gebhart/patrepeval huggingface dataset:
An Investigation of Imidazole and Oxazole Syntheses Using Aryl-Substituted TosMIC Reagents<sup>1</sup> (2000)

This article describes efficient and mild protocols for preparing polysubstituted imidazoles in a single pot from aryl-substituted tosylmethyl isocyanide (TosMIC) reagents and imines generated in situ. Traditional imine-forming reactions employing virtually any aldehyde and amine followed by addition of the TosMIC reagent delivers 1,4,5-trisubstituted imidazoles with predictable regiochemistry. Employing chiral amines and aldehydes, particularly those derived from alpha-amino acids, affords imidazoles with asymmetric centers appended to N-1 or C-5 with excellent retention of chiral purity. 1,4-Disubstituted imidazoles are also readily prepared by a simple variant of the above procedure. Selecting glyoxylic acid as the aldehyde component of this procedure leads to intermediates such as 48, which readily undergo decarboxylation and elimination of the tosyl moiety to deliver 1,4-disubstituted imidazoles in high yields. Alternatively, using NH(4)OH as the amine component in conjunction with a variety of aldehydes delivers 4, 5-disubstituted imidazoles in moderate to good yields in a single pot while avoiding the need for protecting groups. Finally, the facile preparation of mono- and disubstituted oxazoles from these TosMIC reagents and aldehydes is described.
Expression of urokinase-type plasminogen activator (u-PA), u-PA receptor, and tissue-type PA messenger RNAs in human hepatocellular carcinoma. (1998)

Expression of plasminogen activators (PAs) and urokinase-type PA receptor (u-PAR) is associated with tumor growth and invasion. For in vivo human tumor tissues, there is no information on gene expression of PAs in hepatocellular carcinoma (HCC) or other hepatic pathophysiological conditions. In this study we examined the relative levels of u-PA, tissue-type PA (t-PA), and u-PAR mRNA expression in human HCC by reverse transcription-PCR compared with those expressed in peritumoral hepatic tissues. Twenty-five of 25 HCCs expressed u-PA mRNA, as well as 16 of 25 hepatic peritumoral tissues. However, none of the 14 cases of nontumorous liver samples (i.e., normal parenchyma, steatosis, and nonspecific reactive and chronic hepatitis) showed detectable levels of u-PA mRNA. The same samples analyzed for uPAR and t-PA mRNAs exhibited higher levels of these mRNAs in the malignant tissues compared with nontumorous ones. A strong correlation was found between the relative levels of u-PA and t-PA mRNAs detected in the tumor and in the corresponding peritumoral tissues (P < 0.001 for u-PA; P < 0.02 for t-PA). However, there was no correlation between the expression of u-PA and t-PA in HCC (P = 0.565). Furthermore, a significant inverse correlation was found between survival months of male patients and the relative level of u-PA mRNA (P < 0.05) detected at the time of biopsy, whereas no correlation was found in the case of t-PA mRNA. These results are in line with the possible differential biological role of u-PA and t-PA in the tumor etiopathogenesis and suggest that the detection of relative levels of u-PA mRNA may be a useful prognostic factor for male HCC patients.
Immunoglobulin heavy-chain gene rearrangement in adult acute lymphoblastic leukemia reveals preferential usage of JH-proximal variable gene segments (2001)

The aim of this study was to characterize individual-segment and overall patterns of V(H) gene usage in adult B-lineage acute lymphoblastic leukemia (ALL). Theoretical values of V(H) segment usage were calculated with the assumption that all V(H) segments capable of undergoing rearrangement have an equal probability of selection for recombination. Leukemic clones from 127 patients with adult B-lineage acute leukemias were studied by fingerprinting by means of primers for the framework 1 and joining segments. Clones from early preimmune B cells (245 alleles identified) show a predominance of V(H)6 family rearrangements and, consequently, do not conform to this hypothesis. However, profiles of V(H) gene family usage in mature B cells, as investigated in peripheral blood (6 samples), B-cell lymphomas (36 clones) and chronic lymphocytic leukemia (56 clones), are in agreement with this theoretical profile. Sequence analyses of 64 V(H) clones in adult ALL revealed that the rate of V(H) usage is proportional to the proximity of the V(H) gene to the J(H) locus and that the relationship can be mathematically defined. Except for V(H)6, no other V(H) gene is excessively used in adult ALL. V(H) pseudogenes are rarely used (n = 2), which implies the existence of early mechanisms in the pathway to B-cell maturation to reduce wasteful V(H)-(D(H))-J(H) recombination. Finally, similar to early immunoglobulin-H rearrangement patterns in the mouse, B cells of ALL derive from a pool of cells more immature than the cells in chronic lymphoid B-cell malignancies.
Amyloidogenic peptide oligomer accumulation in autophagy-deficient β cells induces diabetes (2014)

