gebhart/patrepeval huggingface dataset:
Isolation and Analysis of cDNA Encoding a Precursor of Canavalia ensiformis Asparaginyl Endopeptidase (Legumain) (1994)

Recently, asparaginyl endopeptidase was purified to homogeneity from jack bean (Canavalia ensiformis) seeds, and its NH2-terminal amino acid sequence was determined for 25 residues [Abe, Y. et al. (1993) J. Biol. Chem. 268, 3525-3529]. On the basis of this sequence information, we searched for seed cDNAs encoding this enzyme. Seven clones were obtained and sequenced. By combining four of them, we obtained a cDNA for a precursor of the enzyme containing the reported NH2-terminal sequence. The other three clones seemed to be for precursors of its isozymes. When the deduced amino acid sequences of these enzyme precursors were compared with those in the GeneBank, EMBL, and NBRF databases, only one protein was found with a homologous sequence. It was a precursor of hemoglobinase from a blood fluke (Schistosoma mansoni). Significant homology was observed only in the range of sequence for the mature form. Although hemoglobinase and asparaginyl endopeptidase behave as cysteine proteinases, their protein natures are distinct from either papain-type proteinases or clostripain. Various plant seeds have been reported to contain asparaginyl endopeptidases. This may be the first report, however, that deals with the primary structure of such a proteinase.
The Use of Neuromodulation for Treatment of Urinary Incontinence (2001)

Urinary incontinence (UI) affects many people in the United States. Although the prevalence of UI increases with age, it should not be considered part of the normal aging process. Medication to relax the bladder and behavioral therapy have been used to treat patients suffering from UI, but they often are unsuccessful or poorly tolerated. Neuromodulation through sacral nerve stimulation is a minimally invasive surgical procedure for treatment of urge incontinence. Neuromodulation is becoming the next logical step at many centers for treating urge incontinence after the failure of more conservative measures.
Novel ’’heat-pipe’’ rotating anode for x-ray lithography (1979)

A unique rotating anode has been developed in which heat is removed from the bombarded target area by conversion of water to vapor. A ’’heat-pipe’’ principle is also incorporated, whereby the vapor is condensed on a cooled plate which is a part of the rotating anode. The condensate is rapidly returned to the reservoir by centrifugal action. The great potential of the heat-pipe rotating anode lies in the fact that, since it is to a large extent hollow, it can be made much lighter than a directly cooled anode of comparable size. Also, the hydrostatic pressures encountered in the heat-pipe anode are very much lower. This makes possible increased diameters and rotation rates for rotating anodes, and consequently x-ray sources with higher power output and brightness.
Transglucosylation into Stevioside by the Enzyme System fromStreptomycessp. (1986)

Journal Article Transglucosylation into Stevioside by the Enzyme System from Streptomyces sp. Get access Satoru Kusama, Satoru Kusama Institute of Applied Biochemistry, University of Tsukuba, Sakura-mura, Niihari-gun, Ibaraki 305, Japan Search for other works by this author on: Oxford Academic Google Scholar Isao Kusakabe, Isao Kusakabe To whom correspondence should be addressed Search for other works by this author on: Oxford Academic Google Scholar Yasuyuki Nakamura, Yasuyuki Nakamura Present address: Iwakuni Institute, Sanyo-Kokusaku Pulp Co., Ltd., 2-8-1 Iida-machi, Iwakuni 740, Japan Search for other works by this author on: Oxford Academic Google Scholar Shigeru Eda, Shigeru Eda Central Research Institute, Nippon Tabacco Co., Ltd., 6–2 Umegaoka, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Kazuo Murakami Kazuo Murakami Institute of Applied Biochemistry, University of Tsukuba, Sakura-mura, Niihari-gun, Ibaraki 305, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 50, Issue 10, 1 October 1986, Pages 2445–2451, https://doi.org/10.1080/00021369.1986.10867771 Published: 01 October 1986 Article history Received: 03 March 1986 Published: 01 October 1986
A modular framework for collaborative multimodal annotation and visualization (2019)

