gebhart/patrepeval huggingface dataset:
A Pyrolytic, Carbon‐Stabilized, Nanoporous Pd Film for Wide‐Range H2 Sensing (2007)

High-performance H2 sensors are becoming increasingly important in detecting and monitoring H2. By using pyrolytic carbon as a transition layer between a Pd film and an anodic aluminum oxide substrate, a nanoporous Pd film sensor is fabricated (see figure) that has a remarkable sensing performance with the ability to detect both dilute and high concentrations of H2 gas quickly and at room temperature.
Structures of RNA Switches: Insight into Molecular Recognition and Tertiary Structure (2007)

RNA switches (riboswitches) have important functions in gene regulation. They comprise an aptamer domain, which is responsible for ligand binding, and an expression platform that transmits the ligand-binding state of the aptamer domain through a conformational change. Riboswitches can regulate gene expression either at the level of transcription or translation, and it has been proposed that riboswitch mechanisms are even used to regulate the processing of mRNA. This Minireview summarizes the current understanding of the structures and mode of action of RNA switches, with particular focus on secondary and tertiary interactions, which stabilize the global RNA structure and thus determine the function of the aptamer domain.
Observation of Measurement-Induced Entanglement and Quantum Trajectories of Remote Superconducting Qubits (2014)

The creation of a quantum network requires the distribution of coherent information across macroscopic distances. We demonstrate the entanglement of two superconducting qubits, separated by more than a meter of coaxial cable, by designing a joint measurement that probabilistically projects onto an entangled state. By using a continuous measurement scheme, we are further able to observe single quantum trajectories of the joint two-qubit state, confirming the validity of the quantum Bayesian formalism for a cascaded system. Our results allow us to resolve the dynamics of continuous projection onto the entangled manifold, in quantitative agreement with theory.
An Artificial Solid Electrolyte Interphase Layer for Stable Lithium Metal Anodes (2015)

A Li3PO4 solid electrolyte interphase (SEI) layer is demonstrated to be stable in the organic electrolyte, even during the Li deposition/dissolution process. Thus, the Li-conducting Li3PO4 SEI layer with a high Young's modulus can effectively reduce side reactions between Li metal and the electrolyte and can restrain Li dendrite growth in lithium-metal batteries during cycling.
Experimental Infection of Chimpanzees with Dengue Viruses (1978)

We describe a prototype digital device for measuring high-order structure functions in turbulence. Because the structure function is a special case of the correlation function, the device may find usage outside the study of turbulence. The device operates at 20 kHz on 12-bits data and updates probability distribution functions of signal differences for 64 arbitrarily chosen time delays in real time.
Cholesteryl Ester Transfer Protein Taq I B2B2 Genotype Is Associated With Higher HDL Cholesterol Levels and Lower Risk of Coronary Heart Disease End Points in Men With HDL Deficiency (2002)

Our data demonstrate that in men with CHD and HDL deficiency, the CETP TaqI B2B2 genotype is (1) significantly reduced and (2) associated with higher levels of plasma HDL-C and lower CHD risk. Together with our earlier report, these results support the concept that increased HDL-C levels, resulting from reduced CETP activity, are associated with decreased CHD risk.
BARNET - A new approach to behavior arbitration (2002)

A new mechanism, termed Behavior Arbitration Network (BARNET) is presented. BARNET is a dynamic adaptive network which is used for arbitration among behaviors and for combining reflexive behaviors and reasoning-driven behaviors in high-functionality intelligent autonomous systems (IASs). BARNET is structured as a networked team of stochastic learning automata, operating in multiple stochastic nonstationary environments as game of automata. The automata team selects the optimal combination of behaviors and their respective level of activation, while properly reacting to continuously changing and unexpected situations and events. BARNET enables a truly hybrid architecture which combines the advantages of both traditional reasoning-driven hierarchical architectures and behavior-based architectures, while lacking their inherent drawbacks. BARNET is embedded within the intelligent autonomous hyper-controller (IAHC) of the IAS. The motivation for developing BARNET, its architecture and algorithms, as well as simulation results, are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mice Lacking Two or All Three Selectins Demonstrate Overlapping and Distinct Functions for Each Selectin (1999)

