gebhart/patrepeval huggingface dataset:
Towards Energy-Efficient Adaptive Mpeg-Dash Streaming Using Hevc (2018)

Green networking and communications have become important factors in nowadays energy-hungry video transmission, where users expect to gain high-quality video regardless of time and place. Modern processors, displays and high-speed mobile networks already enable high-definition video streaming to mobile devices that can decode and playback the stream successfully while still maintaining the device capacity for other tasks. However, user mobility and network congestion can affect even the best machinery and introduce the need for HTTP adaptive streaming, which has popularized among content providers. Still, its optimal utilization especially in terms of energy-efficiency is slightly investigated issue. In this paper, we tackle this issue and evaluate both the content production (headend) as well mobile user (terminal) energy consumption against different adaptation methods considering CPU vs. GPU based approaches. The results indicate that frame rate adaptation provides the lowest consumption in both ends and usage of GPUs can lead to further savings.
Early chimerism threshold necessary to sustain engraftment in prenatal allogeneic chimeras (2008)

Durkin, Emily T. MD; Jones, Kelly A. BS; Elnaggar, Dina BS; Rajesh, Deepika PhD; Shaaban, Aimen F. MD, FACS Author Information
Pharmacodynamic effect of ipilimumab on absolute lymphocyte count (ALC) and association with overall survival in patients with advanced melanoma. (2013)

9052 Background: Ipilimumab (Ipi) is a fully human monoclonal antibody that augments antitumor T-cell responses. Ipi has been shown to improve overall survival (OS) in 2 phase (ph) III trials of advanced melanoma, as monotherapy at 3 mg/kg in previously treated patients (pts) (MDX010-20) or at 10 mg/kg with dacarbazine in previously untreated pts (CA184-024). In preclinical and clinical studies, inhibition of CTLA-4 by Ipi resulted in increases in activation and proliferation of peripheral T cells and increases in ALC. Baseline ALC may be a prognostic biomarker in several cancer types. The current analyses aim to increase understanding of changes in ALC with Ipi treatment and association of these changes with OS. Methods: Data were from 6 studies of Ipi with chemotherapy (CT) (ph I 078; N=59) or without CT (ph III MDX010-20; ph II trials 004, 007, 008, and 022; N=1203), and Ipi monotherapy in an Expanded Access Program (N=117) or with commercially available Ipi (N=71) or BRAF inhibitors (N=39). ALC was measured at baseline, prior to each dose during induction (weeks 1, 4, 7, and 10) and at the end of induction (week 13). Cox proportional hazards models were used to estimate and test associations between ALC measures and OS. Results: In all studies, mean ALC increased significantly over time in pts who received Ipi, with or without CT (P&lt;.0001 to P=.03). There was no significant mean increase in ALC in pts who received gp100 or BRAF-inhibitor monotherapy. In study MDX010-20, pts with a greater rate of change in ALC from baseline to week 7 tended to have longer OS (P=.0003). A similar association was found between OS and ALC ≥1000/µL after 2 Ipi doses. However, pts in MDX010-20 had an OS benefit from Ipi relative to gp100, regardless of rate of change in ALC (P=.14). Conclusions: In these analyses, consistent with inhibition of CTLA-4, Ipi induced an increase in mean ALC, even with the addition of CT. A positive association between rate of ALC increase and OS was observed, but this was not specifically predictive of OS benefit from Ipi. Therefore, ALC cannot currently be used to guide clinical management with Ipi. However, further prospective investigation may be warranted.
POSSIBLE ASSOCIATION OF THE IMMUNOSUPPRESSIVE AND B CELL LYMPHOMA-PROMOTING PROPERTIES OF CYCLOSPORINE (1990)

Central to the immunosuppressive properties of cyclosporine is a drug imposed blockade of the interleukin-2 gene activation. As IL-6 stimulates antigen-activated T cells to release IL-2, we examined the influence of CsA on IL-6 gene expression and IL-6-supported T cell proliferation. Northern blot analysis revealed that CsA failed to abolish IL-6 gene expression in mitogen-activated peripheral blood mononuclear cells. In fact, increased IL-6 gene transcription and increased release of IL-6 bioactivity were detected using mitogen-activated PBMCs cultured with CsA doses (200-800 ng/ml) only slightly in excess of the minimal antiproliferative dose. CsA completely abrogated the IL-6-stimulated proliferative responses of macrophage-depleted T cells stimulated with polyvalent anti-CD3 monoclonal antibodies. It is interesting that CsA-treated patients evidence an increased incidence of polyclonal lymphoproliferative disorders and B cell lymphomas. As IL-6 fosters B cell activation and growth of EBV-transformed B cells, excessive CsA doses may support development of EBV-transformed B cell lymphomas via superinduction of the IL-6 gene.
HoLiSwap: Reducing Wire Energy in L1 Caches (2017)

