gebhart/patrepeval huggingface dataset:
Diagnosis and treatment of portal hypertension (2009)

Major progress has been made in the area of diagnosis and treatment of portal hypertension. Multi-detector row computed tomography (MD-CT) enabled the revelation of the precise overview of portal hemodynamics and was applied into the decision of therapeutic strategies. A noninvasive liver stiffness measurement device, transient elastography, is expected to be applied in the prediction of existence of esophageal varices. Balloon-occluded retrograde transvenous obliteration (B-RTO) is performed mainly in Japan to eradiate the fundic varices and high eradiation rate and low recurrence rate are reported. Partial splenic embolization (PSE) has been performed to improve hypersplenism without serious side-effect and excellent result is reported. Angiotensin receptor blockers (ARBs) are promising drugs for its portal hypotensive effect and antifibrotic effect and more investigation is necessary. Anti-fibrotic therapy, including autologous bone marrow therapy, has the possibility to improve not only liver fibrosis but also portal hypertension.
Sensitivity analysis of agent-based simulation utilizing massively parallel computation and interactive data visualization (2019)

Abstract An essential step in the analysis of agent-based simulation is sensitivity analysis, which namely examines the dependency of parameter values on simulation results. Although a number of approaches have been proposed for sensitivity analysis, they still have limitations in exhaustivity and interpretability. In this study, we propose a novel methodology for sensitivity analysis of agent-based simulation, MASSIVE (Massively parallel Agent-based Simulations and Subsequent Interactive Visualization-based Exploration). MASSIVE takes a unique paradigm, which is completely different from those of sensitivity analysis methods developed so far, By combining massively parallel computation and interactive data visualization, MASSIVE enables us to inspect a broad parameter space intuitively. We demonstrated the utility of MASSIVE by its application to cancer evolution simulation, which successfully identified conditions that generate heterogeneous tumors. We believe that our approach would be a de facto standard for sensitivity analysis of agent-based simulation in an era of ever-growing computational technology. All the result form our MASSIVE analysis is available at https://www.hgc.jp/~niiyan/massive .
Identification of platelet proteins that bind alloantibodies and autoantibodies (1984)

We have used the techniques of radioimmunoprecipitation (RIP) and Western blot to identify the membrane proteins that bind certain alloantibodies. Anti-PlA1 sera precipitated two bands, corresponding to platelet glycoproteins IIb and III, whether or not calcium was present during the procedure. By Western blot, this antibody bound only glycoprotein III. Anti-PlA1 serum does not precipitate proteins from the platelets of a patient with Glanzmann's thrombasthenia. Two monoclonal antibodies reacting with lymphocyte HLA antigens, as well as sera from highly allosensitized patients, precipitated bands of 38,500 and 13,500 daltons. These bands correspond to the molecular weights of the two subunits of the HLA antigen, as it has been described for other cell types. The patients' sera also precipitated a protein of 72,000 daltons from some platelets. The sera of two patients with quinidine-induced thrombocytopenia precipitated a 138,000-dalton band (glycoprotein Ib-alpha) in the presence of quinidine. The purified IgG antibody from one patient did not require other plasma factors to bind to platelets in the presence of quinidine, while purified antibody from a second patient required plasma factors other than, or in addition to von Willebrand factor. Although several sera from patients with idiopathic thrombocytopenic purpura (ITP) were tested, only one precipitated membrane proteins by the RIP method; this serum identified binding proteins corresponding to glycoproteins IIb and III.
3105 An Optimal Design Method in First Order Analysis : Simultaneous Optimization of Cross Sectional and Topological Configurations (2001)

Computer Aided Engineering (CAE) are widely accepted in many mechanical industries such as automotive industries. However, CAE applications are not utilized in the design phase because of the sophisticated operations and a huge amount of time for the analysis. Recently, the concept of a new CAE, First Order Analysis (FOA), has been proposed in order to overcome these problems. In this research, we develop a structural topology optimization methodology in FOA. This optimization method is constructed based on beam elements. The cross sectional dimensions such as the cross sectional area and rotational angle with respect to the principal axis, and the topological configurations of beams are simultaneously treated as design variables. The optimization procedure is developed based on the ground structure approach. Finally, some examples are provided to confirm the optimization method proposed here.
Emotion Recognition from Facial Expressions using Multilevel HMM (2000)

