gebhart/patrepeval huggingface dataset:
Parallel testing of several genes (panel-testing) in patients with ectodermal dysplasia using next-generation sequencing (2012)

Ectodermal dysplasia (ED) is a group of syndromes characterized by abnormalities of structures of ectodermal origin. Up to now more than 150 different syndromes are known. Affected ectodermal structures are mainly hair, teeth, nails and sweat glands. ED can be classified by mode of inheritance (autosomal dominant, autosomal recessive and X-linked), by additional clinical symptoms (e.g. facial abnormalities) or by the structures involved. Hypohidrotic or “classical” ED (HED) is caused by mutations in the genes EDA, EDAR and EDARADD. Mutations in the X-linked EDA gene underlie most cases. EDAR and EDARADD are known to be associated with both autosomal dominant and autosomal recessive forms of HED. As many ED forms show overlapping clinical phenotypes, often many genes have to be analyzed to identify the causative mutation in a patient, therefore Sanger sequencing frequently takes several months and is laborious and cost-intensive. We have designed an accurate and fast molecular test for the 6 most common ED genes using next-generation sequencing. We developed a novel PCR-based protocol on a Roche 454 Junior platform for mutation screening of the genes EDA, EDAR, EDARADD, TP63, GJB6 and WNT10A. The verification and validation process was finished in October 2011, and the “ED panel” is now the routine diagnostic test for ED in our institute. During the last months several mutations in different genes could be identified with this method. A definitive diagnosis could be made rapidly in a number of so far „unsolved cases”. In summary, the next generation sequencing approach has the potential to increase the diagnostic sensitivity by expanding the number of genes that can be screened in parallel while also reducing expenditure of time and costs.
An Open Standard Software Library for High-Performance Parallel Signal Processing: the Parallel VSIPL++ Library (2004)

Real-time signal processing consumes the majority of the world’s computing power. Increasingly, programmable parallel processors are used to address a wide variety of signal processing applications (e.g. scientific, video, wireless, medical, communication, encoding, radar, sonar and imaging). In pro-grammable systems the major challenge is no longer hardware but software. Specifically, the key technical hurdle lies in allowing the user to write programs at high level, while still achieving performance and preserving the portability of the code across parallel computing hardware platforms. The Parallel Vector, Signal, and Image Processing Library (Parallel VSIPL++) addresses this hurdle by providing high level C++ array constructs, a simple mechanism for mapping data and functions onto parallel hardware, and a community-defined portable interface. This paper presents an overview of the Parallel VSIPL++ standard as well as a deeper description of the technical foundations and expected performance of the library. Parallel VSIPL++ supports adaptive optimization at many levels. The C++ arrays are designed to support automatic hardware specialization by the compiler. The computation objects (e.g. Fast Fourier Transforms) are built with explicit setup and run stages to allow for run-time optimization. Parallel arrays and functions in VSIPL++ support these same features, which are used to accelerate communication operations. The parallel mapping mechanism provides an external interface that allows optimal mappings to be generated off-line and read into the system at run-time. Finally, the standard has been developed in collaboration with high performance embedded computing vendors and is compatible with their proprietary approaches to achieving performance.
A lattice model for segmental orientation in deformed polymeric networks. 2. Effect of chain stiffness and thermotropic interactions (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA lattice model for segmental orientation in deformed polymeric networks. 2. Effect of chain stiffness and thermotropic interactionsIvet Bahar, Burak Erman, Andrzej Kloczkowski, and James E. MarkCite this: Macromolecules 1990, 23, 26, 5341–5346Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/ma00228a006https://doi.org/10.1021/ma00228a006research-articleACS PublicationsRequest reuse permissionsArticle Views68Altmetric-Citations25LEARN 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
Antigenic mapping and characterization of Albumin Binding Protein (2010)

Adult females of Leptoconops (Brachyconops) californiensis Wirth & Atchley and 1 female of Leptoconops (Holoconops) sp. near knowltoni were collected from 5 species of lizards in desert sand dune habitats in San Bernardino and Riverside counties, California, and northern Sonora, Mexico. Feeding by L. californiensis was observed on the dorsum (usually the heads) of the lizards, with up to 6 L. californiensis on a host at 1 time. The L. sp. near knowltoni appeared to be trying to feed but did not contain blood. Midges fed during calm, warm daylight periods from March through October. Reptile feeding by Ceratopogonidae is reviewed.
A New Cloning Method for the Preparation of Long Repetitive Polypeptides without a Sequence Requirement (2002)