Abstract Selectins support the capture and rolling of leukocytes in venules at sites of inflammation and in lymphocyte homing. Gene-targeted mice with null mutations at the L-, E-, or P-selectin locus develop normally and show mild (E−/−) to moderate (P−/−, L−/−) defects in inflammatory cell recruitment. Mice lacking both P- and E-selectin (E/P−/−) have severe neutrophilia and spontaneous skin infections that limit their life span. Other combinations of selectin deficiency have not been investigated. We have generated novel mice lacking L- and P-selectin (L/P−/−), L- and E-selectin (L/E−/−), or all three selectins (E/L/P−/−) by bone marrow transplantation. L/P−/− mice (only E-selectin present) show an absence of leukocyte rolling after trauma and severely reduced rolling (by ∼90%) in inflammation induced by TNF-α. Residual rolling in L/P−/− mice was very slow (3.6 ± 0.2 μm/s after TNF-α). L/E−/− mice (only P-selectin present) showed rolling similar to that of L−/− at increased velocities (15.1 ± 0.3 μm/s). The number of adherent leukocytes after 2 or 6 h of TNF-α treatment was not significantly reduced in L/E−/− or L/P−/− mice. E/L/P−/− mice showed very little rolling after TNF-α, all of which was blocked by mAb to α4 integrin. Adherent and emigrated neutrophils were significantly reduced at 6 h after TNF-α. We conclude that any one of the selectins can support some neutrophil recruitment but eliminating all three selectins significantly impairs neutrophil recruitment.
The b matrix in diffusion tensor echo‐planar imaging (1997)

In diffusion tensor imaging (DTI) an effective diffusion tensor in each voxel is measured by using a set of diffusion-weighted images (DWIs) in which diffusion gradients are applied in a multiplicity of oblique directions. However, to estimate the diffusion tensor accurately, one must account for the effects of all imaging and diffusion gradient pulses on each signal echo, which are embodied in the b matrix. For DTI to be practical clinically, one must also acquire DWIs rapidly and free of motion artifacts, which is now possible with diffusion-weighted echo-planar imaging (DW-EPI). An analytical expression for the b matrix of a general DW-EPI pulse sequence is presented and then validated experimentally by measuring the diffusion tensor in an isotropic phantom whose diffusivity is already known. The b matrix is written in a convenient tabular form as a sum of individual pair-wise contributions arising from gradient pulses applied along parallel and perpendicular directions. While the contributions from readout and phase-encode gradient pulse trains are predicted to have a negligible effect on the echo, the contributions from other imaging and diffusion gradient pulses applied in both parallel and orthogonal directions are shown to be significant in our sequence. In general, one must understand and account for the multiplicity of interactions between gradient pulses and the echo signal to ensure that diffusion tensor imaging is quantitative.
DNA Synthesis on a Double-stranded DNA Template by the T4 Bacteriophage DNA Polymerase and the T4 Gene 32 DNA Unwinding Protein (1974)

Abstract T4 DNA polymerase cannot use a nicked duplex DNA molecule as a template-primer for DNA synthesis, apparently because it is unable to displace the 5' end of the strand paired to the strand serving as the template. Addition of the T4 phage gene 32 DNA unwinding protein (32-protein) facilities strand displacement and allows the T4 DNA polymerase to synthesize DNA using nicked duplex T7 DNA as the template-primer. The first product of this reaction is a rapidly renaturable DNA which is found to contain a few large branches when examined by electron microscopy. Later in the reaction there is also synthesis of a product containing predominantly alternating residues of dAMP and dTMP.
Reclassification of the Penicillium Roqueforti Group into Three Species on the Basis of Molecular Genetic and Biochemical Profiles (1996)

