gebhart/patrepeval huggingface dataset:
A comparative study of techniques for differential expression analysis on RNA-Seq data (2014)

Abstract Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
Sexual dysfunctions in breast cancer patients: evidence in context (2023)

In female breast cancer, future research is oriented toward the gain of evidence on combined therapies and long-term data on safety issues on the most promising interventions. The lack of evidence on sexual disturbances in male breast cancer patients remains a major concern.
Stable and noniterative bidirectional beam propagation method (2000)

We present a family of bidirectional beam propagation methods based on the application of Pade approximants to the square-root expressions appearing in the transition operator. We show that the numerical instability associated with the use of real Pade primes can be removed by using branch-cut rotation of the square-root operator.
Fast impedance matching using interval halving of resonator position numbers for a high-power evanescent-mode cavity tuner (2018)

A fast interval-halving search is demonstrated that can be used to optimize power-amplifier load impedance in real-time with a high-power evanescent-mode cavity tuner, consisting of two evanescent-mode resonant cavities. The power-added efficiency is optimized by tuning the resonator position numbers, which map to resonant frequencies, without need for a load-pull characterization. Because no characterization is required, significant time savings in computation is expected, and tuning is expected to be more robust to drift and hysteresis of the tuner characteristics.
Note: Burkholderia thailandensis sp. nov., a Burkholderia pseudomallei-like species (1998)

The presence of a Burkholderia pseudomallei-like species based upon the significant genotypic and phenotypic dissimilarities exhibited between these organisms and true B. pseudomallei strains has been reported previously. In this study, a comprehensive 16S rDNA-based phylogenetic analysis further supports the existence of this newly described Burkholderia species for which the name Burkholderia thailandensis sp. nov. is proposed.
Doping dependence of upper critical field and Hall resistivity in LaFeAsO1-xFx (x = 0, 0.025, 0.05, 0.07, 0.11 and 0.14) (2008)

The electrical resistivity (Rxx) and Hall resistivity (Rxy) of LaFeAsO1-xFx have been measured over a wide fluorine doping range 0 = = 75 T for x = 0.05. This is reminiscent of the composition dependence in high-Tc cuprates and might correlate with opening of a pseudo-gap in the underdoped region. Further, the temperature dependence of Hc2(T) for superconducting samples can be understood in terms of multi-band superconductivity. Rxy data for non-superconducting samples show non-linear field dependence, which is also consistent with a multi-carrier scenario.
Centrality dependence of the pseudorapidity density distribution for charged particles in Pb–Pb collisions at sNN=5.02 TeV (2017)

We present the charged-particle pseudorapidity density in Pb-Pb collisions at s NN = 5.02 TeV in centrality classes measured by ALICE. The measurement covers a wide pseudorapidity range from -3.5 to 5, which is sufficient for reliable estimates of the total number of charged particles produced in the collisions. For the most central (0-5%) collisions we find 21 400 1 300, while for the most peripheral (80-90%) we find 230 38. This corresponds to an increase of (27 4)% over the results at s NN = 2.76 TeV previously reported by ALICE. The energy dependence of the total number of charged particles produced in heavy-ion collisions is found to obey a modified power-law like behaviour. The chargedparticle pseudorapidity density of the most central collisions is compared to model calculations -none of which fully describes the measured distribution. We also present an estimate of the rapidity density of charged particles. The width of that distribution is found to exhibit a remarkable proportionality to the beam rapidity, independent of the collision energy from the top SPS to LHC energies.
Model-Based Data Reconciliation and Bias Detection for Heavy-Duty Industrial Gas Turbines Performance Diagnosis (2011)

Performance diagnoses of heavy-duty industrial gas turbines often rely on measured data from on-site monitoring systems (OSM), subjected to larger uncertainties and possible biases. The measured data are used to analyze gas turbine heat balance and estimate immeasurable performance characteristics such as firing temperature and component health parameters. Traditional heat balance techniques are deterministic, and, thus, calibration uncertainty is not mitigated. In this paper, a method of model-based data reconciliation (MBDR) and bias detection was developed, serving as a probabilistic process of reducing calibration uncertainty while eliminating contamination effects caused by measurement biases. This method utilizes physics-based gas turbine models to reconcile multiple data sets while the model health parameters are inferred simultaneously. Levenberg–Marquardt algorithm was utilized to solve the maximum-likelihood problem, i.e., minimizing Least Squares. A hypothesis test scheme using sequential bias compensation was utilized for bias detection and neutralizing smearing effects. To reduce the computation time in MBDR and bias detection, the Response Surface Methodology (RSM) was applied to generate surrogate model. A systematic way of data selection using Multiscale Principal Component Analysis was also employed, serving as an efficient way of filtering large data sets for the use of MBDR. This proposed methodology was demonstrated by application to GE 7FA gas turbines. Results showed significant reduction in calibration uncertainty and smearing effects.
High-Performance Grid Computing via Distributed Data Access. (2004)

