gebhart/patrepeval huggingface dataset:
Reference Genes for gene expression analysis in Head and Neck Squamous Cell Carcinoma: a Data Science Driven Approach (2022)

Objectives Quantitative real time PCR (qPCR) remains by far the most cost-effective, fast yet sensitive technique to check the gene expression levels in various systems. Traditionally used reference genes over the years were found to be regulated heavily based on sample sources and/or experimental conditions. This paper therefore presents a data science driven -omic approach for selection of reference genes from ~60,000 candidates from The Cancer Genome Atlas (TCGA) and Broad Institute Cancer Cell Line Encyclopaedia (CCLE) for gene expression studies in head and neck squamous cell carcinoma (HNSCC). Materials and Methods mRNA-sequencing data of 500 patient samples and 33 cell lines from publicly available databases were analysed to assess stability of genes in terms of multiple statistical measures. A final set of 12 candidate genes were studied in the Indian set of data in Gene Expression Omnibus (GEO) and validated experimentally using qPCR in 35 different types of samples from platforms like drug sensitive and resistant cell lines, normal and tumor samples, fibroblast and epithelial primary culture derived from HNSCC patients from India. Results The study lead to the choice of five most stable reference genes –TYW5, RIC8B, PLEKHA3, CEP57L1 and GPR89B across three experimental platforms. Conclusion In addition to providing a set of five most stable reference genes for future gene expression analysis experiments across different types of samples in HNSCC, the study also presents an objective framework for assessing reference genes for other disease areas as well.
Magnetic resonance imaging of normal and osteoarthritic trabecular bone structure in the human knee (2002)

High-resolution MRI of the knee joint can provide a noninvasive assessment of trabecular bone structure. Trabecular bone structure, determined by high-resolution MRI, shows significant variation in patients with varying degrees of OA. The impact of OA on trabecular bone is different in the tibia than in the femur, and this difference depends on the extent of the disease.
Application of Film Cooling to an Unshrouded High-Pressure Turbine Casing (2016)

In this paper, we describe the design, modeling, and experimental testing of a film cooling scheme employed on an unshrouded high-pressure (HP) rotor casing. The casing region has high thermal loads at both low and high frequency, with the flow being dominated by the potential field of the rotor and over-tip leakage flows. Increasingly high turbine entry temperatures necessitate internal and film cooling of the casing to ensure satisfactory service life and performance. There are, however, very few published studies presenting computational fluid dynamics (CFD) and experimental data for cooled rotor casings. Experimental testing was performed on a film-cooled rotor casing in the Oxford Turbine Research Facility (OTRF)—a rotating transonic facility of engine scale. Unsteady CFD of an HP rotor blade row with a film-cooled casing was undertaken, uniquely with a domain utilizing a sliding interface in the tip gap. A high density array of thin film heat flux gauges (TFHFGs) was used to obtain time-resolved and time-mean results of adiabatic wall temperature and film cooling effectiveness on the film-cooled rotor casing between −30% and +125% rotor tip axial chord. Results are compared to CFD predictions, and mechanisms for interaction of the coolant with the rotor tip are proposed and discussed. Acoustic effects within casing coolant holes due to the passing of the rotor are demonstrated on a 3D CFD geometry, supporting conclusions drawn in earlier work by the authors on the importance of this effect in a casing film cooling system.
Targeting the MET oncogene in cancer and metastases (2010)

Due to its versatile functions MET is a promising candidate for cancer therapy. Understanding molecular mechanisms of sensitization and resistance to MET inhibitors is a priority to guide tailored therapies and select patients that are most likely to achieve a clinical benefit.
1294-P: Detection and Intervention of Prediabetes in a Large Urban Health System: Systematic Failure or Looming Opportunity? (2019)

