gebhart/patrepeval huggingface dataset:
A Functional Model of Sensemaking in a Neurocognitive Architecture (2013)

Sensemaking is the active process of constructing a meaningful representation (i.e., making sense) of some complex aspect of the world. In relation to intelligence analysis, sensemaking is the act of finding and interpreting relevant facts amongst the sea of incoming reports, images, and intelligence. We present a cognitive model of core information-foraging and hypothesis-updating sensemaking processes applied to complex spatial probability estimation and decision-making tasks. While the model was developed in a hybrid symbolic-statistical cognitive architecture, its correspondence to neural frameworks in terms of both structure and mechanisms provided a direct bridge between rational and neural levels of description. Compared against data from two participant groups, the model correctly predicted both the presence and degree of four biases: confirmation, anchoring and adjustment, representativeness, and probability matching. It also favorably predicted human performance in generating probability distributions across categories, assigning resources based on these distributions, and selecting relevant features given a prior probability distribution. This model provides a constrained theoretical framework describing cognitive biases as arising from three interacting factors: the structure of the task environment, the mechanisms and limitations of the cognitive architecture, and the use of strategies to adapt to the dual constraints of cognition and the environment.
Current Scaling in Aligned Carbon Nanotube Array Transistors With Local Bottom Gating (2010)

A local-bottom-gate (LBG) configuration is introduced for carbon nanotube array field-effect transistors (FETs) (CNTFETs). CNTFETs from highly aligned nanotubes are demonstrated and exhibit the best performance to date, with current density > 40 μA/μm (with no metallic nanotubes), inverse subthreshold slope of 70 mV/decade, and on/off -current ratio > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . Additionally, on-current from LBG-CNTFETs is shown to scale linearly with the number of nanotube channels. These advancements in device geometry and performance provide a new platform for further progress to be made toward high-performance FETs from aligned nanotubes.
Differentially induced expression of C-type lectins in activated lymphocytes (2001)

The human NK gene complex encodes for the leucocyte C-type lectins, CD69, AICL (activation-induced C-type lectin), LLT1 (lectin-like transcript), CD161/NKR-P1A, CD94, and for NKG-2 molecules. These gene products have been implicated in the regulation of the function of natural killer (NK) cells and other lymphocytes. In this study the expression of C-type lectins during the early activation of PMA-stimulated peripheral blood lymphocytes was examined. To investigate the influence of de novo protein synthesis on activation-dependent expression of C-type lectins, cells were cultured in presence of cycloheximide (CHX) and mRNA levels were analyzed by semi-quantitative reverse transcription-polymerase chain reaction. Upregulated levels of CD69, AICL, and LLT1, but less pronounced changes of CD161/NKR-P1A and CD94 mRNA were found at early time points of cellular activation. CD69 was superinduced by CHX at the nuclear precursor transcript and the mRNA level suggesting that regulation of transcriptional activity and mRNA stability contribute to extent of CD69 mRNA accumulation. CHX treatment resulted also in an overexpression of AICL, LLT1, and CD161/NKR-P1A mRNAs. Conversely, CHX blocked CD94 mRNA expression in PMA-stimulated cells, demonstrating that this process is dependent on new protein synthesis. Expression kinetics in context with susceptibility to CHX indicate that the mechanisms responsible for upregulated CD69, AICL, and LLT1 expression are distinct from those which control CD161/NKR-P1A or CD94 expression. J. Cell. Biochem. Suppl. 36: 201-208, 2001.
C-cell hyperplasia. An ultrastructural analysis. (1977)

