gebhart/patrepeval huggingface dataset:
The NH2-terminal 21 amino acid residues are not essential for the papain-inhibitory activity of oryzacystatin, a member of the cystatin superfamily. Expression of oryzacystatin cDNA and its truncated fragments in Escherichia coli. (1988)

Oryzacystatin, a proteinaceous cysteine proteinase inhibitor (cystatin) in rice, is comprised of 102 residues (Met1-Ala102) (Abe, K., Emori, Y., Kondo, H., Suzuki, K., and Arai, S. (1987) J. Biol. Chem. 262, 16793-16797). We constructed an expression plasmid containing a full length oryzacystatin cDNA at the multi-cloning site of pUC18 and produced a lacZ'-oryzacystatin fusion protein in Escherichia coli. The partially purified expressed protein efficiently inhibits papain activity assayed using N-benzoyl-DL-arginine-2-naphthylamide as a substrate. We also constructed expression plasmids lacking the 5'- and 3'-regions of cDNAs that encode NH2- and COOH-terminally truncated oryzacystatins. An N-truncated oryzacystatin lacking Gly5 and retaining Gln53-Val54-Val55-Ala56-Gly57 inhibited papain as efficiently as the full length oryzacystatin, although both Gly5 and Gln53-Gly57 (oryzacystatin numbering) are conserved among members of most cystatin superfamilies. However, another N-truncated oryzacystatin lacking the NH2-terminal 38 residues was almost completely inactive. On the other hand, a COOH-terminally truncated oryzacystatin lacking the COOH-terminal 11 residues possesses potent papain-inhibitory activity, whereas another COOH-terminally truncated oryzacystatin lacking 35 residues shows much less inhibitory activity, although it retains the two well conserved features Gly5 and Gln53-Gly57. These results indicate that the NH2-terminal 21 residues containing Gly5 and the COOH-terminal 11 residues are not essential, suggesting that a portion of the polypeptide segment containing Gln53-Gly57 is necessary for oryzacystatin to elicite its papain-inhibitory activity efficiently.
The Acute Respiratory Distress Syndrome (2015)

The acute respiratory distress syndrome (ARDS) is a major cause of acute respiratory failure. Its development leads to high rates of mortality, as well as short- and long-term complications, such as physical and cognitive impairment. Therefore, early recognition of this syndrome and application of demonstrated therapeutic interventions are essential to change the natural course of this devastating entity. In this review article, we describe updated concepts in ARDS. Specifically, we discuss the new definition of ARDS, its risk factors and pathophysiology, and current evidence regarding ventilation management, adjunctive therapies, and intervention required in refractory hypoxemia.
Unique Cell Surface Expression of Receptor Tyrosine Kinase ROR1 in Human B-Cell Chronic Lymphocytic Leukemia (2008)

The restricted, uniform, and constitutive cell surface expression of ROR1 protein in B-CLL provides a strong incentive for the development of targeted therapeutics such as monoclonal antibodies.
A technique for the treatment of sternal infections using the Vacuum Assisted Closure device. (2001)

The VAC serves as a bridge to sternal wound closure and is a safe and effective therapeutic strategy for patients with impaired physiologic reserve and/or highly contaminated wounds. We feel that it is also reasonable to consider the VAC as a preventive strategy against right ventricular rupture. Furthermore, because the firmness of the vacuum sponge apparatus acts as an impressive sternal stabilizer, post-debridement extubation is possible, reducing the need for prolonged paralysis and mechanical ventilation. This stabilization also allows early postoperative ambulation with the VAC in place. In summary, we believe that the VAC device offers an effective means of managing patients with sternal infections.
Characterization of ion channels involved in the penetration of phage T4 DNA into Escherichia coli cells. (1988)

The hypothesis of a channel-mediated transport of phage DNA into Escherichia coli cytoplasmic membrane has been formulated for a long time. In this paper, we present experimental evidence in favor of this proposal. We have analyzed the kinetics of the K+ efflux induced by T4 phage and ghosts (phage depleted of DNA) using a potassium selective electrode. We show that the K+ efflux is not catalyzed by the K+ transport systems. The Km of K+ efflux is the same for phage and ghosts. The rate of K+ efflux is linearly related to the multiplicity of infection. This suggests that phage and ghosts induce the formation of similar channels and that one channel is induced by one virion. The K+ efflux is associated with an influx of H+ and Na+ or Li+ which compete for entry through the channel. These ion fluxes may be responsible for the cell depolarization. The phage-induced channels allow the passage of DNA. They are only transiently opened, and their closing leads to cellular repolarization. The ghost-induced channels remain open. The insertion and conformation of the channels in the membrane depend on the temperature and their confirmation is voltage-dependent. We give an estimate of their size.
Regulation of Terminal Differentiation of Cultured Mouse Epidermal Cells by lα,25-Dihydroxyvitamin D3* (1983)

