gebhart/patrepeval huggingface dataset:
Summarizing performance for genome scale measurement of miRNA: reference samples and metrics (2018)

The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls. Three pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds. In silico modeling of mixtures provided benchmark values for comparison with physical mixtures. Biomarker development laboratories using next-generation sequencing (NGS) or genome-scale hybridization assays participated in the study and returned data from the samples using their routine workflows. Multiplexed and single assay reverse-transcription PCR (RT-PCR) was used to confirm in silico predicted sample differences. Data visualizations and summary metrics for genome-scale miRNA profiling assessment were developed using this dataset, and a range of performance was observed. These metrics have been incorporated into an online data analysis pipeline and provide a convenient dashboard view of results from experiments following the described design. The website also serves as a repository for the accumulation of performance values providing new participants in the project an opportunity to learn what may be achievable with similar measurement processes. The set of reference samples used in this study provides benchmark values suitable for assessing genome-scale miRNA profiling processes. Incorporation of these metrics into an online resource allows laboratories to periodically evaluate their performance and assess any changes introduced into their measurement process.
Successive interference cancellation (2010)

Successive interference cancellation (SIC) is a physical layer capability that allows a receiver to decode packets that arrive simultaneously. While the technique is well known in communications literature, emerging software radios are making practical experimentation feasible. This motivates us to study the extent of throughput gains possible with SIC from a MAC layer perspective. Contrary to our initial expectation, we find that the gains from SIC are not easily available in many realistic situations. Moreover, we observe that the scope for SIC gets squeezed by the advances in bitrate adaptation, casting doubt on the future of SIC based protocols.
ChemInform Abstract: New Enone Derivatives of Oleanolic Acid and Ursolic Acid as Inhibitors of Nitric Oxide Production in Mouse Macrophages. (1997)

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.
MEMS-based tunable filters for compact IR spectral imaging (2009)

Arrays of independently tunable MEMS Fabry-Perot filters have been developed that enable spectral tuning over the range of 11 - 8 microns with a filter bandwidth of ~ 120 nm. Actuation is provided using a MEMS driver IC that is hybridized to the MEMS chip. Combining the filter array with an IR FPA enables spatially-resolved spectral tuning in a compact architecture. Tunable spectral response data from the first integrated tunable filter / FPA device are presented.
ChemInform Abstract: Phenylselenium Trichloride, Preparation and Use as a Vinylic Chlorination Reagent. (1996)

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.
Ultramark 1621 as a calibration/reference compound for mass spectrometry. II. Positive‐ and negative‐ion electrospray ionization (1994)

Abstract Electrospray ionization of solutions of Ultramark 1621, a commercially available mixture of fluorinated phosphazenes, in solution of 50:23:23:4 v/v of acetonitrile+water+methanol+acetic acid, produced a series of intense singly charged peaks in the m/z range of 900 to ca . 2200 in both positive‐ and negative‐ionization modes. The chemical compositions and accurate masses of ions in both positive‐ and negative‐ion spectra have been reported. An accuracy of approximately 2 ppm has been achieved for the average molecular weight of bovine insulin using Ultramark 1621 peaks as reference standards.
On-Road Motor Vehicle Emissions including NH3, SO2 and NO2 (2009)

The three California cities of San Jose, Fresno and west Los Angeles (LA) were visited during March 2008 to remotely collect on-road emission measurements of carbon monoxide (CO), carbon dioxide, hydrocarbons (HC), nitric oxide (NO), sulfur dioxide, ammonia (NH3) and nitrogen dioxide (NO2) from light-duty vehicles. A database for each site was compiled and contains 24,978 records in San Jose, 13,365 records in Fresno and 17,953 records in LA for which the State of California provided registration information. At the San Jose and LA sites repeat measurements of CO, HC and NO show large fuel specific emission reductions between 1999 and 2008. In Fresno a small fleet of 2007 diesel ambulances was found to have more than 60% of the emitted oxides of nitrogen as NO2. NH3 emissions are again shown to have a strong dependence on model year with NH3 means of 0.49 + 0.02, 0.49 + 0.01 and 0.79 + 0.02 gm/kg of fuel for San Jose, Fresno and LA respectively with the larger in emissions at the LA site likely a result of the more aggressive driving mode.
Effects of Mineral Impurities and Heat on Uranium(VI) Sorption onto Bentonite (Final Report) (2023)