Efficient early detection of prediabetes is critical in order to intervene and reduce conversion to T2DM since lifestyle interventions and/or metformin are proven to reduce progression. Retrospective data from a nationally-ranked tertiary academic medical center were analyzed to determine diagnosis rates, frequency of lifestyle and prescription interventions, and to assess characteristics of patients who were most likely to be clinically identified or treated. Data from the EpicCare EMR were analyzed using the University of Kansas Medical Center i2b2-based clinical data repository (HERON). Data were collected for 69,781 patients established in academically affiliated primary care clinics between 2015 and 2017. After excluding for previous diabetes/prediabetes diagnoses or use of glucose lowering agents, 46,855 patients remained to assess for incident prediabetes (ADA criteria). Clinical recognition of the prediabetes diagnosis, nutrition or weight management referral, and metformin prescription were assessed. Incident prediabetes occurred in 2,581 patients (5%). Thirty eight percent of those received a charted prediabetes diagnosis, 9% received either a referral to nutrition or weight management, and 4% received a metformin prescription. Females (OR 1.57) or those who had higher BMI (OR 1.02) or A1c values (OR 5.67) had higher odds of receiving clinical recognition (p&amp;lt;0.0001). We conclude that relatively few people with prediabetes are clinically noted and even fewer receive interventions that may reduce the conversion to T2DM. There are gender and weight biases; patients with higher BMI, higher A1c values, and females were more likely to have documentation for diagnosis and treatment for prediabetes. These low rates of recognition and treatment are likely to be similar among health care systems across the country. The low rates of recognizing, documenting, and intervening are opportunities to better utilize the EMR and reduce conversion to T2DM. Disclosure E. Newbold: None. S.E. Carlson: Advisory Panel; Self; DSM. Other Relationship; Self; MeadJohnson Nutrition (RB). D.K. Sullivan: None. D.C. Robbins: None. A. Beltramo: None. M. Lowrance: None. L.R. Waitman: None.
Design, Certification, and Deployment of the Colorimetric Water Quality Monitoring Kit (CWQMK) (2010)

In August 2009, an experimental water quality monitoring kit based on Colorimetric Solid Phase Extraction (CSPE) technology was delivered to the International Space Station (ISS) aboard STS-128/17A. The kit, called the Colorimetric Water Quality Monitoring Kit (CWQMK), was developed by a team of scientists and engineers from NASA s Habitability and Environmental Factors Division in the Space Life Sciences Directorate at Johnson Space Center, the Wyle Integrated Science and Engineering Group in Houston, Texas, the University of Utah, and Iowa State University. The CWQMK was flown and deployed as a Station Development Test Objective (SDTO) experiment on ISS. The goal of the SDTO experiment was to evaluate the acceptability of CSPE technology for routine water quality monitoring on ISS. This paper provides an overview of the SDTO experiment, as well as a detailed description of the CWQMK hardware and a summary of the testing and analysis conducted to certify the CWQMK for use on ISS. The results obtained from the SDTO experiment are also reported and discussed in detail.
Production of the Escherichia coli Common Pilus by Uropathogenic E. coli Is Associated with Adherence to HeLa and HTB-4 Cells and Invasion of Mouse Bladder Urothelium (2014)

Uropathogenic Escherichia coli (UPEC) strains cause urinary tract infections and employ type 1 and P pili in colonization of the bladder and kidney, respectively. Most intestinal and extra-intestinal E. coli strains produce a pilus called E. coli common pilus (ECP) involved in cell adherence and biofilm formation. However, the contribution of ECP to the interaction of UPEC with uroepithelial cells remains to be elucidated. Here, we report that prototypic UPEC strains CFT073 and F11 mutated in the major pilin structural gene ecpA are significantly deficient in adherence to cultured HeLa (cervix) and HTB-4 (bladder) epithelial cells in vitro as compared to their parental strains. Complementation of the ecpA mutant restored adherence to wild-type levels. UPEC strains produce ECP upon growth in Luria-Bertani broth or DMEM tissue culture medium preferentially at 26°C, during incubation with cultured epithelial cells in vitro at 37°C, and upon colonization of mouse bladder urothelium ex vivo. ECP was demonstrated on and inside exfoliated bladder epithelial cells present in the urine of urinary tract infection patients. The ability of the CFT073 ecpA mutant to invade the mouse tissue was significantly reduced. The presence of ECP correlated with the architecture of the biofilms produced by UPEC strains on inert surfaces. These data suggest that ECP can potentially be produced in the bladder environment and contribute to the adhesive and invasive capabilities of UPEC during its interaction with the host bladder. We propose that along with other known adhesins, ECP plays a synergistic role in the multi-step infection of the urinary tract.
New Ligands for a General Palladium‐Catalyzed Amination of Aryl and Heteroaryl Chlorides (2004)

