gebhart/patrepeval huggingface dataset:
Rapid Mutation of Endogenous Zebrafish Genes Using Zinc Finger Nucleases Made by Oligomerized Pool ENgineering (OPEN) (2009)

In summary, our study nearly triples the total number of endogenous zebrafish genes successfully modified using ZFNs (from three to eight) and suggests that OPEN provides a reliable method for introducing targeted mutations in nearly any zebrafish gene of interest.
HIV-1 gp41 as a Target for Viral Entry Inhibition (2004)

The recent success of the fusion inhibitor T-20 (enfuvirtide) in clinical studies has ushered in a new chapter in the development of anti-HIV-1 therapeutics. T-20 is the first FDA-approved drug that targets the viral transmembrane protein gp41. This protein, along with gp120, promotes viral entry through a coordinated cascade of conformational transitions that lead to the fusion of the HIV-1 and target cell membranes. The interaction of gp120 with CD4 and a chemokine receptor stimulates gp41 to extend and bridge the space between the virus and cell. Subsequently, gp41 collapses into a trimer-of-hairpins structure that brings the viral and cellular membranes into close proximity necessary for fusion. Enfuvirtide targets the gp41 amino-terminal region exposed in the transient extended state, blocking the ultimate collapse into the trimer-of hairpins and inhibiting membrane fusion. The vulnerability of this transient extended state has stimulated the development of new agents, ranging from small molecules to large proteins, that bind to gp41 and inhibit its structural transformations. The discovery and characterization of these inhibitors have not only led to new antiviral strategies, but have also shed light on the accessibility of gp41 epitopes that might play a role in HIV-1 vaccine development.
Phylogenetic Diversity among Geographically Dispersed Chlamydiales Endosymbionts Recovered from Clinical and Environmental Isolates of Acanthamoeba spp (2000)

The recently proposed reorganization of the order Chlamydiales and description of new taxa are broadening our perception of this once narrowly defined taxon. We have recovered four strains of gram-negative cocci endosymbiotic in Acanthamoeba spp., representing 5% of the Acanthamoeba sp. isolates examined, which displayed developmental life cycles typical of members of the Chlamydiales. One of these endosymbiont strains was found stably infecting an amoebic isolate recovered from a case of amoebic keratitis in North America, with three others found in acanthamoebae recovered from environmental sources in North America (two isolates) and Europe (one isolate). Analyses of nearly full-length 16S rRNA gene sequences of these isolates by neighbor joining, parsimony, and distance matrix methods revealed their clustering with other members of the Chlamydiales but in a lineage separate from those of the genera Chlamydia, Chlamydophila, Simkania, and Waddlia (sequence similarities, <88%) and including the recently described species Parachlamydia acanthamoebae (sequence similarities, 91.2 to 93.1%). With sequence similarities to each other of 91.4 to 99.4%, these four isolates of intra-amoebal endosymbionts may represent three distinct species and, perhaps, new genera within the recently proposed family Parachlamydiaceae. Fluorescently labeled oligonucleotide probes targeted to 16S rRNA signature regions were able to readily differentiate two groups of intra-amoebal endosymbionts which corresponded to two phylogenetic lineages. These results reveal significant phylogenetic diversity occurring among the Chlamydiales in nontraditional host species and supports the existence of a large environmental reservoir of related species. Considering that all described species of Chlamydiales are known to be pathogenic, further investigation of intra-amoebal parachlamydiae as disease-producing agents is warranted.
Reduced immune responses after vaccination with a recombinant herpes simplex virus type 1 vector in the presence of antiviral immunity (2005)

