gebhart/patrepeval huggingface dataset:
The Influenza A Virus NS1 Protein Inhibits Activation of Jun N-Terminal Kinase and AP-1 Transcription Factors (2002)

The influenza A virus nonstructural NS1 protein is known to modulate host cell gene expression and to inhibit double-stranded RNA (dsRNA)-mediated antiviral responses. Here we identify NS1 as the first viral protein that antagonizes virus- and dsRNA-induced activation of the stress response-signaling pathway mediated through Jun N-terminal kinase.
ChemInform Abstract: Transition Metal‐Methylene Complexes. Part 62. Spontaneous Intramolecular Ring Opening of the Cyclopropyl Group at a Metal‐Metal Double Bond. (1986)

Abstract Treatment of the binuclear Rh complex (I) with the diazo Compounds (II), generated in situ from their hydrazone precursor Compounds, results in the formation of the new dimetallacyclopropanes (III).
Abstract A19: Exploring genetic interactions in haploid human cells (2017)

Abstract Gene-associated phenotypes often depend on the activity of other genes resulting in genetic interactions. In model organisms, the large-scale generation of combinations of mutations has resulted in the identification of genetic interactions and provided insights into their contribution to complex phenotypes. Here we use haploid human cells combined with genome-wide mutagenesis to study genetic interactions. We have made a synthetic lethality network using query genes acting in the secretory pathway and observe that human genes frequently engage in genetic interactions. Beyond cell lethality, we search for genes, which upon loss deregulate cellular processes such as signaling pathways. Genetic modifier approaches in those mutants reveals back-up mechanisms or genetic networks contributing to the phenotype of interest. This provides a much-needed window into the robust genetic networks governing human cells. Citation Format: Vincent A. Blomen, Thijn R. Brummelkamp. Exploring genetic interactions in haploid human cells [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A19.
Risk reduction strategy for radiation exposure during percutaneous nephrolithotomy (2012)

It is important to be aware of the amount of radiation patients with nephrolithiasis receive. These patients are at risk for multiple imaging studies and multiple procedures during their lifetime. Whenever possible, the techniques outlined in this review should be implemented to reduce the amount of radiation to which patients are exposed during PNL.
Central vein sign: A diagnostic biomarker in multiple sclerosis (CAVS-MS) study protocol for a prospective multicenter trial (2021)

The specificity and implementation of current MRI-based diagnostic criteria for multiple sclerosis (MS) are imperfect. Approximately 1 in 5 of individuals diagnosed with MS are eventually determined not to have the disease, with overreliance on MRI findings a major cause of MS misdiagnosis. The central vein sign (CVS), a proposed MRI biomarker for MS lesions, has been extensively studied in numerous cross sectional studies and may increase diagnostic specificity for MS. CVS has desirable analytical, measurement, and scalability properties. “Central Vein Sign: A Diagnostic Biomarker in Multiple Sclerosis (CAVS-MS)” is an NIH-supported, 2-year, prospective, international, multicenter study conducted by the North American Imaging in MS Cooperative (NAIMS) to evaluate CVS as a diagnostic biomarker for immediate translation into clinical care. Study objectives include determining the concordance of CVS and McDonald Criteria to diagnose MS, the sensitivity of CVS to detect MS in those with typical presentations, and the specificity of CVS among those with atypical presentations. The study will recruit a total of 400 participants (200 with typical and 200 with atypical presentations) across 11 sites. T2*-weighted, high-isotropic-resolution, segmented echo-planar MRI will be acquired at baseline and 24 months on 3-tesla scanners, and FLAIR* images (combination of FLAIR and T2*) will be generated for evaluating CVS. Data will be processed on a cloud-based platform that contains clinical and CVS rating modules. Imaging quality control will be conducted by automated methods and neuroradiologist review. CVS will be determined by Select6* and Select3* lesion methods following published criteria at each site and by central readers, including neurologists and neuroradiologists. Automated CVS detection and algorithms for incorporation of CVS into McDonald Criteria will be tested. Diagnosis will be adjudicated by three neurologists who served on the 2017 International Panel on the Diagnosis of MS. The CAVS-MS study aims to definitively establish CVS as a diagnostic biomarker that can be applied broadly to individuals presenting for evaluation of the diagnosis of MS.
2,3,7,8 Tetrachlorodibenzo-p-dioxin-induced RNA abundance changes identify Ackr3, Col18a1, Cyb5a and Glud1 as candidate mediators of toxicity (2016)

