gebhart/patrepeval huggingface dataset:
The human Bloom syndrome gene suppresses the DNA replication and repair defects of yeastdna2mutants (2003)

Bloom syndrome is a disorder of profound and early cancer predisposition in which cells become hypermutable, exhibit high frequency of sister chromatid exchanges, and show increased micronuclei. BLM, the gene mutated in Bloom syndrome, has been cloned previously, and the BLM protein is a member of the RecQ family of DNA helicases. Many lines of evidence suggest that BLM is involved either directly in DNA replication or in surveillance during DNA replication, but its specific roles remain unknown. Here we show that hBLM can suppress both the temperature-sensitive growth defect and the DNA damage sensitivity of the yeast DNA replication mutant dna2-1. The dna2-1 mutant is defective in a helicase-nuclease that is required either to coordinate with the crucial Saccharomyces cerevisiae (sc) FEN1 nuclease in Okazaki fragment maturation or to compensate for scFEN1 when its activity is impaired. We show that human BLM interacts with both scDna2 and scFEN1 by using coimmunoprecipitation from yeast extracts, suggesting that human BLM participates in the same steps of DNA replication or repair as scFEN1 and scDna2.
A Direct Measurement of the Terrestrial Mass Accretion Rate of Cosmic Dust (1993)

The mass of extraterrestrial material accreted by the Earth as submillimeter particles has not previously been measured with a single direct and precise technique that samples the particle sizes representing most of that mass. The flux of meteoroids in the mass range 10(-9) to 10(-4) grams has now been determined from an examination of hypervelocity impact craters on the space-facing end of the Long Duration Exposure Facility satellite. The meteoroid mass distribution peaks near 1.5 x 10(-5) grams (200 micrometers in diameter), and the small particle mass accretion rate is (40 +/- 20) x 106 kilograms per year, higher than previous estimates but in good agreement with total terrestrial mass accretion rates found by geochemical methods. This mass input is comparable with or greater than the average contribution from extraterrestrial bodies in the 1-centimeter to 10-kilometer size range.
The enhancement of wordspotting techniques (2005)

This paper presents results of research on the enhancement of speaker independent wordspotting in conversational, telephone bandwidth speech from a variety of talkers. The research involved the comparison of five LPC based parameter sets (filter coefficients, autocorrelation coefficients, cepstral coefficients, vocal tract area functions, and pseudoformants), in three levels of additive white noise, and the evaluation of two methods of noise reduction. The techniques were studied with a dynamic programming based wordspotting system. The performance of the system was measured the percent of keywords spotted with no false alarms. The results show that pseudoformants, without the use of speaker normalization or noise reduction techniques, perform as well as or better than the other parameter sets with these techniques.
Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing (2020)

The human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts encoding human leukocyte antigen (HLA) receptors as well as B cell and T cell receptors (BCR and TCR). Determining which alleles an individual possesses for each HLA gene (high-resolution HLA typing) is essential to establish donor-recipient compatibility in organ and bone marrow transplantations. In turn, the repertoires of millions of unique BCR and TCR transcripts in each individual carry a vast amount of health-relevant information. Both short-read RNA-seq-based HLA typing and BCR/TCR repertoire sequencing (AIRR-seq) currently rely on our incomplete knowledge of the genetic diversity at HLA and BCR/TCR loci. Here, we generated over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used this data set to (1) show that deep and accurate full-length cDNA sequencing can be used to provide isoform-level transcriptome analysis for more than 9000 loci, (2) generate accurate sequences of HLA alleles, and (3) extract detailed AIRR data for the analysis of the adaptive immune system. The HLA and AIRR analysis approaches we introduce here are untargeted and therefore do not require prior knowledge of the composition or genetic diversity of HLA and BCR/TCR loci.
A smooth permittivity function for Poisson–Boltzmann solvation methods (2001)

This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid-based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian-based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions.1 © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 608–640, 2001
A Noninvasive Method of Predicting Pulmonary-Capillary Wedge Pressure (1992)