This paper describes HoLiSwap a method to reduce L1 cache wire energy, a significant fraction of total cache energy, by swapping hot lines to the cache way nearest to the processor. We observe that (i) a small fraction (&lt;3%) of cache lines (hot lines) serve over 60% of the L1 cache accesses and (ii) the difference in wire energy between the nearest and farthest cache subarray can be over 6$\times$. Our method exploits this difference in wire energy to dynamically identify hot lines and swap them to the nearest physical way in a set-associative L1 cache. This provides up to 44% improvement in the wire energy (1.82% saving in overall system energy) with no impact on the cache miss rate and 0.13% performance drop. We also show that HoLiSwap can simplify way-prediction.
64 MHz RF Exposure System for Testing of Implanted Medical Devices in MRI Applications (2019)

Currently whole-body transmit RF coils are the most common RF environment for testing. These RF exposure systems designed for testing of devices are commercially available and currently used in a clinical setting; however, even though head-only transmit/receive (TX/RCV) coils are available on MRI scanners, there is not a validated head-only RF exexposure system available for either 64 or 128 MHz. Testing of active implantable medical devices (AIMDs) is guided by the requirements described in ISO 10974:2018(E). Determining the effects radiofrequency (RF) fields have on AIMDS in an MRI system are of paramount importance. Implanted medical devices in the head and neck experience a different local electric field when being imaged head-only exexposure system. This is a significant difference in local electric field when exposed to a head-only transmit coil versus being exposed to a whole-body transmit coil. To adequately evaluate the safety of these devices in that environment, head-only RF exposure systems are needed. In this paper we summarize the steps in developing and validating a head-only RF exexposure system that is properly tuned to 64 MHz and matched to 50 Ω for the testing of implanted medical devices. These steps include the methods for simulating and developing a head-only RF exexposure system.
Diagnosing causes of increased NO{sub x} at Potomac River Unit 4 (1996)

Potomac River Unit 4, a 108 MW unit, has a corner-fired boiler with conventional burners. Through the use of combustion optimization techniques, the NO{sub x} emissions had been reduced from baseline levels of 0.6 lb/MBtu to values below 0.45 lb/MBtu over the load range, and had been routinely dispatched at this reduced emissions level for extended periods of operation. After a scheduled outage in Fall 1995 for boiler maintenance, windbox modifications and a superheater replacement, the unit was returned to service, and it was found that the full-load NO{sub x} level had increased by approximately 0.1 lb/MBtu. A week of tests was performed and pre- and post-outage data analyzed to determine the factors contributing to the increase in NO{sub x} emissions. The principal cause was found to be a reduction in the amount of boiler air in-leakage arising from boiler casing repairs, and leading to higher air-to-fuel ratios in the furnace. Other, secondary, causes were also determined. Results from the analysis indicate the windbox modifications were actually effective in reducing NO{sub x}, although the benefits were obscured due to the intervening circumstances. This paper describes the diagnostic process which was followed and discusses the findings from the investigation.
CosmoFlow: Using Deep Learning to Learn the Universe at Scale (2018)

Deep learning is a promising tool to determine the physical model that describes our universe. To handle the considerable computational cost of this problem, we present CosmoFlow: a highly scalable deep learning application built on top of the TensorFlow framework. CosmoFlow uses efficient implementations of 3D convolution and pooling primitives, together with improvements in threading for many element-wise operations, to improve training performance on Intel <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Xeon Phi™ processors. We also utilize the Cray PE Machine Learning Plugin for efficient scaling to multiple nodes. We demonstrate fully synchronous data-parallel training on 8192 nodes of Cori with 77% parallel efficiency, achieving 3.5 Pflop/s sustained performance. To our knowledge, this is the first large-scale science application of the TensorFlow framework at supercomputer scale with fully-synchronous training. These enhancements enable us to process large 3D dark matter distribution and predict the cosmological parameters Ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> , σ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> and n <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> with unprecedented accuracy.
Cascade: An Application Pipelining Toolkit for Coarse-Grained Reconfigurable Arrays (2022)

