gebhart/patrepeval huggingface dataset:
Kinetics of the incorporation of dietary fatty acids into serum cholesteryl esters, erythrocyte membranes, and adipose tissue: an 18-month controlled study (1997)

Tissue levels of n-3 fatty acids reflect dietary intake, but quantitative data about rate of incorporation and levels as a function of intake are scarce. We fed 58 men 0, 3, 6, or 9 g/d of fish oil for 12 months and monitored fatty acids in serum cholesteryl esters, erythrocytes, and subcutaneous fat during and after supplementation. Eicosapentaenoic acid (EPA) in cholesteryl esters plateaued after 4-8 weeks; the incorporation half-life was 4.8 days. Steady-state levels increased by 3.9 +/- 0.3 mass % points (+/- SE) for each extra gram of EPA eaten per day. Incorporation of docosahexaenoic acid (DHA) was erratic; plateau values were 1.1 +/- 0.1 mass % higher for every g/d ingested. Incorporation of EPA into erythrocyte membranes showed a half-life of 28 days; a steady state was reached after 180 days. Each g/d increased levels by 2.1 +/- 0.1 mass %. C22:5n-3 levels increased markedly. Changes in DHA were erratic and smaller. EPA levels in adipose tissue rose also; the change after 6 months was 67% of that after 12 months in gluteal and 75% in abdominal fat. After 12 months each gram per day caused an 0.11 +/- 0.01 mass % rise in gluteal fat for EPA, 0.53 +/- 0.07 for C22:5n-3, and 0.14 +/- 0.03 for DHA. Thus, different (n-3) fatty acids were incorporated with different efficiencies, possibly because of interconversions or different affinities of the enzymatic pathways involved. EPA levels in cholesteryl esters reflect intake over the past week or two, erythrocytes over the past month or two, and adipose tissue over a period of years. These findings may help in assessing the intake of (n-3) fatty acids in epidemiological studies.
ABSTRACT: New Concepts for Biodegradation Evaluation in Oil fields, a Combined Geological and Numerical Approach (2002)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Determining DNA Packaging Strategy by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions (2009)

Tailed-bacteriophage virions contain a single linear dsDNA chromosome which can range in size from about 18 to 500 kbp across the known tailed-phage types. These linear chromosomes can have one of several known types of termini as follows: cohesive ends (5'- or 3'-single-strand extensions), circularly permuted direct terminal repeats, short or long exact direct terminal repeats, terminal host DNA sequences, or covalently bound terminal proteins. These different types of ends reflect differing DNA replication strategies and especially differing terminase actions during DNA packaging. In general, complete genome sequence determination does not by itself elucidate the nature of these ends, so directed experimental analysis is usually required to understand the nature of the virion chromosome ends. This chapter discusses these methods.
Kinematic and deformation analysis of 4-D coronary arterial trees reconstructed from cine angiograms (2003)

In the cardiovascular arena, percutaneous catheter-based interventional (i.e., therapeutic) procedures include a variety of coronary and other vascular system interventions. These procedures use two-dimensional (2-D) X-ray-based imaging as the sole or the major imaging modality for procedure guidance and quantification of key parameters. Coronary vascular curvilinearity is one key parameter that requires a four-dimensional (4-D) format, i.e., three-dimensional (3-D) anatomical representation that changes during the cardiac cycle. A new method has been developed for reconstruction and analysis of these patient-specific 4-D datasets utilizing routine cine angiograms. The proposed method consists of three major processes: 1) reconstruction of moving coronary arterial tree throughout the cardiac cycle; 2) establishment of temporal correspondence with smoothness constraints; and 3) kinematic and deformation analysis of the reconstructed 3-D moving coronary arterial trees throughout the cardiac cycle.
Human detection using depth and gray images (2004)

