gebhart/patrepeval huggingface dataset:
Persistent cardiac and urinary tract infections with Borrelia burgdorferi in experimentally infected Syrian hamsters (1991)

The heart can be severely affected in humans with Lyme disease, causing conduction defects and, rarely, heart failure. Although immunodeficient and young mice may develop cardiac lesions, cultivation of Borrelia burgdorferi from cardiac tissues of experimentally infected animals has not been reported previously. We infected Syrian hamsters with B. burgdorferi 297 and found a marked tropism of the spirochete for myocardial and urinary tract tissues. Fifty-six of 57 hearts (98%) and 52 of 58 bladders (90%) were culture positive. The cardiac infection was persistent and could be documented in 21 of 22 hearts (96%) cultured from days 28 to 84 postinfection. The urinary tract was also a site of persistent infection in most animals, with 18 of 23 bladders (78%) being culture positive from days 28 to 84. The persistence of spirochetes was specific for the heart and bladder, as indicated by negative cultures of specimens from the liver and spleen, in which only 1 of 23 cultures was positive from days 28 to 84. Because of the high isolation rates, tropism, and persistence that we found for B. burgdorferi in the hamster heart and bladder, these sites will be useful and important for the cultivation of spirochetes in experimental studies that evaluate the efficacies both of candidate vaccines in preventing infection and of antibiotics in eradicating organisms from privileged sites. In addition, the clear demonstration of persistent cardiac infection with B. burgdorferi may provide a useful model for studying the pathogenesis of cardiac Lyme disease.
Early Diagnosis and Prediction of Sepsis Shock by Combining Static and Dynamic Information Using Convolutional-LSTM (2018)

Deep neural network models, especially Long Short Term Memory (LSTM), have shown great success in analyzing Electronic Health Records (EHRs) due to their ability to capture temporal dependencies in time series data. In this paper, we proposed a general deep neural network framework which incorporates two additional components with the aim of improving LSTM. The first component, a Convolutional Neural Network (CNN), is added before LSTM to obtain local characteristics of EHRs. The second component, a fully connected neural network (FC), introduces static information (e.g., age) to LSTM, which is applied to handle dynamic information (e.g., lab result). The medical condition we aim to predict is septic shock - it is the most advanced complication of sepsis and is due to severe abnormalities in circulation and/or cellular metabolism. Our proposed framework was evaluated for two experimental tasks: visit level early diagnosis (left align) and event level early prediction (right align). Our results show that for visit level early diagnosis, by incorporating both CNN and static information, our framework consistently outperforms the original LSTM. For event level early prediction, the same outcome is observed when predicting <; 5 hours into the future, however, when predicting ≥ 5 hours into the future, the addition of the CNN component alone obtains the best results.
Counting the Zinc-Proteins Encoded in the Human Genome (2005)

Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, or for regulation of their activities or for structural purposes. Genome sequencing projects have provided a huge number of protein primary sequences, but, even though several different elaborate analyses and annotations have been enabled by a rich and ever-increasing portfolio of bioinformatic tools, metal-binding properties remain difficult to predict as well as to investigate experimentally. Consequently, the present knowledge about metalloproteins is only partial. The present bioinformatic research proposes a strategy to answer the question of how many and which proteins encoded in the human genome may require zinc for their physiological function. This is achieved by a combination of approaches, which include: (i) searching in the proteome for the zinc-binding patterns that, on their turn, are obtained from all available X-ray data; (ii) using libraries of metal-binding protein domains based on multiple sequence alignments of known metalloproteins obtained from the Pfam database; and (iii) mining the annotations of human gene sequences, which are based on any type of information available. It is found that 1684 proteins in the human proteome are independently identified by all three approaches as zinc-proteins, 746 are identified by two, and 777 are identified by only one method. By assuming that all proteins identified by at least two approaches are truly zinc-binding and inspecting the proteins identified by a single method, it can be proposed that ca. 2800 human proteins are potentially zinc-binding in vivo, corresponding to 10% of the human proteome, with an uncertainty of 400 sequences. Available functional information suggests that the large majority of human zinc-binding proteins are involved in the regulation of gene expression. The most abundant class of zinc-binding proteins in humans is that of zinc-fingers, with Cys4 and Cys2His2 being the most common types of coordination environment.
Automatic Generation of 3D Building Models for Environmental Education by Straight Skeleton Computation (2018)

