gebhart/patrepeval huggingface dataset:
Simple and ion-pair high performance liquid chromatography as an improved analytical tool for chloramphenicol metabolic profiling. (1983)

Simple and ion-pair reverse phase high performance chromatographic separations combined with selective extraction were developed in order to achieve a qualitative and quantitative analysis of [3H]chloramphenicol (CP) metabolites in rat urine. Complete separation followed by unequivocal identification of all the metabolites was obtained, especially of the toxicologically significant CP-arylamine. Metabolic profiles were established from human and goat urine which confirmed data already available, but was used to identify new acidic metabolites in the latter species. This methodology appears to be a useful research tool in comparative metabolic studies.
The low-density lipoprotein receptor (1991)

The low-density lipoprotein receptor is a model system for the investigation of receptor-mediated endocytosis, lipoprotein metabolism and human genetic diseases. More recently, the low-density lipoprotein receptor has become one of the most extensively studied examples of a protein composed of structural units, that are also called modules or domains.
On the relationship between the perception and learning of Hindi voicing and place contrasts by native speakers of American English. (2008)

Many non-native speech sounds are challenging to perceive and, ultimately, to acquire. Predicting specific learning outcomes from perceptual data has been hampered by (1) problems in quantifying acoustic-phonetic similarity between non-native and native sounds, (2) calculating the perceptual weighting of acoustic cues in the native language, and (3) the high-variability commonly observed in the perceptual assimilation of non-native contrasts to multiple native categories. This variability may reflect long-term persistent patterns in learning or it may represent only a brief early stage prior to fossilization. To examine these two possible accounts, the perceptual assimilation by 15 American English listeners of 7 voicing and place contrasts produced by 6 Hindi speakers was examined before and after training in a paired-associate word learning task. Training utilized tokens from four of the six talkers used in perceptual assimilation tasks. The purpose of the study was to determine whether or not assimilation patterns could be greatly modified and simplified by very limited experience in acquiring the contrasts via word learning. The results showed that limited laboratory training significantly reduced talker and token variability in perceptual assimilation and allowed for non-native contrasts to be categorized more cleanly in terms of their predicted difficulty in learning.
Coefficient test for discrete time learning system stability (2002)

A coefficient test for the stability of discrete time learning systems is developed. The test is based on the Jury criteria. Necessary and sufficient conditions result from the test. Several examples are provided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Acquired Immunodeficiency Syndrome in Persons with Hemophilia (1985)

The widespread use of coagulation factor concentrates prepared from the blood of numerous donors has doubled the life expectancy of persons with hemophilia, but parenteral exposure to alloantigens and infectious agents is not free of risk. The prevalence of the acquired immunodeficiency syndrome (AIDS) now approaches 1% in patients with hemophilia, and laboratory evidence of abnormal immunoregulation is found in at least 50% of treated patients with severe hemophilia. The immune defect is multifactorial. The attack rate of AIDS among patients with severe hemophilia appears to have reached a peak; further evidence suggests that only a minority of those infected with human T-lymphotropic virus type III will develop AIDS. The advent of improved donor screening methods and the application of heat treatment of coagulation factor concentrates should further reduce the risk of AIDS in persons with hemophilia.
HIPO in-flight performance improvements (2014)

The High-speed Imaging Photometer for Occultations (HIPO) is a special purpose science instrument for SOFIA. HIPO can be co-mounted with FLITECAM in the so-called FLIPO configuration for stellar occultation or extrasolar planet transit observations. We gained some flight experience with HIPO and FLITECAM in 2011 as described in a previous publication (Dunham, et al., Proc SPIE, 8446-42, 2012). Since that time a number of improvements to HIPO have been made and a deeper understanding of the airborne environment's impact on photometric precision at optical wavelengths has been obtained. The improvements to HIPO include an improved beamsplitter for the FLIPO configuration, adding deep depletion CCDs as a detector option, expanding the filter set to include a Sloan Digital Sky Survey filter set as well as two custom filters for transit work, and an ability to guide the SOFIA telescope using HIPO data being acquired for science purposes. We now understand that variations in PSF size due to varying static air density has a noticeable impact on photometric stability while the related effect of Mach number is unimportant. The seriousness of ozone absorption in the Chappuis band is now understood and an approach to avoid this has been found. Finally we present demonstration transit data to illustrate our current transit photometry capability.
Lagrange Multipliers and Optimality (1993)

