gebhart/patrepeval huggingface dataset:
Computational Study of <i>Mycobacterium smegmatis</i> Acyl Transferase Reaction Mechanism and Specificity (2018)

The acyl transferase from Mycobacterium smegmatis (MsAcT) catalyzes the acyl transfer between a range of primary and secondary alcohols, whereby its outstanding ability is to perform this reaction in aqueous solution. Therefore, MsAcT opens different options for acylation reactions enabling alternatives for many conventionally hydrolytic enzymes used in biocatalysis. Nevertheless, hydrolysis is still a major side reaction of this enzyme. To provide a detailed understanding of the competition between hydrolysis and transesterification reactions, a combination of density functional theory and free energy perturbation methods have been employed. The relative binding free energies and the energy profiles of the chemical steps involved in the reaction were calculated for a number of substrates. The calculations show that the enzyme active site exhibits a higher affinity for substrates with an aromatic ring. The rate-determining step corresponds to the collapse of a negatively charged tetrahedral intermediate in the substrate acylation half-reaction. The intrinsic barriers of the transesterification and hydrolysis half-reactions are calculated to be of similar heights, suggesting that the determining factor in the MsAcT specificity is the higher binding affinity of the active site for the alcohol substrates relative to water. Finally, the influence of the acyl donor on the MsAcT-catalyzed reaction is also investigated by considering different esters in the calculations.
Integration in or Near Oncogenes Plays Only a Minor Role in Determining the in Vivo Distribution of HIV Integration Sites Before or During Suppressive Antiretroviral Therapy (2020)

Abstract HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 16,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 385,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 6 specific genes, and by clonal expansion. The clones in which a provirus integrated in an oncogene contributed to the survival of the clone comprise only a small fraction of the clones that persist in HIV-infected individuals on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist. Author Summary In HIV-infected individuals, a small fraction of the infected cells persist and divide. This reservoir persists on ART and can rekindle the infection if ART is discontinued. Because the number of possible sites of HIV DNA integration is very large, each infected cell, and all of its descendants, can be identified by the site where the provirus is integrated (IS). To understand the selective forces that determine the fates of infected cells in vivo, we compared the distribution of HIV IS in freshly-infected cells to cells from HIV-infected donors sampled both before and during ART. We found that, as has been previously reported, integration favors highly-expressed genes. However, over time the fraction of cells with proviruses integrated in highly-expressed genes decreases, implying that they grow less well. There are exceptions to this broad negative selection. When a provirus is integrated in a specific region in one of six genes, the proviruses affect the expression of the target gene, promoting growth and/or survival of the cell. Although this effect is striking, it is only a minor component of the forces that promote the growth and survival of the population of infected cells during ART.
Seven subthreshold flip-flop cells (2007)

For ultra-low-power applications, operating the transistors in their subthreshold region is an effective way of reducing the power dissipation of a circuit. This paper presents a comparative study of the performance of seven D-flip-flop cells operating in the subthreshold region, based on simulations in a 90 nm CMOS technology. Simulations have been performed with a supply voltage ranging from 150mV to 350mV. The best PDP and EDP numbers at 175mV is 13 aJ and 10 yJs, respectively.
Characterization of melanosomes and melanogenesis in cells cultured from Ota's nevus. (1997)

Cells from dermis and epidermis of Ota's nevus lesions were cultured to obtain the pigment producing cells that are specific epidermal and dermal melanocytes of nevus Ota. The following media were used: Eagle's minimum essential medium, fortified or not fortified with cholera toxin and phorbol ester. Both epidermal melanocytes and dermal melanocytes grew in the Eagle's minimum essential medium fortified with cholera toxin and phorbol ester. The melanocytes were characterized by 14C-tyrosine uptake and by identification of melanosomes and status of melanogenesis in comparison with those reported in dysplastic nevi and melanomas, as well as those found in Ota's nevus tissue in situ. Eumelanosomes, pheomelanosomes and secondary lysosomal melanosomes appeared in epidermal melanocytes. Pheomelanosomes and melanolysosomes, or myelinosiderosomes appeared predominantly in the dermal melanocytes. These melanosomes seemed to be related to the peculiar skin color of nevus Ota. Some of the abnormal types of melanosomes were very similar to those found in dysplastic nevi and melanomas.
JOSIE (1991)

