gebhart/patrepeval huggingface dataset:
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage (2010)

The generation of genome-wide data derived from methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) has become a major tool for epigenetic studies in health and disease. The computational analysis of such data, however, still falls short on accuracy, sensitivity, and speed. We propose a time-efficient statistical method that is able to cope with the inherent complexity of MeDIP-seq data with similar performance compared with existing methods. In order to demonstrate the computational approach, we have analyzed alterations in DNA methylation during the differentiation of human embryonic stem cells (hESCs) to definitive endoderm. We show improved correlation of normalized MeDIP-seq data in comparison to available whole-genome bisulfite sequencing data, and investigated the effect of differential methylation on gene expression. Furthermore, we analyzed the interplay between DNA methylation, histone modifications, and transcription factor binding and show that in contrast to de novo methylation, demethylation is mainly associated with regions of low CpG densities.
Transmission electron microscopy of saturated hydrocarbon block copolymers (1995)

Abstract Contrast for transmission electron microscopy (TEM) of microphase‐separated saturated hydrocarbon diblock copolymers has been obtained using ruthenium tetroxide (RuO 4 ). This technique exploits differences in the rate of transport of the oxidizing stain in rubbery amorphous versus semicrystalline, or glassy, microdomains. Rapid quenching from above the melting ( T m ), or glass transition ( T g ) temperature is shown to preserve the equilibrium melt morphology in poly(ethylene)‐poly(ethyl‐ethylene) (PE‐PEE), poly(ethylene)‐poly(ethylene‐propylene) (PE‐PEP), and poly(vinylcyclohexane)‐poly(ethyl‐ethylene) (PVCH‐PEE) diblock copolymers; PE melts at 108°C, PVCH is glassy up to about 140°C, while PEE and PEP remain rubbery down to approximately‐20°C and −56°C, respectively. Treatment of ultrathin sections of the quenched specimens with RuO 4 vapor led to welldefined TEM images, that revealed microdomain type and order. These results are consistent with SANS data taken under equilibrium conditions. © 1995 John Wiley &amp; Sons, Inc.
Infrared Instrument for Detecting Hydrogen Fires (2006)

The figure shows an instrument incorporating an infrared camera for detecting small hydrogen fires. The instrument has been developed as an improved replacement for prior infrared and ultraviolet instruments used to detect hydrogen fires. The need for this or any such instrument arises because hydrogen fires (e.g., those associated with leaks from tanks, valves, and ducts) pose a great danger, yet they emit so little visible light that they are mostly undetectable by the unaided human eye. The main performance advantage offered by the present instrument over prior hydrogen-fire-detecting instruments lies in its greater ability to avoid false alarms by discriminating against reflected infrared light, including that originating in (1) the Sun, (2) welding torches, and (3) deliberately ignited hydrogen flames (e.g., ullage-burn-off flames) that are nearby but outside the field of view intended to be monitored by the instrument. Like prior such instruments, this instrument is based mostly on the principle of detecting infrared emission above a threshold level. However, in addition, this instrument utilizes information on the spatial distribution of infrared light from a source that it detects. Because the combination of spatial and threshold information about a flame tends to constitute a unique signature that differs from that of reflected infrared light originating in a source not in the field of view, the incidence of false alarms is reduced substantially below that of related prior threshold- based instruments.
Dideoxyfingerprinting for Mutation Detection (2005)