Artificial Intelligence (AI) research, including machine learning, computer vision, and natural language, requires large amounts of annotated datasets. The current research and development (R&D) pipeline involves each group collecting their own datasets using an annotation tool tailored specifically to their needs, followed by a series of engineering efforts in loading other external datasets and developing their own interfaces, often mimicking some components of existing annotation tools. In departure from the current paradigm, my research focuses on reducing inefficiencies by developing a unified web-based, fully configurable framework that enables researchers to set up an end-to-end R&D experience from dataset annotations to deployment with an application-specific AI backend. Extensible and customizable as required by individual projects, the framework has been successfully featured in a number of research efforts, including conversational AI, explainable AI, and commonsense grounding of language and vision. This submission outlines the various milestones-to-date and planned future work.
Direct, Mild, and Selective Synthesis of Unprotected Dialdo‐Glycosides (2006)

Abstract A direct and highly convenient organocatalytic method for the preparation of 1,5‐dialdo‐pyranosides and 1,4‐dialdo‐furanosides is presented. The method relies on the chemoselective properties of TEMPO in combination with trichloroisocyanuric acid under very mild, basic conditions. Unprotected glycosides are prepared in a single step in high yields and are efficiently purified with the use of solid‐phase imine capture. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Novel trends in affinity biosensors: current challenges and perspectives (2014)

Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ?aptamers? and ?phages? which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives.
Monocyte Chemoattractant Protein-1 Synthesis by Murine Lung Fibroblasts Modulates CD4+ T Cell Activation (1998)

This study addressed the role of endogenous monocyte chemoattractant protein-1 (MCP-1) in Ag-stimulated lymphokine synthesis and proliferation by CD4+ T cells during their coculture with purified lung fibroblasts or splenic macrophages. Initial experiments showed that fibroblasts exposed to IL-4, TNF alpha, or IL-4 and TNF-alpha (all at 10 ng/ml) for 24 h released five- to eightfold more MCP-1 than similarly treated splenic macrophages. In 72-h coculture experiments, the synthesis of IL-4 by OVA-activated CD4+ T cells added to lung fibroblasts or splenic macrophages was significantly inhibited when endogenous MCP-1 was neutralized using polyclonal anti-MCP-1 antiserum. In these same cocultures, IFN-gamma levels were significantly enhanced. Similarly, IFN-gamma levels were significantly enhanced in 72-h cocultures of a purified peptide derivative-activated CD4+ Th1 clone and lung fibroblasts or splenic macrophages following immunoneutralization of MCP-1. In separate experiments, the selective inhibition of MCP-1 synthesis by lung fibroblasts and splenic macrophages using an MCP-1 antisense oligonucleotide significantly enhanced the proliferation of CD4+ T cells during a 96-h coculture. Taken together, these data suggest that MCP-1 exerts an immunomodulatory effect on CD4+ T cell-derived IL-4 and IFN-gamma release and CD4+ T cell proliferation during cell-to-cell interactions.
Measurements of gas permeability and diffusivity of tight reservoir rocks: different approaches and their applications (2009)

Abstract Permeability and diffusivity are critical parameters of tight reservoir rocks that determine their viability for commercial development. Current methods for measuring permeability and/or diffusivity may lead to erroneous results when applied to very tight rocks including gas shales, coal, and tight gas sands, as well as rocks considered as seals for nuclear waste repositories and strata for geological sequestration of CO 2 . The use of He as routinely applied to measure porosity, permeability, and diffusivity may result in non‐systematic errors because of the molecular sieving effect of the fine pore structure to larger molecules such as reservoir gases. Utilizing gases with larger adsorption potentials than He, such as N 2 , and including all reservoir gases to measure porosity or permeability of rocks with high surface area is a viable alternative, but requires correcting for adsorption in the analyses. This study expands several approaches to measure permeability and diffusivity with considerations for gas adsorption, which has not been explicitly considered in previous studies. We present new models that explicitly correct for adsorption during pulse‐decay measurements of core under reservoir conditions, as well as on crushed samples used to approximate permeability or diffusivity. We also present a method to determine permeability or diffusivity from on‐site drill‐core desorption test data as carried out to determine gas in place in coals or gas shales. Our new approach utilizes late‐time data from experimental pressure‐decay tests, which we show to be more reliable and theoretically (and practically) accurate than the early‐time approach commonly used to estimate gas‐transport properties.
First Total Synthesis of the Irciniasulfonic Acids (2005)

