gebhart/patrepeval huggingface dataset:
Enhanced In Vivo Regenerative Potential of HOXB4-Transduced Hematopoietic Stem Cells With Regulation of Their Pool Size (1999)

After bone marrow transplantation (BMT), there is a rapid regeneration to normal pretransplantation levels in the number of hematopoietic progenitors and mature end cells, whereas hematopoietic stem cell (HSC) numbers recover to only 5% to 10% of normal levels. This suggests that HSC are significantly restricted in their self-renewal behavior and hence in their ability to repopulate the host stem cell compartment. Previously, we have reported that HSC engineered to overexpress the homeobox transcription factor HOXB4 have a large repopulation advantage over untransduced cells as assessed at 4 months in a murine transplantation model (Sauvageau et al, Genes Dev 9:1753, 1995). This phenomenon has now been examined in detail for periods extending to 12 months in cohorts of mice transplanted with various numbers of HOXB4-transduced HSC. In all mice analyzed, HOXB4-transduced HSC were capable of fully reconstituting the HSC compartment, resulting, on average, in some 14-fold greater numbers of HSC than observed when transplanting control, non-HOXB4-transduced bone marrow cells. These data indicate that HOXB4 is a limiting factor in the regeneration of HSC to normal levels after BMT. Furthermore, we show that HOXB4-transduced HSC did not expand above levels normally observed in unmanipulated mice, indicating that its overexpression does not override the regulatory mechanisms that maintain the HSC pool size within normal limits.
ChemInform Abstract: THE SYNTHESIS OF A FLUORINATED PHTHALOCYANINE (1979)

Abstract Das durch Sandmeyer‐Reaktion aus dem Cyananilin (I) dargestellte Iodphthalsäure‐dinitril (II) wird mit dem perfluorierten Heptyliodid (III) zum Dinitril (IV) gekuppelt und mit SnCl 2 zum Zinn‐phthalocyanin (V) umgesetzt.
Associations of polymorphisms in the promoter I of bovine <i>acetyl‐CoA carboxylase‐</i><i>α</i> gene with beef fatty acid composition (2009)

The objectives of this study were to identify single nucleotide polymorphisms (SNPs) in the promoter I (PI) region of the bovine acetyl-CoA carboxylase-alpha (ACACA) gene and to evaluate the extent to which they were associated with lipid-related traits. Eight novel SNPs were identified, which were AJ276223:g.2064T>A (SNP1), g.2155C>T (SNP2), g.2203G>T (SNP3), g.2268T>C (SNP4), g.2274G>A (SNP5), g.2340A>G (SNP6), g.2350T>C (SNP7) and g.2370A>G (SNP8). Complete linkage disequilibrium was observed among SNP1, 2, 4, 5, 6 and 8. Phenotypic data were collected from 573 cross-bred steers with six sire breeds, including Hereford, Angus, Brangus, Beefmaster, Bonsmara and Romosinuano. The genotypes of SNP1/2/4/5/6/8 were significantly associated with adjusted backfat thickness. The genotypes of SNP3 were significantly associated with triacylglycerol (TAG) content and fatty acid composition of longissimus dorsi muscle (LM) in Brangus-, Romosinuano- and Bonsmara-sired cattle. Cattle with g.2203GG genotype had greater concentrations of TAG, total lipid, total saturated fatty acid and total monounsaturated fatty acid than did cattle with g.2203GT genotype. The genotypes of SNP7 were significantly associated with fatty acid composition of LM. Cattle with genotype g.2350TC had greater amounts of several fatty acids in LM than did cattle with genotype g.2350CC. Our results suggested that the SNPs in the PI region of ACACA gene are associated with variations in the fatty acid contents in LM.
Continuous wavelength tuning of 850-nm vertical-cavity surface-emitting laser in fiber Fabry-Perot cavity (1998)

Summary form only given. We explore the possibility of wavelength tuning by incorporating VCSELs in fiber Fabry-Perot (FFP) cavities. VCSELs can support robust single longitudinal-mode operation due to wide longitudinal mode spacing of >40,000 GHz, which would allow continuous wavelength tuning without mode hopping by directly changing the cavity length.
ADIP, a Novel Afadin- and α-Actinin-Binding Protein Localized at Cell-Cell Adherens Junctions (2003)