We present an overview of an implemented knowledge system development tool, called JOSIE, that provides a general framework for integrating specialized representation and reasoning facilities. In our presentation we emphasize the problematic issues that arise when integrating specialized representations and the distinctive features of the facilities included in the system. The current system includes assertion, retraction, and query facilities using a predicate-calculus style interface language, a default sentential representation for the interface language, an inference rule language and forward chaining interpreter based on the interface language, a justification-based truth maintenance system that supports restricted nonmonotonic proofs, a frame-based specialized representation system that provides arbitrarily nested slot descriptions and default slot values, and a constraint language and reasoner within the frame system that provides both constraint propagation and symbolic solution of linear equations via Gaussian elimination.
Isocyanate crosslinked polymers for nonlinear optics. 1. Polymers derived from 3-amino-5-[4'-(N-ethyl-N-(2''-hydroxyethyl)amino)benzylidene]rhodanine (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsocyanate crosslinked polymers for nonlinear optics. 1. Polymers derived from 3-amino-5-[4'-(N-ethyl-N-(2''-hydroxyethyl)amino)benzylidene]rhodanineCecil V. Francis, Kenneth M. White, Gary T. Boyd, Robert S. Moshrefzadeh, Sarat K. Mohapatra, Marc D. Radcliffe, John E. Trend, and Robert C. WilliamsCite this: Chem. Mater. 1993, 5, 4, 506–510Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/cm00028a018https://doi.org/10.1021/cm00028a018research-articleACS PublicationsRequest reuse permissionsArticle Views195Altmetric-Citations30LEARN 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
Neurological outcomes of animal models of uterine artery ligation and relevance to human intrauterine growth restriction: a systematic review (2014)

This review concludes that neuronal death, white matter injury, motor abnormalities, and cognitive deficits are important outcomes of uterine artery ligation in animal models. Therefore, this is a clinically relevant type of model, as these findings resemble deficits in human cerebral palsy.
Magnetic and electrical properties of Co-Sm thin films deposited by dc magnetron sputtering (1997)

We investigated the effects of oxidation on the magnetic and electrical properties of the Co-Sm films as a function of film composition and substrate temperature. Co-Sm films were prepared on Si(100) and quartz glass by dc magnetron sputtering, and were characterized by XRD, TEM, VSM, RBS, and 4-point probe. Amorphous Co-Sm thin films deposited at room temperature showed strong ferromagnetic properties. For the films deposited at elevated substrate temperature, the resistivity and coercivity increased, while the saturation magnetization decreased. These phenomena were mainly due to partial oxidation of the Co-Sm films, which was verified by RBS measurement and high-resolution TEM analysis.
TU Elements: a Heterogeneous Family of Modularly Structured Eucaryotic Transposons (1985)

We describe here a family of foldback transposons found in the genome of the higher eucaryote, the sea urchin Strongylocentrotus purpuratus. Two major classes of TU elements have been identified by analysis of genomic DNA and TU element clones. One class consists of largely similar elements with long terminal inverted repeats (IVRs) containing outer and inner domains and sharing a common middle segment that can undergo deletions. Some of these elements contain insertions. The second class is highly heterogeneous, with many different middle segments nonhomologous to those of the first-class and variable-sized inverted repeats that contain only an outer domain. The middle and insertion segments of both classes carry sequences that also are found unassociated from the inverted repeats at many other genomic locations. We conclude that the TU elements are modular structures composed of inverted repeats plus other sequence domains that are themselves members of different families of dispersed repetitive sequences. Such modular elements may have a role in the dispersion and rearrangement of genomic DNA segments.
Breeding melon (Cucumis melo) with resistance to powdery mildew and downy mildew (2022)

