gebhart/patrepeval huggingface dataset:
A Stoichiometric and Pseudo Kinetic Model of Loop Mediated Isothermal Amplification (2020)

Loop mediated isothermal amplification (LAMP) is one of the most popular isothermal DNA amplification techniques for research and commercial applications. The LAMP mechanism is powered by strategic primer design and a strand displacement polymerase, generating products that fold over, creating loops. LAMP leads to generation of products of increasing length over time. These products containing multiple loops are conventionally called cauliflower structures. Existing literature on LAMP provides extremely limited understanding of progression of cascades of reactions involved in the reaction and it is believed that cauliflower structures of increasing length constitute a majority of the product formed in LAMP. This study presents a first of its kind stoichiometric and pseudo kinetic model to comprehend LAMP reactions in deeper depth by (i) classifying LAMP reaction products into uniquely identifiable categories, (ii) generating a condensed reaction network to depict millions of interconnected reactions occurring during LAMP, and (iii) elucidating the pathways for amplicon generation. Despite the inherent limitations of conventional stoichiometric modelling for polymerization type reactions (the network rapidly becomes too large and intractable), our model provides new theoretical understanding of the LAMP reaction pathway. The model shows that while longer length products are formed, it is the smaller length recycle amplicons that contribute more towards the exponential increase in the amount of double stranded DNA. Prediction of concentration of different types of LAMP amplicons will also contribute substantially towards informing design of probe-based assays.
EFFECT OF HEPATIC ISCHEMIA ON ORGANIC ANION (OA) CLEARANCE & OXIDATIVE METABOLISM (1991)

s of Papers to be Presented at the Fifty-first Annual Session American Association for the Surgery of Trauma Wyndham Franklin Plaza Hotel Philadelphia, Pennsylvania September 11–14, 1991: PDF Only
Steam Gasification of Coals with Calcium Hydroxide (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSteam Gasification of Coals with Calcium HydroxideYasuo Ohtsuka and Kenji AsamiCite this: Energy Fuels 1995, 9, 6, 1038–1042Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ef00054a016https://doi.org/10.1021/ef00054a016research-articleACS PublicationsRequest reuse permissionsArticle Views465Altmetric-Citations53LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Automatic watershed segmentation of randomly textured color images (1997)

A new method is proposed for processing randomly textured color images. The method is based on a bottom-up segmentation algorithm that takes into consideration both color and texture properties of the image. An LUV gradient is introduced, which provides both a color similarity measure and a basis for applying the watershed transform. The patches of watershed mosaic are merged according to their color contrast until a termination criterion is met. This criterion is based on the topology of the typical processed image. The resulting algorithm does not require any additional information, be it various thresholds, marker extraction rules, and suchlike, thus being suitable for automatic processing of color images. The algorithm is demonstrated within the framework of the problem of automatic granite inspection. The segmentation procedure has been found to be very robust, producing good results not only on granite images, but on the wide range of other noisy color images as well, subject to the termination criterion.
Development of cytoplasmic male sterile lines and restorer lines of various elite Indica Group rice cultivars using CW-CMS/Rf17 system (2019)

The CW-CMS/Rf17 system will be useful to produce CMS lines and restorer lines of various elite Indica Group rice cultivars.
Nutritional Properties of Starch in Buckwheat Products:  Studies in Vitro and in Vivo (2000)