Terminal differentiation of mouse epidermal cells in primary culture was found to be regulated by 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25(OH)2D3), the hormonal form of vitamin D3 produced by sequential hydroxylations in the liver and kidney. Epidermal differentiation was stimulated dose dependently by 1 alpha,25(OH)2D3 at concentrations of 0.12 nM or more. In the presence of the vitamin, stratified foci increased in number and size and contiguous foci coalesced. Basal cells in the treated cultures decreased sharply and underwent differentiation into squamous and enucleated cells which sloughed off into the medium during cultivation. The size and density of the cells became larger and lighter during the course of differentiation. 1 alpha,25(OH)2D3 markedly stimulated formation of a cornified envelope, a structure with chemically stable cross-links formed beneath the plasma membrane. Of several derivatives of vitamin D3 examined, 1 alpha,25(OH)2D3 was the most potent in inducing epidermal differentiation. Stimulation of epidermal differentiation was also observed in low calcium medium. DNA synthesis was inhibited dose dependently by 1 alpha,25(OH)2D3. A specific receptor for 1 alpha,25(OH)2D3 was found in the cytosol fraction of the epidermal cells. Scatchard plot analysis revealed that the receptor has an apparent dissociation constant (Kd value) of 54 pM and maximum binding value (Nmax) of 43 fmol/mg protein. The specificity of the receptor was demonstrated by analog competition in the following order: 1 alpha,25(OH)2D3 much greater than 25-hydroxyvitamin D3 greater than 1 alpha-hydroxyvitamin D3 greater than 24R,25-dihydroxyvitamin D3.
DNA-dependent protein kinase is not required for accumulation of p53 or cell cycle arrest after DNA damage. (1997)

In response to DNA damage, cells transduce a signal that leads to accumulation and activation of p53 protein, transcriptional induction of several genes, including p21, gadd45, and gadd153, and cell cycle arrest. One hypothesis is that the signal is mediated by DNA-dependent protein kinase (DNA-PK), which consists of a catalytic subunit (DNA-PKcs) and a regulatory subunit (Ku). DNA-PK has several characteristics that support this hypothesis: Ku binds to DNA damaged by nicks or double-strand breaks, DNA-PKcs is activated when Ku binds to DNA, DNA-PK will phosphorylate p53 and other cell cycle regulatory proteins in vitro, and DNA-PKcs shares homology with ATM, which is mutated in ataxia telangiectasia and involved in signaling the p53 response to ionizing radiation. The hypothesis was tested by analyzing early passage fibroblasts from severe combined immunodeficient mice, which are deficient in DNA-PK. After exposure to ionizing radiation, UV radiation, or methyl methane-sulfonate, severe combined immunodeficient and wild-type cells were indistinguishable in their response. The accumulation of p53, induction of p21, gadd45, and gadd153, and arrest of the cell cycle in G1 and G2 occurred normally. Therefore, DNA-PK is not required for the p53 response or cell cycle arrest after DNA damage.
Data Reduction and Error Analysis for the Physical Sciences (1993)

Uncertainties in measurements probability distributions error analysis estimates of means and errors Monte Carlo techniques dependent and independent variables least-squares fit to a polynomial least-squares fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood. Appendices: numerical methods matrices graphs and tables histograms and graphs computer routines in Pascal.
DNA immunization: Induction of higher avidity antibody and effect of route on T cell cytotoxicity (1997)

