gebhart/patrepeval huggingface dataset:
Analysis of Regulatory Network Involved in Mechanical Induction of Embryonic Stem Cell Differentiation (2012)

Embryonic stem cells are conventionally differentiated by modulating specific growth factors in the cell culture media. Recently the effect of cellular mechanical microenvironment in inducing phenotype specific differentiation has attracted considerable attention. We have shown the possibility of inducing endoderm differentiation by culturing the stem cells on fibrin substrates of specific stiffness. Here, we analyze the regulatory network involved in such mechanically induced endoderm differentiation under two different experimental configurations of 2-dimensional and 3-dimensional culture, respectively. Mouse embryonic stem cells are differentiated on an array of substrates of varying mechanical properties and analyzed for relevant endoderm markers. The experimental data set is further analyzed for identification of co-regulated transcription factors across different substrate conditions using the technique of bi-clustering. Overlapped bi-clusters are identified following an optimization formulation, which is solved using an evolutionary algorithm. While typically such analysis is performed at the mean value of expression data across experimental repeats, the variability of stem cell systems reduces the confidence on such analysis of mean data. Bootstrapping technique is thus integrated with the bi-clustering algorithm to determine sets of robust bi-clusters, which is found to differ significantly from corresponding bi-clusters at the mean data value. Analysis of robust bi-clusters reveals an overall similar network interaction as has been reported for chemically induced endoderm or endodermal organs but with differences in patterning between 2-dimensional and 3-dimensional culture. Such analysis sheds light on the pathway of stem cell differentiation indicating the prospect of the two culture configurations for further maturation.
The Sock Electrode Array: A Tool for Determining Global Epicardial Activation during Unstable Arrhythmias (1980)

The conventional technique for mapping the sequence of epicardial activation uses a hand-held electrode moved over the heart to record from a number of epicardial sites one at a time, and requires 5-15 minutes to record from 50 or more sites distributed over the entire ventricular epicardium. This method is inadequate for arrhythmias that are transient or vary from beat to beat. To overcome these limitations the "sock electrode array," a contour-fitting sock containing 26 or 52 electrodes, has been developed. The nylon mesh sock is pulled over the heart and permits simultaneous recording of potentials from electrodes distributed over the entire ventricular epicardium. The electrograms are recorded and converted to digital form for computer generation of isochronous maps. Most of the epicardial activation sequence derived from the sock electrode were compared to those obtained by the hand-held electrode in six normal dogs during sinus rhythm and ventricular pacing. The sequence of local activation times acquired by both methods showed similar areas of early and late activation and comparable isochronous maps. The hand-held electrode technique required 10-15 minutes for data acquisition and another 15-30 minutes for analysis. The sock electrode array allowed electrograms from 26 epicardial electrodes to be recorded simultaneously during one cardiac cycle and computer generated isochronous maps could be displayed within 10 minutes. This method allows rapid recording and analysis of epicardial electrical phenomena and should meet the time constraints imposed during the intraoperative study of ventricular tachyarrhythmias in patients.
Cellular Thymidine Kinase Activity Is Required for the Inhibition of HIV-1 Replication by AZT in Lymphocytes (1994)

In this report, we provide evidence that the cellular thymidine kinase activity is required for the inhibition of HIV replication by zidovudine (AZT) in lymphocytes. The HSV-1 thymidine kinase protein is not able to substitute for the cellular enzyme, in accord with in vitro data that AZT is poorly phosphorylated by the HSV-derived activity.
QuickStart: An Upfront Client-Based Design Advisor for Parallel Data Warehouses (2009)

QuickStart is a tool to automate the physical design of data warehouses for HP's Neoview system. It has been researched and prototyped at HP Labs with close interaction from Neoview design experts. It embodies heuristics and best practices of the experts to search for candidate physical features and uses cost calculations to recommend the features that result in good designs. It has some unique characteristics that differentiate it from other physical design advisors. In particular, it is the only advisor that is client-based, does not require a DBMS server installation and can work off a laptop by simply connecting to the customers' flat files. Another unique characteristic of QuickStart is that it provides the rationale for its recommendations.
Proximity to livestock farms and COVID-19 in the Netherlands, 2020-2021 (2022)