Islet amyloid accumulation is a hallmark of human type 2 diabetes (T2D). In contrast to human islet amyloid polypeptide (hIAPP), murine islet amyloid polypeptide (mIAPP) does not exhibit amyloidogenic propensity. Because autophagy is important in the clearance of amyloid-like proteins, we studied transgenic mice with β cell-specific expression of hIAPP to evaluate the contribution of autophagy in T2D-associated accumulation of hIAPP. In mice with β cell-specific expression of hIAPP, a deficiency in autophagy resulted in development of overt diabetes, which was not observed in mice expressing hIAPP alone or lacking autophagy alone. Furthermore, lack of autophagy in hIAPP-expressing animals resulted in hIAPP oligomer and amyloid accumulation in pancreatic islets, leading to increased death and decreased mass of β cells. Expression of hIAPP in purified monkey islet cells or a murine β cell line resulted in pro-hIAPP dimer formation, while dimer formation was absent or reduced dramatically in cells expressing either nonamyloidogenic mIAPP or nonfibrillar mutant hIAPP. In autophagy-deficient cells, accumulation of pro-hIAPP dimers increased markedly, and pro-hIAPP trimers were detected in the detergent-insoluble fraction. Enhancement of autophagy improved the metabolic profile of hIAPP-expressing mice fed a high-fat diet. These results suggest that autophagy promotes clearance of amyloidogenic hIAPP, autophagy deficiency exacerbates pathogenesis of human T2D, and autophagy enhancers have therapeutic potential for islet amyloid accumulation-associated human T2D.
PAN1/NALP2/PYPAF2, an Inducible Inflammatory Mediator That Regulates NF-κB and Caspase-1 Activation in Macrophages (2004)

Genes encoding proteins with PYRIN/PAAD/DAPIN domains, a nucleotide binding fold (NACHT), and leucine rich repeats have recently been recognized as important mediators in autoimmune inflammatory disorders. Here we characterize the expression and function of a member of the PYRIN and NACHT domain (PAN) family, PAN1 (also known as NALP2 and PYPAF2). PAN1 protein expression is regulated by lipopolysaccharide (LPS) and interferons (IFNbeta and IFNgamma) in THP-1 macrophage cells. In gene transfection studies PAN1 manifests an inhibitory influence on NF-kappaB activation induced by various pro-inflammatory stimuli, including tumor necrosis factor TNFalpha and interleukin-1beta (IL-1beta). Gene transfer-mediated elevations in PAN1 protein also suppressed activation of IkappaB kinases induced by inflammatory cytokines. Conversely, reducing endogenous levels of PAN1 using small interfering RNA enhanced LPS-induced production of ICAM-1 (intercellular adhesion molecule 1), an NF-kappaB-dependent gene. We also show here that PAN1 binds via its PYRIN domain to ASC, an adapter protein involved in caspase-1 activation. This binding is disrupted by mutation of the alpha1 helix of ASC. In gene transfer experiments PAN1 enhances caspase-1 activation and IL-1beta secretion in collaboration with ASC. Conversely, reducing endogenous levels of PAN1 using small interfering RNA significantly reduced LPS-induced secretion of IL-1beta in monocytes. We propose that PAN1 functions as a modulator of the activation of NF-kappaB and pro-caspase-1 in macrophages.
Learning in Dynamic Environments with Ensemble Selection for Autonomous Outdoor Robot Navigation (2009)

