gebhart/patrepeval huggingface dataset:
Ebola virus disease cases among health care workers not working in Ebola treatment units--Liberia, June-August, 2014. (2014)

West Africa is experiencing the largest Ebola virus disease (Ebola) epidemic in recorded history. Health care workers (HCWs) are at increased risk for Ebola. In Liberia, as of August 14, 2014, a total of 810 cases of Ebola had been reported, including 10 clusters of Ebola cases among HCWs working in facilities that were not Ebola treatment units (non-ETUs). The Liberian Ministry of Health and Social Welfare and CDC investigated these clusters by reviewing surveillance data, interviewing county health officials, HCWs, and contact tracers, and visiting health care facilities. Ninety-seven cases of Ebola (12% of the estimated total) were identified among HCWs; 62 HCW cases (64%) were part of 10 distinct clusters in non-ETU health care facilities, primarily hospitals. Early recognition and diagnosis of Ebola in patients who were the likely source of introduction to the HCWs (i.e., source patients) was missed in four clusters. Inconsistent recognition and triage of cases of Ebola, overcrowding, limitations in layout of physical spaces, lack of training in the use of and adequate supply of personal protective equipment (PPE), and limited supervision to ensure consistent adherence to infection control practices all were observed. Improving infection control infrastructure in non-ETUs is essential for protecting HCWs. Since August, the Liberian Ministry of Health and Social Welfare with a consortium of partners have undertaken collaborative efforts to strengthen infection control infrastructure in non-ETU health facilities.
Statistical Challenges in Functional Genomics (2003)

On February 12, 2001 the Human Genome Project announced the completion of a draft physical map of the human genome---the genetic blueprint for a human being. Now the challenge is to annotate this map by understanding the functions of genes and their interplay with proteins and the environment to create complex, dynamic living systems. This is the goal of functional genomics. Recent technological advances enable biomedical investigators to observe the genome of entire organisms in action by simultaneously measuring the level of activation of thousands of genes under the same experimental conditions. This technology, known as microarrays, today provides unparalleled discovery opportunities and is reshaping biomedical sciences. One of the main aspects of this revolution is the introduction of computationally intensive data analysis methods in biomedical research. This article reviews the foundations of this technology and describes the statistical challenges posed by the analysis of microarray data.
Developing Quantum Dot Phosphor‐Based Light‐Emitting Diodes for Aviation Lighting Applications (2012)

We have investigated the feasibility of employing quantum dot (QD) phosphor‐based light‐emitting diodes (LEDs) in aviation applications that request Night Vision Imaging Systems (NVIS) compliance. Our studies suggest that the emerging QD phosphor‐based LED technology could potentially be superior to conventional aviation lighting technology by virtue of the marriage of tight spectral control and broad wavelength tunability. This largely arises from the fact that the optical properties of semiconductor nanocrystal QDs can be tailored by varying the nanocrystal size without any compositional changes. It is envisioned that the QD phosphor‐based LEDs hold great potentials in cockpit illumination, back light sources of monitor screens, as well as the LED indicator lights of aviation panels.
Enhancement of Amygdaloid Neuronal Dendritic Arborization by Fresh Leaf Juice of <i>Centella asiatica</i> (Linn) during Growth Spurt Period in Rats (2007)

Centella asiatica (CeA) is a creeping herb, growing in moist places in India and other Asian Countries. Ayurvedic system of medicine, an alternate system of medicine in India, uses leaves of CeA for memory enhancement. Here, we have investigated the role of CeA fresh leaf juice treatment during growth spurt period of rats on dendritic morphology of amygdaloid neurons, one of the regions concerned with learning and memory. The present study was conducted on neonatal rat pups. The rat pups (7-days-old) were fed with 2, 4 and 6 ml/kg body of fresh leaf juice of CeA for 2, 4 and 6 weeks. After the treatment period, the rats were killed, brains removed and amygdaloid neurons impregnated with Silver nitrate (Golgi staining). Amygdaloid neurons were traced using camera lucida and dendritic branching points (a measure of dendritic arborization) and intersections (a measure dendritic length) quantified. These data were compared with those of age-matched control rats. The results showed a significant increase in dendritic length (intersections) and dendritic branching points along the length of dendrites of the amygdaloid neurons of rats treated with 4 and 6 ml/kg body weight/day of CeA for longer periods of time (i.e. 4 and 6 weeks). We conclude that constituents/active principles present in CeA fresh leaf juice has neuronal dendritic growth stimulating property; hence it can be used for enhancing neuronal dendrites in stress and other neurodegenerative and memory disorders.
Ultra‐thin and Flat Mica as Gate Dielectric Layers (2012)

