gebhart/patrepeval huggingface dataset:
Edema and Lymph Flow (2018)

The lymphatic system plays a critical role in the process of reducing inflammation and edema, as well as a major role in the immune response. It moves fluid (lymph) from interstitial spaces in tissues via a network of collecting vessels to the lymph nodes, where it is mostly emptied into the venous system. Some fluid moves further along the lymphatic chain to other lymph nodes and eventually empties into the thoracic duct. PBM reduces swelling, and it seems likely that the lymphatic system is involved, although limited evidence exists to confirm this. A PubMed search for a range of PBM terms (see Chapter 1) AND edema OR oedema OR swelling returns over 50 abstracts. Most of these abstracts are for post-mastectomy lymphedema, post-surgical swelling, acute soft-tissue injury, and arthritic joints. The mechanism by which light affects edema has not been adequately explored, although it makes sense that it should because nitric oxide (NO) modulates lymphatic vessel contraction and subsequent lymph flow, and it has been established that PBM releases stores of NO8–10 and subsequently improves blood flow. As with blood vessels, NO is produced by endothelial nitric oxide synthase (eNOS) in lymphatic endothelial cells, which in turn affects the dilation and force of lymph vessel contractions. Small amounts of NO are produced (by eNOS) when lymph vessels are stretched (by movement or a stretch/massage technique), and this leads to alternating periods of diastolic filling and systolic ejection of lymphangions (the tiny functional units of the collecting lymphatic system). Excessive amounts of NO produced by inducible nitric oxide synthase (iNOS) during inflammation can overwhelm the NO gradients produced by eNOS. The suppression of eNOS by iNOS disrupts the contraction/relaxation cycle in favor of excessive contraction and subsequent reduced flow.
Ras Activity Regulation by Monoubiquitination (2013)

Ras proteins are critical regulators of cellular growth. The population of activated, GTP‐bound Ras in normal cells is controlled by protein regulators. Oncogenic mutations promote activation by populating the active state of Ras, most frequently by impairing the action of proteins that downregulate its activity. Recently, a novel mechanism of Ras activation was identified, in which modification by ubiquitination was found to populate Ras in its active GTP‐bound state, enhance interactions with downstream effectors and promote Ras‐mediated tumorigenesis. These findings represent a paradigm shift in our understanding of the role monoubiquitination may play in protein regulation. By conducting NMR, modeling, biochemical and biological studies, we find that monoubiquitination of Ras at position 147 has little effect on intrinsic guanine nucleotide binding or hydrolysis, but impairs the ability of GTPase activating proteins to downregulate Ras activity, accounting for the accumulation of Ras‐GTP in cells. These findings reveal that a post‐translational modification can disrupt protein interactions that normally constrain cellular signaling and transformation.
Device Degradation Phenomena in GaN HFET Technology: Status, Mechanisms, and Opportunities (2006)

AlGaN/GaN HFET devices demonstrate remarkable performance. For commercial acceptance of this technology, long-term device stability must meet stringent industry standards. We review the current status of GaN reliability and contrast it with the requirement for commercial viability. Results analyzing degradation pertaining to buffer leakage and gate diode forward failure is presented
Abstract 3628: Improving sequencing quality of libraries prepared from FFPE DNA (2016)