Due to the continuous need for new vaccines, viral vaccine vectors have become increasingly attractive. In particular, herpes simplex virus type 1 (HSV-1)-based vectors offer many advantages, such as broad cellular tropism, large DNA-packaging capacity and the induction of pro-inflammatory responses. However, despite promising results obtained with HSV-1-derived vectors, the question of whether pre-existing virus-specific host immunity affects vaccine efficacy remains controversial. For this reason, the influence of pre-existing HSV-1-specific immunity on the immune response induced with a replication-defective, recombinant HSV-1 vaccine was investigated in vivo. It was shown that humoral as well as cellular immune responses against a model antigen encoded by the vaccine were strongly diminished in HSV-1-seropositive mice. This inhibition could be observed in mice infected with wild-type HSV-1 or with a replication-defective vector. Although these data clearly indicate that pre-existing antiviral host immunity impairs the efficacy of HSV-1-derived vaccine vectors, they also show that vaccination under these constraints might still be feasible.
Synthesis and hypotensive activity of benzamidopiperidylethylindoles (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and hypotensive activity of benzamidopiperidylethylindolesJ. L. Archibald, B. J. Alps, J. F. Cavalla, and J. L. JacksonCite this: J. Med. Chem. 1971, 14, 11, 1054–1059Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://doi.org/10.1021/jm00293a009RIGHTS & PERMISSIONSArticle Views135Altmetric-Citations27LEARN 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 InReddit PDF (636 KB) Get e-Alerts Get e-Alerts
Successful treatment of dermatomyositis with high-dose intravenous immunoglobulin (2006)

This article does not have an abstract.
Superharmonic injection locked oscillators as low power frequency dividers (2002)

Superharmonic injection locking is investigated in a new theoretical approach. Low power frequency dividers are designed using injection locked oscillators with cascode transistors. The Rockwell 0.5 /spl mu/m CMOS process is used to design a 3 mW injection locked frequency divider in the 1800 MHz frequency range. A 200 MHz maximum locking range is achieved in simulations. 2SC3302 Toshiba NPN transistors are also used to build a 1.75 mW injection locked frequency divider in the 800 MHz frequency range to verify the theory.
Receptor tyrosine kinase transmembrane domains (2010)

The transmembrane (TM) domains of receptor tyrosine kinases (RTKs) play an active role in signaling. They contribute to the stability of full-length receptor dimers and to maintaining a signaling-competent dimeric receptor conformation. In an exciting new development, two structures of RTK TM domains have been solved, a break-through achievement in the field. Here we review these structures, and we discuss recent studies of RTK TM domain dimerization energetics, possible synergies between domains, and the effects of pathogenic RTK TM mutations on structure and dimerization.
Alteration in epithelial permeability and ion transport in a mouse model of total parenteral nutrition (2003)

Total parenteral nutrition has significant effects on intestinal epithelial physiology, stimulating ion secretion and reducing epithelial barrier function. Interferon-gamma appears to play an important role in the loss of the epithelial barrier function that is associated with total parenteral nutrition.
Increased expression of eotaxin in bronchoalveolar lavage and airways of asthmatics contributes to the chemotaxis of eosinophils to the site of inflammation (1997)

Presently, there is considerable evidence for the participation of eosinophils in the pathophysiology of human bronchial asthma. Although increased numbers of eosinophils are present in the airways and bronchoalveolar lavage (BAL) fluid of atopic asthmatics, the mechanisms responsible for their preferential accumulation are still largely unknown. Eotaxin is a chemokine that promotes the selective recruitment of eosinophils. We report that atopic asthmatic patients have high concentrations of eotaxin in BAL fluid and an increased expression of eotaxin mRNA and protein in the epithelium and submucosa of their airways when compared with normal controls. In the BAL cells from asthmatic patients, eotaxin immunoreactivity colocalized predominantly to macrophages (62.2%), with a lesser contribution from T cells (16.3%) and eosinophils (8.9%). BAL fluid from asthmatics contained chemotactic activity for eosinophils that was attributable in part to the presence of eotaxin. Moreover, eotaxin was more effective at inducing in vitro eosinophil chemotaxis when eosinophils were stimulated with IL-5 (a cytokine that enhances the effector capacity of mature eosinophils). These observations suggest that eotaxin contributes to the pathogenesis of asthma by the specific recruitment of eosinophils into the airways.
Gas and Vapor Transport Properties of Perfluoropolymers (2006)

This chapter contains sections titled: Introduction Amorphous Perfluoropolymers as Membrane Materials The Nature of Fluorocarbon/Hydrocarbon Interactions Conclusions References
Monensin and brefeldin A differentially affect the phosphorylation and sulfation of secretory proteins. (1992)

