gebhart/patrepeval huggingface dataset:
Expressed sequence tags, DNA chip technology and gene expression profiling. (2003)

Genome-scale cDNA sequencing and DNA microarray analysis opened the door to the exploration and discovery of thousands of new chicken genes. Genome-wide gene expression scans will functionally map the genetic pathways that control immunity, metabolism, growth, development, reproduction and environmental adaptation. Many of the current problems associated with intensive genetic selection and intensive poultry production systems can be addressed with this new knowledge about the chicken's functional genome.
Tungsten-doped thin film materials (2023)

A dielectric thin film material for high frequency use, including use as a capacitor, and having a low dielectric loss factor is provided, the film comprising a composition of tungsten-doped barium strontium titanate of the general formula (Ba.sub.x Sr.sub.1-x)TiO.sub.3, where X is between about 0.5 and about 1.0. Also provided is a method for making a dielectric thin film of the general formula (Ba.sub.x Sr.sub.1-x)TiO.sub.3 and doped with W, where X is between about 0.5 and about 1.0, a substrate is provided, TiO.sub.2, the W dopant, Ba, and optionally Sr are deposited on the substrate, and the substrate containing TiO.sub.2, the W dopant, Ba, and optionally Sr is heated to form a low loss dielectric thin film.
Supplemental material and method from DS-8201a, A Novel HER2-Targeting ADC with a Novel DNA Topoisomerase I Inhibitor, Demonstrates a Promising Antitumor Efficacy with Differentiation from T-DM1 (2023)

&lt;p&gt;Cell line and patient-derived xenograft studies&lt;/p&gt;
Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins (1994)

The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 A resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (ST II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 A. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed.
Diagnosing Road Weather Conditions with Vehicle Probe Data (2010)

Over the past 2 years, the U.S. Department of Transportation RITA funded an IntelliDrive vehicle probe data collection test bed in the northwest Detroit, Michigan, area. The purpose of the test bed was to provide the infrastructure for both public and private organizations to collect, process, and generate a robust observation data set for multiple purposes (e.g., crash avoidance, automated toll services, weather diagnostics). During April 2009, a weather-specific field study was performed over an 11-day period. The resulting data set was processed by a vehicle data translator (VDT), which parsed, quality controlled, and combined these data (with ancillary weather data) in the generation of road weather-specific algorithms. This paper briefly describes the VDT concept and then examines the accuracy of the quality-controlled temperature and pressure data (for several different stratifications) collected from 11 specially equipped vehicles operated during the study time period. Results show that the vehicles accurately measure the temperature (compared with a nearby fixed weather station, KDTW), but are not as accurate at measuring the barometric pressure. In addition, stratification by speed, vehicle type, time of day, and occurrence of precipitation do not affect the accuracy of the temperature and barometric pressure measurements.
ChemInform Abstract: A New Procedure for the Julia—Colonna Stereoselective Epoxidation Reaction under Non‐Aqueous Conditions: The Development of a Catalyst Comprising Polyamino Acid on Silica (PaaSiCat). (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.
Abstract 5487: Identification of super-enhancer-associated cancer genes provides novel therapeutic targets in adult T-cell leukemia/lymphoma (2017)

Abstract Super-enhancers are often enriched at cancer genes in various malignancies. Identification of such enhancers would pinpoint critical factors that directly contribute to pathogenesis. Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive lymphoproliferative disorder that arises from CD4+ mature T-lymphocytes. A recent genome-wide sequencing study revealed a large number of genetic and chromosomal abnormalities. However, there is still a lack of functional evidence for these genetic abnormalities in ATL pathogenesis due to the large mutational burden and the considerable genetic heterogeneity. Here, we performed super-enhancer profiling combined with gene expression analysis in primary ATL samples and cell lines. Super-enhancers are frequently enriched at genes involved in T-cell activation and T-cell receptor signaling pathway in both ATL and normal CD4+ T-cells, reflecting the origin of leukemia cells. Super-enhancers at the CCR4 gene, a known therapeutic target in ATL, were observed in all ATL cases. Additionally, we identified previously-uncharacterized genes that were highly activated in ATL cells and required for cell growth. A small-molecule inhibitor of CDK7 efficiently downregulated the expression of these genes and inhibited cell growth. Our study provides a novel strategy to identify critical cancer genes in cancer. Note: This abstract was not presented at the meeting. Citation Format: Takaomi Sanda, Regina WJ Wong, Phuong TN Cao, Wei Zhong Leong, Alice WY Yam, Tinghu Zhang, Shinsuke Iida, Takashi Okamoto, Ryuzo Ueda, Nathanael S. Gray, Takashi Ishida. Identification of super-enhancer-associated cancer genes provides novel therapeutic targets in adult T-cell leukemia/lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5487. doi:10.1158/1538-7445.AM2017-5487
Transcriptome and Complexity-Reduced, DNA-Based Identification of Intraspecies Single-Nucleotide Polymorphisms in the Polyploid Gossypium hirsutum L. (2014)