We describe and illustrate a new cloning method for the production of long, size-controlled DNA concatemers, which can be expressed as protein polymers without an amino acid sequence requirement. Synthetic genes encoding different numbers of repeats of the amino acid sequence -(Gly-Lys-Gly-Ser-Ala-Gln-Ala)3- were constructed using this cloning technique. The method enables the production of extremely long synthetic genes (e.g., up to 48 DNA repeats, 3024 bp), in a highly controlled fashion by providing higher-order multimers via the reconcatemerization of pre-multimerized genes and also eliminates the specific sequence requirement of the DNA monomer for restriction endonuclease cleavage. Moreover, the effect of intramolecular cyclization, which has a high probability of occurring during the self-ligation reaction and prevents the cloning of long DNA concatemers, is minimized by this approach. DNA multimers encoding a ladder of four differently sized protein polymers (6, 12, 24, and 48 repeats of a 63-bp segment) were expressed in E. coli upon induction with IPTG. Two of the resulting proteins, composed of 277 and 529 amino acid monomers, and each comprising a 10X histidine tag, were purified by immobilized metal affinity chromatography. During the course of the work, the sequence of the DNA concatemers was analyzed and confirmed to be correct by capillary electrophoresis, and the obtainment of the desired protein polymers was confirmed by MALDI−TOF mass spectrum analysis and amino acid compositional analysis. The resultant protein polymers are shown by CD to adopt a random-coil conformation in aqueous solution and to be water-soluble between 20 and 95 °C. This polymer has lysine residues spaced evenly along the polymer backbone, which can be utilized either as derivatizable groups or as cross-linking sites for tissue engineering applications.
Body-mass index and all-cause mortality: individual-participant-data meta-analysis of 239 prospective studies in four continents (2016)

UK Medical Research Council, British Heart Foundation, National Institute for Health Research, US National Institutes of Health.
RNA Polymerase IV Directs Silencing of Endogenous DNA (2005)

Plants encode subunits for a fourth RNA polymerase (Pol IV) in addition to the well-known DNA-dependent RNA polymerases I, II, and III. By mutation of the two largest subunits (NRPD1a and NRPD2), we show that Pol IV silences certain transposons and repetitive DNA in a short interfering RNA pathway involving RNA-dependent RNA polymerase 2 and Dicer-like 3. The existence of this distinct silencing polymerase may explain the paradoxical involvement of an RNA silencing pathway in maintenance of transcriptional silencing.
COCORP seismic profiles near Coalinga, California: Subsurface structure of the western Great Valley (1984)

Research Article| May 01, 1984 COCORP seismic profiles near Coalinga, California: Subsurface structure of the western Great Valley Eric Fielding; Eric Fielding 1Department of Geological Sciences, Cornell University, Ithaca, New York 14853 Search for other works by this author on: GSW Google Scholar Muawia Barazangi; Muawia Barazangi 1Department of Geological Sciences, Cornell University, Ithaca, New York 14853 Search for other works by this author on: GSW Google Scholar Larry Brown; Larry Brown 1Department of Geological Sciences, Cornell University, Ithaca, New York 14853 Search for other works by this author on: GSW Google Scholar Jack Oliver; Jack Oliver 1Department of Geological Sciences, Cornell University, Ithaca, New York 14853 Search for other works by this author on: GSW Google Scholar Sidney Kaufman Sidney Kaufman 1Department of Geological Sciences, Cornell University, Ithaca, New York 14853 Search for other works by this author on: GSW Google Scholar Geology (1984) 12 (5): 268–273. https://doi.org/10.1130/0091-7613(1984)12<268:CSPNCC>2.0.CO;2 Article history first online: 01 Jun 2017 Cite View This Citation Add to Citation Manager Share Icon Share MailTo Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation Eric Fielding, Muawia Barazangi, Larry Brown, Jack Oliver, Sidney Kaufman; COCORP seismic profiles near Coalinga, California: Subsurface structure of the western Great Valley. Geology 1984;; 12 (5): 268–273. doi: https://doi.org/10.1130/0091-7613(1984)12<268:CSPNCC>2.0.CO;2 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract COCORP seismic reflection profiles collected in 1977 on the west side of the San Joaquin Valley near Coalinga in southern California provide information on the Cenozoic and Mesozoic structures in the subsurface of the western Great Valley. The data show evidence of significant normal faulting during the Cretaceous, when this part of California was the site of a forearc basin. Neogene compression, probably associated with transform motion on the nearby San Andreas fault system, may be reactivating these pre-existing faults in a reverse sense and causing the active folding of the southern Coast Ranges. The recent Coalinga earthquake sequence that began on May 2, 1983, appears to correspond to movement on the high-angle reverse fault within the basement that is inferred from the COCORP lines. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Semi-automatic matching of OCT and IVUS images for image fusion (2008)