Afadin is an actin filament (F-actin)-binding protein that is associated with the cytoplasmic tail of nectin, a Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecule. Nectin and afadin strictly localize at cell-cell adherens junctions (AJs) undercoated with F-actin bundles and are involved in the formation of AJs in cooperation with E-cadherin in epithelial cells. In epithelial cells of afadin (-/-) mice and (-/-) embryoid bodies, the proper organization of AJs is markedly impaired. However, the molecular mechanism of how the nectin-afadin system is associated with the E-cadherin-catenin system or functions in the formation of AJs has not yet been fully understood. Here we identified a novel afadin-binding protein, named ADIP (afadin DIL domain-interacting protein). ADIP consists of 615 amino acids with a calculated M(r) of 70,954 and has three coiled-coil domains. Northern and Western blot analyses in mouse tissues indicated that ADIP was widely distributed. Immunofluorescence and immunoelectron microscopy revealed that ADIP strictly localized at cell-cell AJs undercoated with F-actin bundles in small intestine absorptive epithelial cells. This localization pattern was the same as those of afadin and nectin. ADIP was undetectable at cell-matrix AJs. ADIP furthermore bound alpha-actinin, an F-actin-bundling protein known to be indirectly associated with E-cadherin through its direct binding to alpha-catenin. These results indicate that ADIP is an afadin- and alpha-actinin-binding protein that localizes at cell-cell AJs and may have two functions. ADIP may connect the nectin-afadin and E-cadherin-catenin systems through alpha-actinin, and ADIP may be involved in organization of the actin cytoskeleton at AJs through afadin and alpha-actinin.
Express virtual channels (2007)

Due to wire delay scalability and bandwidth limitations inherent in shared buses and dedicated links, packet-switched on-chip interconnection networks are fast emerging as the pervasive communication fabric to connect different processing elements in many-core chips. However, current state-of-the-art packet-switched networks rely on complex routers which increases the communication overhead and energy consumption as compared to the ideal interconnection fabric.
ChemInform Abstract: EFFECT OF STRUCTURAL CHANGE ON ACUTE TOXICITY AND ANTIINFLAMMATORY ACTIVITY IN A SERIES OF IMIDAZOTHIAZOLES AND THIAZOLOBENZIMIDAZOLES (1981)

Abstract Die in situ dargestellten α‐Halogenketone (III) reagieren mit den Mercaptodihydroimidazolen (II) bei Raumtemperatur zu den Hydroxyimidazothiazolen (I) und in siedendem Ethanol zu den Dihydroimidazothiazolen (IV).
Cerebrospinal fluid proteomic biomarkers for Alzheimer's disease (2006)

A panel of possible CSF biomarkers for AD has been identified using proteomic methods.
Active Vibration Isolation of Metrology Frames; A Modal Decoupled Control Design (2005)

For a six degree-of-freedom active vibration isolation system, a control strategy based on modal decoupling is proposed. This has the advantage of controlling the modal directions on a centralized single-input single-output basis. As a consequence, stability and performance can be imposed in each of the modal directions separately. An experimental demonstration is given using a dummy metrology frame. That is, a 1600 kg payload mass supported by three combined pneumatic and Lorentz controlled isolators. With this setup, two unstable modal directions resulting from a high center of gravity are stabilized without compromising performance in any of the remaining directions. In fact, performance in the remaining directions is enhanced using manual loop shaping.
Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver (2015)

Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease--without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER.
High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti‐HER2 therapy (2015)

Quantitative HER2 measurement by SRM-MS is superior to IHC and ISH in predicting outcome after treatment with anti-HER2 therapy.
Composition of robust error control scheme using adaptive coding and its effect on data communication (1990)

Abstract This paper describes a robust error control scheme used for propagation paths especially involving a long time‐frame burst error as in mobile radio communication and its effect on actual data communication channels. This is an adaptive error control scheme based on forward error correction code and composed adaptively of plural coding modes. Here, the BCH code is used as a block code, the diffused code is used as a convolutional code, and 3–5 majority logic is used as a majority voting code. The optimum coding mode is selected automatically according to the status of data transmission channels composed of a radio transmission span and telephone cable transmission lines. Cyclic code is used as an error detection method to evaluate channel status. Under practical transmission circumstances, extremely high throughput efficiency of more than 70 percent is realized for 4800 bit/s data for transmission over the cellular network in Britain. This scheme has been presented at CCITT SG XVII as a standard scheme candidate.
Epitopes in α8β1 and other RGD-binding integrins delineate classes of integrin-blocking antibodies and major binding loops in α subunits (2015)

Identification of epitopes for integrin-blocking monoclonal antibodies (mAbs) has aided our understanding of structure-function relationship of integrins. We mapped epitopes of chicken anti-integrin-α8-subunit-blocking mAbs by mutational analyses, examining regions that harboured all mapped epitopes recognized by mAbs against other α-subunits in the RGD-binding-integrin subfamily. Six mAbs exhibited blocking function, and these mAbs recognized residues on the same W2:41-loop on the top-face of the β-propeller. Loop-tips sufficiently close to W2:41 (<25 Å) contained within a footprint of the mAbs were mutated, and the loop W3:34 on the bottom face was identified as an additional component of the epitope of one antibody, clone YZ5. Binding sequences on the two loops were conserved in virtually all mammals, and that on W3:34 was also conserved in chickens. These indicate 1) YZ5 binds both top and bottom loops, and the binding to W3:34 is by interactions to conserved residues between immunogen and host species, 2) five other blocking mAbs solely bind to W2:41 and 3) the α8 mAbs would cross-react with most mammals. Comparing with the mAbs against the other α-subunits of RGD-integrins, two classes were delineated; those binding to "W3:34 and an top-loop", and "solely W2:41", accounting for 82% of published RGD-integrin-mAbs.
Novel inter and intra prediction tools under consideration for the emerging AV1 video codec (2017)

