gebhart/patrepeval huggingface dataset:
Reduced insulin secretion correlates with decreased expression of exocytotic genes in pancreatic islets from patients with type 2 diabetes (2012)

Reduced insulin release has been linked to defect exocytosis in β-cells. However, whether expression of genes suggested to be involved in the exocytotic process (exocytotic genes) is altered in pancreatic islets from patients with type 2 diabetes (T2D), and correlate to insulin secretion, needs to be further investigated. Analysing expression levels of 23 exocytotic genes using microarray revealed reduced expression of five genes in human T2D islets (χ(2)=13.25; p<0.001). Gene expression of STX1A, SYT4, SYT7, SYT11, SYT13, SNAP25 and STXBP1 correlated negatively to in vivo measurements of HbA1c levels and positively to glucose stimulated insulin secretion (GSIS) in vitro in human islets. STX1A, SYT4 and SYT11 protein levels correspondingly decreased in human T2D islets. Moreover, silencing of SYT4 and SYT13 reduced GSIS in INS1-832/13 cells. Our data support that reduced expression of exocytotic genes contributes to impaired insulin secretion, and suggest decreased expression of these genes as part of T2D pathogenesis.
Production Estimation for Shale Wells with Sentiment-Based Features from Geology Reports (2015)

Shale oil and gas have become very promising unconventional energies in recent years. To optimize operations in oil and gas production, a reservoir model is important for understanding the subsurface appropriately. Generally, sensor data, such as surface seismic data, are most popular data sources in modeling the reservoir with either a numerical simulation model or an Artificial Intelligence (AI)-based model. In this paper, to obtain data that describe the subsurface more exactly, information, including phrases that indicates possible bearing oil or gas and rock colors, is extracted from geology reports. Sentiments of the phrases is identified by sentiment analysis, and sentiment sequence over measured depths is then used to generate features. The rock-color similarities between wells are calculated as well, and integrated as distance metrics into a geology-based regression method. Extensive experiments on Bakken wells in the United States show the effectiveness of using the features extracted from geology reports and the rock colors in terms of estimating well production.
Isolation of intracellular membranes by means of sodium carbonate treatment: application to endoplasmic reticulum. (1982)

A rapid and simple method for the isolation of membranes from subcellular organelles is described. The procedure consists of diluting the organelles in ice-cold 100 mM Na2CO3 followed by centrifugation to pellet the membranes. Closed vesicles are converted to open membrane sheets, and content proteins and peripheral membrane proteins are released in soluble form. Here we document the method by applying it to various subfractions of a rat liver microsomal fraction, prepared by continuous density gradient centrifugation according to Beaufay et al. (1974, J. Cell Biol. 61:213-231). The results confirm and extend those of previous investigators on the distribution of enzymes and proteins among the membranes of the smooth and rough endoplasmic reticulum. In the accompanying paper (1982, J. Cell Biol. 93:103-110) the procedure is applied to peroxisomes and mitochondria.
<i>In vivo</i> continuous‐wave optical breast imaging enhanced with Indocyanine Green (2003)

We investigate the uptake of a nontargeted contrast agent by breast tumors using a continuous wave diffuse optical tomography apparatus. The instrument operates in the near-infrared spectral window and employs 16 sources and 16 detectors to collect light in parallel on the surface of the tumor-bearing breast (coronal geometry). In our protocol an extrinsic contrast agent, Indocyanine Green (ICG), was injected by bolus. Three clinical scenarios with three different pathologies were investigated. A two-compartment model was used to analyze the pharmacokinetics of ICG and preprocess the data, and diffuse optical tomography was used for imaging. Localization and delineation of the tumor was achieved in good agreement with a priori information. Moreover, different dynamical features were observed for differing pathologies. The malignant cases exhibited slower rate constants (uptake and outflow) compared to healthy tissue. These results provide further evidence that in vivo pharmacokinetics of ICG in breast tumors may be a useful diagnostic tool for differentiation of benign and malignant pathologies.
Ethane/ethylene separation in a metal-organic framework with iron-peroxo sites (2018)