Screening for mutations of the thousands of the sequence products provided by human genome analysis has proven to be a daunting task. The gold standard for identifying sequence alterations is direct sequencing. However, this method is labor- intensive and the least costeffective. Since the mid-1980s, the need for rapid, high-throughput, accurate, and economical mutation analysis systems has lead to the development of several technologies, as an alternative to analysis by direct sequencing, which allowed detection of single mutations in long stretches of DNA (200–600 bp). These techniques include restriction endonuclease digestion of polymerase chain reaction (PCR) products (PCR-RFLP), denaturing gradient gel electrophoresis (DGGE), single-strand conformation polymorphism (SSCP), dideoxyfingerprinting (ddF), and heteroduplex mobility assay (HMA). Most of these methods utilize PCR for amplification of a region of the DNA, a physical or chemical treatment of amplified DNA (by restriction digestion or denaturation), separation of the amplicons by gel electrophoresis (by denaturing or nondenaturing), and visualization of the separated sequence strands (by autoradiography or fluorescence-based detection). Most recent modifications in some of these techniques allow the simultaneous separation and detection of DNA fragments with the use of sophisticated equipment such as high-performance liquid chromatography (HPLC) and capillary electrophoresis.
Induction of Blocking Antibodies with T Cell Epitope-Containing Hypoallergenic Recombinant Bet v 1 Fragments (2001)

Bet v 1, the major birch pollen allergen, represents one of the most prominent allergens. It is recognized by serum IgE from more than 95% of birch pollen-allergic patients and 60% of these patients react exclusively with this allergen [1, 2]. Bet v 1 contains conformational IgE epitopes and shares epitopes with major allergens from trees and plant-derived food [3]. We produced by genetic engineering two rBet v 1 fragments, comprising amino acids (aa) 1–74 and aa 75–160 of complete Bet v 1, which due to a loss of their three-dimensional conformation, failed to bind IgE antibodies from allergic patients and had more than 100-fold reduced allergenic activity in histamine release assays and skin tests [4, 5, 6, 7]. Here we show that the recombinant Bet v 1 fragments induced proliferation of PBMC from birch pollen-allergic patients comparable to the rBet v 1 wild type, indicating that both fragments contain most of the Bet v 1-specific T cell epitopes. Interestingly, the C-terminal rBet v 1 fragment aa 75–160 induced significantly higher IFN-γ secretion compared to the N-terminal fragment [4, 8]. Immunization of rabbits and mice with purified rBet v 1 fragments induced IgG antibodies which reacted with rBet v 1 wild type, natural Bet v 1 and cross-reacted with Bet v 1-related allergens present in pollens of trees of the order of Fagales and in plant-derived food. Moreover, rBet v 1 fragment-induced IgG antibodies recognized epitopes defined by patients’ IgE antibodies and inhibited patients’ IgE binding to complete Bet v 1 wild type and to Bet v 1 homologous allergens. Figure 1 shows the inhibition of patients’ IgE binding to rBet v 1 wild type after preincubation with mouse anti-rBet v 1 fragment antibodies. ELISA plate-coupled rBet v 1 was preincubated with mouse anti-rBet v 1 fragment antisera (anti-aa 7–74 antibodies; anti-aa 75–160 antibodies), or, for control purposes, with the corresponding preimmune sera and then incubated with serum IgE from birch pollen-allergic patients. Mouse sera raised against rBet v 1 aa 1–74 in allergic patients inhibited IgE binding to Bet v 1 between 45 and 83% (59.5% mean inhibition) and mouse sera raised against rBet v 1 aa 75–160 inhibited IgE binding to rBet v 1 between 73 and 78% (74.8% mean inhibition) [8](fig. 1).Hypoallergenic rBet v 1 fragments may, therefore, be considered as safe and effective vaccines for specific immunotherapy of tree pollen and associated food allergies. High allergen doses can be administered with a reduced risk of anaphylactic side effects, and thus induce a preferential Th1 response to Bet v 1 accompanied by the induction of high titers of protective Bet v 1-specific IgG antibodies.This study was supported by the ICP program of the Austrian Federal Ministry for Education, Science and Culture and by Grant Y078GEN of the Austrian Science Fund.
Tautology checking using cross-controllability and cross-observability relations (2002)

A novel method is described for verifying the equivalence between a combinational circuit and its specification, when both are given in a modular (e.g., factored) form. It is based on the notion of cross-controllability and cross-observability relations that exist between the internal logic values across a cut of the joint composition of the circuit and the specification. It is proven that even after abstracting input and other internal variables the relations are sufficient to verify the equivalence. The abstraction allows reduction of the size of the relation, thus permitting the verification of much larger circuits. A report is presented on the verification of an 8*8 parallel multiplier using at most 527 BDD (binary decision diagram) cells of 21 variables. Extensions to sequential circuits are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CCR5 Inhibition Prevents Cardiac Dysfunction in the SIV/Macaque Model of HIV (2014)