Chromogranin B and secretogranin II, two members of the granin family, are known to be post-translationally modified by the addition of O-linked carbohydrates to serine and/or threonine, phosphate to serine and threonine, and sulfate to carbohydrate and tyrosine residues. In the present study, chromogranin B and secretogranin II were used as model proteins to investigate in which subcompartment of the Golgi complex secretory proteins become phosphorylated. Monensin, a drug known to block the transport from the medial to the trans cisternae of the Golgi stack, inhibited the phosphorylation of the granins, indicating that this modification occurred distal to the medial Golgi. Monensin also blocked the addition of galactose to O-linked carbohydrates and the sulfation of the granins, confirming previous data that these modifications take place in the trans Golgi. To distinguish, within the trans Golgi, between the trans cisternae of the Golgi stack and the trans Golgi network, we made use of the previous observation that brefeldin A results in the redistribution to the endoplasmic reticulum of membrane-bound enzymes of the trans cisternae of the Golgi stack, but not of the trans Golgi network. Brefeldin A treatment abolished granin sulfation but resulted in the accumulation of phosphorylated and galactosylated granins. Differential effects of brefeldin A on membranes of the Golgi stack versus the trans Golgi network were also observed by immunofluorescence analysis of marker proteins specific for either compartment. Our results suggest that the phosphorylation of secretory proteins, like their galactosylation, largely occurs in the trans cisternae of the Golgi stack, whereas the sulfation of secretory proteins on both carbohydrate and tyrosine residues takes place selectively in the trans Golgi network.
Impact of FOLFIRINOX Compared With Gemcitabine on Quality of Life in Patients With Metastatic Pancreatic Cancer: Results From the PRODIGE 4/ACCORD 11 Randomized Trial (2012)

FOLFIRINOX significantly reduces QoL impairment compared with gemcitabine in patients with metastatic pancreatic cancer. Furthermore, baseline QoL scores improved estimation of survival probability when added to baseline clinical and demographic variables.
Proportion split sort (1996)

This paper introduces a new sorting algorithm called PROPORTION SPLIT SORT. The algorithm splits a sequence into two blocks in the ratio of 1 : p - 1, where p is a fixed constant, then divides them into four blocks with the median of the first block such that the maximum of the left two blocks is less than or equal to the minimum of the right two blocks. Finally, we perform the sorting of the left two blocks and the right two blocks separately. The worst case number of comparisons of this sorting algorithm is bounded by 1/log(2p/(2p - 1))n log n for p > 1. In our simulation, when p = 2, the average number is close to n log n - 1.2n, and for some p (e.g. p = 16), this algorithm is faster than CLEVER QUICKSORT which is referred to as the fastest sorting algorithm.
Prolonged Antibiotic Prophylaxis After Cardiovascular Surgery and Its Effect on Surgical Site Infections and Antimicrobial Resistance (2000)

Our findings confirm that continuing ABP beyond 48 hours after CABG surgery is still widespread; however, this practice is ineffective in reducing SSI, increases antimicrobial resistance, and should therefore be avoided.
Humoral and Cellular Immune Responses to Yersinia pestis Infection in Long-Term Recovered Plague Patients (2011)

Plague is one of the most dangerous diseases and is caused by Yersinia pestis. Effective vaccine development requires understanding of immune protective mechanisms against the bacterium in humans. In this study, the humoral and memory cellular immune responses in plague patients (n = 65) recovered from Y. pestis infection during the past 16 years were investigated using a protein microarray and an enzyme-linked immunosorbent spot assay (ELISpot). The seroprevalence to the F1 antigen in all recovered patients is 78.5%. In patients infected more than a decade ago, the antibody-positive rate still remains 69.5%. There is no difference in the antibody presence between gender, age, and infected years, but it seems to be associated with the F1 antibody titers during infection (r = 0.821; P < 0.05). Except F1 antibody, the antibodies against LcrV and YopD were detected in most of the patients, suggesting they could be the potential diagnostic markers for detecting the infection of F1-negative strains. Regarding cellular immunity, the cell number producing gamma interferon (IFN-γ), stimulated by F1 and LcrV, respectively, in vitro to the peripheral blood mononuclear cells of 7 plague patients and 4 negative controls, showed no significant difference, indicating F1 and LcrV are not dominant T cell antigens against plague for a longer time in humans. Our findings have direct implications for the future design and development of effective vaccines against Y. pestis infection and the development of new target-based diagnostics.
A wavelet clustering technique for the identification of functionally connected regions in the rat brain using resting state fMRI (2012)