The separation of ethane from its corresponding ethylene is an important, challenging, and energy-intensive process in the chemical industry. Here we report a microporous metal-organic framework, iron(III) peroxide 2,5-dioxido-1,4-benzenedicarboxylate [Fe<sub>2</sub>(O<sub>2</sub>)(dobdc) (dobdc<sup>4-</sup>: 2,5-dioxido-1,4-benzenedicarboxylate)], with iron (Fe)-peroxo sites for the preferential binding of ethane over ethylene and thus highly selective separation of C<sub>2</sub>H<sub>6</sub>/C<sub>2</sub>H<sub>4</sub> Neutron powder diffraction studies and theoretical calculations demonstrate the key role of Fe-peroxo sites for the recognition of ethane. The high performance of Fe<sub>2</sub>(O<sub>2</sub>)(dobdc) for the ethane/ethylene separation has been validated by gas sorption isotherms, ideal adsorbed solution theory calculations, and simulated and experimental breakthrough curves. Through a fixed-bed column packed with this porous material, polymer-grade ethylene (99.99% pure) can be straightforwardly produced from ethane/ethylene mixtures during the first adsorption cycle, demonstrating the potential of Fe<sub>2</sub>(O<sub>2</sub>)(dobdc) for this important industrial separation with a low energy cost under ambient conditions.
Excimer-laser-induced crystallization of hydrogenated amorphous silicon (1990)

The electronic transport properties and structural morphology of fast-pulse excimer-laser- crystallized hydrogenated amorphous silicon (a-Si:H) thin films have been measured. The room-temperature dark dc conductivities and Hall mobilities increase by several orders of magnitude at well-defined laser energy density thresholds which decrease as the impurity concentration in the films increases. The structural morphology of the films suggests an impurity-induced reduction of the a-Si:H melt temperature as the origin of this behavior.
CD34-Negative Hematopoietic Stem Cells Isolated from Human Peripheral Blood Cells as Ultimate Precursors of Hematopoietic Progenitors (1997)

<i>Background</i>: The earliest hematopoietic stem cell is still not yet identified. From experiments in dogs there is evidence that the earliest hematopoietic stem cell is a CD 34– fibroblast-like cell which can be isolated from bone marrow stromal cultures. In this set of experiments we wanted to identify such an early CD34– fibroblast4ike cell population from human peripheral blood. <i>Material and Methods</i>: Peripheral blood mononuclear cells (PBMNC) were isolated from healthy volunteer donors and incubated with interleukin-6(IL-6)-containing medium in tissue culture flasks. After establishing an almost confluent adherent layer of fibroblast4ike cells which attach to the plastic surface, the cells were stimulated with various growth factors. The emerging nonadherent cells as well as the adherent cells were applied to a colony-forming unit (CFU) assay in semisolid agar and to long-term culture-initiating cell (LTC-IC) assay. <i>Results:</i> CD34– adherently growing cells could be isolated from human peripheral blood by IL-6-mediated plastic adherence. These cells grow as fibroblast-like cells in culture and differentiation can be induced by stem cell factor (SCF), while IL-6 induces proliferation of these cells. While differentiating, CD34– fibroblast-like cells lose the ability to grow adherently and start to express CD34 and eventually HLA-DR. The differentiating CD34+ cells are also capable of producing CFU and LTC-IC. <i>Conclusion:</i> This set of experiments provides evidence that the earliest identifiable hematopoietic stem cell is a CD34– adherently growing fibroblast-like cell which is part of the marrow microenvironment in vivo and can differentiate into hematopoietic progenitors upon appropriate growth factor signaling. This kind of early stem cell can also be isolated from PBMNC.
High-mobility SiC MOSFET with low density of interface traps using high pressure microwave plasma oxidation* (2020)

The microwave plasma oxidation under the relatively high pressure (6 kPa) region is introduced into the fabrication process of SiO 2 /4H-SiC stack. By controlling the oxidation pressure, species, and temperature, the record low density of interface traps (∼ 4 × 10 10 cm −2 ⋅eV −1 @ E c − 0.2 eV) is demonstrated on SiO 2 /SiC stack formed by microwave plasma oxidation. And high quality SiO 2 with very flat interface (0.27-nm root-mean-square roughness) is obtained. High performance SiC metal–oxide–semiconductor field-effect transistors (MOSFETs) with peak field effect mobility of 44 cm −2 ⋅eV −1 is realized without additional treatment. These results show the potential of a high-pressure plasma oxidation step for improving the channel mobility in SiC MOSFETs.
The design of feedback shift registers and other synchronous counters (1969)