3D building models are important in several fields, such as urban planning and roof report for insurance industries. However, enormous time and labor has to be consumed to create these 3D models, using a 3D modeling software such as 3ds Max or SketchUp. In order to automate laborious steps, a GIS and CG integrated system is proposed for automatically generating 3D building models, based on building polygons (building footprints) on digital maps. Digital maps show most building polygons' edges meet at right angles (orthogonal polygon). In the digital map, however, not all building polygons are orthogonal. In either orthogonal or non-orthogonal polygons, the new system is proposed for automatically generating 3D building models with general shaped roofs by straight skeleton computation. In this paper, the algorithm for shrinking a polygon and forming a straight skeleton are clarified and, the new methodology is proposed for constructing roof models by assuming `the third event' and, at the end of the shrinking process, the shrinking polygon is converged to `a line of convergence'. In our research, extended straight skeleton computation is used for automatic generation of roof models. Based on the monotone polygons which straight skeleton computation forms, roof boards are automatically generated, and a top view of these roof boards can be a roof report for natural disaster damage.
Investigating the effects of polymer chemistry on activity of biocatalytic plastic materials (2000)

The affects of polymer chemistry on the organic solvent activity of alpha-chymotrypsin-containing biocatalytic plastic materials are investigated in this study. To incorporate alpha-chymotrypsin into the polymer, the enzyme is first acryloylated, then solubilized into organic solvents via hydrophobic ion paring with surfactant molecules. Once in the organic solvent, a vinyl monomer and crosslinker are added and copolymerized with the enzyme. Due to the intimate contact between the enzyme and the resulting polymer network, the polymer chemistry plays an important role in the activity of these biocatalytic materials. The chemical composition of the monomer/polymer has the greatest effect on catalytic activity. The activity spans a range of 100-fold and appears to correlate with the hydrophilicity of the monomer, with the lowest activity exhibited for poly(methyl methacrylate) and the highest for poly(2-hydroxyethyl methacrylate). The effect of the chemical structure of the monomer/polymer appears to be an intrinsic kinetic effect, whereas other polymer chemistry conditions investigated, including crosslinker concentration and length and ratio of solvent:monomer during synthesis, appear to effect the rate of substrate diffusion, thereby affecting observed enzyme activity. Changes in the conditions of polymer synthesis can cause as much as a 20-fold change in activity for a given polymeric material. This is most likely due to an increase in the porosity of the materials, and thus a relaxation of diffusional limitations.
ABR service in ATM networks: performance comparison between adaptive stochastic and ERICA flow control schemes with guaranteed minimum cell rate (2002)

Two explicit rate-based flow control schemes for congestion avoidance in ATM networks: explicit rate indication for congestion avoidance (ERICA) and a proposed adaptive stochastic (AS), are compared under heavy load conditions. Neither of the schemes dictates a particular switch architecture. The requirements tested include: utilization, queuing delay, delay variance and queue size. A simple network topology involves an ATM switching node which is modeled as a single server queuing system fed by a number of highly bursty traffic sources. Neither packet discarding, nor packet retransmission mechanisms are included. The controllable sources' allowed cell rates (ACR) have been dynamically shaped by the explicit feedback messages from the switch. The results of a simulation study are presented which suggest that the AS scheme can provide for higher priority traffic considerably shorter queuing delay, delay variance and average queue size, particularly on shorter links, with slightly lower utilization.
Chemotherapeutic potential of cow urine: A review. (2015)

