gebhart/patrepeval huggingface dataset:
The human gastrin/cholecystokinin type B receptor gene: alternative splice donor site in exon 4 generates two variant mRNAs. (1993)

Gastrin and its carboxyl-terminal homolog cholecystokinin (CCK) exert a variety of biological actions in the brain and gastrointestinal tract that are mediated in part through one or more G protein-coupled receptors which exhibit similar affinity for both peptides. Genomic clones encoding a human gastrin/CCKB receptor were isolated by screening a human EMBL phage library with a partial-length DNA fragment which was based on the nucleotide sequence of the canine gastrin receptor. The gene contained a 1356-bp open reading frame consisting of five exons interrupted by 4 introns and was assigned to human chromosome 11p15.4. A region of exon 4, which encodes a portion of the putative third intracellular loop, appears to be alternatively spliced to yield two different mRNAs, one containing (452 amino acids; long isoform) and the other lacking (447 amino acids; short isoform) the pentapeptide sequence Gly-Gly-Ala-Gly-Pro. The two receptor isoforms may contribute to functional differences in gastrin- and CCK-mediated signal transduction.
Identification of Chlamydia pneumoniae by DNA amplification of the 16S rRNA gene (1992)

Chlamydia pneumoniae is an important cause of respiratory disease in humans, but diagnosis of C. pneumoniae is hindered by difficulties in the in vitro growth of the organism. In order to improve detection and identification, we recently developed a polymerase chain reaction (PCR) assay which uses oligonucleotide primers specific for C. pneumoniae. The nucleic acid sequence was determined for the 16S rRNA of C. pneumoniae, and regions in which C. pneumoniae differed from both Chlamydia psittaci and Chlamydia trachomatis were identified. Oligonucleotide primers corresponding to these unique regions were then synthesized and used in a PCR for the detection of C. pneumoniae. The C. pneumoniae-specific primers permitted the identification of six isolates of C. pneumoniae, but no reaction was observed with the 15 serovars of C. trachomatis or two strains of C. psittaci. PCR should prove to be valuable in confirming the identification of C. pneumoniae and in the diagnosis of C. pneumoniae infections.
Purification and properties of guinea-pig submandibular-gland kallikrein (1983)

Guinea-pig submandibular kallikrein has been purified from the glands to electrophoretic homogeneity by conventional procedures. The enzyme is active as a kininogenase, releasing kallidin at a rate of 462 micrograms/min per mg of protein from bovine kininogen, and proved potently hypotensive in the guinea pig and in the dog, properties which indicate its tissue kallikrein nature. The specific activity determined on the substrate N-alpha-benzoyl-L-arginine ethyl ester (11.1 mumol/min per mg of protein) is much lower than that measured with N-acetyl-L-phenylalanyl-L-arginine ethyl ester (483 mumol/min per mg of protein). The latter value is of an order of magnitude comparable with the specific activities of other tissue kallikreins determined with this sensitive kallikrein substrate. The enzyme is a glycoprotein consisting of 237 amino acid residues and containing three to four glucosamine molecules. Its amino acid composition is not identical with that reported for guinea-pig coagulating-gland kallikrein, but is remarkably similar to that of the porcine tissue kallikreins. Apparent Mr values are 29000 (sodium dodecyl sulphate/polyacrylamide-gel electrophoresis) or 34000 (gel filtration). The amino acid sequence of the first 31 N-terminal residues was determined and was found to be closely homologous with that of other tissue kallikreins.
A wafer-scale 3-D circuit integration technology (2006)

The rationale and development of a wafer-scale three-dimensional (3-D) integrated circuit technology are described. The essential elements of the 3-D technology are integrated circuit fabrication on silicon-on-insulator wafers, precision wafer-wafer alignment using an in-house-developed alignment system, low-temperature wafer-wafer bonding to transfer and stack active circuit layers, and interconnection of the circuit layers with dense-vertical connections with sub-Omega 3-D via resistances. The 3-D integration process is described as well as the properties of the four enabling technologies. The wafer-scale 3-D technology imposes constraints on the placement of the first lithographic level in a wafer-stepper process. Control of wafer distortion and wafer bow is required to achieve submicrometer vertical vias. Three-tier digital and analog 3-D circuits were designed and fabricated. The performance characteristics of a 3-D ring oscillator, a 1024 times 1024 visible imager with an 8-mum pixel pitch, and a 64 times 64 Geiger-mode laser radar chip are described
Cow-specific treatment of clinical mastitis: An economic approach (2010)