Lagrange multipliers used to be viewed as auxiliary variables introduced in a problem of constrained minimization in order to write first-order optimality conditions formally as a system of equations. Modern applications, with their emphasis on numerical methods and more complicated side conditions than equations, have demanded deeper understanding of the concept and how it fits into a larger theoretical picture. A major line of research has been the nonsmooth geometry of one-sided tangent and normal vectors to the set of points satisfying the given constraints. Another has been the game-theoretic role of multiplier vectors as solutions to a dual problem. Interpretations as generalized derivatives of the optimal value with respect to problem parameters have also been explored. Lagrange multipliers are now being seen as arising from a general rule for the subdifferentiation of a nonsmooth objective function which allows black-and-white constraints to be replaced by penalty expressions. This paper traces such themes in the current theory of Lagrange multipliers, providing along the way a free-standing exposition of basic nonsmooth analysis as motivated by and applied to this subject.
Towards Optimal Image Stitching for Virtual Microscopy (2005)

In this paper we present an image stitching method based on dynamic programming and describe its application to automated slide acquisition for Virtual Microscopy (VM). Given a large number of fields of view (FOVs) acquired from a single microscope slide, we composite these images into a single large ‘virtual slide’ image. The location of each FOV is determined using a new algorithm based on dynamic programming. We compare the performance of the proposed algorithm to an existing greedy algorithm. In a visual trial it is shown that the new algorithm provides a significant improvement in perceived image quality at image boundaries compared to the existing algorithm.
Failure to abolish reactive hyperemia by indomethacin in denervated kidneys of rabbits (1977)

The effect of indomethacin (10 mg/kg) on the distribution of cortical blood flow during postocclusive reactive hyperemia was evaluated in denervated kidneys of anesthetized rabbits by the radioactive microsphere technique. Renal denervation caused a slight but not significant increase in renal blood flow with no remarkable alteration in the distribution of cortical blood flow. After release of 1-min occlusion of the renal artery, hyperemic responses developed with a fractional flow redistribution toward the inner cortex. The absolute perfusion rate increased in the inner cortex but did not significantly change in the outer cortex. Indomethacin produced a decrease in renal blood flow despite elevated blood pressure. Even in the indomethacin-treated animals, postocclusive reactive hyperemia appeared concomitantly with the fractional flow redistribution to the inner cortex. The percentage repayment by reactive hyperemia of ischemia during the artery clamping was not significantly different before and after indomethacin administration. The findings indicate that indomethacin did not significantly affect the postocclusive vascular response in denervated kidneys of rabbits, thereby giving evidence against the role of prostaglandins as mediators of reactive hyperemia.
Visual hulls from single uncalibrated snapshots using two planar mirrors (2004)

Two mirrors are used to create five views of an object: a view onto the object, two reflections and two reflections of reflections. The five views are captured in a single snapshot. Epipolar geometry of the object&amp;apos;s five silhouettes is determined directly from the image without knowing the poses of the camera or the mirrors. The epipolar geometry provides constraints on the pose of each silhouette, allowing the pose of each silhouette to be computed in a common reference frame using only the silhouette outlines. Once the pose associated with each silhouette has been computed, a five-view visual hull of the object can be computed from the five silhouettes. By capturing several images of a rigid object in different poses, sets of five silhouettes can be combined into a single silhouette set in which the pose of each silhouette is known in a common reference frame. This allows visual hulls of an arbitrary number of views to be computed if more than one image is used. The method is applied to an ornamental cat, and experimental results are shown.
A Human Gut Commensal Ferments Cranberry Carbohydrates To Produce Formate (2017)

Commensal bifidobacteria colonize the human gastrointestinal tract and catabolize glycans that are impervious to host digestion. Accordingly, <i>Bifidobacterium longum</i> typically secretes acetate and lactate as fermentative end products. This study tested the hypothesis that <i>B. longum</i> utilizes cranberry-derived xyloglucans in a strain-dependent manner. Interestingly, the <i>B. longum</i> strain that efficiently utilizes cranberry xyloglucans secretes 2.0 to 2.5 mol of acetate-lactate. The 1.5 acetate:lactate ratio theoretical yield obtained in hexose fermentations shifts during xyloglucan metabolism. Accordingly, this metabolic shift is characterized by increased acetate and formate production at the expense of lactate. α-l-Arabinofuranosidase, an arabinan endo-1,5-α-l-arabinosidase, and a β-xylosidase with a carbohydrate substrate-binding protein and carbohydrate ABC transporter membrane proteins are upregulated (>2-fold change), which suggests carbon flux through this catabolic pathway. Finally, syntrophic interactions occurred with strains that utilize carbohydrate products derived from initial degradation from heterologous bacteria.<b>IMPORTANCE</b> This was a study of bacterial metabolism of complex cranberry carbohydrates termed xyloglucans that are likely not digested prior to reaching the colon. This is significant, as bifidobacteria interact with this dietary compound to potentially impact human host health through energy and metabolite production by utilizing these substrates. Specific bacterial strains utilize cranberry xyloglucans as a nutritive source, indicating unknown mechanisms that are not universal in bifidobacteria. In addition, xyloglucan metabolism proceeds by using an alternative pathway that could lead to further research to investigate mechanisms underlying this interaction. Finally, we observed cross-feeding between bacteria in which one strain degrades the cranberry xyloglucan to make it available to a second strain. Similar nutritive strategies are known to occur within the gut. In aggregate, this study may lead to novel foods or supplements used to impact human health through rational manipulation of the human microbiome.
Assay Development and Screening of Human DGAT1 Inhibitors with an LC/MS-Based Assay: Application of Mass Spectrometry for Large-Scale Primary Screening (2010)

