gebhart/patrepeval huggingface dataset:
Quantitative and Qualitative Preparations of Bacterial Outer Membrane Vesicles (2012)

Gram-negative bacterial outer membrane vesicle production and function have been studied using a variety of quantitative and qualitative methods. These types of analyses can be hampered by the use of impure vesicle preparations. Here we describe a set of techniques that are useful for the quantitative analysis of vesicle production and for preparative yields of highly purified vesicles for studies of vesicle function or composition. Procedures and advice are also included for the purification of vesicles from encapsulated and low-yield strains.
Kinetic and spectroscopic studies of hydrophilic amino acid substitutions in the hydrophobic pocket of human carbonic anhydrase II (1993)

The functional importance and structural determinants of a conserved hydrophobic pocket in human carbonic anhydrase II (CA II) were probed by preparing and characterizing 13 amino acid substitutions at Leu-198, situated at the mouth of the pocket. The pH dependence of the esterase activity reveals that activity decreases (up to 120-fold) as the amino acid size and charge at position 198 are varied while the pKa of the zinc-bound water molecule increases (up to 1 pH unit). Intriguingly, the pH dependence of the Leu-198-->Glu substitution is parabolic (pKas approximately 6 and 9), consistent with introduction of a general base-catalyzed mechanism. Kinetic characterization of CO2/HCO3- interconversion catalyzed by four variants (Leu-198-->Ala, His, Arg, and Glu) reveals that increasing the size of the hydrophobic pocket (Ala) does not compromise catalysis (approximately 3-fold decrease); however, substitution of charged (Arg and Glu) and larger (His) amino acids decreases kcat/KM for CO2 hydration substantially (17-fold, 19-fold, and 10-fold, respectively) but not completely. log kcat/KM for CO2 hydration, HCO3- dehydration, and p-nitrophenyl acetate hydrolysis correlates with the hydrophobicity of the residue at 198, likely reflecting desolvation or electrostatic destabilization of the ground state. The X-ray crystal structures of the Leu-198-->His, Glu, and Arg variants (Nair & Christianson, 1993) indicate that the His and Glu side chains are accommodated by minor structural reorganization leading to a wider mouth for the hydrophobic pocket while the Arg side chain blocks the pocket. Infrared spectroscopy of CO2 bound to either wild-type CA II or the Leu-198-->Arg variant indicates that the Arg substitution both decreases the affinity and alters the position of CO2 binding, suggesting that the hydrophobic pocket forms the CO2 binding site in CA II. Finally, a 1.5-fold increase (Leu-198-->Ala) and 12-fold decrease (Leu-198-->Arg) in kcat for CO2 hydration, indicative of the rate constant for intramolecular proton transfer from zinc-bound water to His-64, are likely mediated by changes in the active site solvent structure.
Structural and Functional Basis of the Serine Protease-like Hepatocyte Growth Factor β-Chain in Met Binding and Signaling (2004)

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Structure of canine pulmonary surfactant apoprotein: cDNA and complete amino acid sequence. (1985)

The apoproteins of pulmonary surfactant (PSAP) are thought to be critical for normal surfactant function. They bind to surfactant phospholipids and enhance their ability to form surface films in vitro. These acidic glycoproteins have monomeric molecular weights of 36,000, 32,000, and 28,000 (PSAP-36, -32, and -28). Each member of this family of proteins has a similar amino acid composition and their differences in electrophoretic mobility are due in part to glycosylation. We have derived the full amino acid sequence of PSAP-32 from the nucleotide sequence of PSAP cDNA. A cDNA library was prepared from canine lung poly(A)+ RNA and screened with oligonucleotide probes that were based on the NH2-terminal amino acids of PSAP-32 determined by Edman degradation. This protein has the striking feature of collagen-like and non-collagen-like sequences in the same polypeptide chain. There are 24 Gly-Xaa-Yaa triplets, where Yaa is often hydroxyproline. These repeats comprise one-third of PSAP near the NH2 terminus. The remaining two-thirds of PSAP is resistant to bacterial collagenase digestion and contains a possible N-glycosylation site near the carboxyl terminus. The NH2-terminal one-third of PSAP-32 probably contains the cysteine involved in interchain disulfide bonds.
Mouse Cathelin-Related Antimicrobial Peptide Chemoattracts Leukocytes Using Formyl Peptide Receptor-Like 1/Mouse Formyl Peptide Receptor-Like 2 as the Receptor and Acts as an Immune Adjuvant (2005)

