gebhart/patrepeval huggingface dataset:
Continuous hydrothermal synthesis of inorganic materials in a near-critical water flow reactor; the one-step synthesis of nano-particulate Ce1 − xZrxO2 (x = 0–1) solid solutions (2001)

Ce1 − xZrxO2 solid solutions are produced continuously by hydrolysis of mixtures of cerium ammonium nitrate and zirconium acetate in near-critical water at ca. 300 °C and 25 MPa using a flow reactor. Rapid hydrothermal coprecipitation leads to nano-particulate Ce1 − xZrxO2 (x = 0–1), the composition of which is largely determined by the initial relative concentrations of Ce4+ and Zr4+ ions in the starting solution. The freshly prepared materials are crystalline, possess very small particle sizes, and have high surface areas. The effects of calcining the products in air at high temperature have been studied. Apart from the 1∶1 Ce∶Zr solid solution, the phases of Ce1 − xZrxO2 remain stable on calcining to 1000 °C, but the particles sinter and the surface areas decrease significantly. The materials have been characterised by Powder X-ray Diffraction (PXD), IR and Raman Spectroscopy, microanalysis, Thermogravimetric Analysis (TGA), X-ray Fluorescence (XRF) and BET (surface area measurements). In selected cases, high resolution Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) images were recorded to examine the particle morphology.
Electrocatalytic Activity of Nitrogen-Doped Carbon Nanotube Cups (2009)

The electrochemical activity of stacked nitrogen-doped carbon nanotube cups (NCNCs) has been explored in comparison to commercial Pt-decorated carbon nanotubes. The nanocup catalyst has demonstrated comparable performance to that of Pt catalyst in oxygen reduction reaction. In addition to effectively catalyzing O(2) reduction, the NCNC electrodes have been used for H(2)O(2) oxidation and consequently for glucose detection when NCNCs were functionalized with glucose oxidase (GOx). Creating the catalysts entirely free of precious metals is of great importance for low-cost fuel cells and biosensors.
Analysis of Movement, Orientation and Rotation-Based Sensing for Phone Placement Recognition (2015)

Phone placement, i.e., where the phone is carried/stored, is an important source of information for context-aware applications. Extracting information from the integrated smart phone sensors, such as motion, light and proximity, is a common technique for phone placement detection. In this paper, the efficiency of an accelerometer-only solution is explored, and it is investigated whether the phone position can be detected with high accuracy by analyzing the movement, orientation and rotation changes. The impact of these changes on the performance is analyzed individually and both in combination to explore which features are more efficient, whether they should be fused and, if yes, how they should be fused. Using three different datasets, collected from 35 people from eight different positions, the performance of different classification algorithms is explored. It is shown that while utilizing only motion information can achieve accuracies around 70%, this ratio increases up to 85% by utilizing information also from orientation and rotation changes. The performance of an accelerometer-only solution is compared to solutions where linear acceleration, gyroscope and magnetic field sensors are used, and it is shown that the accelerometer-only solution performs as well as utilizing other sensing information. Hence, it is not necessary to use extra sensing information where battery power consumption may increase. Additionally, I explore the impact of the performed activities on position recognition and show that the accelerometer-only solution can achieve 80% recognition accuracy with stationary activities where movement data are very limited. Finally, other phone placement problems, such as in-pocket and on-body detections, are also investigated, and higher accuracies, ranging from 88% to 93%, are reported, with an accelerometer-only solution.
Characterization of Drug-Product-Related Impurities and Variants of a Therapeutic Monoclonal Antibody by Higher Energy C-Trap Dissociation Mass Spectrometry (2014)