Abstract — Autonomous robot navigation in unstructured outdoor environments is a challenging area of active research. The navigation task requires identifying safe, traversable paths which allow the robot to progress toward a goal while avoiding obstacles. Machine learning techniques—in particular, classifier ensembles—are well adapted to this task, accomplishing nearto-far learning by augmenting near-field stereo readings in order to identify safe terrain and obstacles in the far field. Composition of the ensemble and subsequent combination of model outputs in this dynamic problem domain remain open questions. Recently, Ensemble Selection has been proposed as a mechanism for selecting and combining models from an existing model library and shown to perform well in static domains. We propose the adaptation of this technique to the time-evolving data associated with the outdoor robot navigation domain. Important research questions as to the composition of the model library, as well as how to combine selected models ’ outputs, are addressed in a two-factor experimental evaluation. We evaluate the performance of our technique on six fully labeled datasets, and show that our technique outperforms memoryless baseline techniques that do not leverage past experience. I.
Enhancing accountability of electronic health record usage via patient-centric monitoring (2012)

Electronic Health Record (EHR) and Personal Health Record (PHR) systems could allow patients to better manage their health information and share it to enhance the quality and efficiency of their healthcare. Unfortunately, misuse of information stored in EHR and PHR systems will create new risks for patients, and we need to empower them to safeguard their health information to avoid problems such as medical identity theft. In this paper, we introduce the notion of accountable use and update of electronic health records and design a patient-centric monitoring system based on it. We develop a system architecture and associated protocols that enable either explicit or implicit patient control over when and how health information is accessed. Our approach provides a reasonable solution rather than addressing the more general information flow control problem in distributed systems. We also implement and evaluate a prototype system motivated by a health record sharing scenario based on NHIN Direct to demonstrate that enhanced accountability can be supported with acceptable performance and integration overheads.
Determination of Junction Avidity of Cytolytic T Cell and Target Cell (1986)

A direct measurement of the avidity of the junction between a cytotoxic T lymphocyte and its target cell was achieved by using a biophysical approach. A micromanipulation technique was used to determine the force required to separate a cytotoxic T cell (human clone F1, with specificity for HLA-DRw6) from its specific target cell (JY: HLA-A2, -B7, -DR4, w6) prior to delivery of the lethal hit. The force required to separate the F1-JY pair is 1.5 X 10(4) dynes per square centimeter. This junction avidity for F1-JY pairs is 6 to 13 times greater than that for F1-F1 and JY-JY pairs; the F1-JY conjugate requires a stronger separating force and is more easily rejoined than the homologous cell pairs. This study provides an estimate of the avidity of cytotoxic T cells for their target cells and insights into the biophysical correlates of the molecular complexes formed in the interaction of cytotoxic T cells and their targets during the cytotoxic process.
Design of High-Activity Mutants of Human Butyrylcholinesterase against (−)-Cocaine: Structural and Energetic Factors Affecting the Catalytic Efficiency (2010)

The present study was aimed to explore the correlation between the protein structure and catalytic efficiency of butyrylcholinesterase (BChE) mutants against (-)-cocaine by modeling the rate-determining transition state (TS1), i.e., the transition state for the first step of chemical reaction process, of (-)-cocaine hydrolysis catalyzed by various mutants of human BChE in comparison with the wild type. Molecular modeling of the TS1 structures revealed that mutations on certain nonactive site residues can indirectly affect the catalytic efficiency of the enzyme against (-)-cocaine through enhancing or weakening the overall hydrogen bonding between the carbonyl oxygen of (-)-cocaine benzoyl ester and the oxyanion hole of the enzyme. Computational insights and predictions were supported by the catalytic activity data obtained from wet experimental tests on the mutants of human BChE, including five new mutants reported for the first time. The BChE mutants with at least ∼1000-fold improved catalytic efficiency against (-)-cocaine compared to the wild-type BChE are all associated with the TS1 structures having stronger overall hydrogen bonding between the carbonyl oxygen of (-)-cocaine benzoyl ester and the oxyanion hole of the enzyme. The combined computational and experimental data demonstrate a reasonable correlation relationship between the hydrogen-bonding distances in the TS1 structure and the catalytic efficiency of the enzyme against (-)-cocaine.
Clonal origin of human erythro-eosinophilic colonies in culture (1982)