A method is presented for extracting pedestrian information from an image sequence taken by a monocular camera. The method makes use of hybrid sensing of depth and gray information and it is shown to work well in an indoor environment. A split-and-merge strategy is proposed to process depth data for object and human detection. Furthermore, human tracking and event detection are also presented to recognize simple behavior such as hand-shaking. This method does not use background subtraction, and therefore it is applicable for scenes taken from mobile platforms. Experimental results are presented to validate our approach.
Zero-Bias Peaks in the Tunneling Conductance of Spin-Orbit-Coupled Superconducting Wires with and without Majorana End-States (2012)

One of the simplest proposed experimental probes of a Majorana bound state is a quantized (2e(2)/h) value of zero-bias tunneling conductance. When temperature is somewhat larger than the intrinsic width of the Majorana peak, conductance is no longer quantized, but a zero-bias peak can remain. Such a nonquantized zero-bias peak has been recently reported for semiconducting nanowires with proximity induced superconductivity. In this Letter we analyze the relation of the zero-bias peak to the presence of Majorana end states, by simulating the tunneling conductance for multiband wires with realistic amounts of disorder. We show that this system generically exhibits a (nonquantized) zero-bias peak even when the wire is topologically trivial and does not possess Majorana end states. We make comparisons to recent experiments, and discuss the necessary requirements for confirming the existence of a Majorana state.
Synthesis of 5,6,7,8‐tetrahydro‐5‐oxopyrido[2,3‐d]pyrimidine‐6‐carbonitriles and ‐6‐carboxylic acid esters (1975)

Abstract Dieckmann ring closure reactions of 4‐[(2‐cyanoethyl)substituted amino]‐2‐phenyl‐5‐pyrimidinecarboxylates (Ha‐f) afforded several 5,6,7,8‐tetrahydro‐5‐oxo‐2‐phenylpyrido[2,3 ‐d] pyrimidine‐6‐ carbonitriles (IIIa‐f). The open‐chain intermediates (IIa‐f) were prepared by dechloroamination of 5‐carbethoxy‐4‐chloro‐2‐phenylpyrimidine (1a) with several 3‐substituted amino‐ propionitriles. Alkylation of the sodium salt of 5,6,7,8‐tetrahydro‐8‐methyl‐5‐oxo‐2‐phenyl‐pyrido[2,3 ‐d] pyrimidine‐6‐ carbonitrile (IIIa) with methyl iodide in DMF resulted in methylation at C‐6 to afford IV. Tosylation of IIIa in pyridine gave the corresponding tosyl ester (V) of the enolic form. Oxidative dehydrogenation at the 6,7‐position resulted when IIIa reacted with thionyl chloride, affording 5,8‐dihydro‐8‐methyl‐5‐oxo‐2‐phenylpyrido[2,3 ‐d] pyrimidine‐6‐ carbonitrile (VII). Dechloroamination of la or 5‐carbethoxy‐4‐chloro‐2‐methylthiopyrimidine (Ib) with ethyl 3‐ethylaminopropionate followed by Dieckmann cyclization of the resulting open‐chain intermediates gave the corresponding ethyl 5,6,7,8‐tetrahydro‐5‐oxopyrido[2,3 ‐d] pyrimidine‐6‐carboxylates IX'a and IX'b, respectively. These exist predominately in the enol form and undergo alkylation and oxidation reactions similar to IIIa.
Ring Group Signatures (2012)

In many applications of group signatures, not only a signer's identity but also which group the signer belongs to is sensitive information regarding signer privacy. In this paper, we study these applications and combine a group signature with a ring signature to create a ring group signature, which specifies a set of possible groups without revealing which member of which group produced the signature. The main contributions of this paper are a formal definition of a ring group signature scheme and its security model, a generic construction and a concrete example of such a scheme. Both the construction and concrete scheme are provably secure if the underlying group signature and ring signature schemes are secure.
Biosynthesis of the Escherichia coli K5 polysaccharide, a representative of group II capsular polysaccharides: polymerization in vitro and characterization of the product (1991)

