gebhart/patrepeval huggingface dataset:
<title>Coding format independent multimedia content adaptation using XML</title> (2003)

Due to the heterogeneity of the current terminal and network infrastructures, multimedia content needs to be adapted to specific capabilities of these terminals and network devices. Furthermore, user preferences and user environment characteristics must also be taken into consideration. The problem becomes even more complex by the diversity of multimedia content types and encoding formats. In order to meet this heterogeneity and to be applicable to different coding formats, the adaptation must be performed in a generic and interoperable way. As a response to this problem and in the context of MPEG-21, we present an approach which uses XML to describe the high-level structure of a multimedia resource in a generic way, i.e., how the multimedia content is organized, for instance in layers, frames, or scenes. For this purpose, a schema for XML-based bitstream syntax descriptions (<i>generic Bitstream Syntax Descriptions</i> or <i>gBSDs</i>) has been developed. A gBSD can describe the high-level structure of a multimedia resource in a coding format independent way. Adaptation of the resource is based on elementary transformation instructions formulated with respect to the gBSDs. These instructions have been separated from the gBSDs in order to use the same descriptions for different adaptations, e.g., temporal scaling, SNR scaling, or semantic adaptations. In the MPEG-21 framework, those adaptations can be steered for instance by the network characteristics and the user preferences. As a result, it becomes possible for coding format agnostic adaptation engines to transform media bitstreams and associated descriptions to meet the requirements imposed by the network conditions, device capabilities, and user preferences.
Big Data Applications in Radiation Oncology (2018)

The era of big data is marked by the enormous amount, speed, and breadth of data that are made available with rapidly advancing technologies in computation, detection, storage, and analysis. In healthcare, big data include medical records, prescription information, medical images, laboratory results, genomic profiles, demographics, and more. The opportunities to improve individual and population health are immense. In oncology, the National Cancer Institute (NCI) had launched pioneering programs in the 2000s to harness big data in support of laboratory and clinical research. Despite their laudable goals, these efforts did not make significant inroads to reap the benefits of big data. The fundamental challenge lies in the large amount of unstructured clinical information that is not readily amenable for electronic analysis. For medical oncology, efforts are now focused on the extraction and reformatting of such clinical data so that they can be queried for analysis from central locations. Progress is being made with data from hundreds of thousands, or even millions, of patients. Somewhat different approaches are being developed for radiation oncology. The Oncospace program from Johns Hopkins University specifically captures structured data during patient encounters; similar to the EuroCat program from Maastro, the researchers send analyses to external databases to retrieve results to avoid the burden of data export. Both radiation oncology programs have been able to produce outcome prediction models that are more effective than those derived by the human practitioners, although the number of patients were less than 500, thus, relatively small. Efforts in oncologic clinical research using big data are clearly in their infancy. Nevertheless, they have provided important insights about the scope of the challenge. It seems only a matter of time that clinical research with big data will have a major impact on the community.
Antisense-Mediated Exon Inclusion (2012)

Exon skipping induced by gene mutations is a common mechanism responsible for many genetic diseases. A practical approach to correct the aberrant splicing of defective genes is to use antisense oligonucleotides (ASOs). The recognition of splice sites and the regulation of splicing involve multiple positive or negative cis-acting elements and trans-acting factors. Base-pairing of ASOs to a negative element in a targeted pre-mRNA blocks the binding of splicing repressors to this cis-element and/or disrupts an unfavorable secondary structure; as a result, the ASO restores exon inclusion. For example, we have recently shown that appropriate 2'-O-(2-methoxyethyl) (MOE) phosphorothioate-modified ASOs can efficiently correct survival motor neuron 2 (SMN2) exon 7 splicing in a cell-free splicing assay, in cultured human cells-including patient fibroblasts-and in both peripheral tissues and the CNS of SMA mouse models. These ASOs are promising drug leads for SMA therapy.
Immunocytochemical Localization of Thyroid Hormone Receptors in the Adult Rat Brain (1991)

