gebhart/patrepeval huggingface dataset:
Identification and cloning of amplified DNA sequences by a modified-in-gel renaturation technique: Isolation of an amplified DNA sequence from a human sarcoma. (1991)

A modified in gel renaturation technique has been developed which detects DNA sequence amplifications of ≥10-fold without prior identification of the target gene. In order to determine the sensitivity of detection and applicability of modified in gel renaturation, primary human tumor cultures and drug resistant human cell lines with identified cellular gene amplifications were assayed. The modified in gel renaturation technique was then used to screen 71 human tumor cell lines and direct tumor biopsies for amplified sequences. Particular emphasis was placed on screening cell lines derived from human melanoma and direct tumor samples from adult sarcomas. Four of 55 cell lines tested had amplification ≥10-fold of previously known cellular oncogenes. None of the 25 melanoma short term cultures tested positive by this assay. One of 16 adult sarcoma samples (a malignant fibrous histiocytoma (MFH)) tested positive for DNA sequence amplification >10-fold. The amplified DNA present in this MFH, (termed ST-23987), was not identified by Southern blot analysis with a panel of oncogene probes previously reported as amplified in other human malignancies. In order to further characterize the amplified DNA in ST-23987, DNA was subjected to in gel renaturation cloning procedures followed by PCR modified cloning. Of 55 clones isolated and analyzed, four cloned inserts (termed pMAC895, pMAC15, pMAC20, and pMAC30) were amplified between 10-to-15-fold in ST-23987DNA. Several other adult sarcomas were probed with these four clones and three other instances of amplification were identified by Southern blot analysis with probes generated from pMAC15 and pMAC30 (found in tumors ST-24609, 870141 and ST-23493). A bacteriophage lambda genomic library was constructed from DNA isolated from a ST-23493. Four clones representing ∼34 kb of the amplified domain (designated 493.1, 493.2, 493.4, and 493.5) were isolated using clones pMAC15 and pMAC30 as probes. Plasmid subclones generated from the EcoRI fragments of the amplified bacteriophage lambda clones (termed p10.5, p6.0, p5.2, p5.0, p4.7, p2.8, and p0.5) were used as probes against Northern blots of sarcoma mRNA in an attempt to identify transcribed sequences within the cloned regions of the amplification unit. The hypothesized target gene carried within the amplification unit will likely be important to the progression, diagnosis and treatment of adult sarcoma, irrespective of the target gene identity.
Corinne Bonnet, Sergio Ribichini & Dirk Steuernagel (a cura di), Religioni in contatto nel Mediterraneo antico. Modalità di diffusione e processi di interferenza. Atti del terzo colloquio su “ Le Religioni orientali nel mondo greco e romano”. Loveno di Menaggio (Como) 26-28 maggio 2006. Pise-Rome, Fabrizio Serra, 2008 (2010)

Van haeperen Françoise. Corinne Bonnet, Sergio Ribichini & Dirk Steuernagel (a cura di), Religioni in contatto nel Mediterraneo antico. Modalità di diffusione e processi di interferenza. Atti del terzo colloquio su “ Le Religioni orientali nel mondo greco e romano”. Loveno di Menaggio (Como) 26-28 maggio 2006. Pise-Rome, Fabrizio Serra, 2008. In: L'antiquité classique, Tome 79, 2010. pp. 544-545.
Prefacio (2005)

En Maruámake (territorio kogui), Sierra Nevada de Santa Marta (Cesar) Simón Te voy a decir una cosa... Tú sabes que, primeramente, por ejemplo, antes de la nueva constitución, nosotros los indígenas éramos como salvajes... pero después que se cambió constitución política en el país, ya uno reconoce como persona... digamos del país... ya se siente mejor porque ya tenemos nuestros senadores en el Congreso, ya hay alcaldes indígenas también, hay Cámara de Representantes y ya hay un espacio donde...
Autonomous Integrity Monitoring for GPS-Based Precision Landing Using Ground-Based Integrity Beacon Pseudolites (1994)

