gebhart/patrepeval huggingface dataset:
Preliminary Gas Turbine Combustor Design Using a Network Approach (1997)

The preliminary design process of a gas turbine combustor often involves the use of cumbersome, geometry restrictive semi-empirical models. The objective of this analysis is the development of a versatile design tool for gas turbine combustors, able to model all conceivable combustor types. A network approach is developed that divides the flow into a number of independent semi-empirical subflows. A pressure-correction methodology solves the continuity equation and a pressure-drop/flow rate relationship. The development of a full conjugate heat transfer model allows the calculation of flame tube heat loss in the presence of cooling films, annulus heat addition, and flame tube feature heat pick-up. A constrained equilibrium calculation, incorporating mixing and recirculation models, simulates combustion processes. Comparison of airflow results to a well-validated combustor design code showed close agreement. The versatility of the network solver is illustrated with comparisons to experimental data from a reverse flow combustor.
ChemInform Abstract: First Synthesis and Further Functionalization of 7‐Chloro‐imidazo[2,1‐b][1,3]thiazin‐5‐ones. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Multivariate analysis and list mode processing of murine hemopoietic subpopulations for cytokinetic studies (1985)

Multivariate analyses and list mode data processing were used to obtain cytokinetic information on flow cytometrically distinct hemopoietic subpopulations. In one application, viable, unfixed hemopoietic subpopulations were discriminated on the basis of cyanine dye fluorescence and orthogonal light scatter; Hoechst dye fluorescence was measured to determine the proliferative status of the subpopulations. In another application, ethanol-fixed mouse bone marrow cells were triply stained with Hoechst dye, rhodamine-conjugated wheat germ agglutinin (WGA), and a fluorescein-labeled monoclonal antibody against bromodeoxyuridine. In both of these studies, flow cytometric data for all three variables were acquired in list mode fashion, stored on magnetic tape, and processed by list mode software on a computer-based multivariable pulse-height analyzer. In the first application, subpopulations distinguished by cyanine dye intensity and light scatter appeared to be more related to cell lineage and cell size than proliferative status. In the second application, WGA affinity discriminated two subpopulations in mouse bone marrow S-phase cells in each subpopulation that actively incorporated bromodeoxyuridine (BrdUrd). List mode data processing obviates the need for routine electronic sorting of cells and thus facilitates characterization of discriminated subpopulations. In this regard, it is particularly useful for the study of flow cytometrically distinct, low frequency subpopulations.
Generation of an Orthogonal Protein–Protein Interface with a Noncanonical Amino Acid (2017)

We have engineered the protein interface of the Escherichia coli chorismate mutase (EcCM) homodimer to be dependent on incorporation of a noncanonical amino acid (ncAA) at residue 72. The large hydrophobic amino acid p-benzoyl phenylalanine (pBzF) was substituted for Tyr72, which led to a catalytically inactive protein. A library of five residues (Leu25', Arg29', Leu76, Ile80' and Asp83') surrounding pBzF72 was generated and subjected to a growth based selection in a chorismate mutase deficient strain. An EcCM variant (Phe25', pBzF72, Thr76, Gly80' and Tyr83') forms a stable homodimer, has catalytic activity similar to the wild type enzyme, and unfolds with a T<sub>m</sub> of 53 °C. The X-ray crystal structure reveals a pi-pi stacking and hydrogen bonding interactions that stabilize the new protein interface. The strategy described here should be useful for generating organisms that are dependent on the presence of a ncAA for growth.
Weight Vector Tuning and Asymptotic Analysis of Binary Linear Classifiers (2022)

