gebhart/patrepeval huggingface dataset:
Molecular and Functional Characterization of Gap Junctions in the Avian Inner Ear (2006)

To analyze the fundamental role of gap junctions in the vertebrate inner ear, we examined molecular and functional characteristics of gap junctional communication (GJC) in the auditory and vestibular system of the chicken. By screening inner ear tissues for connexin isoforms using degenerate reverse transcription-PCR, we identified, in addition to chicken Cx43 (cCx43) and the inner-ear-specific cCx30, an as yet uncharacterized connexin predicted to be the ortholog of the mammalian Cx26. In situ hybridization indicated that cCx30 and cCx26 transcripts were both widely expressed in the cochlear duct and utricle in an overlapping pattern, suggesting coexpression of these isoforms similar to that in the mammalian inner ear. Immunohistochemistry demonstrated that cCx43 was present in gap junctions connecting supporting cells of the basilar papilla, in which its immunofluorescence colocalized with that of cCx30. However, cCx43 was absent from supporting cell gap junctions of the utricular macula. This variation in the molecular composition of gap junction plaques coincided with differences in the functional properties of GJC between the auditory and vestibular sensory epithelia. Fluorescence recovery after photobleaching, adapted to examine the diffusion of calcein in inner ear explants, revealed asymmetric communication pathways among supporting cells in the basilar papilla but not in the utricular macula. This study supports the hypothesis that the coexpression of Cx26/Cx30 is unique to gap junctions in the vertebrate inner ear. Furthermore, it demonstrates asymmetric GJC within the supporting cell population of the auditory sensory epithelium, which might mediate potassium cycling and/or intercellular signaling.
Measurement of prostate-specific membrane antigen in the serum with a new antibody (1996)

Work to date has identified prostate-specific membrane antigen (PSMA) as a membrane-bound glycoprotein with high specificity for prostatic epithelial cells. PSMA reacts with the monoclonal antibody 7E11.C5, which is present in serum, seminal fluid, and prostatic epithelial cells, and is increased in its expression in the presence of a hormone refractory state associated with prostatic cancer. This report confirms these results and further documents the presence of the monoclonal antibody 3F5.4G6, which reacts with the extracellular domain of PSMA. This region of PSMA is also an element present in a truncated version of the protein, so-called PSM'. Immune precipitation with either 7E11.C5 or 3F5.4G6 yields an isolated protein species that are reactive with the reciprocal antibody in Western blot analysis. Thus, 3F5.4G6 recognizes the same PSMA protein as does 7E11.C5, but at different epitopes on essentially opposite ends of the molecule. These two antibodies are well suited for use in a sandwich immunoassay, either one as a capture or detection antibody. Current work on this is underway. This report also confirms that 7E11.C5 Western blots for PSMA are negative with normal human brain tissue. The monoclonal antibody 9H10 does not react with 3F5.4G6 or with 7E11.C5 in studies conducted herein. Moreover, 3F5.4G6 reacts with PSMA found in the LNCaP cell line, but not DU-145 or PC3, which lack PSMA.
Electropolymerization kinetics of a binary mixture of pyrrole and o‐aminobenzoic acid and characterization of the obtained polymer films (2008)

Abstract Poly (pyrrol‐ co ‐ o ‐aminobenzoic acid) has been synthesized electrochemically from an aqueous acid medium. The initial rate of electrocopolymerization reaction on platinum electrode is small and the rate law is: Rate = K 2 [D] 1.02 [HCl] 1.44 [M] 2.00 . The apparent activation energy ( E a ) is found to be 90.11 kJ mol −1 . The polymer films obtained have been characterized by cyclic voltammetry, X‐ray diffraction, elemental analysis, thermogravimetric analysis, scanning electron microscopy, 1 H NMR, and IR‐spectroscopy. The mechanism of the electrochemical polymerization reaction has been discussed. The monomer reactivity ratios ( r 1 and r 2 ) were calculated. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Biomarkers in lupus nephritis (2015)

Lupus nephritis (LN) has significant impact on the outcome of patients with systemic lupus erythematosus (SLE). In the absence of any new breakthrough for management of LN over the last few years, using existing treatment modalities in a more effective manner is the mainstay of improving outcomes. For effectively using the drugs, disease activity needs to be assessed accurately and more objectively, which is not possible with present clinical assessment tools. Biomarkers help in accurate assessment of disease activity and enable the physician to individualize the therapy. Conventional disease activity markers have limitations which need to be addressed and research in the area of biomarker discovery in LN has immensely expanded over the last two decades as evident by the literature. Moreover, biomarkers for LN should be different from the markers of overall disease activity as LN requires significant immunosuppression, unlike other non-renal manifestations of SLE. Newly discovered biomarkers exhibit qualities pertaining to different aspects of disease activity and damage. In this review, we discuss the established as well as new biomarkers of SLE in the light of their role in LN diagnosis, follow-up, prediction of renal flare and correlation with renal histology findings.
Hydrogen Production under Aerobic Conditions by Membrane-Bound Hydrogenases from Ralstonia Species (2008)

