gebhart/patrepeval huggingface dataset:
Differentiation of Cardiomyocytes from Human Pluripotent Stem Cells Using Monolayer Culture (2015)

Human pluripotent stem cells (PSCs) are a promising cell source for cardiac tissue engineering and cell-based therapies for heart repair because they can be expanded in vitro and differentiated into most cardiovascular cell types, including cardiomyocytes. During embryonic heart development, this differentiation occurs under the influence of internal and external stimuli that guide cells to go down the cardiac lineage. In order to differentiate PSCs in vitro, these or similar stimuli need to be provided in a controlled manner. However, because it is not possible to completely recapitulate the embryonic environment, the factors essential for cardiac differentiation of PSCs in vitro need to be experimentally determined and validated. Since PSCs were first developed, significant progress has been made in optimizing techniques for their differentiation toward cardiomyocytes. In this review, we will summarize recent advances in these techniques, with particular focus on monolayer-based methods that have improved the efficiency and scalability of cardiomyocyte differentiation.
Synthesis and evaluation of hexafluorodimethylcarbinol functionalized polymers as microsensor coatings (1991)

Abstract Polystyrenes, polyacrylates, and poly(3,4‐isoprenes) incorporating the hexafluorodimethylcarbinol functionality have been synthesized, characterized, and tested as microsensor coatings on a surface acoustic wave (SAW) device for dimethyl methylphosphonate (DMMP) vapor absorption sensitivity. The syntheses involved monomer functionalization and polymerization or hexafluoroacetone reaction with preformed polymer. All fluoroalcohol functionalized polymer coatings displayed sub parts per million level sensitivity with the slope of the absorption isotherm steepest at low DMMP concentrations. The order of sensitivity for the isomeric polystyrene fluoroalcohols ( meta &gt; para ≫ ortho ) paralleled that of the relative free hydroxyl to hydrogen‐bonded hydroxyl content. Strong hydrogen bonding between the fluoroalcohol polymers and DMMP vapor was observed by IR spectroscopy. Acylation of the fluoroalcohol group markedly reduced the DMMP sensitivity.
Laser and Electron-Beam Induced Growth of Nanoparticles for 2D and 3D Metal Patterning (2002)

3D free-standing and embedded metallic structures with a height of 100 μm (see Figure and also cover) have been microfabricated and characterized. Polymer nanocomposites containing metal nanoparticles, a metal salt, and an appropriate photoreducing dye are found to be efficient precursors for direct laser writing of continuous metal structures. The authors offer a versatile new approach to the 2D and 3D patterning of metals on different length scales.
Adrenal Suppression Following a Single Dose of Etomidate For Rapid Sequence Induction: A Prospective Randomized Study (2008)

The use of etomidate for RSI in trauma patients led to chemical evidence of adrenocortical insufficiency and may have contributed to increased hospital and ICU lengths of stay and increased ventilator days. Further studies should be considered to evaluate the safety profile of this drug in trauma patients.
Total internal reflection fluorescence study of energy transfer in surface-adsorbed and dissolved bovine serum albumin (1983)

A simple adaptation of a commercial spectrofluorometer allows selective excitation of fluorescent biomolecules adsorbed to a solid surface while they are in equilibrium with a bulk solution. As a demonstration of this technique, we have detected a change in the effective singlet-singlet energy transfer in fluorescence-labeled bovine serum albumin (BSA) upon adsorption to a fused silica surface. The technique combines total internal reflection fluorescence excitation of surface-adsorbed BSA with a fluorescence spectroscopic examination of energy transfer between two different fluorophores that are covalently bound to amino groups in each BSA molecule. Two donor--acceptor pairs were used, 4-chloro-7-nitro-2,1,3-benzoxadiazole-rhodamine and dansyl-eosin. For studies of surface-adsorbed BSA, we constructed a device in which the excitation light of a standard fluorescence spectrometer totally internally reflects from a surface at which adsorbed BSA is in equilibrium with the bulk solution. A shallow evanescent wave is created, which excites fluorescence from only those BSA molecules in close proximity to the surface. Spectral examination shows significantly less effective singlet-singlet energy transfer from the donor to the acceptor in surface-adsorbed BSA relative to that in native bulk-dissolved BSA. Under appropriate and reasonable assumptions, the energy transfer change between native and adsorbed states of fluorescent BSA can be interpreted as a conformational change of BSA upon adsorption.
Identification, characterization, and molecular cloning of a novel hyaluronidase, a member of glycosyl hydrolase family 16, fromPenicilliumspp (2010)