2,3,7,8 Tetrachlorodibenzo-p-dioxin (TCDD) is an aromatic, long-lived environmental contaminant. While the pathogenesis of TCDD-induced toxicity is poorly understood, it has been shown that the aryl hydrocarbon receptor (AHR) is required. However, the specific transcriptomic changes that lead to toxic outcomes have not yet been identified. We previously identified a panel of 33 genes that respond to TCDD treatment in two TCDD-sensitive rodent species. To identify genes involved in the onset of hepatic toxicity, we explored 25 of these in-depth using liver from two rat strains: the TCDD-resistant Han/Wistar (H/W) and the TCDD-sensitive Long-Evans (L-E). Time course and dose-response analyses of mRNA abundance following TCDD insult indicate that eight genes are similarly regulated in livers of both strains of rat, suggesting that they are not central to the severe L-E-specific TCDD-induced toxicities. The remaining 17 genes exhibited various divergent mRNA abundances between L-E and H/W strains after TCDD treatment. Several genes displayed a biphasic response where the initial response to TCDD treatment was followed by a secondary response, usually of larger magnitude in L-E liver. This secondary response was most often an exaggeration of the original TCDD-induced response. Only cytochrome b5 type A (microsomal) (Cyb5a) had equivalent TCDD sensitivity to the prototypic AHR-responsive cytochrome P450, family 1, subfamily a, polypeptide 1 (Cyp1a1), while six genes were less sensitive. Four genes showed an early inter-strain difference that was sustained throughout most of the time course (atypical chemokine receptor 3 (Ackr3), collagen, type XVIII, alpha 1 (Col18a1), Cyb5a and glutamate dehydrogenase 1 (Glud1)), and of those genes examined in this study, are most likely to represent genes involved in the pathogenesis of TCDD-induced hepatotoxicity in L-E rats.
Kingfisher: A System for Elastic Cost-aware Provisioning in the Cloud (2010)

Cloud computing platforms allow application providers to rent server capacity to run hosted applications and to dynamically vary the rented capacity to match demand. Today’s cloud platforms offer a plethora of different server configurations for rent and price them differently on a cost-per-core basis. Furthermore, cloud platforms support different replication and migration mechanisms to support elastic provisioning of servers. In this paper, we present Kingfisher a cost-aware provisioning system for cloud applications that can optimize either the rental cost for provisioning a certain capacity or the transition cost of reconfiguring an application’s current capacity. Our system exploits both replication and migration to dynamically provision capacity and uses an integer linear program formulation to optimize cost. We have implemented a prototype of our Kingfisher cloud provisioning system and have evaluated its efficacy on a laboratorybased private Xen cloud as well on the public Amazon EC2 cloud. Our experiments demonstrate the efficacy of Kingfisher in elastically provisioning servers within private and public clouds that see varying application workloads. Our results demonstrate the ability of Kingfisher in reducing server rental costs and reconfiguration overheads over prior costoblivious approaches.
Correction: Cholesteric liquid crystals in rectangular microchannels: skyrmions and stripes (2016)

Correction for 'Cholesteric liquid crystals in rectangular microchannels: skyrmions and stripes' by Yubing Guo et al., Soft Matter, 2016, DOI: 10.1039/c6sm01190j.
Endolysosomal‐Escape Nanovaccines through Adjuvant‐Induced Tumor Antigen Assembly for Enhanced Effector CD8+ T Cell Activation (2018)