Abstract Objectives In the Netherlands, during the first phase of the COVID-19 epidemic, the hotspot of COVID-19 overlapped with the country’s main livestock area, while in subsequent phases this distinct spatial pattern disappeared. Previous studies show that living near livestock farms influence human respiratory health and immunological responses. This study aimed to explore whether proximity to livestock was associated with SARS-CoV-2 infection. Methods The associations between residential (6-digit postal-code) distance to the nearest livestock farm and individuals’ SARS-CoV-2 status was studied in multilevel logistic regression models, comparing individuals notified with a positive SARS-CoV-2 test to the general population in the Netherlands. Data included all reported Dutch laboratory-confirmed patients with disease onset before 1 January 2022. Individuals living in strongly urbanised areas and border areas were excluded. Models were adjusted for individuals’ age categories, the social status of the postal code area, particulate matter (PM 10 )-and nitrogen dioxide (NO 2 )-concentrations. We analysed data for the entire period and population as well as separately for eight time periods (Jan-Mar, Apr-Jun, Jul-Sep and Oct-Dec in 2020 and 2021), four geographic areas of the Netherlands (north, east, west and south), and for five age categories (0-14, 15-24, 25-44, 45-64 and &gt; 65 years). Results Over the period 2020-2021, individuals’ SARS-CoV-2 status was associated with living closer to livestock farms. This association increased from an Odds Ratio (OR) of 1.01 (95% Confidence Interval [CI] 1.01-1.02) for patients living at a distance of 751-1000 m to a farm to an OR of 1.04 (95% CI 1.04-1.04), 1.07 (95% CI 1.06-1.07) and 1.11 (95% CI 1.10-1.12) for patients living in the more proximate 501-750 m, 251-500m and 0-250 m zones around farms, all relative to patients living further than 1000 m around farms. This association was observed in three out of four quarters of the year in both 2020 and 2021, and in all studied geographic areas and age groups. Conclusions In this exploratory study with individual SARS-CoV-2 notification data and high-resolution spatial data associations were found between living near livestock farms and individuals’ SARS-CoV-2 status in the Netherlands. Verification of the results in other countries is warranted, as well as investigations into possible underlying mechanisms.
Identification of a metagenomic gene cluster containing a new class A beta‐lactamase and toxin‐antitoxin systems (2013)

Several reports mention the presence of antibiotic resistance genes in natural and polluted environments, but many studies are based on their detection via polymerase chain reaction (PCR amplification of known genes and not on an activity screening. We constructed a metagenomic fosmid bank from DNA isolated from a polluted river in Brussels, Belgium, the Zenne. A total of 120,000 clones were pooled and plated directly on solid media containing different antibiotics. Several clones were isolated which could grow in the presence of ampicillin. The DNA from several clones was extracted and subjected to restriction analysis and, based on their restriction pattern, two different clones were found. One of the clones was selected for further study as it showed a higher level of resistance to different β-lactams antibiotics (ticarcilline and ceftazidime). To find out which gene is responsible for the resistance, an in vitro transposon mutagenesis was performed and clones having lost the resistance phenotype were analyzed via inverse PCR amplification. Several clones had an insert in a gene encoding a new type of β-lactamase. The amplified fosmid DNA was fully sequenced revealing an insert of 41 kb containing 39 open reading frames (ORFs). Transposon insertions inactivating the resistance to β-lactams were also found in the ORF upstream of the blaA gene, encoding an aminotransferase, suggesting a polar effect on the transcription of the gene downstream. In addition, other genes were found such as histidine biosynthesis genes, which were found to be scattered on the insert, a relA/spoT gene, and genes belonging to type II toxin-antitoxin system. This predicted system was experimentally validated in Escherichia coli using an inducible expression system.
W-Band Free-Space Dielectric Material Property Measurement Techniques for Beamed Energy Applications (2015)

Free-space techniques in W-band (75-110 GHz) using a vector network analyzer and millimeter-wave lenses are applied at room temperature to measure the intrinsic electromagnetic properties of materials, including dielectric constants and dielectric loss factors to characterize millimeter-wave absorption and related electromagnetic interactions with the material. The measurement techniques from the dielectric property measurement experiments will be performed at a range of higher temperatures (up to 2300K) to identify materials of interest for scaled beamed energy heat exchanger measurements and to provide inputs into a coupled analytical model for a scaleable design of a millimeter-wave absorbing heat exchanger for high temperature aerospace and industrial beamed energy processes.
Nanoscale Compositionally Graded Thin‐Film Electrolyte Membranes for Low‐Temperature Solid Oxide Fuel Cells (2012)