Mass spectrometry (MS) characterization of recombinant monoclonal antibody (mAb) drugs and their degraded and/or post-translationally modified counterparts, drug-product-related impurities and variants, is critical for successful development of biotherapeutics. Specifically in this study, drug-product-related impurities of an anti-Clostridium difficile IgG1 mAb drug substance were profiled by cation-exchange liquid chromatography (CEX) followed by the CEX peaks being fraction-collected for MS characterization. A reversed-phase liquid chromatography/mass spectrometry (LC/MS) methodology was developed on a Thermo Q-Exactive orbitrap mass spectrometer for (1) accurate mass measurements of the mAb, its CEX fractionated impurities, and their respective heavy chains and light chains and (2) middle-down LC/MS/MS of the light chains and the heavy chains using higher energy C-trap dissociation (HCD). The accurate mass measurements and the HCD middle-down MS/MS experiments identify that major impurities and variants of the anti-C. difficile mAb are degradation species of the heavy chains at residue Asn101 as well as at the hinge region amino acids, including Cys222, Lys224, His226, and Thr227, with levels ranging from 0.3% to 6.2% of the total drug substance. Additional impurities were identified as light chain C-terminal truncation at Gly93 and oxidized heavy chains at Met40, Met93, and Met430. Our impurity characterization results demonstrate that the middle-down MS method allows direct and accurate identification of drug-product-related impurities of therapeutic mAbs. It is particularly useful for those low-level impurities and variants that are not suitable for further fractionation and characterization by bottom-up MS.
Camptothecin resistance involving steps subsequent to the formation of protein-linked DNA breaks in human camptothecin-resistant KB cell lines. (1996)

To identify mechanisms of camptothecin (CPT) resistance/toxicity, sublines from a human KB cell line were made resistant to CPT by continuous selection in increasing concentrations of CPT. Two CPT-resistant lines, 100 and 300, were 32- and 54-fold resistant to the growth-inhibitory properties of CPT compared to the KB line. After CPT-free culturing, partial revertant lines were established from each resistant line. These partial revertant lines, 100rev and 300rev, were 2.5- and 3.2-fold resistant to CPT compared to KB. When growth inhibition and toxicity were compared, the resistant lines alone displayed an enhanced cytostatic response to CPT. The resistant and partial revertant lines displayed no cross-resistance to etoposide or cisplatin. Comparisons of topoisomerase I (TOPI) activity, content, and protein-linked DNA break production by CPT revealed that resistant and partial revertant lines had one-half the levels as KB, with TOP1 activity that was equally sensitive to CPT in all cell lines tested. However, double-stranded DNA break induction by CPT was significantly reduced only in the resistant lines. Coincubation with 3-aminobenzamide, an inhibitor of poly(ADP-ribosyl) polymerase, potentiated CPT toxicity in the resistant lines alone, without affecting CPT: TOP1 interactions. Therefore, CPT resistance in the 100 and 300 lines was characterized by factors independent of TOP1, specific for CPT, and attenuated by poly(ADP-ribosyl) polymerase inhibition. This resistant phenotype produced fewer double-stranded DNA breaks and enhanced a cytostatic response to CPT.
Figure S4 from Parallel Accumulation of Tumor Hyaluronan, Collagen, and Other Drivers of Tumor Progression (2023)

&lt;p&gt;AsPC-1 parental cells (AsPC-1-P) engineered to overexpress HAS3 (AsPC-1/HAS3, see Materials and Methods) produced more HA in the peritumoral matrix and the stroma.&lt;/p&gt;
Multimodal Routing: Improving Local and Global Interpretability of\n Multimodal Language Analysis (2020)

The human language can be expressed through multiple sources of information\nknown as modalities, including tones of voice, facial gestures, and spoken\nlanguage. Recent multimodal learning with strong performances on human-centric\ntasks such as sentiment analysis and emotion recognition are often black-box,\nwith very limited interpretability. In this paper we propose Multimodal\nRouting, which dynamically adjusts weights between input modalities and output\nrepresentations differently for each input sample. Multimodal routing can\nidentify relative importance of both individual modalities and cross-modality\nfeatures. Moreover, the weight assignment by routing allows us to interpret\nmodality-prediction relationships not only globally (i.e. general trends over\nthe whole dataset), but also locally for each single input sample, meanwhile\nkeeping competitive performance compared to state-of-the-art methods.\n
Sperm DNA Damage Measured by Comet Assay (2012)