Immunizations of mice with plasmid DNAs encoding ovalbumin (OVA), human Ig, and hen egg lysozyme were compared with doses of soluble protein (without adjuvant) that induced similar IgG responses. The route of immunization influenced the magnitude of the antibody (Ab) response in that intradermal (i.d.) injection elicited higher IgG Ab levels than i.m. injection in both DNA- and protein-immunized mice. Although total IgG levels were similar to soluble protein controls, the avidity of the anti-OVA Abs generated by DNA immunization were 100- and 1,000-fold higher via the i.m. or i.d. route, respectively. However, despite the generation of high-avidity Ab in DNA-immunized mice, germinal centers could not be detected in either DNA- or protein-immunized mice. Examination of the IgG subclass response showed that IgG2a was induced by i.m. DNA immunization, coinciding with elevated interferon gamma production, whereas a dominant and elevated IgG1 response, coinciding with detectable interleukin 4 production, was generated after i.d. immunization with DNA or soluble OVA and hen egg lysozyme but not human Ig protein. As expected, cytotoxic T cell (CTL) responses could be detected only after DNA immunization. I.d. immunization produced the strongest CTL responses early (2 weeks) but was similar to i.m. later. Therefore, DNA immunization can differ from protein immunization by its ability to induce rapid CTL responses and higher avidity Ab, both of which are advantageous for vaccination.
From Genome to Proteome: Looking at a Cell's Proteins (1995)

Heidelberg, Germany—It sounds like Mission Impossible: Follow the changes taking place in a cell by identifying the thousands of different proteins the cell produces and watching how they ebband flow over time. But a growing band of researchers believes that improved analytical techniques may soon make such an approach feasible, and they haveeven coined a new term for it: proteome research. Prototype systems that screen and analyze thousands of proteins at a time look promising.
By how much and how quickly does reduction in serum cholesterol concentration lower risk of ischaemic heart disease? (1994)

The results from the cohort studies, international comparisons, and clinical trials are remarkably consistent. The cohort studies, based on half a million men and 18,000 ischaemic heart disease events, estimate that a long term reduction in serum cholesterol concentration of 0.6 mmol/l (10%), which can be achieved by moderate dietary change, lowers the risk of ischaemic heart disease by 50% at age 40, falling to 20% at age 70. The randomised trials, based on 45,000 men and 4000 ischaemic heart disease events show that the full effect of the reduction in risk is achieved by five years.
Structural Analysis and Caco-2 Cell Permeability of the Celiac-Toxic A-Gliadin Peptide 31–55 (2013)

Celiac disease is a chronic enteropathy caused by the ingestion of wheat gliadin and other cereal prolamines. The synthetic peptides 31-43 (P31-43) and 31-49 (P31-49) from A-gliadin are considered to be model peptides for studying innate immunity in celiac disease. Our previous study demonstrated that P31-43 and P31-49 are encrypted within peptide 31-55 (P31-55), which is naturally released from gastropancreatic digestion and is not susceptible to hydrolysis by brush border membrane enzymes. Here, we analyzed the permeability of P31-55 through the epithelial cell layer of confluent Caco-2 cells using high-performance liquid chromatography, mass spectrometry, and fluorescence-activated cell sorting. Twenty-three percent of the P31-55 added to the apical chamber was transported to the basolateral chamber after 4 h of incubation without being degraded by hydrolysis. Treatment of Caco-2 cells with whole gliadin digests extracted from a common wheat cultivar increased the epithelial P31-55 translocation by approximately 35%. Moreover, we observed an atypical chromatographic profile consisting of a double peak. Chromatography using different column temperatures and circular dichroism highlighted the presence of more conformational structures around the amide bond of the two adjacent prolines 38 and 39. These findings confirm that P31-55 is gastrointestinally resistant and is permeable across a Caco-2 monolayer. Moreover, we hypothesize that the various conformations of P31-55 may play a role in the activation of innate immunity.
New Issues, New Results (1992)

This paper surveys empirical studies of the costs of reducing carbon dioxide emissions. It updates and extends an earlier paper, which focused on baseline emission scenarios and the aggregate cost of emission reductions. It attempts to explain some of the differences in simulation results and highlights some major policy issues ...
Color Face Recognition Based on Steerable Pyramid Transform and Extreme Learning Machines (2014)

This paper presents a novel color face recognition algorithm by means of fusing color and local information. The proposed algorithm fuses the multiple features derived from different color spaces. Multiorientation and multiscale information relating to the color face features are extracted by applying Steerable Pyramid Transform (SPT) to the local face regions. In this paper, the new three hybrid color spaces, YSCr, ZnSCr, and BnSCr, are firstly constructed using the Cb and Cr component images of the YCbCr color space, the S color component of the HSV color spaces, and the Zn and Bn color components of the normalized XYZ color space. Secondly, the color component face images are partitioned into the local patches. Thirdly, SPT is applied to local face regions and some statistical features are extracted. Fourthly, all features are fused according to decision fusion frame and the combinations of Extreme Learning Machines classifiers are applied to achieve color face recognition with fast and high correctness. The experiments show that the proposed Local Color Steerable Pyramid Transform (LCSPT) face recognition algorithm improves seriously face recognition performance by using the new color spaces compared to the conventional and some hybrid ones. Furthermore, it achieves faster recognition compared with state-of-the-art studies.
Levetiracetam and ethosuximide in the treatment of acute mania in an open study with an on‐off‐on design (2002)