Together, these findings incriminate SIV/HIV gp120-CCR5 as well as chemokine-CCR5 interactions in HIV-associated cardiac dysfunction. These findings also have important implications for the treatment of HIV-infected individuals: in addition to antiviral properties and reduced chemokine-mediated recruitment and activation of inflammatory cells, CCR5 inhibition may provide a cardioprotective benefit by preventing cardiomyocyte CCR5 signaling.
Supplementary Table 3 from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy (2023)

&lt;p&gt;Proportional Hazards Model of Overall Survival&lt;/p&gt;
Axon Kinematics Change During Growth and Development (2007)

The microkinematic response of axons to mechanical stretch was examined in the developing chick embryo spinal cord during a period of rapid growth and myelination. Spinal cords were isolated at different days of embryonic (E) development post-fertilization (E12, E14, E16, and E18) and stretched 0%, 5%, 10%, 15%, and 20%, respectively. During this period, the spinal cord grew approximately 55% in length, and white matter tracts were myelinated significantly. The spinal cords were fixed with paraformaldehyde at the stretched length, sectioned, stained immunohistochemically for neurofilament proteins, and imaged with epifluorescence microscopy. Axons in unstretched spinal cords were undulated, or tortuous, to varying degrees, and appeared to straighten with stretch. The degree of tortuosity (ratio of the segment's pathlength to its end-to-end length) was quantified in each spinal cord by tracing several hundred randomly selected axons. The change in tortuosity distributions with stretch indicated that axons switched from non-affine, uncoupled behavior at low stretch levels to affine, coupled behavior at high stretch levels, which was consistent with previous reports of axon behavior in the adult guinea pig optic nerve (Bain, Shreiber, and Meaney, J. Biomech. Eng., 125(6), pp. 798-804). A mathematical model previously proposed by Bain et al. was applied to quantify the transition in kinematic behavior. The results indicated that significant percentages of axons demonstrated purely non-affine behavior at each stage, but that this percentage decreased from 64% at E12 to 30% at E18. The decrease correlated negatively to increases in both length and myelination with development, but the change in axon kinematics could not be explained by stretch applied during physical growth of the spinal cord. The relationship between tissue-level and axonal-level deformation changes with development, which can have important implications in the response to physiological forces experienced during growth and trauma.
Congenital Nasal Pyriform Aperture Stenosis: Evidence of Premature Fusion of the Midline Palatal Suture (2021)

Patients with CNPAS have abnormal fusion of the midline palatal suture and exhibit lateral growth restriction of the midface. This may implicate synostosis of the midline palatal suture and abnormal midface growth.
Design of a Low Energy, Self Contained Subsea Burrowing Robot Based on Localized Fluidization Exhibited by Atlantic Razor Clams (2014)

The Atlantic razor clam (Ensis directus) burrows by contracting its valves, fluidizing the surrounding soil and reducing burrowing drag. Moving through a fluidized, rather than static, soil requires energy that scales linearly with depth, rather than depth squared. In addition to providing an advantage for the animal, localized fluidization may provide significant value to engineering applications such as vehicle anchoring and underwater pipe installation. This paper presents the design of a self-actuated, radially expanding burrowing mechanism that utilizes E. directus’ burrowing methods. The device is sized to be a platform for an anchoring system for autonomous underwater vehicles. Scaling relationships presented allow for design of burrowing systems of different sizes for a variety of applications. The minimum contraction time for a given device size governs how quickly the device must move. Contraction displacement necessary to achieve fluidization is presented. The maximum force for a given size mechanism is also calculated, and allows for sizing actuators for different systems. This paper presents the design of a system that will allow testing of these parameters in a laboratory setting. These relationships provide the optimal sizing and power needs for various size subsea borrowing systems.
A ratio scale for brightness perception derived from difference and ratio judgments (1992)

