gebhart/patrepeval huggingface dataset:
Cell-type-specific cDNA probes and the murine I region: the localization and orientation of Ad alpha. (1984)

Labeled cDNA probes highly enriched for B-cell-specific (B-T) and T-suppressor-cell-specific (Ts-B) sequences were used to screen a set of genomic cosmid clones spanning 230 kilobases of the murine immune response (I) region. With the B-cell derived probe, four I-region genes were detectable (A beta, E beta, E beta 2, and E alpha), as well as an additional (fifth) region of hybridization. The T-cell probe, prepared from a putative I-J positive suppressor cell hybridoma, was negative in a parallel experiment. A genomic fragment corresponding to the new region of hybridization seen with the B-cell cDNA probe identified a discrete mRNA species in RNA blotting analysis that had a pattern of expression strikingly similar to E alpha mRNA in a variety of lymphoid tumor lines. This fragment was also used to isolate cDNA clones from a library highly enriched (20-40 times) for B-cell-specific sequences (selected cDNA cloning). DNA sequence analysis of one of these cDNA clones indicates that this gene encodes the A alpha molecule of the d haplotype (Ad alpha). These findings establish that the order of the class II genes in the Ia complex is as follows: centromere-A beta-A alpha-E beta-E beta 2-E alpha.
A Comparison of Observational Studies and Randomized, Controlled Trials (2000)

We found little evidence that estimates of treatment effects in observational studies reported after 1984 are either consistently larger than or qualitatively different from those obtained in randomized, controlled trials.
Role of Extrinsic Innervation in Carbohydrate-Induced Ileal Modulation of Pancreatic Secretion and Upper Gut Function (1997)

Previously we showed that carbohydrate (CHO) in the ileum slowed gastric emptying and increased pancreatic amylase secretion relative to that of other enzymes. Our aim here was to determine if extrinsic innervation of the jejunoileum participates in the CHO-induced ileal modulation of postprandial upper gut function. Six dogs were studied before and 2-3 weeks after in situ neural isolation of the jejunoileum (complete extrinsic denervation). Gastric emptying (GE) and pancreatic amylase secretion were quantitated for 4 h after a 300-ml meal containing 3H-PEH (liquid marker) and 99mTc sulfur colloid cooked with eggs (solid marker). Coincident with feeding, we started a distal ileal infusion of 150 mM NaCl or 40 mg.min-1 CHO. Extrinsic denervation abolished the slowing of GE of liquids and solids and the augmented increase in amylase and trypsin in relation to solid emptying seen in the neurally intact dogs prior to denervation. Denervation also abolished the decrease in total pancreatic exocrine secretion in response to ileal CHO. Increases in plasma concentrations of peptide YY (PYY) were correlated temporally with decreased GE of solids and increased exocrine secretion during ileal CHO in neurally intact dogs, but no increases in PYY release occurred after extrinsic denervation. Extrinsic denervation of the jejunoileum abolished the effect of ileal CHO on GE of liquids and solids, the decrease in total amylase secretion during ileal CHO, and the relative increase in enzyme secretion expressed as total enzyme output per percentage solid marker emptied. Extrinsic innervation of the jejunoileum mediates ileal modulation of GE and the relationship of amylase secretion to GE of solids. The mechanism of this effect may be via neurally mediated release of PYY.
Growth of a-Plane GaN Films on r-Plane Sapphire Substrates by Metalorganic Chemical Vapour Deposition (2004)

Nonpolar a-plane GaN films were grown on r-plane sapphire substrates by metalorganic chemical vapour deposition (MOCVD) under various conditions. The surface morphologies of epitaxial films are studied by atomic force microscopy. The pit density and size both decrease with the increasing growth temperature, decreasing growth pressure or V/III ratio, while the roughness of the surface increases. Formation mechanisms of the pits in the films are discussed.
Optimization by Simulated Annealing (1983)

There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.
Content-based retrieval of segmented images (1994)