The Integrity Beacon Landing System (IBLS), developed
and tested at Stanford University, is a high integrity
solution to GPS-based Category III precision landing.
IBLS is a kinematic GPS system which incorporates
ground-based Integrity Beacon pseudolites placed under
the approach path. The large geometry change that
occurs during pseudolite overtlight ensures observability
for direct cycle ambiguity estimation. Once cycle
ambiguities have been initialized, position fixes accurate
to the centimeter level are possible. The real-time
accuracy performance of IBLS has already been
demonstrated through flight tests in a Piper Dakota.
The large number of redundant measurements resulting
from Integrity Beacon overtlight and the great precision
of carrier phase measurements provide the leverage for
receiver autonomous integrity monitoring @AIM).
Extremely tight detection thresholds may be set without
incurring high false alarm rates (preserving high
continuity). The measurement residual statistic can be
used to detect a wide specuum of fault scenarios,
including cycle slips, intentional tampering or spoofing,
and spacecraft ephemeris errors. The overall level of
IBLS system integrity as well as accuracy, continuity,
and availability is quantitatively assessed through
analysis, simulation, and flight test. Preliminary results
show that the Required Navigation Performance (RNP)
specification for Category III integrity of one undetected
failure in one billion approaches is achievable using
RAIM with Integrity Beacons. Flight tests were
performed in a Piper Dakota with purposely induced
navigation system failures to demonstrate the
effectiveness of real-time autonomous integrity
monitoring with Integrity Beacons. The results of these
experiments are discussed.
Evaluation considerations for EHR-based phenotyping algorithms: A case study for drug-induced liver injury. (2013)

Developing electronic health record (EHR) phenotyping algorithms involves generating queries that run across the EHR data repository. Algorithms are commonly assessed within demonstration studies. There remains, however, little emphasis on assessing the precision and accuracy of measurement methods during the evaluation process. Depending on the complexity of an algorithm, interim refinements may be required to improve measurement methods. Therefore, we develop an evaluation framework that incorporates both measurement and demonstration studies. We evaluate a baseline EHR phenotyping algorithm for drug induced liver injury (DILI) developed in collaboration with electronic Medical Records Genomics (eMERGE) network participants. We conduct a measurement study and report qualitative (i.e., perceptions of evaluation approach effectiveness) and quantitative (i.e., inter-rater reliability) measures. We also conduct a demonstration study and report qualitative (i.e., appropriateness of results) and quantitative (i.e., positive predictive value) measures. Given results from the measurement study, our evaluation approach underwent multiple changes including the addition of laboratory value visualization and an expanded review of clinical notes. Results from the demonstration study informed changes to our algorithm. For example, given the goal of eMERGE to identify patients who may have a genetic susceptibility to DILI, we excluded overdose patients.
On transaction boundaries in active databases: a performance perspective (1991)

A performance model designed for studying active DBMS performance issues is described. The authors present the results of simulation experiments in which system performance was studied as a function of transaction boundary semantics for varying levels of data contention, rule complexity, and data sharing between externally submitted tasks and rule management tasks. The results demonstrate that the way in which transaction boundaries are imposed can have a major impact on the performance of an active DBMS. It is therefore concluded that this aspect of rule semantics must be carefully considered at the time that rules are specified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Light-Emitting Electrochemical Cells and Solution-Processed Organic Light-Emitting Diodes Using Small Molecule Organic Thermally Activated Delayed Fluorescence Emitters (2015)

Two novel charged organic thermally activated delayed fluorescence (TADF) emitters, 1 and 2, have been synthesized. Their TADF behavior is well-supported by the multiexponential decay of their emission (nanosecond and microsecond components) and the oxygen dependence of the photoluminescence quantum yields. Spin-coated electroluminescent devices have been fabricated to make light-emitting electrochemical cells (LEECs) and organic light-emitting diodes (OLEDs). The first example of a non-doped charged small organic molecule LEEC is reported and exhibited an external quantum efficiency (EQE) of 0.39% using 2. With a multilayer architecture, a solution-processed OLED device using neat 2 as the emitting layer gave an EQE of 5.1%, the highest reported to date for a nondoped solution-processed small molecule organic TADF OLED. These promising results open up a new area in light-emitting materials for the development of low-cost TADF LEECs.
Hybrid acoustic models for distant and multichannel large vocabulary speech recognition (2013)

