gebhart/patrepeval huggingface dataset:
In Vivo Gas Transfer Performance of the Intravascular Oxygenator in Acute Respiratory Failure (1994)

The intravascular oxygenator (IVOX) has undergone both animal and clinical trials. Data from the animal studies have demonstrated that the device is capable of transferring up to approximately 100 ml/min of oxygen and carbon dioxide. Initial data from the human trials suggest that gas transfer, although approaching these levels, varied widely in patients with respiratory failure. We studied the factors affecting gas exchange in 26 patients with severe acute respiratory failure who underwent intravenacaval support of gas exchange with IVOX. The patients underwent monitoring of IVOX gas transfer rates, hemodynamics, blood gases, and ventilation parameters at scheduled intervals following device insertion. All devices functioned following implantation. The mean value for O2 transfer was 64 +/- 21 SD ml/min (range 15-114 ml/min) and for CO2 transfer was 48 +/- 17 ml.min-1 (range 14-112 ml/min). CO2 transfer correlated positively with device surface area, cardiac output, and mixed venous Pco2 and negatively with duration of implantation. O2 transfer did not correlate with any patient factors probably due to error inherent in the measurement of this variable. Independent measurements of IVOX gas transfer by respiratory gas exchange in a subset of patients with normal values of mixed venous Pco2 were in good agreement with the routine measurements and indicated that the device provided up to 26% of gas exchange requirements in this subset. We conclude that IVOX transfers clinically useful amounts of oxygen and carbon dioxide in vivo. Factors that influence gas transfer include device surface area, PvCO2, cardiac output, and duration of implantation. Optimization of these factors (such as with permissive hypercapnea) could result in enhanced performance in vivo.
Designing truly one-sided MPI-2 RMA intra-node communication on multi-core systems (2010)

The increasing popularity of multi-core processors has made MPI intra-node communication, including the intra-node RMA (Remote Memory Access) communication, a critical component in high performance computing. MPI-2 RMA model includes one-sided data transfer and synchronization operations. Existing designs in popularly used MPI stacks do not provide truly one-sided intranode RMA communication. They are built on top of twosided send-receive operations, therefore suffering from overheads of two-sided communication and dependency on the remote side. In this paper, we enhance existing shared memory mechanisms to design truly one-sided synchronization. In addition, we design truly one-sided intra-node data transfer using two kernel based direct copy alternatives: basic kernel-assisted approach and I/OAT-assisted approach. Our new design eliminates the overhead of using two-sided operations and eliminates the involvement from the remote side. We also propose a series of benchmarks to evaluate various performance aspects over multi-core architectures (Intel
Specific Localization of Serine 19 Phosphorylated Myosin II during Cell Locomotion and Mitosis of Cultured Cells (1998)

Phosphorylation of the regulatory light chain of myosin II (RMLC) at Serine 19 by a specific enzyme, MLC kinase, is believed to control the contractility of actomyosin in smooth muscle and vertebrate nonmuscle cells. To examine how such phosphorylation is regulated in space and time within cells during coordinated cell movements, including cell locomotion and cell division, we generated a phosphorylation-specific antibody. Motile fibroblasts with a polarized cell shape exhibit a bimodal distribution of phosphorylated myosin along the direction of cell movement. The level of myosin phosphorylation is high in an anterior region near membrane ruffles, as well as in a posterior region containing the nucleus, suggesting that the contractility of both ends is involved in cell locomotion. Phosphorylated myosin is also concentrated in cortical microfilament bundles, indicating that cortical filaments are under tension. The enrichment of phosphorylated myosin in the moving edge is shared with an epithelial cell sheet; peripheral microfilament bundles at the leading edge contain a higher level of phosphorylated myosin. On the other hand, the phosphorylation level of circumferential microfilament bundles in cell-cell contacts is low. These observations suggest that peripheral microfilaments at the edge are involved in force production to drive the cell margin forward while microfilaments in cell-cell contacts play a structural role. During cell division, both fibroblastic and epithelial cells exhibit an increased level of myosin phosphorylation upon cytokinesis, which is consistent with our previous biochemical study (Yamakita, Y., S. Yamashiro, and F. Matsumura. 1994. J. Cell Biol. 124:129-137). In the case of the NRK epithelial cells, phosphorylated myosin first appears in the midzones of the separating chromosomes during late anaphase, but apparently before the formation of cleavage furrows, suggesting that phosphorylation of RMLC is an initial signal for cytokinesis.
Positron Emission Tomography (2004)