The C-cell is the source of the hypocalcemic polypeptide hormone, calcitonin. Sequential increments in calcitonin response to provocative calcium and pentagastrin infusions have been used to identify family members at high risk for the development of medullary thyroid carcinoma, a neoplasm of C-cell origin. Correlative light microscopic and immunohistochemical studies have permitted the identification of a spectrum of C-cell proliferative abnormalities ranging from C-cell hyperplasia (CCH) to invasive medullary thyroid carcinoma. Ultrastructurally, both normal and hyperplastic C-cells occupied an intrafolliculat localization, being separated from the interstitium by the follicular basal lamina and from the luminal colloid by extensions of the follicular cell cytoplasm. These relationships were maintained in areas of advanced hyperplasia where C-cells often completely encircled and displaced the follicular epithelium. Nodular CCH was characterized by the complete obliteration of the follicular space by C-cells. In these areas, prominent reduplications as well as occasional defects in the basal lamina were noted. Some of the solid C-cell nodules adjacent to areas of medullary thyroid carcinoma appeared to form by gradual replacement of follicles by C-cells and did not represent sites of intrathyroidal vascular or lymphatic extension. Two major cell types were noted in cases of CCH. One cell type which was filled with secretory granules measureing 280 nm. in diameter (type I) predominated in areas of diffuse CCH and was also found in control thyroid glands. The larger number of secretory granules in this cell type together with the relative lack of development of granular endoplasmic reticulum and Golgi regions suggested that these cells were in the storage phase of their secretory cycle. The second cell type had fewer secretory granules, which measured 130 nm. in diameter (type II), and was characteristically located in areas of nodular CCH. Type II granules were found in cells with cytologic evidence of active protein synthesis and secretion. Variations in granule morphology and cell ultrastructure may be correlated with functional variations in C-cell populations.
Association of Wilms's Tumor with Aniridia, Hemihypertrophy and Other Congenital Malformations (1964)

WHEN, through epidemiologic study of persons or families, diseases are found to be associated, the opportunities for determining their etiology may be very much increased. The association of leukemia and mongolism1 is an example. An accumulation of case reports in the past decade suggests a link between another childhood cancer, Wilms's tumor, and a rare congenital defect, total hemihypertrophy.2 3 4 5 6 7 8 In addition, isolated cases of Wilms's tumor in horseshoe kidneys have been reported.9 The purpose of this presentation is to define more fully the relation between Wilms's tumor and congenital defects by study of the diagnoses contained in the medical records . . .
The Pfam protein families database (2003)

Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
Pediatric Sepsis Biomarker Risk Model-II: Redefining the Pediatric Sepsis Biomarker Risk Model With Septic Shock Phenotype (2016)

Testing PERSEVERE in the context of septic shock phenotypes prompted a revision incorporating platelet count. PERSEVERE-II performs well upon testing, independent of TAMOF or MOF status. PERSEVERE-II could potentially serve as a prognostic enrichment tool.
Stiffness-Activated GEF-H1 Expression Exacerbates LPS-Induced Lung Inflammation (2014)

Acute lung injury (ALI) is accompanied by decreased lung compliance. However, a role of tissue mechanics in modulation of inflammation remains unclear. We hypothesized that bacterial lipopolysacharide (LPS) stimulates extracellular matrix (ECM) production and vascular stiffening leading to stiffness-dependent exacerbation of endothelial cell (EC) inflammatory activation and lung barrier dysfunction. Expression of GEF-H1, ICAM-1, VCAM-1, ECM proteins fibronectin and collagen, lysyl oxidase (LOX) activity, interleukin-8 and activation of Rho signaling were analyzed in lung samples and pulmonary EC grown on soft (1.5 or 2.8 kPa) and stiff (40 kPa) substrates. LPS induced EC inflammatory activation accompanied by expression of ECM proteins, increase in LOX activity, and activation of Rho signaling. These effects were augmented in EC grown on stiff substrate. Stiffness-dependent enhancement of inflammation was associated with increased expression of Rho activator, GEF-H1. Inhibition of ECM crosslinking and stiffening by LOX suppression reduced EC inflammatory activation and GEF-H1 expression in response to LPS. In vivo, LOX inhibition attenuated LPS-induced expression of GEF-H1 and lung dysfunction. These findings present a novel mechanism of stiffness-dependent exacerbation of vascular inflammation and escalation of ALI via stimulation of GEF-H1-Rho pathway. This pathway represents a fundamental mechanism of positive feedback regulation of inflammation.
Processing seismic ambient noise data to obtain reliable broad-band surface wave dispersion measurements (2007)