Under Dutch circumstances, most clinical mastitis (CM) cases of cows on dairy farms are treated with a standard intramammary antimicrobial treatment. Several antimicrobial treatments are available for CM, differing in antimicrobial compound, route of application, duration, and cost. Because cow factors (e.g., parity, stage of lactation, and somatic cell count history) and the causal pathogen influence the probability of cure, cow-specific treatment of CM is often recommended. The objective of this study was to determine if cow-specific treatment of CM is economically beneficial. Using a stochastic Monte Carlo simulation model, 20,000 CM cases were simulated. These CM cases were caused by Streptococcus uberis and Streptococcus dysgalactiae (40%), Staphylococcus aureus (30%), or Escherichia coli (30%). For each simulated CM case, the consequences of using different antimicrobial treatment regimens (standard 3-d intramammary, extended 5-d intramammary, combination 3-d intramammary+systemic, combination 3-d intramammary+systemic+1-d nonsteroidal antiinflammatory drugs, and combination extended 5-d intramammary+systemic) were simulated simultaneously. Finally, total costs of the 5 antimicrobial treatment regimens were compared. Some inputs for the model were based on literature information and assumptions made by the authors were used if no information was available. Bacteriological cure for each individual cow depended on the antimicrobial treatment regimen, the causal pathogen, and the cow factors parity, stage of lactation, somatic cell count history, CM history, and whether the cow was systemically ill. Total costs for each case depended on treatment costs for the initial CM case (including costs for antibiotics, milk withdrawal, and labor), treatment costs for follow-up CM cases, costs for milk production losses, and costs for culling. Average total costs for CM using the 5 treatments were (US) $224, $247, $253, $260, and $275, respectively. Average probabilities of bacteriological cure for the 5 treatments were 0.53, 0.65, 0.65, 0.68, and 0.75, respectively. For all different simulated CM cases, the standard 3-d intramammary antimicrobial treatment had the lowest total costs. The benefits of lower costs for milk production losses and culling for cases treated with the intensive treatments did not outweigh the higher treatment costs. The stochastic model was developed using information from the literature and assumptions made by the authors. Using these information sources resulted in a difference in effectiveness of different antimicrobial treatments for CM. Based on our assumptions, cow-specific treatment of CM was not economically beneficial.
Gain limit in erbium-doped fiber amplifiers due to internal Rayleigh backscattering (1992)

A very high gain of 51 dB in a single Er-doped fiber is reported. A significant amount of amplified Rayleigh backscattering is also observed. This is predicted to impose an upper limit of 57-70 dB of achievable gain for the investigated fibers. By the insertion of an isolator, a gain of 54 dB is observed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DNA: A Model Compound for Solution Studies of Macromolecules (1991)

Well-defined, monodisperse, homologous series of oligonucleotides and DNA restriction fragments may now be produced and used as models of rigid and semirigid rodlike molecules in solution. Information from optical experiments on these model systems aids in the formulation and testing of theories of macromolecular dynamics in both dilute and concentrated solution.
White Spot Syndrome Virus Infection of Cultured Shrimp in China (1998)