In the grim scenario where presently about 70% of pathogenic bacteria are resistant to at least one of the drugs for the treatment, cue is to be taken from traditional/indigenous medicine to tackle it urgently. The Indian traditional knowledge emanates from ayurveda, where Bos indicus is placed at a high pedestal for numerous uses of its various products. Urine is one of the products of a cow with many benefits and without toxicity. Various studies have found good antimicrobial activity of cow's urine (CU) comparable with standard drugs such as ofloxacin, cefpodoxime, and gentamycin, against a vast number of pathogenic bacteria, more so against Gram-positive than negative bacteria. Interestingly antimicrobial activity has also been found against some resistant strains such as multidrug-resistant (MDR) Escherichia coli and Klebsiella pneumoniae. Antimicrobial action is enhanced still further by it being an immune-enhancer and bioenhancer of some antibiotic drugs. Antifungal activity was comparable to amphotericin B. CU also has anthelmintic and antineoplastic action. CU has, in addition, antioxidant properties, and it can prevent the damage to DNA caused by the environmental stress. In the management of infectious diseases, CU can be used alone or as an adjunctive to prevent the development of resistance and enhance the effect of standard antibiotics.
Minor histocompatibility antigens HA-1-, -2-, and -4-, and HY-specific cytotoxic T-cell clones inhibit human hematopoietic progenitor cell growth by a mechanism that is dependent on direct cell-cell contact (1993)

HLA-identical bone marrow transplantation (BMT) may be complicated by graft-versus-host disease or graft rejection. Both complications are thought to be initiated by recognition of minor histocompatibility (mH) antigens by HLA-restricted mH-antigen-specific T lymphocytes. Using HLA- A2-restricted mH antigens HA-1-, -2-, and -4-, and HY-specific cytotoxic T lymphocyte (CTL) clones, we studied the recognition by these CTL clones of interleukin-2 (IL-2)-stimulated T cells (IL-2 blasts), BM mononuclear cells (BMMNCs), and hematopoietic progenitor cells (HPCs). We showed that, when IL-2 blasts from the BM donors who were investigated were recognized by the HA-1-, -2-, and -4-, and HY- specific CTL clones, their BMMNCs and HPCs were recognized as well by these CTL clones, resulting in antigen-specific growth inhibition of erythrocyte burst-forming units (BFU-E), colony-forming units- granulocyte (CFU-G), and CFU-macrophage (CFU-M). the HA-2-specific CTL clone, however, inhibited BFU-E and CFU-G growth from four donors to a lesser extent than from two other donors. We further investigated whether inhibitory cytokines released into the culture medium by the antigen-specific stimulated CTLs or by stimulated BMMNCs were responsible for suppression of HPC growth or whether this effect was caused by direct cell-cell contact between CTLs and HPCs. HPC growth inhibition was only observed after preincubation of BMMNCs and CTLs together for 4 hours before plating the cells in semisolid HPC culture medium. When no cell-cell contact was permitted before plating, neither antigen-stimulated CTL nor antigen-nonstimulated CTLs provoked HPC growth inhibition. Culturing BMMNCs in the presence of supernatants harvested after incubation of BMMNCs and CTL clones together for 4 or 72 hours did also not result in HPC growth inhibition. Both suppression of HPC growth and lysis of IL-2 blasts and BMMNCs in the 51Cr-release assay appeared to be dependent on direct cell-cell contact between target cells and CTLs and were not caused by the release of inhibitory cytokines into the culture medium by antigen-specific stimulated CTLs or by stimulated BMMNCs. Our results show that mH-antigen-specific CTLs can inhibit HPC growth by a direct cytolytic effect and may therefore be responsible for BM graft rejection after HLA-identical BMT.
Modelling of the Filtration Behaviour Using Coupled DEM and CFD (2012)

