gebhart/patrepeval huggingface dataset:
Cloning of sea urchin actin gene sequences for use in studying the regulation of actin gene transcription (1980)

In order to investigate the regulation of actin gene transcription during early sea urchin development, a specific hybridization probe for actin sequences is required. Such a probe was produced by cloning cDNA transcribed from a sea urchin poly(A)-containing mRNA preparation enriched for actin message. Double-stranded DNA was ligated into the BamHI restriction site of plasmid pBR322, and the resulting hybrid molecules were used to transform the Escherichia coli strain ML100. After preliminary screening of bacterial colonies by antibiotic sensitivity and hybridization back to the original cDNA, clones containing sea urchin DNA were further characterized by a positive translation assay in which total sea urchin mRNA was hybridized to plasmid, and the hybridized message then was eluted and translated in a reticulocyte cell-free protein-synthesizing system. In this way, one clone (pSA38) was found to hybridize selectively to sea urchin mRNA coding for a protein of 43,000 daltons. This protein was identified as actin by three criteria: electrophoretic migration in two-dimensional polyacrylamide gels, affinity for DNase I, and peptide mapping. Restriction endonuclease and heteroduplex mapping of pSA38 indicate that it contains a 1.5-kilobase-pair insert and is therefore likely to contain a large portion of the actin coding sequence. By using pSA38 as a hybridization probe, it has been found that the level of actin-specific RNA sequences increases dramatically during early sea urchin development.
Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases. (1993)

Abasic sites are thought to be the most frequently occurring cellular DNA damage and are generated spontaneously or as the result of chemical or radiation damage to DNA. In contrast to the wealth of information that exists on the effects of abasic sites on DNA polymerases, very little is known about how these lesions interact with RNA polymerases. An in vitro transcription system was used to determine the effects of abasic sites and single-strand breaks on transcriptional elongation. DNA templates were constructed containing single abasic sites or nicks placed at unique locations downstream from two different promoters and were transcribed by SP6 and Escherichia coli RNA polymerases. SP6 RNA polymerase is initially stalled at abasic sites with subsequent, efficient bypass of these lesions. E. coli RNA polymerase also bypassed abasic sites. In contrast, single-strand breaks introduced at abasic sites completely blocked the progression of both RNA polymerases. Sequence analysis of full-length transcripts revealed that SP6 and E. coli RNA polymerases insert primarily, if not exclusively, adenine residues opposite to abasic sites. This finding suggests that abasic sites may be highly mutagenic in vivo at the level of transcription.
Mammalian nuclear transfer (2006)

During development, the genetic content of each cell remains, with a few exceptions, identical to that of the zygote. Differentiated cells, therefore, retain all the genetic information necessary to generate an entire organism (nuclear totipotency). Nuclear transfer (NT) was initially developed to test experimentally this concept by cloning animals from differentiated cells. It has, since then, been used to study the role of genetic and epigenetic alterations during development and disease. In this review, we highlight some of the milestones in mammalian NT reached in the 50 years after the first nuclear transplantations in frogs. We also address problems associated with mammalian nuclear transfer and provide a survey on current NT and stem cell technology. In the long term, nuclear transfer or alternative strategies aim to generate customized pluripotent cells, which would be invaluable to medical research and therapy.
Complement Receptors in Neutrophils (1995)

Human neutrophils contain numerous intracellular granules and vesicles that are exocytosed in a hierarchic manner on stimulation of the neutrophil with inflammatory mediators. Secretory vesicles are mobilized completely to the plasma membrane when neutrophils are stimulated with inflammatory mediators in nanomolar concentrations. There is evidence that secretory vesicles contain at least four different complement receptors, namely, C1qR, CR1, CR3, and CR4. These complement receptors are all transported to the neutrophil surface in parallel by the mobilization of secretory vesicles. A fifth complement receptor, C5aR, is constitutively present on the neutrophil plasma membrane. Because secretory vesicles are mobilized by virtually all inflammatory mediators known to stimulate neutrophils, a prompt upregulation of complement receptors is ensured early in neutrophil activation. The integrins CR3 and CR4 are located both in secretory vesicles and granules, and this diverse subcellular localization may reflect their functional versatility. The residence of complement receptors in several intracellular compartments ensures a graded upregulation of these receptors in response to stimulation.
THE PATH OF CARBON IN PHOTOSYNTHESIS. XXVII. SUGAR-CONJUGATED PLANT GROWTH REGULATORS ENHANCE GENERAL PRODUCTIVITY (2011)