Unlike its intercept, a linear classifier&#x0027;s weight vector cannot be tuned by a simple grid search. Hence, this paper proposes weight vector tuning of a generic binary linear classifier through the parameterization of a decomposition of the discriminant by a scalar which controls the trade-off between conflicting informative and noisy terms. By varying this parameter, the original weight vector is modified in a meaningful way. Applying this method to a number of linear classifiers under a variety of data dimensionality and sample size settings reveals that the classification performance loss due to non-optimal native hyperparameters can be compensated for by weight vector tuning. This yields computational savings as the proposed tuning method reduces to tuning a scalar compared to tuning the native hyperparameter, which may involve repeated weight vector generation along with its burden of optimization, dimensionality reduction, etc., depending on the classifier. It is also found that weight vector tuning significantly improves the performance of Linear Discriminant Analysis (LDA) under high estimation noise. Proceeding from this second finding, an asymptotic study of the misclassification probability of the parameterized LDA classifier in the growth regime where the data dimensionality and sample size are comparable is conducted. Using random matrix theory, the misclassification probability is shown to converge to a quantity that is a function of the true statistics of the data. Additionally, an estimator of the misclassification probability is derived. Finally, computationally efficient tuning of the parameter using this estimator is demonstrated on real data.
ChemInform Abstract: NUCLEOPHILIC RING OPENING OF LACTONES VIA SN2‐TYPE REACTION WITH UNCOMPLEXED PHENYL SELENIDE ANION (1978)

Abstract Das aus Diphenyldiselenid (I) oder Selenophenol (III) erhaltene Natriumphenylselenat (II) spaltet Lactone (IV) zu den ungesättigten Carbonsäuren (V).
[Verrucous carcinoma. Apropos of a case report with palpebral localization]. (1983)

The authors present a case of "verrucous carcinoma" of the eyelid. Such a location never seems to have been described in the literature. As the histological features of the tumor are highly differentiated the exact diagnosis can be ascertained, only upon examination of a large biopsy specimen or of the operative specimen. Clinical, histological and evolutional features are recalled. The therapeutic means of curing this locally malignant and potentially recurrent lesion are discussed. In most cases, recovery depends on early treatment, particularly on surgery.
Microstrip patch antennas feed to optical waveguides in electro-optic modulator for millimeter-wave radar system (2015)

Microstrip patch antennas feed to optical waveguides in an electro-optic (EO) modulator are proposed for millimeter-wave radar system. Reflected millimeter-wave radar signals can be received by the microstrip patch antennas and converted directly to lighwave signals through EO modulation. The lightwave signals can be distributed using low loss optical fibers. Millimeter-wave loss and distortion are almost negligible. Device analysis and experiment for 40GHz millimeter-wave bands are discussed.
Variable renewable energy sources for powering reverse osmosis desalination, with a case study of wave powered desalination for Kilifi, Kenya (2020)

An analysis of reverse osmosis powered by ocean wave power is provided. A commercially available desalination system is connected via a DC/AC converter to a variable DC source and the input voltage is altered to emulate the response of a renewable energy system. Specifically, wave data from Kilifi in Kenya during 2015 is used. The wave resource variations provide variations in estimated power output from a wave energy converter, as well as in estimated freshwater production from a wave powered desalination system. Up to three wave energy converters for desalination are investigated for Kilifi. Also, a hybrid system including solar and wave power is proposed. The experiments show that reverse osmosis desalination systems can function at power levels below the rated values, but with lower freshwater flowrates. It is concluded that wave power, or wave power combined with PV systems, may be considered as power sources for desalination, with or without battery storage.
Supplementary Figure 2 from Low-Calcium Serum-Free Defined Medium Selects for Growth of Normal Prostatic Epithelial Stem Cells (2023)

Supplementary Figure 2 from Low-Calcium Serum-Free Defined Medium Selects for Growth of Normal Prostatic Epithelial Stem Cells
Enhancement of Stochastic Resonance with Tuning Noise and System Parameters (2006)

Stochastic resonance has been increasingly used for signal estimation, signal transmission, signal detection and image processing. The stochastic resonance effect can be realized by tuning system parameters or by adding noise. In our recent paper, we have investigated the possibility to enhance the aperiodic stochastic resonance (ASR) effect by tuning system parameters and adding noise simultaneously for the Gaussian-distribution weak input signal. This paper extends the result to a more general case using standard optimization theory. It is shown that the normalized power norm of the bistable double-well system with a small input signal can reach a larger maximal value by this scheme. An on-line fast-converging optimization algorithm is also proposed for searching the optimal values of system parameters and noise intensity.
Low-Temperature Formation of Silicon Nitride Film by Direct Nitridation Employing High-Density and Low-Energy Ion Bombardment (1999)