Measurement of sperm DNA damage is a useful tool in the evaluation of male infertility, as the sperm nucleus lacks protection against oxidative stress and is vulnerable to oxidation-mediated DNA damage. The Comet assay or single-cell gel electrophoresis is a relatively simple and sensitive method for measuring strand breaks in DNA in individual sperm. During this procedure, sperm cells are embedded in a thin layer of agarose on a microscope slide and lysed with detergent under high salt conditions. This process removes protamines and histones allowing the nucleus to form a nucleoid-like structure containing supercoiled loops of DNA. Alkaline pH conditions result in unwinding of double-stranded DNA, and subsequent electrophoresis results in the migration of broken strands towards the anode, forming a comet tail, when observed under fluorescence microscope. The amount of DNA in the head and tail is reflected by its fluorescent intensity. The relative fluorescence in the tail compared with its head serves as a measure of the level of DNA damage. In this chapter, we describe the alkaline version of the Comet assay, which is highly sensitive for measuring single- and double-strand DNA breaks.
Inverse Heat Conduction (2023)

This book discusses the engineering problem of determining surface heat flux and temperature history based on interior temperature measurements. It also provides the analytical techniques needed to arrive at otherwise difficult solutions, summarizing the findings of the last ten years. Topics include the steady state solution, Duhammel's Theorem, ill-posed problems, single future time step, and more.
Microbial Ecophysiology of Whey Biomethanation: Intermediary Metabolism of Lactose Degradation in Continuous Culture (1986)

The intermediary carbon and electron flow routes for lactose degradation during whey biomethanation were studied in continuous culture. The chemostat was operated under lactose-limited conditions with a 100-h retention time. The carbon balance observed for lactose degradation was 4.65 mmol of CH(4), 4.36 mmol of CO(2) and 1.15 mmol of cellular carbon per mmol of lactose consumed, with other intermediary metabolites (i.e., acetate, lactate, etc.) accounting for less than 2% of the lactose consumed. The carbon and electron recoveries for this biomethanation were 87 and 90%, respectively. C tracer studies demonstrated that lactose biomethanation occurred in three distinct but simultaneous phases. Lactose was metabolized primarily into lactate, ethanol, acetate, formate, and carbon dioxide. During this hydrolytic phase, 82% of the lactose was transformed into lactate. These metabolites were transformed into acetate and H(2)-CO(2) in a second, acetogenic, phase. Finally, the direct methane precursors were transformed during the methanogenic phase, with acetate accounting for 81% of the methane formed. A general scheme is proposed for the exact carbon and electron flow route during lactose biomethanation, which predicts the prevalent microbial populations in this ecosystem.
Toxoplasma serology, parasitemia and antigenemia in patients at risk for toxoplasmic encephalitis (1991)

In order to further characterize the pathogenesis of Toxoplasma gondii infection in patients with AIDS and AIDS-related complex (ARC), a cohort of HIV- and Toxoplasma-infected individuals were identified and prospectively followed. Four hundred and 10 HIV-infected individuals followed in the San Francisco General Hospital AIDS Clinic were screened for antibodies to Toxoplasma between November 1986 and November 1988. Of the 67 (16%) individuals seropositive for Toxoplasma antibodies, 33 (49%) were followed monthly for a mean duration of 7.5 months. One hundred and 11 follow-up blood samples were obtained in order to determine Toxoplasma serology and the incidence of parasitemia. In general, Toxoplasma immunoglobulin (lg) C antibodies remained stable over time. Detection of Toxoplasma antigenemia and parasitemia was uniformly negative, including those specimens obtained from two individuals within 45 days of their developing toxoplasmic encephalitis.
Adaptive nonlinear control of a three-phase three-level neutral point clamped rectifier (2002)