It is generally accepted that thyroid hormones act at the genomic level through an interaction with specific nuclear receptors. Using a monoclonal antibody raised against the rat liver nuclear L-T3 receptor (NTR), we report here the immunocytochemical localization of T3 receptors in the adult rat brain. The strongest NTR immunoreactivity was found in the olfactory bulb, the hippocampus, the dentate gyrus, the amygdala areas, and the neocortex (layers III-VI). An intermediate NTR immunoreactivity was found in the hypothalamus, whereas the thalamus, the caudate-putamen, and the pallidum were weakly NTR-immunoreactive. In the cerebellum, a strong NTR immunoreactivity was found in the nuclei of Purkinje cells, in the internal granular layer, and in some nuclei of cells located in the molecular layer. In the brainstem, a strong NTR immunoreactivity was found in the lateral mamillary nucleus and the interstitial nucleus. A weak to moderate NTR immunoreactivity was observed in the central gray matter, while the substantia nigra and the interpeduncular nucleus were weakly stained. Furthermore, we also found NTR immunoreactivity in the nuclei of ependymocytes, epithelial cells of the choroid plexus, and cells located in the white matter. At the electron microscope level, we confirm that the immunoreactivity was not only localized in the nuclei of neurons but also in the nuclei of astrocytes and medium oligodendrocytes. This study provides new information concerning the distribution of NTR in the rat brain: (1) NTR are present not only in neurons but also in glial and ependymal cells, and (2) there is a regional and cellular heterogeneity in the distribution of NTR in the central nervous system.
Materials processing using radio-frequency ion-sources: Ion-beam sputter-deposition and surface treatment (2019)

The capabilities of ion-beam techniques for thin-film processing, i.e., for materials deposition by ion-beam sputtering and surface treatment, are reviewed. The basic interaction mechanisms between ions and solids are summarized and related to materials processing by ion sources. Typical geometries of ion sources, targets, and samples are discussed for corresponding experimental apparatus. The versatility of ion-beam techniques in the preparation of thin films and multilayer structures is illustrated by several examples: ion-beam sputter-deposition of various binary oxide materials (including crystalline MgO, NiO, ZnO, Sn<sub>x</sub>O<sub>y</sub>, and Cu<sub>x</sub>O<sub>y</sub>) as well as combinatorial growth of materials libraries of amorphous ternary oxides. Furthermore, controlled ion-beam etching of surfaces is discussed.
A reduced-rank approach to single-channel noise reduction (2014)

This paper investigates the application of the so-called reduced-rank principle to the problem of single-channel noise reduction. Under the reduced-rank framework, we develop reduced-rank Wiener and tradeoff filters. In comparison to the classical Wiener filter, the reduced-rank Wiener one can provide a degree of freedom to control the compromise between noise reduction and speech distortion. Similarly, the reduced-rank tradeoff filter offers one more degree of flexibility than the traditional tradeoff filter to optimize the noise reduction performance. Experiments are carried out and preliminary results indicate that the reduced-rank optimal filters are more interesting than their conventional counterparts in many aspects.
The Time Course of Clinical Oxygenator Failure Due to Clot Formation (2020)

Abstract Background Long-term use of extracorporeal membrane oxygenation (ECMO) remains limited because of poor biocompatibility, which often leads to clot formation and device failure. Despite this common pathway to failure, there are no published studies on the rate of clot formation and resulting performance deficits in current oxygenators. Methods ECMO cases with either Maquet’s CardioHelp (CH, n=28) or Quadrox (Qx, n=14) oxygenators were evaluated over a three-month period. Data was collected prospectively and included patient characteristics and hematological data. The inlet-outlet oxygen content difference (ΔC O2 ) and blood flow resistance were calculated as measures of device function, and device failure due to clot formation was defined as a resistance increase greater than 1 mmHg/(L/min)/day for more than one day. Results There were no statistically significant differences in patient age, total days on ECMO, platelet count (PLT) prior to ECMO, activated partial thromboplastin time during ECMO, initial resistance, and device blood flow rate. During ECMO, the Qx group had a significantly greater change in PLT (Qx: - 34±10%; CH: 7±15%), rapidity to failure due to clot formation, and a greater decline in ΔC O2 (all p&lt;0.05). Clot burden was focused at the center of the CH oxygenator, farthest from all inlets, whereas Qx devices developed a more diffuse clot pattern. Conclusions Qx oxygenators clot earlier than CH oxygenators with a correlated drop in ΔC O2 and greater PLT reduction. These differences are likely due to the distributed, four-inlet CH design vs. the single inlet Qx design and differences in pump-induced platelet activation.
Predictability of the progression of chronic renal failure. (1983)