These preliminary data indicate that a simple noninvasive method can accurately predict the PCWP and changes in the PCWP in response to medical therapy.
RF power amplifiers, classes A through S-how they operate, and when to use each (2002)

With at least ten lettered classes of RF power amplifiers, and several combinations of those classes, it is not surprising that many RF engineers are confused about power amplifiers. The complexity of the subject is compounded by the fact that the RF power transistor acts either as a high-resistance current source or as a low-resistance switch, or -in some amplifiers-as a high-resistance current source during part of the "on" interval and as a low-resistance switch during another part of the "on" interval ("mixed-mode" operation. Inspection ofthe circuit topology is not sufficient to define unambiguously the transistor operating mode or the amplifier class of operation. Examples are given of the same circuit topology operating as a Class B, C, or E amplifier, depending on how the transistor is biased and driven, and on the specific L-R-C values in the load network. Modes of operation and applications of each type of amplifier are discussed.
Analysis of side-chain organization on a refined model of charybdotoxin: structural and functional implications (1992)

The spatial organization of side chains on a refined model of charybdotoxin is presented. First, the structural role of two groups of well-defined, low-accessible side chains (Thr3, Val5, Val16, Leu20, Cys33 and Leu20, His21, Thr23, Cys17, Cys35) is discussed. These side chains are conserved in three out of the five known scorpion toxins acting on K+ channels. Interestingly, they are not conserved in scyllatoxin which presents a slightly different secondary structure organization. Second, the spatial organization of all positively charged residues is analyzed. Comparison with the results presented by Park and Miller [(1992) Biochemistry (preceding paper in this issue)] shows that all functionally important positive residues are located on the beta-sheet side of the toxin. These results are different from those obtained by Auguste et al. [(1992) Biochemistry 31, 648-654] on scyllatoxin, which blocks a different type of K+ channel. This study shows, in fact, that functionally important positive residues are located on the helix side of the toxin. Thus, charybdotoxin and scyllatoxin, which present the same global fold, interact with two different classes of K+ channels by two different parts of the motif.
Analysis of the resistance mediated by several R-factors to Tetracycline and Minocycline (1972)

SUMMARY The resistance levels conferred by the T-determinants in four R-factors to Tetracycline and Minocycline in cells of Escherichia coli K 12, before and after induction of maximum resistance by treatment with sub-inhibitory concentrations of the drugs, are measured by simple growth-and-challenge tests. The effect of a plasmid T K which confers tetracycline resistance on its host Klebsiella aerogenes is tested in the same way. The five T-determinants fall into a high-level and a low-level group for resistance, the former giving 3- to 4-fold higher resistance in both induced and uninduced cells than the latter. The T-determinants all confer much lower resistance to Minocycline (a tetracycline molecule modified at the C-6 and C-7 positions) than to Tetracycline. The main cause of this difference is that cells carrying a T-determinant exclude Minocycline much less efficiently than Tetracycline, but in addition Minocycline is less effective than Tetracycline in inducing increased resistance. These results are discussed in the light of a model put forward to explain the inducible nature of R-factor resistance to the tetracyclines.
Cell-Free Extracts from Mammalian Oocytes Partially Induce Nuclear Reprogramming in Somatic Cells1 (2009)