Abstract We have found that applications of sugar-conjugated plant growth regulators (SPGRs) by exposures of roots or shoots to millimolar (mM) SPGRs are key to their uptake and transport for enhancement of vegetative productivity of the entire plant as compared to control populations. Initial surveys utilizing foliar applications of identically nutrient-supplemented 0.3 mM cytokinin glycosides, N6-benzyladenine glycosides, kinetin glycosides; and a 0.3 mM auxin glycoside, indoxyl-β-D-glucopyranoside (IG) resulted in significant shoot enhancements over controls. Foliar application of 0.3 mM kinetin glucoside resulted in significant root increase above the control. Foliar application of 3 mM to 6 mM IG resulted in enhanced root and shoot growths over controls. Similarly, increases of root and shoot yields over controls were observed as a result of foliar application of 3 mM indoxyl-β-D-glucuronide. Foliar application of 1 mM trans-zeatin-β-D-glucoside was particularly effective, resulting in significant enhancement of root and shoot growth with no phytotoxicity. Keywords: carbonbrassicasmanganese
Algorithms and software for ordinary differential equations and differential- algebraic equations, Part I: Euler methods and error estimation (1995)

Department Editor: William J. Thompson
Relationship between the association of rat epididymal protein ?DE? with spermatozoa and the behavior and function of the protein (2000)

Rat epididymal glycoprotein DE associates with the dorsal region of the sperm head during sperm maturation, migrates to the equatorial segment (ES) with the acrosome reaction (AR), and is involved in gamete membrane fusion. In the present study we examined the association of DE with the sperm surface and the relationship of this interaction with the behavior and function of the protein. Cloning and sequencing of DE revealed a lack of hydrophobic domains and the presence of 16 cysteine residues in the molecule. Experiments in which cauda epididymal sperm were subjected to different extraction procedures indicated that while most of the protein is removable from sperm by mild ionic strength, a low amount of DE, resistant to even 2 M NaCl, can be completely extracted by agents that remove integral proteins. However, the lack of hydrophobic domains in the molecule and the failure of DE to interact with liposomes, does not support a direct insertion of the protein into the lipid bilayer. These results, and the complete extraction of the tightly bound protein by dithiothreitol, suggest that this population would correspond to a peripheral protein bound to a membrane component by strong noncovalent interactions that involve disulfide bonds. While ELISA experiments showed that no protein could be extracted by NaCl from capacitated sperm, indirect immunofluorescence studies revealed the ability of the NaCl-resistant protein to migrate to the ES. Together, these results support the existence of two populations of DE: a major, loosely bound population that is released during capacitation, and a minor strongly bound population that remains after capacitation, migrates to the ES with the AR, and thus would correspond to the one with a role in gamete fusion.
Novel Path to Activation of Vascular Smooth Muscle Cells: Up-Regulation of gp130 Creates an Autocrine Activation Loop by IL-6 and Its Soluble Receptor (1999)

This study describes a novel path to the activation of smooth muscle cells (SMC) by the IL-6/soluble IL-6 receptor (sIL-6R) system. Human vascular SMC constitutively express only scant amounts of IL-6R and so do not respond to stimulation with this cytokine. We show that SMC also do not constitutively express appreciable levels of gp130, which would render them sensitive to transsignaling by the IL-6/sIL-6R complex. Because gp130 is generally believed not to be subject to regulation, SMC would thus appear not to qualify as targets for the IL-6/sIL-6R system. However, we report that treatment of SMC with IL-6/sIL-6R provokes marked up-regulation of gp130 mRNA and surface protein expression. This is accompanied by secretion of IL-6 by the cells, so that an autocrine stimulation loop is created. In the wake of this self-sustaining system, there is a selective induction and secretion of MCP-1, up-regulation of ICAM-1, and marked cell proliferation. The study identifies SMC as the first example of cells in which gp130 expression is subject to substantive up-regulation, and discovers a novel amplification loop involving IL-6 and its soluble receptor that drives SMC into a proinflammatory state.
Sensing polygon poses by inscription (2002)