The synthesis and application of monodentate N-substituted heteroarylphosphines is described. In general, the ligands are conveniently prepared by selective metallation at the 2-position of the respective N-substituted heterocycle (pyrrole, indole) by using n-butyllithium/tetramethylethylenediamine (TMEDA) followed by quenching with dialkyl- or diarylchlorophosphines. Of the different ligands prepared, the new dialkyl-2-(N-arylindolyl)phosphines (cataCXium P) perform excellently in the palladium-catalyzed amination of aryl and heteroaryl chlorides. Coupling of both activated and deactivated chloroarenes proceeds under mild conditions (room temperature to 60 degrees C). By using optimized conditions remarkable catalyst productivity (total turnover number, TON, up to 8000) and activity (turnover frequency, TOF=14000 h(-1) at 75% conversion) are observed.
Experiments and simulations of wall running and transferring of a climbing robot (2015)

This paper reports experimental and simulation results of a compact wall-climbing robot. The robot has been developed with the aim to detect or repair inspections and flaws on walls. First, the mechanical structure of the robot is summarized, and the remote and autonomous control system is also described. Next, we focus on running on walls and transferring between two different walls. The experimental results are compared to the simulation results based on the dynamical model of the robot. Two proposed methods for wall transferring are experimentally verified, and these experiments have good agreements with the simulations.
Mitochondrial function in cardiomyocytes: target for cardioprotection (2005)

It appears that mitochondria regulate the life and death of cardiac cells by manipulating several factors, including bioenergetics, mitochondrial permeability transition pore and redox-sensing genes. Redox signaling is likely to be critically involved in this process.
Hydrogen water chemistry for BWRs (1985)

Laboratory tests show that hydrogen water chemistry is less aggressive than normal BWR water chemistry toward plant structural materials. Limited field tests indicate that the reduced corrosion cracking promised by the laboratory test results can be realized in an operating plant.
Intelligent Edge Computing for IoT-Based Energy Management in Smart Cities (2019)

In recent years, green energy management systems (smart grid, smart buildings, and so on) have received huge research and industrial attention with the explosive development of smart cities. By introducing Internet of Things (IoT) technology, smart cities are able to achieve exquisite energy management by ubiquitous monitoring and reliable communications. However, long-term energy efficiency has become an important issue when using an IoT-based network structure. In this article, we focus on designing an IoT-based energy management system based on edge computing infrastructure with deep reinforcement learning. First, an overview of IoT-based energy management in smart cities is described. Then the framework and software model of an IoT-based system with edge computing are proposed. After that, we present an efficient energy scheduling scheme with deep reinforcement learning for the proposed framework. Finally, we illustrate the effectiveness of the proposed scheme.
First-class variability modeling in Matlab/Simulink (2013)

Modern cars exist in an vast number of variants. Thus, variability has to be dealt with in all phases of the development process, in particular during model-based development of software-intensive functionality using Matlab/Simulink. Currently, variability is often encoded within a functional model leading to so called 150%-models which easily become very complex and do not scale for larger product lines. To counter these problems, we propose a modular variability modeling approach for Matlab/Simulink based on the concept of delta modeling [8, 9, 24]. A functional variant is described by a delta encapsulating a set of modifications. A sequence of deltas can be applied to a core product to derive the desired variant. We present a prototypical implementation, which is integrated into Matlab/Simulink and offers graphical editing of delta models.
Lack of usefulness of epidermal growth factor receptor expression determination for cetuximab therapy in patients with colorectal cancer (2006)