A flexible and concise first total synthesis of the irciniasulfonic acids is reported.
Identification of the ligand‐binding domain of the surface‐located fibrinogen receptor (clumping factor) of Staphylococcus aureus (1995)

The ability of Staphylococcus aureus to bind to fibrinogen and fibrin is believed to be an important factor in the initiation of foreign-body and wound infections. Recently, we reported the cloning and sequencing of the gene clfA encoding the fibrinogen receptor (clumping factor, ClfA) of S. aureus strain Newman and showed that the gene product was responsible for the clumping of bacteria in soluble fibrinogen and for the adherence of bacteria to solid-phase fibrinogen. This was confirmed here by showing that antibodies raised against purified Region A inhibited both of these properties. Also, immunofluorescent microscopic analysis of wild-type Newman and a clfA::Tn917 mutant of Newman with anti-ClfA Region A sera confirmed that Region A is exposed on the bacterial cell surface. Furthermore, polystyrene beads coated with the Region A protein formed clumps in soluble fibrinogen showing that the ClfA protein alone is sufficient for the clumping phenotype. Western immunoblotting with anti-ClfA Region A antibodies identified the native ClfA receptor as a 185 kDa protein that was released from the cell wall of S. aureus by lysostaphin treatment. A single extensive ligand-binding site was located within Region A of the ClfA protein. Truncated ClfA proteins were expressed in Escherichia coli. Lysates of E. coli and proteins that had been purified by affinity chromatography were tested for (i) their ability to bind fibrinogen in Western ligand blotting experiments, (ii) for their ability to inhibit clumping of bacteria in fibrinogen solution and adherence of bacteria to solid-phase fibrinogen, and (iii) for their ability to neutralize the blocking activity of anti-ClfA Region A antibody. These tests allowed the ligand-binding domain to be localized to a 218-residue segment (residues 332-550) within Region A.
Bcl-2 and FKBP12 bind to IP3 and ryanodine receptors at overlapping sites: the complexity of protein–protein interactions for channel regulation (2015)

The 12- and 12.6-kDa FK506-binding proteins, FKBP12 (12-kDa FK506-binding protein) and FKBP12.6 (12.6-kDa FK506-binding protein), have been implicated in the binding to and the regulation of ryanodine receptors (RyRs) and inositol 1,4,5-trisphosphate receptors (IP3Rs), both tetrameric intracellular Ca2+-release channels. Whereas the amino acid sequences responsible for FKBP12 binding to RyRs are conserved in IP3Rs, FKBP12 binding to IP3Rs has been questioned and could not be observed in various experimental models. Nevertheless, conservation of these residues in the different IP3R isoforms and during evolution suggested that they could harbour an important regulatory site critical for IP3R-channel function. Recently, it has become clear that in IP3Rs, this site was targeted by B-cell lymphoma 2 (Bcl-2) via its Bcl-2 homology (BH)4 domain, thereby dampening IP3R-mediated Ca2+ flux and preventing pro-apoptotic Ca2+ signalling. Furthermore, vice versa, the presence of the corresponding site in RyRs implied that Bcl-2 proteins could associate with and regulate RyR channels. Recently, the existence of endogenous RyR-Bcl-2 complexes has been identified in primary hippocampal neurons. Like for IP3Rs, binding of Bcl-2 to RyRs also involved its BH4 domain and suppressed RyR-mediated Ca2+ release. We therefore propose that the originally identified FKBP12-binding site in IP3Rs is a region critical for controlling IP3R-mediated Ca2+ flux by recruiting Bcl-2 rather than FKBP12. Although we hypothesize that anti-apoptotic Bcl-2 proteins, but not FKBP12, are the main physiological inhibitors of IP3Rs, we cannot exclude that Bcl-2 could help engaging FKBP12 (or other FKBP isoforms) to the IP3R, potentially via calcineurin.
Wet autoclave pretreatment for antigen retrieval in diagnostic immunohistochemistry (1994)

