gebhart/patrepeval huggingface dataset:
Cloning and Expression of a cDNA Coding for a Rat Liver Plasma Membrane Ecto-ATPase (1989)

The amino acid sequence of the ecto-ATPase from rat liver was deduced from analysis of cDNA clones and a genomic clone. Immunoblots with antibodies raised against a peptide sequence deduced from the cDNA sequence indicated that the determined amino acid sequence is that of the ecto-ATPase. The deduced sequence predicts a 519-amino acid protein with a calculated molecular mass of 57,388 daltons. There are 16 potential asparagine-linked glycosylation sites in the protein. Hydropathy analysis of the deduced amino acid sequence indicates that the protein has two hydrophobic stretches. One is located at the N-terminal and the other is near the C-terminal end. A full-length clone encoding the ecto-ATPase was expressed transiently in mouse L cells and human HeLa cells. The cell lysate from the transfected cells contained immunoreactive ecto-ATPase and Ca2+-stimulated ATPase activities. The expressed protein is glycosylated and has an apparent molecular weight (100,000) similar to that of the rat liver plasma membrane ecto-ATPase.
Nonsense-mediated mRNA decay in mammals (2005)

Nonsense-mediated mRNA decay (NMD) in mammalian cells generally degrades mRNAs that terminate translation more than 50-55 nucleotides upstream of a splicing-generated exon-exon junction (reviewed in [Maquat, 2004a][1]; [Nagy and Maquat, 1998][2]). Notably, dependence on exon-exon junctions
Use of laser reflectometry for end-point detection during the etching of magnetic thin films (1997)

Laser reflectometry at a wavelength of 679 nm has been employed for monitoring and detection of the end point during the etching of thin films of magnetic materials. Oscillations in the detected reflected signal due to the periodicity of multilayer structures for Pt/Co and Cu/Co with periods as small as 3 nm have been recorded. Known details of the structures have been used to model the normal incidence reflectance to compare with the observed results. This technique allows the etching to be stopped after removal of the thin magnetic multilayer film to an accuracy of better than 5 nm in the cases cited.
Release of soluble peptidoglycan from growing conococci: demonstration of anhydro-muramyl-containing fragments (1980)

Previous analysis of soluble peptidoglycan (PG) fragments released by exponentially growing gonococci implicated the combined action of both hexosaminidase and amidase activities in PG turnover. Current studies further characterized PG fragments which were labeled in the glycan with D-glucosamine and in the peptide moiety with meso-diaminopimelic acid of L- and D-alanine. Labeled PG fragments were isolated by gel filtration and characterized on the bases of (i) KD values, (ii) free amino group analysis using fluorodinitrobenzene, (iii) borohydride reduction, (iv) alkali-catalyzed beta-elimination, (v) paper chromatography in various solvents, (vi) electrophoretic mobility at various pH values, (vii) digestibility by Charonia lampas glycosidases, and (viii) content of labeled D- and L-alanine. A set of well-characterized PG fragments was used as standards. The monomer fraction (the major extracellular product) was found to contain two components. Most (about 80%) appeared to be N-acetylglucosaminyl-beta-1 leads to 4-1,6-anhydro-N-acetylmuramyl-L-ala-D-glu-meso-diaminopimelic acid; the remainder was the corresponding disaccharide tetrapeptide containing a C-terminal D-alanine. An unusual feature of these products was the presence of the anhydro-muramyl (non-reducing) ends, reflecting the activity of a gonococcal transglycosylase, and the near absence of products containing detectable reducing ends. Otherwise, the structures of the monomer fragments were typical of those expected for a gram-negative bacterium (chemotype I). The corresponding peptide-cross-linked dimer and the free disaccharide also contained nonreducing ends, exclusively. Free peptides (products of amidase activity) consisted of both tripeptide and tetrapeptide. In summary, all gonococci examined appear to possess an unusual transglycosylase activity which contributes to the release of soluble PG fragments containing nonreducing, anhydro-muramyl ends. The release of these fragments in vivo might be a unique aspect of gonococci-host interactions.
Post‐irradiation approaches to treatment of radiation injuries in the context of radiological terrorism and radiation accidents: a review (2004)