We have observed the presence of erythropoietic bursts containing eosinophils and their precursors in methylcellulose culture of human peripheral blood and marrow nucleated cells in the presence of erythropoietin and medium conditioned by phytohemagglutinin-stimulated leukocytes (PHA-LCM). It was possible to identify these bursts (colonies) in situ in methylcellulose culture on the basis of their unique red and black colors. Transmission electron microscopy revealed that the constituent erythroid and eosinophilic cells lay intermixed with each other, and through close intercellular connections formed compact colonies and bursts consisting of several sub-colonies. Differential counts of individual erythro-eosinophil colonies (EEo colonies) revealed only a small percentage of blast cells in most of the colonies. Replating experiments of single EEo colonies yielded only eosinophilic colonies and clusters and erythroid colonies. The clonal nature of the EEo colonies was documented by analysis of Y-chromatin- positive cells in individual EEo colonies derived from cocultures of male and female peripheral blood mononuclear cells. Comparison of conditioned media indicated that PHA-LCM is the best stimulator for EEo colonies. These studies suggest that the differentiation capabilities of the progenitors for EEo colonies are restricted to erythroid and eosinophilic differentiation.
Pattern recognition for automated DNA sequencing: I. On-line signal conditioning and feature extraction for basecalling. (1993)

The massive scale of DNA sequencing for the Human Genome Initiative compels efforts to reduce the cost and increase the throughput of DNA sequencing technology. Contemporary automated DNA sequencing systems do not yet meet estimated performance requirements for cost-effective and timely completion of this project. Greater accuracy of basecalling software would minimize manual review and editing of basecalling results, and facilitate assembly of primary sequences to large contig(uous) arrays. In this report we describe a neural network model for photometric signal conditioning during raw data acquisition with an automated DNA sequencer. This network supports on-line extraction and evaluation of informative arrays of oligomer separations and yields, as a feature table for accurate, real-time basecalling.
Development of a Stable Isotope Dilution Analysis with Liquid Chromatography−Tandem Mass Spectrometry Detection for the Quantitative Analysis of Di- and Trihydroxybenzenes in Foods and Model Systems (2006)

A straightforward stable isotope dilution analysis (SIDA) for the quantitative determination of the di- and trihydroxybenzenes catechol (1), pyrogallol (2), 3-methylcatechol (3), 4-methylcatechol (4), and 4-ethylcatechol (5) in foods by means of liquid chromatography-tandem mass spectrometry was developed. With or without sample preparation involving phenylboronyl solid phase extraction, the method allowed the quantification of the target compounds in complex matrices such as coffee beverages with quantification limits of 9 nmol/L for 4-ethylcatechol, 24 nmol/L for catechol, 3-methyl-, and 4-methylcatechol, and 31 nmol/L for pyrogallol. Recovery rates for the analytes ranged from 97 to 103%. Application of the developed SIDA to various commercial food samples showed that quantitative analysis of the target compounds is possible within 30 min and gave first quantitative data on the amounts of di- and trihydroxybenzenes in coffee beverage, coffee powder, coffee surrogate, beer, malt, roasted cocoa powder, bread crust, potato crisps, fruits, and cigarette smoke and human urine. Model precursor studies revealed the carbohydrate/amino acid systems as well as the plant polyphenols catechin and epicatechin as precursors of catechol and 5-O-caffeoylquinic acid, caffeic acid as a precursor of catechol and 4-ethylcatechol, and gallocatechin, epigallocatechin, and gallic acid as precursors of pyrogallol.
Parthenogenetic activation of mouse and rabbit eggs by electric stimulation in vitro (1989)

The present study was undertaken to determine conditions for parthenogenetic activation of mouse and rabbit eggs by electric stimulation in vitro. The cumulus-free eggs were submitted to square direct current pulses at output voltage of 1.0 to 2.5 kV/cm for 25 to 200 microseconds. The best conditions for the activation of mouse eggs were 1.5 kV/cm for 100 microseconds, in which 78% of eggs were activated, 32% of which developed to blastocysts in vitro. When the nonelectric solution (0.3M mannitol) was used for electric stimulation, the activation rate was quite low (16%). Optimal conditions for activation of rabbit eggs were 1.5 kV/cm for 200 microseconds, in which 77% of eggs were activated, 25% of which developed to blastocysts. Unlike mouse eggs, rabbit eggs frequently had three pronuclei after electric stimulation. It is clearly shown that electric stimulus can induce parthenogenetic activation of the mouse and rabbit eggs in vitro.
BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES (2000)