The activation of tumor-specific effector immune cells is key for successful immunotherapy and vaccination is a powerful strategy to induce such adaptive immune responses. However, the generation of effective anticancer vaccines is challenging. To overcome these challenges, a novel straight-forward strategy of adjuvant-induced tumor antigen assembly to generate nanovaccines with superior antigen/adjuvant loading efficiency is developed. To protect nanovaccines in circulation and to introduce additional functionalities, a biocompatible polyphenol coating is installed. The resulting functionalizable nanovaccines are equipped with a pH (low) insertion peptide (pHLIP) to facilitate endolysosomal escape and to promote cytoplasmic localization, with the aim to enhance cross-presentation of the antigen by dendritic cells to effectively activate CD8<sup>+</sup> T cell. The results demonstrate that pHLIP-functionalized model nanovaccine can induce endolysosomal escape and enhance CD8<sup>+</sup> T cell activation both in vitro and in vivo. Furthermore, based on the adjuvant-induced antigen assembly, nanovaccines of the clinically relevant tumor-associated antigen NY-ESO-1 are generated and show excellent capacity to elicit NY-ESO-1-specific CD8<sup>+</sup> T cell activation, demonstrating a high potential of this functionalizable nanovaccine formulation strategy for clinical applications.
Oxidation, Impurity Diffusion, and Defect Growth in Silicon—An Overview (1981)

As a result of a large body of literature on oxidation, impurity diffusion, and defect growth in silicon, a consistent picture has emerged of oxidation‐enhanced diffusion (OED) and oxidation‐induced stacking fault growth (OISF). It is believed that silicon self‐interstitials can be generated at an oxidizing interface as a result of an incomplete half‐cell reaction involving silicon and oxygen. Those interstitials that do not participate in surface regrowth participate in raising the steady‐state concentration of self‐interstitials in the surface region. OED can be explained in terms of a partial interstitialcy mechanism involving the surface‐generated self‐interstitials. The growth of OISF will occur if the relative steady‐state self‐interstitial concentration around the fault exceeds the emitted concentration of interstitials from the fault line. It is shown that this model predicts that OISF growth is limited by the production rate of self‐interstitials at the interface. The retrogrowth of OISF and the reduction of OED both occur when the concentration of generated self‐interstitials decreases. The introduction of chlorine‐bearing compounds into the oxidation tube can also cause retrogrowth. The reaction of chlorine with silicon at the interface creates vacancies which can recombine with generated self‐interstitials and reduce their concentration. Calculations show that the chlorine compound formed at the interface is .
Multifunctional actuation systems responding to chemical gradients (2012)

The ability to manipulate the movement of surface microstructures is essential for the development of dynamic, responsive materials. We demonstrate that in addition to bulk actuation upon drying, a unique type of highly localized, directional actuation can be achieved when microstructures embedded in pH responsive gel are exposed to pH gradients. Theory and modelling elucidates the underlying mechanism behind this novel approach to inducing responsive actuation.
SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing (2020)

Abstract Segmental duplications are important for understanding human diseases and evolution. The challenge to distinguish allelic and duplication sequences has hindered their phased assembly as well as characterization of structural variant calls. Here we have developed a novel graph-based approach that leverages single nucleotide differences in overlapping reads to distinguish allelic and duplication sequences information from long read accurate PacBio HiFi sequencing. These differences enable to generate allelic and duplication-specific overlaps in the graph to spell out phased assembly used for structural variant calling. We have applied our method to three public genomes: CHM13, NA12878 and HG002. Our method resolved 86% of duplicated regions fully with contig N50 up to 79 kb and produced &lt;800 structural variant phased calls, outperforming state-of-the-part SDA method in terms of all metrics. Furthermore, we demonstrate the importance of phased assemblies and variant calls to the biologically-relevant duplicated genes such as SMN1, SRGAP2C, NPY4R and FAM72A. Our phased assemblies and accurate variant calling specifically in duplicated regions will enable the study of the evolution and adaptation of various species.
The maximum number of points on a curve of genus 4 over F_8 is 25 (2002)

