gebhart/patrepeval huggingface dataset:
Life-Time Prediction for Anchorage Systems (2016)

The life-time prediction of fastening systems under sustained loads requires, among others, a suitable numerical solution strategy and viscoelastic constitutive models that can reproduce well the material specific characteristics. The formulation and calibration of viscoelastic models can be based on a topdown approach from observed macroscopic response or, alternatively, a bottom-up approach can be pursued. In the simplest case a fine scale model can represent the system response of bonded and mechanical anchors with contributions of each component, namely (i) concrete, (ii) steel, and (iii) mortar, and the respective interfaces, which are calibrated individually based on quasistatic tests and creep tests. Further homogenization steps allow the derivation of each materials creep response from their respective sources at lower scales hydrates for concrete and the polymer matrix.
Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences (2013)

The heterogeneous collection of nucleosome remodelling and deacetylation (NuRD) complexes can be grouped into the MBD2- or MBD3-containing complexes MBD2-NuRD and MBD3-NuRD. MBD2 is known to bind to methylated CpG sequences in vitro in contrast to MBD3. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here, we show that MBD2-NuRD, in contrast to MBD3-NuRD, converts open chromatin with euchromatic histone modifications into tightly compacted chromatin with repressive histone marks. Genome-wide, a strong enrichment for MBD2 at methylated CpG sequences is found, whereas CpGs bound by MBD3 are devoid of methylation. MBD2-bound genes are generally lower expressed as compared with MBD3-bound genes. When depleting cells for MBD2, the MBD2-bound genes increase their activity, whereas MBD2 plus MBD3-bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes.
Ras–MEK Signaling Mediates a Critical Chk1-Dependent DNA Damage Response in Cancer Cells (2017)

Cancer cell line profiling to identify previously unrecognized kinase dependencies revealed a novel nonmutational dependency on the DNA damage response checkpoint kinase Chk1. Although Chk1 is a promising therapeutic target in p53-deficient cancers, we found that Ras-MEK signaling engages Chk1 in a subset of osteosarcoma, ovarian, and breast cancer cells to enable their survival upon DNA damage, irrespective of p53 mutation status. Mechanistically, Ras-MEK signaling drives Chk1 expression and promotes cancer cell growth that produces genotoxic stress that requires Chk1 to mediate a response to the consequent DNA damage. Reciprocally, Chk1 engages a negative feedback loop to prevent hyperactivation of Ras-MEK signaling, thereby limiting DNA damage. Furthermore, exogenous DNA damage promotes Chk1 dependency, and pharmacologic Chk1 inhibition combined with genotoxic chemotherapy potentiates a DNA damage response and tumor cell killing. These findings reveal a mechanism-based diagnostic strategy to identify cancer patients that may benefit from Chk1-targeted therapy. <i>Mol Cancer Ther; 16(4); 694-704. ©2017 AACR</i>.
In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data (2011)

To investigate 3'-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3'-untranslated region (3' UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3' UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3' UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15-30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3'-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3'-end-processing signals are similar to those in yeast and plants, some notable differences exist between them.
Parachute use to prevent death and major trauma when jumping from aircraft: randomized controlled trial (2018)

Parachute use did not reduce death or major traumatic injury when jumping from aircraft in the first randomized evaluation of this intervention. However, the trial was only able to enroll participants on small stationary aircraft on the ground, suggesting cautious extrapolation to high altitude jumps. When beliefs regarding the effectiveness of an intervention exist in the community, randomized trials might selectively enroll individuals with a lower perceived likelihood of benefit, thus diminishing the applicability of the results to clinical practice.
<title>Force and membrane compliance measurements using laser interferometry and optical trapping</title> (1993)