This paper is concerned with digital sub-systems comprising bistable flip-flops connected to a common source of clock-pulses. This configuration, of which the feedback shift register is the most important special case, is useful for the generation of periodic binary codes and sequences. It is assumed that the building-blocks for these circuits are integrated J-K flip-flops and NAND gates, and design techniques appropriate for this situation are described.
Crystal Structure of the Nuclear Matrix Targeting Signal of the Transcription Factor Acute Myelogenous Leukemia-1/Polyoma Enhancer-binding Protein 2αB/Core Binding Factor α2 (1999)

Transcription factors of the acute myelogenous leukemia (AML)/polyoma enhancer-binding protein (PEBP2alpha)/core-binding factor alpha (CBFA) class are key transactivators of tissue-specific genes of the hematopoietic and bone lineages. AML-1/PEBP2alphaB/CBFA2 proteins participating in transcription are associated with the nuclear matrix. This association is solely dependent on a highly conserved C-terminal protein segment, designated the nuclear matrix targeting signal (NMTS). The NMTS of AML-1 is physically distinct from the nuclear localization signal, operates autonomously, and supports transactivation. Our data indicate that the related AML-3 and AML-2 proteins are also targeted to the nuclear matrix in situ by analogous C-terminal domains. Here we report the first crystal structure of an NMTS in an AML-1 segment fused to glutathione S-transferase. The model of the NMTS consists of two loops connected by a flexible U-shaped peptide chain.
KNIME: The Konstanz Information Miner (2006)

Abstract. The Konstanz Information Miner is a modular environment, which en-ables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the de-sign aspects of the underlying architecture and briefly sketch how new nodes can be incorporated. 1
Surface nuclear magnetic relaxation and dynamics of water and oil in macroporous media (2001)

Proton nuclear spin-relaxation studies on water- or oil-saturated granular packings and limestone rocks allow estimating surface molecular dynamical parameters. Measurements were performed at various conditions of temperature, magnetic field strengths, and pore size. We show by low field NMR relaxation that changing the amount of surface paramagnetic impurities leads to striking different pore-size dependences of the relaxation times T1 and T2 of liquids in pores. These dependences are well supported by surface-limited or diffusion-limited relaxation models. Surface relaxivity parameters rho(1) and rho(2) are deduced from the pore-size dependence in the surface-limited regime. We evidence the frequency and temperature dependence of the surface relaxivity rho(1) by field cycling NMR relaxation and relevant theoretical models. The typical frequency dependence found allows an experimental separation of the surface and bulk microdynamics in porous media. Several surface dynamical parameters, such as diffusion coefficients, activation energies, time of residence, and coefficient of surface affinity, were therefore determined. The methods presented here give a powerful analysis of the surface microdynamics of confined liquids, which can be applied to the study of oil-bearing rocks.
Novel binder system for ultraviolet‐curable coatings based on tobacco seed (<i>Nicotiana rustica</i>) oil derivatives as a renewable resource (2007)

Abstract Several coatings have been developed to reduce volatile organic component emissions, such as water‐borne coatings, high‐solid coatings, powder coatings, and radiation‐curable coatings. Ultraviolet‐curable coatings are one such boon to paint industries, not only reducing volatile organic components but also increasing productivity. Most polymers industrially produced nowadays are based on petroleum, which is a limited resource. Developing new procedures for making polymers based on natural renewable resources is a resounding theme for this decade and the future also. In response to both these needs, we have investigated the use of tobacco seed ( Nicotiana rustica ) oil in the synthesis of radiation‐curable coatings. In this work, the alcoholysis of oil in various ratios with polyhydroxyl compounds was performed to prepare novel polyols, and these different polyols were reacted further with excess polyisocyanate to produce isocyanate‐terminated prepolymers. The prepolymer were further reacted with hydroxyethyl methacrylate to produce urethane acrylate oligomers. The radiation‐curable coating compositions were than prepared by the mixing of these oligomers with different reactive diluents, photoinitiators, and activators. These coating compositions were studied for their various physical and film characteristics, and certain coating compositions from tobacco seed oil were found to show very excellent overall coating properties. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Restriction Enzymes as a Target for DNA-Based Sensing and Structural Rearrangement (2018)