A ratio scale for brightness perception derived from difference and ratio judgments
Evaluation of in vivo THz sensing for assessing human skin hydration (2020)

Abstract Terahertz (THz) in vivo reflection imaging can be used to assess the water content of the surface of the skin. This study presents the results of treating 20 subjects with aqueous, anhydrous and water-oil emulsion samples and observing the changes induced in the skin using THz sensing. These regions were also measured with a corneometer, the present gold standard for skin hydration assessment within the cosmetics industry. We find that THz sensing is effective at observing the presence of oil and water on the surface of the skin, these results can be verified with the measurements of capacitance taken by the corneometer. The THz measurements reveal a distinction between the responses of subjects with initially dry or well hydrated skin, this observation is particularly noticeable with the oil-based samples. Additionally, moderate correlation was found between the THz reflected amplitude and capacitance of untreated skin with a correlation coefficient of r = −0.66, suggesting THz sensing has promising potential for assessing skin hydration.
Titelbild (2001)

Das Titelbild zeigt eine durcheinander gewirbelte Mischung aus Übergangsmetallbruchstücken und einfachen organischen Liganden, aus denen sich supramolekulare Koordinationsverbindungen aufbauen, die man am Rand des Wirbels aufsteigen sieht. Die Synthese solcher großer Strukturen erfordert Strategien, die die entropischen Kosten in Rechnung stellen, damit keine Oligomere höheren Grades oder Polymere entstehen. Der Einsatz von Übergangsmetallionen als Bausteine für supramolekulare Verbindungen ist inzwischen zu einer weit verbreiteten Strategie bei der Herstellung solcher Strukturen geworden. In diesem schnell wachsenden Arbeitsgebiet kristallisierten sich drei allgemein anwendbare Syntheseansätze für die durch Metallzentren gesteuerte Bildung supramolekularer Koordinationsverbindungen heraus. Sie werden von B. J. Holliday und C. A. Mirkin auf S. 2076 ff. beschrieben.
Comprehensive gene expression profile of human activated Th1- and Th2-polarized cells (2001)

In response to antigen stimulation, T(h) cells differentiate into two types of effector cells, T(h)1 and T(h)2. T(h)1 cells predominantly mediate cellular immunity, whereas T(h)2 cells induce humoral allergic responses. We have conducted here serial analysis of gene expression (SAGE) in human activated T(h)1- and T(h)2-polarized cells from cord blood. SAGE analysis of 64,510 tags (32,219 and 32,291 tags from T(h)1 and T(h)2 cells respectively) allowed identification of 22,096 different transcripts. In activated T(h)1 cells, many of the known genes (12 genes, P: < 0.01; 56 genes, P: < 0.05), including genes encoding IFN-gamma, lymphotactin, osteopontin, MIP-1alpha, MIP-1beta, perforin, beta-catenin and CD55, are highly expressed. On the other hand, in activated T(h)2 cells rather limited numbers of known genes (four genes, P: < 0.01; 10 genes; P: < 0.05), such as genes encoding FUS, ILF-2, IL-13 and E2-EPF, are found to be selectively expressed. The comprehensive identification of genes selectively expressed in human activated T(h)1 or T(h)2 cells should contribute to our understanding of the molecular basis of T(h)1/T(h)2-dominated human diseases and may provide genetic information to diagnose these diseases.
Toeplitz Structured Subspace for Multi-Channel Blind Identification Methods (2021)

Abstract This paper addresses the problem of blind identification of multichannel systems. It proposes three different novel algorithms by exploiting the inherent Toeplitz /Sylvester structures impeded in the system model. The first algorithm is the structured signal subspace (SSS) method, which involves direct estimation of the signal from a multiple-input multiple-output (MIMO) system. The second algorithm is the structured channel subspace (SCS) method, whereby the MIMO channel matrix is estimated by employing its embedded Toeplitz structure. The last algorithm deals with the bilinear blind identification by utilizing the information (embedded structure) of both row and column subspaces of the received signals. The proposed methods exploit the block Sylvester structure of the signal and the channel matrix to formulate a quadratic cost function whose minimization enables us to estimate the desired system parameters. The simulation results of the proposed structured subspace methods are appealing in different scenarios.
Interleukin-1β–Driven Inflammation Promotes the Development and Invasiveness of Chemical Carcinogen–Induced Tumors (2007)