Biosynthesis of the capsular K5 polysaccharide of Escherichia coli, which has the structure 4)-beta GlcA-1,4-alpha GlcNAc-(1, was studied with membrane preparations from an E. coli K5 wild-type strain and from a recombinant K-12 strain expressing the K5 capsule. Polymerization occurs at the inner face of the cytoplasmic membrane without the participation of lipid-linked oligosaccharides. The serological K5 specificity of the in vitro product was determined with a K5-specific monoclonal antibody in an antigen-binding assay. The K5 polysaccharide, as obtained from the membranes after an in vitro incubation, has 2-keto-3-deoxyoctulosonic acid as the reducing sugar, which indicates that the polysaccharide grows by chain elongation at the nonreducing end.
The Drosophila dorsal morphogen represses the tolloid gene by interacting with a silencer element. (1994)

The dorsal protein (DL) regulates the transcriptional activity of several genes that determine cell fate along the dorsoventral axis of the Drosophila melanogaster embryo. DL is present at high levels in ventral nuclei, where it activates some genes (twi and sna) and represses others (zen, dpp, and tld). DL shows homology to the Rel family of proteins and interacts with specific DNA sequences in the regulatory regions of its target genes. The distal portion of the zen gene acts as a silencer that can mediate the repression of a heterologous promoter in ventral regions of the embryo. It contains four DL binding sites which alone are sufficient for activation but not repression. Here we analyze the interaction of DL with another one of its repressed targets, the tolloid (tld) gene. Approximately 800 bp of 5'-flanking sequences upstream of the tld coding region were shown to drive an expression pattern indistinguishable from the wild-type pattern. A 423-bp fragment located within these sequences contains two DL binding sites and was shown to act as a silencer to mediate ventral repression. Point mutations in the sites abolish not only DNA binding but also ventral repression. We discuss a comparison of the DNA sequences from the zen and tld promoters and the possible mechanisms of transcriptional silencing.
Presence‐Only Data and the EM Algorithm (2008)

In ecological modeling of the habitat of a species, it can be prohibitively expensive to determine species absence. Presence-only data consist of a sample of locations with observed presences and a separate group of locations sampled from the full landscape, with unknown presences. We propose an expectation-maximization algorithm to estimate the underlying presence-absence logistic model for presence-only data. This algorithm can be used with any off-the-shelf logistic model. For models with stepwise fitting procedures, such as boosted trees, the fitting process can be accelerated by interleaving expectation steps within the procedure. Preliminary analyses based on sampling from presence-absence records of fish in New Zealand rivers illustrate that this new procedure can reduce both deviance and the shrinkage of marginal effect estimates that occur in the naive model often used in practice. Finally, it is shown that the population prevalence of a species is only identifiable when there is some unrealistic constraint on the structure of the logistic model. In practice, it is strongly recommended that an estimate of population prevalence be provided.
An Enhanced Algorithm for Linear Multivariate Calibration (1998)

We present a new method of linear multivariate calibration that can generate better prediction results than those obtained by partial least squares (PLS). This is accomplished by incorporating the spectrum of the desired species into the calibration procedure. The method combines the advantages of different standard methods and is therefore called hybrid linear analysis (HLA). In side-by-side tests using both simulated and experimental data, HLA produced lower prediction errors than PLS in all instances. We recommend HLA over PLS in situations where the spectrum of the desired species is available.
Frequent Endonuclease Cleavage at Off-target Locations In Vivo (2010)

Target-site DNA breaks increase recombination frequencies, however, the specificity of the enzymes used to create them remains poorly defined. The location and frequency of off-target cleavage events are especially important when rare-cutting endonucleases are used in clinical settings. Here, we identify noncanonical cleavage sites of I-SceI that are frequently cut in the human genome by localizing adeno-associated virus (AAV) vector-chromosome junctions, demonstrating the importance of in vivo characterization of enzyme cleavage specificity.
Effect of exogenous opioid peptides on TNF-alpha-induced human neutrophil apoptosis in vitro. (2003)

