gebhart/patrepeval huggingface dataset:
Trans catalysis in Tn 5 transposition (2000)

Synaptic complexes in prokaryotic transposons occur when transposase monomers bind to each of two specific end-binding sequences and then associate to bring the proteins and the two ends of the transposon together. It is within this complex of proteins and DNA that identical catalytic reactions are carried out by transposase on each of the ends of the transposon. In this study, we perform in vitro transposition reactions by combining the methylated inside end (IE(ME)) biased hyperactive Tn5 transposase, Tnp sC7 version 2.0, and the outside end (OE) biased hyperactive Tn5 transposase, Tnp EK/LP, with plasmid DNA containing a transposon defined by one IE(ME) and one OE. These two proteins cooperate to facilitate double end cleavage of the transposon from the plasmid and conversion into transposition products via strand transfer. When one of the hyperactive Tnps is replaced with a catalytically inactive version containing the mutation EA326 (DDE mutant), the predominant reaction product is a linearized plasmid resulting from single end cleavage. Restriction analysis of these linear products reveals that cleavage is occurring on the end distal to that which is bound by the transposase with an intact active site or in trans. Similar in vitro experiments performed with precut transposons and a supercoiled target plasmid demonstrated that the strand transfer reaction is also facilitated by a trans active DDE motif.
Focus on Primary Care Postmenopausal Osteoporosis: An Update (2000)

Osteoporosis is a common and costly condition that can cause disability or death. Evaluation of patients for possible secondary causes is important. Bone density testing permits identification of individuals who are at high risk of fracture and is recommended for all women age 65 and older and for younger women who have clinical risk factors. Measurement of bone markers, particularly collagen cross links, may add some information. Adequate calcium, vitamin D, and weight-bearing exercise are important for everyone and are fundamental to any program for prevention of bone loss or treatment of osteoporosis. Effective pharmacologic agents are available for prevention of bone loss in recently menopausal women and for treatment of established osteoporosis. Pharmacologic intervention is indicated for women who have osteoporosis, defined either as a fracture or BMD T-score of -2.5 and below.
Avian adenovirus isolated from pigeons affected with inclusion body hepatitis. (1990)

Avian adenoviruses were isolated from two pigeons affected with inclusion body hepatitis (IBH) by using chicken embryo liver cell cultures. One of the isolates, designated strain S-PL1, replicated in the cell nuclei forming intranuclear inclusion bodies, showed adenovirus-like morphology by electron microscopy, and cross-reacted serologically with strain SR-48 known as serotype 2 of fowl adenovirus. The strain S-PL1 killed day-old chicks by subcutaneous inoculation, and its 50% chicken lethal dose was 10(3.8) plaque forming units per bird. Severe lesions characterized with IBH and pancreatitis, were produced in chicks inoculated with the virus. Intranuclear inclusion bodies were also recognized in the liver, pancreas, kidney, proventriculus, small intestine, and caecum. By indirect immunofluorescence test, intranuclear viral antigens were detected in the liver, pancreas and other tissues.
Development of human factors guidelines for Advanced Traveler Information Systems (ATIS) and commercial vehicle operations (CVO): Comparable systems analysis (1996)

A comparable systems analysis was performed on seven systems selected for their relevance to the features and functions of the Advanced Traveler Information Systems (ATIS) and Commercial Vehicle Operations (CVO) components of the Intelligent Transportation Systems (ITS) program. The seven systems were selected for their relevance to ATIS/CVO concepts, user time-sharing characteristics, technology level, dynamics of information flow, level of implementation, and accessibility. Five of the systems were highway transportation or CVO in-vehicle information systems, two were comparable systems featuring advanced navigation and decision aiding in Army aviation. Analyses of the seven systems resulted in human factors lessons learned. The lessons learned were compiled into preliminary human factors design guidelines for ATIS/CVO.
Effects of modulation strength in guided-mode resonant subwavelength gratings at normal incidence (2000)

A comparative study of the reflection spectral resonances in weakly and strongly modulated subwavelength gratings is presented. The effects of strong modulation in resonant subwavelength gratings have been largely ignored in the literature. We show that the spectral stability of resonances as a function of angle of incidence around normal can be greatly enhanced with strongly modulated gratings while the desirable narrow line-width associated with weakly modulated gratings is still maintained.
Evaluating glymphatic pathway function utilizing clinically relevant intrathecal infusion of CSF tracer (2013)