The development of the single beam gradient force optical trap has improved the experimental capabilities available to cell biologists for noninvasive micromanipulation and mechanical measurement on living cells. Laser traps can be used not only to optically manipulate particles including bacteria, yeast cells, and intracellular organelles ranging in size from 25 nm to 25 micrometers with fine control of position (10 nm) but also to measure small (0.1 pN) forces in biological systems. For a given particle, trapping forces are linearly related to the laser power so that a relatively simple way of measuring force is to trap a particle at high power and gradually reduce it until the particle just escapes from the trap. The `escape' power, which is usually calibrated against the viscous drag of the aqueous medium at varying laser power levels, is a measure of the force.
Differential frequency hopping performance in Doppler-inducing underwater acoustic communication channels. (2011)

The relationships between the parameters of Doppler spread-inducing underwater environments and the bit-error performance of differential frequency hopping (DFH) modulation in the underwater acoustic channel are characterized. Wind speed determines the nature of the effect that the water surface imposes on the acoustic DFH wavefoms propagating underwater. Low wind speeds result in an essentially flat, low-absorption sea surface. In this regime, strong surface reflections and little frequency spreading make intersymbol interference (ISI) the dominant effect on the received waveforms. At high wind speeds, the higher density of air bubbles in the surface layer absorbs almost all energy incident on the surface, resulting in no surface reflections reaching the receiver. In this regime, the surface has little effect on the received signal, either in the form of ISI or frequency spreading. The intermediate ranges of wind speed, with a mix of ISI and surface-induced Doppler spread, pose the most challenging conditions. Simulations and at-sea experiments show that recent algorithmic improvements to the receiver make DFH robust to a variety of environmental conditions and that DFH modulation parameters can be easily adapted to a variety of operationally relevant scenarios based on environmental information.
ChemInform Abstract: UNFUSED HETEROBICYCLES AS AMPLIFIERS OF PHLEOMYCIN. III. THIAZOLYLPYRIDINES AND BIPYRIMIDINES WITH STRONGLY BASIC SIDE CHAINS (1982)

Abstract Nach bekannten Literatur‐Methoden werden die 2‐substituierten 4‐Pyridylthiazole (III), (VI), (VIII) und (XI) sowie die 4‐ und/oder 5‐substituierten Analogen (XIII), (XVI) und (XVII) synthetisiert und zusammen mit analog substituierten 2,4′‐, 4,5′‐ und 5,5′‐Bipyrimidinen auf ihre Wirkung als Verstärker der wachstumshemmenden Aktivität von Phleomxcin gegenüber Escherichia coli (in vitro) getestet.
Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein (2008)

We report direct evidence for deprotonation of a lysine side chain buried in the hydrophobic core of a protein, demonstrating heteronuclear 1H-15N NMR data on the Lys-66 side chain amine (Nzeta) group in the delta-PHS/V66K variant of staphylococcal nuclease. Previous crystallographic study has shown that the Lys-66 Nzeta group is completely buried in the hydrophobic core. On the basis of double and triple resonance experiments, we found that the 1Hzeta and 15Nzeta chemical shifts at pH 8.0 and 6 degrees C for the buried lysine are 0.81 and 23.3 ppm, respectively, which are too abnormal to correspond to the protonated (NH3+) state. Further investigations using a model system suggested that the abnormal 1H and 15N chemical shifts represent the deprotonated (NH2) state of the Lys-66 Nzeta group. More straightforward evidence for the deprotonation was obtained with 2D F1-1H-coupled 1H-15N heteronuclear correlation experiments. Observed 15N multiplets clearly indicated that the spin system for the Lys-66 Nzeta group is AX2 (NH2) rather than AX3 (NH3+). Interestingly, although the amine group is buried in the hydrophobic core, the hydrogen exchange between water and the Lys-66 Nzeta group was found to be relatively rapid (93 s(-1) at -1 degrees C), which suggests the presence of a dynamic process such as local unfolding or water penetration. The partial self-decoupling effect on 15Nzeta multiplets due to the rapid hydrogen exchange is also discussed.
Ordered macroporous titania photonic balls by micrometer-scale spherical assembly templating (2005)