The nutritional characteristics of buckwheat starch were studied to identify the possibility for reduced postmeal metabolic responses to various buckwheat products. The in vitro rate of starch hydrolysis and resistant starch (RS) formation in boiled buckwheat groats and in a series of breads, baked with 30-70% of buckwheat flour (BWF) or groats (BWG), respectively, were evaluated in vitro. In parallel, postprandial glucose and insulin responses and also the satiety score to BWG and wheat bread with 50% BWG as compared with the reference white wheat bread (WWB) were studied in healthy humans. The highest concentration of RS was found in boiled BWG (6% total starch basis). The RS level in bread products based on different proportions of BWF or BWG (30-70%) varied from 0.9 to 4.4%. The rate of in vitro amylolysis was significantly lower (P < 0.05) in all buckwheat products in comparison with the reference WWB. The calculated hydrolysis indices (HI) were lowest in boiled BWG (HI = 50) and in bread with 70% BWG (HI = 54). Consumption of boiled BWG or bread based on wheat flour and 50% BWG induced significantly lower postprandial blood glucose and insulin responses compared with the WWB. The calculated glycemic and insulinemic indices (GI and II) for boiled BWG were 61 and 53 and for the buckwheat bread, 66 and 74, respectively. The highest satiety score was found with boiled BWG. It is concluded that buckwheat has potential use in the design of foods with lower GI properties.
Mass Action and Conservation of Current (2016)

Abstract The law of mass action does not force a series of chemical reactions to have the same current flow everywhere. Interruption of far-away current does not stop current everywhere in a series of chemical reactions (analyzed according to the law of mass action), and so does not obey Maxwell’s equations. An additional constraint and equation is needed to enforce global continuity of current. The additional constraint is introduced in this paper in the special case that the chemical reaction describes spatial movement through narrow channels. In that case, a fully consistent treatment is possible using different models of charge movement. The general case must be dealt with by variational methods that enforce consistency of all the physical laws involved. Violations of current continuity arise away from equilibrium, when current flows, and the law of mass action is applied to a non-equilibrium situation, different from the systems considered when the law was originally derived. Device design in the chemical world is difficult because simple laws are not obeyed in that way. Rate constants of the law of mass action are found experimentally to change from one set of conditions to another. The law of mass action is not robust in most cases and cannot serve the same role that circuit models do in our electrical technology. Robust models and device designs in the chemical world will not be possible until continuity of current is embedded in a generalization of the law of mass action using a consistent variational model of energy and dissipation.
Identifying repeated structural elements in folded proteins (1994)

A previously described method for partitioning amino acid dihedral angle space generates a set of cluster centers which may be used to represent residue backbones in three dimensional protein structures [Id]. 99 non-homologous polypeptide chains are eztracted from Brookhaven Protein D ata B ank files and abstracted into sequences of these cluster centers, then this data set is ezamined for repeated sub-sequences. Repeated sequences of amino acid conformational clusters indicate duplicated motifs or sub-structures in folded proteins, independent of amino acid sequence identity. This representation is significantly more detailed than standard secondary structure descriptors (heliz, strand, turn, etc.) and facilitates the identification of common structural elements without regard to sequence length. The current work ezamines the degree to which three ezample proteins share sub-structures with the remainder of the data set (ribonuclease A, erythrocruorin, and actinozanthin), the specification of a-helices and &strands under this system, and the sensitivity of the method to visual diflerences between structures.
Microkinetic Modeling of Homogeneous and Gold Nanoparticle-Catalyzed Oxidation of Cyclooctene (2018)

Small gold nanoparticles (AuNPs) have recently shown potential to act as a catalyst for oxidation reactions mediated by free radicals, with their role postulated to be facilitating hydrogen abstraction by gold superoxo species and/or activation of hydroperoxides. Cyclooctene oxidation using molecular oxygen as the oxidant at 373 K showed high selectivity to the epoxide product, cyclooctene oxide, with either tert-butyl hydroperoxide as an initiator or in the presence of small AuNPs (5–8 atoms). While previous studies have investigated the mechanism leading to high epoxide selectivity using density functional theory, a full microkinetic model was developed in this work using automated network generation to determine the relative contributions of elementary reactions and the role of AuNPs. A cycle of radical addition of peroxy and alkoxy radicals with subsequent epoxidation reactions can justify the observed activity and selectivity to epoxide at multiple temperatures and initiator concentrations. The alcohol, ketone, and hydroperoxide minor products are formed when the peroxy and alkoxy radicals perform hydrogen abstraction or β-scission. The overall selectivity is determined by the competition between the addition and hydrogen abstraction reactions. With the underlying homogeneous reaction model validated, the effect of the AuNPs was determined through an expanded model that includes cycles for both hydrogen abstraction by superoxo gold species and hydroperoxide decomposition via species derived from AuNPs. The model suggests that hydrogen abstraction by the superoxo gold species dominates at short times compared to homogeneous initiation, increasing the activity during the induction period and reducing the time before radical chain oxidation commences. On the time scale of an hour, hydroperoxide decomposition is significantly catalyzed by the presence of gold species, increasing the overall rate of chain propagation.
Acute otitis media. Histopathological changes: a post mortem study on temporal bones. (2000)