Lumbar intrathecal contrast delivery is a clinically useful approach that could be used in conjunction with dynamic contrast enhanced MRI nuclear imaging to assess glymphatic pathway function in humans.
Encapsulation of basic fibroblast growth factor in thermogelling copolymers preserves its bioactivity (2010)

In this paper, we present a new approach of using thermogelling copolymers for the encapsulation of basic fibroblast growth factor and the preservation of its bioactivity without the need for stabilizing agents. Thermogelling poly(ether urethane)s consisting of poly(ethylene/butylene) (PEB), poly(ethylene glycol) (PEG), and poly(propylene glycol) (PPG) segments were investigated as potential encapsulation and delivery agents for basic fibroblast growth factors (bFGFs). Thermogels form when micelles aggregate as the temperature increases. This leads to the formation of gels without the need for crosslinking. The mobility of the protein encapsulated within the gel matrix was found to be closely related with the rheological property of the copolymer gel. Lysozyme and BSA release studies were conducted to understand the effects of gel concentration, protein size and protein concentration on the kinetics of protein release. Based on the calculated diffusion coefficients, the mobility of the protein within the gel matrix was determined. Finally, basic fibroblast growth factor (bFGF) was encapsulated in the gels. The immunoreactivities and bioactivities of the cytokines encapsulated in the gel were well preserved for up to 5 days, as determined by enzyme-linked immunosorbent assay (ELISA) measurements as well as cell culture assays. This finding suggests that thermogelling polymers could potentially be used as an injectable gel depot for the release of bioactive cytokines for tissue repair and other related applications.
Application of a panel of antiganglioside monoclonal antibodies to cytologic specimens. (1992)

The cytologic evaluation of poorly differentiated tumors frequently poses a diagnostic dilemma as to the tissue of origin. To assess the diagnostic utility of monoclonal antibodies (MAbs) in these situations, we applied a panel of three highly purified MAbs specific for tumor-associated ganglioside epitopes to a diverse series of cytologic specimens. The panel was composed of DMAb-3, reactive with the epitope GalNAc beta 1-4 (NeuAc alpha 2-3)Gal- of GM2; DMAb-7, reactive with the epitope (NeuAc alpha 2-8NeuAc alpha 2-3)Gal beta 1-4(Glc or GlcNAc)- of GD3 and 3'8'-LD1; and DMAb-20, reactive with the epitope GalNAc beta 1-4(NeuAc alpha 2-8NeuAc alpha 2-3)Gal- of GD2. The cytologic material consisted of air-dried Cytospin preparations prepared predominantly from fine needle aspirates and stained with the ABC immunohistochemical method. Positive reactivity was recognized when greater than 5% of tumor cells stained with the antibody; lesser reactivity was called negative. DMAb-3 stained 9/14 (64%) glial tumors, 4/13 (31%) nonglial central nervous system tumors, 1/21 (5%) melanomas, 7/38 (18%) non-small cell carcinomas (NSCC), 1/15 (7%) small cell carcinomas (SCC), 0/9 (0%) lymphomas/leukemias, 2/10 (20%) sarcomas, 1/7 (14%) miscellaneous tumors and 2/2 (100%) reactive fluids. DMAb-7 recognized 14/14 (100%) glial tumors, 9/13 (69%) non-glial central nervous system tumors, 19/22 (86%) melanomas, 19/43 (44%) NSCC, 5/15 (33%) SCC, 2/9 (22%) lymphomas/leukemias, 6/10 (60%) sarcomas, 1/7 (14%) miscellaneous tumors and 4/4 (100%) reactive fluids. DMAb-20 stained 6/14 (43%) glial tumors, 2/13 (15%) nonglial central nervous system tumors, 1/21 (5%) melanomas, 4/38 (10%) NSCC, 0/15 (0%) SCC, 0/9 (0%) lymphomas/leukemias, 1/10 (10%) sarcomas, 1/7 (14%) miscellaneous tumors and 1/3 (33%) reactive fluids. The GD3-reactive DMAb-7 recognized a large portion of many tumor types and thus is not diagnostically useful alone. DMAb-3 and DMAb-20 were more selective and showed the strongest reactivity for glial tumors and minimal reactivity for melanomas, small cell carcinomas, and lymphomas or leukemias. DMAb-3 and DMAb-20 may be useful as components of a larger panel of MAbs in distinguishing between poorly differentiated tumors in samples derived from the central nervous system.
The application of a novel thrombin sensitive site in genetic engineering. (1997)