While coarse-grained reconfigurable arrays (CGRAs) have emerged as promising programmable accelerator architectures, pipelining applications running on CGRAs is required to ensure high maximum clock frequencies. Current CGRA compilers either lack pipelining techniques resulting in low performance or perform exhaustive pipelining resulting in high energy and resource consumption. We introduce Cascade, an application pipelining toolkit for CGRAs, including a CGRA application frequency model, automated pipelining techniques for CGRA application compilers that work with both dense and sparse applications, and hardware optimizations for improving application frequency. Cascade enables 7 - 34x lower critical path delays and 7 - 190x lower EDP across a variety of dense image processing and machine learning workloads, and 2 - 4.4x lower critical path delays and 1.5 - 4.2x lower EDP on sparse workloads, compared to a compiler without pipelining.
Motif-Based Visual Analysis of Dynamic Networks (2022)

Many data analysis problems rely on dynamic networks, such as social or communication network analyses. Providing a scalable overview of long sequences of such dynamic networks remains challenging due to the underlying large-scale data containing elusive topological changes. We propose two complementary pixel-based visualizations, which reflect occurrences of selected sub-networks (motifs) and provide a time-scalable overview of dynamic networks: a network-level census (motif significance profiles) linked with a node-level sub-network metric (graphlet degree vectors) views to reveal structural changes, trends, states, and outliers. The network census captures significantly occurring motifs compared to their expected occurrences in random networks and exposes structural changes in a dynamic network. The sub-network metrics display the local topological neighborhood of a node in a single network belonging to the dynamic network. The linked pixel-based visualizations allow exploring motifs in different-sized networks to analyze the changing structures within and across dynamic networks, for instance, to visually analyze the shape and rate of changes in the network topology. We describe the identification of visual patterns, also considering different reordering strategies to emphasize visual patterns. We demonstrate the approach’s usefulness by a use case analysis based on real-world large-scale dynamic networks, such as the evolving social networks of Reddit or Facebook.
Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions (1997)

In bacteriophage T7 the gene 2.5 single-stranded DNA-binding protein and the gene 4 helicase together promote the annealing of homologous regions of two DNA partners to form a joint molecule and subsequent strand transfer. In this reaction T7 gene 2.5 protein is essential for joint molecule formation, but is not required for T7 gene 4 protein-mediated strand transfer. T7 gene 4 helicase alone is able to mediate strand transfer, provided that a joint molecule is available. The present paper shows that, in addition, strand transfer proceeds at a normal rate even when both DNA partners contain ultraviolet-induced pyrimidine dimers (0.6 dimer per 100 nt). An insert of a relatively long (842-nt) segment of nonhomologous DNA in the single-stranded DNA partner has no effect on strand transfer, whereas its presence in the double-stranded partner prevents strand transfer. A short insert (37 nt) can be tolerated in either partner. Thus, DNA helicase is able to participate in recombinational DNA repair through its role in strand exchange, providing a pathway distinct from nucleotide excision repair.
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation (2023)

Abstract During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes defining fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, accompanied by changes in 3D organization and local changes in DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.
1-Deoxy-L-mannitol (6-deoxy-L-mannitol or L-rhamnitol) (2008)

The crystalline form of 1-de-oxy-l-mannitol, C(6)H(14)O(5), exists as an extensively hydrogen-bonded structure with each mol-ecule acting as a donor and acceptor for five hydrogen bonds. There are no unusual crystal-packing features; the absolute configuration was determined from the use of 6-de-oxy-l-mannose (l-rhamnose) as the starting material.
Skyrmion Echo in a System of Interacting Skyrmions (2022)

We consider helical rotation of skyrmions confined in the potentials formed by nanodisks. Based on numerical and analytical calculations we propose the skyrmion echo phenomenon. The physical mechanism of the skyrmion echo formation is also proposed. Because of the distortion of the lattice, impurities, or pinning effect, confined skyrmions experience slightly different local fields, which leads to dephasing of the initial signal. The interaction between skyrmions also can contribute to the dephasing process. However, switching the magnetization direction in the nanodiscs (e.g., by spin transfer torque) also switches the helical rotation of the skyrmions from clockwise to anticlockwise (or vice versa), and this restores the initial signal (which is the essence of skyrmion echo).
Formation Process of Microstructure in Laser Powder Bed Fusion with WC Cemented Carbide Powder (2020)