Varietal single nucleotide polymorphisms (SNPs) are the differences within one of the two subgenomes between different tetraploid cotton varieties and have not been practically used in cotton genetics and breeding because they are difficult to identify due to low genetic diversity and very high sequence identity between homeologous genes in cotton. We have used transcriptome and restriction site-associated DNA sequencing to identify varietal SNPs among 18 G. hirsutum varieties based on the rationale that varietal SNPs can be more confidently called when flanked by subgenome-specific SNPs. Using transcriptome data, we successfully identified 37,413 varietal SNPs and, of these, 22,121 did not have an additional varietal SNP within their 20-bp flanking regions so can be used in most SNP genotyping assays. From restriction site-associated DNA sequencing data, we identified an additional 3090 varietal SNPs between two of the varieties. Of the 1583 successful SNP assays achieved using different genotyping platforms, 1363 were verified. Many of the SNPs behaved as dominant markers because of coamplification from homeologous loci, but the number of SNPs acting as codominant markers increased when one or more subgenome-specific SNP(s) were incorporated in their assay primers, giving them greater utility for breeding applications. A G. hirsutum genetic map with 1244 SNP markers was constructed covering 5557.42 centiMorgan and used to map qualitative and quantitative traits. This collection of G. hirsutum varietal SNPs complements existing intra-specific SNPs and provides the cotton community with a valuable marker resource applicable to genetic analyses and breeding programs.
Continuous Flow Peritoneal Dialysis: Is There a Need for it? (2001)

Automated peritoneal dialysis (APD) is the fastest growing technique of peritoneal dialysis. However, recently APD has displayed some limitations imposed by the characteristics of the technique and by the characteristics of the peritoneal membrane of some patients. In general, the advent of a new technique such as continuous flow peritoneal dialysis (CFPD) should be seen as a benefit for several patients based on different considerations: CFPD is a high-efficiency technique which could overcome some of the limitations imposed by other techniques in terms of adequacy targets and performance. CFPD may become a useful tool to keep patients on PD who would otherwise be transferred to hemodialysis. CFPD may present advantages in terms of biocompatibility and also in terms of the possible modulation of the peritoneal solution to patient needs. Recent developments in technology seem to have made CFPD easily feasible and well tolerated. A new era of PD is probably beginning and CFPD will definitely represent one of the key issues in the future of PD.
NUMERICAL SIMULATION OF LAP-SHEAR AND PRESTRESS FORCE RELEASE TESTS OF FRP STRIPS GLUED ON CONCRETE: CONSIDERATIONS ABOUT THE ROLE OF MIXED-MODE FRACTURE PROCESSES (2023)

Lap-shear tests carried out on Externally Bonded (EB) FRP strips or, more recently, prestress force release tests have established in the scientific community as experimental methods intended at determining the actual bearing capacity of EB FRP strips glued to concrete. The results of these tests are employed to scrutinize the interface behavior between FRP and supporting materials, which is generally modelled as a pure mode II fracture process. This paper shows the results of a numerical study intended at further unveiling the role of mixed-mode fracture parameters in the debonding process between FRP strips and concrete in lap-shear and prestress force releasing tests.
Micro-power sources enabling robotic outpost based deep space exploration (2001)

Robotic outpost based exploration represents a fundamental shift in mission design from conventional, single spacecraft missions towards a distributed risk approach with many miniaturized semi-autonomous robots and sensors. This approach can facilitate wide-area sampling and exploration, and may consist of a web of orbiters, landers, or penetrators. To meet the mass and volume constraints of deep space missions such as the Europa Ocean Science Station, the distributed units must be fully miniaturized to fully leverage the wide-area exploration approach. However, presently there is a dearth of available options for powering these miniaturized sensors and robots. This group is currently examining miniaturized, solid state batteries as candidates to meet the demand of applications requiring low power, mass, and volume micro-power sources. These applications may include powering microsensors, battery-backing rad-hard CMOS memory and providing momentary chip back-up power. Additional information is contained in the original extended abstract.
Magnetic Polymer Brushes: Towards Tailor-Made Stabilization of Magnetic Fluids by Surface-Initiated Polymerization (2006)

Summary Novel surfactant-free magnetic fluids based on magnetite nanoparticles stabilized by a covalently attached polymeric brush were characterized in terms of their dispersion properties by DLS. We found that the molecular weight of the stabilizing surface-tethered polymeric arms has a direct impact on the hydrodynamic diameter d h of the well-dispersed particles. An increase of d h from 10 nm (octylcarboxylate-stabilized magnetite particles) to more than 100 nm for similar magnetite cores with a densely grafted poly(ε-caprolactone) (PCL) shell of 12300 g mol −1 is observed. The experimental results are compared to the expected values in the case of completely stretched polymeric chains.
Atom Interferometry on Atom Chips-A Novel Approach Towards Precision Inertial Navigation Systems (PINS) (2008)