Abstract Targeted cancer therapy based on genomic alterations can be remarkably effective, and has made significant strides with the recent advances in next-generation sequencing (NGS) technology. Although samples of blood and other bodily fluids are being actively explored for early disease diagnosis and treatment monitoring, DNA isolated from FFPE samples is currently the main source for NGS-based cancer profiling in clinical settings. Unfortunately, sequencing DNA from FFPE samples is challenging due to limited quantities and poor quality, a result of DNA damage incurred during fixation and storage. Artifacts associated with FFPE DNA have limited the mutation detection sensitivity to ≥ 5% mutant allele frequency (Frampton et al, Nature Biotechnology 2013), which would unfortunately leave many low-abundance genetic variants of clinical significance undetected. For example, clinical resistance-causing KIT and EGFR mutations can be present in tumors at levels &amp;lt;&amp;lt; 1% (Milbury et al, Clin. Chem. 2012). In this study, we investigated the effects of DNA repair and different sample handling workflows on sequencing quality of libraries prepared from FFPE samples. Careful analysis of sequencing data showed that base calling qualities for all 4 bases are improved, and aberrant G:C to A:T mutations were significantly reduced upon DNA repair. Because the large majority of mutations encountered in human tumors are G:C to A:T mutations (Greenman, C. Nature 2007), we expect that lowering the damage induced background noise of FFPE DNA would allow more reliable detection of clinically important, actionable mutations at lower abundance. In addition, we observed specific sequencing artifacts associated with the method of handling FFPE samples and have since identified effective measurements to avoid such artifacts. We expect that these improvements in sequencing quality of FFPE samples would ultimately enable more sensitive and robust detection of many low level genetic variations in clinically and biologically relevant cancer genes. Citation Format: pingfang liu, Lixin Chen, Laurence Ettwiller, Christine Sumner, Fiona J. Stewart, Eileen T. Dimalanta, Theodore B. Davis, Evans C. Thomas. Improving sequencing quality of libraries prepared from FFPE DNA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3628.
Determination of bacteriocin-encoding plasmids of Pediococcus acidilactici strains by Southern hybridization (1994)

A 3.5 kb (2.3 MDa) plasmid probe (pRBI) containing the pap gene (pediocin AcH production) was used in Southern hybridization tests to determine the presence or absence of a plasmid-encoded pediocin gene in various isolates of Pediococcus. This probe hybridized with a 9.4 kb (6.2 MDa) plasmid found present in all pediocin-producing Pediococcus acidilactici strains tested. Conversely, this probe showed no reactions with Ped. acidilactici RS2-1, AB6-1 and PC, strains which did not produce pediocin and lacked the 9.4 kb (6.2 MDa) plasmid. This probe also did not hybridize with the plasmids from a bacteriocin producing Ped. pentosaceus strain.
The Influence of Printing Parameters and Cell Density on Bioink Printing Outcomes (2020)

Bioink printability persists as a limiting factor toward many bioprinting applications. Printing parameter selection is largely user-dependent, and the effect of cell density on printability has not been thoroughly investigated. Recently, methods have been developed to give greater insight into printing outcomes. This study aims to further advance those methods and apply them to study the effect of printing parameters (feedrate and flowrate) and cell density on printability. Two printed structures, a crosshatch and five-layer tube, were established as printing standards and utilized to determine the printing outcomes. Acellular bioinks were printed using a testing matrix of feedrates of 37.5, 75, 150, 300, and 600 mm/min and flowrates of 21, 42, 84, 168, and 336 mm<sup>3</sup>/min. Structures were also printed with cell densities of 5, 10, 20, and 40 × 10<sup>6</sup> cell/mL at 150 mm/min and 84 mm<sup>3</sup>/min. Only speed ratios (defined as flowrate divided by feedrate) from 0.07 to 2.24 mm<sup>2</sup> were suitable for analysis. Increasing speed ratio dramatically increased the height, width, and wall thickness of tubular structures, but did not influence radial accuracy. For crosshatch structures, the area of pores and the frequency of broken filaments were decreased without impacting pore shape (<i>Pr</i>). Within speed ratios, feedrate and flowrate had negligible, inconsistent effects. Cell density did not affect any printing outcomes despite slight rheological changes. Printing outcomes were dominated by the speed ratio, with feedrate, flowrate, and cell density having little impact on printing outcomes when controlling for speed ratio within the ranges tested. The relevance of these results to other bioinks and printing conditions requires continued investigation by the bioprinting community, as well as highlight speed ratio as a key variable to report and suggest that rheology is a more sensitive measure than printing outcomes.
Evolution of Novartis’ Small Molecule Screening Deck Design (2020)