Many attractive targets for therapeutic intervention are enzymes that catalyze biological reactions involving small molecules such as lipids, fatty acids, amino acid derivatives, nucleic acid derivatives, and cofactors. Some of the reactions are difficult to detect by methods commonly used in high-throughput screening (HTS) without specific radioactive or fluorescent labeling of substrates. In addition, there are instances when labeling has a detrimental effect on the biological response. Generally, applicable assay methodologies for detection of such reactions are thus required. Mass spectrometry (MS), being a label-free detection tool, has been actively pursued for assay detection in HTS in the past several years. The authors have explored the use of multiparallel liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) for high-throughput detection of biochemical reactions. In this report, we describe in detail the assay development and screening with a LC/MS-based system for inhibitors of human diacylglycerol acyltransferase (DGAT1) with a chemical library of approximately 800,000 compounds. Several strategies and process improvements have been investigated to overcome technical challenges such as data variation and throughput. Results indicated that, through these innovative approaches, the LC/MS-based screening method is both feasible and suitable for high-throughput primary screening.
ChemInform Abstract: Studies Towards the Stereoselective Synthesis of Polyquinane Frameworks from Acyclic Precursors via Radical Cyclizations (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
NOX2 (gp91phox) is a predominant O2 sensor in a human airway chemoreceptor cell line: biochemical, molecular, and electrophysiological evidence (2012)

Pulmonary neuroepithelial bodies (NEBs), composed of clusters of amine [serotonin (5-HT)] and peptide-producing cells, are widely distributed within the airway mucosa of human and animal lungs. NEBs are thought to function as airway O(2)-sensors, since they are extensively innervated and release 5-HT upon hypoxia exposure. The small cell lung carcinoma cell line (H146) provides a useful model for native NEBs, since they contain (and secrete) 5-HT and share the expression of a membrane-delimited O(2) sensor [classical NADPH oxidase (NOX2) coupled to an O(2)-sensitive K(+) channel]. In addition, both native NEBs and H146 cells express different NADPH oxidase homologs (NOX1, NOX4) and its subunits together with a variety of O(2)-sensitive voltage-dependent K(+) channel proteins (K(v)) and tandem pore acid-sensing K(+) channels (TASK). Here we used H146 cells to investigate the role and interactions of various NADPH oxidase components in O(2)-sensing using a combination of coimmunoprecipitation, Western blot analysis (quantum dot labeling), and electrophysiology (patchclamp, amperometry) methods. Coimmunoprecipitation studies demonstrated formation of molecular complexes between NOX2 and K(v)3.3 and K(v)4.3 ion channels but not with TASK1 ion channels, while NOX4 associated with TASK1 but not with K(v) channel proteins. Downregulation of mRNA for NOX2, but not for NOX4, suppressed hypoxia-sensitive outward current and significantly reduced hypoxia -induced 5-HT release. Collectively, our studies suggest that NOX2/K(v) complexes are the predominant O(2) sensor in H146 cells and, by inference, in native NEBs. Present findings favor a NEB cell-specific plasma membrane model of O(2)-sensing and suggest that unique NOX/K(+) channel combinations may serve diverse physiological functions.
Cu-Based Bulk Glassy Alloys with Good Mechanical Properties in Cu-Zr-Hf-Ti System (2001)

