gebhart/patrepeval huggingface dataset:
Production of nanoparticles using organisms (2009)

Recent developments in the biosynthesis of nanomaterials have demonstrated the important role of biological systems and microorganisms in nanoscience and nanotechnology. These organisms show a unique potential in environmentally friendly production and accumulation of nanoparticles with different shapes and sizes. Therefore, researchers in the field of nanoparticle synthesis are focusing their attention to biological systems. In order to obtain different applied chemical compositions, controlled monodispersity, desired morphologies (e.g., amorphous, spherical, needles, crystalline, triangular, and hexagonal), and interested particle size, they have investigated the biological mechanism and enzymatic process of nanoparticle production. In this review, most of these organisms used in nanoparticle synthesis are shown.
How do Data Science Workers Collaborate? Roles, Workflows, and Tools (2020)

Today, the prominence of data science within organizations has given rise to teams of data science workers collaborating on extracting insights from data, as opposed to individual data scientists working alone. However, we still lack a deep understanding of how data science workers collaborate in practice. In this work, we conducted an online survey with 183 participants who work in various aspects of data science. We focused on their reported interactions with each other (e.g., managers with engineers) and with different tools (e.g., Jupyter Notebook). We found that data science teams are extremely collaborative and work with a variety of stakeholders and tools during the six common steps of a data science workflow (e.g., clean data and train model). We also found that the collaborative practices workers employ, such as documentation, vary according to the kinds of tools they use. Based on these findings, we discuss design implications for supporting data science team collaborations and future research directions.
N-Acylethanolamine Signaling in Tobacco Is Mediated by a Membrane-Associated, High-Affinity Binding Protein (2003)

N-Acylethanolamines (NAEs) are fatty acid derivatives found as minor constituents of animal and plant tissues, and their levels increase 10- to 50-fold in tobacco (Nicotiana tabacum) leaves treated with fungal elicitors. Infiltration of tobacco leaves with submicromolar to micromolar concentrations of N-myristoylethanolamine (NAE 14:0) resulted in an increase in relative phenylalanine ammonia-lyase (PAL) transcript abundance within 8 h after infiltration, and this PAL activation was reduced after co-infiltration with cannabinoid receptor antagonists (AM 281 and SR 144528). A saturable, high-affinity specific binding activity for [(3)H]NAE 14:0 was identified in suspension-cultured tobacco cells and in microsomes from tobacco leaves (apparent K(d) of 74 and 35 nM, respectively); cannabinoid receptor antagonists reduced or eliminated specific [(3)H]NAE 14:0 binding, consistent with the physiological response. N-Oleoylethanolamine activated PAL2 expression in leaves and diminished [(3)H]NAE 14:0 binding in microsomes, whereas N-linoleoylethanolamine did not activate PAL2 expression in leaves, and did not affect [(3)H]NAE 14:0 binding in microsomes. The nonionic detergent dodecylmaltoside solubilized functional [(3)H]NAE 14:0-binding activity from tobacco microsomal membranes. The dodecylmaltoside-solubilized NAE-binding activity retained similar, but not identical, binding properties to the NAE-binding protein(s) in intact tobacco microsomes. Additionally, high-affinity saturable NAE-binding proteins were identified in microsomes isolated from Arabidopsis and Medicago truncatula tissues, indicating the general prevalence of these binding proteins in plant membranes. We propose that plants possess an NAE-signaling pathway with functional similarities to the "endocannabinoid" pathway of animal systems and that this pathway, in part, participates in xylanase elicitor perception in tobacco.
A necessary and sufficient condition for quantization errors to be uniform and white (1977)

In this paper, a necessary and sufficient condition is given to model the output of a quantizer as an infinite-precision input and an additive, uniform, white noise. The statistical properties of the quantization error are studied, and a detailed analysis for Gaussian distributed inputs is given.
Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing (2012)

Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis.
Calories and gastric emptying: a regulatory capacity with implications for feeding (1979)

Gastric emptying in four unanesthetized male Macaca mulatta was studied with the serial test meal method of Hunt and Spurrell. Liquid meals were infused into the stomach through a chronic indwelling Silastic cannula. Saline meals empty rapidly and exponentially. Doubling the volume of saline from 150 to 300 ml increased the emptying rate so that the half-life remained unchanged (15 min). The 150-ml glucose meals (0.05, 0.125, and 0.25 g/ml) emptied more slowly than saline, progressively more slowly with increasing concentrations (0.05--1.8, 0.125--0.78, and 0.25--0.37 ml/min) and linearly through most of their course. Doubling the volume of 0.125 g/ml-glucose meal did not change the rate of emptying. Converting grams of glucose to their caloric content, the emptying rate in kcal/min becomes constant (approx 0.4 kcal/min) in this range of concentrations. Isocaloric casein hydrolysate and medium-chain triglyceride oil meals at 0.5 kcal/ml empty at the same rate as glucose. The precision of this regulation is sufficient to give it a role in preabsorptive satiety and the control of caloric intake.
Photochromism of Salicylidene Aniline (1968)