In 1993 and 1994, an epizootic of disease (white spot) occurred among cultured shrimp in China, resulting in mass mortality. During the periods of outbreak epizootiological surveys were undertaken. Based on these surveys it is known that the disease occurred among populations of cultured Penaeus chinensis, P. japonicus, and P. monodon, infecting shrimp from 2.4 cm to adult. The disease presumably spread among farms as a result of transport of contaminated shrimp seedlings and seawater. Water temperatures exceeding 25°C caused the disease to spread more rapidly. Challenge experiments showed the causative agent was highly virulent. Both naturally and experimentally infected shrimp exhibited white spots on the carapace. Moribund shrimp contained turbid hemolymph, hypertrophied lymphoid organ, and a necrotic hepatopancreas. By electron microscopy, viral particles were observed in gills, stomach, lymphoid organ, and hypodermal tissue of infected shrimp. The virions were slightly ovoid with an envelope and averaged 350 × 150 nm and nucleocapsids measured 325 × 120 nm in size. By use of negative stains, complete virions were 375 × 157 nm and unenveloped nucleocapsids averaged 395 × 83 nm.
The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. (1995)

The histones of all eukaryotes show only a low degree of primary structure homology, but our earlier crystallographic results defined a three-dimensional structural motif, the histone fold, common to all core histones. We now examine the specific architectural patterns within the fold and analyze the nature of the amino acid residues within its functional segments. The histone fold emerges as a fundamental protein dimerization motif while the differentiations of the tips of the histone dimers appear to provide the rules of core octamer assembly and the basis for nucleosome regulation. We present evidence for the occurrence of the fold from archaebacteria to mammals and propose the use of this structural motif to define a distinct family of proteins, the histone fold superfamily. It appears that evolution has conserved the conformation of the fold even through variations in primary structure and among proteins with various functional roles.
A bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probes (2014)

Small molecules are useful tools for probing the biological function and therapeutic potential of individual proteins, but achieving selectivity is challenging when the target protein shares structural domains with other proteins. The Bromo and Extra-Terminal (BET) proteins have attracted interest because of their roles in transcriptional regulation, epigenetics, and cancer. The BET bromodomains (protein interaction modules that bind acetyl-lysine) have been targeted by potent small-molecule inhibitors, but these inhibitors lack selectivity for individual family members. We developed an ethyl derivative of an existing small-molecule inhibitor, I-BET/JQ1, and showed that it binds leucine/alanine mutant bromodomains with nanomolar affinity and achieves up to 540-fold selectivity relative to wild-type bromodomains. Cell culture studies showed that blockade of the first bromodomain alone is sufficient to displace a specific BET protein, Brd4, from chromatin. Expansion of this approach could help identify the individual roles of single BET proteins in human physiology and disease.
Improved molecular diagnosis of dystrophinopathies in an unselected clinical cohort (2005)

Mutations in the DMD gene result in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Readily available clinical tests detect only deletions of one exon or greater, which are found in approximately 60% of cases. Mutational analysis of other types of DMD mutations, such as premature stop codons and small frameshifting insertions or deletions, has historically been hampered by the large size of the gene. We have recently reported a method that allows the rapid and economical sequencing of the entire coding region of the DMD gene, and that is more sensitive than methods based on single-strand conformational polymorphism (SSCP) screening or other preliminary screening steps. Here we use single condition amplification/internal primer (SCAIP) sequencing analysis, in combination with multiplex amplifiable probe hybridization (MAPH) analysis of duplications, to report the frequency of mutations in a large cohort of unselected dystrophinopathy patients from a single clinic. Our results indicate that 7% of dystrophinopathy patients do not have coding region mutations, suggesting that intronic mutations are not uncommon. The availability of rapid and thorough mutation analysis from peripheral blood samples, along with an improved estimate of the percentage of non-coding region mutations, will be of benefit for improved genetic counseling and in identification of cohorts for clinical trials.
Social Indexing of TV Programs: Detection and Labeling of Significant TV Scenes by Twitter Analysis (2012)

Technology to analyze the content of TV programs, especially the extraction and annotation of important scenes and events within a program, is beneficial for users to enjoy recorded programs. In this paper, we propose a method of detecting significant scenes in TV programs and automatically annotating the content of the extracted scenes through Twitter analysis. Experiments conducted on baseball games indicate that the proposed method is capable of detecting major events in a baseball game with an accuracy of 90.6%. Moreover, the names of persons involved in the events were detected with an accuracy of 87.2%, and labels describing the event were applied with an accuracy of 66.8%. The proposed technology is very helpful, because it enables users to skip to the highlights of a recorded program.
Stanniocalcin-1 regulates endothelial gene expression and modulates transendothelial migration of leukocytes (2006)