To obtain high efficiency of cleavage of thrombin in fusion protein containing alpha-ANP fused to Ref peptides, the linker sequence designed as VIAGR which was different from GVRGPR formerly used was studied. Plasmid pHL carrying the fusion gene Ref-NT-ANP downstream from PL promoter was derived from expression vector pLY1 by inserting the fragment of NT-ANP into it. The expression of fusion gene was induced at 42 degrees C, and the interested protein Ref-NT-ANP accumulated as inclusion bodies was isolated by gradient centrifuge and then dissolved in 7 mol/L guanidinehydrochloride (Gdn-HCl). After dilution, renaturation and dialyzation, the cleavage of thrombin was examined using samples with 1.1 mol/L Gdn-HC1 and samples free of Gdn-HCl respectively. Digestion result showed that the novel-adopted cleavage sequence was highly sensitive to thrombin when the substrate dissolved in 1.1 mol/L Gdn-HCl. The time needed for 87% cleavage (the ratio of substrate to thrombin was 50 micrograms/u) was less than 24 hours. This sequence described here which was specifically recognized by thrombin might be broadly applied in other fusion systems.
Initial Diagnostic Work-Up of Acute Leukemia: ASCO Clinical Practice Guideline Endorsement of the College of American Pathologists and American Society of Hematology Guideline (2018)

Twenty-seven guideline statements were reviewed. Some discussion points were included to better assess CNS involvement in leukemia and to provide novel insights into molecular diagnosis and potential markers for risk stratification and target therapy. These discussions are categorized into four sections: (1) initial diagnosis focusing on basic diagnostics and determination of risk parameters, (2) molecular markers and minimal residual disease detection, (3) context of referral to another institution with expertise in the management of AL, and (4) reporting and record keeping for better outlining and follow-up discussion. Additional information is available at: www.asco.org/hematologic-malignancies-guidelines .
Recognition of Human Proinsulin Leader Sequence by Class I–Restricted T-Cells in HLA-A*0201 Transgenic Mice and in Human Type 1 Diabetes (2008)

We defined class I-restricted epitopes located within the leader sequence of human preproinsulin through in vivo (transgenic mice) and ex vivo (diabetic patients) assays, illustrating the possible role of preproinsulin-specific CD8(+) T-cells in human type 1 diabetes.
Syringe-vacuum microfluidics: A portable technique to create monodisperse emulsions (2011)

We present a simple method for creating monodisperse emulsions with microfluidic devices. Unlike conventional approaches that require bulky pumps, control computers, and expertise with device physics to operate devices, our method requires only the microfluidic device and a hand-operated syringe. The fluids needed for the emulsion are loaded into the device inlets, while the syringe is used to create a vacuum at the device outlet; this sucks the fluids through the channels, generating the drops. By controlling the hydrodynamic resistances of the channels using hydrodynamic resistors and valves, we are able to control the properties of the drops. This provides a simple and highly portable method for creating monodisperse emulsions.
Human Genes Other than CD4 Facilitate HIV-1 Infection of Murine Cells (1991)

The human CD4 glycoprotein is a specific receptor for the HIV family of retroviruses. When expressed on human cell lines, this molecule binds virus through direct interactions with the gp 120 viral envelope glycoprotein thus allowing virus infection to occur. Subsequent to binding, conformational changes in the viral envelope glycoproteins are thought to facilitate virus entry into the target cell through direct fusion of the virus with the cell membrane. In contrast to the infection observed in human cell lines, infection of murine cell lines even in the presence of the CD4 receptor does not readily occur. We have examined this species tropism of HIV infection. We report that the inability to infect murine cells is not a function of the receptor for HIV or a suppressive function of the murine cellular background. Human CD4 expression, configuration and down-modulation on the murine background are similar if not identical to expression on the human cell background. Utilizing a panel of interspecific cell hybridomas, we have been able to bypass the barrier to infectivity of human CD4-positive murine cells. We demonstrate that there are at least two different restrictions to infectivity on the mouse background which can be complemented by the human genome. One restriction appears to be an extremely early postbinding function likely to be molecules necessary for viral entry into cells, the second restriction is necessary for high levels of virus production. Our mapping studies suggest that fewer than five human chromosomes are necessary for reconstituting infectivity in the murine background. These results have implications for models of HIV-induced pathogenesis and infectivity.
Aluminum Neurotoxicity in Experimental Animals (1993)