Photochromic properties of two crystalline forms of salicylidene aniline have been investigated, emphasizing properties not previously evaluated. A broad band with maximum absorbance at 480 mmu is induced by near uv radiation; 380 mmu is most effective. Occurring spontaneously, the reverse change is accelerated by visible radiation; 480 mmu is most effective. The two crystalline forms require similar energy for inducing the 480-mmu band, but differ markedly in energy for the reverse change and in the kinetics of spontaneous fading. For thin films, maximum absorbance change divided by thickness is about 0.5mu(-1). The compound resists fatigue excellently when cycled by radiation most effective for photochromic changes.
Molecular Mechanisms of TRPV4‐Mediated Neural Signaling (2008)

In signal transduction of metazoan cells, ion channels of the family of transient receptor potential (TRP) have been identified to respond to diverse external and internal stimuli, among them osmotic stimuli. This review highlights a specific member of the TRPV subfamily, the TRPV4 channel, initially named vanilloid-receptor related osmotically activated channel (VR-OAC) or OTRPC4. In a striking example of evolutionary conservation of function, mammalian TRPV4 has been found to rescue osmo- and mechanosensory deficits of the TRPV mutant strain osm-9 in Caenorhabditis elegans. This is an astounding finding given the <26% orthology between OSM-9 and TRPV4 proteins. Here, recent findings pertaining to TRPV4's mechano- and osmosensory function in endothelia, in the alveolar unit of the lung, and in intestinal sensory innervation are reviewed, namely, transduction of mechanical shear stress in endothelia, maintenance of alveolar integrity on the endothelial side, and intestinal mechanosensation of noxious stimuli by dorsal root ganglion sensory neurons, which can be potently sensitized to mechanical stimuli by activation of the proteinase-activated receptor 2 (PAR-2), in a strictly TRPV4-dependent manner.
The Dialectic of Bottom-up and Top-down Emergence in Social Systems (1970)

In this paper we will present a theoretical explanation of the relationship between so-called individual emergence and the emergence of social systems. We want to take as our point of departure the assumption that from the perspective of hierarchical systems theory self-organization on the level of social systems includes a bottom-up process as well as a top-down process. The bottom-up process refers to what in sociology is called agency, the top-down process refers to what is called structure. We will show that it is convenient to suggest that these processes be linked in a dialectical manner. In this respect we will discuss problems of determinism and indeterminism. This is the background against which we will try to clarify the notion of individual emergence. Our rather general considerations will be illustrated by how ideology, that is consciousness in a collective as well as an individual sense, is conceived of by a number of theories and how it should be conceived of when aspects of self-organization are included. We will conclude with a statement that makes clear why consciousness is a property of individuals that emerges only when individuals participate in society and why society emerges only when individuals are endowed with consciousness.
Elk Basin Madison heterogeneity--its influence on performance (1968)

The 920-ft thick Madison limestone of Mississippian is one of the 7 producing horizons in the Elk Basin field, located on the Wyoming-Montana border near Yellowstone Park. Full section coring, done nearly 20 yr after the horizon was discovered and after more than 65,000,000 bbl oil had been produced, has shown the reservoir rock to be distorted highly by ground-water erosion, solution, and remineralization that took place at the end of Mississippian deposition. Geologic interpretation of the new data has helped to define reservoir discontinuities and to explain anomalies previously noted in reservoir performance, and has provided a better basis for analyzing current performance. An improved understanding of reservoir heterogeneity led to a development drilling program which has increased production from 16,000 bopd to a peak rate of 24,600 bopd. Waterflood efficiency also has been improved by adjusting injection water distribution to account for difference is subzone performance and for discontinuities.
Orosomucoid 1 Attenuates Doxorubicin‐Induced Oxidative Stress and Apoptosis in Cardiomyocytes via Nrf2 Signaling (2020)