Highly ordered macroporous photonic balls (i.e. inverse opaline structure) composed of titania frameworks were fabricated by using a titania precursor templated around polystyrene spheres which had been assembled into polymer photonic balls (i.e. opaline structure). Narrow disperse polymer photonic balls consisting of monodisperse surface-modified polystyrene (PS) latex particles were prepared by utilizing a suspension system. The diameters of the opaline balls can be controlled in a range of a few or a few tens of micrometers. The macroporous titania structure made by this method was well-defined because the PS spheres making up the polymer photonic balls were close-packed and ordered in three-dimensions. Furthermore, crystalline types of titania (anatase or rutile) were readily adjusted through tuning the calcination temperatures, so the macroporous titania inverse opaline balls composed of anatase or rutile can be used for various applications.
[Gene mutation in the areas of PreC/C and BCP of HBV DNA]. (2005)

The mutations in the areas of Pre C/C and BCP of HBV DNA might possibly be associated with liver fibrosis. There are many mutation sites in HBV DNA and mutation occurs frequently, therefore gene sequencing is helpful to the design of gene chip and to clinical application.
Genetically Engineered Mouse Models for Drug Discovery: New Chemical Genetic Approaches (2004)

While standard transgenic and knockout mouse technologies have provided a wealth of information for target selection and validation, there have been great advances in using more sophisticated modeling techniques to achieve temporal and spatial regulation of individual genes in adult animals. Recent developments in RNA interference (RNAi) technology in in vivo models promise to further improve upon the static and irreversible features of gene knockouts. Chemical genetic approaches create novel functional alleles of targets and allow fine modulation of protein function in vivo by small molecules, providing the most pharmacologically relevant target validation. Using these advanced models, one can not only ask whether the function of the target is critical for the initiation and maintenance of the disease, but also whether therapies designed to alter the function of the target would be safe and efficacious. In this review, we describe various in vivo tools for target validation in mouse models, discuss advantages and disadvantages of each approach, and give examples of their impact on drug discovery.
Analysis of Differential Display RT-PCR Products Using Fluorescent Primers and GENESCAN TM Software (1997)

Differential display reverse transcription PCR (DDRT-PCR) is a procedure used to identify the induction or repression of gene expression. In most DDRT-PCR protocols, radioisotopes are incorporated during PCR and the cDNA products are detected by autoradiography. This report describes the fluorescent labeling of cDNAs and their detection on automated sequencers from PE Applied Biosystems. A fluorescent tag can be incorporated into the PCR product by using either a labeled primer or a labeled dUTP. The fluorescent signals are analyzed by GENESCAN software. Fluorescent DDRT-PCR increases throughput and obviates the handling of hazardous radioisotopes. A PCR cycling profile, expected to give improved reproducibility, is also described. Because amplified cDNAs can't be recovered from the automated sequencer gel, suggestions are given for the identification and recovery of differentially expressed cDNAs.
Layered Poly(ethylene-co-vinyl acetate)/Poly(ethylene-co-vinyl alcohol) Membranes with Enhanced Water Separation Selectivity and Performance (2017)

A three-layered membrane based on poly(ethylene-co-vinyl acetate) (EVA) and hydrolyzed EVA-poly(ethylene-co-vinyl alcohol) (EVOH), was elaborated by the surface hydrolysis of a dense EVA membrane. Because of the chemical modifications, the three-layered EVOH/EVA/EVOH membrane was characterized by the particular microstructure (amorphous EVA and semicrystalline EVOH) and the tunable hydrophilic/hydrophobic balance. Also, these modifications led to the membrane with the selective barrier properties compared with the pure EVA and completely hydrolyzed EVOH membranes. The water barrier behavior was related to the strong hydrogen-bond interactions of water and vinyl alcohol groups, whereas the weak chemical interactions were revealed for gases (N<sub>2</sub> and O<sub>2</sub>). Furthermore, the influence of the polymer rubbery or glassy state on the permeation kinetics was established. In the case of the three-layered membrane, the considerably high selectivity values were obtained for H<sub>2</sub>O/O<sub>2</sub> (∼11 900) and H<sub>2</sub>O/N<sub>2</sub> (∼48 000) at 25 °C. In addition to these highly selective properties, the three-layered structure does not present delamination features due to its elaboration procedure. Thus, these new layered membranes are very promising as selective materials for the water and gas separation and can be potentially used in food packaging or for the gas dehydration.
Paraneoplastic syndromes of the spinal cord, nerve, and muscle (2000)