Human-computer intelligent interaction (HCII) is an emerging field of science aimed at providing natural ways for humans to use computers as aids. It is argued that for the computer to be able to interact with humans, it needs to have the communication skills of humans. One of these skills is the ability to understand the emotional state of the person. The most expressive way humans display emotions is through facial expressions. This work focuses on automatic facial expression recognition from live video input using temporal cues. Methods for using temporal information have been extensively explored for speech recognition applications. Among these methods are template matching using dynamic programming methods and hidden Markov models (HMM). This work exploits existing methods and proposes a new architecture of HMMs for automatically segmenting and recognizing human facial expression from video sequences. The novelty of this architecture is that both segmentation and recognition of the facial expressions are done automatically using a multilevel HMM architecture while increasing the discrimination power between the different classes. In the work we explore person-dependent and person-independent recognition of expressions.
A novel mechanism of olanzapine-induced lipid accumulation (2011)

Introduction Second generation antipsychotic drugs (SGADs) including olanzapine trigger adverse metabolic alterations possibly by a direct action on adipocytes. Objectives and aims The system of the inflammatory 5-lipoxygenase (5-LOX) and its activating protein (FLAP) have been implicated in lipid dysfunction in obesity. We investigated whether this system could participate in the adipogenic action of olanzapine. Methods Experiments were performed in 3T3-L1 adipocytes in vitro. Cells were treated with olanzapine and a FLAP inhibitor MK-886. Their lipid content, 5-LOX and FLAP mRNA content, and FLAP protein content were measured. Results Olanzapine treatment did not affect the cell content of 5-LOX mRNA; however, it decreased FLAP mRNA content at day five but not 24 hours after olanzapine addition. The inhibitory effect of olanzapine on FLAP expression was confirmed by quantitative Western blot assays. In the absence of a FLAP inhibitor, low concentrations of olanzapine (0.5 and 5 μM) increased lipid content only by about 13% (compared to about a 56% increase induced by 50 μM olanzapine) whereas in the presence of MK-886 these concentrations of olanzapine produced lipid increases comparable to the increase caused by 50 μM. In these experimental conditions, MK-886 alone did not alter the cell content of lipids. Conclusions 5-LOX system may be involved in lipid dysfunction not only in conditions of obesity but possibly in SGAD-related metabolic alterations. The known polymorphism in the genes of the human 5-LOX system could play a role in setting a variable individual susceptibility to the metabolic side effects of SGADs.
Optimal competitiveness for Symmetric Rectilinear Steiner Arborescence\n and related problems (2013)

We present optimal competitive algorithms for two interrelated known problems\ninvolving Steiner Arborescence. One is the continuous problem of the Symmetric\nRectilinear Steiner Arborescence (SRSA), studied by Berman and Coulston.\n A very related, but discrete problem (studied separately in the past) is the\nonline Multimedia Content Delivery (MCD) problem on line networks, presented\noriginally by Papadimitriu, Ramanathan, and Rangan. An efficient content\ndelivery was modeled as a low cost Steiner arborescence in a grid of\nnetwork*time they defined. We study here the version studied by Charikar,\nHalperin, and Motwani (who used the same problem definitions, but removed some\nconstraints on the inputs).\n The bounds on the competitive ratios introduced separately in the above\npapers are similar for the two problems: O(log N) for the continuous problem\nand O(log n) for the network problem, where N was the number of terminals to\nserve, and n was the size of the network. The lower bounds were Omega(sqrt{log\nN}) and Omega(sqrt{log n}) correspondingly. Berman and Coulston conjectured\nthat both the upper bound and the lower bound could be improved.\n We disprove this conjecture and close these quadratic gaps for both problems.\nWe first present an O(sqrt{log n}) deterministic competitive algorithm for MCD\non the line, matching the lower bound. We then translate this algorithm to\nbecome a competitive optimal algorithm O(sqrt{log N}) for SRSA. Finally, we\ntranslate the latter back to solve MCD problem, this time competitive optimally\neven in the case that the number of requests is small (that is, O(min{sqrt{log\nn},sqrt{log N}})). We also present a Omega(sqrt[3]{log n}) lower bound on the\ncompetitiveness of any randomized algorithm. Some of the techniques may be\nuseful in other contexts.\n
Fractionation of Phosphorus in Sludge‐Affected Soils (1983)