Abstract : Considerable progress was made during the grant period toward establishing a chip based atom interferometer. At the beginning of the gBECi period, no coherent on-chip beam splitter had been demonstrated. During the funding period, we developed two area enclosing interferometers with demonstrated coherence preservation: one using optical pulses, the other one using RF dressed potentials. Technical improvements in the moving guide technique should provide a 1cm2 enclosed area in a device with a length ~ 1 cm. We addressed in several studies the role of interactions in a Bose-Einstein condensate. This can lead to phase diffusion and phase fluctuations. We showed that a BEC interferometer can be robust against phase fluctuations, that interactions can lead to number squeezing, which slows down phase diffusion, and led to a considerable enhancement of the coherence time, and finally, that soliton-type excitations in an interacting condensate can be used to read out the phase of the interferometer after recombining the split condensate. Technical breakthroughs include improved atom chip fabrication methods, and continuous non-destructive optical readout of the interferometer phase. In related work, we demonstrated quantum reflection with normal incidence and studied it for different surfaces. Single photon sources have been developed.
Convergent Synthesis of the Renin Inhibitor Aliskiren Based on C5–C6 Disconnection and CO2H–NH2 Equivalence (2016)

A novel synthesis of the renin inhibitor aliskiren based on an unprecedented disconnection between C5 and C6 was developed, in which the C5 carbon acts as a nucleophile and the amino group is introduced by a Curtius rearrangement, which follows a simultaneous stereocontrolled generation of the C4 and C5 stereogenic centers by an asymmetric hydrogenation. Operational simplicity, step economy, and a good overall yield makes this synthesis amenable to manufacture on scale.
E7.1 - Miniaturized SMD-Reflow-Capable Photoacoustic CO2-Sensor Using a Dual-Chamber Approach (2023)

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Requirements of power amplifier on super high bit rate massive MIMO OFDM transmission using higher frequency bands (2014)

To actualize the 5th generation (5G) radio access network with a super high bit rate and high capacity, small cells using both higher frequency bands and Massive MIMO technology are needed. Massive MIMO OFDM transmissions in the 20-GHz band at 20 Gbps that take advantage of higher beamforming (BF) gain have been studied. However, Massive MIMO OFDM causes a high peak to average power ratio (PAPR) because of the large number of subcarriers and multiplexed streams, and thus nonlinear distortion of the power amplifier (PA) degrades the transmission performance. On the other hand, Massive MIMO SC-FDMA may reduce the PAPR by sacrificing the BF gain with subband-precoding matrices. In order to achieve a low-cost Massive MIMO transceiver integrated circuit including a PA in the 20-GHz band, this paper compares the performance of Massive MIMO OFDM and SC-FDMA based on link level simulations with 256 transmitter antennas in the presence of PA nonlinear distortion in order to achieve a low-cost Massive MIMO transceiver integrated circuit including a power amplifier (PA) in the 20-GHz band. Simulation results show that the throughput for Massive MIMO OFDM is higher than that for Massive MIMO SC-FDMA. This paper also presents PA requirements for 20-Gbps Massive MEVIO OFDM in terms of throughput and out-of-band radiation.
HCV genotype 3 and squamous cell carcinoma antigen (SCCA)‐IgM are independently associated with histological features of NASH in HCV‐infected patients (2015)

Nonalcoholic steatohepatitis (NASH) enhances the risk of progressive liver disease. In chronic hepatitis C (CHC), liver steatosis is frequent, especially in genotype 3, but its clinical significance is debated. As squamous cell carcinoma antigen (SCCA)-IgM has been associated with advanced liver disease and risk of tumour development, we evaluated its occurrence in CHC and the possible relation with NASH at liver biopsy. Using a validated ELISA, serum SCCA-IgM was measured in 91 patients with CHC at the time of liver biopsy performed before antiviral treatment, at the end of treatment and 6 months thereafter, and in 93 HCV-negative patients with histological diagnosis of nonalcoholic fatty liver disease, as controls. SCCA-IgM was detected in 33% of CHC patients and in 4% of controls. This biomarker was found more elevated in CHC patients with histological NASH, and at multivariate analysis, SCCA-IgM and HCV genotype 3 were independently associated with NASH [OR (95% CI): 6.94 (1.21-40) and 27.02 (4.44-166.6)]. As predictors of NASH, HCV genotype 3 and SCCA-IgM had a specificity and a sensitivity of 97% and 44%, and of 95% and 27%, respectively. PPV and NPV were 80% and 86% for HCV genotype 3 vs 73% and 72% for SCCA-IgM. In patients with sustained virologic response to therapy, SCCA-IgM levels decreased significantly, while these remained unchanged in nonresponders. In conclusion, SCCA-IgM is detectable in one-third of patients with CHC and significantly correlates with histological NASH.
LYMPHOCYTE SUBPOPULATIONS ANALYSIS IN PERIPHERAL BLOOD IN POLYMYALGIA RHEUMATICA/GLANT CELL ARTERITIS (1993)