This work presents a new data-driven method for the identification of functionally connected regions in the rat brain, using agglomerative clustering based on the discrete wavelet transform (DWT). The proposed approach is evaluated on resting state fMRI data and no a priori assumptions about the distribution of the signals or anatomical ROIs are made. The coefficients of the DWT are used as features in the clustering algorithm, and the performance of the classifier is evaluated as the capability to produce clusters that best correlate with known anatomical regions in the sensorimotor cortex of the brain. Wavelet features that best represent salient characteristics in the spectrum of the voxel signals are found to produce best clustering results.
A Nanomesoporous Catalyst from Modified Red Mud and Its Application for Methane Decomposition to Hydrogen Production (2016)

A type of nanomesoporous modified red mud (MRM) catalyst was prepared and utilized for catalytic methane decomposition (CMD) to produce hydrogen. The modification process significantly simplified the mineral composition of the red mud (RM); in the meantime, the physical and chemical structure of RM was changed. TEM images suggested that MRM was a kind of nanomesoporous material assembled by a number of uniformly nanoscale particles, BET results showed that the pore size distributions of MRM were ranged from 3 to 12 nm, and the specific surface area and total pore volumes of red mud improved from 8.00 m 2 /g and 0.08 cm 3 /g to 190.61 m 2 /g and 0.39 cm 3 /g, respectively. The catalytic performance of the catalysts has been tested at 800°C; the results showed that MRM exhibited much higher activity and stability than RM for CMD.
Object databases in a distributed scientific workflow application (2002)

The construction of large scientific experiments (such as the Compact Muon Solenoid experiment being undertaken for CERN) necessitates the use of complex production management operations, often distributed over many geographically separated research institutes. These workflow operations are often only loosely-defined at the outset of the construction and can evolve rapidly as the results of experiments are analysed. Existing commercial workflow management systems are largely based on relational database management systems (RDBMSs) and are unable to cope with the requirements of such scientific workflow environments and, in particular, with the dynamic schema evolution which results from the rapidly evolving scientific workflow definitions. This paper reports on the requirements for object repositories in the implementation of a prototype scientific workflow management system entitled CRISTAL (Cooperating Repositories and an Information System for Tracking Assembly Lifecycles) and considers issues surrounding data duplication between object repositories and scientific workflow management in CRISTAL.
Scale for the assessment and rating of ataxia (2006)

The Scale for the Assessment and Rating of Ataxia is a reliable and valid measure of ataxia, making it an appropriate primary outcome measure for clinical trials.
Over‐expression of hsp70 confers tumorigenicity to mouse fibrosarcoma cells (1995)

Over-expression of the major heat-shock protein hsp70 in WEHI-S tumor cells renders them resistant to the cytotoxic effects of tumor necrosis factor (TNF). To study the significance of this resistance in vivo, the tumorigenic potential of WEHI-S cells transfected with human hsp70 in sense and anti-sense orientation was investigated in athymic and in normal syngenic mice. A striking correlation was observed between the level of hsp70 expression and tumorigenicity in athymic mice. Hsp70 expression rendered WEHI cells tumorigenic also in normal mice, but higher numbers of cells were required for tumor formation than in athymic mice. Over-expression of hsp70 in WEHI-S cells did not enhance their anchorage-dependent growth in vitro or their ability to form colonies in soft agar. The hsp70-transfected cells exhibited greatly increased resistance against killing by murine natural cytotoxic cells and macrophages in vitro. A similar tumorigenic phenotype could also be induced independently of hsp70 by prolonged culture of WEHI-S cells with TNF. These results suggest that over-expression of hsp70 increases the tumorigenic potential of WEHI-S cells in mice, by allowing these cells to escape from the early TNF-mediated anti-tumor immune surveillance.
Asymptomatic left ventricular dysfunction: an overlooked part of the continuum of heart failure. (2002)