Penicillium roqueforti is currently divided into two varieties, one used for cheese starter cultures, P. roqueforti var. roqueforti, and one ubiquitous patulin-producing variety, P. roqueforti var. carneum. The ribosomal regions comprising the 5.8S gene and the internal transcribed spacers, ITS I and ITS II, have been analysed from 10 isolates belonging to each variety. The 10 P. roqueforti var. carneum isolates were separated into two groups of five on the basis of 12 base-pair differences in the ITS regions. One of the groups of P. roqueforti var. carneum, in the following designated P. carneum, differed from P. roqueforti var. roqueforti, here designated P. roqueforti, in just two positions, while the other group, here called P. paneum, differed from P. roqueforti in 12 positions. Random Amplified Polymorphic DNA (RAPD) analysis substantiated these findings, and a comparison of secondary metabolites produced by the three groups showed that the P. roqueforti isolates all produce Penicillium Roqueforti (PR) toxin, marcfortines and fumigaclavine A, while the P. carneum isolates produce patulin, penitrem A and mycophenolic acid, as well as unidentified metabolites. P. paneum produces secondary metabolites in five chromophore families including the known mycotoxins patulin and botryodiploidin. On the basis of these findings it is proposed that P. roqueforti is reclassified into three species named P. roqueforti, P. carneum and P. paneum.
Fast Computation and Applications of Genome Mappability (2012)

We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of massively parallel sequencing experiments. We investigate the properties of the mappability of eukaryotic DNA/RNA both as a whole and at the level of the gene family, providing for various organisms tracks which allow the mappability information to be visually explored. In addition, we show that mappability varies greatly between species and gene classes. Finally, we suggest several practical applications where mappability can be used to refine the analysis of high-throughput sequencing data (SNP calling, gene expression quantification and paired-end experiments). This work highlights mappability as an important concept which deserves to be taken into full account, in particular when massively parallel sequencing technologies are employed. The GEM mappability program belongs to the GEM (GEnome Multitool) suite of programs, which can be freely downloaded for any use from its website (http://gemlibrary.sourceforge.net).
Looking at the surprise: Bottom-up attentional control of an active camera system (2008)

Inspired by the expectation-based perception of humans, a surprise-driven active vision system is proposed. This vision system not only considers spatial saliency of objects in the environment, but also investigates temporal novelty in the neighborhood. Surprise is defined as the difference of the saliency probability distributions of two consecutive input images, which is measured using Kullback-Leibler divergence. The high-speed gaze shift capability of the camera platform and the parallel computation with the aid of GPUs enable a real-time tracking of the surprising event.
Identification of glypican-3-derived long peptides activating both CD8+and CD4+T cells; prolonged overall survival in cancer patients with Th cell response (2015)

In a recent phase I clinical trial, a vaccine consisting of glypican-3 (GPC3)-derived CTL epitopes was found to be safe and induced measurable immune and clinical responses in patients with hepatocellular carcinoma (HCC). The aim of this study was to identify GPC3-derived long peptides (GPC3-LPs) carrying promiscuous HLA class II-restricted T helper (Th) cell epitopes. Using a computer algorithm, we predicted GPC3-LPs that can bind to promiscuous HLA class II molecules. Their antigenicity for induction of specific CD4<sup>+</sup> T cells in healthy donors or patients with HCC, before and after vaccination with GPC3-SPs, was proven by IFNγ enzyme-linked immunospot assays. Natural processing of these epitopes was confirmed by the immune response of helper T cells to dendritic cells (DCs) loaded with GPC3 proteins. Cross-presentation capacity was assessed <i>in vitro</i> using human DCs and LPs encapsulated in liposomes and <i>in vivo</i> in HLA-A2 transgenic mice (Tgm). All five LPs could induce Th1 cells and were presented by several frequently occurring HLA class II molecules <i>in vitro</i>. Four of them were likely to be naturally processed. One of the LPs encapsulated in liposomes was well cross-presented <i>in vitro</i>; it cross-primed CTLs in HLA-A2 Tgm. LP-specific and HLA class II-restricted CD4<sup>+</sup> T-cell responses were observed in 14 of 20 HCC patients vaccinated with GPC3-SPs. Repeated vaccinations enhanced GPC3-LP-specific responses in 8 of 13 patients with HCC. Moreover, the presence of the specific Th cell was correlated with prolonged overall survival (OS). GPC3-LPs can be useful for cancer immunotherapy.
Wireless communications in the automated factory environment (1988)

The networking issues involved in the use of infrared communications in a factory environment are described. A brief history of the use of infrared and radio for indoor (factory environment) communications is given, and the physical infrared environment is reviewed. Topology and protocol alternatives are compared.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
One-Step Conversion of Aldehydes to Oxazolines and 5,6-Dihydro-4H-1,3-oxazines Using 1,2- and 1,3-Azido Alcohols (1996)