Medical imaging is essential in the diagnosis of atherosclerosis. In this paper, we propose the semi-automatic matching of two promising and complementary intravascular imaging techniques, Intravascular Ultrasound (IVUS) and Optical Coherence Tomography (OCT), with the ultimate goal of producing hybrid images with increased diagnostic value for assessing arterial health. If no ECG gating has been performed on the IVUS and OCT pullbacks, there is typically an anatomical shuffle (displacement in time and space) in the image sequences due to the catheter motion in the artery during the cardiac cycle, and thus, this is not possible to perform a 3D registration. Therefore, the goal of our work is to detect semi-automatically the corresponding images in both modalities as a preprocessing step for the fusion. Our method is based on the characterization of the lumen shape by a set of Gabor Jets features. We also introduce different correction terms based on the approximate position of the slice in the artery. Then we train different support vector machines based on these features to recognize these correspondences. Experimental results demonstrate the usefulness of our approach, which achieves up to 95% matching accuracy for our data.
Secretion of α-Amylase from <i>Pseudoalteromonas haloplanktis</i> TAB23: Two Different Pathways in Different Hosts (2002)

Secretion of cold-adapted alpha-amylase from Pseudoalteromonas haloplanktis TAB23 was studied in three Antarctic bacteria. We demonstrated that the enzyme is specifically secreted in the psychrophilic hosts even in the absence of a protein domain that has been previously reported to be necessary for alpha-amylase secretion in Escherichia coli. The occurrence of two different secretion pathways in different hosts is proposed.
PERCEPTUAL, MOTOR AND ATTENTIONAL DEFICITS IN SWEDISH PRIMARY SCHOOL CHILDREN. SOME CHILD PSYCHIATRIC ASPECTS (1983)

One hundred and forty-one seven-year-old children took part in an extensive neuropsychiatric study. Eight-two of these children had been selected and sampled from a group of 3448 children for whom questionnaires concerning motor control, perception and attention/behaviour had been completed by pre-school teachers. They all showed pre-school signs of both attention deficit and motor/perception dysfunction. The fifty-nine remaining children had been randomly sampled from the group of 3448 children to serve as controls. The study was carried out in a blind fashion. The present paper reports on results of the neuropsychiatric study with special regard to psychiatric disorders in so-called MBD syndromes, defined in accordance with operational criteria. Prevalence figures for marked psychiatric abnormality in MBD were shown to be higher than for psychiatric abnormality in children with 'neuroepileptic' disorders in the Isle of Wight study. Psychotic behaviour was found to be specifically associated with MBD. Hereditary and neuropathogenic factors singly or together possibly caused the 'MBD handicap'. Non-optimal psychosocial factors appear to interact with the MBD syndrome in the moulding of psychiatric disorders.
[The effect on gastric secretion and the anti-ulcer action of imidazo[1,2-A]benzimidazole derivatives]. (1990)

The experiments on rats showed that of 16 studied imidazo [1,2-a]benzimidazole derivatives only the compounds with phenyl at the second carbon atom and nitrogen-containing radical of the ninth nitrogen atom inhibit the gastric acid secretion. The binding of oxymethyl group to phenyl, its substitution through adamantyl, displacement of nitrogen-containing substitute to the first nitrogen atom or its substitution were found to decrease or stop the inhibiting action of these substances on the gastric parietal cells. Dihydrochloride 2-phenyl-9 (beta-diethyl-aminoethyl)imidazo [1,2-a]denzimidazole was more potent than cimetidine and omeprazole in inhibiting the gastric acid secretion, pepsin output and antiulcer action.
Pummerer reaction of 2-vinylcyclopropyl sulfoxides: generation and reactions of butadienylthionium ion intermediates (1998)

Generation of butadienylthionium ions in the Pummerer reactions of 2-vinylcyclopropyl sulfoxides has been investigated. Although the Pummerer reactions of 2-vinylcyclopropyl sulfoxides 1 are complicated, benzothiazinone derivatives 10 smoothly react with trifluoroacetic anhydride to give 1,3-dienes in good yields. The reactions proceed via butadienylthionium ions by proton abstraction from the 2′-methyl group or the cyclopropane ring. Reactions of disubstituted benzothiazinones 10e–h provided cyclic dienes while treatment of mono- or un-substituted derivatives gave acyclic conjugated dienes 11a–d. 2-Vinylcyclopropyl sulfoxides 1 and 10 were prepared by MCPBA oxidation of the corresponding 2-vinylcyclopropyl sulfides 19 and 23, respectively, which were obtained by cyclopropanation of α-chloro sulfides with 1,3-dienes via the 5,6-dihydro-2H-thiopyranium intermediate 22.
Cathodoluminescence study of GaAs quantum wells and of submicron dots fabricated by magnetron reactive ion etching (1997)

Cathodoluminescence has been employed to investigate the luminescence and lateral transport properties of excited carriers at 8 K in GaAs-AlGaAs quantum well material and in submicron features fabricated in this material by magnetron reactive ion etching. A carrier diffusion length of 0.85±0.04 μm in quantum wells and a surface recombination velocity (5.4±0.8)×103 m/s at etched sidewalls were measured. Also, the effect of feature size on luminescence efficiency was examined and compared with model calculations using the measured values of diffusion length and surface recombination velocity.
Application de l'oxydoréduction Détermination de la pollution organique des eaux, mesure de la demande chimique en oxygène (2004)