Doxorubicin (DOX) is an effective anticancer drug, but its therapeutic use is limited by its cardiotoxicity. The principal mechanisms of DOX-induced cardiotoxicity are oxidative stress and apoptosis in cardiomyocytes. Orosomucoid 1 (ORM1), an acute-phase protein, plays important roles in inflammation and ischemic stroke; however, the roles and mechanisms of ORM1 in DOX-induced cardiotoxicity remain unknown. Therefore, in the present study, we aimed to investigate the function of ORM1 in cardiomyocytes experiencing DOX-induced oxidative stress and apoptosis. A DOX-induced cardiotoxicity animal model was established in C57BL/6 mice by administering an intraperitoneal injection of DOX (20 mg/kg), and the control group was intraperitoneally injected with the same volume of sterilized saline. The effects were assessed after 7 d. Additionally, H9c2 cells were stimulated with DOX (10 <i>μ</i>M) for 24 h. The results showed decreased ORM1 and increased oxidative stress and apoptosis after DOX stimulation in vivo and in vitro. ORM1 overexpression significantly reduced DOX-induced oxidative stress and apoptosis in H9c2 cells. ORM1 significantly increased the expression of nuclear factor-like 2 (Nrf2) and its downstream protein heme oxygenase 1 (HO-1) and reduced the expression of the lipid peroxidation end product 4-hydroxynonenal (4-HNE) and the level of cleaved caspase-3. In addition, Nrf2 silencing reversed the effects of ORM1 on DOX-induced oxidative stress and apoptosis in cardiomyocytes. In conclusion, ORM1 inhibited DOX-induced oxidative stress and apoptosis in cardiomyocytes by regulating the Nrf2/HO-1 pathway, which might provide a new treatment strategy for DOX-induced cardiotoxicity.
An XML-based system for management and query of video databases with user identifiable and annotated scenes (2014)

Video is one type of document. However, unlike traditional documents and databases that are searchable, video is not. At the same time, video is typically lengthy and contains large amount of useful and/or useless information. Therefore, it is desired to make the video manageable and searchable. Metadata and scene annotation are two keys to resolve this challenge. In this thesis we designed and implemented an XML-based Movie Database Manager (MDM) as a proof of concept. The video information is well organized in its natural way and stored in one single XML file. Videos are divided into user defined scenes with annotations for quick and exact query with build-in query engine. Users can also create, edit, and delete scenes annotations without physically split them in the video files. MDM integrates the query builder to help users run pre-defined queries or create and maintain their own ones. These queries can be stored in the same XML file. A full functional video player is also implemented to help user play their query results, create / edit / delete scene annotations.
Social presence and e-commerce B2B chat functions (2020)

Purpose Currently, online chat is in common use in e-commerce. By adding social interaction to the online context, companies hope to increase customers’ purchasing intentions. However, previous studies have not investigated how social presence is embedded in online business-to-business (B2B) chat conversations between buyers and sellers. Moreover, the functions of online chat in B2B sales have not been investigated. Design/methodology/approach The data was collected at a case company over the course of four years, from which the authors analyzed 157 online chat conversations between buyers ( n = 157) and sellers ( n = 9) with a theory-driven thematic analysis. In addition, data from the company’s customer relationship management system was collected to specify buyer types. Findings The results reveal that social presence was embedded in online B2B chat via buyers’ interactive, affective and relationship maintenance responses. Social presence differed depending on the type of buyer, with only existing customers having relationship maintenance responses. E-commerce B2B chat functions can be described as multiple and changing depending on the buyer–seller relationship stage. Research limitations/implications Having data only from one case company limits the results to one type of industry. Practical implications The results can be used in sales training and when developing online chat services. Originality/value Results bring scientific utility to B2B sales and marketing research, as the authors build a bridge between social presence, the existing theoretical model on B2B buyer–seller relationship development and online chat as a communication medium. Other researchers may use this understanding when exploring B2B buyer–seller interaction in different digitalized communication media.
Adsorption characteristics of certain antibiotics to veegum and activated charcoal. (1984)

Adsorption of streptomycin sulphate and neomycin sulphate to veegum and activated charcoal in water or buffered solution was studied. Both antibiotics demonstrated a significant reduction in their activity, particularly in water. The activity of streptomycin sulphate decreased in the following order: veegum in water greater than activated charcoal in water greater than veegum in buffer greater than activated charcoal in buffer and their calculated adsorption coefficients were 111 X 10(-3), 57 X 10(-3), 33 X 10(-3) and 25 X 10(-3) (respectively), while neomycin sulphate was affected in the following decreasing order: activated charcoal in water greater than activated charcoal in buffer greater than veegum in water greater than veegum in buffer. The calculated adsorption coefficients were 64 X 10(-3), 47 X 10(-3), 34 X 10(-3) and 26 X 10(-3) (respectively). The mechanism of adsorption was discussed.
Designing Constructed Wetlands for Nitrogen Removal (1994)

Many constructed wetlands adequately treat BOD5, TSS, and bacteria. However, a review of nitrogen (N) data from 52 constructed and natural wetlands in the North American data base confirmed that N removal was variable. Nitrification and denitrification require aerobic and anaerobic conditions. This paper presents case histories of systems that use alternating shallow and deep water zones to create both environments. Regression analysis of N removal and N loadings in 18 shallow-deep water systems suggested that NH4+ loading (kg N/ha/day) could be used to predict effluent NH4+ values. Combinations of shallow water-emergent vegetation and deep water-submergent vegetation with low NH4+ (and TKN) loading rates can produce very low levels of discharged NH4+.
Protein <i>O</i> -fucosyltransferase 1 is an essential component of Notch signaling pathways (2003)