Nuclear transfer has been regarded as the only reliable tool for studying nuclear reprogramming of mammalian somatic cells by oocytes. However, nuclear transfer is not well suited for biochemical analyses of the molecular mechanisms of reprogramming. A cell-free system from oocytes is an attractive alternative way to mimic reprogramming in vitro, since a large number of cells can be treated and analyzed. Nevertheless, a cell-free system using oocytes has not been developed in mammals. Here, cell extracts from porcine oocytes were prepared and their ability to induce nuclear reprogramming was evaluated. Extracts from metaphase II (MII) oocytes erased the machinery for regulating gene expression in reversibly permeabilized somatic cells. For example, the extracts caused histone deacetylation and the disappearance of TATA box-binding protein from the nuclei. However, MII-extract-treated cells did not show any obvious changes after cell culture. In contrast, extracts from germinal vesicle (GV) oocytes activated pluripotent marker genes, especially NANOG, and induced partial dedifferentiation after cell culture. The activation of pluripotent marker genes by GV extracts was associated with histone acetylation that was induced during extract treatment. These results indicate that GV- and MII-oocyte extracts have different roles on nuclear reprogramming. Furthermore, both oocyte extracts induced site-specific demethylation in the upstream region of NANOG. These results indicate that cell-free extracts derived from GV- and MII-oocytes could be useful for studying the mechanisms involved in nuclear reprogramming.
Botulinum Neurotoxin a Blocks Synaptic Vesicle Exocytosis but Not Endocytosis at the Nerve Terminal (1999)

The supply of synaptic vesicles in the nerve terminal is maintained by a temporally linked balance of exo- and endocytosis. Tetanus and botulinum neurotoxins block neurotransmitter release by the enzymatic cleavage of proteins identified as critical for synaptic vesicle exocytosis. We show here that botulinum neurotoxin A is unique in that the toxin-induced block in exocytosis does not arrest vesicle membrane endocytosis. In the murine spinal cord, cell cultures exposed to botulinum neurotoxin A, neither K(+)-evoked neurotransmitter release nor synaptic currents can be detected, twice the ordinary number of synaptic vesicles are docked at the synaptic active zone, and its protein substrate is cleaved, which is similar to observations with tetanus and other botulinal neurotoxins. In marked contrast, K(+) depolarization, in the presence of Ca(2+), triggers the endocytosis of the vesicle membrane in botulinum neurotoxin A-blocked cultures as evidenced by FM1-43 staining of synaptic terminals and uptake of HRP into synaptic vesicles. These experiments are the first demonstration that botulinum neurotoxin A uncouples vesicle exo- from endocytosis, and provide evidence that Ca(2+) is required for synaptic vesicle membrane retrieval.
Fabrication of highly ordered metallic nanowire arrays by electrodeposition (2001)

Highly ordered hexagonal arrays of parallel metallic nanowires (Ni, Bi) with diameters of about 50 nm and lengths up to 50 μm were synthesized by electrodeposition. Hexagonal-close-packed nanochannel anodized aluminum oxide film was used as the deposition template. The deposition was performed in an organic bath of dimethylsulfoxide with metal chloride as the electrolyte. A high degree of ordering and uniformity in these arrays can be obtained with this technique by fine-tuning the electrodeposition parameters. Moreover, an unprecedentedly high level of uniformity and control of the wire length was achieved. The arrays are unique platforms for explorations of collective behavior in coupled mesoscopic systems, and are useful for applications in high-density data storage, field emission displays, and sensors.
S-3-Amino-phthalimido-glutarimide inhibits angiogenesis and growth of B-cell neoplasias in mice. (2002)

Thalidomide has recently been shown to be useful in the treatment of multiple myeloma and may also be useful in the treatment of other hematological malignancies. We have identified a new derivative of thalidomide, S-3-[3-amino-phthalimido]-glutarimide (S-3APG) with dual activity against B-cell neoplasias. S-3APG was able to directly inhibit the proliferation of myeloma and Burkitt's lymphoma cell lines in vitro without showing toxicity to normal bone marrow stromal cells or hematopoietic progenitor cells. In vivo, S-3APG treatment of drug resistant myeloma cell tumors in mice was able to produce complete and sustained regressions without any observed toxicity. Additionally, S-3APG induced complete regressions of Burkitt's lymphoma cell tumors. Furthermore, S-3APG inhibited angiogenesis more potently than thalidomide in the murine corneal micropocket model. We conclude that S-3APG is a powerful anti-myeloma and anti-B-cell-lymphoma agent that has both antiproliferative and antiangiogenic effects.
The Neutralization of Type I IFN Biologic Actions by Anti-IFNAR-2 Monoclonal Antibodies Is Not Entirely Due to Inhibition of Jak-Stat Tyrosine Phosphorylation (2000)