The mammalian counterpart of the fish calcium-regulating hormone stanniocalcin-1 (STC1) inhibits monocyte chemotactic protein-1- and stromal-derived factor-1alpha (SDF-1alpha)-mediated chemotaxis and diminishes chemokinesis in macrophage-like RAW264.7 and U937 cells in a manner that may involve attenuation of the intracellular calcium signal. STC1 is strongly induced in the kidney following obstructive injury. We hypothesized that STC1 may serve to attenuate the influx of inflammatory cells to the site of tissue injury. In this study, we examined the effect of STC1 on the migration of freshly isolated human macrophages, neutrophils, and T and B lymphocytes through quiescent or IL-1beta-treated human umbilical vein endothelial cell (HUVEC) monolayers. STC1 inhibited transmigration of macrophages and T lymphocytes through quiescent or IL-1beta-activated HUVECs but did not attenuate the transmigration of neutrophils and B lymphocytes. STC1 regulates gene expression in cultured endothelial cells and is detected on the apical surface of endothelial cells in vivo. The data suggest that STC1 plays a critical role in transendothelial migration of inflammatory cells and is involved in the regulation of numerous aspects of endothelial function.
Efficacy of a Mycoplasma hyopneumoniae bacterin in pigs challenged with two contemporary pathogenic isolates ofM hyopneumoniae (2008)

Materials and methods: Two challenge studies were performed in which pigs received two doses of either saline (nonvaccinated groups) or an M hyo bacterin (vaccinated groups), followed 3 weeks later by intratracheal inoculation of each pig with one of two M hyo field isolates. Necropsies were performed 28 or 30 days post challenge. Vaccine efficacy was determined by evaluating macroscopic lung lesions, DNA levels of M hyo in bronchial alveolar lavage fluids (BALF), Peer ­reviewed
A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes (1995)

A system for generating chromosomal insertions in lactococci is described. It is based on the conditional replication of lactococcal pWV01-derived Ori+ RepA- vector pORI19, containing lacZ alpha and the multiple cloning site of pUC19. Chromosomal AluI fragments of Lactococcus lactis were cloned in pORI19 in RepA+ helper strain Escherichia coli EC101. The frequency of Campbell-type recombinants, following introduction of this plasmid bank into L. lactis (RepA-), was increased by combining the system with temperature-sensitive pWV01 derivative pVE6007. Transformation of L. lactis MG1363 (pVE6007) with the pORI19 bank of lactococcal chromosomal fragments at the permissive temperature allowed replication of several copies of a recombinant plasmid from the bank within a cell because of the provision in trans of RepA-Ts from pVE6007. A temperature shift to 37 degrees C resulted in loss of pVE6007 and integration of the pORI19 derivatives at high frequencies. A bank of lactococcal mutants was made in this way and successfully screened for the presence of two mutations: one in the monocistronic 1.3-kb peptidoglycan hydrolase gene (acmA) and one in the hitherto uncharacterized maltose fermentation pathway. Reintroduction of pVE6007 into the Mal- mutant at 30 degrees C resulted in excision of the integrated plasmid and restoration of the ability of ferment maltose. The integration plasmid (pMAL) was rescued by using the isolated plasmid content of a restored Mal+ colony to transform E. coli EC101. Nucleotide sequencing of the 564-bp chromosomal fragment in pMAL revealed an internal part of an open reading frame of which the translated product showed significant homology with ATP-binding proteins MalK of E. coli, Salmonella typhimurium, and Enterobacter aerogenes and MsmK of Streptococcus mutans. This combined use of two types of conditional replicating pWV01-derived vectors represents a novel, powerful tool for chromosomal gene inactivation, targeting, cloning, and sequencing of the labelled gene.
Suppressive Effect of Receptor-interacting Protein 140 on Coregulator Binding to Retinoic Acid Receptor Complexes, Histone-modifying Enzyme Activity, and Gene Activation (2003)