Polymorphonuclear leukocyte (neutrophil) apoptosis is an important mechanism regulating the life span and some functions of neutrophils at inflamed sites. Opioid peptides are present in the peripheral circulation and their concentrations rapidly increase as a result of stress and inflammation. The effect of opioid peptides such as met-enkephalin (M-ENK) and beta-endorphin (beta-END) on tumor necrosis factor (TNF)-alpha-induced apoptosis in human neutrophils in vitro was investigated. Neutrophils isolated from peripheral blood were cultured in the absence or presence of 10(-6)-10(-10) M of opioid peptides for 8, 12 and 18 h. Features of apoptotic neutrophils were measured by a flow cytometric method based on analysis of the apoptotic nuclei (DNA content). We found that M-ENK and beta-END enhanced both uninduced and TNF-alpha-induced neutrophil apoptosis in vitro in a dose-dependent manner. The effect of opioid peptides on the modulation of neutrophil apoptosis was not reversed by the opioid-receptor antagonist naloxone. The results suggest that M-ENK and beta-END can regulate neutrophil life span via apoptosis and in this way may participate in the resolution of inflammation.
Self-starting diode-pumped femtosecond Nd fiber laser (1993)

A self-starting passively mode-locked diode-pumped neodymium fiber laser with a semiconductor antiresonant Fabry-Perot saturable absorber (A-FPSA) is demonstrated for the first time to our knowledge. Mode locking can be initiated and maintained by the semiconductor absorber, and pulse durations down to 260 fs are routinely obtained. Alternatively, shorter pulses (60 fs) were generated by exploition of nonlinear polarization evolution in the fiber (in combination with a stronger pump source) where the A-FPSA simply initiates the pulse-forming process.
A sequential expression system for high‐throughput functional genomic analysis (2007)

A method employing sequential rounds of cell-free protein synthesis (CFPS) was developed to identify gene products influencing the complex metabolic systems that result in protein accumulation and folding in vitro. The first round of CFPS creates an array of cell extracts individually enriched with a single gene product expressed in-parallel from linear DNA expression templates (ETs). The cell extract is engineered to enhance template stability and to provide reaction conditions conducive for general protein activation. Following first-round expression, linear templates are selectively degraded and a plasmid template for a reporter enzyme is added to initiate a subsequent round of protein expression. Reporter concentration and activity identify first-round gene products that affect amino acid and nucleic acid stability, energy supply, protein expression, stability, and activation. This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities.
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655 (2003)

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.
Efficacy and Safety of Intranasal Esketamine for the Rapid Reduction of Symptoms of Depression and Suicidality in Patients at Imminent Risk for Suicide: Results of a Double-Blind, Randomized, Placebo-Controlled Study (2018)

These preliminary findings indicate that intranasal esketamine compared with placebo, given in addition to comprehensive standard-of-care treatment, may result in significantly rapid improvement in depressive symptoms, including some measures of suicidal ideation, among depressed patients at imminent risk for suicide.
Development and Preliminary Clinical Validation of a High Sensitivity Assay for Cardiac Troponin Using a Capillary Flow (Single Molecule) Fluorescence Detector (2006)

The European Society of Cardiology and the American College of Cardiology (ESC/ACC) have redefined the criteria for the diagnosis of acute myocardial infarction, requiring an increase in the concentration of cardiac troponin in the clinical context of myocardial ischemia (1). A subgroup of this committee has recommended that the cutoff concentration be established at the 99th percentile of the reference range, with an acceptable interassay imprecision of ≤10% (2). The use of a low troponin cutoff concentration enables the detection of more patients who have minor myocardial damage and are at short-term risk for adverse cardiac events (3). In a study conducted by the IFCC, none of the manufacturers of troponin assays cleared by the Food and Drug Administration in 2004 had a sensitivity for detecting troponin at the 99th percentile with the requisite precision (4). Therefore, troponin assays with higher analytical sensitivity and precision are needed to meet the guidelines of The European Society of Cardiology and the American College of Cardiology.

