gebhart/patrepeval huggingface dataset:
Uncoupling of the <i>recBC</i> ATPase from DNase by DNA Crosslinked with Psoralen (1972)

Exonucleolytic cleavage of DNA by the recBC DNase is accompained by a DNA-dependent ATP hydrolysis that ceases when the DNA that has been digested to a limit. On the other hand, DNA that has been crosslinked by 4,5',8-trimethylpsoralen in the presence of 360-nm light remains an effective cofactor in the ATPase reaction, but is resistant to digestion by the enzyme. Psoralentreated DNA is degraded by pancreatic DNase, micrococcal nuclease, and Escherichia coli B restriction enzyme, but not by Neurospora crassa nuclease, suggesting that crosslinking did not grossly distort the duplex structure of the DNA. The psoralen-DNA is not a potent inhibitor, but competes with single-stranded DNA from bacteriophage fd for the recBC DNase to roughly the same extent as does normal duplex DNA. DNA treated with psoralen in the dark, exposed to 360-nm light in the absence of psoralen, or treated with the intercalating agents ethidium bromide, 9-aminoacridine, ICR-191, or actinomycin D, responds to the enzyme no differently from untreated DNA. However, DNA crosslinked with mitomycin C or nitrogen mustard behaves similarly to psoralen-treated DNA. The relationship of these findings to models for the function and control of the recBC ATPase and nuclease, and the advantages of psoralen as a DNA crosslinking agent, are discussed.
Mucopolysaccharidosis type VI (MPS VI) and molecular analysis: Review and classification of published variants in the<i>ARSB</i>gene (2018)

Maroteaux-Lamy syndrome (MPS VI) is an autosomal recessive lysosomal storage disorder caused by pathogenic ARSB gene variants, commonly diagnosed through clinical findings and deficiency of the arylsulfatase B (ASB) enzyme. Detection of ARSB pathogenic variants can independently confirm diagnosis and render genetic counseling possible. In this review, we collect and summarize 908 alleles (201 distinct variants, including 3 polymorphisms previously considered as disease-causing variants) from 478 individuals diagnosed with MPS VI, identified from literature and public databases. Each variant is further analyzed for clinical classification according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results highlight the heterogeneity of ARSB alleles, with most unique variants (59.5%) identified as missense and 31.7% of unique alleles appearing once. Only 18% of distinct variants were previously recorded in public databases with supporting evidence and clinical significance. ACMG recommends publishing clinical and biochemical data that accurately characterize pathogenicity of new variants in association with reporting specific alleles. Variants analyzed were sent to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), and MPS VI locus-specific database (http://mps6-database.org) where they will be available. High clinical suspicion coupled with diagnostic testing for deficient ASB activity and timely submission and classification of ARSB variants with biochemical and clinical data in public databases is essential for timely diagnosis of MPS VI.
Analog microwave photonic link based on a high power directly modulated laser, a high power photodiode and passive impedance matching (2012)

International audience
Some chemical and biological studies on an exotoxin from Bacillus thuringiensis var. thuringiensis Berliner (1969)

Research Article| August 01 1969 Some chemical and biological studies on an exotoxin from Bacillus thuringiensis var. thuringiensis Berliner R P M Bond; R P M Bond 1‘Shell’ Research Ltd., Milstead Laboratory of Chemical Enzymology, Sittingbourne, Kent Search for other works by this author on: This Site PubMed Google Scholar C B C Boyce; C B C Boyce 1‘Shell’ Research Ltd., Milstead Laboratory of Chemical Enzymology, Sittingbourne, Kent Search for other works by this author on: This Site PubMed Google Scholar V K Brown; V K Brown 1‘Shell’ Research Ltd., Milstead Laboratory of Chemical Enzymology, Sittingbourne, Kent Search for other works by this author on: This Site PubMed Google Scholar J D Tipton J D Tipton 1‘Shell’ Research Ltd., Milstead Laboratory of Chemical Enzymology, Sittingbourne, Kent Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1969) 114 (1): 1P. https://doi.org/10.1042/bj1140001Pa Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation R P M Bond, C B C Boyce, V K Brown, J D Tipton; Some chemical and biological studies on an exotoxin from Bacillus thuringiensis var. thuringiensis Berliner. Biochem J 1 August 1969; 114 (1): 1P. doi: https://doi.org/10.1042/bj1140001Pa Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1969 The Biochemical Society1969 Article PDF first page preview Close Modal You do not currently have access to this content.
Cytokinin from Soluble RNA of <i>Escherichia coli</i> : 6-(3-Methyl-2-butenylamino)-2-methylthio-9-β-D-ribofuranosylpurine (1968)