Hyaluronidase (HAase) activity was detected in the culture supernatants of Penicillium purpurogenum and Penicillium funiculosum. The HAase from Penicillium spp. (HAase-P) was a hyaluronate 4-glycanohydrolase, which catalyzed the endolytic hydrolysis of the β-1,4 glycosidic linkage, as do vertebrate HAases. The gene encoding HAase-P was cloned and expressed in Escherichia coli. According to homology analyses of the deduced amino acid sequences, HAase-P is not classified into any of the known HAase groups, but belongs to glycoside hydrolase family 16, which includes endo-β-1,3(4)-glucanase. Regarding the substrate specificities, no chondroitinase and glucanase activities were detected. Judging from homology analyses and enzymatic properties, HAase-P seems to be a new type of HAase.
BugNet: Continuously Recording Program Execution for Deterministic Replay Debugging (2005)

Significant time is spent by companies trying to reproduce and fix the bugs that occur for released code. To assist developers, we propose the BugNet architecture to continuously record information on production runs. The information collected before the crash of a program can be used by the developers working in their execution environment to deterministically replay the last several million instructions executed before the crash. BugNet is based on the insight that recording the register file contents at any point in time, and then recording the load values that occur after that point can enable deterministic replaying of a program's execution. BugNet focuses on being able to replay the application's execution and the libraries it uses, but not the operating system. But our approach provides the ability to replay an application's execution across context switches and interrupts. Hence, BugNet obviates the need for tracking program I/O, interrupts and DMA transfers, which would have otherwise required more complex hardware support. In addition, BugNet does not require a final core dump of the system state for replaying, which significantly reduces the amount of data that must be sent back to the developer.
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays (2008)

Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). The information in a single lane of Illumina sequencing data appears comparable to that in a single array in enabling identification of differentially expressed genes, while allowing for additional analyses such as detection of low-expressed genes, alternative splice variants, and novel transcripts. Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology.
Acute Effects of TASER X26 Discharges in a Swine Model (2007)

Immediately after the discharge, two deaths occurred because of ventricular fibrillation. In this model of prolonged EID exposure, clinically significant acid-base and cardiovascular disturbances were clearly seen. The severe metabolic and respiratory acidosis seen here suggests the involvement of a primary cardiovascular mechanism.
Understanding the Structural Properties of a Homologous Series of Bis-diphenylphosphine Oxides (2000)