Most nuclear waste disposal options include compacted bentonite, consisting of montmorillonite clay, as part of a barrier system to minimize contaminant mobility. Uranium (U) is the primary element in spent nuclear fuel, and from an environmental perspective, a potential contaminant of water resources. Furthermore, uranium may control nuclear fuel degradation rates and the consequent release of other radioactive contaminants based on its diffusive transport away from waste canisters. Uranium sorption onto clay and other mineral surfaces is expected to limit U(VI) mobility in these systems. However, at this point a prediction of U(VI) sorption and transport behavior in performance assessment (PA) models is complicated by a series of factors, such as: (1) the presence of various U(VI) solution species with different charges and sorption characteristics; (2) the complex microstructure of montmorillonite clay resulting in two types of clay porosities and multiple sorption sites; (3) the largely unknown effects of bentonite mineral impurities on pore water chemistry, U(VI) sorption and diffusion behavior; and (4) the potential impacts of heat, generated by the decay of spent fuel, on mineralogical and microstructural transformations, and any subsequent effects on radionuclide sorption and mobility. In this project, we investigated the effects of calcite impurities on U(VI) sorption and diffusion onto montmorillonite before and after mineral exposure to heat. Overall, our main goals were to: 1. Gain a mechanistic understanding of the effects of calcite impurities on U(VI) sorption and diffusion in montmorillonite/bentonite at variable chemical conditions, and before and after mineral exposure to heat; and to 2. Work towards the development of new surface complexation and diffusion models to predict U(VI) sorption and mobility in montmorillonite/bentonite while accounting for the impacts of calcite impurities and heat. In order to achieve these goals, we pursued the following research objectives and tasks: 1. Characterize the effects of calcite impurities on U(VI) sorption onto Na-montmorillonite, and evaluate if and how these effects change due to solids’ exposure to heat (Task 1). 2. Characterize U(VI) surface speciation in solid samples from Task 1, with a particular focus on U(VI) precipitates and co-precipitates (Task 2). 3. Test the relevance of observed changes in U(VI) sorption characteristics for U(VI) diffusive transport behavior in bentonite barriers (Task 3). 4. Evaluate the exclusion of anionic U(VI) solution complexes from clay nanopores (Task 4). 5. Building on Tasks 1-4, start the development of new surface complexation and reactive transport models that can simulate and predict U(VI) sorption and diffusion in complex bentonite systems (Task 5). A detailed description of all tasks, and their specific results and conclusions is provided in this report.
Nickel silicide contacts formed by excimer laser annealing for high efficiency solar cells (2013)

ABSTRACT Driven by the relatively high cost of silver (Ag), interest has grown in the photovoltaic (PV) industry to substitute conventional screen printed (SP) Ag front contacts with copper (Cu) plated contacts. The approach chosen here applies selective laser ablation of the front anti‐reflection coating (ARC), then forming self‐aligned nickel silicides (NiSi x ) contacts, and thickening the lines by Cu plating to achieve the desired line conductivity. A successful implementation of this scheme requires annealing to form NiSi x with low contact resistance. However, it has been shown that industrial shallow emitters can be damaged severely upon conventional annealing of nickel. In this paper, we show that by using large area excimer laser annealing (ELA), NiSi x contacts can be formed on industrial shallow emitters without the associated junction degradation. On the basis of sheet resistance, transmission electron microscopy, and lifetime measurements, we demonstrate that NiSi x formation by ELA can be achieved in narrow contact openings without damaging the passivation and reflectance properties of the neighboring ARC. In addition, the thresholds for NiSi x formation for different Ni thicknesses are quantified by rigorous finite element simulations and compared with experimental data. Finally, high efficiency passivated emitter and rear cell type solar cells featuring a shallow 85 Ω/sq emitter have been processed on large area CZ–Si using laser ablation of the ARC and subsequent NiSi x formation by ELA. These cells show an average efficiency gain of 0.4% abs compared with cells processed with reference SP contacts. In this work, the best performing cell with the ELA process reached 20.0% energy conversion efficiency. Copyright © 2013 John Wiley &amp; Sons, Ltd.
Natural Abundance N-15 NMR of the Solids from the Reaction of HCN and Ammonia (1982)