To study alcohol’s effects on the structure and function of the brain in living human beings, researchers can use various imaging techniques. Positron emission tomography (PET) is a functional imaging approach used to study the metabolism and physiology of the brain. PET studies have found that both acute and chronic alcohol ingestion alter blood flow and metabolism in various brain regions, including the frontal lobes and cerebellum. Other analyses focusing on alcohol’s effects on brain chemical (i.e., neurotransmitter) systems have found that both acute and chronic alcohol consumption alter the activities of the inhibitory neurotransmitter gamma­ aminobutyric acid (GABA) and the excitatory neurotransmitters glutamate, dopamine, and serotonin. These alterations may contribute to the reinforcing and rewarding effects of alcohol as well as to symptoms of alcohol withdrawal. Imaging studies also have demonstrated that some of alcohol’s adverse effects on brain function can be reversed by abstinence or alcoholism treatment interventions. In addition, imaging studies may help in the development of new medications for alcoholism treatment.
Transcriptome-wide N<sup>6</sup>-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification (2014)

N(6)-methyladenosine (m(6)A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m(6)A modification becomes feasible. Here we present a transcriptome-wide m(6)A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m(6)A-modified genes, respectively. The m(6)A peak (m(6)A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m(6)A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m(6)A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m(6)A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m(6)A-modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m(6)A modification.
Extrusion Processing and Properties of Protein‐Based Thermoplastics (2009)

Abstract Increasing interest in competitive, sustainable, and biodegradable alternatives to petroleum‐based plastics has encouraged the developmentof protein‐based plastics. The formation of a homogeneous protein melt during extrusion occurs through: denaturation, dissociation, unraveling, and alignment of polymer chains. The presence of covalent cross‐links is unfavorable, decreasing chain mobility, increasing viscosity and preventing homogenization. Proteins have high softening temperatures, often above their decomposition temperatures. To avoid degradation, the required chain mobility is achieved by plasticizers. By understanding a protein's physiochemical nature, additives can be selected that lead to a bioplastic with good processability. The final structural and functional properties are highly dependent on the protein and processing conditions. magnified image
Continuous Security Metrics for Prevalent Network Threats: Introduction and First Four Metrics (2012)

Abstract : The goal of this work is to introduce meaningful security metrics that motivate effective improvements in network security. We present a methodology for directly deriving security metrics from realistic mathematical models of adversarial behaviors and systems and also a maturity model to guide the adoption and use of these metrics. Four security metrics are described that assess the risk from prevalent network threats. These can be computed automatically and continuously on a network to assess the effectiveness of controls. Each new metric directly assesses the effect of controls that mitigate vulnerabilities, continuously estimates the risk from one adversary, and provides direct insight into what changes must be made to improve security. Details of an explicit maturity model are provided for each metric that guide security practitioners through three stages where they (1) develop foundational understanding, tools and procedures, (2) make accurate and timely measurements that cover all relevant network components and specify security conditions to test, and (3) perform continuous risk assessments and network improvements. Metrics are designed to address specific threats, maintain practicality and simplicity, and motivate risk reduction. These initial four metrics and additional ones we are developing should be added incrementally to a network to gradually improve overall security as scores drop to acceptable levels and the risks from associated cyber threats are mitigated.
Circovirus in Tissues of Dogs with Vasculitis and Hemorrhage (2013)

We characterized the complete genome of a novel dog circovirus (DogCV) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. DogCV was detected by PCR in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. Co-infection with other canine pathogens was detected for 13/19 (68%) DogCV-positive dogs with diarrhea. DogCV capsid proteins from different dogs varied by up to 8%. In situ hybridization and transmission electron microscopy detected DogCV in the lymph nodes and spleens of 4 dogs with vascular compromise and histiocytic inflammation. The detection of a circovirus in tissues of dogs expands the known tropism of these viruses to a second mammalian host. Our results indicate that circovirus, alone or in co-infection with other pathogens, might contribute to illness and death in dogs.
Model-based high-precision tuning of NOR flash memory cells for analog computing applications (2016)

High-precision individual cell tuning was experimentally demonstrated, for the first time, in analog integrated circuits redesigned from a commercial NOR flash memory. The tuning is fully automatic, and relies on a write-verify algorithm, with the optimal amplitude of each write pulse determined from runtime measurements, using a compact model of cell's dynamics, fitted to experimental results. The algorithm has allowed tuning of each cell of a 100-cell array to any desired state within a 4-orders-of-magnitude dynamic range. With 10 write pulses, the average tuning accuracy is about 3%, while with 35 pulses the precision reaches ~0.3%. Taking into account the dynamic range, the last number is equivalent to ~1,500 levels, i.e. 10+ bits.
Tissue-Specific Regulation of Peptidyl-Glycine α-Amidating Monooxygenase Expression* (1989)