Mammalian antimicrobial proteins, such as defensins and cathelicidin, have stimulating effects on host leukocytes. Cathelin-related antimicrobial peptide (CRAMP), the orthologue of human cathelicidin/LL-37, is the sole identified murine cathelicidin. CRAMP has been shown to have both antimicrobial and angiogenic activities. However, whether CRAMP, like human cathelicidin/LL-37, also exhibits a direct effect on the migration and function of leukocytes is not known. We have observed that CRAMP, like LL-37, was chemotactic for human monocytes, neutrophils, macrophages, and mouse peripheral blood leukocytes. CRAMP also induced calcium mobilization and the activation of MAPK in monocytes. CRAMP-induced calcium flux in monocytes was desensitized by MMK-1, an agonistic ligand specific for formyl peptide receptor-like-1 (FPRL1), and vice versa, suggesting the use of FPRL1 by CRAMP as a receptor. Furthermore, CRAMP induced the chemotaxis of human embryonic kidney 293 cells transfected with either FPRL1 or mouse formyl peptide receptor-2, the mouse homologue of FPRL1, but not by untransfected parental human embryonic kidney 293 cells, confirming the use of FPRL1/mouse formyl peptide receptor-2 by CRAMP. Injection of CRAMP into mouse air pouches resulted in the recruitment predominantly of neutrophils and monocytes, indicating that CRAMP acts as a chemotactic factor in vivo. Finally, simultaneous administration of OVA with CRAMP to mice promoted both humoral and cellular Ag-specific immune responses. Thus, CRAMP functions as both a chemoattractant for phagocytic leukocytes and an enhancer of adaptive immune response.
Dose Responsive Effects of PDGF-BB, PDGF-AA, EGF, and bFGF on Granulation Tissue in a Guinea Pig Partial Thickness Skin Excision Model (1993)

A guinea pig partial thickness skin excision model was used to evaluate the effects of recombinant human PDGF-BB, PDGF-AA, EGF, and bFGF on granulation tissue (neodermis) formation. These growth factors tended to increase the thickness of the granulation tissue bed when assessed histologically at day 7. Using only four animals per group, PDGF-BB at 30 and 100 micrograms/ml consistently and significantly increased the thickness of the granulation bed 2-3 times that of control. Except for the increased thickness, the granulation tissue appeared normal. PDGF-AA and EGF also significantly increased the granulation tissue thickness, and bFGF gave indications of an effect. There was no evidence of synergistic effects between PDGF-BB, EGF, and/or bFGF.
Directionally controlled drilling to horizontally intercept selected strata, upper Freeport coalbed, Greene County, Pa. [8 refs] (1977)

A 3-inch pilot hole was directionally drilled to intercept the Freeport coalbed horizon horizontally at Mather, Pa., as part of a Bureau of Mines degasification project. The original concept was to continue the horizontal drilling into the coalbed, after the initial intercept, with a total of three horizontal holes eventually being completed. However, the erratic thickness (0.0 to 4.3 feet) of the Freeport coalbed at Mather was not sufficient to support the horizontal drilling degasification technique, and the site was abandoned after six attempts to locate adequate continuous coal thicknesses. The drilling of coreholes in the immediate vicinity of proposed well paths to evaluate coal thickness is essential prior to future slant hole operations. Although mechanical failures of the new directional drilling equipment, mud pump and rig breakdowns, directional control problems, and exploratory horizontal drilling in the Freeport horizon more than doubled the anticipated cost of the pilot hole, continuing improvements in directional drilling equipment and techniques should significantly reduce the time and costs of future drilling operations.
A Biomechanical Analysis of Atlantoaxial Stabilization Methods Using a Bovine Model (1993)