Natural-abundance cross-polarization 15 N NMR spectra of the complex solids from the reaction of HCN and ammonia have been obtained at 9.12 MHz with magic-angle sample spinning at 1.5 kHz. The spectra are interpreted in terms of the relative concentrations of nitrile-, aromatic-, amide-, urea-, and ammonia-like nitrogen present. The spectrum of the water-insoluble polymeric fraction of the reaction products shows a diversity of nitrogen functionality as broad as that observed for an isolated bacterial RNA.
Viscosity transitions in aqueous suspensions of hydrogel microspheres (1997)

Large transitions in viscosity are demonstrated for suspensions of environmentally sensitive gel microspheres upon application of external stimuli. Depending on the number concentration of microspheres, these suspensions may thicken to become semisolid, essentially undergoing a sol-gel transition. These reversible viscosity transitions are directly related to the volume transitions observed previously in the literature for individual environmentally sensitive gels. Temperature-sensitive poly-N-isopropyl-acrylamide microspheres were synthesized, and the effects of microsphere concentration on the temperature-induced viscosity transitions were measured. The viscosity of poly-N-isopropylacrylamide microsphere suspensions could also be increased by addition of sodium dodecyl sulfate. Non-temperature-sensitive, commercially available poly-acrylamide microspheres were used to demonstrate viscosity transitions as a function of solvent composition in acetone/water mixtures. Potential applications for these systems were suggested. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 63: 1369–1372, 1997
Two Classes of Broadly Neutralizing Antibodies within a Single Lineage Directed to the High-Mannose Patch of HIV Envelope (2014)

Development of an HIV vaccine is of vital importance for prevention of new infections, and it is thought that elicitation of HIV bnAbs will be an important component of an effective vaccine. Increasingly, bnAbs that bind to the cluster of high-mannose glycans on the HIV envelope glycoprotein, gp120, are being highlighted as important templates for vaccine design. In particular, bnAbs from IAVI donor 36 (PGT125 to PGT131) have been shown to be extremely broad and potent. Combination of these bnAbs enhanced neutralization breadth considerably, suggesting that an optimal immunogen should elicit several antibodies from this family. Here we study the evolution of this antibody family to inform immunogen design. We identify two classes of bnAbs that differ in their recognition of the high-mannose patch and show that different immunogens may be required to elicit these different classes.
Robust and flexible FPGA-based digital PUF (2014)

We have developed the first FPGA-based digital physical unclonable function (PUF) by leveraging the reconfigurability of an FPGA and introducing a new way of using the standard analog delay PUF. The key observation is that for any analog delay PUF, there is a subset of challenge inputs for which the PUF output is stable regardless of operation and environmental conditions. We use only such stable inputs to initialize the look-up tables (LUTs) that are configured in such a way that the digital PUF is formed. We demonstrate the effectiveness of the new security primitive using extensive simulation and experimental results. For example, we show that the new PUF is resistant against a wide spectrum of security attacks and its output stream passes all the NIST randomness tests.
Role of genetics in prevention of coronary atherosclerosis (2003)