We have isolated a compound responsible for the cytokinin activity of soluble RNA from Escherichia coli. The structure, indicated as 6-(3-methyl-2-butenylamino)-2-methylthio-9-beta-D-ribofuranosylpurine, C(16)H(23)N(5)0(4)S, on the basis of low-and high-reso!ution mass spectrometry, was established by unequivocal synthesis. The mass spectra, chromatographic behavior, and ultraviolet spectra of the compounds from natural and synthetic sources were identical.
Detection of mitochondrial fission with orientation‐dependent optical Fourier filters (2011)

We utilize a recently developed optical imaging method based on Fourier processing with Gabor-like filters to detect changes in light scattering resulting from alterations in mitochondrial structure in endothelial cells undergoing apoptosis. Imaging based on Gabor filters shows a significant decrease in the orientation of subcellular organelles at 60 to 100 minutes following apoptosis induction and concomitant with mitochondrial fragmentation observed by fluorescence. The optical scatter changes can be detected at low resolution at the whole cell level. At high resolution, we combine fluorescence imaging of the mitochondria with optical Fourier-based imaging to demonstrate that the dynamic decrease in organelle orientation measured by optical Gabor filtering is spatially associated with fluorescent mitochondria and remains largely absent from nonfluorescent subcellular regions. These results provide strong evidence that the optical Gabor responses track mitochondrial fission during apoptosis and can be used to provide label-free, rapid monitoring of this morphological process within single cells.
Reduction of abstinence induced withdrawal and craving using nicotine replacement therapy (2006)

Rationale Decreasing withdrawal and craving during smoking cessation is a major aim of cessation medications. Prior studies have shown that Nicotine Replacement Therapy (NRT) decreases withdrawal symptom severity but have relied on retrospective reports and lacked robust measures of baseline symptoms or symptoms during unmedicated abstinence. Objectives and methods We tested the effect of high-dose (35 mg) nicotine patch on withdrawal and craving during abstinence using real-time assessment with electronic diaries during ad libitum smoking, a brief period of experimentally directed trial abstinence, and the first 3 days of cessation. Subjects were 324 smokers randomized to high-dose nicotine patches or placebo. Results Treatment with active patches reduced withdrawal and craving during cessation and completely eliminated deprivation-related changes in affect or concentration. Conclusion High-dose NRT reduces withdrawal symptoms and craving and can eliminate some symptoms entirely.
Fragger: a protein fragment picker for structural queries (2018)

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.
The effect of Mach number on the stability of a plane supersonic wake (1990)

Recent interest in supersonic combustion and problems of transatmospheric flight has prompted renewed research efforts in laminar–turbulent free-shear flow transition. In the present work, the influence of Mach number on the stability of supersonic planar wake flows is investigated to gain insight into the physics of linear, nonlinear, and three-dimensional (3-D) stages of transition. The effect of varying the relative phase difference between a fundamental instability mode and its subharmonic is investigated as a possible means of controlling the evolution of a wake. From a linear stability analysis, it is found that the influence of increasing Mach number is stabilizing, resulting in a growth rate at a Mach number of 3 which is 60% that of an incompressible wake. Direct numerical simulations of the time-dependent compressible Navier–Stokes equations in two and three dimensions are performed for a forced time-developing wake using a spectral collocation method. The results of the two-dimensional (2-D) simulations show the slow rollup of spanwise vortices at high Mach numbers that is attributed to the influence of baroclinic and dilatational effects. Finally, the results of three-dimensional simulations forced with the most unstable Kelvin–Helmholtz wave and a pair of oblique three-dimensional waves show that, depending on the initial phasing between the 2-D and 3-D waves, vortex loops may or may not form as a result of the interaction between the streamwise and spanwise vorticity.
Trypanosoma brucei prenylated-protein carboxyl methyltransferase prefers farnesylated substrates (2002)