Ambient noise tomography is a rapidly emerging field of seismological research. This paper presents the current status of ambient noise data processing as it has developed over the past several years and is intended to explain and justify this development through salient examples. The ambient noise data processing procedure divides into four principal phases: (1) single station data preparation, (2) cross-correlation and temporal stacking, (3) measurement of dispersion curves (performed with frequency—time analysis for both group and phase speeds) and (4) quality control, including error analysis and selection of the acceptable measurements. The procedures that are described herein have been designed not only to deliver reliable measurements, but to be flexible, applicable to a wide variety of observational settings, as well as being fully automated. For an automated data processing procedure, data quality control measures are particularly important to identify and reject bad measurements and compute quality assurance statistics for the accepted measurements. The principal metric on which to base a judgment of quality is stability, the robustness of the measurement to perturbations in the conditions under which it is obtained. Temporal repeatability, in particular, is a significant indicator of reliability and is elevated to a high position in our assessment, as we equate seasonal repeatability with measurement uncertainty. Proxy curves relating observed signal-to-noise ratios to average measurement uncertainties show promise to provide useful expected measurement error estimates in the absence of the long time-series needed for temporal subsetting.
[Influence of indole-3-alkanecarboxylic acids on glucose utilization in rats]. (1975)

The influence of various indole-3-alkane-carboxylic acids (indole-3-propionic acid, indole-3-butyric acid and derivatives of this substance) on some parameters of carbohydrate, fat and insulin metabolism were studied in normal and experimentally induced diabetic rats. Earlier it had been shown, by Schillinger and Loge (1973) using rat liver slices for in vitro studies and adrenalectomized rates for in vivo experiments that indole-3-butyric acid and its analogues investigated suppress gluconeogenesis from pyruvate and that these substances have a hypoglycaemic effect when administered orally at doses of 50-250 mg/kg. Indole-3-propionic acid, indole-3-butyric acid, 1-methyl-indole-3-butyric acid, 2-methyl-indole-3-butyric acid and 1-carboxy-6-fluor-1,2,3,4-tetrahydrocarbazol, administered orally at doses up to 1000 mg/kg, had either only a slight or no hypoglycaemic effect at all in intact and streptozotocin-diabetic rats. The suppression of gluconeogenesis observed in vitro thus only has an appreciable effect on blood glucose in vivo when the capacity of the liver to synthetize glucose is reduced. In normal rats indole-3-propionic acid and indole-3-butyric acid led to a deterioration of glucose tolerance following i.v. glucose loading and to a reduction of 14C-U-glucose oxidation. An increase in the concentration of serum free fatty acids (FFA) measured after treatment with indole-3-butyric acid and its 1- and 2-methylated derivatives was not--in accordance with a theory of an interference of the glucose and fatty acid utilization published in literature--considered to be the primary cause since the reduced formation of 14CO2 from radioactive glucose is not normalized when the increased FFA content is reduced by an inhibitor of lipolysis (5-methyl-isoxazol-3-carboxylic acid)...
The Dr1/DRAP1 heterodimer is a global repressor of transcription in vivo (1997)

A general repressor extensively studied in vitro is the human Dr1/DRAP1 heterodimeric complex. To elucidate the function of Dr1 and DRAP1 in vivo, the yeast Saccharomyces cerevisiae Dr1/DRAP1 repressor complex was identified. The repressor complex is encoded by two essential genes, designated YDR1 and BUR6. The inviability associated with deletion of the yeast genes can be overcome by expressing the human genes. However, the human corepressor DRAP1 functions in yeast only when human Dr1 is coexpressed. The yDr1/Bur6 complex represses transcription in vitro in a reconstituted RNA polymerase II transcription system. Repression of transcription could be overcome by increasing the concentration of TATA-element binding protein (TBP). Consistent with the in vitro results, overexpression of YDR1 in vivo resulted in decreased mRNA accumulation. Furthermore, YDR1 overexpression impaired cell growth, an effect that could be rescued by overexpression of TBP. In agreement with our previous studies in vitro, we found that overexpression of Dr1 in vivo also affected the accumulation of RNA polymerase III transcripts, but not of RNA polymerase I transcripts. Our results demonstrate that Dr1 functions as a repressor of transcription in vivo and, moreover, directly targets TBP, a global regulator of transcription.
Positioning using time-difference of arrival measurements (2004)