We investigate the application of deep neural network (DNN)-hidden Markov model (HMM) hybrid acoustic models for far-field speech recognition of meetings recorded using microphone arrays. We show that the hybrid models achieve significantly better accuracy than conventional systems based on Gaussian mixture models (GMMs). We observe up to 8% absolute word error rate (WER) reduction from a discriminatively trained GMM baseline when using a single distant microphone, and between 4-6% absolute WER reduction when using beamforming on various combinations of array channels. By training the networks on audio from multiple channels, we find the networks can recover significant part of accuracy difference between the single distant microphone and beamformed configurations. Finally, we show that the accuracy of a network recognising speech from a single distant microphone can approach that of a multi-microphone setup by training with data from other microphones.
Using Impedance Spectroscopy to Detect the Selective Sorption of Iodine by MOF ZIF-8. (2019)

Abstract not provided.
Porous Hydroxyapatite Reinforced with Collagen Protein (1996)

Porous hydroxyapatite (HAP) with certain porosity and pore size was prepared, and incorporated with bovine collagen protein. The composition and structure of the HAP was confirmed by X-Ray Diffraction (XRD) and ICP. Scanning Electron Microscopy (SEM), mechanical tests and in vitro degradation were performed. Collagen protein with low antigenicity was obtained from bovine tendon by enzyme digestion, and was then forced to fill in the HAP matrix to form composites. Scanning Electron Microscopy (SEM), Mechanical tests and in vitro degradation were performed. The test results show that first, HAP thus made has specific pore size and directions; second, mechanical properties of the composites have been markedly improved; third, the in vitro degradation rate of the composite is almost the same as and mainly controlled by the degradation rate of collagen.
mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites (2021)

Abstract Background Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease which involves multiple body systems (e.g., immune, nervous, digestive, circulatory) and research domains (e.g., immunology, metabolomics, the gut microbiome, genomics, neurology). Despite several decades of research, there are no established ME/CFS biomarkers available to diagnose and treat ME/CFS. Sharing data and integrating findings across these domains is essential to advance understanding of this complex disease by revealing diagnostic biomarkers and facilitating discovery of novel effective therapies. Methods The National Institutes of Health funded the development of a data sharing portal to support collaborative efforts among an initial group of three funded research centers. This was subsequently expanded to include the global ME/CFS research community. Using the open-source comprehensive knowledge archive network (CKAN) framework as the base, the ME/CFS Data Management and Coordinating Center developed targeted metadata collection, smart search capabilities, and domain-agnostic data integration to support data findability and reusability while reducing the barriers to sustainable data sharing. Results We designed the mapMECFS data portal to facilitate data sharing and integration by allowing ME/CFS researchers to browse, share, compare, and download molecular datasets from within one data repository. At the time of publication, mapMECFS contains data curated from public data repositories, peer-reviewed publications, and current ME/CFS network researchers. Conclusions mapMECFS is a disease-specific data portal to improve data sharing and collaboration among ME/CFS researchers around the world. mapMECFS is accessible to the broader research community with registration. Further development is ongoing to include novel systems biology and data integration methods.
Motion-Compensated FDG PET/CT for Oesophageal Cancer (2020)