The role of microenvironment interleukin 1 (IL-1) on 3-methylcholanthrene (3-MCA)-induced carcinogenesis was assessed in IL-1-deficient mice, i.e., IL-1beta(-/-), IL-1alpha(-/-), IL-1alpha/beta(-/-) (double knockout), and mice deficient in the naturally occurring inhibitor of IL-1, the IL-1 receptor antagonist (IL-1Ra). Tumors developed in all wild-type (WT) mice, whereas in IL-1beta-deficient mice, tumors developed slower and only in some of the mice. In IL-1Ra-deficient mice, tumor development was the most rapid. Tumor incidence was similar in WT and IL-1alpha-deficient mice. Histologic analyses revealed fibrotic structures forming a capsule surrounding droplets of the carcinogen in olive oil, resembling foreign body-like granulomas, which appeared 10 days after injection of 3-MCA and persisted until the development of local tumors. A sparse leukocyte infiltrate was found at the site of carcinogen injection in IL-1beta-deficient mice, whereas in IL-1Ra-deficient mice, a dense neutrophilic infiltrate was observed. Treatment of IL-1Ra-deficient mice with recombinant IL-1Ra but not with an inhibitor of tumor necrosis factor abrogated the early leukocytic infiltrate. The late leukocyte infiltrate (day 70), which was dominated by macrophages, was also apparent in WT and IL-1alpha-deficient mice, but was nearly absent in IL-1beta-deficient mice. Fibrosarcoma cell lines, established from 3-MCA-induced tumors from IL-1Ra-deficient mice, were more aggressive and metastatic than lines from WT mice; cell lines from IL-1-deficient mice were the least invasive. These observations show the crucial role of microenvironment-derived IL-1beta, rather than IL-1alpha, in chemical carcinogenesis and in determining the invasive potential of malignant cells.
Chemical synthesis of staphyloferrin A and its application for Staphylococcus aureus detection (2014)

The chemical synthesis of staphyloferrin A, a siderophore used by Staphylococcus bacteria for ferric iron retrieval, has been achieved with 79% yield via solid phase peptide synthesis (SPPS). Biological activity of synthetic staphyloferrin A has been confirmed by demonstrating its capture and uptake by live S. aureus.
Thermal Conductivity of Si/SiGe Superlattices (2001)

Abstract The cross-plane and in-plane thermal conductivity of four Si/Si0.7Ge0.3 superlattice structures with periods from 45 Å to 300 Å are experimentally investigated using the 3-ω measurement technique. The experiment is conducted over a temperature range from 70 to 340 K. Results indicate that the cross-plane thermal conductivity decreases with decreasing period thickness (i.e. increasing number of interfaces per unit length). The superlattice with the shortest period exhibits a cross-plane thermal conductivity similar to that of a SiGe alloy. The in-plane thermal conductivity follows a similar decreasing trend with period thickness for the three larger period superlattices, but jumps to higher values for the shortest period superlattice. Additionally, the in-plane conductivity can be 3–4 times higher than the cross-plane value.
Experiments and model for the oscillatory oxidation of benzaldehyde (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExperiments and model for the oscillatory oxidation of benzaldehydeAnne M. Reimus, Jean Marie Massie, and John L. HudsonCite this: Ind. Eng. Chem. Res. 1989, 28, 5, 590–599Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ie00089a015https://doi.org/10.1021/ie00089a015research-articleACS PublicationsRequest reuse permissionsArticle Views57Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Blockade of Brain Angiotensin II Type 1 Receptor Inhibits the Development of Atrial Fibrillation in Hypertensive Rats (2014)

Brain AT1R blockade suppresses AF inducibility and maintenance independent of depressor response in hypertensive rats.