Prokaryotic cyanobacteria express robust circadian (daily) rhythms, even when growing with doubling times that are considerably faster than once every 24 h. This biological clock orchestrates cellular events to occur in an optimal temporal program. Competition experiments demonstrate that fitness is enhanced when the circadian period resonates with the period of the environmental cycle.
Transfer Learning by Sharing Support Vectors (2012)

? This work was supported in part by the ERC MicroNano project. Abstract. Machine Learning techniques play an increasingly vital role in the analysis of Biomedical imagery, as in all other areas of Computer Vision. However, in this specific context, they suffer from the fact that experimental conditions and protocols change often and that acquiring sufficient amounts of new training data after each image acquisition is impractical. In this paper, we propose an effective method to train a non-linear SVM using a very small amount of new data by leveraging data obtained under different conditions. Unlike earlier approaches, ours takes full advantage of the kernelized SVM formulation, does not depend on a loss function that is sensitive to outliers, and yields a quadratic optimization problem. We demonstrate its effectiveness for the purpose of classifying pixels in electron microscope image stacks and delineating linear structures in optical microscopy and retinal scans. Our method outperforms two state-of-the-art transfer-learning approaches in terms of accuracy and computational complexity.
Carrier Envelope Offset of Nondegenerate, Doubly-Resonant, Midinfrared GaAs Optical Parametric Oscillators (2013)

We demonstrate that the carrier-envelope offset frequency of a mid-infrared frequency comb from a nondegenerate and doubly-resonant GaAs-based optical parametric oscillator is locked to that of the 2 µm thulium-fiber pump laser.
251 (2012)

Introduction: Lung ultrasound has been shown to help diagnose patients with various lung ailments such as pleural effusion, interstitial edema, or pneumothorax. Congestive heart failure (CHF) exacerbation is suggested by the presence of a large number of “B-Lines.” Hypothesis: We hypothesized that daily lung ultrasound scans (LUS) would show a decrease in the number of “B-lines” during treatment of CHF exacerbations. Methods: All patients presenting to the Emergency Department with a high clinical suspicion of CHF exacerbation were eligible for the study. A convenience sample of patients was enrolled, based on operator availability. Ultrasound-trained physicians performed the initial LUS at presentation and on the second day of hospital admission. All patients received routine management of CHF exacerbations from their treating physicians, who were unaware of the LUS results. LUS were performed using a Sonosite M-Turbo ultrasound device with a phased-array cardiac transducer. Six-second clips were recorded in 8 lung zones. Two operators blinded to clinical data reviewed all clips. A B-line score was generated for each LUS by adding the individual scores of each of the 8 zones. We compared the B-line scores between the two time points using a paired two-way Student’s t-test. Spearman’s rank correlation coefficients were determined for all possible pairs of the clinical variables collected, including total B-line score. Results: Twenty patients were enrolled in the study after giving consent. The mean total B-line score on Day 1 was 26.4 (SD 10.1), compared to 15.7 (SD 9.0) on Day 2 (p = 0.0025). Day 1 total B-line scores were positively correlated with age (r = 0.57, p < 0.05), and negatively correlated with Killip class (r = -0.50, p < 0.05). All patients indicated an improvement in symptoms on the following day. Neither Day 2 B-line values or the difference between Day 1 values and Day 2 values, were correlated with any other clinical variables. Conclusions: The total B-line score significantly decreased after treatment for CHF exacerbation, in parallel to clinical improvement. These data suggest that the B-line score may be used to monitor patients’ response to treatment for CHF exacerbations.
Application of non-negative matrix factorization for the deconvolution of petroleum mixtures using mid FTIR analysis (2015)