Most general content-based image retrieval techniques use colour and texture as main retrieval indices. A recent technique uses colour pairs to model distinct object boundaries for retrieval. These techniques have been applied to overall image contents without taking into account the characteristics of individual objects. While the techniques work well for the retrieval of images with similar overall contents (including backgrounds), their accuracies are limited because they are unable to take advantage of individual object's visual characteristics, and to perform object-level retrieval. This paper looks specifically at the use of colour-pair technique for fuzzy object-level image retrieval. Three extensions are applied to the basic colour-pair technique: (a) the development of a similarity-based ranking formula for colour-pairs matching; (b) the use of segmented objects for object-level retrieval; and (c) the inclusion of perceptually similar colours for fuzzy retrieval. A computer-aided segmentation technique is developed to segment the images' contents. Experimental results indicate that the extensions have led to substantial improvements in the retrieval performance. These extensions are sufficiently general and can be applied to other content-based image retrieval techniques.
Comprehensive investigation of disease‐specific short peptides in sera from patients with systemic sclerosis: Complement C3f‐des‐arginine, detected predominantly in systemic sclerosis sera, enhances proliferation of vascular endothelial cells (2007)

This comprehensive peptidomics analysis revealed the predominance of DRC3f in the sera of patients with SSc. Investigation of DRC3f may be a useful tool for the diagnosis and evaluation of disease activity in SSc. Moreover, its demonstrated effects on endothelial cells suggest a potential role for DRC3f in the pathophysiologic mechanisms of SSc.
Studies on Changes of Protein by Dye Sensitized Photooxidation (1970)

Photooxidation products of amino acid residues of lysozyme were identified as kynurenine and 3-oxykynurenine from tryptophan, alanine from histidine, methionine sulfoxide and methionine sulfone from methionine, cysteic acid from cystine, glutamic acid from arginine and serine from tyrosine by isolating peptides in tryptic hydrolysate, although the yield of each product did not always reach 100%. Higher intensity of incident rays caused breakage of peptide chain, the mechanism of which was divided into two steps; the first predominated at the earlier stage of illumination with oxidation of tryptophan, the second predominated at the later stage of illumination accompaning the formation of amide and α-keto acid groups. Carbonyls and peroxides liberated during illumination were also determined.
Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling (2008)

To correlate gene expression profiles to fundamental biological processes such as cell growth, differentiation and migration, it is essential to work at the single cell level. Gene expression analysis always starts with the relatively low efficient reverse transcription (RT) of RNA into complementary DNA (cDNA), an essential step as unprocessed RNAs will not be analysed further. In this paper, we present a novel method for RT that uses microfluidics to manipulate nanolitre volumes. We compare our method to conventional protocols performed in microlitre volumes. More specifically, reverse transcription was performed either in a polydimethylsiloxane (PDMS) rotary mixer or in a tube, using a single cell amount of mouse brain RNA (10 pg), and was followed by a template-switching PCR (TS-PCR) amplification step. We demonstrate that, using the microfluidic protocol, 74% of the genes expressed in mouse brain were detected, while only 4% were found with the conventional approach. We next profiled single neuronal progenitors. Using our microfluidic approach, i.e. performing cell capture, lysis and reverse transcription on-chip followed by TS-PCR amplification in tube, a mean of 5000 genes were detected in each neuron, which corresponds to the expected number of genes expressed in a single cell. This demonstrates the outstanding sensitivity of the microfluidic method.
Shiga Toxin Activates Complement and Binds Factor H: Evidence for an Active Role of Complement in Hemolytic Uremic Syndrome (2009)