Studies have been carried out to establish the ability of O2-tolerant membrane-bound [NiFe] hydrogenases (MBH) from Ralstonia sp. to catalyze H2 production in addition to H2 oxidation. These hydrogenases are not noted for H2-evolution activity, and this is partly due to strong product inhibition. However, when adsorbed on a rotating disk graphite electrode the enzymes produce H2 efficiently, provided the H2 product is continuously removed by rapidly rotating the electrode and flowing N2 through the gastight electrochemical cell. Electrocatalytic H2 production proceeds with minimal overpotentiala significant observation because lowering the overpotential (the electrochemically responsive activation barrier) is seen as crucial in developing small-molecule catalysts for H2 production. A mutant having a high KM for H2 oxidation did not prove to be a better H2 producer relative to the wild type, thus suggesting that weak binding of H2 does not itself confer a tendency to be a H2 producer. Inhibition by H2 is much stronger than inhibition by CO and, most significantly, even O2. Consequently, H2 can be produced sustainably in the presence of O2 as long as the H2 is removed continuously, thereby proving the feasibility for biological H2 production in air.
Inverse electrocardiographic imaging to assess electrical dyssynchrony in cardiac resynchronization therapy patients (2012)

Electrical dyssynchrony is postulated to be one of the main factors contributing to non-response of patients to cardiac resynchronization therapy (CRT). We applied inverse epicardial imaging computed from patient-specific geometry and body-surface potential recordings to assess global and regional electrical dyssynchrony. Patients were imaged pre- and post-device implantation, without and with pacing function (P-OFF and P-ON). The reconstructed maps of activation in the dyssynchronous pre-CRT rhythm agree with published contact mapping activation maps with earliest activation starting on the RV free wall and slowly spreading to the LV in a U-shaped pattern. The new ΔQRSi metric captures global pre-CRT dyssynchrony showing negative values (−0.32±0.10) with minimal variability beats (coefficient of variation 10±3.6%) while post-CRT pacing indicates positive values (0.18±0.11). The imaging method is well-suited to study electrical dyssynchrony and potentially guide CRT lead placement.
New Response Evaluation Criteria in Solid Tumors (RECIST) Guidelines for Advanced Non–Small Cell Lung Cancer: Comparison With Original RECIST and Impact on Assessment of Tumor Response to Targeted Therapy (2010)

RECIST 1.1 provided almost perfect agreement in response assessment after erlotinib therapy compared with RECIST 1.0. Assessment with PET/CT was a major factor that influenced the difference in best response assessment between RECIST 1.1 and RECIST 1.0.
Ultra-high-speed wavelength conversion in a silicon photonic chip (2011)

We have successfully demonstrated all-optical wavelength conversion of a 640-Gbit/s line-rate return-to-zero differential phase-shift keying (RZ-DPSK) signal based on low-power four wave mixing (FWM) in a silicon photonic chip with a switching energy of only ~110 fJ/bit. The waveguide dispersion of the silicon nanowire is nano-engineered to optimize phase matching for FWM and the switching power used for the signal processing is low enough to reduce nonlinear absorption from two-photon-absorption (TPA). These results demonstrate that high-speed wavelength conversion is achievable in silicon chips with high data integrity and indicate that high-speed operation can be obtained at moderate power levels where nonlinear absorption due to TPA and free-carrier absorption (FCA) is not detrimental. This demonstration can potentially enable high-speed optical networks on a silicon photonic chip.
High electron mobility in modulation-doped Si/SiGe quantum well structures (1991)

Modulation-doped multiple quantum well structures based on Si/SiGe have been grown by molecular beam epitaxy. Low-temperature electron mobilities up to 17 000 cm2/V s have been achieved in narrow Si quantum wells. The electronic properties of the strain symmetrized Si/SiGe multilayer structures were studied by magnetotransport and cyclotron resonance experiments. The results are consistent with subband calculations which take the strain-induced splitting of the conduction band and the lowering of two valleys into account.
The Relationship Between Reduction in Periodontal Inflammation and Diabetes Control: A Report of 9 Cases (1992)