A homologous series of bis-diphenylphosphine oxides (C6H5)2PO(CH2)(n)PO(C6H5)2 (with n = 2-8; denoted 2-8] have been investigated to explore the effects of a range of competing and cooperative intermolecular and intramolecular interactions on the structural properties in the solid state. The important factors influencing the structural properties include intramolecular aspects such as the conformation of the aliphatic chain and the intramolecular interaction between the two P=O dipoles in the molecule, and intermolecular aspects such as long-range electrostatic interactions (dominated by the arrangement of the P=O dipoles), C-H...O interactions, C-H...pi interactions and pi...pi interactions. Compounds 3 and 5 could be crystallized only as solvate co-crystals (3 water and 5 x (toluene)2], whereas the crystal structures of all the other compounds contain only the bis-diphenylphosphine oxide molecule. The crystal structures have been determined from single-crystal X-ray diffraction data, with the exception of 7 (which has been determined here from powder X-ray diffraction data) and 4 (which was known previously). The compounds with even n represent a systematic structural series, exhibiting characteristic, essentially linear P=O...P=O...P=O dipolar arrays, together with C-H...O and C-H...pi interactions. For the compounds with odd n, on the other hand, uniform structural behaviour is not observed across the series, although certain aspects of these crystal structures contribute in a general sense to our understanding of the structural properties of bis-diphenylphosphine oxides. Importantly, for the compounds with odd n, there is "frustration" with regard to the molecular conformation, as the preferred all-anti conformation of the aliphatic chain gives rise to an unfavourable parallel alignment of the two P=O dipoles within the molecule. Clearly the importance of avoiding a parallel alignment of the P=O dipoles becomes greater as n decreases. Local structural aspects (investigated by high-resolution solid-state 31P NMR spectroscopy) and thermal properties of the bis-diphenylphosphine oxide materials are also reported.
Construction and field validation of a self‐administered screener for testosterone deficiency (hypogonadism) in ageing men (2000)

To design a self-administered screening questionnaire to inform men about their risk for testosterone deficiency. The screener was developed in two phases. First was a construction phase in which relevant risk factors and a scoring algorithm were defined from multiple logistic regression analyses of survey data. In the second phase, the screener's accuracy (based on sensitivity, specificity, and Receiver Operating Characteristic (ROC) curves) was tested using patients from a primary care clinic. All subjects provided blood samples for endocrine testing. Survey data from 1660 men aged 40-79 years participating in the Massachusetts Male Ageing Study (MMAS) were analysed in the first phase. The clinic sample consisted of 304 men aged 40-79 years presenting at a large Massachusetts primary health care clinic for routine check-ups or minor medical problems. The primary outcome was testosterone deficiency, defined as serum total testosterone below 12.1 nmol/l. Self-reported variables considered as potential risk factors included age, obesity, chronic diseases, health behaviour, the Jackson dominance scale, and symptoms of stress. The prevalence of testosterone deficiency was 20.4% in the MMAS and 42.1% in the clinic sample. An eight-item screener was developed based on age, body mass index, diabetes, asthma, headaches, sleep patterns, dominance preferences, and smoking status. The screener performed significantly better than chance in identifying men with low testosterone levels; the area under the ROC curve was 0.66 in the MMAS sample and 0.67 in the clinic sample. The self-scored screener developed in this study reliably detects men at risk of hypogonadism. The screener encourages at risk men to seek professional evaluation of their testosterone levels.
Schizophrenia: Do the Genetics and Neurobiology of Neuregulin Provide a Pathogenesis Model? (2006)

The sequencing of the human genome and an emerging dense map of markers across the human genome have spawned new approaches to search for risk genes for human diseases with complex genetics. These approaches are particularly relevant to the search for risk genes for bipolar disorder and schizophrenia. A gene called neuregulin 1 has been reported to be a risk gene for schizophrenia. This article reviews aspects of the genetics, cellular neurobiology, and biochemistry of neuregulin 1 and attempts to integrate several observations from disparate fields into a model for the pathogenesis of schizophrenia. The model outlines experimental approaches that may, in the future, shed more light on its validity.
The Influence of Morphology on High‐Performance Polymer Field‐Effect Transistors (2008)

The influence of molecular packing on the performance of polymer organic field-effect transistors is illustrated in this work. Both close π-stacking distance and long-range order are important for achieving high mobilities. By aligning the polymers from solution, long-range order is induced, yielding hole mobilities of up to µsat = 1.4 cm2 V−1 s−1 and current on/off ratios Ion/Ioff of 105. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Paving the path (2001)