Infections with enterohemorrhagic Escherichia coli (EHEC) are a major cause of hemolytic uremic syndrome (HUS). Shiga toxins (Stxs), especially Stx2, are believed to represent major virulence factors of EHEC, contributing to HUS pathogenesis. Beside EHEC-associated HUS, there are hereditary atypical forms of HUS, which are mostly caused by mutations of complement regulators. The aim of the present study was to investigate whether or not complement is also involved in the pathogenesis of EHEC-induced typical HUS, by being activated either directly or indirectly by involvement of its inhibitors. Purified Stx2 markedly activated complement via the alternative pathway and was found to bind to factor H (FH), however, only when it was active. No apparent cleavage or destruction of FH was visible, and cofactor activity in fluid phase was unaffected, but clearly delayed for surface-attached FH, where it is essential for host cell protection. Binding studies using FH constructs revealed that Stx2 binds to short consensus repeats (SCRs) 6-8 and SCRs18-20, but not to SCRs16-17, i.e., to regions involved in the surface recognition function of FH. In conclusion, complement, and in particular FH, not only plays an important role in atypical HUS, but most probably also in EHEC-induced HUS.
Texture design using a simplicial complex of morphable textures (2005)

We present a system for designing novel textures in the space of textures induced by an input database. We capture the structure of the induced space by a simplicial complex where vertices of the simplices represent input textures. A user can generate new textures by interpolating within individual simplices. We propose a morphable interpolation for textures, which also defines a metric used to build the simplicial complex. To guarantee sharpness in interpolated textures, we enforce histograms of high-frequency content using a novel method for histogram interpolation. We allow users to continuously navigate in the simplicial complex and design new textures using a simple and efficient user interface. We demonstrate the usefulness of our system by integrating it with a 3D texture painting application, where the user interactively designs desired textures.
ChemInform Abstract: Antagonists of the Human CCR5 Receptor as anti‐HIV‐1 Agents. Part 1. Discovery and Initial Structure—Activity Relationships for 1‐Amino‐2‐phenyl‐4‐(piperidin‐1‐yl)butanes. (2001)

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.
Spatio-temporal coding for wireless communication (1998)

Multipath signal propagation has long been viewed as an impairment to reliable communication in wireless channels. This paper shows that the presence of multipath greatly improves achievable data rate if the appropriate communication structure is employed. A compact model is developed for the multiple-input multiple-output (MIMO) dispersive spatially selective wireless communication channel. The multivariate information capacity is analyzed. For high signal-to-noise ratio (SNR) conditions, the MIMO channel can exhibit a capacity slope in bits per decibel of power increase that is proportional to the minimum of the number multipath components, the number of input antennas, or the number of output antennas. This desirable result is contrasted with the lower capacity slope of the well-studied case with multiple antennas at only one side of the radio link. A spatio-temporal vector-coding (STVC) communication structure is suggested as a means for achieving MIMO channel capacity. The complexity of STVC motivates a more practical reduced-complexity discrete matrix multitone (DMMT) space-frequency coding approach. Both of these structures are shown to be asymptotically optimum. An adaptive-lattice trellis-coding technique is suggested as a method for coding across the space and frequency dimensions that exist in the DMMT channel. Experimental examples that support the theoretical results are presented.
Low-energy electron beam enhanced etching of Si(100)-(2×1) by molecular hydrogen (1992)

The use of low-energy electrons to enhance the rate of the reaction between H2 and Si to produce SiHx has been investigated. Etching was accomplished by steady-state application of H2 and electrons, with quadrupole mass spectrometer (QMS) detection of etch products. After etching, low-energy electron diffraction (LEED) was used to check for surface damage. Ultraviolet photoelectron spectroscopy and thermally stimulated desorption were used to determine the surface composition after etching. Experiments of this type have been conducted with electron energies from 200–1000 eV, hydrogen flux held constant, and the sample at room temperature. All have shown qualitatively similar results: the QMS detected species do not represent the fragmentation pattern of SiH4, the thermodynamically predicted product, and LEED shows that the surface has not been damaged.
The serine/threonine kinase Pim-2 is a transcriptionally regulated apoptotic inhibitor (2003)