Atherosclerosis is currently regarded as a complex disorder, triggered by gene-gene and gene-environment interactions. Despite the difficulties of multifactorial disease genetic analysis, significant progress has been achieved in the search for atherosclerosis susceptibility genes. Here, we review these advances with regard to genome scan results and candidate gene analysis.
Effects of PRKAR1A mutations in behavior and brain function (2014)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Runtime Precomputation of Data-Dependent Parameters in Embedded Systems (2018)

In many modern embedded systems, the available resources (e.g., CPU clock cycles, memory, and energy) are consumed nonuniformly while the system is under exploitation. Typically, the resource requirements in the system change with different input data that the system process. These data trigger different parts of the embedded software, resulting in different operations executed that require different hardware platform resources to be used. A significant research effort has been dedicated to develop mechanisms for runtime resource management (e.g., branch prediction for pipelined processors, prefetching of data from main memory to cache, and scenario-based design methodologies). All these techniques rely on the availability of information at runtime about upcoming changes in resource requirements. In this article, we propose a method for detecting upcoming resource changes based on preliminary calculation of software variables that have the most dynamic impact on resource requirements in the system. We apply the method on a modified real-life biomedical algorithm with real input data and estimate a 40% energy reduction as compared to static DVFS scheduling. Comparing to dynamic DVFS scheduling, an 18% energy reduction is demonstrated.
A CMOS image sensor with 2.5-e − random noise and 110-ke − full well capacity using column source follower readout circuits (2009)

A low noise CMOS image sensor without degradation of saturation performance has been developed by using column amplifiers of the gains of about 1.0 in a lateral overflow integration capacitor technology. The 1/4-inch, 4.5-µm pitch, 800H × 600V pixels CMOS image sensor fabricated by a 0.18-µm 2P3M technology including a buried pinned photo-diode structure has achieved fully linear response, 0.98 column readout gain, 100-µV/e− conversion gain, 2.5-e− random noise, 110,000-e− full well capacity and 93-dB dynamic range in one exposure.
Scanning (1999)

This chapter discusses the process of converting a hardcopy image into a digital image using a scanner. The components of a scanner are described in some detail: illumination source, optics, scanning mechanical components, image sensor, and electronics. Special attention is paid to the factors that influence the quality of the scanner output. A number of image processing functions often integrated with scanners are also described.
The insulin receptor as a universal marker of activated lymphocytes (1978)

Abstract Although resting, rat thymus‐derived spleen lymphocytes do not bear insulin receptors, these receptors emerge upon the membrane of alloimmune rat T cells subsequent to skin grafting. These studies examine conditions that permit the emergence of lymphocyte insulin receptors upon T or B‐enriched rat lymphocyte populations. Allogeneic stimulation was accomplished in vivo by skin grafting from (Lewis × Brown Norway)F 1 (LBN) to Lewis male rats or by Graft‐ vs. ‐host (GVH) reaction established by intraperitoneal injections of 2 × 10 8 Lewis leukocytes each week for a total of four injections into LBN animals. In vitro allogeneic stimulation was provided by one‐way mixed lymphocyte cultures between the same strains. Lastly, both T and B‐enriched populations were interacted with mitogens concanavalin A (Con A), phytohemagglutinin (PHA‐P), and lipopolysaccharide (LPS). The T‐enriched populations were highly enriched for T lymphocytes (90%) and macrophage‐depleted while B‐enriched populations contained nearly 85% B cells. Insulin receptors emerged upon T‐enriched cell populations consequent to allogeneic skin grafting with saturability, specificity and high affinity (k d = 1.1 nM) as well as after GVH. Responder strain lymphocytes developed an insulin receptor during allogeneic mixed lymphocyte cultures within 72 h of initiation. Specific insulin‐binding sites also appeared upon T‐enriched populations after culture with PHA‐P and Con A but not LPS. Conversely, B cells developed an insulin receptor after interactions with LPS but not PHA‐P or Con A. Anti‐Ig and complement but not rat anti‐T cell antibody abrogated the ability of LPS to induce an insulin receptor on B‐enriched cells. Binding specificity was demonstrated by the inhibition of [ 125 I]‐labeled insulin in the order porcine insulin ≊ desalanine insulin &gt; proinsulin ≫ desoctapeptide insulin with growth hormone exhibiting no such inhibition. These data demonstrate that a true insulin receptor appears upon both T and B cells consequent to activation. The lymphocyte insulin receptor is a universal marker of cellular activation as it is not restricted to clone or species and may be applied to B and T lymphocytes of mouse, rat and man.
A phosphorylated β-catenin peptide that is presented by HLA-A2 generates strong phosphospecific T cell responses against melanoma (101.10) (2010)