The Path of Carbon in Photosynthesis evolved in the minds of Sam Ruben and Martin Kamen as they followed incorporation of radioactive 11CO2 in their many experiments, 1938 to 1942. With the concepts and collaboration of C. B. van Niel it became clear that reduction of CO2 can occur in the dark and may require processes similar to bacterial systems. It could not involve the century-old A. von Baeyer theory's photochemical reduction of CO2 adsorbed on chlorophyll which had guided decades of painstaking efforts, of R. Willstatter and A. Stoll and many others, in vain searches for formaldehyde. In 1942 Sam Ruben gave me all of his home-made 14CO2 to look for the first steps of the path of carbon in photosynthesis. Measurements were tedious and activities low but progress was real. Liquid-liquid partition of the radioactivity indicated chemical properties of the products and their derivatives. Interrupted by the war and Sam Ruben?s tragic accidental death, I accepted Melvin Calvin's invitation to continue The Path and we established our lab in the Old Radiation Laboratory next to Ernest Lawrence's cyclotron. Pre-illuminated algae rapidly reduced 14CO2 in the dark! Simple 'partition'-based separations on paper chromatograms extended the earlier methodology. Sedoheptulose and ribulose made surprise appearances. Soon it became clear that Nature had selected ribulose bisphosphate as its universal CO2 acceptor molecule. Finally, our isolation of carboxydismutase in 1954 revealed its identity with Sam Wildman's Fraction 1 protein. The Path was paved with one of this planet's major proteins!
Athermal demodulator for 42.7-Gb/s DPSK signals (2005)

We report an athermal optical-delay-interferometer capable of demodulating any OC-768 DPSK signal on the ITU 50-GHz-grid over the C+L band. Receiver sensitivity of -35.5 dBm is achieved for a 42.7-Gb/s nonreturn-to-zero DPSK signal. (2 pages)
Chemistry of the Diazeniumdiolates. 3. Photoreactivity (2001)

We have found O(2)-substituted diazeniumdiolates, compounds of structure R(2)N-N(O)=NOR' that are under development for various possible pharmaceutical uses, to be rather photosensitive. With R = ethyl and R' = methyl, benzyl, or 2-nitrobenzyl, the observed product distributions suggest that two primary pathways are operative. A minor pathway involves the extrusion of nitrous oxide (N(2)O) with simultaneous generation of R(2)N(*) and R'O(*), which may then form amines, aldehydes, and alcohols. The major reaction pathway is an interesting photochemical cleavage of the N=N bond to form a nitrosamine (R(2)NN=O) and an oxygen-substituted nitrene (R'ON). The intermediacy of the O-nitrene was inferred from the production of abundant oxime, via rearrangement of the O-nitrene to a C-nitroso compound (R'ON --> O=NR'), and subsequent tautomerization to the more stable oxime. Involvement of the O-nitrene was confirmed by trapping with 2,3-dimethyl-2-butene to form the aziridine and with oxygen to generate the nitrate ester. 2-Nitro substitution on the benzyl derivative had surprisingly little effect on the reaction course. For each compound examined, minor amounts of nitric oxide (NO), presumably produced by secondary photolysis of the nitrosamine, were observed. Time-resolved infrared experiments provided additional support for the above reaction pathways and confirmed that the nitrosamine is a primary photoproduct. We have also found that the relative contributions of the reaction pathways can be altered in certain derivatives. For example, when R' = 2,4-dinitrophenyl, the contribution of the nitrosamine/O-nitrene-forming pathway was diminished. Pharmacological implications of these results are discussed.
Improved Survival with MEK Inhibition in BRAF-Mutated Melanoma (2012)

Trametinib, as compared with chemotherapy, improved rates of progression-free and overall survival among patients who had metastatic melanoma with a BRAF V600E or V600K mutation. (Funded by GlaxoSmithKline; METRIC ClinicalTrials.gov number, NCT01245062.).
A Quality-of-Service Mechanism for Interconnection Networks in System-on-Chips (2005)