High-integrity silicon nitride films can be obtained at a temperature of 400°C using a newly developed high-density (&gt;10 12 cm -3 ) plasma characterized by low ion bombardment energies of below 7 eV. It was found for the first time that stoichiometric silicon nitride can be formed at a temperature of 400°C by precise control of nitrogen partial pressure to generate N 2 + in plasma. The growth rate and the electrical properties of this silicon nitride are similar to those of thermally grown nitride. Moreover, hysteresis of the C – V curve attributed to charge traps in the silicon nitride film disappeared with the addition of hydrogen to Ar/N 2 plasma, and the leakage current of the nitride film was decreased dramatically by irradiating in Ar/N 2 /H 2 plasma after Ar/N 2 plasma nitridation. These technologies are very promising for fabricating feature metal substrate silicon-on-insulator (SOI) devices and silicon nitride gate metal-insulator-semiconductor field effect transistors (MISFETs).
A survey of trust in internet applications (2000)

Trust is an important aspect of decision making for Internet applications and particularly influences the specification of security policy, i.e., who is authorized to perform actions as well as the techniques needed to manage and implement security to and for the applications. This survey examines the various definitions of trust in the literature and provides a working definition of trust for Internet applications. The properties of trust relationships are explained and classes of different types of trust identified in the literature are discussed with examples. Some influential examples of trust management systems are described.
Detection of Promoter Hypermethylation in Salivary Rinses as a Biomarker for Head and Neck Squamous Cell Carcinoma Surveillance (2011)

We were able to confirm an elevated rate of promoter hypermethylation in HNSCC saliva of patients by using a panel of gene promoters previously described as methylated specifically in HNSCC. Detection of hypermethylation in pretreatment saliva DNA seems to be predictive of local recurrence and overall survival. This finding has potential to influence treatment and surveillance of HNSCC patients.
Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides (2017)

Antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages are broadly used as research tools and therapeutic agents. Chemically modified PS-ASOs can mediate efficient target reduction by site-specific cleavage of RNA through RNase H1. PS-ASOs are known to be internalized via a number of endocytotic pathways and are released from membrane-enclosed endocytotic organelles, mainly late endosomes (LEs). This study was focused on the details of PS-ASO trafficking through endocytic pathways. It was found that lysobisphosphatidic acid (LBPA) is required for release of PS-ASOs from LEs. PS-ASOs exited early endosomes (EEs) rapidly after internalization and became co-localized with LBPA by 2 hours in LEs. Inside LEs, PS-ASOs and LBPA were co-localized in punctate, dot-like structures, likely intraluminal vesicles (ILVs). Deactivation of LBPA using anti-LBPA antibody significantly decreased PS-ASO activities without affecting total PS-ASO uptake. Reduction of Alix also substantially decreased PS-ASO activities without affecting total PS-ASO uptake. Furthermore, Alix reduction decreased LBPA levels and limited co-localization of LBPA with PS-ASOs at ILVs inside LEs. Thus, the fusion properties of ILVs, which are supported by LBPA, contribute to PS-ASO intracellular release from LEs.
FourArabidopsis RPPLoci Controlling Resistance to theNoco2Isolate ofPeronospora parasiticaMap to Regions Known to Contain OtherRPPRecognition Specificities (1996)