The aim of this study was to develop an efficient, in terms of both time and cost, but still reliable methodology, capable of identifying the chemical fractions in complex commercial petroleum products. The performance of a methodology based on Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) analytical signals is demonstrated, combined with a modified factorization algorithm to solve this “mixture problem”. The results of this innovative work, regarding both the application of the adapted deconvolution technique to petroleum analysis and its self-adaptation to data without any former initialization, indicate that it is possible to reveal the content in a chemically complex petroleum mixture, working solely with the infrared signals of a limited number of samples and without any other a priori information. A focus application of the proposed methodology is the quality control of commercial gasoline by identifying and quantifying the individual fractions used for its formulation.
09282 Abstracts Collection – Foundations for Forgery-Resilient Cryptographic Hardware (2010)

From 05.07 to 08.07.2009, the Dagstuhl Seminar 09282 "Foundations for Forgery-Resilient Cryptographic Hardware" was held in Schloss Dagstuhl - Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available
Visualization and Fundamental Analysis of Liquid Atomization by Fuel Slingers in Small Gas Turbine Engines (2002)

There are strong engineering motivations for wanting to place the design of fuel slingers and the understanding of their performance on an improved technical foundation. To date, however, there have been no studies conducted at a fundamental level of the basic physical processes involved in fuel slinger operation, or of the design and performance rules that are implied by these. We present results from visualization experiments of liquid atomization in a variety of fuel slinger geometries over a range of operating conditions. These visualizations then lead to a fundamental technical analysis that develops broadly applicable design and performance rules for round-hole fuel slingers in small gas turbines. The results from this analysis provide excellent correlation of experimental data by Morishita (1981) on the atomization performance of gas turbine slingers for various combinations of slinger diameters, number of holes, hole sizes, liquid flow rates, and slinger rotation rates. The results provide a basis for understanding the performance of existing fuel slingers, for guiding the design of improved fuel slingers, and for pointing to potentially dramatic new improvements in fuel slinger technology for small gas turbines.
Next-generation sequencing reveals the biological significance of the N 2,3-ethenoguanine lesion in vivo (2015)

Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N(2),3-ethenoguanine (N(2),3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2'-fluoro-2'-deoxyribose analog of N(2),3-εG was used to quantify directly its genotoxicity and mutagenicity. A multiplex method involving next-generation sequencing enabled a large-scale in vivo analysis, in which both N(2),3-εG and its isomer 1,N(2)-ethenoguanine (1,N(2)-εG) were evaluated in various repair and replication backgrounds. We found that N(2),3-εG potently induces G to A transitions, the same mutation previously observed in VC-associated tumors. By contrast, 1,N(2)-εG induces various substitutions and frameshifts. We also found that N(2),3-εG is the only etheno lesion that cannot be repaired by AlkB, which partially explains its persistence. Both εG lesions are strong replication blocks and DinB, a translesion polymerase, facilitates the mutagenic bypass of both lesions. Collectively, our results indicate that N(2),3-εG is a biologically important lesion and may have a functional role in VC-induced or inflammation-driven carcinogenesis.
$\hbox{Ge-Si}_{x}\hbox{Ge}_{1 - x}$ Core–Shell Nanowire Tunneling Field-Effect Transistors (2010)

We report the fabrication and experimental investigation of Ge-Si <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-</sub> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> core-shell nanowire (NW) tunneling field-effect transistors (TFETs), consisting of p-i-n device structures realized by low-energy ion implantation. We investigate the NW TFET device characteristics as a function of drain doping, channel length, and temperature. Our devices show on-state currents of up to <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> ~ 5μA/μm, with an ambipolar behavior that can be suppressed by varying the drain doping concentration. The subthreshold swing of NW TFETs shows little temperature dependence down to 77 K, consistent with band-to-band tunneling as being the dominant carrier injection mechanism.
RV Pacing Percentage (2020)