A panel of monoclonal antibodies (mAb) derived against human interferon-alpha/beta receptor-2 (IFNAR-2) was evaluated for their ability to antagonize the biologic effects of type 1 interferons (IFN-alpha1, IFN-alpha2a, and IFN-beta). Anti-IFNAR-2 mAb 117.7, 35.9, 53.2, and 51.44 neutralized type I IFN-mediated antiviral, antiproliferative, and major histocompatibility complex (MHC) class I upregulation functions. However, only mAb 51.44 neutralized IFN-alpha2a and IFN-beta-mediated natural killer (NK) cell cytotoxicity. In BIAcore and cell binding studies, only mAb 51.44 and 234.28 inhibited IFN-alpha2a and IFN-beta binding to its receptor. The receptor blockade by mAb 51.44 and 234.28 resulted in the inhibition of IFN-alpha2a and IFN-beta-induced tyrosine phosphorylation of Jak1, Tyk2, Stat1/2/3, and IFNAR-1/2 and inhibition of IFN-stimulated gene factor 3 (ISGF3) formation. mAb 117.7, 35.9, and 53.2, although antagonists of IFN's biologic activities, did not block the binding of IFN-alpha/beta to its receptor. The 117.7 mAb, representative of this class of receptor nonblocking mAb, induced hyper-tyrosine phosphorylation of IFNAR-2 in the presence of IFN-alpha/beta but did not inhibit IFN-alpha/beta-induced Jak-Stat tyrosine phosphorylation and ISGF3 complex formation. These results show that the neutralization of type I IFN biologic actions by anti-IFNAR-2 mAb cannot be entirely explained by inhibition of Jak-Stat tyrosine phosphorylation.
The Berkeley Lower Extremity Exoskeleton (2005)

The first functional load-carrying and energetically autonomous exoskeleton was demonstrated at the University of California, Berkeley, walking at the average speed of 1.3m∕s(2.9mph) while carrying a 34kg(75lb) payload. Four fundamental technologies associated with the Berkeley lower extremity exoskeleton were tackled during the course of this project. These four core technologies include the design of the exoskeleton architecture, control schemes, a body local area network to host the control algorithm, and a series of on-board power units to power the actuators, sensors, and the computers. This paper gives an overview of one of the control schemes. The analysis here is an extension of the classical definition of the sensitivity function of a system: the ability of a system to reject disturbances or the measure of system robustness. The control algorithm developed here increases the closed-loop system sensitivity to its wearer’s forces and torques without any measurement from the wearer (such as force, position, or electromyogram signal). The control method has little robustness to parameter variations and therefore requires a relatively good dynamic model of the system. The trade-offs between having sensors to measure human variables and the lack of robustness to parameter variation are described.
Cloning and sequence analysis of the gene encoding 3-hexulose-6-phosphate synthase from the methylotrophic bacterium, Methylomonas aminofaciens 77a, and its expression in Escherichia coli (1996)

A DNA fragment of 550 bp was specifically amplified by PCR with primers based on the N-terminal sequence of the purified 3-hexulose-6-phosphate synthase from Methylomonas aminofaciens 77a and on that of a lysyl endopep(idase-derived peptide. Using this PCR product as a probe, a gene coding for 3-hexulose-6-phosphate synthase in M. aminofaciens 77a chromosomal DNA was cloned in Escherichia coli JM109. Sequencing analysis revealed that the gene encoding 3-hexulose-6-phosphate synthase contained a 624-bp open reading frame, encoding a protein composed of 208 amino acid residues with a calculated relative molecular mass of 21 224.
G Protein-Coupled Receptor Fusion Proteins in Drug Discovery (2004)