Interactions between Arabidopsis thaliana and the downy mildew fungus Peronospora parasitica provide a model system to study the genetic and molecular basis of plant-pathogen recognition. With the use of the Noco2 isolate of P. parasitica, the reaction phenotypes of 46 accessions of Arabidopsis were examined and 31 accessions exhibited resistance. Resistance phenotypes examined ranged from distinct necrotic pits or flecks to a weak necrosis accompanied by late and sparse fungal sporulation. Segregating populations generated from crosses between the susceptible accession Col-0 and the resistant accessions Ws-0, Pr-0, Oy-0, Po-1, Bch-1, Ge-1, Di-1, Ji-1, and Te-0 were also screened with Noco2. The genetic data were consistent with the presence of single resistance (RPP) loci in all of these accessions except Oy-0, in which resistance was inherited as a digenic trait. As a first step to molecular cloning, the map positions of four resistance loci were determined. These have been designated RPP14.1 from Ws-0, RPP14.2 from Pr-O, and RPP14.3 and RPP5.2 from Oy-0. RPP14.1 was mapped to a 3.2-cM interval on chromosome 3 that is linked to a region between the markers Gl-1 and m249 known to contain other P. parasitica resistance specificities. RPP14.2 from Pr-0 and RPP14.3 from Oy-0 were also positioned in this interval. Moreover, RPP14.1 and RPP14.2 showed linkage of < 0.05 cM, suggesting possible allelism. The second RPP locus from Oy-0, RPP5.2, was located on chromosome 4 and exhibited strong linkage (< 2 cM) to RRP5.1, a locus previously identified in the Arabidopsis accession Landsberg-erecta. The results reinforce evidence for RPP gene clustering in the Arabidopsis genome and provide new targets for cloning and examination of RPP gene structure, function, allelic variation, and organization within defined loci.
All-pole modeling of speech based on the minimum variance distortionless response spectrum (2000)

We present all-pole models based upon the minimum variance distortionless response (MVDR) spectrum for spectral modeling of speech. The MVDR method, which is popular in array processing, provides all-pole spectra that are robust for modeling both voiced and unvoiced speech. Although linear prediction (LP) is a popular method for obtaining all-pole model parameters, LP spectral envelopes overestimate and overemphasize the medium and high pitch voiced speech spectral powers, thereby featuring unwanted sharp contours, and do not improve in spectral envelope modeling performance as the filter order is increased. In contrast, the MVDR all-pole spectrum which can be easily obtained from the LP coefficients, features improved spectral envelope modeling as the filter order is increased. In particular, the high order MVDR spectrum models voiced speech spectra very well, particularly at the perceptually important harmonics, and features a smooth contoured envelope. Furthermore, the MVDR spectrum can be based upon either conventional time domain correlation estimates or upon spectral samples, a task that is common in frequency domain speech coding. In particular, the MVDR spectrum of sufficient order provides an all-pole envelope that models a set of spectral samples exactly. In addition, the MVDR all-pole spectrum is also suitable for modeling unvoiced speech spectra.
A Modified “Cross-talk” between Histone H2B Lys-120 Ubiquitination and H3 Lys-79 Methylation (2010)

Western blot analysis is currently the major method utilized for quantitatively assessing histone global modifications. However, there is a growing need to develop a highly specific, accurate, and multisite quantitative method. Herein, we report a liquid chromatography-tandem mass spectrometry-multiple reaction monitoring method to simultaneously quantify multisite modifications with unmatched specificity, sensitivity, and throughput. With one set of purification of histones by high pressure liquid chromatography or SDS-PAGE, nearly 20 modification sites including acetylation, propionylation, methylation, and ubiquitination were quantified within 2 h for two samples to be compared. Using this method, the relative levels of H2B ubiquitination and H3 Lys-79 methylation were quantified in the U937 human leukemia cell line, U937 derivative cell lines overexpressing anti-secretory factor 10 (AF10) and mutant AF10 with the deletion of the hDot1 binding domain OM-LZ. We found that H2B ubiquitination is inversely correlated with H3 Lys-79 methylation. Therefore, we propose that a catalytic and inhibitory loop mechanism may better describe the cross-talk relationship between H2B ubiquitination and H3 Lys-79 methylation.
Top–Down Attentional Modulation in Human Frontal Cortex: Differential Engagement during External and Internal Attention (2020)