A classification of otitis media is proposed and the histopathological changes of otitis media with effusion are reviewed post mortem on two temporal bones. A case of adhesive otitis media is observed on temporal bone slides. The clinical and therapeutic aspect are examined and treatment guidelines are proposed.
Alignment and small oscillation of superparamagnetic iron oxide nanoparticle in liquid under alternating magnetic field (2019)

It is important to understand the rotational behavior of magnetic nanoparticles (MNPs) in liquids under an alternating magnetic field for their successful application in biomedical fields. These applications include magnetic hyperthermia therapy and magnetic particle imaging. In particular, recent theoretical studies suggest that the physical rotation of MNP itself causes a significant change in the magnetization response of MNPs. However, because it is hard to distinguish the contribution of the physical rotation to the magnetization curve, its behavior under an alternating field has not been established to date. In this study, we measured the absorbance change of maghemite MNP suspension. We observed magnetically induced linear dichroism under a damped oscillatory magnetic field (DOMF) with Faraday configuration, where the propagation of light was parallel to the magnetic field. Accompanied by the application of DOMF, an absorbance change was observed. Through numerical simulations, it was revealed that the waveform of the absorbance change reflects the behavior of the physical rotation. From the analysis of the waveform, it was experimentally found that the easy axis of the MNP aligns partially and oscillates with the small amplitude under an alternating magnetic field. The rotation mechanism of the MNP in liquids under an alternating magnetic field is proposed based on the observed waveform of the absorbance change. We also investigated the influences of the viscosity and the field frequency on the rotation behavior and confirmed that these results were consistent with the mechanism.
Overcoming Multi-Model Forgetting (2019)

We identify a phenomenon, which we refer to as multi-model forgetting, that occurs when sequentially training multiple deep networks with partially-shared parameters; the performance of previously-trained models degrades as one optimizes a subsequent one, due to the overwriting of shared parameters. To overcome this, we introduce a statistically-justified weight plasticity loss that regularizes the learning of a model's shared parameters according to their importance for the previous models, and demonstrate its effectiveness when training two models sequentially and for neural architecture search. Adding weight plasticity in neural architecture search preserves the best models to the end of the search and yields improved results in both natural language processing and computer vision tasks.
A time‐resolved fluorescence resonance energy transfer‐based screen for identification of a novel claudin‐4 binder that modulates the epithelial tight junction barrier (2020)