Growth factor withdrawal results in the termination of factor-dependent transcription. One transcript that declines rapidly following growth factor deprivation of hematopoietic cells is the serine/threonine kinase pim-2. When constitutively expressed, Pim-2 conferred long-term resistance to a variety of apoptotic stimuli including growth factor withdrawal and endogenous levels of Pim-2 contributed to growth factor-mediated apoptotic resistance. Pim-2 expression maintained cell size and mitochondrial potential independently of the PI3K/Akt/TOR pathway. Pim-2-dependent maintenance of cell size and survival correlated with its ability to maintain rapamycin-resistant phosphorylation of the translational repressor 4E-BP1 and phosphorylation of the BH3 protein BAD. These results establish Pim-2 as a direct link between growth factor-induced transcription and a novel, kinase-dependent pathway that promotes cell-autonomous survival.
Time-gated optical system for depth-resolved functional brain imaging (2006)

We present a time-domain optical system for functional imaging of the adult head. We first describe the instrument, which is based on a Ti:Sapphire pulsed laser (wavelength 750-850 nm) and an intensified CCD camera enabling parallel detection of multiple fibers. We characterize the system in terms of sensitivity and signal-to-noise ratio, instrument response function, cross-talk, stability, and reproducibility. We then describe two applications of the instrument: the characterization of baseline optical properties of homogeneous scattering media, and functional brain imaging. For the second application, we developed a two-part probe consisting in two squares of 4 x 4 sources and 3 x 3 detectors. The laser source is time-multiplexed to define 4 states of 8 sources that can be turned on during the same camera frame while minimizing cross-talk. On the detection side, we use for each detector 7 fibers of different lengths creating an optical delay, and enabling simultaneous detection in 7 windows (by steps of 500 ps) for each detector. This multiple window detection allows depth sensitivity. The imaging probe was tested on dynamic phantoms and a preliminary result on an adult performing a motor task shows discrimination between superficial and cortical responses to the stimulus on both hemispheres.
Indoleamine 2,3-Dioxygenase Expression in Transplanted NOD Islets Prolongs Graft Survival After Adoptive Transfer of Diabetogenic Splenocytes (2002)

Indoleamine 2,3-dioxygenase (IDO) catalyzes the breakdown of the amino acid tryptophan into kyneurenine. It has been shown that IDO production by placental trophoblasts prevents the attack of maternal T-cells activated in response to the paternal HLA alleles expressed by the tissues of the fetus. In this article, we show that adenoviral gene transfer of IDO to pancreatic islets can sufficiently deplete culture media of tryptophan and consequently inhibit the proliferation of T-cells in vitro. Experiments in vivo have also demonstrated that transplantation of IDO-expressing islets from prediabetic NOD mouse donors into NODscid recipient mice is associated with a prolongation in islet graft survival after adoptive transfer of NOD diabetogenic T-cells. This protection is attributed to the depletion of tryptophan at the transplantation site beneath the kidney capsule. These results suggest that local modulation of tryptophan catabolism may be a means of facilitating islet transplantation as a therapy for type 1 diabetes.
Human prostate carcinoma cells express functional alphaIIb(beta)3 integrin. (1996)

