gebhart/patrepeval huggingface dataset:
Angiopoietin-2 induces human glioma invasion through the activation of matrix metalloprotease-2 (2003)

A hallmark of highly malignant human gliomas is their infiltration of the brain. We analyzed a large number of primary human glioma biopsies and found high levels of expression of an angiogenic regulator, angiopoietin-2 (Ang2), in the invasive areas, but not in the central regions, of those tumors. In the invasive regions where Ang2 was overexpressed, increased levels of matrix metalloprotease-2 (MMP-2) were also apparent. Consonant with these features, intracranial xenografts of glioma cells engineered to express Ang2 were highly invasive into adjacent brain parenchyma compared with isogenic control tumors. In regions of the Ang2-expressing tumors that were actively invading the brain, high levels of expression of MMP-2 and increased angiogenesis were also evident. A link between these two features was apparent, because stable expression of Ang2 by U87MG cells or treatment of several glioma cell lines with recombinant Ang2 in vitro caused activation of MMP-2 and acquisition of increased invasiveness. Conversely, MMP inhibitors suppressed Ang2-stimulated activation of MMP-2 and Ang2-induced cell invasion. These results suggest that Ang2 plays a critical role in inducing tumor cell infiltration, and that this invasive phenotype is caused by activation of MMP-2.
De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects (2016)

Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.
Novel Benzamide-Based Histamine H3 Receptor Antagonists: The Identification of Two Candidates for Clinical Development (2015)

The preclinical characterization of novel phenyl(piperazin-1-yl)methanones that are histamine H3 receptor antagonists is described. The compounds described are high affinity histamine H3 antagonists. Optimization of the physical properties of these histamine H3 antagonists led to the discovery of several promising lead compounds, and extensive preclinical profiling aided in the identification of compounds with optimal duration of action for wake promoting activity. This led to the discovery of two development candidates for Phase I and Phase II clinical trials.
Plasma heating in the multimirror trap GOL-3 by prolongated pulse REB (2008)

To analyze fusion prospects of E-beam heating the plasma in multimirror trap, the beam generator U-2 at the GOL-3 facility was modified for prolongation of 9μs beam pulse. Energy transfer from the beam to plasma column was investigated on the base of measurements of the energy distribution functions both plasma electrons (Thomson scattering of Nd-glass laser light) and beam electrons (multifoil analyzer). This measuring with diamagnetic signals gave new knowledge on dynamics of plasma heating by relativistic E-beam.
Successive Convex Approximation Algorithms for Sparse Signal Estimation With Nonconvex Regularizations (2018)

In this paper, we propose a successive convex approximation framework for sparse optimization where the nonsmooth regularization function in the objective function is nonconvex and it can be written as the difference of two convex functions. The proposed framework is based on a nontrivial combination of the majorization–minimization framework and the successive convex approximation framework proposed in literature for a convex regularization function. The proposed framework has several attractive features, namely, first, flexibility, as different choices of the approximate function lead to different types of algorithms; second, fast convergence, as the problem structure can be better exploited by a proper choice of the approximate function and the stepsize is calculated by the line search; third, low complexity, as the approximate function is convex and the line search scheme is carried out over a differentiable function; fourth, guaranteed convergence to a stationary point. We demonstrate these features by two example applications in subspace learning, namely the network anomaly detection problem and the sparse subspace clustering problem. Customizing the proposed framework by adopting the best-response type approximation, we obtain soft-thresholding with exact line search algorithms for which all elements of the unknown parameter are updated in parallel according to closed-form expressions. The attractive features of the proposed algorithms are illustrated numerically.
Atherosclerotic Plaque Component Segmentation in Combined Carotid MRI and CTA Data Incorporating Class Label Uncertainty (2014)