Carboxyl methylation of the C-terminal prenylated cysteine, which occurs in most farnesylated and geranylgeranylated proteins, is a reversible step and is implicated in the regulation of membrane binding and cellular functions of prenylated proteins such as GTPases. The gene coding for prenylated-protein carboxyl methyltransferase (PPMT) of the protozoan parasite Trypanosoma brucei has been cloned and expressed in the baculovirus/Sf9 cell system. The protein of 245 amino acids has 24-28% sequence identity to the orthologues from other species including human and Saccharomyces cerevisiae. Methyltransferase activity was detected in the membrane fraction from Sf9 cells infected with the recombinant baculovirus using N -acetyl- S -farnesylcysteine (AFC) and S -adenosyl[ methyl -(3)H]methionine ([(3)H]AdoMet) as substrates. Recombinant T. brucei PPMT prefers AFC to N -acetyl- S -geranylgeranylcysteine (AGGC) by 10-50-fold based on the V (max)/ K (m) values. Native PPMT activity detected in the membrane fraction from T. brucei procyclics displays similar substrate specificity ( approximately 40-fold preference for AFC over AGGC). In contrast, mouse liver PPMT utilizes both AFC and AGGC as substrates with similar catalytic efficiencies. Several cellular proteins of the T. brucei bloodstream form were shown to be carboxyl methylated in a cell-free system. Incorporation of [(3)H]methyl group from [(3)H]AdoMet into most of the proteins was significantly inhibited by AFC but not AGGC at 20 microM, suggesting that T. brucei PPMT acts on farnesylated proteins in the cell. Cells of the T. brucei bloodstream form show higher sensitivity to AFC and AGGC (EC(50)=70-80 microM) compared with mouse 3T3 cells (EC(50)>150 microM).
Über die Veresterung von Glycerinaldehyd‐diethylacetal mit einigen Aminosäuren (1982)

On the Esterification of Glyceraldehyde Diethyl Acetal with Some Amino Acids Glyceraldehyde diethylacetal was selectively esterified in the 2‐ and 3‐position, respectively, by several Z‐amino acids. Attempts to remove the protective groups usually result in hydrogenolytic or hydrolytic cleavage of the ester bond.
The pharmacology of batrachotoxin. 3. Effect on the heart Purkinje fibers. (1971)

The effects of batrachotoxin (BTX) on the electrogenic properties of Purkinje fibers isolated from the dog heart were studied with intracellular techniques. BTX caused a depolarization of the Purkinje fiber membrane and in a few cases the membrane potential reached values of +20 mV. Application of anodal hyperpolarizing current, 1 mM Na-sucrose solution or tetrodotoxin to the Purkinje fiber previously depolarized by BTX, restored the membrane potential to values similar to control conditions. High extracellular calcium concentration prolonged the time course of the BTX effect but did not prevent it. Prior to the onset of membrane depolarization, BTX caused an increase in the duration of the plateau and negative afterpotential of the action potential. Simultaneous with the depolarization induced by BTX, a decremise in the upstroke velocity and overshoot of the spike potential occurred together with an increase in the rate of depolarization during the diastolic interval. When the membrane was depolarized to values less than -20 mV. excitability was lost. These effects of BTX on heart Purkinje fibers were antagonized by tetrodotoxin. The results raise the possibility of the existence of functionally different sodium channels. It is concluded that BTX acts on the heart Purkinje fiber to selectively increase sodium permeability.
Sialic acid methylation refines capillary electrophoresis laser‐induced fluorescence analyses of immunoglobulin G <i>N</i>‐glycans of ovarian cancer patients (2014)