Industrial assembly involves sensing the pose (orientation and position) of a part. Efficient and reliable sensing strategies can be developed for an assembly task if the shape of the part is known in advance. In this paper the authors investigate the problem of determining the pose of a convex n-gon from a set of m supporting cones, i.e., cones with both sides supporting the polygon. An algorithm with running time O(nm) which almost always reduces to O(n+m log n) is presented to solve for all possible poses of the polygon. As a consequence, the polygon inscription problem of finding all possible poses for a convex n-gon inscribed in another convex m-gon, can be solved within the same asymptotic time bound. The authors prove that the number of possible poses cannot exceed 6n, given m/spl ges/2 supporting cones with distinct vertices. Experiments demonstrate that two supporting cones are sufficient to determine the real pose of the n-gon in most cases. The authors' results imply that sensing in practice can be carried out by obtaining viewing angles of a planar part at multiple exterior sites in the plane. As a conclusion, the authors generalize this and other sensing methods into a scheme named sensing by inscription.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A whole word recurrent neural network for keyword spotting (1992)

The authors present a neural network which is trained on word examples to perform the wordspotting task. This network has multiple recurrent connections with time delay to account for temporal dynamics. A single network may be trained to recognize one word or many words. A hybrid wordspotter is evaluated in which a conventional wordspotter (based on dynamic time warping word matching) is used to screen incoming speech for potential keywords which are then passed to the network for the final accept/reject decision. Initial tests on a standard wordspotting test corpora resulted in improved keyword recognition at false alarm rates above zero.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lipolysis Produces Changes in the Immunoreactivity and Cell Reactivity of Very Low Density Lipoproteins (1979)

Smaller very low density lipoprotein (VLDL) remnants interact more readily with tissues than do larger "intact" VLDL. This may be related to changes in the availability of VLDL apoproteins on the surface of the lipoproteins. To test this hypothesis VLDL were incubated at 37 degrees C with bovine milk lipase (LPL), and the abilities of LPL-treated VLDL preparations to compete with (125)I-low density lipoproteins (LDL) for interaction with cultured normal human fibroblasts were measured. At the same time, the immunologic activities of these preparations were also tested by double antibody radioimmunoassay. Triglyceride (TG) contents of VLDL fell by 30-90% during incubation with LPL and, on zonal ultracentrifugation, VLDL of faster Svedberg unit of flotation (S(f1.063)) rates (>150) were gradually converted to smaller VLDL with lower S(f) rates (21-60). LPL-treated VLDL competed two to five times more effectively with (125)I-LDL for binding to cellular receptors than did control VLDL. Control VLDL incubated with heat-inactivated LPL at 37 degrees C, or with active LPL at 4 degrees C had unaltered cell reactivities and TG contents compared with VLDL incubated without any enzyme. The direct uptake and degradation of LPL-treated VLDL was also assessed by using VLDL (125)I-labeled in apoprotein (Apo)B. LPL-treated VLDL-(125)I-ApoB were taken up and degraded by fibroblast at greater rates than were control VLDL-(125)I-ApoB. Thus, hydrolysis of VLDL lipids was accompanied by an increased ability of VLDL to interact with fibroblasts. The immunoreactivity of ApoB in the same VLDL preparations, expressed as the "apparent ApoB contents" of LPL-treated VLDL, increased by 10-50% (P < 0.02) in those assays that contained anti-LDL antisera, but the ApoB of control VLDL remained constant. However, assays that contained antisera directed against ApoB isolated from VLDL did not distinguish between LPL-treated and control VLDL. Thus, VLDL lipid hydrolysis was accompanied by changes in the immunoreactivity of VLDL-ApoB, which probably reflect changes in the disposition of ApoB on the surface of VLDL. The altered disposition of ApoB on VLDL "remnants" may be related to their enhanced interaction with cells.
Neurokinin 1 receptor and relative abundance of the short and long isoforms in the human brain (2003)