A wide range of pharmacological approaches are being developed in the laboratory that could greatly expand the ability to treat acute and chronic radiation injuries. However, there are currently a variety of practical and legal barriers that would prevent the actual clinical use of most of the approaches. There are also the potential weaknesses in most of the current programmes for dealing with the consequences of radiation accidents or nuclear terrorism, including the absence of widespread radiation biodosimetry capabilities and the resulting inability to triage. If a major radiation accident or terrorist event occurs, the lack of biodosimetry and treatment capabilities will be compounded by widespread public fear of 'radiation'.
Tumor Formation and β-Glucuronidase Expression in Phaseolus vulgaris Inoculated with Agrobacterium tumefaciens (1994)

Ten common bean ( Phaseolus vulgaris L.) lines—including cultivars, breeding lines, and one wild line—were evaluated for susceptibility to Agrobacterium tumefaciens strain C58 by stab-inoculating intact shoot tips of germinating seeds. Significant differences for tumor frequency and size were found on the resulting 3-week-old seedlings. UW 325, a wild bean, had the highest rate of tumorigenesis; `Olathe', a dry bean cultivar, had the lowest. Uninoculated excised shoot tips cultured in media with BA or BA plus NAA exhibited differences in phytohormone sensitivity, as evidenced by callusing and root initiation. The cultivar Montcalm seemed to be highly sensitive, while `Olathe' was relatively insensitive. Fluorometric GUS assays of shoot tips from germinating seeds inoculated with the disarmed GUS-containing A. tumefaciens strain C58C1(pGV3850/pKIWI105) showed that UW 325 had the highest level of GUS activity. `Montcalm' had a high rate of tumorigenesis but a low level of GUS activity; this anomaly was attributed to its high phytohormone sensitivity. The use of the virulence-inducing compound acetosyringone in the inoculum culture medium did not alter genotypic differences (ranks) in susceptibility. Histochemical GUS assays of inoculated UW 325 shoot tips showed that 60% of the apexes exhibited one or more transformation events. Chemical names used: β-glucuronidase (GUS); α-naphthaleneacetic acid (NAA); N -(phenylmethyl)-1 H -purin-6-amine (BA).
The significance of delusions in depressive disorders (2001)

When reviewing clinical research on delusional depression published since 1999 the following results have emerged: (1) Mood-congruent delusions are indicators of severity of depressive episodes. (2) Among the new generation antidepressants fluvoxamine has a hgh response rate (79%) in patients with mood-congruent delusional major depression. (3) Among the new generation (atypical) antipsychotics neither risperidone nor quetiapine has been found effective. (4) However, quetiapine has been found effective in schizoaffective disorder. This is in agreement with research on cognitive functioning which has placed schizoaffective disorders closer to schizophrenia than to mood disorders.
Looks Good To Me: Visualizations As Sanity Checks (2018)

Famous examples such as Anscombe's Quartet highlight that one of the core benefits of visualizations is allowing people to discover visual patterns that might otherwise be hidden by summary statistics. This visual inspection is particularly important in exploratory data analysis, where analysts can use visualizations such as histograms and dot plots to identify data quality issues. Yet, these visualizations are driven by parameters such as histogram bin size or mark opacity that have a great deal of impact on the final visual appearance of the chart, but are rarely optimized to make important features visible. In this paper, we show that data flaws have varying impact on the visual features of visualizations, and that the adversarial or merely uncritical setting of design parameters of visualizations can obscure the visual signatures of these flaws. Drawing on the framework of Algebraic Visualization Design, we present the results of a crowdsourced study showing that common visualization types can appear to reasonably summarize distributional data while hiding large and important flaws such as missing data and extraneous modes. We make use of these results to propose additional best practices for visualizations of distributions for data quality tasks.
The Structural Complexity of Lithium-Rich Li1+x(Mn0.5Ni0.5)1-xO2 and Li1+x(Mn0.33Ni0.33Co0.33)1-xO2Electrodes for Lithium Batteries (2006)

Abstract not Available.
Soft-Tissue Penetration of Ceftobiprole in Healthy Volunteers Determined by In Vivo Microdialysis (2009)