Ultra-thin and flat mica-based carbon nanotube field-effect transistors reveal the excellent gate control capability and low leakage current due to the high dielectric constant and high dielectric strength of ultra-thin mica as the gate dielectric. Subthreshold swing of 110 mV/dec and carrier mobility improvement are achieved. The ultra-thin mica retains its surface flatness, indicating the potential application for low-dimensional materials in which surface roughness scattering is significant. 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.
Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer (2014)

Lymphocytic infiltration is associated with a favourable prognosis and predicts response to chemotherapy in many cancer types, including the aggressive triple-negative breast cancer (TNBC). However, it is not well understood owing to the high levels of spatial heterogeneity within tumours, which is difficult to analyse by traditional pathological assessment. This paper describes an unbiased methodology to statistically model the spatial distribution of lymphocytes among tumour cells based on automated analysis of haematoxylin-and-eosin-stained whole-tumour section images, which is applied to two independent TNBC cohorts of 181 patients with matched microarray gene expression data. The novelty of the proposed methodology is the fusion of image analysis and statistical modelling for an integrative understanding of intratumour heterogeneity of lymphocytic infiltration. Using this methodology, a quantitative measure of intratumour lymphocyte ratio is developed and found to be significantly associated with disease-specific survival in both TNBC cohorts independent to standard clinical parameters. The proposed image-based measure compares favourably to a number of gene expression signatures of immune infiltration. In addition, heterogeneous immune infiltration at the morphological level is reflected at the molecular scale and correlated with increased expression of CTLA4, the target of ipilimumab. Taken together, these results support the fusion of high-throughput image analysis and statistical modelling to offer reproducible and robust biomarkers for the objective identification of patients with poor prognosis and treatment options.
FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator <i>CONSTANS</i> in <i>Arabidopsis</i> (2012)

Many plants monitor day-length changes throughout the year and use the information to precisely regulate the timing of seasonal flowering for maximum reproductive success. In Arabidopsis thaliana, transcriptional regulation of the CONSTANS (CO) gene and posttranslational regulation of CO protein are crucial mechanisms for proper day-length measurement in photoperiodic flowering. Currently, the CYCLING DOF FACTOR proteins are the only transcription factors known to directly regulate CO gene expression, and the mechanisms that directly activate CO transcription have remained unknown. Here we report the identification of four CO transcriptional activators, named FLOWERING BHLH 1 (FBH1), FBH2, FBH3, and FBH4. All FBH proteins are related basic helix-loop-helix-type transcription factors that preferentially bind to the E-box cis-elements in the CO promoter. Overexpression of all FBH genes drastically elevated CO levels and caused early flowering regardless of photoperiod, whereas CO levels were reduced in the fbh quadruple mutants. In addition, FBH1 is expressed in the vascular tissue and bound near the transcription start site of the CO promoter in vivo. Furthermore, FBH homologs in poplar and rice induced CO expression in Arabidopsis. These results indicate that FBH proteins positively regulate CO transcription for photoperiodic flowering and that this mechanism may be conserved in diverse plant species. Our results suggest that the diurnal CO expression pattern is generated by a concert of redundant functions of positive and negative transcriptional regulators.
A Reconfigurable Architecture for Multi-Gigabit Speed Content-Based Routing (2006)

This paper presents a reconfigurable architecture for high-speed content-based routing. Our architecture goes beyond simple pattern matching by implementing a parsing engine that defines the semantics of patterns that are parsed within the data stream. Defining the semantics of patterns allows for more accurate processing and routing of packets using any fields that appear within the payload of the packet. The architecture consists of several components, including a pattern matcher, a parsing structure, and a routing module. Both the pattern matcher and parsing structure are automatically generated using an application-specific compiler that is described in this paper. The compiler accepts a grammar specification as input and outputs a data parser in VHDL. The routing module receives control signals from both the pattern matcher and the parsing structure that aid in the routing of packets. We illustrate how a content-based router can be implemented with our technique using an XML parser as an example. The XML parser presented was designed, implemented, and tested in a Xilinx Virtex XCV2000E FPGA on the FPX platform. It is capable of processing 32-bits of data per clock cycle and runs at 100 MHz. This allows the system to process and route XML messages at 3.2 Gbps
Infrared and visible image fusion via saliency analysis and local edge-preserving multi-scale decomposition (2017)

To retain the details of a visible image with a discernible target area, we propose a multi-scale decomposition image fusion method based on a local edge-preserving (LEP) filter and saliency detection. We first use a LEP filter to decompose the infrared and visible images. Then, a modified saliency detection method is utilized to detect the salient target areas of an infrared image, which determine the base layer's weights of fusion strategy. Finally, each layer is reconstructed to obtain a visually pleasing fused image. Comparison with 11 other state-of-the-art methods reveals the superiority of the proposed method in terms of quality and quantity results.
Thrombosis in inflammatory bowel disease: clinical setting, procoagulant profile and factor V Leiden (1997)