The reactions of 1,2- and 1,3-hydroxy azides with aldehydes under acidic conditions were examined. A variety of Lewis acids were examined, of which BF3·OEt2 was found the most convenient. Trimethylsilyl ether derivatives of the alcohols could also be reacted using trimethylsilyl triflate as the promoter. Twenty-five examples that proceed in moderate to quantitative yields are reported.
Production and characterization of monoclonal and polyclonal antibodies against digoxin. (1990)

Three hybridoma cell lines (DIG 64. 2B. 5, DIG 104. H10.1 and DIG 222. 4D. 5) producing monoclonal antibodies against digoxin were established, and the properties of these monoclonal antibodies were characterized and compared with three polyclonal rabbit anti-digoxin antisera. Both polyclonal and monoclonal antibodies gave association constants ranging from 10(9) to 10(10) (M-1). The monoclonal antibodies were of the IgG1(kappa) or IgG2b(kappa) subclass. Cross-reactivities of these monoclonal antibodies and polyclonal antisera with various related cardenolides and their aglycones were determined by competitive radioimmunoassay. The monoclonal antibodies were specific for digoxigenin-containing glycosides such as lanatoside C and deslanoside, but not for digitoxigenin-containing glycosides. On the other hand, the specificities of the polyclonal antisera were less strict than the monoclonal antibodies and relatively cross-reactive with digitoxin. It was shown that the RIA for digoxin using DIG 64. 2B. 5 is sensitive enough to detect 0.2-0.3 nM (30-60 pg/tube) of digoxigenin-containing cardenolides.
Tumor-Specific Urinary Matrix Metalloproteinase Fingerprinting: Identification of High Molecular Weight Urinary Matrix Metalloproteinase Species (2008)

This study is the first to identify a tumor-specific urinary MMP fingerprint that may noninvasively facilitate identification of cancer presence and type. This information may be of diagnostic and prognostic value in the detection and/or clinical monitoring of disease progression and therapeutic efficacy in patients with bladder or prostate cancer.
Targeted Genomic Integration of a Selectable Floxed Dual Fluorescence Reporter in Human Embryonic Stem Cells (2012)

The differentiation of pluripotent stem cells involves transition through a series of specific cell states. To understand these cell fate decisions, the field needs improved genetic tools for the labeling, lineage tracing and selection of specific cell types from heterogeneous differentiating populations, particularly in the human embryonic stem cell (hESC) system. We used zinc finger nuclease technology to stably insert a unique, selectable, floxed dual-fluorescence reporter transgene into the AAVS1 locus of RUES2 hESCs. This "stoplight" transgene, mTmG-2a-Puro, strongly expresses membrane-localized tdTomato red fluorescent protein until Cre-dependent recombination causes a switch to expression of membrane-localized enhanced green fluorescent protein (eGFP) and puromycin resistance. First, to validate this system in undifferentiated cells, we transduced transgenic hESCs with a lentiviral vector driving constitutive expression of Cre and observed the expected phenotypic switch. Next, to demonstrate its utility in lineage-specific selection, we transduced differentiated cultures with a lentiviral vector in which the striated muscle-specific CK7 promoter drives Cre expression. This yielded near-homogenous populations of eGFP(+) hESC-derived cardiomyocytes. The mTmg-2a-Puro hESC line described here represents a useful new tool for both in vitro fate mapping studies and the selection of useful differentiated cell types.
Practical Wyner-Ziv Switching Scheme for Multiple Bit-Rate Video Streaming (2006)

In this paper, we propose a novel bit-stream switching scheme for the multiple bit-rate (MBR) video streaming, in which a Wyner-Ziv coded frame is used to overcome the mismatch between the MBR streams when the switching occurs. With the proposed technique, the MBR streams can be independently encoded without losing any coding efficiency. Similar to distributed video coding, the proposed Wyner-Ziv switching scheme also faces the challenge of rate allocation at the server side. To solve this problem, we propose a new correlation model based on the analysis on the reconstructed frames from the streams with different bit rates. Accordingly, the number of transmitted bits can be on-line calculated based on the correlation model without any feedback from the decoder. With the proposed technique, the actually transmitted Wyner-Ziv bits are only few more than the truly requested bits. However, the delay due to the bit requesting process can be avoided.
Anodal transcranial direct current stimulation of the visual cortex for migraine prevention: a proof-of-concept study (2013)