Walden J, Langosch J, Born C, Schaub G, Grunze H. Levetiracetam and ethosuximide in the treatment of acute mania in an open study with an on‐off‐on design. Bipolar Disord 2002: 4(Suppl. 1): 114. © Blackwell Munksgaard, 2002
An Evaluation of Rapid Point-of-Collection Oral Fluid Drug-Testing Devices (2003)

New technology is currently being marketed to rapidly test oral fluids for drugs of abuse at the point of collection (POC). There are no nationally accepted standards or cutoff concentrations for detecting drugs in oral fluids and for most analytes there are significant differences in cutoff concentrations across devices. Four devices were evaluated (OralLab), RapiScan, Drugwipe, and SalivaScreen) for their ability to meet manufacturers claims, and proposed federal standards for criminal justice and workplace programs. Human oral fluid fortified with known quantities of drug [drug(s) or metabolite(s)] was used to test these devices. Overall, the performance of these rapid POC oral fluid drug-testing devices was quite variable. Some devices performed well for the analysis of some drug classes but poorly for others. In general, most devices performed well for the detection of methamphetamine and opiates, but all performed poorly for the detection of cannabinoids. The ability to accurately and reliably detect cocaine and amphetamine was dependent on the individual device.
The indirect association of human T-cell leukemia virus tax protein with DNA results in transcriptional activation (1991)

trans-activator p40tax of human T-cell leukemia virus type I activates specific enhancers and stimulates transcription of the viral and some cellular genes but does not bind directly to the enhancer sequences. We demonstrated here that a fusion protein of p40tax and GAL4 DNA binding domain activated transcription dependent on the GAL4-binding site in the reporter plasmid. Mutants of p40tax were also tested in the fusion protein, and their activities were found to be in parallel with those of their free forms on the original target long terminal repeat. This activation with GAL4 fusion protein was interfered with by the free form of p40tax. These results suggest that p40tax associates with DNA through interaction with DNA binding protein(s) and also interacts with another transcription factor(s) to elicit the activation.
Weka: Practical machine learning tools and techniques with Java implementations (1999)

Introduction The Waikato Environment for Knowledge Analysis&amp;lt;E-174&amp;gt; (Weka) is a comprehensive suite of Java class&amp;lt;E-188&amp;gt; libraries that implement many state-of-the-art&amp;lt;E-145&amp;gt; machine learning and data mining algorithms.&amp;lt;E-161&amp;gt; Weka is freely available on the World-Wide Web&amp;lt;E-189&amp;gt; and accompanies a new text on data mining [1]&amp;lt;E-196&amp;gt; which documents and fully explains all the&amp;lt;E-195&amp;gt; algorithms it contains. Applications written using&amp;lt;E-186&amp;gt; the Weka class libraries can be run on any&amp;lt;E-193&amp;gt; computer with a Web browsing capability; this&amp;lt;E-193&amp;gt; allows users to apply machine learning techniques&amp;lt;E-165&amp;gt; to their own data regardless of computer platform.&amp;lt;E-162&amp;gt; Tools are provided for pre-processing data, feeding&amp;lt;E-178&amp;gt; it into a variety of learning schemes, and analyzing&amp;lt;E-169&amp;gt; the resulting classifiers and their performance. An&amp;lt;E-196&amp;gt; important resource for navigating through Weka is&amp;lt;E-202&amp;gt; its on-line documentation, which is automatically&amp;lt;E-153&amp;gt; generated from the source.&amp;lt;E-77&amp;gt; The pri
Interferon-γ, But Not Interferon-αβ, Synergizes with Tumor Necrosis Factor-α and Lipid A in the Induction of Nitric Oxide Production by Murine L929 Cells (1993)