Neurotoxic effects of aluminum (Al) were recognized > 100 years ago, but have only recently been studied in detail. By far, the most dramatic effect of Al is that of producing intraneuronal perikaryal neurofilamentous aggregates, which consist of phosphorylated neurofilaments. Several species have been used to demonstrate this effect, rabbit being most common; the effect also is seen in in vitro systems. Besides its role in producing neurofibrillary pathology, Al appears to modify the blood-brain barrier and exert cholinergic and noradrenergic effects. Possible mechanisms of Al neurotoxicity could be related to cell damage via free radical production, impairment of glucose metabolism, and effects on signal transduction.
Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry (2000)

Multiplexed SNP genotyping by OLA with flow cytometric analysis of fluorescent microspheres is an accurate and rapid method for the analysis of SNPs.
Design Guidelines for Automotive Fuel Level Sensors (2002)

&lt;div class="htmlview paragraph"&gt;Most current automotive and light truck fuel level sensors are essentially rotary potentiometers that have been designed to survive the chemically harsh environments found in the fuel tank. This paper will chronicle the design improvements made from the early wire wound versions to today's more robust thick film ink systems. The paper will highlight potential failure modes and discuss techniques to reduce noise and increase wear life. Data will be provided regarding changes in the circuit layout, ink compositions, and contact materials. Special consideration will be given to the adverse effects associated with the reactive sulfur prevalent in today's fuels.&lt;/div&gt;
Design of a Peptide Inhibitor that Blocks the Cell Fusion Mediated by Glycoprotein 41 of Human Immunodeficiency Virus Type 1 (2000)

Fusion between the envelope of HIV and the plasma membrane of target cells is mediated by gp41, the envelope glycoprotein of HIV. Peptides derived from the membrane-proximal helical motif of the extracellular domain of gp41 effectively inhibit the infection of HIV, and their inhibitory activities are known to be correlated with the helical propensity of the peptides. We have designed small peptides that can form a stable alpha helix and thereby inhibit gp120/41-mediated cell fusion. A 19-mer peptide from the membrane-proximal helical motif of gp41 had no secondary structure in solution, and failed to block gp41-mediated cell fusion. When amino acids with low helical propensity were substituted, and helix-capping sequences were introduced at both ends of the peptides, the modified peptides formed a stable helical structure. They also bound to the coiled-coil motif of gp41 presented at the C terminus of thioredoxin and blocked the cell fusion mediated by gp120/41. These results implied that such modification was enough to change a short peptide derived from gp41 into a potent inhibitor against the infection of HIV.
CROWDSOURCING A WORD–EMOTION ASSOCIATION LEXICON (2012)

Even though considerable attention has been given to the polarity of words (positive and negative) and the creation of large polarity lexicons, research in emotion analysis has had to rely on limited and small emotion lexicons. In this paper, we show how the combined strength and wisdom of the crowds can be used to generate a large, high‐quality, word–emotion and word–polarity association lexicon quickly and inexpensively. We enumerate the challenges in emotion annotation in a crowdsourcing scenario and propose solutions to address them. Most notably, in addition to questions about emotions associated with terms, we show how the inclusion of a word choice question can discourage malicious data entry, help to identify instances where the annotator may not be familiar with the target term (allowing us to reject such annotations), and help to obtain annotations at sense level (rather than at word level). We conducted experiments on how to formulate the emotion‐annotation questions, and show that asking if a term is associated with an emotion leads to markedly higher interannotator agreement than that obtained by asking if a term evokes an emotion.
Effects of long-term treatment with the luteinizing hormone-releasing hormone (LHRH) agonist Decapeptyl and the LHRH antagonist Cetrorelix on the levels of pituitary LHRH receptors and their mRNA expression in rats (2002)