Abstract PurposeRespiratory-induced motion of oesophageal tumours and lymph nodes can influence positron emission tomography/computed tomography (PET/CT). The aim was to compare standard three-dimensional (3D) and motion-compensated PET/CT regarding standardized uptake value (SUV), metabolic tumour volume (MTV) and detection of lymph node metastases. MethodsThis prospective observational study (NCT02424864) included thirty-seven newly diagnosed oesophageal cancer patients. Diagnostic PET/CT was reconstructed in 3D and motion-compensated PET/CT. MTVs of the primary tumour were calculated using an automated region-growing algorithm with SUV thresholds of 2.5 (MTV2.5) and ≥50% of SUVmax (MTV50%). Blinded for reconstruction method, a nuclear medicine physician assessed all lymph nodes showing 18 F-fluorodeoxyglucose uptake for their degree of suspicion. ResultsThe mean (95% CI) SUVmax of the primary tumour was 13.1(10.6-15.5) versus 13.0(10.4-15.6) for 3D and motion-compensated PET/CT, respectively. MTVs were also similar between the two techniques. Bland-Altman analysis showed mean differences between both measurements (95% limits of agreement) of 0.08(-3.60 - 3.75), -0.26(-2.34 – 1.82), 4.66(-29.61 – 38.92)cm 3 and -0.95(-19.9 – 18.0)cm 3 for tumour SUVmax, lymph node SUVmax, for MTV2.5 and MTV50%, respectively. Lymph nodes were classified as highly suspicious (30/34 nodes), suspicious (20/22) and dubious (66/59) for metastases on 3D/motion-compensated PET/CT. No additional lymph node metastases were found on motion-compensated PET/CT. SUVmax of the most intense lymph nodes was similar for both scans: mean (95% CI) 6.6(4.3-8.8) and 6.8(4.5-9.1) for 3D and motion-compensated, respectively.ConclusionsSUVmax of the primary oesophageal tumour and lymph nodes was comparable on 3D and motion-compensated PET/CT. The use of motion-compensated PET/CT did not improve lymph node detection. Trial registration(www.clinicaltrials.gov: NCT02424864)
Geophysical characterization of the Devonian Nisku Formation for the Wabamun area CO2 sequestration project (WASP), Alberta, Canada (2011)

Geophysical characterization of the Devonian Nisku Formation in the Wabamun area, Alberta, Canada for large-scale CO2 sequestration project has been successful in revealing two primary groups of anomalies. The first group is interpreted to be due to contrasts in lithology of the Nisku Formation. This interpretation is supported by constraints provided by well control, seismic modeling and petrophysical data. The second group is interpreted to be footprints of geological discontinuities which are induced by dissolution and karsting in a geologic formation shallower in the stratigraphy. Even though there is no evidence to indicate that the integrity of the Nisku Formation or the overlying caprock has been compromised, such geologic discontinuities should be taken into consideration if supercritical CO2 were to be injected into the Nisku Formation. The analysis has identified favorable low-impedance high-porosity locations that could be developed for a CO2 injection site. Those locations exhibit a good correlation with relatively high porosity-permeability zones of the Nisku Formation on maps derived from wireline data and core analysis using petrophysical analysis. Finally, fluid replacement modelling was undertaken to predict the feasibility of time-lapse seismic monitoring for detecting an injected CO2 plume. The results suggest that changes in seismic response will most likely be subtle and that the plume will probably be at the lower threshold of seismic detectability.
Improved lasing performance of KrCl excimer laser (1983)

A compact, small active volume (70 cc) discharge pumped KrCl laser with UV preionization is described. The results obtained show that KrCl compares well with the performance obtainable from the well established XeCl and KrF lasers. Considerably improved laser output energy density (≂2.5 J/1) is achieved at very high discharge power loadings (≂24 MW/cc), with a good power conversion efficiency (0.8%) and a long gas static lifetime. The output laser beam is reproducible and uniform with a cross section of 2×1 cm2.
Phase Change Materials by Design: How to realize fast optical switches (2018)