Patients with inflammatory bowel disease have an increased frequency of thromboembolism, and microvascular thrombosis has been proposed as a contributory pathogenic factor. The mechanism of enhanced procoagulant activity is not understood. We examined the clinical setting of thromboembolic events in 52 patients with Crohn's disease or ulcerative colitis, and assessed the procoagulant laboratory profile, including Factor V Leiden, in a subset of 20 patients to identify procoagulant risk factors. Patients who developed thrombosis tended to be young; 60% of thrombotic events occurred in patients under 50 years. Multiple thromboembolic episodes occurred in 13% and unusual sites of thrombosis (e.g. intracardiac, cerebral, inominate veins) in 11%. No risk factor was identifiable in 52% of cases and two-thirds of thromboses occurred in an out-patient setting. The mortality rate was 8%. Evidence for inflammatory disease activity was found in only 45% of patients with ulcerative colitis at the time of the thromboembolic event, in contrast to 89% of those with Crohn's disease. Assays for specific coagulation defects were negative in all cases tested (protein S, C were normal in 17/17; anti-thrombin III, anti-phospholipid antibodies and activated protein C resistance were negative in 20/20, and only 1/20 patients was found to be heterozygous for Factor V leiden. Thrombosis in inflammatory bowel disease is important because it occurs in a young population, often in unusual sites, and has a high mortality. The development of thrombosis is related to active inflammatory disease in most patients with Crohn's disease but apparently not in those with ulcerative colitis. Since approximately half of the patients had no other identifiable risk factor, there remains a substantial group of patients with IBD who develop thrombosis for unknown reasons.
Mutations of NOTCH1, FBXW7, and prognosis in T-lineage acute lymphoblastic leukemia (2009)

et al. 21 in the current issue represents a significant step forward in this chain as it links biology to prognosis by showing that lower risk non-del(5q) MDS patients with RPS14 haplo-insufficiency tend to have a prolonged survival. Be that as it may, the fact remains that defective ribosomal biogenesis, a previously unsuspected mechanism, is emerging as a surprise contender for the lead role in disrupting erythropoiesis in a variety of anemias. An entirely original subject of research has exploded on the MDS scene, one which links congenital and acquired anemias, and which is likely to produce exciting biological insights in the future, especially when combined with the emerging improved technology.
Computational Probability and Statistics (1973)

A change in attitude to applied mathematics is described, with more emphasis on solving problems motivated by questions from outside of mathematics and less on purely, methodological development. A consequence of this change is the need for a better understanding of what current computer technology can do for applied mathematics in making it more realistic. This is studied in the special context of mathematical statistics (probability, inference, data analysis). A number of problems are discussed in the range from very concrete decision problems to rather theoretical questions in the calculus of probability. An experimental and rather pragmatic approach is used, stressing the aid to our intuitive understanding that is offered by the mathematical experiment employing the computer as a laboratory and as a way of generating imagery closer to real life than the standard analytical model. Some attention is given to the technical difficulties encountered, especially those concerned with programming and use of computer graphics in mathematical statistics.
Survey of Public Key Infrastructure (2004)

With the development of e-commerce and e-government, Public Key Infrastructure (PKI)has played an important role in the information system security as a security infrastructure. Although PKI has been developed and deployed rapidly.there're still many risks and problems to be solved to meet the new requirements of the information security. In this paper, we introduce and analyze some new solutions,services and techniques of PKI,including the techniques of the secod generation PKI.
The controversial role of the Polycomb group proteins in transcription and cancer: how much do we not understand Polycomb proteins? (2014)

Polycomb group proteins (PcGs) are a large protein family that includes diverse biochemical features assembled together in two large multiprotein complexes. These complexes maintain gene transcriptional repression in a cell type specific manner by modifying the surrounding chromatin to control development, differentiation and cell proliferation. PcGs are also involved in several diseases. PcGs are often directly or indirectly implicated in cancer development for which they have been proposed as potential targets for cancer therapeutic strategies. However, in the last few years a series of discoveries about the basic properties of PcGs and the identification of specific genetic alterations affecting specific Polycomb proteins in different tumours have converged to challenge old dogmas about PcG biological and molecular functions. In this review, we analyse these new data in the context of the old knowledge, highlighting the controversies and providing new models of interpretation and ideas that will perhaps bring some order among apparently contradicting observations.
MANEJO NUTRICIONAL Y REPRODUCTIVO DE VAQUILLONAS EN RECRIA DE UN TAMBO DEL PARTIDO DE LOBOS. EVALUACIÓN DE LAS CONSECUENCIAS PRODUCTIVAS Y ECONOMICAS (2015)