Cancer can affect the peripheral nervous system by non-metastatic, sometimes immune-mediated mechanisms. Recognition of these paraneoplastic syndromes is important because it can lead to the detection of the tumor, and also helps to avoid unnecessary studies to determine the cause of the neurologic symptoms in patients with cancer. Many paraneoplastic syndromes of the peripheral nervous system are not associated with serum antibodies that serve as markers of paraneoplasia. For this group of disorders the diagnosis depends on the clinician's index of suspicion and conventional electrophysiologic and laboratory tests. Treatment of the tumor, immunotherapy, or both may improve some of these syndromes. This review focuses on paraneoplastic syndromes of the spinal cord, peripheral nerve, and muscle. © 2000 John Wiley & Sons, Inc. Muscle Nerve 23: 1800–1818, 2000
Attosecond Pump-Probe Spectroscopy of Electron Correlation Dynamics in the Double Ionization of Benzene (2016)

Using newly developed three-dimensional (3D) two-electron angular streaking (3D-2eAS) method, we show the emission time delay between two electrons in a double ionization event can be measured from zero attosecond to more than one femtosecond.
Defects of the Classic Formulation of a Nonsteady EHL Problem for a Journal Bearing. New Problem Formulation (1999)

A nonsteady problem for an elastohydrodynamically lubricated (EHL) journal bearing is considered. It is shown that under certain circumstances contact pressure and shaft normal velocity are discontinuous functions of time. The initial normal velocity of the shaft has a certain value which is predetermined by the shaft initial position and applied load. Therefore, the EHL solution cannot accommodate any different initial normal velocity of the shaft. These defects pertain to any nonsteady EHL problem in the “classic” formulation. The main goal of this paper is to propose a modified formulation of the EHL problem free from the above defects. For purely squeezed lubrication film an analytical and numerical analysis of a dynamic bearing response to abrupt changes in external load is performed based on the classic and “modified” problem formulations leading to discontinuous and smooth solutions, respectively.
2D Human Pose Estimation: New Benchmark and State of the Art Analysis (2014)

Human pose estimation has made significant progress during the last years. However current datasets are limited in their coverage of the overall pose estimation challenges. Still these serve as the common sources to evaluate, train and compare different models on. In this paper we introduce a novel benchmark "MPII Human Pose" that makes a significant advance in terms of diversity and difficulty, a contribution that we feel is required for future developments in human body models. This comprehensive dataset was collected using an established taxonomy of over 800 human activities [1]. The collected images cover a wider variety of human activities than previous datasets including various recreational, occupational and householding activities, and capture people from a wider range of viewpoints. We provide a rich set of labels including positions of body joints, full 3D torso and head orientation, occlusion labels for joints and body parts, and activity labels. For each image we provide adjacent video frames to facilitate the use of motion information. Given these rich annotations we perform a detailed analysis of leading human pose estimation approaches and gaining insights for the success and failures of these methods.
A new approach for ovarian stimulation in IVF using Corifollitropin Alfa in combination with GnRH analogues to trigger final oocyte maturation. A pilot study. (2014)