The problem of position estimation from time difference of arrival (TDOA) measurements occurs in a range of applications from wireless communication networks to electronic warfare positioning. Correlation analysis of the transmitted signal to two receivers gives rise to one hyperbolic function. With more than two receivers, we can compute more hyperbolic functions, which ideally intersect in one unique point. With TDOA measurement uncertainty, we face a non-linear estimation problem. We suggest and compare a Monte Carlo based method for positioning and a gradient search algorithm using a nonlinear least squares framework. The former has the feature of being easily extended to a dynamic framework where a motion model of the transmitter is included. A small simulation study is presented.
Optical Photopolymers: Design and Applications (1998)

The combination of precise optically recorded patterns and changes in the physical properties upon light-induced polymerization leads to the unique function and utility of photopolymers in enabling improvements in the display of information or data storage. The authors focus on the newest photopolymers under development at DuPont—optical photopolymers—and their commercialization. A description of the materials is followed by a discussion of several applications under development, e.g., laser eye protection filters, liquid crystal display systems, optical interconnection, and holographic data storage.
Atmospheric pressure plasma jets: an overview of devices and new directions (2015)

Atmospheric pressure plasma jets have a long history of more than 50 years. During this time their design and plasma generation mechanism has been developed and adapted to various fields of applications. This review aims at giving an overview of jet devices by starting with a brief history of their development. This is followed by an overview of commonly used terms and definitions as well as a survey of different classification schemes (e.g. geometry, excition frequency or specific energy input) described in literature. A selective update of new designs and novel research achievments on atmospheric pressure plasma jets published in 2012 or later shows the impressive variety and rapid development of the field. Finally, a brief outlook on the future trends and directions is given.
Gene Therapy of Cancer: Activation of Nucleoside Prodrugs withE. coliPurine Nucleoside Phosphorylase (1999)

During the last few years, many gene therapy strategies have been developed for various disease targets. The development of anticancer gene therapy strategies to selectively generate cytotoxic nucleoside or nucleotide analogs is an attractive goal. One such approach involves the delivery of herpes simplex virus thymidine kinase followed by the acyclic nucleoside analog ganciclovir. We have developed another gene therapy methodology for the treatment of cancer that has several significant attributes. Specifically, our approach involves the delivery of E. coli purine nucleoside phosphorylase, followed by treatment with a relatively non-toxic nucleoside prodrug that is cleaved by the enzyme to a toxic compound. This presentation describes the concept, details our search for suitable prodrugs, and summarizes the current biological data.
Reconstitution of cytokeratin filaments in vitro: further evidence for the role of nonhelical peptides in filament assembly. (1984)

The in vitro renaturation and assembly of cytokeratin molecules to form intermediate filaments (IF) illustrates that these molecules contain all of the structural information necessary for IF information. These molecules contain nine structural domains: the amino- and carboxyterminal extra helical regions, and three conserved extra helical segments that separate four helical rod-like domains. Chymotrypsin treatment of these molecules removes the end-peptide domains and inhibits the self-assembly process. We have examined the renaturation and assembly of cytokeratin molecules using solution conditions that favor the presence of intermediate forms of IF organization. Dialysis against low salt buffers revealed the presence of bead-like chains of filaments in which the 6-8-nm beads are separated by a distance of 21 nm. These data suggest that a lateral stagger of protofilaments was among the primary events in IF assembly. Chymotrypsin-modified cytokeratin enriched for alpha-helix barely initiated a turbidity increase at conditions favoring self-assembly. Addition of small amounts of intact cytokeratin accelerated the rate and extent of this reaction. These results indicate that the nonhelical peptides on intact cytokeratin potentiate the assembly of IF by orientating the stagger of laterally associated protofilaments.
Regulation of Human Clara Cell 10 kD Protein Expression by Chicken Ovalbumin Upstream Promoter Transcription Factors (COUP-TFs) (2002)