The reliability and initial postoperative stability of six widely used C1-C2 surgical constructs were evaluated by nondestructive biomechanical testing of ten fresh bovine upper cervical spine segments. The six fixation techniques were the simple midline sublaminar C1 wiring (SMW), the modified Gallie wiring (MGW), the Brook wedge arthrodesis (BWA), the bilateral lateral mass screw (LMS), and the Clark arthrodesis without (CWO) and with (CW) the adjunctive use of polymethylmethacrylate (PMMA) cement. Instability was produced by resection of the base of the dens. Intact, destabilized, and instrumented constructs were tested in unconstrained flexion, extension, torsion, anterior, and posterior shear forces. The LMS and CW techniques proved the most effective in achieving C1-C2 stability. Sublaminar C2 wiring methods tended to have greater torsional and shear stiffness. Less rigid fixation techniques frequently loosened. All non-PMMA-enhanced wired constructs failed to restore the ability to adequately resist the posterior translation of C1 on C2. Stabilization of an unstable atlantoaxial articulation is best accomplished by a lateral mass screw or sublaminar C1-C2 PMMA-enhanced technique. Other techniques provided less consistent and reliable surgical fixation. Because of the inadequacy of wired constructs to resist posterior shear in patients with this instability pattern, the usual treatment may need to be modified to include more prolonged or protective external immobilization or more rigid fixation techniques. Although less rigid, the SMW and the MGW techniques are safer because they require less-frequent passage of sublaminar wires, avoid potential problems with PMMA, and obviate the hazards of further lateral dissection and insertion of the transarticular screws.
Randomised controlled trials investigating pharmacological and psychological interventions for treatment-refractory depression (2002)

There is little evidence to guide the management of depression that has not responded to a course of antidepressants. Treatment-refractory depression is an important public health problem and large pragmatic trials are needed to inform clinical practice.
How interleukin‐1β induces gouty arthritis (2010)

Recent clinical trials with IL-1β blockade have revealed an impressive and sustained reduction in recurrent attacks of gouty arthritis (1).Even with the use of allopurinol to reduce the systemic levels of uric acid and the anti-inflammatory properties of colchicine, there is no dearth of patients with recurrent episodes of painful gouty arthritis poorly controlled with these regimens who require intermittent courses of glucocorticoids.Thus, the success of IL-1β blocking therapies is a welcome addition for treating refractory gouty arthritis in these patients.Despite the availability of several widely used TNFα blocking therapies for rheumatoid arthritis and other autoimmune diseases, there is a paucity of reports that blocking TNFα provides an effective reduction in gout severity.One explanation for the lack of clinical trials of TNFα blockade in gout attacks is reluctance of subjecting these patients to suppression of host-defense by TNFα blockers.An alternative explanation is that efficacy of TNFα blockade in refractory gout is less than expected.One study reports a weak response with rather high doses of infliximab (2).There are also few publications on monosodium urate (MSU) crystals inducing TNFα from human and mouse cells unless co-stimulated with endotoxins.Therefore, IL-1β blockade may be used for inducing long-term remissions in refractory patients and replace glucocorticoids.If IL-1β blockade becomes the standard of care in refractory gout, it would be consistent with the unique role of IL-1β in the pathogenesis of auto-inflammatory diseases.
Protective Effect of Avian Myelomonocytic Growth Factor in Infection with Marek’s Disease Virus (2002)