Ceftobiprole is a promising new broad-spectrum cephalosporin with activity against several multidrug-resistant gram-positive and gram-negative species, including methicillin-resistant Staphylococcus aureus. In order to make efficacy predications against these resistant bacteria in soft-tissue infections, i.e., skin and skin structure infections, ceftobiprole's ability to reach the site of action should be explored. Therefore, a microdialysis study was conducted in 12 healthy volunteers to determine the penetration of ceftobiprole into skeletal muscle and subcutaneous (s.c.) adipose tissue after a single intravenous dose of 500 mg. Plasma and tissue interstitial space fluid (ISF) drug concentrations were measured for 24 h from the start of the 2-h intravenous infusion. Pharmacokinetic parameters were determined using noncompartmental analysis. The penetration of ceftobiprole into the ISF of tissues was assessed by comparing the ratios between tissue and plasma of the free drug area under the concentration-time curve (fAUC). It was found that ceftobiprole distributes into the muscle (fAUC(muscle)/fAUC(plasma) of 0.69 +/- 0.13) and s.c. adipose tissue (fAUC(s.c.adipose)/fAUC(plasma) of 0.49 +/- 0.28). The concentrations in both skeletal muscle and s.c. adipose tissue met the efficacy breakpoint (percentage of the time that free drug concentrations remained above the MIC) for at least 40% of the 8-h dosing interval for organisms with a MIC of 2 mg/liter. Therefore, ceftobiprole qualifies as a potential agent with drug penetration capabilities to treat complicated skin and skin structure infections due to both gram-negative and gram-positive pathogens with MICs equal to or below 2 mg/liter.
The eight-item treatment-outcome post-traumatic stress disorder scale (1997)

This preliminary report describes a new brief interview based assessment of post-traumatic stress disorder using an 8-item treatment-outcome post-traumatic stress disorder scale (TOP-8). The TOP-8 was developed from a larger post-traumatic stress disorder evaluation scale based on items which occurred frequently in the population and which responded substantially to treatment across time. The 8 resultant items were drawn from all three symptom clusters for post-traumatic stress disorder, and showed an improved ability to detect drug versus placebo differences in comparison with the original scale. The eight-item treatment-outcome post-traumatic stress disorder scale also correlated significantly with a self-rated measure of post-traumatic stress disorder and distinguished at a highly significant level between responders and non-responders on an independently judged Clinical Global Impressions measure. The results of this study are discussed and future directions suggested.
Transdermal Nicotine for Mildly to Moderately Active Ulcerative Colitis (1997)

Transdermal nicotine administered at the highest tolerated dosage (< or = 22 mg/d) for 4 weeks is efficacious for controlling clinical manifestations of mildly to moderately active ulcerative colitis.
THE EFFECTS OF CYCLOSPORINE AND CYCLOSPORINE METABOLITES IN EXPERIMENTAL SMALL INTESTINAL TRANSPLANTATION (1990)

Cyclosporine metabolites (CM) were compared with cyclosporine for their in vitro and in vivo immunosuppressive, nephrotoxic, and hepatotoxic effects using (A) in vitro mixed lymphocyte induction of monocyte/macrophage procoagulant activity (PCA), an accurate marker of allograft rejection; (B) in vitro toxic effects on renal cells in culture; and (C) a unidirectional rejection model of rat small intestinal transplantation (SIT). CM were composed of OL1, OL17, OL18, and two additional peaks C and H, (peak C: mass = 1235, 15.3% of total CM, peak H: mass = 1205, 6.3% of total CM). In vitro, CM fully suppressed the one-way mixed lymphocyte culture-induced PCA from 52.5 +/- 8.2 mU/10(6) PBM to the basal level 22.3 +/- 6.6 mU/10(6) PBM (P less than 0.01), which was comparable to CsA (21.3 +/- 5.5 mU/10(6) PBM). Lewis rats that had received Lewis-Brown Norway F1 hybrid intestinal allografts when treated with CM, demonstrated near-normal histology with minimal signs of rejection as compared with the fulminant clinical and histological rejection observed in the control (untreated and Cremaphor/NaCl treated) animals. PCA was markedly elevated in the control animals, 278 +/- 172 (untreated) and 160 +/- 98 mU/10(6) PBM (Cremaphor/normal saline treated), whereas CsA-treated allogeneic transplants expressed only basal levels of PCA (14.0 +/- 4 mU/10(6) PBM) (P less than 0.01), associated with normal histology. CM-treated animals expressed PCA levels of 27.0 +/- 10 mU/10(6) PBM, which was significantly different from both control and CsA-treated animals (P less than 0.01). In contrast to CsA-treated animals, CM-treated allogeneic transplants demonstrated no apparent renal or hepatic toxicity, as measured by blood urea nitrogen (25.3 +/- 9.5 vs. 10.0 +/- 5.3 mg/dl), alkaline phosphatase (160.7 +/- 29.3 vs. 100.3 +/- 19.5 U/L), and aspartate transaminase (96.7 +/- 23.7 vs. 61.7 +/- 11.7 U/L) (P less than 0.01). Similarly, in contrast to CsA, CM had minimal or no toxicity in renal epithelial and mesangial cells in culture, as measured by minimal or no inhibition of DNA, RNA, and protein synthesis. These results suggest that CM have potent immunosuppressive properties with no apparent nephrotoxicity and hepatotoxicity in vitro and in vivo.
A Web-based design center for vector-based siRNA and siRNA cassette (2004)