A wide range of peptides and polypeptides can be appended to either the N- or C-terminus of G protein-coupled receptors without disrupting substantially ligand binding and signal transduction. Following fusion of fluorescent proteins, reporter gene constructs or G protein alpha subunits to the C-terminal tail of a receptor high content and G protein activation assays can be employed to identify agonist ligands. Further modification of the receptor fusions to introduce enhanced levels of constitutive activity and to physically destabilise the protein allows antagonist/inverse agonists screens to be developed in parallel. Equivalent C-terminal addition of pairs of complementary, non-functional, polypeptide fragments allows the application of enzyme complementation techniques. Introduction of N-terminal tags to receptors has also allowed the introduction of novel assay techniques based on a pH-sensitive cyanine dye. These have the capacity to overcome certain limitations of GPCR-fluorescent protein fusions.
Genetics of Type 1 Diabetes (2011)

Children with the HLA-risk genotypes DR3/4-DQ8 or DR4/DR4 who have a family history of type 1 diabetes have more than a 1 in 5 risk for developing islet autoantibodies during childhood, and children with the same HLA-risk genotype but no family history have approximately a 1 in 20 risk. Determining extreme genetic risk is a prerequisite for the implementation of primary prevention trials, which are now underway for relatives of individuals with type 1 diabetes.
Diamond/Ir/SrTiO 3 : A material combination for improved heteroepitaxial diamond films (1999)

Heteroepitaxial diamond films with highly improved alignment have been realized by using the layer sequence diamond/Ir/SrTiO3(001). In a first step, epitaxial iridium films with a misorientation &amp;lt;0.2° have been deposited on polished SrTiO3(001) surfaces by electron-beam evaporation. Using the bias-enhanced nucleation procedure in microwave plasma chemical vapor deposition, epitaxial diamond grains with a density of 109 cm−2 could be nucleated on these substrates. The orientation relationship for this layer system is diamond(001)[100]∥Ir(001)[100]∥SrTiO3(001)[100]. The polar and azimuthal spread for the crystal orientation of a 600 nm thick diamond film is about 1° in each case. For an 8 μm thick diamond film a significantly improved alignment of 0.34° (polar) and 0.65° (azimuthal) has been measured. The latter values, which to the best of our knowledge are superior to those of all former reports about epitaxial diamond films on alternative substrates, indicate the high potential of the substrate Ir/SrTiO3 for the realization of large-area single-crystalline diamond films.
Rolling Ball Viscometer (1943)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRolling Ball ViscometerRobert Hubbard and George BrownCite this: Ind. Eng. Chem. Anal. Ed. 1943, 15, 3, 212–218Publication Date (Print):March 1, 1943Publication History Published online1 May 2002Published inissue 1 March 1943https://pubs.acs.org/doi/10.1021/i560115a018https://doi.org/10.1021/i560115a018research-articleACS PublicationsRequest reuse permissionsArticle Views906Altmetric-Citations59LEARN 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 options Get e-Alerts
Mutation analysis and association studies of the UCHL1 gene in German Parkinsonʼs disease patients (2000)

Recently, an Ile93Met substitution has been identified in the ubiquitin carboxy-terminal hydrolase L1 (UCHL1) gene in a single German PD family with autosomal dominant inheritance. To determine whether mutations in the UCHL1 gene are causative for Parkinson's disease (PD) a detailed mutation analysis was performed in a large sample of German sporadic and familial PD patients. We found no disease-causing mutation in the coding region of the UCHL1 gene. Direct sequencing revealed six intronic polymorphisms in the UCHL1 gene. Analysis of an S18Y polymorphism in exon 3 of the UCHL1 gene in sporadic PD patients and controls showed carriers of allele 2 (tyrosine) significantly less frequent in patients with a reduced risk of 0.57 (CI = 0.36-0.88; p = 0.012, p(c) = 0.047, chi2 = 6.31). Our study shows that sequence variations in the coding region of UCHL1 are a rare event. A protective effect of a certain UCHL1 variant in the pathogenesis of sporadic PD is suggested, underlining the relevance of UCHL1 in neurodegeneration.