The phenotypic characteristics of peripheral blood lymphocytes were investigated in 22 patients suffering from active polymyalgia rheumatica/giant cell arteritis (PMR/GCA) prior to steroid treatment. We observed a significant reduction in the absolute number and the relative percentage of CD4-, CD8+ and CD3+, CD16+ and/or CD56+ cells compared to controls. Fifteen patients were investigated prospectively over a 6-month period of prednisone therapy. At the end of the study CD4-CD8+ cells had increased significantly compared to baselines, CD3+ CD16+ and/or CD56+ cells remained significantly lower when compared to controls. We did not observe any abnormalities in the absolute number and percentage of HLA-DR+ T lymphocytes, CD5+ B cells and NK cell phenotypes before or during steroid treatment. Our study confirms that there was significant increase in the absolute number of CD8+ T cells during steroid treatment in the PMR/GCA patients, but indicates the persistence of an immunological alteration despite the control of disease manifestations.
A Recovery Process for Spent Polyurethane-Based Propellants (1995)

The valuable inorganic components—energetics and fuel—of solid propellants are successfully separated and recovered by using swelling and ultrasound. In this study, the inert polyurethane-based propellant is first comminuted in various solvents as swelling media, and an appropriate solvent is then selected. Subsequently an ultrasound induced cavitational reaction for interfacial treatment is performed with the use of a mild oxidant. Through the process, the polymer binders are partially degraded and the propellant network is destroyed, enabling inorganic and metallic constituents to be released and separated.
Service-Delivery Modeling and Optimization (2015)

Service-delivery modeling and optimization is a complex problem involving multiple service levels, skill sets, request classes, and service times. In this paper, we describe a comprehensive and scalable end-to-end analytical methodology that we developed and implemented at a global information technology service delivery provider. This methodology provides predictive insight and prescriptive solutions to the problem of staffing service-delivery units in this complex environment. Our solution has been deployed globally at more than 640 service-delivery units and has yielded more than $52 million in cost savings and cost avoidance to date.
Solute Removal Characteristics of The Dialyzer: New Concept of Design for The Internal Filtration Enhanced Dialyzer (2012)

The fluid and solute transfer performances of dialyzers have been improved as a result of advances in membrane and device technology. To date, many types of dialyzers with high performance membranes have been developed. In some of these dialyzers, the pressure drop in the blood and dialysate streams occurs in a countercurrent manner, inducing internal filtration/back filtration (IF/BF). Namely, filtration from the blood through the membrane and to the dialysate occurs in the upstream of the blood flow and back filtration from the dialysate to the blood occurs in the downstream.Recently, several types of dialyzer with enhanced internal filtration have been introduced for clinical application as a means of improving the efficiency of solute removal, and the enhanced internal filtration in these dialyzers has increased the convective transport of the solute besides the diffusive transport. The internal filtration flow rates (QIF) of the dialyzer, however, have never been evaluated precisely. During our studies, blood flow velocity in a cross-sectional plane of a dialyzer was measured by pulse Doppler ultrasonography to evaluate QIF. An in vitro study using bovine blood was carried out to determine the profile of local blood flow velocity with a probe slider that enables the probe to move in parallel along a dialyzer. The Doppler ultrasonography is a useful method for bedside monitoring of QIF in several dialyzers, because it is noninvasive to the patient and produces reliable data with higher reproducibility.
Large-Scale Clustering of cDNA-Fingerprinting Data (1999)

Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for our algorithm is oligonucleotide fingerprinting-a method for simultaneous determination of expression level for every active gene of a specific tissue-although the algorithm can be applied as well to other large-scale projects like EST clustering and qualitative clustering of DNA-chip data. As a pairwise similarity measure between two p-dimensional data points, x and y, we introduce mutual information that can be interpreted as the amount of information about x in y, and vice versa. We show that for our purposes this measure is superior to commonly used metric distances, for example, Euclidean distance. We also introduce a modified version of mutual information as a novel method for validating clustering results when the true clustering is known. The performance of our algorithm with respect to experimental noise is shown by extensive simulation studies. The algorithm is tested on a subset of 2029 cDNA clones coming from 15 different genes from a cDNA library derived from human dendritic cells. Furthermore, the clustering of these 2029 cDNA clones is demonstrated when the entire set of 76,032 cDNA clones is processed.