Abstract Phosphorus accumulated in sludge‐treated soils was chemically fractionated by a sequential extraction procedure. Samples used for the study were obtained from experimental plots of a sludge land application site, where composted sludges at rates 0, 22.5, 45, and 90 t ha −1 y −1 , and liquid sludges at rates of 0, 3.75, 7.5, and 15 cm/y have been applied for 5 y. There were also experimental plots whose liquid sludge treatments were terminated after 3 y. The experimental field was cropped with winter barley ( Hordeum vulgare ) after the sludge applications. In soils not treated with sludges, the Ca‐bound P accounted for 50–60% of the total P. An accumulation of Al‐ and Fe‐bound P occurred in all sludge‐treated soils. In the top 15 cm of surface soil, after 5 y of composted sludge treatment at a rate of 90 t ha −1 y −1 (1980), the Al‐ and Fe‐bound P was &gt; 60% of the total P. Concentrations of water‐soluble P in sludge‐treated soils also increased. There were indications that the organically bound P in sludge‐treated soils was the most likely form to leach. Three years after the termination of sludge applications, there was little change in the distribution pattern of sludge‐borne P in the soil profile.
Serine Proteases and their Inhibitors in Human Airway Epithelial Cells: Effects on Influenza Virus Replication and Airway Serine Proteases and their Inhibitors in Human Airway Epithelial Cells: Effects on Influenza Virus Replication and Airway Inflammation (2016)

Influenza virus replication and the production of inflammatory cytokines are associated with symptoms, including fever, and exacerbation of bronchial asthma and chronic obstructive pulmonary disease. Proteolytic activation of influenza viruses by serine proteases that are produced by airway epithelial cells is essential for viral entry and replication. Transmembrane protease serine S1 member (TMPRSS) 2, TMPRSS4 and TMPRSS11D have been detected certain cells, including the human alveolar epithelial cell line A549 and the surface epithelial cells of the human nasal mucosa, the trachea, the distal airways, and the lung. Several protease inhibitors, including aprotinin, reduce influenza virus replication. We previously demonstrated the following: (1) TMPRSSs (TMPRSS2, 4, and 11D) are present in primary cultures of human tracheal epithelial cells; (2) serine protease inhibitors, such as camostat and aprotinin, reduce the influenza virus replication and the release of the cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)- into cell supernatants; and (3) camostat reduces the cleavage of an influenza virus precursor protein, HA0, into the subunit HA1. These findings suggest that serine proteases expressed by human tracheal epithelial cells induce the proteolytic activation of influenza viruses and that serine protease inhibitors may reduce viral replication and the resultant production of inflammatory cytokines. Thus, serine protease inhibitors are potential candidates for anti-influenza virus drugs.
Analysis of a Thermotoga maritima DNA fragment encoding two similar thermostable cellulases, CelA and CelB, and characterization of the recombinant enzymes (1996)

Recombinant Escherichia coli clones displaying thermostable beta-glucanase activity were isolated from two different gene libraries of the hyperthermophilic bacterium Thermotoga maritima MSB8 (DSM 3109), and the nucleotide sequence of a 1,4-beta-glucanase gene designated celA was determined. Amino-terminal sequencing of cellulase I previously detected in T. maritima cells indicated that the celA gene encodes this beta-glucanase, which is now designated CelA. CelA, which has a calculated molecular mass of 29,732 Da, was purified from a recombinant E. coli strain to apparent homogeneity as judged by SDS-PAGE with a 44% yield. The enzyme was most active against soluble substrates such as mixed-linkage beta-glucan and CM-cellulose. CelA displayed remarkable thermostability, which was enhanced in the presence of high concentrations of salt. Downstream of the celA gene we found a second open reading frame, celB, whose nucleotide sequence was 58% identical to celA. Experimental proof that celB also encodes a beta-glucanase was obtained by separation from celA and expression in E. coli under the control of an efficient host promoter. According to the deduced amino acid sequences, CelB, in contrast to CelA, contains a signal peptide at the amino terminus. CelB and CelA had similar substrate specificities and temperature optima, but differed in their pH optima. Also, the addition of salt had a less stabilizing effect on CelB than on CelA. Nine 30 bp direct repeats, each itself representing a sequence with imperfect dyad symmetry, were detected upstream of the celA-celB cellulase gene cluster.
An improved spectral subtraction method based on modified MCRA noise estimate and magnitude compensation (2013)