Google started the WebM Project in 2010 to develop open source, royalty- free video codecs designed specifically for media on the Web. The second generation codec released by the WebM project, VP9, is currently served by YouTube, and enjoys billions of views per day. Realizing the need for even greater compression efficiency to cope with the growing demand for video on the web, the WebM team embarked on an ambitious project to develop a next edition codec AV1, in a consortium of major tech companies called the Alliance for Open Media, that achieves at least a generational improvement in coding efficiency over VP9. In this paper, we focus primarily on new tools in AV1 that improve the prediction of pixel blocks before transforms, quantization and entropy coding are invoked. Specifically, we describe tools and coding modes that improve intra, inter and combined inter-intra prediction. Results are presented on standard test sets.
Uncertainty in photoluminescence-based effective carrier lifetime measurements (2012)

Photoluminescence-based effective carrier lifetime measurements have received increased attention in recent years due to their high sensitivity, even at very low excess carrier concentration. Like any other measurement technique, knowledge regarding the experimental uncertainty is crucial in order to distinguish significant differences between samples. However, until now, the uncertainty of the photoluminescence based measurements has not been comprehensively analysed. This paper presents a preliminary study of the uncertainty associated with photoluminescence based lifetime measurements. The uncertainty of both the excess carrier concentration and the effective carrier lifetime is expressed by the uncertainty of the input parameters, such as calibration constants, bulk dopant concentration, wafer thickness and front surface reflection. The paper illustrates the importance of accurate determination of the calibration constant A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> and bulk resistivity in order to reduce the measurement uncertainty.
Constant switching frequency techniques for sliding mode control in DC-DC converters (2011)

Sliding mode is a very effective control strategy for switch mode DC-DC converters. However, its widespread adoption has been hampered by some of the drawbacks inherent to this control technique. Among these, the most important is apparently the varying operating frequency, which can cause electromagnetic interference (EMI) problems. This problem is particularly critical in portable devices (e.g. smartphones, e-readers) where it is highly desirable that the DC-DC converters operate at a constant switching frequency to avoid interferences with other parts of the system. Several methods have been proposed in previous literature to stabilize the operating frequency of sliding mode controllers. In this paper, some of the most promising techniques are evaluated and applied to a specific test case, i.e. a Buck converter for a wireless system. A detailed model of the DC-DC converter has been developed in order to obtain realistic results. The system parameters have been chosen to reflect an actual commercial application.
Stopping Light on a Defect (2001)

Gap solitons are localized nonlinear coherent states which have been shown both theoretically and experimentally to propagate in periodic structures. Although theory allows for their propagation at any speed $v$, $0\le v\le c$, they have been observed in experiments at speeds of approximately 50% of $c$. It is of scientific and technological interest to trap gap solitons. We first introduce an explicit multiparameter family of periodic structures with localized defects, which support linear defect modes. These linear defect modes are shown to persist into the nonlinear regime, as {\it nonlinear defect modes}. Using mathematical analysis and numerical simulations we then investigate the capture of an incident gap soliton by these defects. The mechanism of capture of a gap soliton is resonant transfer of its energy to nonlinear defect modes. We introduce a useful bifurcation diagram from which information on the parameter regimes of gap soliton capture, reflection and transmission can be obtained by simple conservation of energy and resonant energy transfer principles.
An optical interconnect layer on silicon (2007)

We demonstrate an optical interconnection link on silicon. Compact InP-based micro-disk lasers and photodetectors (PDs) are connected via Si photonic waveguides on top of a Si wafer. The photonic devices are fabricated in a way compatible with wafer scale processing steps, guaranteeing compatibility towards future generation electronic IC processing. Device design, fabrication, integration scheme and preliminary measurements of the full optical link are described in this paper.
Diazo-based assay for total bilirubin in a coated thin film evaluated. (1984)

Abstract We compared results for total bilirubin as measured on a coated thin film and by the Evelyn-Malloy and Jendrassik-Gróf methods. We examined serum samples from patients and studied the effects of protein, hemoglobin, and lipids on bilirubin measurement. Results from the thin-film assay compared favorably with those of the other methods. Total and within-day precision (CV), assessed over a one-year period, were better than 6% and 3%, respectively, at all concentrations. Analytical recovery was 99 +/- 3%. Samples from individuals having a wide range of liver diseases demonstrated, by linear regression, good correlation between the thin-film method and the two wet-chemistry methods (correlation coefficients of 0.990 and 0.994). We conclude that the thin-film method offers a valid alternative assay for total bilirubin.
Analysis by RNA-RNA hybridization assay of intertypic rotaviruses suggests that gene reassortment occurs in vivo (1987)