International audience
ChemInform Abstract: 4‐Functionally Substituted 3‐Hetarylpyrazoles. Part 6. 1,3‐Diaryl‐4‐isocyanatopyrazoles. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
O-006 Pharmaco-mechanical clot disruption using a balloon infusion wire in an acute rabbit common carotid artery thromboembolic occlusion model (2011)

Purpose Recanalization using intra-arterial fibrinolytic therapy in combination with mechanical clot disruption may be a more effective strategy for early reestablishment of cerebral blood flow in acute ischemic stroke. To validate our hypothesis, we evaluated a prototype balloon infusion wire (NeuroInterventions, Pittsburgh Pa) for delivering rtPA directly within the clot and compared its performance with the HyperGlide compliant balloon (eV3 Neurovascular, Irvine, CA) and microcatheter directed rtPA infusion in a rabbit common carotid artery (CCA) thromboembolic occlusion model. Materials and Methods New Zealand white rabbits (n=7) were selected for this work due to their similar response to rtPA as in humans. They were anesthetized and >50% luminal stenosis of the CCA was created bilaterally with 3-0 silk suture. Allogenic clot was injected through a 6F guide catheter and lodged consistently in the CCA proximal to the stenosis (arrows, A). The stenosis was released one hour post clot injection allowing sufficient time for clot-vessel lumen interaction. DSA was performed bilaterally to confirm the occlusion and assess the Thrombolysis in Cerebral Infarction (TICI) score. Each vessel was assigned to receive the device, balloon angioplasty, or microcatheter directed rtPA. The negative control group received no therapy. The primary endpoint was flow restoration. The secondary endpoint was time to recanalization and vascular safety, which was assessed by histological response on luminal scanning electron microscopy (SEM) and H&E staining. An assessment of the vascular safety from controlled operation of the infusion device and balloon occlusion in unembolized rabbit CCA was also made. Results We successfully created consistent thromboembolic occlusions with TICI 0 flow at the predetermined location within the CCA. The balloon infusion wire achieved an earlier recanalization with a TICI 2B score (B, 2D perfusion post MTT) in 14 min requiring 2.8 mg rtPA. In comparison, microcatheter directed rtPA achieved TICI 2B score in 29 min requiring 4 mg rtPA. Balloon angioplasty, when used alone, achieved an inferior TICI 2A final recanalization score in 20 min post treatment and often failed to recanalize the CCA. Histomorphometry and luminal SEM evaluation revealed that the operation of the infusion device is comparable to balloon angioplasty with endothelial cell denudation and an exposure of the internal elastic lamina, an acceptable level of disruption for mechanical revascularization devices. Conclusion Combined pharmaco-mechanical disruption achieves a high recanalization grade with a lower thombolytic dose more rapidly in comparison to either therapy (balloon angioplasty and thrombolysis) used alone. Abstract O-006 Figure 1
The sensitivity of bladder wash flow cytometry, bladder wash cytology, and voided cytology in the detection of bladder carcinoma (1987)

The sensitivity of voided urinary cytology (VUC), bladder wash cytology (BWC), and bladder wash flow cytometry (BWFCM) in detecting cancer was studied in 70 patients with biopsy-proven bladder tumors. There were 11 Grade I papillomas, 14 Grade II TA, 18 Grade II-III TIS, 19 Grade II-III T1, and eight Grade II-III T2 carcinomas. One to five VUCs per patient (mean, 2.63) were obtained within the 24 hours preceding biopsy. At endoscopy a bladder wash specimen was obtained and divided for cytologic and flow cytometric examinations. For all tumor categories combined, the sensitivity for one, two, and three voided cytology examinations per patient was 41%, 41%, and 60%, respectively. The sensitivity of a single BWC was 61%, of a single BWFCM, 83%. Thus, one BWFCM is more sensitive than three VUC (binomial test; P = 0.006); one BWC is more sensitive than two VUC (P = 0.01); and one BWFCM is more sensitive than one BWC (P = 0.003). These findings remain significant when papillomas are excluded from the analysis (P less than or equal to 0.03) and when papillomas and T2 tumors are jointly excluded (P less than or equal to 0.02). Only four of 70 patients (6%) had their cancers detected by VUC and/or BWC rather than BWFCM. In summary, irrigation cytology specimens are more sensitive than voided urinary cytology, and bladder wash flow cytometry is more sensitive than either in diagnosing bladder cancer. Flow cytometry is more sensitive because of the better sampling of bladder irrigation compared with voided urine and because of the measurement technique itself.