Peptidyl-glycine alpha-amidating monooxygenase (PAM; EC 1.14.17.3) is present in a variety of tissues, where it plays a vital role in the processing of numerous peptide substrates, often conferring bioactivity. PAM is present in high amounts in heart atrial myocytes and the pituitary gland, where activity is present in both soluble and membrane forms. We used AtT-20 cells, a mouse corticotrope tumor cell line, and primary heart atrial cultures to establish the occurrence of tissue-specific regulation of PAM expression. In the AtT-20 cells, PAM expression is regulated in parallel with the source of its peptide substrate, pro-ACTH/endorphin. PAM mRNA levels are increased to 132 +/- 5% of control values by treatment with (Bu)2-cAMP and decreased to 55 +/- 7% of control values by treatment with dexamethasone. Treatment with (Bu)2cAMP decreases PAM specific activity in the AtT-20 cells to 68 +/- 4% of the control value, presumably due to secretion of enzyme from the cells; dexamethasone treatment decreases PAM specific activity to 57 +/- 1% of the control value. In contrast, in heart atrial cultures, dexamethasone stimulates PAM expression. In atrial cultures exposed to dexamethasone for 48 h, PAM mRNA and PAM specific activity are elevated to 230 +/- 50% and 220 +/- 20% of control values, respectively; secretion of PAM activity is increased to 230% of the control value. As for AtT-20 cells, treatment of atrial cultures with (Bu)2cAMP increases PAM mRNA levels. Thus, PAM expression is regulated in a tissue-specific manner by dexamethasone in the two tissues examined. In AtT-20 cells, time-course studies and studies with cycloheximide indicate that dexamethasone exerts its effects on PAM mRNA levels by an indirect mechanism involving protein synthesis.
2'-Deoxycoformycin-induced hemolysis in the mouse. (1982)

2'-Deoxycoformycin (dCF), a tight-binding inhibitor of adenosine deaminase, has recently been entered into clinical trials. Toxicity has included lymphopenia, seizures, coma, conjunctivitis, renal failure, and hemolysis. Mice treated with dCF on a variety of schedules exhibited massive hemolysis. Hemolysis was brief, lasting about 20 hours, and did not recur upon readministration of the drug unless readministration was delayed for at least 6 days after initial exposure, which suggests that a sensitive subpopulation of cells was selectively destroyed. Splenectomy failed to protect the animals from dCF-induced hemolysis. Administration of adenosine or 2'-deoxyadenosine without dCF did not cause hemolysis, and use of these two agents with dCF did not potentiate the observed hemolysis. ATP and dATP levels were measured in erythrocytes, and changes in levels of these nucleotides did not correspond with the development of hemolysis.
Genomics of Mycobacterium tuberculosis: old threats & new trends. (2004)

Tuberculosis (TB) has been declared as a global health emergency by the World Health Organization (WHO). This has been mainly due to the emergence of multiple drug resistant strains and the synergy between tubercle bacilli and the human immunodeficiency virus (HIV). Genomic analysis of strains for outbreak investigations is in vogue for about a decade now. However, information available from whole genome sequencing efforts and comparative genomics of laboratory and field strains is likely to revolutionize efforts towards understanding molecular pathogenesis and dissemination dynamics of this dreaded disease. Genomic information is also going to fuel discovery projects where new targets will be identified and explored towards a new drug for TB. Besides this, efforts of information technologists, chemists, population biologists, freelance workers, media persons, non-governmental organizations and administrators to needed to handle the problem of tuberculosis to prevent it from becoming a pandemic.
Optimizing Loop Operation and Dataflow in FPGA Acceleration of Deep Convolutional Neural Networks (2017)

As convolution layers contribute most operations in convolutional neural network (CNN) algorithms, an effective convolution acceleration scheme significantly affects the efficiency and performance of a hardware CNN accelerator. Convolution in CNNs involves three-dimensional multiply and accumulate (MAC) operations with four levels of loops, which results in a large design space. Prior works either employ limited loop optimization techniques, e.g. loop unrolling, tiling and interchange, or only tune some of the design variables after the accelerator architecture and dataflow are already fixed. Without fully studying the convolution loop optimization before the hardware design phase, the resulting accelerator can hardly exploit the data reuse and manage data movement efficiently. This work overcomes these barriers by quantitatively analyzing and optimizing the design objectives (e.g. required memory access) of the CNN accelerator based on multiple design variables. We systematically explore the trade-offs of hardware cost by searching the design variable configurations, and propose a specific dataflow of hardware CNN acceleration to minimize the memory access and data movement while maximizing the resource utilization to achieve high performance. The proposed CNN acceleration scheme and architecture are demonstrated on a standalone Altera Arria 10 GX 1150 FPGA by implementing end-to-end VGG-16 CNN model and achieved 645.25 GOPS of throughput and 47.97 ms of latency, which is a >3.2× enhancement compared to state-of-the-art FPGA implementations of VGG model.
Dietary Fat and Carbohydrates Are Independently Associated With Circulating Insulin-Like Growth Factor 1 and Insulin-Like Growth Factor–Binding Protein 3 Concentrations in Healthy Adults (1999)