In this paper, the microstructure formation process of WC cemented carbide manufactured by Laser Powder Bed Fusion (LPBF) was investigated with WC/25 wt%Co agglomerated and sintered powder. The internal structure of the as-built cemented carbide specimen was categorized into two regions. The first region included many pores and a unique microstructure which was not observed from the samples fabricated with conventional manufacturing methods. In this region, W2C and W3Co3C were formed due to a WC decomposition and an evaporation of graphite and Co during laser irradiation. On the other hand, the second region showed the similar microstructure to the conventional method. The microstructure of the first region revealed that the powder was completely melted during a laser scanning process. The precipitation process of W2C, W3Co3C, and Graphite phase was considered with calculated liquidus projection of a C-Co-W ternary phase diagram.
Direct amplification of picosecond pulses in erbium fibre to 127 kW peak power without pulse break-up (2008)

Picosecond pulses are directly amplified in a core pumped erbium fibre with effective area 1170-mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> to record diffraction limited 67- nJ pulse energy and 127- kW peak power without pulse break-up.
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans (2022)

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.
Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer (2019)

Apolipoprotein E is a 299-residue lipid carrier protein produced in both the liver and the brain. The protein has three major isoforms denoted apoE2, apoE3, and apoE4 which differ at positions 112 and 158 and which occur at different frequencies in the human population. Genome-wide association studies indicate that the possession of two apoE4 alleles is a strong genetic risk factor for late-onset Alzheimer’s disease (LOAD). In an attempt to identify a small molecule stabilizer of apoE4 function that may have utility as a therapy for Alzheimer’s disease, we carried out an NMR-based fragment screen on the N-terminal domain of apoE4 and identified a benzyl amidine based fragment binder. In addition to NMR, binding was characterized using various other biophysical techniques, and a crystal structure of the bound core was obtained. Core elaboration ultimately yielded a compound that showed activity in an IL-6 and IL-8 cytokine release assay.
Experimental demonstration of active equalization and ASE suppression of three 2.5-Gb/s WDM-network channels over 2500 km using AOTF as transmission filters (1997)

By using acoustooptic tunable filters with active feedback, we have experimentally demonstrated the dynamic channel-power equalization of the nonuniform EDFA gain as well as interchannel ASE suppression. The AOTF's have multiple independent passbands and act as dynamic wavelength-dependent loss elements. After 2500 km, the power differential is reduced from over 20 dB to /spl sim/1 dB for three 2.5-Gb/s WDM channels covering an /spl sim/8-nm wavelength range, and a 10/sup -9/ BER can be achieved for all channels.
Vascular Endothelial Growth Factor-B in Physiology and Disease (2014)

Vascular endothelial growth factor-B (VEGF-B), discovered over 15 years ago, has long been seen as one of the more ambiguous members of the VEGF family. VEGF-B is produced as two isoforms: one that binds strongly to heparan sulfate in the pericellular matrix and a soluble form that can acquire binding via proteolytic processing. Both forms of VEGF-B bind to VEGF-receptor 1 (VEGFR-1) and the neuropilin-1 (NRP-1) coreceptor, which are expressed mainly in blood vascular endothelial cells. VEGF-B-deficient mice and rats are viable without any overt phenotype, and the ability of VEGF-B to induce angiogenesis in most tissues is weak. This has been a puzzle, as the related placenta growth factor (PlGF) binds to the same receptors and induces angiogenesis and arteriogenesis in a variety of tissues. However, it seems that VEGF-B is a vascular growth factor that is more tissue specific and can have trophic and metabolic effects, and its binding to VEGFR-1 shows subtle but important differences compared with that of PlGF. VEGF-B has the potential to induce coronary vessel growth and cardiac hypertrophy, which can protect the heart from ischemic damage as well as heart failure. In addition, VEGF-B is abundantly expressed in tissues with highly active energy metabolism, where it could support significant metabolic functions. VEGF-B also has a role in neuroprotection, but unlike other members of the VEGF family, it does not have a clear role in tumor progression. Here we review what is hitherto known about the functions of this growth factor in physiology and disease.
Automated Framework for Time-Domain Piecewise-Linear Fitting Method Based on Digital Wave Processing of $S$ -Parameters (2019)

An innovative full time-domain macromodeling technique for general, linear multiport systems is described. The methodology is defined in a digital wave framework and time-domain simulations are performed via an efficient method called Segment Fast Convolution (SFC). It is based on a piecewise-constant (PWC) model of the impulse response of scattering parameters, computed starting from a piecewise-linear fitting of their step response (PWLFIT). Such step response is directly available from time-domain reflectometer measurements (TDR/TDT) or equivalent simulations. The model-building phase is performed in a fast automated framework and an analytic formulation of computational efficiency of the SFC with respect to the standard time-domain convolution is given. Two application examples are used to verify the PWLFIT performance and to perform a comparison with macromodeling methods defined in the frequency-domain, such as Vector Fitting (VF).