Antigenic characterization of human and animal rotaviruses by the plaque reduction neutralization assay has shown the existence of naturally occurring intertypes. Antiserum to M37, a rotavirus strain isolated from an asymptomatic neonate, neutralizes both Wa and ST3 strains, which are classified as serotype 1 and serotype 4 human rotaviruses, respectively. Likewise, antiserum to SB-1A, a porcine rotavirus, neutralizes rotavirus strains belonging to serotype 4 or 5. Plaque reduction neutralization assay of reassortant rotaviruses produced in vitro from these intertypes indicates that these viruses share one antigenically related outer capsid protein, VP3, with one serotype and another antigenically related outer capsid protein, VP7, with the other serotype. Thus, M37 is related to ST3 on the basis of its fourth-gene product, VP3, and to Wa on the basis of its ninth-gene product, VP7, whereas SB-1A is related to Gottfried (serotype 4 porcine rotavirus) via VP7 and to OSU (serotype 5 porcine rotavirus) via VP3. RNA-RNA hybridization studies revealed a high degree of homology between the VP3 or VP7 gene segments responsible for shared serotype specificity. Thus, the fourth gene segments of M37 and ST3 were highly homologous, while M37 and Wa had homology between their ninth gene segments. SB-1A and Gottfried were homologous not only with respect to the ninth gene but had complete homology in all other genes except the fourth gene. The fourth gene of SB-1A was highly homologous with the fourth gene of OSU. These observations suggested that SB-1A was a naturally occurring reassortant between Gottfried-like and OSU-like porcine rotavirus strains. Our observations also suggested that intertypes may result from genetic reassortment in nature.
Co-gasification of pyrolysis oil and black liquor - a new track for production of chemicals and transportation fuels from biomass (2015)

Pressurized oxygen-blown entrained flow black liquor (BL) gasification, the Chemrec technology, has been demonstrated in a 3 MWth pilot plant in Pitea, Sweden for more than 25,000 h. The plant is owned and operated by Lulea University of Technology since 2013. It is well known that catalytic activity of alkali metals is important for the high reactivity of black liquor, which leads to a highly efficient BL gasification process. The globally available volume of BL is however limited and strongly connected to pulp production. By co-gasifying pyrolysis oil (PO) with BL it is possible to utilize the catalytic activity also for PO conversion to syngas. Adding PO leads to larger feedstock flexibility with the possibility of building larger biofuels plants based on BL gasification technology. This presentation summarizes new results from research activities aimed at developing and assessing the PO/BL co-gasification process. Results from laboratory experiments with PO/BL mixtures show that pyrolysis behavior and char gasification reactivity are similar to pure BL. This means that the decrease in the alkali metal concentration due to the addition of PO in the mixture does not decrease the reactivity. Pure PO is much less reactive. Mixing tests show that the fraction of PO that can be mixed into BL is limited by lignin precipitation as a consequence of PO acidity. Pilot scale PO/BL co-gasification experiments have been executed following design and construction of a new feeding system to allow co-feeding of PO with BL. The results confirm the conclusions from the lab scale study and prove that the co-gasification concept is practically applicable. Process performance of the pilot scale co-gasification process is similar to gasification of BL only with high carbon conversion and clean syngas generation. This indicates that the established BL gasification technology can be used for co-gasification of PO and BL without major modifications.
From Thumbnails to Summaries - A single Deep Neural Network to Rule Them All (2018)

Video summaries come in many forms, from traditional single-image thumbnails, animated thumbnails, storyboards, to trailer-like video summaries. Content creators use the summaries to display the most attractive portion of their videos; the users use them to quickly evaluate if a video is worth watching. All forms of summaries are essential to video viewers, content creators, and advertisers. Often video content management systems have to generate multiple versions of summaries that vary in duration and presentational forms. We present a framework ReconstSum that utilizes LSTM-based autoencoder architecture to extract and select a sparse subset of video frames or keyshots that optimally represent the input video in an unsupervised manner. The encoder selects a subset from the input video while the decoder seeks to reconstruct the video from the selection. The goal is to minimize the difference between the original input video and the reconstructed video. Our method is easily extendable to generate a variety of applications including static video thumbnails, animated thumbnails, storyboards and "trailer-like" highlights. We specifically study and evaluate two most popular use cases: thumbnail generation and storyboard generation. We demonstrate that our methods generate better results than the state-of-the-art techniques in both use cases.