Clara cell 10 kD protein (CC10) is expressed specifically in a portion of nonciliated airway epithelial cells. The molecular mechanisms that determine its high specificity are not clear. Transcription factors implicated in the regulation of CC10 in rodents do not show the same level of cell specificity. We report here that a 3.3 kb human CC10 DNA fragment, containing the 5' flanking region and promoter, directs lacZ reporter expression in a small portion of Clara cells of the airway epithelia of transgenic mice, indicating the requirement of additional regulatory elements for expression. Addition of an intron containing a transcription enhancer from the human cytokeratin 18 gene greatly enhances the level of transgene expression and broadens epithelial specificity. To gain insight into the mechanisms underlying the cell specificity of human CC10 expression, we performed a promoter analysis of the CC10 gene and a yeast one-hybrid screening to identify factors that regulate the promoter. We have found that chicken ovalbumin upstream promoter transcription factors (COUP-TFs) interact with a proximal promoter region and confirmed the interaction by gel-shift assays. Cotransfection analyses with reporter constructs in cultured cells indicated that COUP-TFs inhibit human CC10 expression. These experiments suggest that COUP-TFs may play a pivotal role in cell specificity of the human CC10 gene by inhibiting its expression in nonpermissive cells.
A human monoclonal antibody to a complex epitope in the V3 region of gp120 of human immunodeficiency virus type 1 has broad reactivity within and outside clade B (1995)

We have used virus neutralization and antibody-binding techniques to define the epitope for a human monoclonal antibody, designated 19b, within the V3 region of the gp120 surface glycoprotein of human immunodeficiency virus type 1. Unusually, the 19b epitope encompasses residues on both flanks of the V3 loop. However, 19b binding to gp120 is independent of sequences at the crown of the V3 loop, provided that they are compatible with the formation of a type II beta turn that is presumably necessary to juxtapose the antigenic residues on the V3 flanks. By comparing the V3 sequences of virus gp120s able and unable to bind 19b, we were able to define the canonical 19b epitope as -I----G--FY-T, where residues at the positions indicated by the gaps do not contribute directly to the 19b-binding site. A few conservative substitutions at the more critical residues are also compatible with 19b binding. Inspection of V3 sequences in the human immunodeficiency virus database indicated that the canonical 19b epitope is well conserved among isolates from the North American-European clade B and also among clade E isolates from Thailand and clade F isolates from Brazil. A minority of gp120s from clades A and C also possess the 19b epitope. Consistent with the theoretical predictions of its cross-clade reactivity, 19b was found to bind to gp120s from clades A, B, C, E, and F in immunoassays. However, 19b was not able to reduce the infectivity of primary viruses from clades A, E, and F that were predicted to possess the 19b epitope and only modestly reduced the infectivity of a clade C virus at low input virus concentrations. Cross-clade neutralization via V3-directed antibodies may, therefore, be difficult, even if the antibodies show broad reactivities in binding assays and the viruses theoretically possess the relevant binding site.
Neural Systems Responding to Degrees of Uncertainty in Human Decision-Making (2005)

Much is known about how people make decisions under varying levels of probability (risk). Less is known about the neural basis of decision-making when probabilities are uncertain because of missing information (ambiguity). In decision theory, ambiguity about probabilities should not affect choices. Using functional brain imaging, we show that the level of ambiguity in choices correlates positively with activation in the amygdala and orbitofrontal cortex, and negatively with a striatal system. Moreover, striatal activity correlates positively with expected reward. Neurological subjects with orbitofrontal lesions were insensitive to the level of ambiguity and risk in behavioral choices. These data suggest a general neural circuit responding to degrees of uncertainty, contrary to decision theory.