Notch receptor signaling regulates cell growth and differentiation, and core components of Notch signaling pathways are conserved from Drosophila to humans. Fringe glycosyltransferases are crucial modulators of Notch signaling that act on epidermal growth factor (EGF)-like repeats in the Notch receptor extracellular domain. The substrate of Fringe is EGF-O-fucose and the transfer of fucose to Notch by protein O-fucosyltransferase 1 is necessary for Fringe to function. O-fucose also occurs on Cripto and on Notch ligands. Here we show that mouse embryos lacking protein O-fucosyltransferase 1 die at midgestation with severe defects in somitogenesis, vasculogenesis, cardiogenesis, and neurogenesis. The phenotype is similar to that of embryos lacking downstream effectors of all Notch signaling pathways such as presenilins or RBP-J kappa, and is different from Cripto, Notch receptor, Notch ligand, or Fringe null phenotypes. Protein O-fucosyltransferase 1 is therefore an essential core member of Notch signaling pathways in mammals.
Clostero virus‐Like Particles of Two Types Associated with Diseased Grapevines (1984)

Abstract Previous work led to the characterization of, and the production of an antiserum to a closterovirus referred to as grapevine stem pitting‐associated virus (GSP‐AV). Using this antiserum and immunoelectron microscopy, we now show that GSP‐AV is widespread in grapevines and that a second serologically distinct closterovirus‐like particle is also widely present. One or both of the closterovirus‐like particles were often but not always associated with leafroll symptoms. However, some plants indexed as suffering from stem pitting also contained one or both of the particles. As “grapevine stem pitting‐associated virus” no longer seems appropriate as a name, we suggest changing it to grapevine virus A (GVA). We provisionally refer to the second closterovirus‐like virus as grapevine virus B (GVB).
[Senile amyloidosis of the eye as a manifestation of senile cerebral amyloidosis]. (1993)

Senile amyloidosis affects brain vessels and meninges, eye vessels and extraocular structures, and appears during the 6th decade of the life. Its, incidence in patients with senile or presenile dementia and senile plaques is higher than in patients having only senile plaques (the data are based on the examination of 165 patients who died at psychiatric clinics and charitable institutions for old people in Volgograd from 1987 to 1992.
RELATION BETWEEN INELASTIC DEFORMABILITY AND THERMAL EXPANSION OF GLASS IN ITS ANNEALING RANGE* (1946)

A bstract In accordance with experience concerning the behavior of glass at temperatures within its annealing range, an equation is proposed which relates the various extraordinary heat effects to the inelastic deformability and to the degree of superheating or undercooling. By using this equation in connection with the thermal‐expansion curves of a glass within its annealing range, certain constants that are related to the coefficient of viscosity and its changes with temperature and the degree of superheating or undercooling have been determined with reasonable results. Such results make it possible to estimate the inelastic deformability of a glass in its various conditions at all annealing temperatures and are therefore valuable in connection with problems that are encountered in the process of annealing glass. The apparent success achieved in applying the proposed equation to experimental data suggests that the concepts underlying this equation are fundamental and must be considered in any theory concerning the constitution of glass or that of any other extremely viscous liquid.
Evidence for redox regulation of the transcription factor NtcA, acting both as an activator and a repressor, in the cyanobacterium Anabaena PCC 7120 (1997)

NtcA has been identified as a nitrogen-responsive regulatory protein required for nitrogen assimilation and heterocyst differentiation in cyanobacteria. It is proposed that NtcA functions through the formation of DNA-protein complexes with its specific target sequence within the promoter regions of the regulated genes. In vitro, NtcA of Anabaena PCC 7120 binds to upstream regions of the genes whose products are involved in nitrogen assimilation, but also to the upstream region of rbcLS (carbon-fixation gene), xisA (encoding a site-specific recombinase expressed during heterocyst differentiation) and ntcA (encoding NtcA itself). However, the mechanism by which NtcA serves as a critical regulator for such diverse processes is not understood. With the use of electrophoretic mobility shift assays, NtcA from Anabaena PCC 7120 was here shown to interact with the promoter sequence of the gor gene, encoding glutathione reductase, thereby providing a novel example of NtcA's acting as a repressor, previously found only for the rbcLS gene. Furthermore we demonstrate that the binding of DNA by NtcA is regulated in vitro by a redox-dependent mechanism involving cysteine residues of the NtcA protein. These findings suggest that NtcA is a transcriptional regulator that responds not only to the nitrogen status but also to the cellular redox status, a function that might be particularly significant during heterocyst differentiation.