Recently, we have demonstrated that tumor necrosis factor (TNF)-sensitive tumor cells produce nitric oxide (NO) in response to TNF whereas TNF-resistant cells do not. Because the addition of interferon-gamma (IFN-gamma) augmented NO production, we were interested in investigating this phenomenon further and comparing the effects of IFN-gamma with those of IFN-alpha beta. We found that cell lines that are sensitive to TNF-mediated cytotoxicity (TMC) produced NO in response to TNF and IFN-gamma, but not in response to IFN-alpha beta. The effect of IFN-gamma on NO production was dose dependent, but IFN-gamma by itself did not induce NO production. A TNF-resistant cell line (MCA) did not produce NO under any of the conditions tested. Different results were obtained when the effect of IFNs on TMC was assayed. TNF-sensitive L929 cells were rendered less sensitive to TNF after treatment with both types of IFN. In contrast, another TNF-sensitive cell, WEHI 164, was rendered more sensitive to TMC after treatment with both types of IFN. The effect of IFNs on WEHI cells was dose dependent. Neither IFN had any effect on TNF sensitivity of TNF-resistant MCA cells. The addition of lipid A (LA) had no effect on TMC under any condition. However, L929 cells treated with LA, TNF, and IFN-gamma produced twice as much NO as cells treated with TNF and IFN-gamma only. Northern analysis for cytokine-inducible NO synthase (NOS) mRNA steady-state levels indicated that TNF synergized with IFN-gamma to induce increased accumulation of NOS mRNA.(ABSTRACT TRUNCATED AT 250 WORDS)
Kinetics of a naltrexone sustained-release preparation (1984)

A biodegradable sustained-release naltrexone bead preparation containing 70% naltrexone in a physical mixture with a copolymer of 90% lactic acid and 10% glycolic acid was evaluated in three male subjects. Each subject received a 10-mg iv dose of naltrexone HCl and a 63-mg dose by subcutaneous implantation of naltrexone beads. Kinetics of naltrexone estimated from the intravenous dose indicated a plasma clearance range of 3.1 to 3.4 l/min and a t 1/2 range of 1.7 to 3.7 hr. After bead implantation, average plasma naltrexone levels were maintained at 0.3 to 0.4 ng/ml and naltrexol levels were at 0.4 to 1.0 ng/ml for a period of approximately 1 mo, during which urine naltrexone and naltrexol levels were about 20 to 30 and 70 to 200 ng/ml. It was estimated that approximately 70% to 77% of the dose was absorbed after bead implantation. There were no serious adverse effects other than tissue irritation in two of the three subjects.
Involvement of mannose receptor in cytokine interleukin-1beta (IL-1beta), IL-6, and granulocyte-macrophage colony-stimulating factor responses, but not in chemokine macrophage inflammatory protein 1beta (MIP-1beta), MIP-2, and KC responses, caused by attachment of Candida albicans to macrophages (1997)

The production of chemotactic cytokines (chemokines) and other cytokines by macrophages in response to fungal infection is thought to be critical during the course of candidiasis. However, the mechanism of cytokine synthesis by macrophages in response to fungi is not well understood. Therefore, the response of macrophages to Candida albicans was examined in terms of receptor-mediated chemokine and other cytokine mRNA induction. Attachment of C. albicans to murine thioglycollate-elicited peritoneal macrophages induced increased mRNA levels of the cytokines interleukin-1beta (IL-1beta), IL-6, and granulocyte-macrophage colony-stimulating factor (GM-CSF) and the chemokines macrophage inflammatory protein 1beta (MIP-1beta), MIP-2, and KC (a member of the platelet factor 4 neutrophil chemoattractant family), as determined by quantitative reverse transcription-PCR. However, treatment of macrophages with alpha-methyl-D-mannoside significantly reduced the cytokine GM-CSF response to C. albicans but did not affect the chemokine MIP-2 response. Antisense oligodeoxynucleotide (ODN) to mannose receptor (MR) mRNA inhibited the expression and function of MR in macrophages as determined by Western blot analysis and 125I-labeled mannose-bovine serum albumin (BSA) binding, and also inhibited the elevation of cytokine IL-1beta, IL-6, and GM-CSF mRNA levels induced by C. albicans attachment. Elevation of chemokine MIP-1beta, MIP-2, and KC mRNA levels induced by C. albicans was not affected in macrophages whose MR expression was suppressed by antisense ODN treatment. Furthermore, IL-4 treatment of macrophages, which up-regulated MR expression as determined by Western blot analysis and fluorescein isothiocyanate-labeled mannose-BSA uptake, enhanced the level of cytokine GM-CSF mRNA induced by C. albicans but not the level of the chemokine MIP-2 mRNA. These results indicate that selected cytokine responses of macrophages to C. albicans are mediated by MR, while some chemokine responses may be mediated by other receptors.