Phase change media utilize a remarkable property portfolio including the ability to rapidly switch between the amorphous and the crystalline state, which differ significantly in their properties. This property combination makes them very attractive for photonic applications ranging from data storage to fast optical switches, employing the pronounced difference of optical properties between the amorphous and crystalline state. This talk will discuss the origin of the unique material properties, which characterize phase change materials. In particular, it will be shown that only a rather small group of materials utilizes ‘metavalent bonding’, a novel, yet fundamental bonding mechanism, which can explain many of the characteristic features of phase change materials. This insight is employed to predict systematic property trends and to explore the limits in stoichiometry for photonic applications of this material class. It will be demonstrated how this concept can be used to tailor fast optical switches. Yet, the discoveries presented here also force us to revisit the concept of chemical bonding and bring back a history of vivid scientific disputes about ‘the nature of the chemical bond’.
Coronary and Abdominal Aorta Calcification in Rheumatoid Arthritis: Relationships with Traditional Cardiovascular Risk Factors, Disease Characteristics, and Concomitant Treatments (2014)

Our study demonstrates that in patients with RA, (1) CAC and AAC are more prevalent and more severe compared with age-matched and sex-matched control participants, (2) current use of MTX is a major determinant of the absence of CAC, and (3) erosive arthritis is a major determinant of AAC.
Geomorphology variables predict fish assemblages for forested and endorheic rivers of two continents (2021)

Stream fishes are restricted to specific environments with appropriate habitats for feeding and reproduction. Interactions between streams and surrounding landscapes influence the availability and type of fish habitat, nutrient concentrations, suspended solids, and substrate composition. Valley width and gradient are geomorphological variables that influence the frequency and intensity that a stream interacts with the surrounding landscape. For example, in constrained valleys, canyon walls are steeply sloped and valleys are narrow, limiting the movement of water into riparian zones. Wide valleys have long, flat floodplains that are inundated with high discharge. We tested for differences in fish assemblages with geomorphology variation among stream sites. We selected rivers in similar forested and endorheic ecoregion types of the United States and Mongolia. Sites where we collected were defined as geomorphologically unique river segments (i.e., functional process zones; FPZs) using an automated ArcGIS-based tool. This tool extracts geomorphic variables at the valley and catchment scales and uses them to cluster stream segments based on their similarity. We collected a representative fish sample from replicates of FPZs. Then, we used constrained ordinations to determine whether river geomorphology could predict fish assemblage variation. Our constrained ordination approach using geomorphology to predict fish assemblages resulted in significance using fish taxonomy and traits in several watersheds. The watersheds where constrained ordinations were not successful were next analyzed with unconstrained ordinations to examine patterns among fish taxonomy and traits with geomorphology variables. Common geomorphology variables as predictors for taxonomic fish assemblages were river gradient, valley width, and valley slope. Significant geomorphology predictors of functional traits were valley width-to-floor width ratio, elevation, gradient, and channel sinuosity. These results provide evidence that fish assemblages respond similarly and strongly to geomorphic variables on two continents.
Evaluation of the risk of hypoglycemias using a questionnaire in patients with type 2 diabetes (2018)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Simulation of 3D Streamer branching using High Performance Computing (2018)

International audience
Structural Determinants for the Interactions of Chemically Modified Nucleic Acids with the Stabilin-2 Clearance Receptor (2018)

The Stabilin receptors are systemic clearance receptors for some classes of chemically modified nucleic acid therapeutics. In this study, the recombinant human secreted ecto-domain of the small isoform of Stabilin-2 (s190) was purified from cell culture and evaluated for direct binding with a multitude of antisense oligonucleotides (ASOs) using a fluorescence polarization-based assay. The tested ASOs varied in their backbone composition, modification of the ribose 2' position, overall length of the oligo, and sequence of the nucleotide bases. A fully phosphorothioate (PS) ASO with a 5-10-5 pattern of flanking 2'- O-methoxyethyl modifications was then used to test the effects of pH and salt concentration on receptor binding. These tests concluded that the PS backbone was the primary determinant for ASO binding and that decreasing pH and increasing salt generally increased the rate of ligand dissociation and fit within the biological parameters expected of a constitutive recycling receptor. These results will be useful in the rational design of therapeutic oligonucleotides for enhancing their affinity or avoidance of the Stabilin receptors.