Claudins, a 27‐member family of proteins with four transmembrane domains each, play a pivotal role in maintaining tight junction (TJ) seals in epithelial and endothelial tissue. The C‐terminal fragment of Clostridium perfringens enterotoxin (C‐CPE) binds to claudin‐4, which is a key functional and structural component of the TJ in mucosal epithelial cells. Upon binding, C‐CPE reversibly modulates TJ seals, yielding an enhancement of the paracellular transport of solutes. However, the use of C‐CPE as an absorption enhancer is limited by the molecule’s immunogenicity and manufacturing cost. In the present study, we developed a high‐throughput screening system using Time‐Resolved Fluorescence Resonance Energy Transfer (TR‐FRET) to identify small‐molecule compounds that bind to claudin‐4. Using this system, we performed a claudin‐4 binding screen of a library containing 2642 biologically active small molecules, and identified thiostrepton as a novel claudin‐4 binder. Thiostrepton decreased the transepithelial electrical resistance and increased flux of 4‐kDa FITC‐dextran in Caco‐2 cell monolayers without cell toxicity. Immunoblotting analysis revealed that thiostrepton changed the level of claudin‐4 in the Triton‐X soluble fraction, which contains TJ components, without altering the localization of claudin‐4. Furthermore, treatment of isolated rat jejunum with thiostrepton increased absorption of 4‐kDa FITC‐dextran. The TR‐FRET‐based screening system described here is expected to be of use in identifying compounds that modulate the permeability of the intestinal epithelial cell barrier; these compounds might serve as novel absorption enhancers in the intestine. Support or Funding Information This study was supported in part by Grants‐in‐Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan (19H04468, 18K19400); a grant for Research on Development of New Drugs from the Japan Agency for Medical Research and Development (AMED); and grants from the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research [BINDS]) of AMED (JP19am0101077, JP19am0101084, JP19am0101090).
MMP-9 inhibition promotes anti-tumor immunity through disruption of biochemical and physical barriers to T-cell trafficking to tumors (2018)

Matrix metalloproteinase-9 (MMP-9), whose expression is frequently dysregulated in cancer, promotes tumor growth, invasion, and metastasis by multiple mechanisms, including extracellular matrix remodeling and growth-factor and cytokine activation. We developed a monoclonal antibody against murine MMP-9, which we found decreased growth of established primary tumors in an orthotopic model of HER2-driven breast cancer (HC11-NeuT) in immunocompetent mice. RNA sequencing (RNAseq) profiling of NeuT tumors and additional mouse model tumors revealed that anti-MMP-9 treatment resulted in upregulation of immune signature pathways associated with cytotoxic T-cell response. As there is a need to boost the low response rates observed with anti-PDL1 antibody treatment in the clinical setting, we assessed the potential of anti-MMP-9 to improve T-cell response to immune checkpoint inhibitor anti-PDL1 in NeuT tumors. Anti-MMP-9 and anti-PDL1 cotreatment reduced T-cell receptor (TCR) clonality and increased TCR diversity, as detected by TCR sequencing of NeuT tumors. Flow cytometry analyses of tumors showed that the combination treatment increased the frequency of CD3+ T cells, including memory/effector CD4 and CD8 T cells, but not regulatory T cells, among tumor-infiltrating leukocytes. Moreover, in vitro enzymatic assays corroborated that MMP-9 cleaves key T-cell chemoattractant CXC receptor 3 ligands (CXC ligand [CXCL] 9, CXCL10, and CXCL11) and renders them inactive in T-cell migration assays. Consistent with our in vitro experiments, analysis of NeuT tumor protein lysates showed that anti-MMP-9 treatment increases expression of CXCL10 and other T cell-stimulating factors, such as interleukin (IL)-12p70 and IL-18. We show that inhibition of MMP-9, a key component of the tumor-promoting and immune-suppressive myeloid inflammatory milieu, increases T-helper cell 1 type cytokines, trafficking of effector/memory T cells into tumors, and intratumoral T-cell diversity.
MR evaluation of cervical cancer in hysterectomy specimens: Correlation of quantitative T2 measurement and histology (1994)