Substance P exerts its various biochemical effects mainly via interactions through neurokinin-1 receptors (NK1). Recently, the NK1 receptor has attracted considerable interest for its possible role in a variety of psychiatric disorders including depression and anxiety. However, little is known regarding the anatomical distribution of NK1 in the human central nervous system (CNS). Riboprobe in situ hybridization, quantitative PCR and in vitro autoradiography were performed. Highest NK1 mRNA levels were localized in the locus coeruleus and ventral striatum, while moderate hybridization signals were observed in the cerebral cortex (most abundant in the visual cortex), hippocampus and different amygdaloid nuclei. Very low levels of the NK1 mRNA were detected in the cerebellum and thalamus. In view of the existence of a long and short isoform of the NK1 receptor, it was of interest to assess whether there was a differential distribution of the two splice variants in the human CNS and peripheral tissues. A quantitative TaqMan PCR analysis showed that the long NK1 isoform was the most prevalent throughout the human brain, while in peripheral tissues the truncated form was the most represented. 3H-Substance P autoradiography revealed a good correlation between receptor binding sites and NK1 mRNA expression throughout the brain, with the highest levels of binding in the locus coeruleus. These results provide the anatomical evidence that the NK1 receptors have a strong association with neuronal systems relevant to mood regulation and stress in the human brain, but do not suggest a region-specific role of the two isoforms in the CNS.
Array of Molecularly Mediated Thin Film Assemblies of Nanoparticles:  Correlation of Vapor Sensing with Interparticle Spatial Properties (2007)

The ability to tune interparticle spatial properties of nanoparticle assemblies is essential for the design of sensing materials toward desired sensitivity and selectivity. This paper reports findings of an investigation of molecularly mediated thin film assemblies of metal nanoparticles with controllable interparticle spatial properties as a sensing array. The interparticle spatial properties are controlled by a combination of alpha,omega-difunctional alkyl mediators (X-(CH(2))(n)-X) such as alkyl dithiols, dicarboxylate acids, and alkanethiol shells capped on nanoparticles. Alkanethiolate-capped gold and gold-silver alloy nanoparticles (2-3 nm) were studied as model building blocks toward the thin film assemblies, whereas the variation of alkyl chain length manipulates the interparticle spacing. The thin films assembled on an interdigitated microelectrode array platform are characterized for determining their responses to the sorption of volatile organic compounds (VOCs). The correlation between the response sensitivity and the interparticle spacing properties revealed not only a clear dependence of the sensitivity on alkyl chain length but also the occurrence of a dramatic change of the sensitivity in a region of chain length for the alkyl mediator comparable with that of the capping alkyl chains. This finding reflects a balance between the interparticle chain-chain cohesive interdigitation and the nanostructure-vapor interaction which determines the relative change of the electrical conductivity of the inked nanoparticle thin film in response to vapor sorption. The results, along with statistical analysis of the sensor array data in terms of sensitivity and selectivity, have provided important insights into the detailed delineation between the interparticle spacing and the nanostructured sensing properties.
Generation and Comprehension of Unambiguous Object Descriptions (2015)

We propose a method that can generate an unambiguous description (known as a referring expression) of a specific object or region in an image, and which can also comprehend or interpret such an expression to infer which object is being described. We show that our method outperforms previous methods that generate descriptions of objects without taking into account other potentially ambiguous objects in the scene. Our model is inspired by recent successes of deep learning methods for image captioning, but while image captioning is difficult to evaluate, our task allows for easy objective evaluation. We also present a new large-scale dataset for referring expressions, based on MS-COCO. We have released the dataset and a toolbox for visualization and evaluation, see https://github.com/mjhucla/Google_Refexp_toolbox
Molecular characterization of the VH region of murine autoantibodies from neonatal and adult BALB/c mice (1989)