Abstract Controllable fabrication of compositionally graded Gd 0.1 Ce 0.9 O 2‐δ and Y 0.16 Zr 0.84 O 2‐δ electrolytes using co‐sputtering is demonstrated. Self‐supported membranes were lithographically fabricated to employ the new electrolytes into thin film solid oxide fuel cells. Devices integrating such electrolytes demonstrate performance of over 1175 mW cm −2 and 665 mW cm −2 at 520 °C using hydrogen and methane as fuel, respectively. The results present a general strategy to fabricate nanoscale functionally graded materials with selective interfacial functionality for energy conversion.
Quinolone‐Based IMPDH Inhibitors: Introduction of Basic Residues on Ring D and SAR of the Corresponding Mono, Di and Benzofused Analogues. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Second order flamenco fractal antenna for industrial scientific and medical applications (2017)

Novel second order fractal geometry is presented in this paper for exhibiting radiation characteristics feasible for biomedical applications. The Flamenco fractal is iterated upto second order for attaining resonance covering Industrial, Scientific and Medical (ISM) band for off-body Wireless Body Area Networks (WBAN) communications. The antenna is designed in monopole configuration with the fractal geometry placed on the top layer of the printed circuit board and ground plane embedded on the bottom layer. The frequency response plot is presented for the verification of the radiation characteristics of proposed antenna for ISM band covering frequencies 2.4-2.48 GHz. The gain patterns presented verifies the omni-directional radiations for the Flamenco fractal providing suitability for wireless communications.
Property enhancement in polypropylene ternary blend nanocomposites via a novel poly(ethylene oxide)‐grafted polystyrene‐block‐poly(ethylene/butylene)‐block‐polystyrene toughener–compatibilizer system (2018)

Abstract Synthesis and characterization of a novel toughener–compatibilizer for polypropylene (PP)–montmorillonite (MMT) nanocomposites were conducted to provide enhanced mechanical and thermal properties. Poly(ethylene oxide) (PEO) blocks were synthetically grafted onto maleic anhydride‐grafted polystyrene‐ block ‐poly(ethylene/butylene)‐ block ‐polystyrene (SEBS‐ g ‐MA). Special attention was paid to emphasize the effect of PEO‐grafted SEBS (SEBS‐ g ‐PEO) against SEBS‐ g ‐MA on morphology, static/dynamic mechanical properties and surface hydrophilicity of the resultant blends and nanocomposites. It was found that the silicate layers of neat MMT are well separated by PEO chains chemically bonded to nonpolar SEBS polymer without needing any organophilic modification of the clay as confirmed by X‐ray diffraction and transmission electron microscopy analyses. From scanning electron microscopy analyses, elastomeric domains interacting with MMT layers via PEO sites were found to be distributed in the PP matrix with higher number and smaller sizes than the corresponding blend. As a benefit of PEO grafting, SEBS‐ g ‐PEO‐containing nanocomposite exhibited not only higher toughness/impact strength but also increased creep recovery, as compared to corresponding SEBS‐ g ‐MA‐containing nanocomposite and neat PP. The damping parameter of the same nanocomposite was also found to be high in a broad range of temperatures as another advantage of the SEBS‐ g ‐PEO toughener–compatibilizer. The water contact angles of the blends and nanocomposites were found to be lower than that of neat hydrophobic PP which is desirable for finishing processes such as dyeing and coating. © 2018 Society of Chemical Industry
Multicomponent encapsulation into fully degradable protein nanocarriers via interfacial azide–alkyne click reaction in miniemulsion allows the co-delivery of immunotherapeutics (2022)