The integrin alphaIIb(beta)3 was initially believed to be expressed only in cells from the megakaryocytic lineage, such as platelets or HEL cells. In this study, we report for the first time that human prostate carcinoma PC-3 and DU-145 cells express alphaIIb(beta)3. Reverse transcription-PCR from HEL (positive control), PC-3, and DU-145 cells amplified a predicted alphaIIb fragment that hybridized to the full-length alphaIIb cDNA probe. DNA sequencing of the PCR fragments revealed 100% sequence homology to the corresponding extracellular domain of platelet alphaIIb but minimal sequence homology to integrins (alpha)v or a5. An RNase protection assay was used to confirm the results from reverse transcription-PCR. An antisense riboprobe to alphaIIb mRNA hybridized to total RNA from HEL, PC-3, and DU-145 cells, suggesting that alphaIIb mRNA is transcribed in these tumor cells. In situ hybridization on surgical specimens from human prostate tumor tissue stained positive with an antisense riboprobe to alphaIIb mRNA. The expression of alphaIIb(beta)3 protein in PC-3 and DU-145 cells was demonstrated by Western and dot blotting and flow cytometry with monoclonal antibodies (mAbs) to alphaIIb (MAB 1990), beta3, and alphaIIb(beta)3 (AP-2). A protein kinase C activator, phorbol 12-myristate 13-acetate, increased the adhesion of PC-3 cells to PAC-1, a mAb specific to the high-affinity state of alphaIIb(beta)3, by more than 80-fold. The invasion of DU-145 cells through a reconstituted basement membrane was blocked 40-50% by mAbs AP-2 or PAC-1. These data collectively suggest that: (a) prostate tumor cells express alphaIIb(beta)3; (b) surface expression of alphaIIb(beta)3 integrin is regulated by protein kinase C; and (c) mAbs to this receptor inhibit invasion of prostate cancer cells through a reconstituted basement membrane.
Chemical and biological approaches to improve the efficiency of homologous recombination in human cells mediated by artificial restriction DNA cutter (2012)

A chemistry-based artificial restriction DNA cutter (ARCUT) was recently prepared from Ce(IV)/EDTA complex and a pair of pseudo-complementary peptide nucleic acids. This cutter has freely tunable scission-site and site specificity. In this article, homologous recombination (HR) in human cells was promoted by cutting a substrate DNA with ARCUT, and the efficiency of this bioprocess was optimized by various chemical and biological approaches. Of two kinds of terminal structure formed by ARCUT, 3'-overhang termini provided by 1.7-fold higher efficiency than 5'-overhang termini. A longer homology length (e.g. 698 bp) was about 2-fold more favorable than shorter one (e.g. 100 bp). When the cell cycle was synchronized to G2/M phase with nocodazole, the HR was promoted by about 2-fold. Repression of the NHEJ-relevant proteins Ku70 and Ku80 by siRNA increased the efficiency by 2- to 3-fold. It was indicated that appropriate combination of all these chemical and biological approaches should be very effective to promote ARCUT-mediated HR in human cells.
Human catechol-O-methyltransferase pharmacogenetics: description of a functional polymorphism and its potential application to neuropsychiatric disorders (1996)

Catechol-O-methyltransferase (COMT) inactivates catecholamines and catechol drugs such as L-DOPA. A common genetic polymorphism in humans is associated with a three-to-four-fold variation in COMT enzyme activity and is also associated with individual variation in COMT thermal instability. We now show that this is due to G-->A transition at codon 158 of the COMT gene that results in a valine to methionine substitution. The two alleles can be identified with a PCR-based restriction fragment length polymorphism analysis using the restriction enzyme Nla III. The identification of a gentic marker associated with significant alterations in enzyme activity will facilitate the analysis of a possible role for the COMT gene in neuropsychiatric conditions in which abnormalities in catecholamine neurotransmission are believed to occur, including mood disorders, schizophrenia, obsessive compulsive disorder, alcohol and substance abuse, and attention deficit hyperactivity disorder. In addition, this polymorphism may have pharmacogenetic significance in that it will help make it possible to identify patients who display altered metabolism of catechol drugs.
Platinum catalysed 1,4-diboration of α,β-unsaturated ketones (1997)

Diborane(4) compounds react with α,β-unsaturated ketones to give the 1,4-addition product in the presence of a platinum catalyst at 80 °C.
Development of novel cell-permeable DNA sensitive dyes using combinatorial synthesis and cell-based screeningElectronic supplementary information (ESI) available: experimental section. See http://www.rsc.org/suppdata/cc/b3/b303960a/ (2003)

A novel cell-permeable DNA fluorescence sensor was developed based on combinatorially-created styryl dyes and cell-based localization screening.