Alterations in IgG N-glycosylation coincide with the development of a number of diseases including cancer and could potentially be used as diagnostic markers. CE-LIF of 8-aminopyrene-1,3,6-trisulfonic acid labeled N-glycans is a well-established rapid method to characterize IgG N-glycans that needs only low amounts of starting material. However,sialylated N-glycans have short migration times due to their negative charge. As a result,some of them are not well resolved and co-migrate with neutral glycans. In this work, we neutralized the negative charge of sialic acids by methylation and optimized the protocol using the commercially available disialylated biantennary oligosaccharide (A2G2S2). IgGN-glycans isolated from healthy human serum were then analyzed using this method. We could demonstrate that co-migration of A2, FA2G2S1, and FA2B[3]G1S1 was prevented,which allowed an accurate quantification of these N-glycans. Finally, we investigated the IgG N-glycan profiles of patients suffering from ovarian cancer using the conventional and methylation methods.With both methods, we observed an increase of agalactosylated structures that was accompanied by a decrease in digalactosylated structures. Finally, using the methylation protocol, we could further demonstrate an increase of A2, which was technically impossible with the conventional method.
Normal distributions of thermal and vibration sensory thresholds (1998)

The distributions of sensory thresholds were estimated in a healthy population while controlling for potential covariates. Using the method of levels and the two-alternative forced choice, thermal and vibration thresholds respectively were measured in the hand and foot of 148 subjects. Age was uniformly distributed between 20 and 86 years. Independent effects of age, gender, height, and skin temperature were estimated using multiple linear regression. Parametric and nonparametric methods were used to estimate the distributions of interest. Significant age-related increases were observed for all vibration thresholds (P < 0.0001), and for thermal thresholds in the foot (P < 0.0002). Percentiles were estimated for thermal thresholds in the hand and age-adjusted continuous distributions were calculated for all other thresholds. Height was positively associated with vibration thresholds in the foot (P < 0.003), and appropriate corrections were made. Our results provide reference values for thermal and vibration sensory thresholds in a healthy population, allowing for the accurate diagnosis of disordered sensory function.
In Situ Polymerized Wicks for Passive Water Management and Humidification of Dry Gases (2009)

Abstract not Available.
A Novel Polymorphism, 70Leu/Phe, Disrupts a Consensus Leu Residue within the Leucine-rich Repeat Sequence of Platelet Glycoprotein Ibα (2002)

Platelet glycoprotein (GP) Ib/IX/V complex mediates high-shear dependent platelet activation through an interaction with the von Willebrand factor (vWF). All four subunits of the complex have a structural motif, the leucine-rich repeat (LRR) sequence, with leucines in conserved positions. Here we report a new polymorphism, Leu/Phe at residue 70 of GPIbalpha, which disrupts the consensus sequence of the LRR in the vWF binding domain. Genotype frequencies among 142 healthy Japanese subjects were 92.3%, 7.7%, and 0.0%, for the 70Leu/Leu, 70Leu/Phe, and 75Phe/Phe genotypes, respectively. Ristocetin-induced or shear-induced platelet aggregation was not significantly different between the 70Leu/Leu and 70Leu/Phe genotypes. In in vitro studies, a recombinant GPIbalpha fragment with 70Phe (L70F) as compared to that with 70Leu (WT) had low reactivity to anti-GPIbalpha monoclonal antibodies, GUR20-5 and Hip1, both of which recognize conformation-specific epitopes within the 45-kDa domain. Ristocetin-induced 125I-vWF binding to L70F, however, did not differ from that to WT.
ExonMiner: Web service for analysis of GeneChip Exon array data (2008)

ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.
Combined Parameter and Function Estimation in Heat Transfer With Application to Contact Conductance (1988)