The effects of depot formulations of the luteinizing hormone-releasing hormone (LHRH) agonist Decapeptyl (25 microg/day) for 30 days or LHRH antagonist Cetrorelix pamoate (100 microg/day) for 30 days and daily injections of 100 microg of Decapeptyl for 10 days on the expression of mRNA for pituitary LHRH receptor (LHRH-R) and the levels of LHRH-R protein were evaluated in rats. Serum sex steroid concentrations and the weights of the reproductive organs were greatly reduced in all groups treated with analogs, demonstrating an efficient blockade of the pituitary-gonadal axis. Decapeptyl microcapsules elevated serum LH in female rats, but decreased it in male rats. LHRH-R mRNA expression in female pituitaries was reduced to 41% and 56-65% on days 10 and 30, respectively, whereas LHRH-R protein was 64% of control on day 10 and returned to pretreatment levels on day 30. Decapeptyl microcapsules reduced LHRH-R mRNA expression in male pituitaries to 58% on day 30 but not LHRH-R protein. Daily injections of Decapeptyl caused a desensitization of LH responses in female rats, while raising LHRH-R mRNA expression in female rats by 23% and LHRH-R protein levels by 119%. Cetrorelix pamoate reduced serum LH in female rats and diminished LHRH-R mRNA to 30% and 26% and LHRH-R protein to 57% and 48% on days 10 and 30, respectively. Elevated LHRH-R protein levels of ovariectomized rats were reduced after 10-day treatment with Cetrorelix or 100 microg/day Decapeptyl. Thus, changes in the mRNA expression after treatment with Cetrorelix, but not always Decapeptyl, paralleled those of LHRH-R protein. The inhibitory effect of Cetrorelix on serum LH, pituitary LHRH-R mRNA, and LHRH-R protein was greater than that of Decapeptyl.
Glucose Regulates Insulin Gene Transcription by Hyperacetylation of Histone H4 (2003)

Induction of insulin gene expression in response to high blood glucose levels is essential for maintaining glucose homeostasis. Although several transcription factors including Beta-2, Ribe3b1, and Pdx-1 have been shown to play a role in glucose stimulation of insulin gene expression, the exact molecular mechanism(s) by which this regulation occurs is unknown. Previous data demonstrate that the transcription factors Beta-2/NeuroD1 and Pdx-1, which are involved in glucose-stimulated insulin gene expression, interact with the histone acetylase p300, suggesting a role for histone acetylation in glucose regulation of the insulin gene expression. We report that exposure of mouse insulinoma 6 cells to high concentrations of glucose results in hyperacetylation of histone H4 at the insulin gene promoter, which correlates with the increased level of insulin gene transcription. In addition, we demonstrate that hyperacetylation of histone H4 in response to high concentrations of glucose also occurs at the glucose transporter-2 gene promoter. Using histone deacetylase inhibitors, we show that increases in histone H4 acetylation cause stimulation of insulin gene transcription even in the absence of high concentrations of glucose. Furthermore, we show that fibroblasts, which lack insulin gene expression, also lack histone acetylation at the insulin gene promoter. In summary, our data support the idea that high concentrations of glucose stimulate insulin gene expression by causing hyperacetylation of histone H4 at the insulin gene promoter.
Construction and characterization of cDNA library for IRM-2 mice (2010)

Objective To screen and isolate the radioresistance related genes of IRM-2 mice.Methods cDNA library of IRM-2 mice was constructed by SMART technique.Total RNA was isolated from spleens of IRM-2 male mice.The first-strand cDNA was synthesized by using PowerScript reverse transeriptase,and double-strand cDNA was synthesized and amplified by long PCR.The PCR products were purified,digested with restriction enzyme Sfi I.The ds-cDNA fragment lessthan 500 bp was fractionated and ligated to the Sfi I-digested pDNR-LIB vector.The ligation mixture was transformed into E.coil DH5α by electroporution transformation to generate the unamplified cDNA library.The quality of cDNA library was identified by PCR technique.130 clones from cDNA library were sequenced and compared with GenBank database.Results The cDNA library contained 2.25 x 106 independent clones with an average insert size of 1.2 kb.The ratio of recombination and full-length was 95% and 55%,respectively.21 pieces of EST sequences from cDNA library were not the same as the known mice genes and registered into GenBank EST database,with registered number DW474856-DW474876.Conclusions cDNA library of IRM-2 mice has been constructed successfully.21 pieces of EST implies that radioresistance correlative genes may be in IRM-2 mice,which will lay a foundation for isolating and identifying radioresistance related genes in further study.

Key words: 
IRM-2 mice; cDNA library; SMART techique