Decades of electrophysiological research on top-down control converge on the role of the lateral frontal cortex in facilitating attention to behaviorally relevant external inputs. However, the involvement of frontal cortex in the top-down control of attention directed to the external versus internal environment remains poorly understood. To address this, we recorded intracranial electrocorticography while subjects directed their attention externally to tones and responded to infrequent target tones, or internally to their own thoughts while ignoring the tones. Our analyses focused on frontal and temporal cortices. We first computed the target effect, as indexed by the difference in high frequency activity (70-150 Hz) between target and standard tones. Importantly, we then compared the target effect between external and internal attention, reflecting a top-down attentional effect elicited by task demands, in each region of interest. Both frontal and temporal cortices showed target effects during external and internal attention, suggesting this effect is present irrespective of attention states. However, only the frontal cortex showed an enhanced target effect during external relative to internal attention. These findings provide electrophysiological evidence for top-down attentional modulation in the lateral frontal cortex, revealing preferential engagement with external attention.
Changes in Frailty After Kidney Transplantation (2015)

After KT, in adult recipients of all ages, frailty initially worsens but then improves by 3 months. Although KT recipients who were frail at KT had higher frailty scores over the long term, they were most likely to show improvements in their physiological reserve after KT, supporting the transplantation in these individuals and suggesting that pretransplant frailty is not an irreversible state of low physiological reserve.
A Prodomain Fragment from the Proteolytic Activation of Growth Differentiation Factor 11 Remains Associated with the Mature Growth Factor and Keeps It Soluble (2017)

Growth differentiation factor 11 (GDF11), a member of the transforming growth factor β (TGF-β) family, plays diverse roles in mammalian development. It is synthesized as a large, inactive precursor protein containing a prodomain, pro-GDF11, and exists as a homodimer. Activation requires two proteolytic processing steps that release the prodomains and transform latent pro-GDF11 into active mature GDF11. In studying proteolytic activation in vitro, we discovered that a 6-kDa prodomain peptide containing residues 60-114, PDP<sub>60-114</sub>, remained associated with the mature growth factor. Whereas the full-length prodomain of GDF11 is a functional antagonist, PDP<sub>60-114</sub> had no impact on activity. The specific activity of the GDF11/PDP<sub>60-114</sub> complex (EC<sub>50</sub> = 1 nM) in a SMAD2/3 reporter assay was identical to that of mature GDF11 alone. PDP<sub>60-114</sub> improved the solubility of mature GDF11 at neutral pH. As the growth factor normally aggregates/precipitates at neutral pH, PDP<sub>60-114</sub> can be used as a solubility-enhancing formulation. Expression of two engineered constructs with PDP<sub>60-114</sub> genetically fused to the mature domain of GDF11 through a 2x or 3x G4S linker produced soluble monomeric products that could be dimerized through redox reactions. The construct with a 3x G4S linker retained 10% activity (EC<sub>50</sub> = 10 nM), whereas the construct connected with a 2x G4S linker could only be activated (EC<sub>50</sub> = 2 nM) by protease treatment. Complex formation with PDP<sub>60-114</sub> represents a new strategy for stabilizing GDF11 in an active state that may translate to other members of the TGF-β family that form latent pro/mature domain complexes.
Explainable AI for ECG-based prediction of cardiac resynchronization therapy outcomes: learning from machine learning? (2022)

In the first phase the ECG is encoded by breaking it down to its principal factors, which contain all important signal information if the compression is lossless. Since the factors contain all essential information, a decoder reconstructs the ECG and can be used to identify the most important features (FactorECG). Additionally, these factors are used to predict CRT outcomes (second phase). Modification of the factors allows generation of an ECG that corresponds to specific outcomes, and corresponding ECGs can be generated to indicate signal feature changes associated with the outcomes.
METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning (2023)

Abstract Imaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated. METASPACE-ML is a machine learning-based approach addressing this challenge which incorporates new scores and computationally-efficient False Discovery Rate estimation. For training and evaluation, we use a comprehensive set of 1,710 datasets from 159 researchers from 47 labs encompassing both animal and plant-based datasets representing multiple spatial metabolomics contexts derived from the METASPACE knowledge base. Here we show that, METASPACE-ML outperforms its rule-based predecessor, exhibiting higher precision, increased throughput, and enhanced capability in identifying low-intensity and biologically-relevant metabolites.