Gene induction by retinoic acid (RA) is suppressed by overexpression of receptor-interacting protein 140 (RIP140). RIP140-mediated suppression was reversed most effectively by overexpressing the coactivator p300/CREB-binding protein-associated factor (P/CAF). Immunoprecipitation demonstrated coexistence of holoreceptors complexed with RIP140 or P/CAF. Chromatin immunoprecipitation revealed rapid RA-enhanced recruitment of RIP140, but delayed P/CAF recruitment, to an RA-targeted promoter in COS-1 cells supplemented with RIP140. In RA-induced P19 cells, endogenous RIP140 was rapidly (within 4 h) and significantly recruited to both the RARbeta2 and TR2 genes, whereas the peak of endogenous P/CAF recruitment occurred much later (48 h) and to a lesser degree. Consistent with these observations, significant histone acetylation of endogenous RA receptor (RAR) targets was only observed 48 h following RA treatment. In vitro experiments confirmed RA-induced transcription from a chromatin template, which was reduced by adding RIP140. This study presents evidence for coexistence of multiple RAR-coregulator complexes and a preferential RA-induced recruitment of RIP140 to endogenous RAR-targeted promoters after short term RA treatment, which correlates with suppressed induction of RA-regulated gene expression in the presence of RIP140.
Filling-in by joint interpolation of vector fields and gray levels (2001)

A variational approach for filling-in regions of missing data in digital images is introduced. The approach is based on joint interpolation of the image gray levels and gradient/isophotes directions, smoothly extending in an automatic fashion the isophote lines into the holes of missing data. This interpolation is computed by solving the variational problem via its gradient descent flow, which leads to a set of coupled second order partial differential equations, one for the gray-levels and one for the gradient orientations. The process underlying this approach can be considered as an interpretation of the Gestaltist's principle of good continuation. No limitations are imposed on the topology of the holes, and all regions of missing data can be simultaneously processed, even if they are surrounded by completely different structures. Applications of this technique include the restoration of old photographs and removal of superimposed text like dates, subtitles, or publicity. Examples of these applications are given. We conclude the paper with a number of theoretical results on the proposed variational approach and its corresponding gradient descent flow.
Genome Editing of Human Embryonic Stem Cells and Induced Pluripotent Stem Cells With Zinc Finger Nucleases for Cellular Imaging (2012)

Our study demonstrates a novel application of ZFN technology to the targeted genetic engineering of human pluripotent stem cells and their progeny for molecular imaging in vitro and in vivo.
ReMotENet: Efficient Relevant Motion Event Detection for Large-scale Home Surveillance Videos (2018)

This paper addresses the problem of detecting relevant motion caused by objects of interest (e.g., person and vehicles) in large scale home surveillance videos. The traditional method usually consists of two separate steps, i.e., detecting moving objects with background subtraction running on the camera, and filtering out nuisance motion events (e.g., trees, cloud, shadow, rain/snow, flag) with deep learning based object detection and tracking running on cloud. The method is extremely slow and therefore not cost effective, and does not fully leverage the spatial-temporal redundancies with a pre-trained off-the-shelf object detector. To dramatically speedup relevant motion event detection and improve its performance, we propose a novel network for relevant motion event detection, ReMotENet, which is a unified, end-to-end data-driven method using spatial-temporal attention-based 3D ConvNets to jointly model the appearance and motion of objects-of-interest in a video. ReMotENet parses an entire video clip in one forward pass of a neural network to achieve significant speedup. Meanwhile, it exploits the properties of home surveillance videos, e.g., relevant motion is sparse both spatially and temporally, and enhances 3D ConvNets with a spatial-temporal attention model and reference-frame subtraction to encourage the network to focus on the relevant moving objects. Experiments demonstrate that our method can achieve comparable or event better performance than the object detection based method but with three to four orders of magnitude speedup (up to 20k times) on GPU devices. Our network is efficient, compact and light-weight. It can detect relevant motion on a 15s surveillance video clip within 4-8 milliseconds on a GPU and a fraction of second (0.17-0.39) on a CPU with a model size of less than 1MB.