A pilot study of 10 patients undergoing IVF stimulation, using the new combination of Corifollitropin Alfa with highly purified hMG and GnRH antagonists has been performed, whereas final oocyte maturation was induced by GnRH analogues. The hormonal profiles were analyzed, as well as the clinical outcome. All patients were recruited between March 1st 2013 and June 30(th) 2013. They were all younger than 38 years, had a normal BMI (between 18,0 and 32,0) and did not have more than three previous IVF stimulations. The combination of long acting FSH with hphMG, and under protection of GnRH antagonists against spontaneous LH-surge, provided a normal hormonal profile for estradiol, progesterone, LH, and FSH. The average oocyte quality and embryo quality were excellent, which resulted in four pregnancies out of ten. We conclude that the described combination is a safe, efficient, and patient friendly alternative for the classical IVF stimulation.
Mastitis: I. In Vitro Antimicrobial Activity of Alkyl Amines Against Mastitic Bacteria (1979)

The activities of branched and straight chain amines (10 to 18 carbons chain length) were compared in inhibiting the growth of five microorganisms that cause about 95% of bovine mastitis. Three gram-positive (Streptococcus agalactiae, Streptococcus uberis, Staphylococcus aureus) and two gram-negative (Escherichia coli, Klebsiella pneumoniae) bacteria were used in a trypticase soy broth tube culture growth assay. Sixty-two compounds were screened at concentrations of 200, 100, 50, 25, 10, 5, and 1 ppm in broth culture to determine the effective minimum inhibitory concentration. Alkyl secondary N-substituted monoethyl [CH3(CH2)nNHCH2CH3] and tertiary N,N-substituted dimethyl [CH3(CH2) nN(CH3)2] amines with chain lengths of 11 to 14 carbon atoms were active against both gram-positive and gram-negative organisms. Antimicrobial activity against gram-positive organisms increased with increasing chain length and carbon-14 to 18 amines were active at 1 to 5 ppm. The carbon-11 to 13 alkyl amines were most active against gram-positive organisms; longer chain amines (more than 14 carbons) were inactive. Branching of the alkyl chain caused a loss of activity against gram-negative but not against gram-positive bacteria. Antimicrobial testing of monoamines, polyamines, and the influence of order substituents were investigated to correlate structure-acitivity relationships.
Ethanol Electro-Oxidation on Ternary Platinum–Rhodium–Tin Nanocatalysts: Insights in the Atomic 3D Structure of the Active Catalytic Phase (2014)

Novel insights in the synthesis–structure–catalytic activity relationships of nanostructured trimetallic Pt–Rh–Sn electrocatalysts for the electrocatalytic oxidation of ethanol are reported. In particular, we identify a novel single-phase Rh-doped Pt–Sn Niggliite mineral phase as the source of catalytically active sites for ethanol oxidation; we discuss its morphology, composition, chemical surface state, and the detailed 3D atomic arrangement using high-energy (HE-XRD), atomic pair distribution function (PDF) analysis, and X-ray photoelectron spectroscopy (XPS). The intrinsic ethanol oxidation activity of the active Niggliite phase exceeded those of earlier reports, lending support to the notion that the atomic-scale neighborhood of Pt, Rh, and Sn is conducive to the emergence of active surface catalytic sites under reaction conditions. In situ mechanistic Fourier transform infrared (in situ FTIR) analysis confirms an active 12 electron oxidation reaction channel to CO2 at electrode potentials as low as 450 mV/RHE, demonstrating the favorable efficiency of the PtRhSn Niggliite phase for C–C bond splitting.
Coronary MR Angiography in patients with coronary artery disease using image-based respiratory motion compensation (2015)

Background Respiratory motion remains a major impediment in a substantial amount of patients undergoing coronary magnetic resonance angiography (CMRA). Studies in healthy subjects have shown that image-based navigation (iNAV) improves respiratory motion compensation compared to the state-of-the art method. Here, we used iNAV for respiratory motion compensated CMRA in 22 patients with known or suspected coronary artery disease.
Site trials of concrete barriers for landfill liners (2002)

Presentation to American Concrete Institute “Research in Progress” session. Detroit Michigan, April 22, 2002.\n