Marek's disease virus (MDV) is a herpesvirus that induces T lymphomas in chickens. The aim of this study was to assess the role of the macrophage activator chicken myelomonocytic growth factor (cMGF) in controlling MDV infection. B13/B13 chickens, which are highly susceptible to MD, were either treated with cMGF delivered via a live fowlpox virus (fp/cMGF) or treated with the parent vector (fp/M3) or were left as untreated controls. Seven days later, when challenged with the very virulent RB-1B strain of MDV, the spleens of chickens treated with fp/cMGF showed increased expression of the inducible nitric oxide synthase (iNOS) gene compared to those of control chickens and fp/M3-treated chickens. Increased iNOS gene expression was also accompanied by greater induction of gamma interferon and macrophage inflammatory protein (K203) gene expression, both possible activators of iNOS. fp/cMGF treatment also increased the number of monocytes and systemic NO production in contrast to fp/M3 treatment. Even though cMGF treatment was unable to prevent death for the chickens, it did prolong their survival time, and viremia and tumor incidence were greatly reduced. In addition, cMGF treatment improved the partial protection induced by vaccination with HVT (herpesvirus isolated from turkeys) against RB-1B, preventing 100% mortality (versus 66% with vaccination alone) and greatly reducing tumor development. Treatment with fp/M3 did not have such effects. These results suggest that cMGF may play multiple roles in protection against MD. First, it may enhance the innate immune response by increasing the number and activity of monocytes and macrophages, resulting in increased NO production. Second, it may enhance the acquired immune response, indicated by its ability to enhance vaccine efficacy.
Immunization of Pigs with a Particle-Mediated DNA Vaccine to Influenza A Virus Protects against Challenge with Homologous Virus (1998)

Particle-mediated delivery of a DNA expression vector encoding the hemagglutinin (HA) of an H1N1 influenza virus (A/Swine/Indiana/1726/88) to porcine epidermis elicits a humoral immune response and accelerates the clearance of virus in pigs following a homotypic challenge. Mucosal administration of the HA expression plasmid elicits an immune response that is qualitatively different than that elicited by the epidermal vaccination in terms of inhibition of the initial virus infection. In contrast, delivery of a plasmid encoding an influenza virus nucleoprotein from A/PR/8/34 (H1N1) to the epidermis elicits a strong humoral response but no detectable protection in terms of nasal virus shed. The efficacy of the HA DNA vaccine was compared with that of a commercially available inactivated whole-virus vaccine as well as with the level of immunity afforded by previous infection. The HA DNA and inactivated viral vaccines elicited similar protection in that initial infection was not prevented, but subsequent amplification of the infection is limited, resulting in early clearance of the virus. Convalescent animals which recovered from exposure to virulent swine influenza virus were completely resistant to infection when challenged. The porcine influenza A virus system is a relevant preclinical model for humans in terms of both disease and gene transfer to the epidermis and thus provides a basis for advancing the development of DNA-based vaccines.
Application of a Leukocyte Migration-Inhibition Agarose Test to Swine Dysentery (1980)

Cell-mediated immunity (CMI) was demonstrated in swine naturally affected with swine dysentery (SD) by a leukocyte migration-inhibition agarose test (LMAT). Migration of leukocytes from SD-affected pigs was inhibited in the presence of soluble antigen of Treponema hyodysenteriae, whereas migration of leukocytes from noninfected swine was not inhibited by exposure to the same antigen. Cell-mediated immunity was detected initially after the appearance of clinical signs of the disease, and a peak migration index (MI) of 0.11 (P less than 0.01) was detected at 2 weeks thereafter. The MI gradually decreased over the remaining 3 weeks of the experiment. Humoral antibody correlated well with CMI, since both showed maximum production within the same time interval. Leukocytes of swine naturally affected with SD 4 months previously had a significant MI response of 0.73 (P less than 0.05), whereas uninfected swine of comparable age and weight showed a MI of 0.94 that was not significant (P less than 0.05). The results indicated that the LMAT may be useful for the diagnosis of SD.
The genetic contribution to human T-cell receptor repertoire. (1991)