The Web-based design tools are available at GenScript Website (siRNA design center). http://www.genscript.com or http://www.genscript.com/rnai.html#design or http://www.genscript.com/sirna_ca.html#design
Effects of Natural Organic Matter and Ionic Species on Membrane Surface Charge (2002)

The surface charges of clean and natural organic matter (NOM)-adsorbed membrane surfaces of two different types of membranes (a UF and a NF membrane composed of the same material but having different pore sizes) were investigated. Concentrated NOM and its fractionated constituents were used as adsorbate and interacting macromolecules nearthe membrane surface. The zeta potential and the acidity of membranes were measured using electrophoresis and potentiometric titration methods, respectively, from the perspective of charge characterization, along with demonstration of ionic strength effects. The membrane surface was also characterized with attenuated total refractive Fourier transform infrared spectra to determine intrinsic functional groups and those changes before and after NOM adsorption. As a comparative study for the electrokinetic property of membrane, the zeta potentials for both examined polymeric membranes were determined by the electrophoresis and the streaming potential measurement methods as functions of ionic strength and the pH of measuring solution. Selectivity tests were performed to decide the relative importance of charge valence of cation in terms of the surface charge of membrane. It was demonstrated that divalent cations (Ca2+, Mg2+) increase zeta potentials relatively compared to monovalent cations (Na+, K+) because divalent cations have a greater potential in approaching membrane surfaces (i.e., inside the Stern layer). Thus, divalent cations can provide a greater double layer compaction and, when near the shear plane (available for both the zeta potential measurement methods), exist to a lesser extent than monovalent cations.
Retroviral RNA identified in the cerebrospinal fluids and brains of individuals with schizophrenia (2001)

Schizophrenia is a serious brain disease of uncertain etiology. A role for retroviruses in the etiopathogenesis of some cases of schizophrenia has been postulated on the basis of clinical and epidemiological observations. We found sequences homologous to retroviral pol genes in the cell-free cerebrospinal fluids (CSFs) of 10 of 35 (29%) individuals with recent-onset schizophrenia or schizoaffective disorder. Retroviral sequences also were identified in the CSFs of 1 of 20 individuals with chronic schizophrenia. However, retroviral sequences were not identified in any of the CSFs obtained from 22 individuals with noninflammatory neurological diseases or from 30 individuals without evidence of neurological or psychiatric diseases (chi(2) = 19.25, P < 0.001). The nucleotide sequences identified in the CSFs of the individuals with schizophrenia or schizoaffective disorder were related to those of the human endogenous retroviral (HERV)-W family of endogenous retroviruses and to other retroviruses in the murine leukemia virus genus. Transcription of RNA homologous to members of the HERV-W family of retroviruses also was found to be up-regulated differentially in the frontal cortex regions of brains obtained postmortem from individuals with schizophrenia, as compared with corresponding tissue from individuals without psychiatric diseases. The transcriptional activation of certain retroviral elements within the central nervous system may be associated with the development of schizophrenia in at least some individuals. The further characterization of retroviral elements within the central nervous system of individuals with schizophrenia might lead to improved methods for the diagnosis and management of this disorder.
Stem Cells as a Source of Regenerative Cardiomyocytes (2006)

The realization of regenerative cardiac medicine depends on the availability of cardiomyocytes in sufficient numbers for transplantation of cardiac tissue and the accompanying blood vessels. Embryonic stem (ES) cells, bone marrow (BM) stem cells, and tissue-derived stem cells are all potential cell sources. Although ES cells are highly proliferative and suitable for mass production, an efficient protocol is yet to be established to ensure selective cardiomyocyte induction using these cells. Recent advances in developmental biology have clarified the involvement of critical factors in cardiomyocyte differentiation, including bone morphogenic protein and Wnt signaling proteins, and such factors have the potential to improve the efficiency of stem cell induction. Initial studies of the intracoronary administration of BM mononuclear cells after myocardial infarction has yielded promising results; however, intensive investigation of the underlying molecular mechanisms at play as well as double-blinded clinical trials will be necessary to establish the extent of both migration of the BM stem cells into the damaged cardiac tissue and their differentiation into cardiomyocytes. Several types of cardiac tissue stem cells have also been reported, but an accurate and extensive comparison of these cells with regard to their characteristics and multipotency remains to be done. An integrative study involving developmental biology, stem cell biology, and tissue engineering is required to achieve the full potential of cardiac regeneration.
On the energy efficiency of MIMO cooperative relaying networks (2009)