The progression of chronic renal failure has been claimed to be predictable by means of mathematical models. The present study assesses, in 110 adult patients, the prediction error caused by the application of these models. The study shows that the prediction error has a wide range, which indicates that these models should be used with caution for prediction purposes in individual patients. Improvements of the models are proposed, and a new approach is demonstrated.
Platelet Adhesion and Aggregation Under Flow using Microfluidic Flow Cells (2009)

Platelet aggregation occurs in response to vascular injury where the extracellular matrix below the endothelium has been exposed. The platelet adhesion cascade takes place in the presence of shear flow, a factor not accounted for in conventional (static) well-plate assays. This article reports on a platelet-aggregation assay utilizing a microfluidic well-plate format to emulate physiological shear flow conditions. Extracellular proteins, collagen I or von Willebrand factor are deposited within the microfluidic channel using active perfusion with a pneumatic pump. The matrix proteins are then washed with buffer and blocked to prepare the microfluidic channel for platelet interactions. Whole blood labeled with fluorescent dye is perfused through the channel at various flow rates in order to achieve platelet activation and aggregation. Inhibitors of platelet aggregation can be added prior to the flow cell experiment to generate IC50 dose response data.
Associations between Particulate Matter and Otitis Media in Children: A Meta-Analysis (2020)

Particulate matter (PM), a primary component of air pollution, is a suspected risk factor for the development of otitis media (OM). However, the results of studies on the potential correlation between an increase in the concentration of PM and risk of developing OM are inconsistent. To better characterize this potential association, a meta-analysis of studies indexed in three global databases (PubMed, EMBASE, and The Cochrane Library) was conducted. These databases were systematically screened for observational studies of PM concentration and the development of OM from the time of their inception to 31 March 2020. Following these searches, 12 articles were analyzed using pooled odds ratios generated from random-effects models to test for an association between an increased concentration of PM and the risk of developing OM. The data were analyzed separately according to the size of particulate matter as PM<sub>2.5</sub> and PM<sub>10</sub>. The pooled odds ratios for each 10 μg/m<sup>3</sup> increase in PM<sub>2.5</sub> and PM<sub>10</sub> concentration were 1.032 (95% confidence interval (CI), 1.005-1.060) and 1.010 (95% CI, 1.008-1.012), respectively. Specifically, the pooled odds ratios were significant within the short-term studies (PM measured within 1 week of the development of OM), as 1.024 (95% CI, 1.008-1.040) for PM<sub>2.5</sub> concentration and 1.010 (95% CI, 1.008-1.012) for PM<sub>10</sub> concentration. They were significant for children under 2 years of age with pooled odds ratios of 1.426 (95% CI, 1.278-1.519) for an increase in the concentration of PM<sub>2.5</sub>. The incidence of OM was not correlated with the concentration of PM, but was correlated with an increase in the concentration of PM. In conclusion, an increase in the concentration of PM<sub>2.5</sub> is more closely associated with the development of OM compared with an increase in the concentration of PM<sub>10</sub>; this influence is more substantial in shorter-term studies and for younger children.
Synthesis of Isotactic Polypropene-block-Poly(methyl methacrylate) Using Magnesium Bromide-Terminated Isotactic Polypropene (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Isotactic Polypropene-block-Poly(methyl methacrylate) Using Magnesium Bromide-Terminated Isotactic PolypropeneTakeshi Shiono, Yoshihide Akino, and Kazuo SogaCite this: Macromolecules 1994, 27, 21, 6229–6231Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/ma00099a046https://doi.org/10.1021/ma00099a046research-articleACS PublicationsRequest reuse permissionsArticle Views156Altmetric-Citations17LEARN 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
A novel faecalLachnoclostridiummarker for the non-invasive diagnosis of colorectal adenoma and cancer (2019)