The established correlation between diabetes and periodontal diseases and the increasing prevalence of Type II diabetes in the general population indicate that dental practitioners will probably treat an increasing number of diabetic patients. Despite the fact that there is little scientific evidence to support the concept, it has been generally accepted that treatment for periodontal disease in diabetic patients may reduce insulin requirements and improve metabolic balance. However, to date no one has evaluated the effects of periodontal therapy on the metabolic state of the poorly-controlled diabetic patient. The purpose of this pilot study was to evaluate the effect of controlling gingival inflammation on blood glucose levels as determined by glycosylation of hemoglobin and albumin.
DFG-out Mode of Inhibition by an Irreversible Type-1 Inhibitor Capable of Overcoming Gate-Keeper Mutations in FGF Receptors (2014)

Drug-resistance acquisition through kinase gate-keeper mutations is a major hurdle in the clinic. Here, we determined the first crystal structures of the human FGFR4 kinase domain (FGFR4K) alone and complexed with ponatinib, a promiscuous type-2 (DFG-out) kinase inhibitor, and an oncogenic FGFR4K harboring the V550L gate-keeper mutation bound to FIIN-2, a new type-1 irreversible inhibitor. Remarkably, like ponatinib, FIIN-2 also binds in the DFG-out mode despite lacking a functional group necessary to occupy the pocket vacated upon the DFG-out flip. Structural analysis reveals that the covalent bond between FIIN-2 and a cysteine, uniquely present in the glycine-rich loop of FGFR kinases, facilitates the DFG-out conformation, which together with the internal flexibility of FIIN-2 enables FIIN-2 to avoid the steric clash with the gate-keeper mutation that causes the ponatinib resistance. The structural data provide a blueprint for the development of next generation anticancer inhibitors through combining the salient inhibitory mechanisms of ponatinib and FIIN-2.
IL-1 receptor antagonist and IL-1 beta production in human monocytes are regulated differently (1991)

Human monocytes may synthesize simultaneously both the agonist IL-1 beta and a specific receptor antagonist of IL-1 (IL-1ra). These studies examined whether monocyte production of these two structurally related cytokines was regulated differently. IL-1ra and IL-1 beta protein levels in cell supernatants and lysates were measured with specific ELISA. Relative steady-state mRNA levels, relative transcriptional rates as determined by the nuclear run-on technique, and mRNA stability were all assessed using specific cDNA probes. Monocytes were stimulated with LPS alone, adherent IgG, or both LPS and adherent IgG. Monocytes stimulated with LPS produced near equivalent amounts of IL-1ra and IL-1 beta proteins over 22 h; relative steady-state mRNA levels paralleled the protein levels. In addition, LPS-induced monocytes exhibited enhanced rates of transcription for both IL-1ra and IL-1 beta, in comparison to adherent control cells without LPS. mRNA half-lives in LPS-induced monocytes also were similar for IL-1ra and IL-1 beta. Monocytes cultured on adherent IgG exhibited a low level of IL-1 beta transcription with an absence of protein production. In contrast, adherent IgG led to a high and prolonged rate of IL-1ra protein production. Furthermore, monocytes cultured on adherent IgG exhibited a specific induction of IL-1ra transcription and a marked prolongation in IL-1ra mRNA stability. However, LPS in a high concentration, 1 microgram/ml, reversed the IgG induction of IL-1ra production by decreasing both transcriptional rate and mRNA stability. These results indicate that production of IL-1ra by human monocytes is characterized by different patterns of regulation in comparison with IL-1 beta. LPS induces production of both proteins whereas adherent IgG stimulates only IL-1ra production. The effects of IgG and LPS on induction of IL-1ra production in human monocytes are mediated at both transcriptional and post-transcriptional levels.
The coagulation cascade: initiation, maintenance, and regulation (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe coagulation cascade: initiation, maintenance, and regulationEarl W. Davie, Kazuo Fujikawa, and Walter KisielCite this: Biochemistry 1991, 30, 43, 10363–10370Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/bi00107a001https://doi.org/10.1021/bi00107a001research-articleACS PublicationsRequest reuse permissionsArticle Views7359Altmetric-Citations1406LEARN 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
Inventory management of repairable service parts for personal computers (1996)

Notes, in recent years, an increase of interest in the field of service parts inventory ‐ particularly in the computer industry. Explains that the computer industry is a highly competitive industry; products have to be repaired as quickly as possible, since slow repair can lead to loss of future business to competitors with better service reputations. Maintains that a good reputation is therefore closely linked to the availability of spare parts on the market. Using a real‐life case study, elaborates on the management and control of service‐parts inventory and gives a brief overview of the contemporary literature on the subject. Presents the solution approach adopted and the results of the study, which indicate that significant savings can be realized through good management of service‐parts inventory.
Comparison of analog and digital nanosystems: Issues for the nano-architect (2008)