In patients with metastatic colorectal cancer, the use of cetuximab currently requires a documented tumoral epidermal growth factor receptor positivity. Responses to cetuximab, however, have been described in patients with epidermal growth factor receptor-negative tumors. We have used cetuximab in all eligible patients with metastatic colorectal cancer, whether their tumor expressed epidermal growth factor receptor or not. We assessed the cetuximab efficacy with regard to tumoral epidermal growth factor receptor expression. Twenty patients with metastatic colorectal cancer were treated off study with cetuximab and irinotecan after failure of oxaliplatin- and irinotecan-based regimens. Tumors were analyzed in all patients for epidermal growth factor receptor expression by immunohistochemistry. Tumors were positive for epidermal growth factor receptor in 12 cases and negative in eight cases. An objective response to cetuximab-based therapy was obtained in four patients (20%). Tumors of these four patients were negative for epidermal growth factor receptor expression. These results provide further evidence for the lack of usefulness of epidermal growth factor receptor detection by immunohistochemistry for cetuximab therapy in patients with metastatic colorectal cancer.
Warmer and Wetter Soil Stimulates Assimilation More than Respiration in Rainfed Agricultural Ecosystem on the China Loess Plateau: The Role of Partial Plastic Film Mulching Tillage (2015)

Effects of agricultural practices on ecosystem carbon storage have acquired widespread concern due to its alleviation of rising atmospheric CO2 concentrations. Recently, combining of furrow-ridge with plastic film mulching in spring maize ecosystem was widely applied to boost crop water productivity in the semiarid regions of China. However, there is still limited information about the potentials for increased ecosystem carbon storage of this tillage method. The objective of this study was to quantify and contrast net carbon dioxide exchange, biomass accumulation and carbon budgets of maize (Zea maize L.) fields under the traditional non-mulching with flat tillage (CK) and partial plastic film mulching with furrow-ridge tillage (MFR) on the China Loess Plateau. Half-hourly net ecosystem CO2 exchange (NEE) of both treatments were synchronously measured with two eddy covariance systems during the growing seasons of 2011 through 2013. At same time green leaf area index (GLAI) and biomass were also measured biweekly. Compared with CK, the warmer and wetter (+1.3°C and +4.3%) top soil at MFR accelerated the rates of biomass accumulation, promoted greater green leaf area and thus shortened the growing seasons by an average value of 10.4 days for three years. MFR stimulated assimilation more than respiration during whole growing season, resulting in a higher carbon sequestration in terms of NEE of -79 gC/m2 than CK. However, after considering carbon in harvested grain (or aboveground biomass), there is a slight higher carbon sink (or a stronger carbon source) in MFR due to its greater difference of aboveground biomass than that of grain between both treatments. These results demonstrate that partial plastic film mulched furrow-ridge tillage with aboveground biomass exclusive of grain returned to the soil is an effective way to enhance simultaneously carbon sequestration and grain yield of maize in the semiarid regions.
Operation of the Longitudinal Shock Wave Ferroelectric Generator Charging a Capacitor Bank (2007)

Summary form only given. Systematic experimental and theoretical investigations of explosive-driven ferroelectric generators (FEGs) charging capacitor banks of a wide range of capacitance were performed. The FEG operation is based on the physical effect of longitudinal (shock wave propagates along the polarization vector P) shock wave depolarization of lead zirconate titanate Pb(Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">52</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">48</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> polycrystalline ferroelectrics. Experimental data are presented for FEGs containing Pb(Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">52</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> piezoelectric energy-carrying elements of different dimensions. A model for digital simulation of an explosive-driven FEG operating in the charging mode has been developed and is addressed.
Entanglement-area law for general bosonic harmonic lattice systems (14 pages) (2006)