We examined the analytical performance of the ZeptX™ System (Singulex) assay for cardiac troponin I (cTnI), evaluating its sensitivity, precision, and recovery. We assessed the assay’s clinical performance by comparing assay results for 97 specimens from patients with chest pain with results from the 1st-generation Bayer Centaur cTnI assay. With samples from 88 healthy individuals, we determined the 99th percentile cutoff for the ZeptX assay. We also determined the analytical limit of detection (LoD) across 15 sequential assays and calculated the LoD as the mean value of the zero standard plus 3 SDs from quadruplicate intraassay determinations.

The ZeptX System consists of flow …
Optimal Patterns for Alignment (1974)

Patterns with optimal autocorrelation functions are sometimes optimal for optical alignment. When the finest gratings that can be resolved exceed those that actually can be used, errors of alignment can be reduced by nearly a factor of 2 by incorporating segments of a grating into the patterns. Under some conditions, resolution of the inspecting device need not limit accuracy of alignment. Bull's-eye patterns may be optimal for visual alignment.
Mucosa-Associated Bacteria in the Human Gastrointestinal Tract Are Uniformly Distributed along the Colon and Differ from the Community Recovered from Feces (2002)

The human gastrointestinal (GI) tract harbors a complex community of bacterial cells in the mucosa, lumen, and feces. Since most attention has been focused on bacteria present in feces, knowledge about the mucosa-associated bacterial communities in different parts of the colon is limited. In this study, the bacterial communities in feces and biopsy samples from the ascending, transverse, and descending colons of 10 individuals were analyzed by using a 16S rRNA approach. Flow cytometric analysis indicated that 10(5) to 10(6) bacteria were present in the biopsy samples. To visualize the diversity of the predominant and the Lactobacillus group community, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was performed. DGGE analysis and similarity index comparisons demonstrated that the predominant mucosa-associated bacterial community was host specific and uniformly distributed along the colon but significantly different from the fecal community (P < 0.01). The Lactobacillus group-specific profiles were less complex than the profiles reflecting the predominant community. For 6 of the 10 individuals the community of Lactobacillus-like bacteria in the biopsy samples was similar to that in the feces. Amplicons having 99% sequence similarity to the 16S ribosomal DNA of Lactobacillus gasseri were detected in the biopsy samples of nine individuals. No significant differences were observed between healthy and diseased individuals. The observed host-specific DGGE profiles of the mucosa-associated bacterial community in the colon support the hypothesis that host-related factors are involved in the determination of the GI tract microbial community.
Role of 4-Hydroxybutyrate-CoA Synthetase in the CO2 Fixation Cycle in Thermoacidophilic Archaea (2012)

Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific genes, except for the one responsible for ligation of coenzyme A (CoA) to 4HB. Although several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. In this report, transcriptomic analysis of cells grown under strict H(2)-CO(2) autotrophy was consistent with the involvement of Msed_0406 and Msed_0394. Recombinant versions of these enzymes catalyzed the ligation of CoA to 4HB, with similar affinities for 4HB (K(m) values of 1.9 and 1.5 mm for Msed_0406 and Msed_0394, respectively) but with different rates (1.69 and 0.22 μmol × min(-1) × mg(-1) for Msed_0406 and Msed_0394, respectively). Neither Msed_0406 nor Msed_0394 have close homologs in other Sulfolobales, although low sequence similarity is not unusual for acyl-adenylate-forming enzymes. The capacity of these two enzymes to use 4HB as a substrate may have arisen from simple modifications to acyl-adenylate-forming enzymes. For example, a single amino acid substitution (W424G) in the active site of the acetate/propionate synthetase (Msed_1353), an enzyme that is highly conserved among the Sulfolobales, changed its substrate specificity to include 4HB. The identification of the 4-HB CoA synthetase now completes the set of enzymes comprising the 3HP/4HB cycle.