Atherosclerotic plaque composition can indicate plaque vulnerability. We segment atherosclerotic plaque components from the carotid artery on a combination of in vivo MRI and CT-angiography (CTA) data using supervised voxelwise classification. In contrast to previous studies the ground truth for training is directly obtained from 3D registration with histology for fibrous and lipid-rich necrotic tissue, and with μCT for calcification. This registration does, however, not provide accurate voxelwise correspondence. We therefore evaluate three approaches that incorporate uncertainty in the ground truth used for training: I) soft labels are created by Gaussian blurring of the original binary histology segmentations to reduce weights at the boundaries between components, and are weighted by the estimated registration accuracy of the histology and in vivo imaging data (measured by overlap), II) samples are weighted by the local contour distance of the lumen and outer wall between histology and in vivo data, and III) 10% of each class is rejected by Gaussian outlier rejection. Classification was evaluated on the relative volumes (% of tissue type in the vessel wall) for calcified, fibrous and lipid-rich necrotic tissue, using linear discriminant (LDC) and support vector machine (SVM) classification. In addition, the combination of MRI and CTA data was compared to using only one imaging modality. Best results were obtained by LDC and outlier rejection: the volume error per vessel was 0.9±1.0% for calcification, 12.7±7.6% for fibrous and 12.1±8.1% for necrotic tissue, with Spearman rank correlation coefficients of 0.91 (calcification), 0.80 (fibrous) and 0.81 (necrotic). While segmentation using only MRI features yielded low accuracy for calcification, and segmentation using only CTA features yielded low accuracy for necrotic tissue, the combination of features from MRI and CTA gave good results for all studied components.
Discovery of Novel Candidate Therapeutics and Diagnostics Based on Engineered Human Antibody Domains (2014)

The smallest independently folded antibody fragments, the domains, are emerging as promising scaffolds for candidate therapeutics and diagnostics that bind specifically targets of interest. The discovery of such binders is based on several technologies including structure-based design and generation of libraries of mutants displayed on phage or yeast, next-generation sequencing for diversity analysis, panning and screening of the libraries, affinity maturation of selected binders, and their expression, purification, and characterization for specific binding, function, and aggregation propensity. In this review, we describe these technologies as applied for the generation of engineered antibody domains (eAds), especially those derived from the human immunoglobulin heavy chain variable region (VH) and the second domain of IgG1 heavy chain constant region (CH2) as potential candidate therapeutics and diagnostics, and discuss examples of eAds against HIV-1 and cancer-related proteins.
Improved mode selection in hybrid error concealment for multi-broadcast-reception (2010)

Digital TV signals are often degraded by lost macro blocks or slices if received with mobile devices. Recently, we introduced a technique for inter-sequence error concealment in multi-broadcast scenarios which reconstruct lost image blocks of video signals by inserting error-free blocks of corresponding reference signals. The algorithm outperforms state-of-the-art techniques by up to 15 dB PSNR <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</sub> . The quality of reconstructed image blocks can he further enhanced by combining inter-sequence error concealment with a temporal concealment approach as we showed in 2009. To enhance the robustness of this hybrid error concealment, we propose a novel metric for mode selection in this paper which takes into account local image statistics. While keeping the complexity of hybrid error concealment nearly constant, a mean gain of up to 2.1 dB and a peak gain of up to 10.1 dB in terms of PSNR <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</sub> can be achieved additionally.
Molecular basis for N-terminal alpha-synuclein acetylation by human NatB (2020)

NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and <i>Candida albicans</i> NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.
Learning to produce 3D media from a captured 2D video (2011)

Due to the advances in display technologies and the commercial success of 3D motion pictures in recent years, there is renewed interest in enabling consumers to create 3D content. While new 3D content can be created using more advanced capture devices (i.e., stereo cameras), most people still use 2D capture devices. Furthermore, enormously large collections of captured media exist only in 2D. We present a system for producing stereo images from captured 2D videos. Our system detects "good" stereo frames from a 2D video, which was captured a priori without any constraints on camera motion or content. We use a trained classifier to detect pairs of video frames that are suitable for constructing stereo images. In particular, for a given frame It at time t, we determine if t̂ exists such that It+t̂ and It can form an acceptable stereo image. We verify the performance of our method for producing stereo media from captured 2D videos in a psychovisual evaluation using both professional movie clips and amateur home videos. To the best of our knowledge, detecting good stereo pairs from a captured 2D video has been adequately addressed in the literature.
A Lithium-Ion Battery Balancing Circuit Based on Synchronous Rectification (2019)