Conventional spectral subtraction algorithm is limited by its stationary noise assumption. However, most of the nonstationary noises are encountered in real world. In this paper, a novel refined spectral subtraction algorithm for speech enhancement is proposed. The algorithm based on both MCRA (Minima Controlled Recursive Averaging) noise estimate algorithm and magnitude compensation algorithm, which could keep residual noise and speech distortion under a lower level.
FOXM1 modulates 5-FU resistance in colorectal cancer through regulating TYMS expression (2019)

Resistance to 5-Fluoruracil (5-FU) has been linked to elevated expression of the main target, thymidylate synthase (TYMS), which catalyses the de novo pathway for production of deoxythymidine monophosphate. The potent oncogenic forkhead box transcription factor, FOXM1 is is regulated by E2F1 which also controls TYMS. This study reveals a significant role of FOXM1 in 5-FU resistance. Overexpression and knock-down studies of FOXM1 in colon cancer cells suggest the importance of FOXM1 in TYMS regulation. ChIP and global ChIP-seq data also confirms that FOXM1 can also potentially regulate other 5-FU targets, such as TYMS, thymidine kinase 1 (TK-1) and thymidine phosphorylase (TYMP). In human colorectal cancer tissue specimens, a strong correlation of FOXM1 and TYMS staining was observed. Elevated FOXM1 and TYMS expression was also observed in acquired 5-FU resistant colon cancer cells (HCT116 5-FU Res). A synergistic effect was observed following treatment of CRC cells with an inhibitor of FOXM1, thiostrepton, in combination with 5-FU. The combination treatment decreased colony formation and migration, and induced cell cycle arrest, DNA damage, and apoptosis in CRC cell lines. In summary, this research demonstrated that FOXM1 plays a pivotal role in 5-FU resistance at least partially through the regulation of TYMS.
Classification of breast lesions using cross-modal deep learning (2017)

Automatic detection and classification of lesions in medical images is a desirable goal, with numerous clinical applications. In breast imaging, multiple modalities such as X-ray, ultrasound and MRI are often used in the diagnostic workflow. Training robust classifiers for each modality is challenging due to the typically small size of the available datasets. We propose to use cross-modal transfer learning to improve the robustness of the classifiers. We demonstrate the potential of this approach on a problem of identifying masses in breast MRI images, using a network that was trained on mammography images. Comparison between cross-modal and cross-domain transfer learning showed that the former improved the classification performance, with overall accuracy of 0.93 versus 0.90, while the accuracy of de-novo training was 0.94. Using transfer learning within the medical imaging domain may help to produce standard pre-trained shared models, which can be utilized to solve a variety of specific clinical problems.
Cryopreservation of Gene Disrupted Mouse Spermatozoa. (1998)

Cryopreservation of mouse spermatozoa has recently become available for use. In this study, we attempted to apply this technique to the maintenance of gene disrupted mouse lines. Cauda epididymides that were taken from Et1tm1Csk and Gktm1Csk mice were minced in 100 μl of a cryopreservation solution which consisted of 18% raffinose and 3% skim milk. Sperm suspensions in plastic straws were cooled rather rapidly by being placed in the gas phase above liquid nitrogen, and then were stored at -196°C. The frozen straws were thawed rapidly being by immersing in a water bath at 30°C. For in vitro fertilization, 1 μl of thawed sperm suspensions from each mouse strain was added directly to oocytes contained in 200 μl of medium. Following pre-incubation of the frozen-thawed spermatozoa, ICR oocytes were introduced into the medium containing the frozen-thawed spermatozoa. The fertilization rates of the oocytes inseminated with Et1tm1Csk and Gktm1Csk frozen-thawed spermatozoa were 71% and 77%, respectively. The development rates into young after embryo transfer were in a range of 32-65%. Progeny tests revealed that the mutated locus/loci were transmitted to the next generation according to the Mendelian law of the inheritance of characteristics. These results indicate that cryopreservation of spermatozoa provides an effective alternative to embryo freezing for maintenance of gene disrupted mouse strains.
Virtualization of Linux Based Computers: The Linux-VServer Project (2005)