High-strength Cu-based bulk glassy alloys were synthesized in Cu–Zr–Ti and Cu–Hf–Ti ternary and Cu–Zr–Hf–Ti quaternary systems by copper mold casting. The critical diameter was 4 mm for the Cu60Zr30Ti10 and Cu60Hf25Ti15 ternary alloys and the Cu60Zr20Hf10Ti10 and Cu60Zr10Hf15Ti15 quaternary alloys. As the substitution amount of Zr or Hf by Ti in Cu60Zr40 and Cu60Hf40 alloys increases, the glass transition temperature (Tg), crystallization temperature (Tx) and temperature interval of supercooled liquid region ΔTx(=Tx−Tg) decrease, while the liquidus temperature (Tl) has a minimum of 1127 K around 20%Ti, resulting in a maximum Tg⁄Tl of 0.63 in the vicinity of 20%Ti. The high glass-forming ability was obtained at the compositions with high Tg⁄Tl. The bulk glassy alloys exhibit high fracture strength of 2040–2190 MPa and plastic elongations of 0.3 to 1.9%. The finding of the Cu-based bulk glassy alloys with high Tg⁄Tl above 0.60, high fracture strength above 2000 MPa and distinct plastic elongation is encouraging for the subsequent development as a new type of bulk glassy alloys which can be used for structural materials.
CRISPR as a Diagnostic Tool (2021)

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
Adopting orphans: comprehensive genetic testing of Mendelian diseases of childhood by next-generation sequencing (2011)

Orphan diseases are individually uncommon but collectively contribute significantly to pediatric morbidity, mortality and healthcare costs. Current molecular testing for rare genetic disorders is often a lengthy and costly endeavor, and in many cases a molecular diagnosis is never achieved despite extensive testing. Diseases with locus heterogeneity or overlapping signs and symptoms are especially challenging owing to the number of potential targets. Consequently, there is immense need for scalable, economical, rapid, multiplexed diagnostic testing for rare Mendelian diseases. Recent advances in next-generation sequencing and bioinformatic technologies have the potential to change the standard of care for the diagnosis of rare genetic disorders. These advances will be reviewed in the setting of a recently developed test for 592 autosomal recessive and X-linked diseases.
Efficacy of TG101348, a Selective JAK2 Inhibitor, in Treatment of a Murine Model of JAK2V617F-Induced Polycythemia Vera. (2007)

Abstract The JAK2V617F mutation is present in the majority of cases of myeloproliferative disease, including polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF), and is an attractive candidate for molecularly targeted therapy. However, the potential toxicities of JAK2 inhibition in vivo, and identification of appropriate surrogate endpoints for response, are challenges that may limit clinical usefulness in treatment of these relatively indolent diseases. We report efficacy and assessment of surrogate endpoints for response of a small molecule JAK2 inhibitor, TG101348 in a murine model of polycythemia vera. TG101348 is selective for JAK2 with an in vitro IC50 of ∼3 nM that is ∼334 fold more potent than for inhibition of JAK3. TG101348 showed therapeutic efficacy in the murine model of PV that included a statistically significant reduction in hematocrit, normalization of white blood cell count, a dose dependent reduction/elimination of extramedullary hematopoiesis in the spleen and liver, and marked attenuation of myelofibrosis. Consistent with its selective inhibition of JAK2 and not JAK3, there was no significant change in T-cell number in treated animals. These clinical responses correlated with surrogate endpoints for response, including reduction or elimination of JAK2V617F expressing clones based on quantitative genomic PCR, suppression of JAK2V617F positive endogenous erythroid colony growth of JAK2V617F MPD bone marrow, and inhibition of JAK-STAT signal transduction as assessed by phosphoflow cytometry for phosphorylated STAT5. Thus, TG101348 is efficacious in treatment of a murine model of PV, and surrogate endpoints have been identified that may be of value in clinical trials in humans.
Quantification of Bacteria in Oral Samples by Competitive Polymerase Chain Reaction (1999)

Information about the total amount of bacteria in oral samples contributes to assessment of an individual's risk of contracting dental caries or developing periodontitis and the prediction of that individual's clinical course. Since existing techniques are often time-consuming and expensive, it seemed attractive to look for alternative methods for the quantification of eubacteria. With their high specificity and sensitivity, polymerase chain-reaction (PCR) techniques have the potential of supplying fast and reliable results. We developed a method of competitive PCR for the quantification of eubacteria. We designed forward and reverse PCR primers which bind to highly conserved sequences of the bacterial 16S rRNA gene. A homologous competitor was synthesized with Escherichia coli 16S rDNA as a template, with the reverse primer and a hybrid primer which binds 67 bases downstream to the forward primer and carries the forward primer sequence at its 5' end. Specificity controls with 30 different bacterial species, 5 Archaea, 3 fungi, human astrocytoma cells, and rat hepatoblastoma cells were carried out. Results were positive for all eubacteria and negative for all other cells tested. Calibration curves were obtained by co-amplification of known amounts of E. coli cells in the presence of the homologous competitor. The developed method was successfully applied to assessment of the accumulation of bacteria during an oral hygiene cessation experiment. The competitive PCR method proved to be a reliable and fast method for the quantification of bacterial DNA and cultured eubacteria, as well as of bacteria in biological samples. It may find further applications not only in periodontology and cariology but also in other fields of medical microbiology.