DNA nanostructures have been shown viable for the creation of complex logic-enabled sensing motifs. To date, most of these types of devices have been limited to the interaction with strictly DNA-type inputs. Restriction endonuclease represents a class of enzyme with endogenous specificity to DNA, and we hypothesize that these can be integrated with a DNA structure for use as inputs to trigger structural transformation and structural rearrangement. In this work, we reconfigured a three-arm DNA switch, which utilizes a cyclic Förster resonance energy transfer interaction between three dyes to produce complex output for the detection of three separate input regions to respond to restriction endonucleases, and investigated the efficacy of the enzyme targets. We demonstrate the ability to use three enzymes in one switch with no nonspecific interaction between cleavage sites. Further, we show that the enzymatic digestion can be harnessed to expose an active toehold into the DNA structure, allowing for single-pot addition of a small oligo in solution.
Near-optimal Nonmyopic Value of Information in Graphical Models (2012)

A fundamental issue in real-world systems, such as sensor networks, is the selection of observations which most effectively reduce uncertainty. More specifically, we address the long standing problem of nonmyopically selecting the most informative subset of variables in a graphical model. We present the first efficient randomized algorithm providing a constant factor (1-1/e-epsilon) approximation guarantee for any epsilon > 0 with high confidence. The algorithm leverages the theory of submodular functions, in combination with a polynomial bound on sample complexity. We furthermore prove that no polynomial time algorithm can provide a constant factor approximation better than (1 - 1/e) unless P = NP. Finally, we provide extensive evidence of the effectiveness of our method on two complex real-world datasets.
Frontiers and Opportunities in Chemoenzymatic Synthesis (2010)

Natural product biosynthetic pathways have evolved enzymes with myriad activities that represent an expansive array of chemical transformations for constructing secondary metabolites. Recently, harnessing the biosynthetic potential of these enzymes through chemoenzymatic synthesis has provided a powerful tool that often rivals the most sophisticated methodologies in modern synthetic chemistry and provides new opportunities for accessing chemical diversity. Herein, we describe our research efforts with enzymes from a broad collection of biosynthetic systems, highlighting recent progress in this exciting field.
Distillation columns containing structured packing (1990)

Presentation de methodes pour l'evaluation et la prediction de la capacite d'engorgement, de la perte de charge et du transfert de masse dans les lits a garnissage structure. Etude limitee aux geometries d'elements metalliques ondules tels que Intalox, Gempak, Flexipac, Mellapak, Sulzer et Montz
Simulation of Diffraction Intensity Distribution of a Superconductor Containing Stacking Faults in the Bi-Sr-Ca-Cu-O System (1988)

A superconducting material with a T c ∼110 K in the Bi-Sr-Ca-Cu-O system is liable to contain stacking faults as suggested by the broadened diffraction. The diffraction intensity is simulated by applying the matrix method based on assumed models of stacking faults. The calculated intensity distributions explain the features of the observed powder X-ray diffraction patterns of the high- T c specimens.
Reproductive Hormones, Aging, and Sleep (1999)

Insomnia, disturbed sleep, and fatigue are among the most frequent health complaints of perimenopausal women. Estrogen replacement therapy (ERT) usually improves sleep, most likely by alleviating vasomotor symptoms. However, sleep difficulties are not restricted to the perimenopausal period. Older postmenopausal women typically experience longer latencies to sleep onset, increased nocturnal waking, increased fragmentation of sleep, and less slow wave (deep) sleep. These sleep changes in older women may be partially related to the postmenopausal profile of sex steroid hormones. Estrogen has powerful effects on several biological factors that directly influence sleep, including body temperature regulation, circadian rhythms, and stress reactivity. The link between sleep disturbance in older women and these CNS effects of estrogen is largely speculative at present. This article reviews what is known, what remains to be addressed, and some clinical implications.
Interactive Medical Image Segmentation Using PDE Control of Active Contours (2013)