The development of genome sequencing and DNA microarray analysis of gene expression gives rise to the demand for data-mining tools. BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs. BioProspector uses zero to third-order Markov background models whose parameters are either given by the user or estimated from a specified sequence file. The significance of each motif found is judged based on a motif score distribution estimated by a Monte Carlo method. In addition, BioProspector modifies the motif model used in the earlier Gibbs samplers to allow for the modeling of gapped motifs and motifs with palindromic patterns. All these modifications greatly improve the performance of the program. Although testing and development are still in progress, the program has shown preliminary success in finding the binding motifs for Saccharomyces cerevisiae RAP1, Bacillus subtilis RNA polymerase, and Escherichia coli CRP. We are currently working on combining BioProspector with a clustering program to explore gene expression networks and regulatory mechanisms.
Overexpression of the EMT Driver Brachyury in Breast Carcinomas: Association With Poor Prognosis (2014)

The studies reported here provide the rationale for the use of a vaccine targeting brachyury for the therapy of human breast cancer, either as a monotherapy or in combination therapies.
A family of surface-exposed proteins of 20 kilodaltons in the genus Borrelia (1994)

Relapsing fever and Lyme disease spirochetes of the genus Borrelia display at their surfaces abundant lipoproteins: Vmp proteins in Borrelia hermsii and Osp proteins in Borrelia burgdorferi. Vmp and Osp proteins largely determine serotype specificity, and neutralizing antibodies of infected or immunized animals are directed at them. For the present study, we examined B. hermsii serotype 33, which is unique among strain HS1 serotypes in the low frequency of switches to other serotypes during infections and in vitro cultivation. Failing to clone the complete vmp33 gene, we accomplished its further characterization by (i) determining three partial amino acid sequences, (ii) designing oligonucleotide primers based on these amino acid sequences, (iii) cloning and sequencing the central portion of vmp33, and (iv) using outwardly directed primers and the inverse PCR to clone the 5' and 3' ends of the gene and flanking regions. The transcriptional start site was identified by primer extension analysis. Vmp33 was a polypeptide of 211 amino acids; the three partial amino acid sequences were identified in the open reading frame. Vmp33 was found to be more similar to other 20-kDa Vmp proteins of B. hermsii and to OspC proteins of B. burgdorferi than it was to 35- to 39-kDa Vmp proteins of the same strain. Moreover, OspC proteins were more similar to Vmp33 than they were to OspA, -B, or -D proteins of B. burgdorferi. These sequence similarities were consistent with Western blot (immunoblot) findings of cross-reactions between Vmp33 and OspC with anti-Vmp33 and anti-OspC sera. The promoter for the expressed vmp33 gene was found to be different from the expression site for other active vmp genes characterized to date. These results indicate that Vmp33 and other small Vmp's belong with OspC to a genus-wide family of 20-kDa proteins and that expression of these proteins may be coordinated with expression of other Vmp and Osp proteins in Borrelia spp.
Partial Chemical Characterization of Corn Root Cell Walls (1968)

The present study reports on chemical changes which occur in the cell wall of Zea mays during early phases of growth. Roots of seedling corn plants were divided into a meristematic zone, the zone of elongation, and the maturation zone, and the cell wall isolated from each of these zones. The wall preparations were then extracted sequentially to obtain pectin, hemicellulose, cellulose, and lignin fractions. Each of these, except for the lignin fraction, was hydrolyzed and the resultant sugars isolated, identified, and estimated quantitatively. Quantitative analysis of the products of hydrolysis of these fractions demonstrated that the classical scheme of fractionation is a valuable indicator of the changes in solubility properties which the various polysaccharide components for the wall undergo. It does not however yield definite chemical entities. For example, the "pectin" fraction contains only about 3% galacturonic acid; the bulk of it being composed of glucose, xylose, and galactose. By summation of analysis of these various fractions, it was found that substances yielding glucose and xylose upon hydrolysis increase with advancing age of the tissue. Galactose- and arabinose-yielding compounds decrease and mannose appears during maturation. Anhydrouronic acids first decrease, then increase. Most interestingly, of the total dry weight of the cell wall, only 24, 45, and 50% of the meristematic, elongation, and maturation zones respectively are accounted for as simple sugars in the acid hydrolysates. Oligosaccharides were not encountered in large amounts so that the 50 to 75% of the wall weight unaccounted for would consist of polysaccharides or oligosaccharides not precipitated by ethanol from the extracting solutions employed and by polysaccharides in the hemicellulose fraction which are resistant to acid hydrolysis.