This article summarizes the evolution of the screening deck at the Novartis Institutes for BioMedical Research (NIBR). Historically, the screening deck was an assembly of all available compounds. In 2015, we designed a first deck to facilitate access to diverse subsets with optimized properties. We allocated the compounds as plated subsets on a 2D grid with property based ranking in one dimension and increasing structural redundancy in the other. The learnings from the 2015 screening deck were applied to the design of a next generation in 2019. We found that using traditional leadlikeness criteria (mainly MW, clogP) reduces the hit rates of attractive chemical starting points in subset screening. Consequently, the 2019 deck relies on solubility and permeability to select preferred compounds. The 2019 design also uses NIBR's experimental assay data and inferred biological activity profiles in addition to structural diversity to define redundancy across the compound sets.
Phase II Evaluation of Docetaxel Plus Exisulind in Patients With Androgen Independent Prostate Carcinoma (2006)

: Overall, our trial indicated that the toxicity profile and efficacy of this regimen is unlikely to be substantially better than single agent docetaxel.
STAG2 deficiency induces interferon responses via cGAS-STING pathway and restricts virus infection (2018)

Cohesin is a multi-subunit nuclear protein complex that coordinates sister chromatid separation during cell division. Highly frequent somatic mutations in genes encoding core cohesin subunits have been reported in multiple cancer types. Here, using a genome-wide CRISPR-Cas9 screening approach to identify host dependency factors and novel innate immune regulators of rotavirus (RV) infection, we demonstrate that the loss of STAG2, an important component of the cohesin complex, confers resistance to RV replication in cell culture and human intestinal enteroids. Mechanistically, STAG2 deficiency results in spontaneous genomic DNA damage and robust interferon (IFN) expression via the cGAS-STING cytosolic DNA-sensing pathway. The resultant activation of JAK-STAT signaling and IFN-stimulated gene (ISG) expression broadly protects against virus infections, including RVs. Our work highlights a previously undocumented role of the cohesin complex in regulating IFN homeostasis and identifies new therapeutic avenues for manipulating the innate immunity.
Iterative Water-filling for Load-balancing in Wireless LAN or Microcellular Networks (2006)

This paper presents an efficient iterative load-balancing algorithm for time and bandwidth allocation among access points (APs) and users subject to heterogeneous fairness and application requirements. The algorithm can be carried out either at a central network switch with site-specific propagation predictions, or in a decentralized manner. The algorithm converges to maximum network resource utilization from any starting point, and usually converges in 3 to 9 iterations in various network conditions including users joining, leaving, and moving within a network and various network sizes. Such a fast convergence allows real-time implementations of our algorithm. Simulation results show that our algorithm has merits over other schemes especially when users exhibit clustered patterns: Our algorithm, when assuming multiple radios at each user, achieves 48% gain of median throughput as compared with the max-min fair load-balancing scheme (also with the multi-radio assumption) while losing 14% of fairness index; we also achieve 26% gain of median throughput and 52% gain of fairness index over the strongest-signal-first scheme (which assumes each user has only a single radio). When only a single radio is used, our algorithm is similar to the max-min fairness scheme, and is still better than SSF with 44% gain of 25-percentile throughput and 37% gain of fairness index
Coupled Electrorotation: Two Proximate Microspheres Spin in Registry with an AC Electric Field (2002)