Segmentation of injured or unusual anatomic structures in medical imagery is a problem that has continued to elude fully automated solutions. In this paper, the goal of easy-to-use and consistent interactive segmentation is transformed into a control synthesis problem. A nominal level set partial differential equation (PDE) is assumed to be given; this open-loop system achieves correct segmentation under ideal conditions, but does not agree with a human expert's ideal boundary for real image data. Perturbing the state and dynamics of a level set PDE via the accumulated user input and an observer-like system leads to desirable closed-loop behavior. The input structure is designed such that a user can stabilize the boundary in some desired state without needing to understand any mathematical parameters. Effectiveness of the technique is illustrated with applications to the challenging segmentations of a patellar tendon in magnetic resonance and a shattered femur in computed tomography.
A hierarchical image clustering cosegmentation framework (2012)

Given the knowledge that the same or similar objects appear in a set of images, our goal is to simultaneously segment that object from the set of images. To solve this problem, known as the cosegmentation problem, we present a method based upon hierarchical clustering. Our framework first eliminates intra-class heterogeneity in a dataset by clustering similar images together into smaller groups. Then, from each image, our method extracts multiple levels of segmentation and creates connections between regions (e.g. superpixel) across levels to establish intra-image multi-scale constraints. Next we take advantage of the information available from other images in our group. We design and present an efficient method to create inter-image relationships, e.g. connections between image regions from one image to all other images in an image cluster. Given the intra & inter-image connections, we perform a segmentation of the group of images into foreground and background regions. Finally, we compare our segmentation accuracy to several other state-of-the-art segmentation methods on standard datasets, and also demonstrate the robustness of our method on real world data.
1-H MRS changes in dorsolateral prefrontal cortex after donepezil treatment in patients with mild to moderate Alzheimer's disease. (2011)

Magnetic resonance spectroscopy (MRS) noninvasively provides information on the concentration of some cerebral metabolites in vivo. Among those measurable by proton magnetic resonance spectroscopy (1H-MRS), N-acetyl-aspartate (NAA) is decreased, and myo-inositol (ml) and choline (Cho) levels are increased in patients with Alzheimer's disease (AD). Donepezil, an acetylcholinesteraze inhibitor, has proven effect on cognitive symptoms in patients with AD. In previous studies, treatment response was associated with an increase of NAA and NAA/Cr in the parietal lobe and hippocampi. Correlation of longitudinal changes of 1H-MRS detectable metabolites in dorsolateral prefrontal cortex (DLPFC) with clinically observable changes is a poorly researched topic. The objective of this non-interventional study is to assess whether changes in 1H-MRS measurable metabolites correlate with clinical outcome after donepezil treatment. Twelve patients with mild to moderate AD were evaluated during 26 weeks of donepezil treatment. 1H-MRS parameters in DLPFC were assessed before and after 26 weeks of donepezil treatment. Cognition was assessed with Alzheimer's Disease Assessment Scale cognitive subscale (ADAS-Cog). A significant increase in NAA/Cr ratio and significantly lower decrease in mI/Cr ratio were found in AD patients with positive treatment response. The results of this study indicate possible modest donepezil effect on prevention of neuronal functional deterioration in DLPFC which correlates with clinical outcome and point the use of 1HMRS as technique of help in assessment of drug effect.
Rethinking 'multi-user' (2011)

Multi-touch tabletops have been much heralded as an innovative technology that can facilitate new ways of group working. However, there is little evidence of these materialising outside of research lab settings. We present the findings of a 5-week in-the-wild study examining how a shared planning application - designed to run on a walk-up-and-use tabletop - was used when placed in a tourist information centre. We describe how groups approached, congregated and interacted with it and the social interactions that took place - noting how they were quite different from research findings describing the ways groups work around a tabletop in lab settings. We discuss the implications of such situated group work for designing collaborative tabletop applications for use in public settings.