There have been numerous studies focusing on normal aging in previous decades which is accompanied by the structural and functional decline in the hippocampus, while the pattern of hippocampal alteration with age remains unclear. Figuring out the mechanism of hippocampal changes precisely is beneficial for a better understanding of the aging process. In this study, we included a total of 451 T1 MRI scans of subjects of age 50-90 who were labeled as normal in the Alzheimer's Disease Neuroimaging Initiative. Taking 10 years of age as an age band, we divided the subjects into four groups (denoted as HC1, HC2, HC3, and HC4, respectively), with the youngest being 50-60 and the oldest 81-90. Then the Multivariate Morphometry Statistics (MMS) of the hippocampus segmented from the four groups were extracted by surface reconstruction, mesh generation, and surface registration. Finally, the significant differences between the youngest group and the other three were statistically analyzed. Results showed that the earliest deformation region of the left hippocampus located in the frontal subiculum and the dorsal CA1 of the tail part and gradually expanded with aging, while the right hippocampal deformation mainly concentrated in the dorsal CA1 and spread to the posterior CA2-3, which occurred later than that of the left. All the results illustrated that the hippocampus is truly a vulnerable structure in the course of aging, and the MMS are sensitive metrics for detecting the changes in the subcortical convex structure.
Diagnosis and testing for growth hormone deficiency across the ages: a global view of the accuracy, caveats, and cut-offs for diagnosis (2023)

Growth hormone deficiency (GHD) is a clinical syndrome that can manifest either as isolated or associated with additional pituitary hormone deficiencies. Although diminished height velocity and short stature are useful and important clinical markers to consider testing for GHD in children, the signs and symptoms of GHD are not always so apparent in adults. Quality of life and metabolic health are often impacted in patients with GHD; thus, making an accurate diagnosis is important so that appropriate growth hormone (GH) replacement therapy can be offered to these patients. Screening and testing for GHD require sound clinical judgment that follows after obtaining a complete medical history of patients with a hypothalamic-pituitary disorder and a thorough physical examination with specific features for each period of life, while targeted biochemical testing and imaging are required to confirm the diagnosis. Random measurements of serum GH levels are not recommended to screen for GHD (except in neonates) as endogenous GH secretion is episodic and pulsatile throughout the lifespan. One or more GH stimulation tests may be required, but existing methods of testing might be inaccurate, difficult to perform, and can be imprecise. Furthermore, there are multiple caveats when interpreting test results including individual patient factors, differences in peak GH cut-offs (by age and test), testing time points, and heterogeneity of GH and insulin-like growth factor 1 assays. In this article, we provide a global overview of the accuracy and cut-offs for diagnosis of GHD in children and adults and discuss the caveats in conducting and interpreting these tests.
Quinoxalineimide as a Novel Electron-accepting Building Block for Organic Optoelectronics (2015)

Abstract Organic semiconductors with a donor–acceptor–donor architecture based on the novel acceptor unit of quinoxalineimide (QI) were designed and synthesized. They absorbed wider wavelength light compared to PC61BM, and functioned as acceptor materials for solution-processed bulk-heterojunction organic photovoltaic devices. In addition, the relatively shallow LUMO levels, due to the electron-withdrawing pyrazine and imide groups of the QI unit, resulted in a high open-circuit voltage of the devices.
ChemInform Abstract: Selective Complexation and Membrane Transport of Guanidinium Salts by Calix(6)arene Amides. (1993)

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.
ChemInform Abstract: THE (E)‐ AND (Z)‐α‐HYDROXY AND α‐METHOXYIMINO‐4‐NITRO‐1H‐IMIDAZOLE‐1‐ACETIC ACIDS AND ESTERS. SPECTRAL PROPERTIES, CONFORMATIONS AND PHOTOISOMERIZATION OF THE NEW COMPOUNDS (1980)

Abstract E‐ und Z‐Isomere (I)‐(III) werden in bekannter Weise hergestellt.