Recent studies in mice have highlighted the importance of polymorphic genetic loci such as the major histocompatibility complex (MHC) or minor lymphocyte-stimulating antigen (Mls) in determining the nature of the peripheral T-cell receptor (TcR) population. As our knowledge of the equivalent process in humans is incomplete, we have utilized a modification of the polymerase chain reaction (PCR) to determine the overall genetic contribution to the normal human TcR variable V beta gene repertoire. These data demonstrate that the normal human T-cell population contains members of all the major TcR V beta families and that there is considerable variation in the relative amounts of specific TcR V beta transcripts between individuals. We have established that the normal peripheral TcR V beta repertoire is more concordant in identical twins than in unrelated individuals. The relative importance of genetic factors in determining the peripheral TcR repertoire is emphasized by these results and suggests that, in humans, the genetic control of immune responsiveness is mediated in part by the peripheral TcR repertoire.
Application of risk score analysis to low‐coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13 (2015)

We conclude that simplified MPS can be used to stratify the risk of pregnancies for trisomy 21, trisomy 18, and trisomy 13 and accurately determine fetal sex. © 2015 John Wiley & Sons, Ltd.
Increase of hybridoma formation by human lymphocytes after stimulation in vitro; effect of antigen, endothelial cells, and PWM. (1982)

Peripheral blood lymphocytes from antibody-producing Rh- donors were fused with mouse myeloma cells, and the hybrids were screened for anti-Rh antibody production. Although the resulting hybrids were not stable in long-term culture, they provided a useful test system for an investigation of ways to stimulate human lymphocytes in vitro before fusion in order to maximize the recovery of hybrids producing antibodies with a desired specificity. Although 6-day culture with PWM or with antigen (Rh+ erythrocytes) increased slightly the yield of desired hybrids, exposure of the PBL to antigen in the presence of human endothelial cells was dramatically more effective. This effect was not produced with endothelial cell culture supernatants (HECS) that had been shown previously to enhance hybridoma growth. Culture of PBL before fusion with both PWM and antigen also improved the proportion of active hybridomas, and incubation with antigen plus endothelial cells plus PWM resulted in a very high number of hybridomas, with a very high proportion producing antibody to the immunizing antigen. There are several alternatives to explain the mechanisms involved, but in any case, the technique should be particularly useful when the possibility of fusion of human PBL with a human myeloma line becomes more widely available.
Purine nucleosides. XXIX. Synthesis of 21-deoxy-L-adenosine and 21-deoxy-L-guanosine and their .alpha. anomers (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurine nucleosides. XXIX. Synthesis of 21-deoxy-L-adenosine and 21-deoxy-L-guanosine and their .alpha. anomersMorris J. Robins, Tasneem A. Khwaja, and Roland K. RobinsCite this: J. Org. Chem. 1970, 35, 3, 636–639Publication Date (Print):March 1, 1970Publication History Published online1 May 2002Published inissue 1 March 1970https://pubs.acs.org/doi/10.1021/jo00828a019https://doi.org/10.1021/jo00828a019research-articleACS PublicationsRequest reuse permissionsArticle Views178Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Factors affecting the performance of parallel mining of minimal unique itemsets on diverse architectures (2009)

Abstract Three parallel implementations of a divide‐and‐conquer search algorithm (called SUDA2) for finding minimal unique itemsets (MUIs) are compared in this paper. The identification of MUIs is used by national statistics agencies for statistical disclosure assessment. The first parallel implementation adapts SUDA2 to a symmetric multi‐processor cluster using the message passing interface (MPI), which we call an MPI cluster; the second optimizes the code for the Cray MTA2 (a shared‐memory, multi‐threaded architecture) and the third uses a heterogeneous ‘group’ of workstations connected by LAN. Each implementation considers the parallel structure of SUDA2, and how the subsearch computation times and sequence of subsearches affect load balancing. All three approaches scale with the number of processors, enabling SUDA2 to handle larger problems than before. For example, the MPI implementation is able to achieve nearly two orders of magnitude improvement with 132 processors. Performance results are given for a number of data sets. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Quantum computation using geometric algebra (2002)

vi LIST OF TABLES .....................................................................................................................x LIST OF FIGURES ............................................................................................................... xiii CHAPTER 1