This paper presents a control strategy for a three-phase three-level neutral-point-clamped boost rectifier, which consists of applying an adaptive nonlinear control. The exact nonlinear multiple-input multiple-output state space model of the rectifier was obtained in the (d,q,0) reference frame using the power balance between the input and output sides. Applying a change of coordinates and nonlinear feedback linearization technique to the nonlinear model results in a linear and decoupled model, a robust model-based reference adaptive control scheme is proposed for the feedback-linearized system in order to control line-currents, output and neutral point voltages and also to reduce the influence of the parameter uncertainty. This control uses a 3 kHz pulse width modulator. Computer simulations based on the use of Power System Blockset and Simulink/Matlab verify the robustness of the proposed control law in balanced output load conditions. The line-current THD and output voltage ripples are very low.
Molecular Classification of Medullobastomas by Whole Genome Expression Profiling. (2019)

Molecular classification of MBs has been established in our institution allowing better understanding of this heterogeneous disease and helping clinicians in therapeutic planning in affected patients. This work was supported by the Czech Ministry of Health grant No. 16-33209A. All rights reserved. he authors declare they have no potential confl icts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 1. 3. 2019 Accepted: 4. 3. 2019.
Screening for control genes in rat global cerebral ischemia using high‐density oligonucleotide array (2004)

From conventional relative gene expression analyses (Northern blotting, in situ hybridization, and RT-PCR), it has been reported that the expression of control genes, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin, used as references may be affected by ischemia. Therefore, we extended searching and evaluation at the mRNA level of transcripts whose expression levels were not changed by cerebral ischemia, using a high-density oligonucleotide array and statistical analysis in a rat global cerebral ischemia and reperfusion model. We added a hyperthermic factor and localization factor to ischemia and identified transcripts with a stable expression level under conditions even more disadvantageous than ischemia only. Screening of more than 8,000 transcripts with the Rat Genome U34A array yielded 28 transcripts, which we listed and classified according to their expression level. Widely used control genes, GAPDH and beta-actin, were not included, although cyclophilin A was included. In addition, we conducted a functional classification based on gene ontology. Under the functional classification of the 28 transcripts, many genes tended to be associated with metabolism. In conclusion, use of several transcripts is recommended, such as those we identified, as references in the analysis of gene expression in pathological models of ischemia.
The organization of behavior into temporal and spatial neighborhoods (2012)

The mot <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> framework [1] is a system for learning behaviors while organizing them across a two-dimensional, topological map such that similar behaviors are represented in nearby regions of the map. The current paper introduces temporal coherence into the framework, whereby temporally extended behaviors are more likely to be represented within a small, local region of the map. In previous work, the regions of the map represented arbitrary parts of a single global policy. This paper introduces and examines several different methods for achieving temporal coherence, each applying updates to the map using both spatial and temporal neighborhoods, thus encouraging parts of the policy that commonly occur together in time to reside within a common region. These methods are analyzed experimentally in a setting modeled after a human behavior-switching game, in which players are rewarded for producing a series of short but specific behavior sequences. The new methods achieve varying degrees-in some cases high degrees-of temporal coherence. An important byproduct of these methods is the automatic decomposition of behavior sequences into cohesive groupings, each represented individually in local regions.
Chi-3's: their characterization and understanding (2002)

This paper will discuss in general the so-called third-order nonlinear optical susceptibility X(3). Values for this quantity are often quoted that vary wildly in magnitude depending on the material and source used, in particular the source pulsewidth. It would be "nice" if X(3) were constant rather than depending on the illumination parameters.
284. High-Efficiency Targeted Introduction of an Anti-CD19 CAR Into the CCR5 Locus in Primary Human T Cells (2015)