As Moore's Law continues to fuel the ability to build ever increasing complex systems-on-chips (SoCs), achieving performance goals is rising as a critical challenge to completing designs. In particular, the system interconnect must efficiently service a diverse set of data flows with widely ranging quality-of-service (QoS) requirements. However the known solutions for off-chip interconnects, such as large-scale networks, are not necessarily applicable to the on-chip environment. Latency and memory constraints for on-chip interconnects are quite different from larger-scale interconnects. The paper introduces a novel on-chip interconnect arbitration scheme. We show how this scheme can be distributed across a chip for high-speed implementation. We compare the performance of the arbitration scheme with other known interconnect arbitration schemes. Existing schemes typically focus heavily on either low latency of service for some initiators or on guaranteed bandwidth delivery for other initiators. Our scheme allows service latency on some initiators to be traded off smoothly against jitter bounds on other initiators, while still delivering bandwidth guarantees. This scheme is a subset of the QoS controls that are available in the SonicsMX/spl trade/ (SMX) product.
Photoreceptor cell tumors in transgenic mice. (1994)

These mice represent an animal model system for human trilateral retinoblastoma, in which retinoblastomas are accompanied by pineal tumors.
Characteristics of a grating-external-cavity semiconductor laser containing intracavity prism beam expanders (1992)

A grating tuned external cavity semiconductor laser incorporating a gradient-index rod lens and a pair of intracavity silicon prism beam expanders was constructed using a configuration aimed at simultaneously achieving the following objectives: the ability to operate at any external cavity longitudinal mode without tuning gaps caused by residual resonances of the laser diode cavity, stable feedback coupling between the diode and external cavities, narrow optical linewidth, and a high degree of external cavity longitudinal sidemode suppression.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oligosaccharide Library-based Assessment of Heparan Sulfate 6-O-Sulfotransferase Substrate Specificity (2003)

Heparan sulfate mediates numerous complex biological processes. Its action critically depends on the amount and the positions of O-sulfate groups (iduronyl 2-O-sulfates, glucosaminyl 6-O- and 3-O-sulfates) that form binding sites for proteins. The structures and distribution of these protein-binding domains are influenced by the expression and substrate specificity of heparan sulfate biosynthetic enzymes. We describe a general approach to assess substrate specificities of enzymes involved in glycosaminoglycan metabolism, here applied to 6-O-sulfotransferases involved in heparan sulfate biosynthesis. To understand how 2-O-sulfation affects subsequent 6-O-sulfation reactions, the substrate specificity of 6-O-sulfotransferase 3 was probed using substrates from a heparin-based octasaccharide library. Purified 3H-labeled N-sulfated octasaccharides from a library designed to sample 2-O-sulfated motifs were used as sulfate acceptors, 3'-phosphoadenosine 5'-phosphosulfate as sulfate donor, and cell extract from 6-O-sulfotransferase 3-overexpressing 293 cells as enzyme source in the 6-O-sulfotransferase-catalyzed reactions. The first 6-O-sulfate group was preferentially incorporated at the internal glucosamine unit of the octasaccharide substrate. As the reaction proceeded, the octasaccharides acquired three 6-O-sulfate groups. The specificities toward competing octasaccharide substrates, for 6-O-sulfotransferase 2 and 6-O-sulfotransferase 3, were determined using overexpressing 293 cell extracts and purified octasaccharides. Both 6-O-sulfotransferases showed a preference for 2-O-sulfated substrates. The specificity toward substrates with two to three 2-O-sulfate groups was three to five times higher as compared with octasaccharides with no or one 2-O-sulfate group.
Identification and Functional Analysis of an Immunoreactive DsbA-Like Thio-Disulfide Oxidoreductase of Ehrlichia spp (2002)

Novel homologous DsbA-like disulfide bond formation (Dsb) proteins of Ehrlichia chaffeensis and Ehrlichia canis were identified which restored DsbA activity in complemented Escherichia coli dsbA mutants. Recombinant Ehrlichia Dsb (eDsb) proteins were recognized by sera from E. canis-infected dogs but not from E. chaffeensis-infected patients. The eDsb proteins were observed primarily in the periplasm of E. chaffeensis and E. canis.