Abstract Introduction Chronic right ventricular pacing (RVP) has been associated with dyssynchrony, leading to increased mortality. However, there have been discrepancies in previous reports in the effect of RVP levels. Objective To sub-stratify mortality risk by age for different RVP level groups within a large real-world ICD cohort. Methods Optum® de-identified electronic health records were linked to the Medtronic Carelink data to identify dual chamber ICD recipients (2007–2017). RVP level was based on median daily pacing during the first 90 days post-implant and categorized either into groups with a cutoff of 40%, or with groups of 0–9%, 10–19%, 20–29%, 30–39%, 40–49%, and 50–100%. The endpoint was death more than 90 days post-implant. Kaplan-Meier survival curves, log-rank tests, and Cox regression were used to analyze the relationship between RVP and risk of death. Results Among 14,832 ICD patients (median age 67; 74.0% male), there were 2,602 deaths within 10 years after implant. In unadjusted comparisons, high RVP (&amp;gt;40%) increased the risk of death relative to low RVP (≤40%) (p&amp;lt;0.001). This effect remained significant in older cohort (≥67 years old at implant) (p&amp;lt;0.001), but not in younger cohort (&amp;lt;67 years old) (p=0.955) (Figure). After controlling for age, gender, pacing mode, MI, SCA, HF hospitalization, diabetes, and renal dysfunction, similar or increased risk was associated with higher pacing groups relative to the 0–9% pacing group in the older cohort, but not in the younger cohort. Conclusions Our data from a large contemporaneous real-world source suggests that older age or characteristics associated with age make patients more sensitive to chronic RVP effects. These results help reconcile differences observed in prior studies. Funding Acknowledgement Type of funding source: Private company. Main funding source(s): Medtronic, Inc.
Performance Investigation of Power Inverter Components Submersed in Subcooled Liquid Nitrogen for Electric Aircraft (2022)

Investigating the performance of power electronics devices and thus power inverters at cryogenic temperatures for electric aircraft systems are of great interest. Accordingly, the purpose of this study is to examine the inverter circuit technologies used in cryogenically-cooled electric aircraft applications from three perspectives: inverter topologies, power capabilities, and electromagnetic interference (EMI) that may occur. At a cryogenic temperature, the characteristics of five power semiconductor switches with different technologies (Si MOS, SiC MOS, and GaN HEMT) used in cryogenically-cooled electric aircraft inverters were tested and the results were presented. Furthermore, the low-temperature performance of three types of capacitors commonly used in power electronics inverters was investigated. The research findings provide crucial considerations for the research and development of power inverters cooled by sub-cooled liquid nitrogen for modern electric aircraft.
<title>Overview of FTTH networks: past history, current status, and future designs</title> (1996)

Fiber-to-the-home (FTTH) networks have always been the ultimate solution to a future-proof, broadband access- network. In the past, the major obstacle to implementing FTTH has been cost, coupled with the lack of symmetrical, bandwidth intensive applications. In recent years, however, there have been several technological, commercial, and regulatory developments that brighten the outlook on FTTH. This paper outlines these changes, and presents architectures that may be deployed in the near future. First, the current motivations driving FTTH, including high bandwidth, high reliability, and low operations cost, are discussed. This is then be followed by a review of various FTTH systems. This emphasizes key developments and trends that are influencing present system configurations. After this background, some recent technology developments that impact FTTH are presented. These include high-temperature loop lasers, battery technology, video compression, and ATM transport. It is shown how oak of these advances makes FTTH more attainable. In general, a FTTH system can be characterized by its service capability, network topology, and signal format. By specifying different combinations of these characteristics, one can generate many different systems which can then be compared to identify optimal designs. From these considerations, for distinct FTTH networks, including TDM-PON, FDM-PON, dense-WDM-PON, and FTTC with fiber drops are described and analyzed in view of their future potential.
A novel enantioselective synthesis of (S)-(?)- and (R)-(+)-nornicotine via alkylation of a chiral 2-hydroxy-3-pinanone ketimine template (1999)

An asymmetric synthesis of the optically pure isomers of the minor tobacco alkaloid and CNS nicotine metabolite, nornicotine, has been achieved with moderately high optical purity. The synthetic pathway involves alkylation of a chiral ketimine, prepared from either 1R,2R,5R-(+)- or 1S,2S,5S-(-)-2-hydroxy-3-pinanone and 3-(aminomethyl)pyridine with 3-bromopropan-1-ol. After cleavage of the respective C-alkylated ketimines with NH2OH.HCl, and treatment of the resulting amino alcohols with HBr, followed by base-catalyzed intramolecular ring closure, (S)-(-)-nornicotine and (R)-(+)-nornicotine were obtained with ee values of 91% and 81%, respectively.