We report a novel approach to micro- and nanoparticle rotation, uniting the fine translational control afforded by optical trapping with the flexibility and simplicity of dipole-field-induced coupled electrorotation (CER). Fluorescence imaging using a microparticle photopatterning technique was combined with optical trapping to quantify both the senses and speeds of rotation for individual pairs of particles. Laser tweezers allowed controlled positioning of a pair of particles within a dipole field while simultaneously providing an axis about which the particles rotated. The particle-particle interactions inherent in CER offer several distinct advantages compared with electrorotation in multipole fields. Results from several investigations highlight the utility of this approach, including quantification of rotation in spheres as small as 750 nm in diameter, observation of rotation rates as high as 1800 rpm, fabrication of coupled electrorotational "antigears", trapping and rotation of sphere dimers, and exploitation of the registry of sphere rotation to probe the dielectric properties of immobile objects.
Appendix A Review of Electromagnetic Wave Propagation (2012)

Some sections of this book rely on the reader's familiarity with various aspects of EM field theory. This appendix briefly reviews wave propagation, the idea of a complex refraction index, the Poynting vector, and the diffraction limit. The concepts introduced here are reviewed only - not fully developed. Maxwell's equations are used as the starting point. SI units (meter, kilogram, second, ampere) are used throughout.
High Efficiency Water Heating Technology Development Final Report, Part II: CO<sub>2</sub> and Absorption-Based Residential Heat Pump Water Heater Development (2017)

The two objectives of this project were to 1.demonstrate an affordable path to an ENERGY STAR qualified electric heat pump water heater (HPWH) based on low-global warming potential (GWP) CO2 refrigerant, and 2.demonstrate an affordable path to a gas-fired absorption-based heat pump water heater with a gas energy factor (EF) greater than 1.0. The first objective has been met, and the project has identified a promising low-cost option capable of meeting the second objective. This report documents the process followed and results obtained in addressing these objectives.
ChemInform Abstract: Synthesis and Identification of Conformationally Constrained Selective MMP Inhibitors. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Increased TRAIL-resistance of pancreatic cancer stem cells (2008)

Introduction: Due to chemoresistance and early metastasis formation pancreatic cancer still demonstrates disastrous survival rates. According to the cancer stem cell model only a small proportion of cancer cells, termed cancer stem cells, possesses the capacity of unlimited self-renewal which, supplemented by chemoresistance, cause tumor relapse and metastasis formation. CD44 has been published as a tumor stem cell marker for pancreatic cancer. Triggering the extrinsic pathway of apoptosis induction, TNF-related apoptosis-inducing ligand (TRAIL) induces apoptosis in many tumor cells but not in most normal tissues.
Making faces (1998)

We have created a system for capturing both the three-dimensional geometry and color and shading information for human facial expressions. We use this data to reconstruct photorealistic, 3D animations of the captured expressions. The system uses a large set of sampling points on the face to accurately track the three dimensional deformations of the face. Simultaneously with the tracking of the geometric data, we capture multiple high resolution, registered video images of the face. These images are used to create a texture map sequence for a three dimensional polygonal face model which can then be rendered on standard 3D graphics hardware. The resulting facial animation is surprisingly life-like and looks very much like the original live performance. Separating the capture of the geometry from the texture images eliminates much of the variance in the image data due to motion, which increases compression ratios. Although the primary emphasis of our work is not compression we have investigated the use of a novel method to compress the geometric data based on principal components analysis. The texture sequence is compressed using an MPEG4 video codec. Animations reconstructed from 512x512 pixel textures look good at data rates as low as 240 Kbits per second.
Electromagnetic properties of dry and water saturated basalt rock, 1-110 GHz (1998)

This paper reports on the measured electromagnetic properties of dry and water saturated basalt rock over a frequency range of 1-110 GHz. Tests were conducted in standard waveguides below 12 GHz and with free-space systems above 12 GHz. The basalt used in this investigation was found to be nonmagnetic. Measured relative permittivities for the dry basalt varied from approximately (8.19,-0.71) at 1.12 GHz to (6.80,-0.49) at 110 GHz. The porosity of the basalt was determined to be roughly 10%. Properties of water saturated basalt were also measured at several frequencies and compared to theoretical predictions based on a simple Maxwell-Garnett mixing theory. Finally, the potential of using microwave tomography on basalt rock was examined based on the resulting properties.
A unified fast channel change framework for IPTV networks (2011)