The filtration by cake formation is an effective method to drain a particle suspension. One possibility to improve the filtration process is the formation of flocs, which deposit faster. The aim of this work is to predict the filtration behavior, the effects of flocculation and simulate the flow rate during generation and compression of the porous ultrafine particle packings by coupling Discrete Element Method and Computational Fluid Dynamics in two dimensions within the micron range. A Press-Shear-Cell was used to investigate the filtration behaviour of the consolidated particle packings and to measure the most important material properties. It was shown that the time dependency of specific filtrate volume and cake height for the flocculated and non-flocculated suspension can be predicted by this method. It is observed that a flocculation causes an increase in porosity and permeability of the filter cake. This results in decreasing filter cake resistances and increasing permeabilities. The filtration times are decreasing. A stable suspension with dominant repulsion produces a compact filter cake with small porosity, large filter cake resistance and poor permeability. The compressibility of the flocculated cake is higher compared to the stable suspension and can be categorized as very compressible.
Cell cycle-regulated multi-site phosphorylation of Neurogenin 2 coordinates cell cycling with differentiation during neurogenesis (2011)

During development of the central nervous system, the transition from progenitor maintenance to differentiation is directly triggered by a lengthening of the cell cycle that occurs as development progresses. However, the mechanistic basis of this regulation is unknown. The proneural transcription factor Neurogenin 2 (Ngn2) acts as a master regulator of neuronal differentiation. Here, we demonstrate that Ngn2 is phosphorylated on multiple serine-proline sites in response to rising cyclin-dependent kinase (cdk) levels. This multi-site phosphorylation results in quantitative inhibition of the ability of Ngn2 to induce neurogenesis in vivo and in vitro. Mechanistically, multi-site phosphorylation inhibits binding of Ngn2 to E box DNA, and inhibition of DNA binding depends on the number of phosphorylation sites available, quantitatively controlling promoter occupancy in a rheostat-like manner. Neuronal differentiation driven by a mutant of Ngn2 that cannot be phosphorylated by cdks is no longer inhibited by elevated cdk kinase levels. Additionally, phosphomutant Ngn2-driven neuronal differentiation shows a reduced requirement for the presence of cdk inhibitors. From these results, we propose a model whereby multi-site cdk-dependent phosphorylation of Ngn2 interprets cdk levels to control neuronal differentiation in response to cell cycle lengthening during development.
Text/Non-text Ink Stroke Classification in Japanese Handwriting Based on Markov Random Fields (2007)

In this paper, we present an approach for separating text and non-text ink strokes in online handwritten Japanese documents based on Markov random fields (MRFs), which effectively utilize the spatial relationship between strokes. Support vector machine (SVM) classifiers are trained for individual stroke and stroke pair classification, and on converting the SVM outputs to probabilities, the likelihood clique potentials of MRF are derived. In experiments on the TUAT Kon-date database, the proposed MRF approach yield superior performance compared to individual stroke classification and sequence classification based on hidden Markov models (HMMs).
FPGA implementation of edge detection for Sobel operator in eight directions (2018)

Sobel edge detection algorithm is an important research method in image processing and computer vision, but for most edge detection is obtained through PC-side processing, it can not be directly detected locally. This paper proposes that FPGA(Field Programmable Gate Array) can implement modular and local detection of the algorithm. First, the principle and advantages of multidirectional Sobel algorithm are described. Secondly, the FPGA implementation of the algorithm is studied and the preliminary experimental results are obtained. Finally, The detection images obtained by using the eight-direction Sobel algorithm and FPGA are compared with those obtained by matlab, It is found that the hardware can realize the edge detection of local real-time processing while ensuring the image detection effect.
Message Passing Multi-Agent GANs (2016)