Over 4.7 million Americans have heart failure, and 50000 new cases of heart failure are diagnosed every year. In addition, a significant proportion of the population may have asymptomatic left ventricular (LV) systolic dysfunction. Population studies estimate that the prevalence of asymptomatic LV dysfunction ranges from 0.9-5.9%. Of these, a substantial number will eventually develop symptomatic heart failure. Diagnosing and treating these patients before they develop symptoms may help to delay or prevent the development of symptomatic heart failure. This review highlights the currently available data on the epidemiology, pathophysiology, diagnosis, and treatment of asymptomatic LV systolic dysfunction.
Pharmacokinetics of Levodopa (1984)

Departments of Neurology and Pharmacology, and Biochemistry, Oregon Health Sciences University, Portland, Oregon
Reactions of [RhCl(diene)]2with Bi- and Terdentate Nitrogen Ligands. X-ray Structures of Five-Coordinate Complexes (1997)

Reaction of [RhCl(diene)]2 (diene = 1,5-cyclooctadiene (COD) or bicyclo[2.2.1] hepta-2,5-diene (NBD)) with the N−N−N nitrogen ligands 2,6-(C(R1)N−R2)2C5H3N in CD2Cl2 or CH2Cl2 yielded the five-coordinate complexes [RhCl(2,6-(C(H)N−R2)2C5H3N)(diene)] (diene = NBD; R2 = i-Pr, t-Bu, and p-anisyl), which has been isolated for NBD but not for COD. A single-crystal X-ray determination showed that [RhCl(2,6-(C(H)N−p-anisyl)2C5H3N)(NBD)] has a distorted trigonal bipyramidal configuration with the pyridyl N-atom, one imine N-atom, and one alkene double bond in the equatorial plane, while the second alkene bond and the chloride atom occupy the axial positions. This conformation containing one noncoordinated imine moiety is clearly retained at 183 K in CD2Cl2, as is also the case for the other complexes. For the COD complexes, the reaction is more complicated, as the intermediates that are observed depend on the substituents R1 and R2 of the N−N−N nitrogen ligand. The five-coordinate complexes [RhCl(2,6-(C(R1)N−R2)2C5H3N)(COD)] could be observed at low temperatures for R1 = H and R2 = i-Pr, t-Bu, and p-anisyl, while for R1 = Me and R2 = p-anisyl, this intermediate could not be observed; instead, [Rh(2,6-(C(Me)N−p-anisyl)2C5H3N)2]+Cl- was found, which shows the presence of one N−N−N ligand bonded as a bidentate ligand and one N−N−N ligand bonded as a terdentate ligand at low temperatures. Further reaction of [Rh(2,6-(C(Me)N−p-anisyl)2C5H3N)2]+Cl- with [RhCl(COD)]2 afforded [RhCl(2,6-(C(Me)N−p-anisyl)2C5H3N)] and subsequently, via oxidative addition of CD2Cl2, the complex [RhCl2(CD2Cl)(2,6-(C(Me)N−p-anisyl)2C5H3N)]. The dynamic properties of the five-coordinate diene complexes [RhCl(2-(C(H)N−R2)-6-(Me)C5H3N)(NBD)] (R2 = i-Pr, t-Bu, and p-anisyl), which contain N−N nitrogen ligands, and of the new complexes [Rh(2-(C(H)N−R2)-6-(Me)C5H3N)(NBD)]OTf (R2 = i-Pr, t-Bu, and p-anisyl) and of [Rh(2,2‘-bipyrimidine)(NBD)]OTf have been investigated. A single-crystal X-ray determination of [RhCl(2-(C(H)N−i-Pr)-6-(Me)C5H3N)(NBD)] showed structural features which are analogous to those of [RhCl(2,6-(C(H)N−p-anisyl)2C5H3N)(NBD)].
A Comprehensive Approach to the Recognition, Diagnosis, and Severity-Based Treatment of Focal Hyperhidrosis: Recommendations of the Canadian Hyperhidrosis Advisory Committee (2007)

These guidelines offer a rapid method to assess disease severity and to treat primary focal hyperhidrosis according to severity.