This study identifies a novel bacterial marker <i>m3</i> for the non-invasive diagnosis of colorectal adenoma.
Nanometer scale patterning and pattern transfer on amorphous Si, crystalline Si, and SiO2 surfaces using self-assembled monolayers (1997)

Microcontact printing was used to form nanometer scale patterns of self-assembled monolayers (SAMs) on amorphous Si, crystalline Si, and SiO2 using octadecyltrichlorosilane (OTS) as the ink and an elastomer as the stamp. The patterns were subsequently transferred into crystalline Si substrates or amorphous Si films using the SAM of OTS as the resist film. Atomic force microscopy was used to characterize the quality of the SAM and the resulting patterns. Using a Si pillar structure as the master, “pancakes” of less than 80 nm in size were formed by over etching of the patterned OTS film on amorphous Si using KOH. The size of the resulting amorphous Si pancakes can be controlled by the etching time.
Novel CH1:CL interfaces that enhance correct light chain pairing in heterodimeric bispecific antibodies (2017)

Targeting two unique antigens with a single bispecific antibody is an attractive approach with potential broad therapeutic applicability. However, the production of heterodimeric bispecific antibodies (bsAbs) presents a challenge, requiring the co-expression and accurate pairing of two distinct heavy and light chain units. Several undesirable by-products can be formed in the production process, including heavy chain homodimers and non-cognate light chain pairings. Although additional downstream purification methods exist, they are often time consuming and restrict practical large-scale production. In this study, we identify and validate novel Fab interface mutations that increase cognate light chain pairing efficiencies within heterodimeric bsAbs. Importantly, the variable domains remain unaltered as interface mutations were restricted to the CH1 and CL domains. We performed several biochemical assays to demonstrate that the novel engineered interfaces do not adversely impact bispecific antibody expression, stability, affinity and biological function. The designs reported here can easily be applied in a generic manner to use existing antibodies as building blocks for bsAbs which will help to accelerate the identification and production of next generation bispecific antibody therapeutics.
Administering truncated receive functions in a parallel messaging interface (2023)

Administering truncated receive functions in a parallel messaging interface (`PMI`) of a parallel computer comprising a plurality of compute nodes coupled for data communications through the PMI and through a data communications network, including: sending, through the PMI on a source compute node, a quantity of data from the source compute node to a destination compute node; specifying, by an application on the destination compute node, a portion of the quantity of data to be received by the application on the destination compute node and a portion of the quantity of data to be discarded; receiving, by the PMI on the destination compute node, all of the quantity of data; providing, by the PMI on the destination compute node to the application on the destination compute node, only the portion of the quantity of data to be received by the application; and discarding, by the PMI on the destination compute node, the portion of the quantity of data to be discarded.
COBRApy: COnstraints-Based Reconstruction and Analysis for Python (2013)

http://opencobra.sourceforge.net/
Change of high-voltage conduction mechanism in vertical GaN–on–GaN Schottky diodes at elevated temperatures (2020)

Current-voltage-temperature characteristics (0 °C to 150 °C) of SBDs on highly compensated 15 μm and 30 μm n-type GaN drift layer were measured for voltages up to −300 V and up to −800 V, respectively. When the temperature is between 75 °C and 100 °C, both SBDs exhibited a similar change in conduction mechanism from thermionic field emission (TFE) to thermionic emission (TE) due to the activation of N-vacancies (VN) (Ea = −1.67 ± 0.02 eV). However, at high voltages when the temperature is >100 °C, the conduction mechanism changes from TE to TFE due to the de-trapping of electrons from activated carbon-traps (Ea = +0.69 eV) in the grown drift layers.
Dynamic Underground Stripping Demonstration Project. Interim progress report, 1991 (1992)