This article presents the available programs that can provide, with different technology, a virtualization of Linux computers. We define some usage criteria that allows the reader to chose the relevant virtualization technology according to its specific needs. We focus on the Linux-VServer technology, which is a very lightweight and effective technology for the regular Linux user not interested in Kernel hacking. The Linux-VServer project also supports additional security options and resources limitation that can be very useful. This is also the most mature open-source technology and several users have production servers using this technology for years now.
Synthèse d'oligosaccharides de chondroitines sulfate D (2001)

Les chondroitines sulfate sont des polysaccharides microheterogenes de la famille des proteoglycanes. Elles sont constituees d'unites disaccharidiques repetitives d'une N-acetyl-D-galactosamine et d'un acide D-glucoronique, pouvant comporter sur certains hydroxyles des substitutions par des esters sulfuriques. L'interet pour ce type de molecules repose sur leur participation a de nombreux processus biologiques (pathologie rhumatologique, reconnaissance cellulaire, angiogenese,. . . ) ainsi que sur la recherche fondamentale liee a leur biosynthese. Dans le but de mieux comprendre ces differents phenomenes, nos travaux ont porte sur la synthese par voie chimique de fragments de tailles variees de chondroitines sulfate de type D. A partir de produits commerciaux peu couteux, nous avons pu mettre au point des syntheses efficaces des differents monomeres : les monosaccharides a structure D-galactosamine ont ainsi pu etre obtenus a partir du chlorhydrate de D-glucosamine par epimerisation de la position 4 au cours de la synthese. La construction des motifs de tailles superieures a ensuite pu etre realisee avec de bons rendements et la stereochimie souhaitee, justifiant une nouvelle fois l'utilisation de glycosides donneurs de nature trichloroacetimidate ainsi que celle de groupements participant 2-trichloroacetamido. En outre, l'utilisation de la voie de synthese par blocs disaccharidiques qui a ete etudiee a donne lieu a des resultats tres satisfaisants. Des molecules di-, tetra- et hexasaccharidiques ont pu etre obtenues et ont ete formellement caracterisees par des etudes RMN.
Research concerning the radioprotective and immunostimulating effects of deuterium-depleted water. (2002)

Mice fed for 15 days with Deuterium-Depleted Water (30 ppm deuterium) had a statistically significant increased survival rate compared with control groups fed with normal distilled water (150 ppm deuterium), after 8.5 Gy irradiation (61% survival in the test group versus 25% in the control group). The hematological picture showed that normal WBC, RBC and platelet counts were maintained in the test groups. Immunological parameters (serum opsonic and bactericidal capacity, bactericidal capacity of the peritoneal macrophages) showed a marked increase in the test groups compared to a severe decrease in the control groups. Auxiliary tests using chemical radiomimetics (hydrochloric embihine) and immunosuppressors (cyclophosphamide) showed a strong protective effect of deuterium-depleted water against the decrease of the leukocyte counts and other immunologic parameters. In conditions of experimental inflammation induced with subcutaneous-implanted pellets, deuterium-depleted water feeding resulted in a statistically significant increase of the inflammatory response, demonstrated by increased percentages of PMN and lymphocytes in the peripheral blood and the increased phagocytic capacity of the peripheral blood PMN. Experimental infections induced with K. pneumoniae 506 and S. pneumoniae 558 in mice irradiated or treated with cyclophosphamide showed increased, non-specific immunity parameters. All results show a marked intensification of the immune defenses and increased proliferation of the peripheral blood cells, probably accounting for the radioprotective effects.