Communicating and sharing intelligence among agents is an important facet of achieving Artificial General Intelligence. As a first step towards this challenge, we introduce a novel framework for image generation: Message Passing Multi-Agent Generative Adversarial Networks (MPM GANs). While GANs have recently been shown to be very effective for image generation and other tasks, these networks have been limited to mostly single generator-discriminator networks. We show that we can obtain multi-agent GANs that communicate through message passing to achieve better image generation. The objectives of the individual agents in this framework are two fold: a co-operation objective and a competing objective. The co-operation objective ensures that the message sharing mechanism guides the other generator to generate better than itself while the competing objective encourages each generator to generate better than its counterpart. We analyze and visualize the messages that these GANs share among themselves in various scenarios. We quantitatively show that the message sharing formulation serves as a regularizer for the adversarial training. Qualitatively, we show that the different generators capture different traits of the underlying data distribution.
Luminescence properties of stoichiometric EuM<sub>2</sub>S<sub>4</sub> (M = Ga, Al) conversion phosphors for white LED applications (2012)

Abstract EuM 2 S 4 (M = Ga, Al) phosphors were synthesized using the solid‐state reaction method. The structure and photoluminescence (PL) properties of the phosphors were investigated in detail. XRD pattern results indicated that the two phosphors are isostructures to the orthorhombic structure. The PL spectra showed that the EuGa 2 S 4 and EuAl 2 S 4 phosphors can be excited efficiently by UV–visible light from 350 to 480 nm and that they emit intense green and bluish‐green light, with emission bands peaking at 545 and 506 nm, respectively. The fluorescence lifetimes of Eu 2+ were calculated to be 0.076 and 0.064 µs for EuGa 2 S 4 and EuAl 2 S 4 , respectively. The thermal quenching temperature was 412 K for EuGa 2 S 4 . A green LED was fabricated by the combination of a near‐UV InGaN chip and the prepared EuGa 2 S 4 phosphor. The EuGa 2 S 4 phosphor exhibits much better green color purity than EuAl 2 S 4 . As a result, EuGa 2 S 4 might be a promising green phosphor candidate for solid‐state lighting LED technology.
Panorama maps with non-linear ray tracing (2007)

We present a framework for the interactive generation of 3D panorama maps. Our approach addresses the main issue that occurs during panorama map construction: non-linear projection or deformation of the terrain in order to minimize the occlusion of important information such as roads and trails. Traditionally, panorama maps are hand-drawn by skilled illustrators. In contrast, our approach provides computer support for the rendering of non-occluded views of 3D panorama maps, where deformations are modeled by nonlinear ray tracing. The deflection of rays is influenced by 2D and 3D force fields that directly consider the shape of the terrain. In addition, our framework allows the user to further modify the force fields to have fine control over the deformations of the panorama map. User interaction is facilitated by our real-time rendering system in terms of linked multiple views of both linear and non-linear projected terrain and the deformed view rays. Fast rendering is achieved by GPU-based non-linear ray tracing. We demonstrate the usefulness of our modeling and visualization method by several examples.
Evaluation of perceptual resolution of printed matter (Fogra L-Score evaluation) (2014)

A new method has been developed to address the objective evaluation of perceived resolution of printed matter. To achieve this, a psychophysical experiment has been designed and conducted that ranked typical test prints representing the manifold of printing processes and substrates. A scanner based method has been developed that computes a score value between 0 and 100 termed Fogra L-Score. It is based on the idea to identify a predefined signal in an image (print). The predefined signal is a perfect representation of the “perceived resolution domain” by means of a test target (RIT ConRes-target) that covers systematic variations of the two governing parameters of perceived resolution namely contrast and spatial resolution. The printed images to be evaluated have been scanned and pre-processed. The level of closeness between the reference (digital representation) and the printed matter (scanned print) have been determined by a 2-dimensional normalized cross-correlation (on the CIEL*-channel). The resulting correlation coefficients have been compared against findings of the performed psychophysical experiment. Finally a framework will be presented that also allows for spatial filtering to address different intended viewing distances as well as chromatic test charts. Publisher’s Note: The first printing of this volume was completed prior to the SPIE Digital Library publication and this paper has since been replaced with a corrected/revised version.