Abstract Using metal ion affinity chromatography and mass spectrometry, we have previously shown that phosphorylated peptides are endogenously processed and presented by many different MHC I and II molecules, and have identified differentially displayed phosphopeptides presented by HLA-A2 on cancer cells. Many of the source proteins for these phosphopeptides are involved in tumorigenesis and metastasis. These peptides are appealing immunotherapeutic targets since mutations in or downregulation of the source proteins as a means of immune escape may compromise malignancy. We focused on one phosphopeptide spanning residues 30-39 of β-catenin (βcatpS33). When used to immunize HLA-A2 transgenic mice, βcatpS33 was very weakly immunogenic. Replacement of a suboptimal Ala anchor residue at P10 with a Val (βcatpS33(V)) enhanced the HLA-A2 binding affinity 10 fold and substantially improved immunogenicity. CD8 T cells from βcatpS33(V)-immunized mice were crossreactive to βcatpS33. The T cells also recognized endogenously processed βcatpS33 on several HLA-A2+ melanoma cells. Thus, crossreactivity to the natural βcatpS33 phosphopeptide can be maintained by making minimal changes in the sequence while preserving the ability of T cells to discriminate between the phosphorylated and unphosphorylated forms of the peptide. Enhancing immunogenicity by fine-tuning such an attractive tumor antigen linked to tumorigenic and metastatic processes should improve the efficiency of tumor control.
A 38 GHz cellular outage study for an urban outdoor campus environment (2012)

Wireless systems require increasingly large system bandwidths that are only available at millimeter-wave frequencies. Such spectrum bands offer the potential for multi-gigabit-per-second data rates to low-cost massively broadband® devices. To enable mobile outdoor millimeter-wave cellular-type applications, it is necessary to determine the coverage potential of base stations in real-world environments. This paper presents the results of a measurement campaign of 38 GHz outdoor urban cellular channels using directional antennas at both the mobile and the base station, and assesses outage probabilities at two separate transmitter locations on the campus of The University of Texas at Austin. Our measurements demonstrate the viability of directional antennas and site-specific planning for future mm-wave cellular, and show that cell radii of ~200 M will provide a very high probability of coverage in an urban environment. As production costs for millimeter-wave technologies continue to fall [1], we envision millimeter-wave cellular systems with dense base station deployments as a cost effective means of delivering multi-Gbps data rates to mobile cell phone and internet users.
Is Peer Review Censorship? (2009)

“A censor is an expert in cutting remarks.” —Laurence J. Peter ([22][1]) 

Given the unpleasantness of having one's work rejected ([10][2]), as well as a desire for more-rapid communication of scientific findings, some scientists have expressed nostalgia for the good old days when nearly any
Live Neuron Morphology Automatically Reconstructed From Multiphoton and Confocal Imaging Data (2008)

We have developed a fully automated procedure for extracting dendritic morphology from multiple three-dimensional image stacks produced by laser scanning microscopy. By eliminating human intervention, we ensure that the results are objective, quickly generated, and accurate. The software suite accounts for typical experimental conditions by reducing background noise, removing pipette artifacts, and aligning multiple overlapping image stacks. The output morphology is appropriate for simulation in compartmental simulation environments. In this report, we validate the utility of this procedure by comparing its performance on live neurons and test specimens with other fully and semiautomated reconstruction tools.