Specimens from modified radical hysterectomies performed for invasive carcinoma of the cervix were analyzed with quantitative T2 magnetic resonance (MR) imaging and histologic study to determine to what degree there was a correlation between the findings of the two modalities. The mean T2 of cervical stroma was 48 msec, while the outer zone of the cervix had a mean T2 of 62 msec and the central canal region typically had T2 values of 115 msec +/- 20 (standard deviation). A total of nine cervical cancers were analyzed, and their mean T2 value was 79 msec. Separation between cervical stroma and tumor was good, with stromal T2 values ranging from 30 to 66 msec, while tumor T2s ranged from 60 to 97 msec. Statistical analysis indicated that these data were associated with a sensitivity of 89% and a specificity of 95%, with 95% confidence intervals of [50%, 99.4%] and [74%, 99.7%], respectively, for separating tumor from stroma on the basis of T2 value. Quantitative T2 imaging was found to provide an effective, nonsubjective means of classifying cervical anatomy and neoplastic disease.
A case report of same-day denture repair using magnetic attachments (2016)

We report clinical uses of magnetic attachments for the repair of dentures and retainers on the same day. This report describes three clinical cases. In all cases, the abutment teeth that act as retention elements for the dentures were detached due to secondary caries, and, without abutment teeth, retention was extremely poor. The patients were dissatisfied with the dynamic stability and retention of their dentures. Therefore, keepers of the magnetic attachments were fixed with composite resin material to the remaining radicular teeth, and magnetic assemblies were attached to the dentures. The magnetic attachments used were MAGFIT® RKR (AICHI STEEL, Japan) in cases 1 and 2 and GIGAUSS® (GC, Japan) in case 3. As a result, patients’ complaints of functional dissatisfaction were resolved.
Fluorescence Imaging Topography Scanning System for intraoperative multimodal imaging (2017)

Fluorescence imaging is a powerful technique with diverse applications in intraoperative settings. Visualization of three dimensional (3D) structures and depth assessment of lesions, however, are oftentimes limited in planar fluorescence imaging systems. In this study, a novel Fluorescence Imaging Topography Scanning (FITS) system has been developed, which offers color reflectance imaging, fluorescence imaging and surface topography scanning capabilities. The system is compact and portable, and thus suitable for deployment in the operating room without disturbing the surgical flow. For system performance, parameters including near infrared fluorescence detection limit, contrast transfer functions and topography depth resolution were characterized. The developed system was tested in chicken tissues ex vivo with simulated tumors for intraoperative imaging. We subsequently conducted in vivo multimodal imaging of sentinel lymph nodes in mice using FITS and PET/CT. The PET/CT/optical multimodal images were co-registered and conveniently presented to users to guide surgeries. Our results show that the developed system can facilitate multimodal intraoperative imaging.
Postphenomenology vs Postpositivism : Don Ihde vs Bruno Latour (2014)

Our presentation will try to clarify the differences between Postphenomenology and Postpositivism. Contemporary studies of technology and its relation to science are very much inspired by the works of Don Ihde and Bruno Latour.Updated February 2016.
Radio communications: components, systems, and networks (2011)

Dear readers: In this issue of the series, our focus is back on the basic techniques and building blocks of communications systems such as transceivers and modulation. In addition, we provide a look into new standardization activity in the area of cognitive radios.
The Equity Risk Premium Essays and Explorations (2006)

Abstract This book aims to create a strong understanding of the empirical basis for the equity risk premium. Through the research and anaylsis of two scholars who are experts in this field, this volume presents the key issues that are paramount to investors, including whether or not to use historical data as a method of equity investing, and can the equity premium reflect changes in fundamental values and cash flows of the market.
Efficacy and safety of empagliflozin for type 2 diabetes mellitus (2018)

Our evidence supports the application of EMPA in treatment of patients with T2DM who are obesity or at risk of weight gain.
Methylphenidate in Hyperkinetic Children: Differences in Dose Effects on Learning and Social Behavior (1977)

Methylphenidate (Ritalin) is widely prescribed for hyperkinetic children. This study showed a peak enchancement of learning in children after being given a dose of 0.3 milligram per kilogram of body weight, and a decrement in learning in those given larger doses; social behavior showed the most improvement in children given 1.0 milligram per kilogram. These results had been hypothesized from theoretical dose-response curves which indicate different target behaviors would improve at different doses.