合作中继技术能极大地改进多重输入和多重输出(MIMO ) 的能力无线系统。为各种各样的中继协议的 transmit 力量分配(TPA ) 策略为改进精力效率变得很重要。这篇文章在中继系统的 MIMO 合作社建议新奇 TPA 计划。二种不同情形被考虑。一个人是在的混合 decode-and-forward (HDF ) 协议零力量(ZF ) 过程被操作中继，并且其它是有继电器节点和天线选择策略的 decode-and-forward (DF ) 协议。模拟结果显示建议计划能由利用继电器连接的性质引起重要电容获得。另外，当有更少继电器节点的相等的 TPA 使用了，在 HDF 系统的建议 TPA 计划能完成一样的能力。最后，当继电器节点的分发范围膨胀时，有建议计划的电容获得增加。
DNA-Thumb Interactions and Processivity of T7 DNA Polymerase in Comparison to Yeast Polymerase η (2004)

The replicative polymerase of bacteriophage T7 is structurally and mechanistically well characterized. The crystal structure of T7 DNA polymerase or gene 5 protein complexed to its processivity factor, Escherichia coli thioredoxin, a primer-template, and a dideoxynucleotide reveals how this enzyme interacts with the 3'-end of the primer-template, but does not show how thioredoxin confers processivity to the polymerase. In the crystal structure highly conserved amino acids Asn(335) and Ser(338) of the thumb subdomain of T7 DNA polymerase are seen to interact with phosphates 7 and 8 of the DNA template strand. Results with a mutant T7 DNA polymerase in which aliphatic residues are substituted for these amino acids and experiments with different length and methylphosphonate-modified primer-templates demonstrate that these interactions are essential for processive synthesis and d(A.T)(n) tract bypass. Our data with methylphosphonate-modified DNA suggests that thioredoxin confers processivity to T7 DNA polymerase in part by causing an interaction with the phosphate backbone or minor groove of DNA. Residues Asn(335) and Ser(338) may also function with a nearby helix-loop-helix motif located at residues 339-372 to enclose the DNA during processive synthesis. Our results suggest that this structure must be held close to the DNA by ionic interactions to function. These interactions also allow for DNA sliding but physically block the passage of a 3T bulge in the template. In contrast, yeast polymerase eta, a polymerase that non-mutagenically repairs cis-syn thymidine dimers, allows the same bulge to slide past its thumb subdomain during synthesis. A relaxed thumb interaction with the DNA could account for the notably low processivity of polymerase eta.
Structural mapping of Fc receptor bound immunoglobulin E: proximity to the membrane surface of the antibody combining site and another site in the Fab segments (1985)

Resonance energy-transfer methods have been used to investigate the structure of immunoglobulin E (IgE) bound to its high-affinity receptor on plasma membrane vesicles derived from rat basophilic leukemia cells. The structural mapping of receptor-bound IgE was initiated in an earlier study [Holowka, D., & Baird, B. (1983) Biochemistry 22, 3475], and it is based on measuring the minimal distance from IgE sites that are selectively labeled with donor probes to a plane of amphipathic acceptors at the membrane surface. This paper describes the use of monoclonal IgE specific for 5-(dimethylamino)naphthalene-1-sulfonyl (DNS) to place a donor probe, DNS-L-Lys, in the antibody combining sites. The distance from these sites to the membrane surface was determined to be greater than 100 A with two different amphipathic acceptor probes. Another site in the Fab segments of monoclonal IgE (anti-dinitrophenyl) could be labeled selectively with N-[4-[7-(diethylamino)-4-methylcoumarin-3-yl]phenyl]maleimide (CPM) in the absence of reducing agents [CPM(-)], and the reaction could not be blocked by prereaction with N-ethylmaleimide. The pattern of CPM(-)-labeled proteolytic fragments and the lack of fluorescence quenching by (trinitrophenyl)lysine in the antibody combining sites suggested the CPM(-)-labeled site to be in the C epsilon 1 domain of IgE. The distance between this site on receptor-bound IgE and the membrane surface was determined to be 75-87 A with two different amphipathic acceptors.(ABSTRACT TRUNCATED AT 250 WORDS)