This paper discusses parameter estimation, function estimation, and a combination of the two. An example of parameter estimation is the determination of thermal conductivity of solids from transient temperature measurements. An example of function estimation is the inverse heat conduction problem, which uses transient temperature measurements to determine the surface heat flux history. The examples used herein involve the determination of the thermal contact conductance. Two sets of very good data are analyzed. One set of steady-state data was obtained by Antonetti and Eid (1987). The other set was obtained by Moses and Johnson (1986) under transient conditions for periodic contact. Both sets of data are used to illustrate parameter, function, and combined estimation. It is demonstrated that the proposed methods are more powerful then commonly accepted methods. Many other heat transfer problems can be treated using the proposed techniques.
Cleanliness Requirements For The Air In A BRDF Facility (1990)

A method is presented for estimating the cleanliness level of the air contained in a BRDF measurement facility. The use of HEPA filters is assumed and a set of reasonable assumptions are set which provide a minimum criterion for the class of clean room required for a given minimum measurable BRDF desired. The basis of the method is the use of Rayleigh scattering theory.
Characterization of Withania somnifera Leaf Transcriptome and Expression Analysis of Pathogenesis – Related Genes during Salicylic Acid Signaling (2014)

Withania somnifera (L.) Dunal is a valued medicinal plant with pharmaceutical applications. The present study was undertaken to analyze the salicylic acid induced leaf transcriptome of W. somnifera. A total of 45.6 million reads were generated and the de novo assembly yielded 73,523 transcript contig with average transcript contig length of 1620 bp. A total of 71,062 transcripts were annotated and 53,424 of them were assigned GO terms. Mapping of transcript contigs to biological pathways revealed presence of 182 pathways. Seventeen genes representing 12 pathogenesis-related (PR) families were mined from the transcriptome data and their pattern of expression post 17 and 36 hours of salicylic acid treatment was documented. The analysis revealed significant up-regulation of all families of PR genes by 36 hours post treatment except WsPR10. The relative fold expression of transcripts ranged from 1 fold to 6,532 fold. The two families of peroxidases including the lignin-forming anionic peroxidase (WsL-PRX) and suberization-associated anionic peroxidase (WsS-PRX) recorded maximum expression of 377 fold and 6532 fold respectively, while the expression of WsPR10 was down-regulated by 14 fold. Additionally, the most stable reference gene for normalization of qRT-PCR data was also identified. The effect of SA on the accumulation of major secondary metabolites of W. somnifera including withanoside V, withaferin A and withanolide A was also analyzed and an increase in content of all the three metabolites were detected. This is the first report on expression patterns of PR genes during salicylic acid signaling in W. somnifera.
Memory, Excess & the Fictional Self (2010)

When recalling a sense of a past Self I suggest that characteristics can be identified - ones that have been discarded as well as some that are celebrated in the present moment. Acts of remembrance form the basis of this research document, where I look to explore the construction, through experience, of a person’s sense of their queer sexual Self. In exploring common links between two memories, I will look to question the possibility of being able to consciously and continuously inhabit a space where there is the possibility of recognition of something that is not entirely visible to one’s Self. Sarah Ahmed suggests in ‘Queer Phenomenology’ that ‘things become queer precisely given how bodies are touched by objects’ and frames these ‘things’ or ‘experiences’ and ‘interactions’ in the context of ‘here’, ‘there’ and ‘within’. It is this sense of queering experience that will look to challenge commonly understood notions that discuss memory as integral to the construct of Self. I will suggest that through acts of remembrance, a space is continually sought to create a space for an invisible Self - a sexual Self, a gendered Self and a Self that is not continually visible, rather, only visible in relation to Richard Dyers ‘orientation towards others’. In considering this, the emphasis will be placed upon the fluid nature of sexuality and desire and their ability to move between non-fictional, ‘real’ states of being to the socially constructed. Furthermore, parallels will be drawn between excess, Deleuzian notions of ‘vibration’. Derrida’s ‘under erasure’ will also be integral to this research chapter insofar as suggesting that our ‘secret’ Self gains meaning from its absence.