Serum IGF-1 and/or IGFBP-3 concentrations are associated with red meat, carbohydrate intake, and fat intake and, thus, may mediate the effect of these dietary factors on the pathogenesis of several disease states. Additional studies are needed to further quantify these associations and elucidate the underlying mechanisms.
Expression of Interleukin (IL)-1β, IL-8, IL-10 and IL-13 in Chronic Adult Periodontitis Progression (2017)

Introduction: Cytokines play a major role in the pathogenesis of periodontal disease and may be used as markers in diagnosis. We aimed to evaluate correlation between progression of periodontal disease and plasma expression of several interleukins.
Latest Advances Towards Ras Inhibition: A Medicinal Chemistry Perspective (2016)

Owing to their high occurrence rate across many human cancers and their lack of druggability so far, mutant forms of the signaling protein Ras are currently among the most attractive (and elusive) oncology targets. This strong appeal explains the sustained effort in the field, and the ensuing progress has rekindled optimism regarding the discovery of Ras inhibitors. In this Minireview, we discuss the most recent advances towards irreversible inhibitors, and highlight approaches to inhibitors of Ras-effector interactions that have been overshadowed by the current focus on direct Ras inhibition. At the same time, we provide a critical assessment from a medicinal chemistry perspective.
Corneal graft rejection associated with anterior iris adhesion: case report. (1978)

A patient's corneal graft rejection arose at the site of an anterior iris adhesion and was reduced by removal of the adhesion.
PURSUING AUTOMATED CLASSIFICATION OF HISTORIC PHOTOGRAPHIC PAPERS FROM RAKING LIGHT IMAGES (2014)

Surface texture is a critical feature in the manufacture, marketing, and use of photographic paper. Raking light reveals texture through a stark rendering of highlights and shadows. Though close-up raking light images effectively document surface features of photographic paper, the sheer number and diversity of textures used for historic papers prohibits efficient visual classification. This work provides evidence that automatic, computer-based classification of texture documented with raking light is feasible by demonstrating an encouraging degree of success sorting a set of 120 images made from samples of historic silver gelatin paper. Using this dataset, four university teams applied different image-processing strategies for automatic feature extraction and degree of similarity quantification.All four approaches successfully detected strong affinities and outliers built into the dataset. The creation and deployment of the algorithms was carried out by the teams without prior knowledge of the distributions of similarities and outliers.These results indicate that automatic classification of silver gelatin photographic paper based on close-up texture images is feasible and should be pursued. To encourage the development of other classification schemes, the 120-sample “training” dataset used in this work is available to other academic researchers at http://www.PaperTextureID.org.
Postnatal development of perineuronal nets in wild-type mice and in a mutant deficient in tenascin-R (2000)

The extracellular matrix glycoprotein tenascin-R (TN-R), colocalizing with hyaluronan, phosphacan, and aggregating chondroitin sulphate proteoglycans in the white and grey matter, is accumulated in perineuronal nets that surround different types of neurons in many brain regions. To characterize the role of TN-R in the formation of perineuronal nets, we studied their postnatal development in wild-type mice and in a TN-R knock-out mutant by using the lectin Wisteria floribunda agglutinin and an antibody to nonspecified chondroitin sulphate proteoglycans as established cytochemical markers. We detected the matrix components TN-R, hyaluronan, phosphacan, neurocan, and brevican in the perineuronal nets of cortical and subcortical regions. In wild-type mice, lectin-stained, immature perineuronal nets were first seen on postnatal day 4 in the brainstem and on day 14 in the cerebral cortex. The staining intensity of these nets for TN-R, hyaluronan, phosphacan, neurocan, and brevican was extremely weak or not distinguishable from that of the surrounding neuropil. However, all markers showed an increase in staining intensity of perineuronal nets reaching maximal levels between postnatal days 21 and 40. In TN-R-deficient animals, the perineuronal nets tended to show a granular component within their lattice-like structure at early stages of development. Additionally, the staining intensity in perineuronal nets was reduced for brevican, extremely low for hyaluronan and neurocan, and virtually no immunoreactivity was detectable for phosphacan. The granular configuration of perineuronal nets became more predominant with advancing age of the mutant animals, indicating the continued abnormal aggregation of chondroitin sulphate proteoglycans complexed with hyaluronan. As shown by electron microscopy in the cerebral cortex, the disruption of perineuronal nets was not accompanied by apparent changes in the synaptic structure on net-bearing neurons. The regional distribution patterns and the temporal course of development of perineuronal nets were not obviously changed in the mutant. We conclude that the lack of TN-R initially and continuously disturbs the molecular scaffolding of extracellular matrix components in perineuronal nets. This may interfere with the development of the specific micromilieu of the ensheathed neurons and adjacent glial cells and may also permanently change their functional properties.