Improvements in manufacturing and assembly of novel devices such as the carbon nanotube (CNT) and semiconductor nanowires has led to the exploration of new nano-architectures utilizing such devices for applications such as general purpose computing, image processing etc. This paper discusses different possible nanoscale implementations of cellular neural networks (CNN). It is seen that while an analog nanoscale implementation of the CNN may be difficult with self-assembly based approaches given the requirements for customization of devices and arbitrary routing, a digital equivalent may be realizable in the near term. One such digital CNN design based on the NASIC nanoscale fabric is shown. A specialized architecture for CNN with resonant tunneling diodes (RTD) is also discussed.
Multielectrode spiral cuff for selective stimulation of nerve fibres (1992)

In this paper we present the modelling, design, and initial experimental testing of a nerve cuff multielectrode system for selective stimulation of fibres in superficial peripheral nerve trunk regions which is capable of making a selective activation of multiple muscles. The developed multielectrode nerve cuff consists of 14 platinum stimulating electrodes embedded within a self-curling sheet of biocompatible insulation, exhibiting a spiral transverse cross-section. The spiral shape of the system is such that the number of stimulating electrodes which can be utilized depends on the diameter of the stimulated nerve. Nerves with a greater diameter automatically make use of more electrodes than thin ones. The development was based on results obtained by a histological examination of the peripheral nerves which were planned to be stimulated, and on models of excitation of myelinated nerve fibres. The modelling objectives were to determine the electric field that would be generated within a nerve trunk by a specific electrode. Moreover, the extent of initial excitation of the nerve fibres within the superficial region of the dog sciatic nerve elicited by a certain discrete stimulating electrode was predicted. For this purpose a calculation of activating function for six positions where the nerve fibres were supposed to lie within the longitudinally dissected sciatic nerve was performed. In two acute experiments on the sciatic nerve of the dog the objective was to characterize the effectiveness of the multielectrode system in monopolar selective stimulation of the superficial regions, innervating the gastrocnemius and tibialis anterior muscle. A selectivity preliminary tested by measuring the myoelectric activity of the gastrocnemius and tibialis anterior muscle after 2 months showed good results in both animals.
Differential expression analysis for sequence count data (2010)

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation (2015)

Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation.
Antibody Response in Individuals Infected with Avian Influenza A (H5N1) Viruses and Detection of Anti‐H5 Antibody among Household and Social Contacts (1999)

The first documented outbreak of human respiratory disease caused by avian influenza A (H5N1) viruses occurred in Hong Kong in 1997. The kinetics of the antibody response to the avian virus in H5N1-infected persons was similar to that of a primary response to human influenza A viruses; serum neutralizing antibody was detected, in general, >/=14 days after symptom onset. Cohort studies were conducted to assess the risk of human-to-human transmission of the virus. By use of a combination of serologic assays, 6 of 51 household contacts, 1 of 26 tour group members, and none of 47 coworkers exposed to H5N1-infected persons were positive for H5 antibody. One H5 antibody-positive household contact, with no history of poultry exposure, provided evidence that human-to-human transmission of the avian virus may have occurred through close physical contact with H5N1-infected patients. In contrast, social exposure to case patients was not associated with H5N1 infection.
Whole Genome Sequence of the Rifamycin B-Producing Strain Amycolatopsis mediterranei S699 (2011)

Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic, rifamycin B. Semisynthetic derivatives of rifamycin B are used for the treatment of tuberculosis, leprosy, and AIDS-related mycobacterial infections. Here, we report the complete genome sequence (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.
Climbing the Branches of the Strigolactones Pathway One Discovery at a Time (2010)

Branching habit is intrinsic to every higher plant species. Consider, for example, a pine tree ( Pinus spp.) and an oak tree ( Quercus spp.). Although the characteristic architecture of each species is mainly determined by genetics, the sessile nature of plants demands a high degree of plasticity.
Characterization of a Factor VII Molecule Carrying a Mutation in the Second Epidermal Growth Factor-like Domain (1998)

A missense mutation at codon 100 in the second epidermal growth factor-like domain, resulting in Gln100-->Arg, was detected in 19 out of 21 available severely factor VII (FVII) deficient patients in Norway. Seventeen patients were homozygous, and the two remaining were compound heterozygotes. In the homozygous patients, FVII antigen was measured to 10-28%, and activity to 0.6-6.5% of that in normal pooled plasma. Recombinant FVII containing the mutation was expressed transiently in CHO cells to a mean antigen level of 57% of the wild type FVII protein, and with a specific activity of 6% of wild type. The mutant protein had a 14-fold reduction in affinity for tissue factor (TF), whereas binding of FX seemed unaffected. In line with the experimental data, molecular modelling of the mutation based on the coordinates of the tissue factor/FVIIa complex showed that substituting arginine for glutamine disrupts the interface between the catalytic and second epidermal growth factor-like domains.