Encapsulation of multiple adjuvants along with antigens into nanocarriers allows a co-delivery to antigen-presenting cells for the synergistic induction of robust immune responses. However, loading cargoes of different molar masses, polarities, and solubilities in high efficiencies remains a challenge. Therefore, we developed a strategy to encapsulate a triple combination of the so-called adjuvants, <i>i.e.</i> with Resiquimod (R848), muramyl dipeptide (MDP) and polyinosinic-polycytidylic acid (Poly(I : C)) into human serum albumin (HSA) nanocarriers. The loading is conducted <i>in situ</i> while the nanocarrier is formed by an orthogonal and metal-free click reaction at the interface of an inverse miniemulsion. By this unique approach, high encapsulation efficiency without harming the cargo during the nanocarrier formation process and regardless of their physical properties is achieved, thus keeping their bioactivity. Furthermore, we demonstrated high control over the encapsulation efficiency and varying the amount of each cargo did not influence the efficiency of multicomponent encapsulation. Azide-modified HSA was crosslinked with hexanediol dipropiolate (HDDP) at the interface of a water-in-oil miniemulsion. Varying the crosslinker amount allowed us to tailor the density and degradation rates of the protein shell. Additional installation of disulfide bonds into the crosslinker created redox-responsive nanocarriers, which degraded both by protease and under reducing conditions with dithiothreitol. The prepared HSA nanocarriers were efficiently taken up by dendritic cells and exhibited an additive cell activation and maturation, exceeding the nanocarriers loaded with only a single drug. This general protocol allows the orthogonal and metal-free encapsulation of various drugs or adjuvants at defined concentrations into the protein nanocarriers.
Oxidation and Reduction (2007)

This chapter contains sections titled: Oxidation by Metal Ions Oxidation by Compounds of Non-metallic Elements Ozonolysis and Ozonation Peracids, Peroxides, and Superoxide Singlet Oxygen Autoxidation and Other Reactions of Triplet Oxygen Miscellaneous Oxidations Reduction by Complex Hydrides Reduction by Metals, Metal Complexes, and Ions Miscellaneous Reductions Hydrogenation Reductions and Oxidations of Biological Interest
Joint equalization and timing recovery for coherent fiber optic receivers (2008)

A new low-complexity, dispersion-robust digital timing recovery for coherent systems is presented as a joint implementation with the FIR-equalizer, demonstrated for 112 Gb/s RZ-CP-QPSK.
First Demonstration of 80-km Long-Haul Transmission of 12.5-Gb/s Data Using Silicon Microring Resonator Electro-Optic Modulator (2010)

First demonstration of long-haul transmission reaching bandwidth-distance product of 1-Tb-km/s, using silicon microring resonator electro-optic modulator, sets new precedence for silicon photonic applications. 12.5-Gb/s bit-error-rate and power penalty measurements confirm 80-km of feasible fiber propagation.
Automatic communication optimizations through memory reuse strategies (2012)

Modern parallel architectures are emerging with sophisticated hardware consisting of hierarchically placed parallel processors and memories. The properties of memories in a system vary wildly, not only quantitatively (size, latency, bandwidth, number of banks) but also qualitatively (scratchpad, cache). Along with the emergence of such architectures comes the need for effectively utilizing the parallel processors and properly managing data movement across memories to improve memory bandwidth and hide data transfer latency. In this paper, we describe some of the high-level optimizations that are targeted at the improvement of memory performance in the R-Stream compiler, a high-level source-to-source automatic parallelizing compiler. We direct our focus in this paper on optimizing communications (data transfers) by improving memory reuse at various levels of an explicit memory hierarchy. This general concept is well-suited to the hardware properties of GPGPUs, which is the architecture that we concentrate on for this paper. We apply our techniques and obtain performance improvement on various stencil kernels including an important iterative stencil kernel in seismic processing applications where the performance is comparable to that of the state-of-the-art implementation of the kernel by a CUDA expert.
Abstract 16563: Genetic and Pharmacological Inactivation of ANGPTL3 is Associated With Reduced Atherosclerotic Cardiovascular Disease (2016)

Introduction: Loss of function (LoF) variants in ANGPTL3 have been associated with low plasma low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) and triglycer...
Validation of a Self-Administered iPad®- and iPod®-Based Tool for Assessing Information Processing (P5.302) (2014)