In this paper, a battery balancing circuit is proposed for the series-connected lithium-ion battery cells based on the principle of synchronous rectification. The proposed balancing circuit, also referred to as an equalizer, mainly includes a buck–boost converter (BBC), a multiport half-bridge converter (MHBC), and a driving circuit. The MHBC is coupled with a multiwinding transformer. Compared with the conventional congeneric methods, the number of transformer windings is almost reduced by half, leading to a more compact size and lower cost. Moreover, the secondary <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mosfet</small> s of the MHBC are synchronously driven by the primary half-bridge converter (HBC) without the need of additional isolated <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mosfet</small> gate drivers and power supplies, dramatically reducing the circuit cost and complexity. In addition, the proposed equalizer can realize the module-to-multi-cell (M2MC) equalization under severe imbalance conditions to improve the balancing speed, and work at the any-cell-to-any-cell (AC2AC) self-balancing mode under slight imbalance conditions to improve the balancing efficiency and effectiveness, which achieves a good trade-off between balancing speed and effectiveness. The expressions of the equalization current and efficiency are derived and verified by experimental results. The proposed equalizer is experimentally evaluated for a string with 12 series-connected lithium-ion cells.
Asymmetric Growth of Bilayer Graphene on Copper Enclosures Using Low-Pressure Chemical Vapor Deposition (2014)

In this work, we investigated the growth mechanisms of bilayer graphene on the outside surface of Cu enclosures at low pressures. We observed that the asymmetric growth environment of a Cu enclosure can yield a much higher (up to 100%) bilayer coverage on the outside surface as compared to the bilayer growth on a flat Cu foil, where both sides are exposed to the same growth environment. By simultaneously examining the graphene films grown on both the outside and inside surfaces of the Cu enclosure, we find that carbon can diffuse from the inside surface to the outside via exposed copper regions on the inside surface. The kinetics of this process are examined by coupling the asymmetric growth between the two surfaces through a carbon diffusion model. Finally, using these results, we show that the coverage of bilayer graphene can be tuned simply by changing the thickness of the Cu foil, further confirming our model of carbon delivery through the Cu foil.
Intracerebral grafting of cultured autologous skin fibroblasts into the rat striatum: An assessment of graft size and ultrastructure (1991)

To identify a suitable donor cell population for gene therapy applications to the central nervous system, primary fibroblasts isolated from skin biopsies and maintained in culture are employed as autologous cells for intracerebral grafting within the adult rat striatum. Results from the present investigation reveal that cultured primary skin fibroblasts cease to proliferate once they reach confluence; these cells are thus contact inhibited in vitro. Following implantation within the striatum, the volume of the primary fibroblast grafts, stained immunohistochemically for fibronectin, does not differ significantly at 3 and 8 weeks. The graft size is dependent on the density of the cell suspension, but not dependent on either the number of passages the cells are taken through in culture prior to grafting or on the postoperative survival period. Ultrastructural evidence reveals that at 8 weeks the grafts are composed primarily of collagen and fibroblasts with rough endoplasmic reticulum and vesicles. Reactive astrocytic processes and phagocytic cells are also present in the grafts. The grafts are extensively vascularized with capillaries composed of nonfenestrated endothelium; intercellular junctions are evident at sites of apposition between endothelial cells. It is concluded that primary skin fibroblasts are able to survive for at least 8 weeks following intracerebral implantation and continue to synthesize collagen and fibronectin in vivo. Also, the grafts maintain a constant volume between 3 and 8 weeks, thereby indicating that primary skin fibroblasts do not produce tumors. Finally, dynamic host-to-graft interactions--including phagocytic migration, astrocytic hypertrophy and infiltration within the grafts, and angiogenesis--are features that constitute the structural integration of primary skin fibroblasts grafted within the adult rat central nervous system.
A standards-based framework for real-time media in immersive scenes (2022)