This paper proves that the maximum number of rational points on a smooth, absolutely irreducible genus 4 curve over the field of 8 elements is 25. The body of the paper shows that 27 points is not possible using techniques from algebraic geometry. The appendix shows that 26 points is not possible by examining the zeta functions.
Pareto-optimized coding configurations for VVenC, a fast and efficient VVC encoder (2021)

The Versatile Video Coding (VVC) standard was finalized in July 2020. It has since been studied in the literature with regards to both compression efficiency and complexity. Most of the experiments regarding VVC were performed based on the VTM reference software using its full configuration, usually compared to the test model of its predecessor, High Efficiency Video Coding (HEVC), HM. In this paper, we present a comprehensive and in-depth analysis of the VVC encoding complexity by using the fast and efficient open VVC encoder implementation VVenC. As a practical non-reference encoder, it offers alternative tradeoffs between compression efficiency and complexity. To find those, we approximate the Pareto set of the configuration space in an iterative process, encompassing search space extending encoding tools as well as search space pruning fast algorithms. While the VVenC Pareto set is derived based on HD and UHD video encoding results, it is validated and improved for alternative input material, namely for low-resolution and screen content video. Based on this optimization, five presets are defined constituting approximate Pareto-optimal encoding points for various content types as well as for multi-threaded operation. Without multi-threading, the presets span working points from faster at 4.7% HM runtime at 11% BD-rate gain through medium providing 38% BD-rate gain over HM at a quarter of the HM runtime, up to slower providing all of VTM’s gain at less than half of its runtime.
Fragmentation mechanisms occurring during an energetic fuel-coolant interaction (1980)

It seems that by investing in user-friendly systems with better technical quality and good support for feedback that professionals perceive as being beneficial would improve the work-related well-being and overall well-being of physicians. Moreover, improving physicians' skills related to information systems by giving them training could help to lessen the stress that results from poorly functioning information systems and improve physicians' well-being.
Learning-Assisted Optimization for Energy-Efficient Scheduling in Deadline-Aware NOMA Systems (2019)

In this paper, we study a class of minimum-energy scheduling problems in non-orthogonal multiple access (NOMA) systems. NOMA is adopted to enable efficient channel utilization and interference mitigation, such that base stations can consume minimal energy to empty their queued data in presence of transmission deadlines, and each user can obtain all the requested data timely. Due to the high computational complexity in resource scheduling and the stringent execution-time constraints in practical systems, providing a time-efficient and high-quality solution to 5G real-time systems is challenging. The conventional iterative optimization approaches may exhibit their limitations in supporting online optimization. We herein explore a viable alternative and develop a learning-assisted optimization framework to improve the computational efficiency while retaining competitive energy-saving performance. The idea is to use deep-learning-based predictions to accelerate the optimization process in conventional optimization methods for tackling the NOMA resource scheduling problems. In numerical studies, the proposed optimization framework demonstrates high computational efficiency. Its computational time is insensitive to the input size. The framework is able to provide optimal solutions as long as the learning-based predictions satisfy a derived optimality condition. For the general cases with imperfect predictions, the algorithmic solution is error-tolerable and performance scaleable, leading the energy-saving performance close to the global optimum.
The More (Antennas), the Merrier: A Survey of Silicon-Based mm-Wave Phased Arrays Using Multi-IC Scaling (2019)

Phased-array antenna technology has had a broad impact for more than half a century, spanning radio astronomy and radar, and is about to ignite a significant shift in the operation of mobile communications. Its general principle is to use an array of wireless transmitters (Txs) or receivers (Rxs) to focus and steer energy. The focus is achieved by creating an interference pattern from the antenna array to enable constructive interference in the desired direction and destructive interference in all of the other directions; the steering is accomplished by modifying the delays at each antenna element in the array to control the directions of constructive and destructive interference [1]-[3].
HEARTMATE III (2002)