OBJECTIVE: To determine the feasibility and validity of quantifying information processing through simple (SRT) and choice reaction time (CRT) paradigms developed on tablet and mobile devices. BACKGROUND:Information processing and decision-making are common areas of cognitive-motor decline observed in patients with neurologic pathology, injury, and normal aging. Self-administered SRT and CRT tasks were internally developed on iPad and iPod and compared with the technician-administered Lafayette Visual Choice Reaction Time device. DESIGN/METHODS: Sixty healthy controls (age 18-24) completed two sessions separated by one hour, including SRT and CRT tasks on the technician-administered Lafayette device and either the iPad or iPod devices. For iPad and Lafayette devices, the participant lifted their index finger in response to stimulus presentation. For iPod, participants lifted their thumb. CRT tasks on iOS devices also involved a distractor stimulus. Test-retest reliability and concurrent validity of the three devices were determined. RESULTS:SRT performance was not significantly different between the three devices. Lafayette CRT performance was significantly faster due to presence of distractor stimulus in iOS tasks. All device-task combinations showed no significant test-retest difference. SRT and CRT on iOS devices displayed moderate concurrent validity with the Lafayette Reaction Timer (r = 0.46-0.67), indicating that the iOS and Lafayette tasks assess comparable information processing capabilities. Test-retest reliability was strong for all three devices, with concordance ranging from 0.57 (iPad-CRT) to 0.84 (Lafayette-CRT). CONCLUSIONS: Information processing capabilities can be accurately and reliably quantified using tablet and mobile devices. These portable electronic modes of data collection displayed favorable psychometric properties when compared with similar tasks on a validated mechanical method of assessment. Mobile devices hold promise for the valid and reliable evaluation of information processing of neurological patients in clinical and non-clinical settings. We are currently using this approach to characterize information processing changes post-concussion (results will be presented). Study Supported by: The Lincy Foundation
Mitigating Vibration for a Heavy-Duty Diesel Cylinder Deactivation Truck (2021)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Commercial vehicles require fast aftertreatment heat up in order to move the selective catalyst reduction (SCR) into the most efficient temperature range to meet upcoming NOx regulations. Heavy duty cylinder deactivation (CDA) is an important technology to meet these regulations. One of the challenges with implementing CDA in the heavy-duty market is to ensure acceptable engine and vehicle vibration. The purpose of this paper is to mitigate CDA vibration on a vehicle to acceptable levels. Emphasis was placed at the idle operating condition. Idle is the most challenging operating mode to enable, as deactivating cylinders reduces the frequency of the forcing function due to engine firing, which leads to a need to isolate these lower frequencies. A focused modal analysis of the engine (source), frame (path), and cabin (path/receiver) was used to characterize the vehicle system. The work showed that a change in cab mounts reduced the observed vibration levels dramatically while operating in CDA. This work shows that mitigation of vibration in a heavy-duty truck while operating in CDA mode is feasible.&lt;/div&gt;&lt;/div&gt;
Expansion of the HSV-2-specific T cell repertoire in skin after immunotherapeutic HSV-2 vaccine (2022)

The skin at the site of HSV-2 reactivation is enriched for HSV-2-specific T cells. To evaluate whether an immunotherapeutic vaccine could elicit skin-based memory T cells, we studied skin biopsies and HSV-2-reactive CD4<sup>+</sup> T cells from peripheral blood mononuclear cells (PBMCs) by T cell receptor β (<i>TRB</i>) sequencing before and after vaccination with a replication-incompetent whole virus HSV-2 vaccine candidate (HSV529). The representation of HSV-2-reactive CD4<sup>+</sup> <i>TRB</i> sequences from PBMCs in the skin <i>TRB</i> repertoire increased after the first vaccine dose. We found sustained expansion after vaccination of unique, skin-based T-cell clonotypes that were not detected in HSV-2-reactive CD4<sup>+</sup> T cells isolated from PBMCs. In one participant a switch in immunodominance occurred with the emergence of a T cell receptor (TCR) αβ pair after vaccination that was not detected in blood. This TCRαβ was shown to be HSV-2-reactive by expression of a synthetic TCR in a Jurkat-based NR4A1 reporter system. The skin in areas of HSV-2 reactivation possesses an oligoclonal <i>TRB</i> repertoire that is distinct from the circulation. Defining the influence of therapeutic vaccination on the HSV-2-specific <i>TRB</i> repertoire requires tissue-based evaluation.