In this paper we introduce a distributed channel change framework that utilizes a dedicated server and session peers to support the fast channel change process. Support peers represent the prior choice to deliver the channel change packets to the zapping users. The dedicated server, which we refer to as the Channel Switch Coordinator (CSC), is essentially responsible for the coordination of the channel change requests. To minimize the average channel change delay for all the users connected to the same CSC server, CSC server is also responsible for the delivery of channel change and proactive repair packets, whenever peer-based delivery fails to achieve the desired performance results in terms of channel change latency. Because of the increased scalability offered by the use of support peers during the channel change process, the proposed approach allows the use of longer group-of-picture (GOP) sizes for the transmission of the IPTV content.
Using Internet of Things Technologies for an Efficient Data Collection in Maintenance 4.0 (2019)

The digital transformation in the manufacturing world raised an additional interest in data collection and connectivity, preferably to the one performed in real time. Internet of Things (IoT) and Machine to Machine (M2M) technologies allow the collection of the huge amount of generated data in the shop floor, at the desired rates and without any human intervention. This paper describes the application of IoT technologies to create an automatic data collection solution for an industrial metal stamping unit, supporting its posterior processing, aiming to develop monitoring, prediction and optimization in an industrial intelligent and predictive maintenance system.
Dynamics and control of a 4-dof wearable cable-driven upper arm exoskeleton (2009)

In this paper, we present the dynamics, control, and preliminary experiments on a wearable upper arm exoskeleton intended for human users with four degrees-of-freedom (dof), driven by six cables. The control of this cable-driven exoskeleton is complicated because the cables can transmit forces to the arm only under tension. The standard PD controllers or computed torque controllers perform only moderately since the cables need to be in tension. Future efforts will seek to refine these control strategies and their implementations to improve functionality of a human user.
What are the risk factors and settings for non‐alcoholic fatty liver disease in Asia–Pacific? (2007)

The risk factors and settings for non-alcoholic fatty liver disease (NAFLD) in Asians are reviewed comprehensively. Based particularly on large community-based studies using ultrasonography, case-control series and prospective longitudinal studies, the prevalence of NAFLD in Asia is between 12% and 24%, depending on age, gender, locality and ethnicity. Further, the prevalence in China and Japan has nearly doubled in the last 10-15 years. A detailed analysis of these data shows that NAFLD risk factors for Asians resemble those in the West for age at presentation, prevalence of type 2 diabetes mellitus (T2DM) and hyperlipidemia. The apparent differences in prevalence of central obesity and overall obesity are related to criteria used to define waist circumference and body mass index (BMI), respectively. The strongest associations are with components of the metabolic syndrome, particularly the combined presence of central obesity and obesity. Non-alcoholic fatty liver disease appears to be associated with long-standing insulin resistance and likely represents the hepatic manifestation of metabolic syndrome. Not surprisingly therefore, Asians with NAFLD are at high risk of developing diabetes and cardiovascular disease. Conversely, metabolic syndrome may precede the diagnosis of NAFLD. The increasing prevalence of obesity, coupled with T2DM, dyslipidemia, hypertension and ultimately metabolic syndrome puts more than half the world's population at risk of developing NAFLD/non-alcoholic steatohepatitis/cirrhosis in the coming decades. Public health initiatives are clearly imperative to halt or reverse the global 'diabesity' pandemic, the underlying basis of NAFLD and metabolic syndrome. In addition, a perspective of NAFLD beyond its hepatic consequences is now warranted; this needs to be considered in relation to management guidelines for affected individuals.
At‐home sperm testing for epidemiologic studies: Evaluation of the Trak male fertility testing system in an internet‐based preconception cohort (2019)

The Trak System provides a simple and potentially cost-effective means of measuring important semen parameters and may be useful in population-based epidemiologic fertility studies.