PURPOSE: HeartMate III is a centrifugal LVAD featuring a magnetically levitated impeller and integrated control electronics. The goal of our ongoing work is to demonstrate biocompatibility, low hemolysis, and good thermal characteristics in chronic bovine in vivo studies. METHODS: Three implantable titanium prototypes have been built with textured blood-contacting surfaces. To date, pumps have been implanted in three calves (≤ 100 kg at implant) instrumented for pump flow, pump housing temp, and carotid artery pressure measurements. Upon explant, histological and biochemical characteristics of tissue ingrowth within the pump were studied and compared to previous HeartMale I pumps. RESULTS: Two studies were terminated at 14 and 23 days, while one study is ongoing at 93 days. PFH was 6.8 ± 2.6 mg/dl. For the two animals with intact temp probes, the difference between pump and mediastinal temp was 1.3 ± 0.3 and 0.9 ± 0.3 °C. All measured biochemical indicators of end organ function have remained within normal range. Pumps have functioned as designed with no failures. CONCLUSIONS: Our preliminary data suggest that hemolysis and tissue heating will be clinically acceptable with HeartMate III. In chronic bovine implants, the textured surfaces in HeartMate III pumps perform comparably to those in pulsatile HeartMate I pumps.
Designing Robust Checkers in the Presence of Massive Timing Errors (2006)

So far, performance and reliability of circuits have been determined by worst-case characterization of silicon and environmental noise. As new deep sub-micron technologies exacerbate process variations and reduce noise margins, worst-case design will eventually fail to meet an aggressive combination of objectives in performance, reliability, and power. In order to circumvent these difficulties, researchers have recently proposed a new design paradigm: self-calibrating circuits. Design parameters (e.g., operating points) of self-calibrating circuits are set by monitoring correctness of their operation, thus enabling to dynamically trade reliability for power or performance, depending on actual silicon capabilities and noise conditions. In this paper, we study the problem of detecting errors caused by self-calibration of the supply voltage and frequency of an on-chip link. These errors are caused by operation at sub-critical voltage and may be numerous. We attack the problem with a coding technique. We also discuss an alternative approach using double sampling flip-flops. We stress the complementarily of the two approaches and show how they can be combined. Finally, we consider extending our work to computation. We give preliminary research directions on the detection of errors induced by self-calibration for an adder
Smart Small Cell for 5G: Theoretical Feasibility and Prototype Results (2015)

In this article, we present a real-time three dimensional (3D) hybrid beamforming for fifth generation (5G) wireless networks. One of the key concepts in 5G cellular systems is a small cell network, which settles the high mobile traffic demand and provides uniform user-experienced data rates. The overall capacity of the small cell network can be enhanced with the enabling technology of 3D hybrid beamforming. This study validates the feasibility of the 3D hybrid beamforming, mostly for link-level performances, through the implementation of a real-time testbed using a software-defined radio (SDR) platform and fabricated antenna array. Based on the measured data, we also investigate system-level performances to verify the gain of the proposed smart small cell system over long term evolution (LTE) systems by performing system-level simulations based on a 3D ray-tracing tool.
A technique for large-area position-controlled growth of GaAs nanowire arrays (2016)

We demonstrate a technique for fabricating position-controlled, large-area arrays of vertical semiconductor nanowires (NWs) with adjustable periods and NW diameters. In our approach, a Au-covered GaAs substrate is first coated with a thin film of photoresponsive azopolymer, which is exposed twice to a laser interference pattern forming a 2D surface relief grating. After dry etching, an array of polymer islands is formed, which is used as a mask to fabricate a matrix of gold particles. The Au particles are then used as seeds in vapour-liquid-solid growth to create arrays of vertical GaAs NWs using metalorganic vapour phase epitaxy. The presented technique enables producing NWs of uniform size distribution with high throughput and potentially on large wafer sizes without relying on expensive lithography techniques. The feasibility of the technique is demonstrated by arrays of vertical NWs with periods of 255-1000 nm and diameters of 50-80 nm on a 2 × 2 cm area. The grown NWs exhibit high long range order and good crystalline quality. Although only GaAs NWs were grown in this study, in principle, the presented technique is suitable for any material available for Au seeded NW growth.