Interest has recently been shown in adapting the microwave oven heating technique for antigen retrieval to routine diagnostic immunocytochemical practice. Although it has proved effective as a specialist method for individual antigen localization in many laboratories, it has certain drawbacks which have hampered its wider routine application. These include the need to monitor the sections during the microwave treatment to prevent damage or drying, the limited number of sections that can be accommodated in the microwave oven, and the inevitable alteration in nuclear morphology induced by the microwaves. In order to obviate these difficulties, we have modified the wet autoclave method of Shin et al. (Lab Invest 1991; 64: 693-702) as a routine technique for retrieval of a variety of cell surface, cytoplasmic, and nuclear antigens in formalin-fixed and paraffin-embedded tissue. The technique produces even enhancement of several refractory antigens in anatomically different sites and has the potential to handle reliably up to 200 sections at a time without significant damage to the section or to nuclear morphology.
Three Acylated Saponins and a Related Compound from Pithecellobium dulce (1997)

Four new oleanane-type triterpene glycosides, pithedulosides H-K (1-4), were isolated from the seeds of Pithecellobium dulce. Their structures were established by extensive NMR experiments and chemical methods. Compounds 1-3 comprised acacic acid as the aglycon and either monoterpene carboxylic acid and its xyloside or monoterpene carboxylic acid as the acyl moiety at C-21. The oligosaccharide moieties linked to C-3 and C-28 were determined as alpha-L-arabinopyranosyl-(1-->2)-alpha-L-arabinopyranosyl-(1 -->6)- [beta-D-glucopyranosyl-(1-->2)]-beta-D-glucopyranosyl and alpha-L-arabinofuranosyl-(1-->4)-[beta-D-glucopyranosyl-(1-->3)]-alpha- rhamnopyranosyl-(1-->2)-beta-D-glucopyranosyl ester, respectively. Compound 4 was established as an echinocystic acid 3-O-glycoside having the same sugar sequences as 1-3. Also obtained in this investigation was the known compound 5, which was identified as echinocystic acid 3-O-beta-D-xylopyranosyl- (1-->2)-alpha-L-arabinopyranosyl-(1-->6)-[beta-D-glucopyranosyl-(1 -->2)]- beta-D-glucopyranoside.
Genetic Alterations of Microsatellites on Chromosome 18 in Human Breast Carcinoma (1995)

Allelic alterations of chromosome 18 microsatellites were determined using normal and tumor DNA pairs from 29 patients with infiltrating ductal carcinoma of the breast. Loss of heterozygosity was detected in 62% (18 of 29 patients) of the tumors at one or more of these microsatellites. Eight of the 18 patients exhibited deletions in the region at 18q21.1. This chromosomal band is known to contain a tumor suppressor gene (DCC) whose expression is frequently inactivated in several types of cancer. Ten other patients had deletions in regions not included in the DCC locus. Five of these patients revealed a common deletion at the D18S50 locus (18q23), and the other five patients had deletions in various other regions of the chromosome. No apparent correlation between loss of heterozygosity of chromosome 18 microsatellites and the clinical stage was found in this series. The results indicate that, in addition to the DCC locus, the 18q23 region is likely to contain a second tumor suppressor gene relevant to breast carcinogenesis. Four percent of all microsatellites tested in these patients showed allelic differences in the sizes of repeat units between tumor and the corresponding constitutional DNAs. The pattern of allele instability observed in breast carcinoma differed from that originally reported in a hereditary type of colorectal carcinoma. The observation suggests that this phenomenon is not a mechanism specific to neoplastic processes in breast carcinoma.
Regulation of Gene Expression by Cyclic GMP (2003)