Se plantea un cambio de manejo y de alimentación durante la recría en una alternativa denominada semi intensiva Se realizaron balances forrajeros para la propuesta, usando los recursos existentes y una suplementación energética y proteica mayor a la actual.
The Essential Oil of Sicilian<i>Thymus capitatus</i>(L.) Hoffmanns, et Link (1992)

ABSTRACT GC analysis of the essential oil of wild Sicilian Thymus capitatus showed the presence of 31 compounds. The main components, accounting for 90.5% of the oil, were carvacrol (86.3%), β-caryophyllene (2.8%) and α-elemol (1.4%).
The effect of pH and cations on the theramal denaturation of trypsin. (1953)

Dialysed or very dilute solutions of crystalline trypsin are rapidly and irreversibly inactivated at 40�C. At this temperature and in dilute solution the enzyme is most stable at pH values of about 2.7, 6.6, and 10.7, with intermediate regions of instability.
Integrating species life‐history traits and patterns of deforestation in amphibian conservation planning (2009)

Abstract Aim To identify priority areas for amphibian conservation in southeastern Brazil, by integrating species life‐history traits and patterns of deforestation. Location State of São Paulo, Brazil. Methods We used the software M arxan to evaluate different scenarios of amphibian conservation planning. Our approach differs from previous methods by explicitly including two different landscape metrics; habitat split for species with aquatic larvae, and habitat loss for species with terrestrial development. We evaluated the effect of habitat requirements by classifying species breeding habitats in five categories (flowing water, still water permanent, still water temporary, bromeliad or bamboo, and terrestrial). We performed analyses using two scales, grid cells and watersheds and also considered nature preserves as protected areas. Results We found contrasting patterns of deforestation between coastal and inland regions. Seventy‐six grid cells and 14 watersheds are capable of representing each species at least once. When accounting for grid cells already protected in state and national parks and considering species habitat requirements we found 16 high‐priority grid cells for species with one or two reproductive habitats, and only one cell representing species with four habitat requirements. Key areas for the conservation of species breeding in flowing and permanent still waters are concentrated in southern state, while those for amphibians breeding in temporary ponds are concentrated in central to eastern zones. Eastern highland zones are key areas for preserving species breeding terrestrially by direct or indirect development. Species breeding in bromeliads and bamboos are already well represented in protected areas. Main conclusions Our results emphasize the need to integrate information on landscape configuration and species life‐history traits to produce more ecologically relevant conservation strategies.
Low-constant parallel algorithms for finite element simulations using linear octrees (2007)

In this article we propose parallel algorithms for the construction of conforming finite-element discretization on linear octrees. Existing octree-based discretizations scale to billions of elements, but the complexity constants can be high. In our approach we use several techniques to minimize overhead: a novel bottom-up tree-construction and 2:1 balance constraint enforcement; a Golomb-Rice encoding for compression by representing the octree and element connectivity as an Uniquely Decodable Code (UDC); overlapping communication and computation; and byte alignment for cache efficiency. The cost of applying the Laplacian is comparable to that of applying it using a direct indexing regular grid discretization with the same number of elements. Our algorithm has scaled up to four billion octants on 4096 processors on a Cray XT3 at the Pittsburgh Supercomputing Center. The overall tree construction time is under a minute in contrast to previous implementations that required several minutes; the evaluation of the discretization of a variable-coefficient Laplacian takes only a few seconds.
Binding‐Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids (2015)

We introduce the concept and operation of a binding-induced DNA nanomachine that can be activated by proteins and nucleic acids. This new type of nanomachine harnesses specific target binding to trigger assembly of separate DNA components that are otherwise unable to spontaneously assemble. Three-dimensional DNA tracks of high density are constructed on gold nanoparticles functionalized with hundreds of single-stranded oligonucleotides and tens of an affinity ligand. A DNA swing arm, free in solution, is linked to a second affinity ligand. Binding of a target molecule to the two ligands brings the swing arm to AuNP and initiates autonomous, stepwise movement of the swing arm around the AuNP surface. The movement of the swing arm, powered by enzymatic cleavage of conjugated oligonucleotides, cleaves hundreds of oligonucleotides in response to a single binding event. We demonstrate three nanomachines that are specifically activated by streptavidin, platelet-derived growth factor, and the Smallpox gene. Substituting the ligands enables the nanomachine to respond to other molecules. The new nanomachines have several unique and advantageous features over DNA nanomachines that rely on DNA self-assembly.
Field results of liner rotation during cementing (1984)

Improving liner cementing success has been a constant objective of the industry for years. Recent developments in rotating liner hanger technology have made this primary cementing technique applicable to more wells than before. Presented here is an analysis of the results of 45 jobs over a year and a half. The study examines success ratios in light of liner size, depth, length, method of rotation, setting tool types, deviation, casing hardware (centralizers, scratchers, etc.), and bearing load.