LLNL is collaborating with the UC Berkeley College of Engineering to develop and demonstrate a system of thermal remediation and underground imaging techniques for use in rapid cleanup of localized underground spills. Called ``Dynamic Stripping`` to reflect the rapid and controllable nature of the process, it will combine steam injection, direct electrical heating, and tomographic geophysical imaging in a cleanup of the LLNL gasoline spill. In the first 8 months of the project, a Clean Site engineering test was conducted to prove the field application of the techniques before moving to the contaminated site in FY 92.
Cutthroat Trout Avoidance of Metals and Conditions Characteristic of a Mining Waste Site: Coeur d'Alene River, Idaho (1997)

The South Fork basin of the Coeur dˈAlene River, Idaho, has been an area of heavy mining activity since the 1880s. The mining operations have resulted in elevated concentrations of metals in surface water, most notably cadmium, lead, zinc, and, to a lesser extent, copper. The metals affected surface water quality downstream in the Coeur dˈAlene basin and are suspected to be one of the primary reasons for the reduction in populations of native westslope cutthroat trout Oncorhynchus clarki lewisi. The avoidance response of a surrogate species, Snake River cutthroat trout O. clarki (unnamed subspecies), was evaluated against conditions simulating those in the Coeur dˈAlene River basin. Cutthroat trout avoided a metals mixture of these concentrations: Cd (0.30 μg/L), Cu (6.0 μg/L), Pb (0.6 μg/L), and Zn (28 μg/L). The avoidance response to either Cu or Zn alone was similar to the avoidance response to the mixture, suggesting that avoidance to the mixture was due to these metals. After acclimation to Zn at 55 μg/L for 90 d, cutthroat trout detected and preferred a lower Zn concentration of 28 μg/L. The lowest Zn concentrations avoided (28 μg/L) were 1/6 to 1/78 the Zn concentrations measured in the South Fork and lower Coeur dˈAlene River basins. Avoidance of metals-contaminated habitats by cutthroat trout may be, in part, responsible for reduced fish populations.
Differential pressure distribution measurement with an MEMS sensor on a free-flying butterfly wing (2012)

An insect can perform various flight maneuvers. However, the aerodynamic force generated by real insect wings during free flight has never been measured directly. In this study, we present the direct measurement of the four points of the differential pressures acting on the wing surface of a flying insect. A small-scale differential pressure sensor of 1.0 mm × 1.0 mm × 0.3 mm in size was developed using microelectromechanical systems (MEMS) and was attached to a butterfly wing. Total weight of the sensor chip and the flexible electrode on the wing was 4.5 mg, which was less than 10% of the wing weight. Four points on the wing were chosen as measurement points, and one sensor chip was attached in each flight experiment. During takeoff, the wing's flapping motion induced a periodic and symmetric differential pressure between upstroke and downstroke. The average absolute value of the local differential pressure differed significantly with the location: 7.4 Pa at the forewing tip, 5.5 Pa at the forewing center, 2.1 Pa at the forewing root and 2.1 Pa at the hindwing center. The instantaneous pressure at the forewing tip reached 10 Pa, which was ten times larger than wing loading of the butterfly.
<title>Cyclic peptidase substrates for fluorescent analysis of Caspase 3 enzyme activity</title> (2000)

Cyclic Caspase 3 peptidase substrates derived from the fluorophore Rhodamine 110, as well as their cleavage products, were prepared by step-wise synthesis, using three independent methods. 3D energy minimized structural analysis as well as Mass Spectral analysis indicate that the cyclic substrates can bind positively charged cations. Enzymatic assays indicate that the substrates are cleaved by the Caspase 3 enzyme. Cellular assays showed cell specific staining of apoptosis induced cell lines. Application of these substrates to the high-throughput screening analysis of apoptosis induction in whole cells was developed.