Cyclic GMP, produced in response to nitric oxide and natriuretic peptides, is a key regulator of vascular smooth muscle cell contractility, growth, and differentiation, and is implicated in opposing the pathophysiology of hypertension, cardiac hypertrophy, atherosclerosis, and vascular injury/restenosis. cGMP regulates gene expression both positively and negatively at transcriptional as well as at posttranscriptional levels. cGMP-regulated transcription factors include the cAMP-response element binding protein CREB, the serum response factor SRF, and the nuclear factor of activated T cells NF/AT. cGMP can regulate CREB directly, through phosphorylation by cGMP-dependent protein kinase, or indirectly, through activation of mitogen-activated protein kinase pathways; regulation of SRF and NF/AT by cGMP is indirect, through modulation of RhoA and calcineurin signaling, respectively. Downregulation of the RNA-binding protein HuR by cGMP leads to destabilization of guanylate cyclase mRNA, but this posttranscriptional mechanism may affect many more cGMP-regulated genes. In this review, we discuss the role of cGMP-regulated gene expression in (patho)physiological processes most relevant to the cardiovascular system, such as regulation of vascular tone, cardiac hypertrophy, phenotypic modulation of vascular smooth muscle cells, and regulation of cell proliferation and apoptosis.
Febrile Infants at Low Risk for Serious Bacterial Infection—An Appraisal of the Rochester Criteria and Implications for Management (1994)

Objective. Prospective studies were conducted to test the hypothesis that infants unlikely to have serious bacterial infections (SBI) can be accurately identified by low risk criteria. Methods. Febrile infants (rectal T ≥ 38°C) ≤60 days of age were considered at low risk for SBI if they met the following criteria: 1) appear well; 2) were previously healthy; 3) have no focal infection; 4) have WBC count 5.0-15.0 x 109 cells/L (5000-15 000/mm3), band form count≤ 1.5 x 109 cells/L (≤1500/mm3), ≤10 WBC per high power field on microscopic examination of spun urine sediment, and ≤5 WBC per high power field on microscopic examination of a stool smear (if diarrhea). The recommended evaluation included the culture of specimens of blood, cerebrospinal fluid, and urine for bacteria. Outcomes were determined. The negative predictive values of the low risk criteria for SBI and bacteremia were calculated. Results. Of 1057 eligible infants, 931 were well appearing, and, of these, 437 met the remaining low risk criteria. Five low risk infants had SBI including two infants with bacteremia. The negative predictive value of the low risk criteria was 98.9% (95% confidence interval, 97.2% to 99.6%) for SBI, and 99.5% (95% confidence interval, 98.2% to 99.9%) for bacteremia. Conclusions. These data confirm the ability of the low risk criteria to identify infants unlikely to have SBI. Infants who meet the low risk criteria can be carefully observed without administering antimicrobial agents.
Validation of a semiquantitative food frequency questionnaire to assess energy and macronutrient intakes of Cuban Americans (2005)

Compared with 3-day food records, the Willett FFQ is a reasonable instrument to assess the intakes of most macronutrients and alcohol among Cuban Americans. Further studies should be conducted to validate the usefulness of the Willett FFQ in Cuban Americans for other nutrients.
Cloning, characterization, and expression of a G-protein-coupled receptor from Lymnaea stagnalis and identification of a leucokinin-like peptide, PSFHSWSamide, as its endogenous ligand. (1997)

Neuropeptides are known to be important signaling molecules in several neural systems of the pond snail Lymnaea stagnalis. Although the functions of these peptides have been studied in many neurons, the nature of the postsynaptic signal transduction is mainly unknown. The cloning and characterization of neuropeptide receptors in Lymnaea thus would be very valuable in further elucidating peptidergic pathways. Indirect evidence suggests that these neuropeptides operate via G-protein-coupled mechanisms indicating the presence of G-protein-coupled receptors as the initial postsynaptic targets. Here we describe the cloning of a neuropeptide receptor from Lymnaea and the isolation of an endogenous ligand. This peptide, PSFHSWSamide, belongs to the leucokinin family of peptides, and, thus, this Lymnaea receptor is the first example of a leucokinin-like neuropeptide receptor, representing a new subfamily of G-protein-coupled neuropeptide receptors.