of the organic carbon sources. The data in this study suggests that P. tricomutum could provide high lipid productivity combined of high oil content and biomass in mixotrophic culture, which offers a promise to be one of the sources of biodiesel.

	 

	Key words: Lipid productivity, mixotrophic growth, organic carbon sources,Phaeodactylum tricornutum.
Magnetic Resonance Imaging the Velocity Vector Components of Fluid Flow (1985)

Encoding the precession phase angle of proton nuclei for Fourier analysis has produced accurate measurement of fluid velocity vector components by MRI. A pair of identical gradient pulses separated in time by exactly 1/2 TE, are used to linearly encode the phase of flow velocity vector components without changing the phase of stationary nuclei. Two-dimensional Fourier transformation of signals gave velocity density images of laminar flow in angled tubes which were in agreement with the laws of vector addition. These velocity profile images provide a quantitative method for the investigation of fluid dynamics and hemodynamics.
Room-temperature atmospheric pressure plasma plume for biomedical applications (2005)

As low-temperature nonequilibrium plasmas come to play an increasing role in biomedical applications, reliable and user-friendly sources need to be developed. These plasma sources have to meet stringent requirements such as low temperature (at or near room temperature), no risk of arcing, operation at atmospheric pressure, preferably hand-held operation, low concentration of ozone generation, etc. In this letter, we present a device that meets exactly such requirements. This device is capable of generating a cold plasma plume several centimeters in length. It exhibits low power requirements as shown by its current-voltage characteristics. Using helium as a carrier gas, very little ozone is generated and the gas temperature, as measured by emission spectroscopy, remains at room temperature even after hours of operations. The plasma plume can be touched by bare hands and can be directed manually by a user to come in contact with delicate objects and materials including skin and dental gum without causing any heating or painful sensation.
Fasting insulin, adiponectin, hs-CRP levels, and the components of metabolic syndrome. (2007)

there is a relationship between the number of components of metabolic syndrome and the increasing levels of fasting insulin, and hs-CRP, and low levels of adiponectin. These may explain in part the risk of cardiovascular events among individuals with metabolic syndrome.