Prophylaxis is challenging in migraine because of the low efficiency/tolerability ratio of most drugs [1]. Abnormal excitability of the cerebral cortex seems implicated in migraine pathophysiology [2]. Transcranial direct current stimulation (tDCS) can durably modify the activity of a target cortex and thus be a promising treatment [3]. We have shown that the cerebral cortex, namely the visual cortex, is hyperreactive in migraineurs between attacks and hypothesized that this may be related more to a decreased preactivation level than to hyperexcitability per se [2]. Anodal, rather than cathodal, tDCS might be the stimulation modality of choice in migraine.
Practical semen analysis: from A to Z (2010)

Accurate semen analysis is critical for decisions about patient care, as well as for studies addressing overall changes in semen quality, contraceptive efficacy and effects of toxicant exposure. The standardization of semen analysis is very difficult for many reasons, including the use of subjective techniques with no standards for comparison, poor technician training, problems with proficiency testing and a reluctance to change techniques. The World Health Organization (WHO) Semen handbook (2010) offers a vastly improved set of standardized procedures, all at a level of detail that will preclude most misinterpretations. However, there is a limit to what can be learned from words and pictures alone. A WHO-produced DVD that offers complete demonstrations of each technique along with quality assurance standards for motility, morphology and concentration assessments would enhance the effectiveness of the manual. However, neither the manual nor a DVD will help unless there is general acknowledgement of the critical need to standardize techniques and rigorously pursue quality control to ensure that laboratories actually perform techniques 'according to WHO' instead of merely reporting that they have done so. Unless improvements are made, patient results will continue to be compromised and comparison between studies and laboratories will have limited merit.
Cardiac Dynamics of the Langendorff Perfused Heart (1985)

The Langendorff perfused heart is studied in a closed system with (i) automatic regulations to maintain constancy of the perfusion column (Krebs-Henseleit + 0.5% albumin or 25-30% washed erythrocyte suspension), (ii) continuous recording of rate, coronary flow, and supravalvular aortic pressure. A microcomputer with software interface is used for storage treatment and on-line analysis of the recorded variables. In 38 preparations perfused with Krebs-Henseleit, minimal diastolic (61.2 +/- 2.8 mm Hg) is significantly below and peak systolic (98.7 +/- 3.6 mm Hg) significantly above perfusion pressure (80 mm Hg). Pressure difference between minimal diastolic and peak systolic (delta P) is 37.5 +/- 1.8 mm Hg. Increases in perfusion pressure will be associated with increases of coronary flow and delta P, which is also increased by isoprenaline administration. Oxygen consumption decreased by 76% when perfusion pressure was lowered from 80 to 60 mm Hg in hearts perfused with a 30% erythrocyte suspension. All of these experimental results were interpreted as indicating that delta P measured in this system resulted from an ejected volume (x acceleration) from the heart. The ejected volume corresponds to a valvular leak caused by the rigid nature of the system which is devoid of aortic compliance. delta P may be considered an index of left ventricular performance, an indication that the Langendorff preparation studied under the present conditions is a working heart. A 100-microliter volume constant infusion syringe for time administration of cardioactive drugs may be inserted at the base of the perfusion column to obtain dose-response effects.
Scalable Deep Learning on Distributed Infrastructures (2020)

Deep Learning (DL) has had an immense success in the recent past, leading to state-of-the-art results in various domains, such as image recognition and natural language processing. One of the reasons for this success is the increasing size of DL models and the proliferation of vast amounts of training data being available. To keep on improving the performance of DL, increasing the scalability of DL systems is necessary. In this survey, we perform a broad and thorough investigation on challenges, techniques and tools for scalable DL on distributed infrastructures. This incorporates infrastructures for DL, methods for parallel DL training, multi-tenant resource scheduling, and the management of training and model data. Further, we analyze and compare 11 current open-source DL frameworks and tools and investigate which of the techniques are commonly implemented in practice. Finally, we highlight future research trends in DL systems that deserve further research.