The safety and efficacy of anti-CD19 chimeric antigen receptor (CD19-CAR) therapeutic cell transfer for treatment of CD19+ B cell malignancies is currently being evaluated in multiple clinical trials. Current protocols employ randomly integrating lentiviral or gamma-retroviral vectors to introduce the CAR into patient- or donor-derived T cells. This strategy carries with it an inherent risk of insertional mutagenesis as well as variable CAR expression. Here we have developed a method of targeting a CD19-CAR construct directly into the CCR5 locus by homology directed recombination (HDR). Using a CCR5 megaTAL nuclease (an engineered homing endonuclease and TALEN chimera) and an AAV donor template (comprised of an MND promoter-CD19CAR-T2A-BFP expression cassette between CCR5 homology arms), we obtained efficient targeting rates in primary human T cells. CAR expression was confirmed by flow cytometry and homologous recombination within the CCR5 locus was verified by PCR analysis and by direct sequencing. Rates of biallelic HDR were assessed using single cell PCR. T cells with the CD19-CAR at the CCR5 locus demonstrated activation, cytokine production and specific killing in the presence of CD19+ cells. Activity levels were indistinguishable from T cells transduced with LV expressing an identical CD19-CAR construct. Seamless targeting to CCR5 has important therapeutic advantages over traditional viral delivery, including a reduced potential for oncogenic insertions and uniform levels of gene expression, in parallel with effective disruption of the co-receptor for CCR5-tropic HIV-1. Further, the targeting methods used are directly amenable to clinical application. As HIV patients develop aggressive B cell lymphomas at increased rates, we believe this technique has substantial potential for clinical implementation including the protection of autologous CD19-CAR effector T cell products from HIV infection in vivo.
Fatgraph Models of Proteins (2009)

We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore amenable to fast computer implementation. Applications include the refinement of structural protein classifications and the prediction of geometric and other properties of proteins from their chemical structures.
International Federation of Clinical Chemistry (IFCC). Recommendation on mean molar activity coefficients and single ion activity coefficients of solutions for calibration of ion-selective electrodes for sodium, potassium and calcium determination. (1997)

In principle, flame photometry measures substance concentration, and ion-selective electrodes (ISEs) measure ion activity. However, the situation regarding the comparison of results from the two techniques when applied to blood plasma is complex. The problem can be approached experimentally from the point of view of calibration of ion-selective electrodes with concentration calibrators, and similar procedures are adopted for commercial ISE-based clinical analysers. Nevertheless, there is interest in the evaluation of single ion activities in blood plasma and solutions simulating its ionic composition. Solutions are proposed for calibrating ion-selective electrodes for the determination of sodium, potassium and calcium. It is recommended that the values for single ion activities derived from the Pitzer treatment of mixed electrolyte solutions be adopted, because, although this has some empirical features, it has a sounder theoretical basis than the previously used Stokes-Robinson-Bates hydration approach.
Prognostic and predictive factors in prostate cancer: Historical perspectives and recent international consensus initiatives (2005)

An understanding of prognosis in cancer medicine is important for patient care, research and cancer control programs. In prostate cancer, prognostic (predictive) factors are particularly important given the marked heterogeneity of this disease at clinical, morphologic and biomolecular levels. Clinical stage and histologic grade have historically played major roles in defining heterogeneity in prostate cancer. More recently, serum prostate-specific antigen measurement has assumed a significant prognostic role. Over the last two decades there has been an explosion of research into biomarkers, many of which have been purported to have prognostic significance. In this paper we present an overview of the various consensus initiatives that have transpired over the last dozen years. Criteria for evaluating prognostic factors and classifications of predictive factors have emerged that have proven useful and advanced our understanding of the biology of prostate cancer. The results of these consensus initiatives form a foundation on which the current international consultation on prognosis (prediction) in prostate cancer is built. Advances in our understanding of the new and promising prognostic factors will require a more rigorous evidence-based approach to the analysis of published studies. Furthermore, appropriate mathematical models for the analysis of the multiple factors that influence a prognostic system will have to be employed.