Immersive media experiences are anticipated to become the norm in entertainment and communication in the near future, enabled by advances in computer graphics, capture and display systems, and networking technology. Immersive experiences are based on a rich 3D scene that enables immersion, fusion with the real world, and rich interactivity. However, 3D scenes are large, rich and complex - and hence stored and processed not only on devices, but on cloud systems. MPEG is currently working on specifying a set of functionalities that address different aspects of immersive media, including formats, access and delivery, and compression of these emerging media types.
Innovations in microwave filters and multiplexing networks for communications satellite systems (1992)

The evolution of microwave filters and multiplexers for space application is described. The many advances are described within the context of the design of the overall communication subsystem. Emphasis is placed on the multipaction and passive intermodulation (PIM) considerations in designing high-power multiplexers. The impact of microwave filter technology in the channel characterization of satellite systems is described. The future directions of research and development are briefly discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Size–speed trade-off in optical switching elements (1995)

The basic building blocks of an interconnection network are the switching elements. We examine two optical implementations for a basic switching element: (1) ferroelectric liquid-crystal light valves and (2) Fabry-Perot étalons. For these two examples we report a trade-off between the size, i.e., the number of input and output channels, and the switching speed. We speculate that it may be a general property of optical switching elements that size and speed cannot be optimized simultaneously.
The secret lives of single cells (2021)

Looking back fondly on the first 15 years of Microbial Biotechnology, a trend is emerging that biotechnology is moving from studies that focus on whole-cell populations, where heterogeneity exists even during robust growth, to those with an emphasis on single cells. This instils optimism that insights will be made into myriad aspects of bacterial growth in communities.
Fusion product bombardment of a tokamak first wall (1977)

A method of calculating the wall loading due to fusion products escaping from the plasma in a tokamak is described. For this purpose, the small-banana-width approximation is eliminated, yielding an analytic formulation for high-energy orbits and associated loss-cone limits. Wall-loading profiles (as a function of poloidal angle) are presented for various experimental devices (PLT, TFTR, and ORNL-EPR) and for a typical reactor (UWMAK-I). Peak-to-average alpha flux ratios of the order of 1.4 to 2.3 combined with average fluxes of ∼ 1011 alphas per cm2 per second, suggest that localized blistering may be a serious source of impurity atoms as well as a wall erosion mechanism. Special wall panels in regions of high flux are suggested. Other implications include a unique suggestion for fuel injection along special orbits intercepted via a bundle divertor.
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models (2010)

After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild-type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild-type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM-computed optimal growth states.
Insight into live bird markets of Bangladesh: an overview of the dynamics of transmission of H5N1 and H9N2 avian influenza viruses (2017)

Highly pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2 viruses have been recognized as threats to public health in Bangladesh since 2007. Although live bird markets (LBMs) have been implicated in the transmission, dissemination, and circulation of these viruses, an in-depth analysis of the dynamics of avian transmission of H5N1 and H9N2 viruses at the human-animal interface has been lacking. Here we present and evaluate epidemiological findings from active surveillance conducted among poultry in various production sectors in Bangladesh from 2008 to 2016. Overall, the prevalence of avian influenza viruses (AIVs) in collected samples was 24%. Our data show that AIVs are more prevalent in domestic birds within LBMs (30.4%) than in farms (9.6%). Quail, chickens and ducks showed a high prevalence of AIVs (>20%). The vast majority of AIVs detected (99.7%) have come from apparently healthy birds and poultry drinking water served as a reservoir of AIVs with a prevalence of 32.5% in collected samples. HPAI H5N1 was more frequently detected in ducks while H9N2 was more common in chickens and quail. LBMs, particularly wholesale markets, have become a potential reservoir for various types of AIVs, including HPAI H5N1 and LPAI H9N2. The persistence of AIVs in LBMs is of great concern to public health, and this study highlights the importance of regularly reviewing and implementing infection control procedures as a means of reducing the exposure of the general public to AIVs.Emerging Microbes & Infections (2017) 6, e12; doi:10.1038/emi.2016.142; published online 8 March 2017.