We report on the molecular characterization of the heavy (H) chain variable (V) region of two murine autoantibodies reacting with a conventional self antigen, thyroglobulin (Tg), originated from unimmunized/unstimulated neonatal mice (clone B10H2) and from an adult hyperimmunized mouse (clone 62), respectively. Serologically, both hybridoma antibodies express the same idiotype (Id). By cloning and sequencing we demonstrated that their VH regions are encoded by identical VDJ gene elements including the VD and DJ joints. This VH belongs to the VH 7183 gene family, the most 3'-end proximal family in the murine genome. The D segment is unique and only 50% similar to any murine D segment. The J segment utilized is germ-line JH4. The cloned DNA rearrangement was transfected into the J558L myeloma cells and the secreted antibody was found to express the reference Id on the H chain, hence proving that the productive VDJ rearrangement had been identified. These results show that a spontaneously arising and an antigen-induced autoantibody use an identical VDJ gene rearrangement and that after hyperimmunization somatic mutation did not occur. The significance of this finding with respect to ontogeny of the B cell repertoire is discussed.
A PROSPECTIVE, RANDOMIZED MULTICENTER TRIAL COMPARING CELSIOR?? TO STANDARD CARDIAC PRESERVATION SOLUTION. (1999)

442 The impact of variable preservation solutions on early graft function has not been measured. Currently, no cardiac preservation solution has FDA clearance; therefore, a clinical standard does not exist. Celsior® has been developed specifically for heart preservation. A multi-center trial was conducted to compare the safety and efficacy of Celsior® (SangStat Medical Corporation, Menlo Park, CA USA) and local preservation solutions. Donor hearts were prospectively randomized to be flushed and stored in 1-2 L of either Celsior® or the local preservation solution. The primary endpoint was 7-day patient (PT) survival. Secondary endpoints included 30 day PT and graft survival, cardiac and non-cardiac adverse events (AE), and death with a treatment related etiology. A total of 131 patients were enrolled. Demographic characteristics did not differ between treatment groups. (Table)TableUtilizing this study design, Celsior® appears to have at least equivalent safety, efficacy to currently utilized commercial and in-house preservation solutions. This study design may provide a benchmark for evaluating preservation solutions in this transplant population. This study was sponsored by in part by SangStat Medical Corporation.
Product platform design and customization: Status and promise (2004)

In an effort to improve customization for today's highly competitive global marketplace, many companies are utilizing product families and platform-based product development to increase variety, shorten lead times, and reduce costs. The key to a successful product family is the product platform from which it is derived either by adding, removing, or substituting one or more modules to the platform or by scaling the platform in one or more dimensions to target specific market niches. This nascent field of engineering design has matured rapidly in the past decade, and this paper provides a comprehensive review of the flurry of research activity that has occurred during that time to facilitate product family design and platform-based product development for mass customization. Techniques for identifying platform leveraging strategies within a product family are reviewed along with metrics for assessing the effectiveness of product platforms and product families. Special emphasis is placed on optimization approaches and artificial intelligence techniques to assist in the process of product family design and platform-based product development. Web-based systems for product platform customization are also discussed. Examples from both industry and academia are presented throughout the paper to highlight the benefits of product families and product platforms. The paper concludes with a discussion of potential areas of research to help bridge the gap between planning and managing families of products and designing and manufacturing them.
Effects of exenatide versus sitagliptin on postprandial glucose, insulin and glucagon secretion, gastric emptying, and caloric intake: a randomized, cross-over study (2008)

Although this study was limited by a 2-week duration of exposure, these data demonstrate that, exenatide had: (i) a greater effect than sitagliptin to lower postprandial glucose and (ii) a more potent effect to increase insulin secretion and reduce postprandial glucagon secretion in T2D patients. In contrast to sitagliptin, exenatide slowed gastric emptying and reduced caloric intake. These key findings differentiate the therapeutic actions of the two incretin-based approaches, and may have meaningful clinical implications.