Melon (Cucumis melo L.) production is often restricted by a plethora of pests and diseases, including powdery mildew and downy mildew caused respectively by the fungal species Podosphaera xanthii/Golovinomyces orontii and oomycete species Pseudoperonospora cubensis. Many efforts have been directed on identification of resistant sources by screening (wild) melon germplasm. In the current review, we summarized such efforts from various publications of the last 50 plus years. Resistance to powdery mildew has been identified in 239 melon accessions and downy mildew resistance in 452 accessions of both C. melo and the wild relative species C. figarei. Among the resistance sources, C. melo var. cantalupensis accessions PMR 45, PMR 5, PMR 6, and WMR 29 as well as C. melo var. momordica accessions PI 124111, PI 124112, and PI 414723 have been considered as the most valuable germplasm because multiple resistance genes have been identified from these accessions and are widely used in melon resistance breeding. Further genetic mapping in a number of resistant sources has enabled identification of 25 dominant genes, two recessive genes and seven QTLs conferring powdery mildew resistance, as well as eight dominant genes and 11 QTLs for downy mildew resistances. Based on the reported sequences of associated markers, we anchored physically (many of) these genes and QTLs to chromosomes of the melon cv. DHL92 genome. In addition to presenting a comprehensive overview on powdery mildew and downy mildew resistance in (wild) melon germplasm, we suggest strategies aiming at breeding melon with durable and broad-spectrum resistance to pathogens and pests.
The Practice of Urethral Dilation for Voiding Dysfunction Among Fellows of the Section on Urology of the American Academy of Pediatrics (2002)

Urethral dilation is rarely used as primary treatment for pediatric voiding dysfunction, is usually reserved until all other treatments have failed and appears to have long-term efficacy in less than 50% of patients. To define better the need for this treatment modality and its efficacy, a randomized prospective trial is mandatory.
Formvar membrane laid on artificial medium induces haustorium-like structure formation in powdery mildew fungi (2019)

We aimed to develop an artificial membrane system to observe the infection process of the obligate biotrophic powdery mildew fungi without the use of living plant cells. The conidia of Blumeria graminis and Erysiphe pisi conidia were inoculated on a formvar membrane laid on an artificial medium. Germinated conidia frequently formed appressoria and then penetrated the membrane to form haustorium-like structures in the artificial medium. Secondary hyphae elongation was also observed after the formation of haustorium-like structures. These results suggested that the formvar membrane laid on artificial medium induced the formation of haustorium-like structures that have roles in the formation of secondary hyphae.
Pyogranulomatous meningoencephalitis in a dog (2017)

Meningoencephalitis defines a pathological inflammation of the brain parenchyma and meninges classically dichotomised into infectious and non‐infectious meningoencephalitides. Pyogranulomatous meningoencephalitides have been sporadically reported in the veterinary literature associated with various infectious agents ( Mycobacteria species, Cladophialophora bantiana or Actinomyces species). The following outlines a case of pyogranulomatous meningoencephalitides suspected secondary to Aureimonas altamirensis infection. To the authors' knowledge, this is only the second report of A. altamirensis resulting in clinical disease in a dog.
Steam Gasification of Cellulose and Wood in a Fluidized Bed of Porous Clay Particles (2009)

Potential of biomass steam gasification with porous clay-derived materials that holds tar inside the reactor to enhance gas production was investigated. Tar capturing ability was compared for commercial FCC particles, commercial activated clay, lightly acidified bentonite, raw bentonite, porous silica particles and silica sand by using a laboratory scale fluidized bed reactor. FCC particles and all clay materials, even raw bentonite, were found to reduce heavy tar and water-soluble species emissions, and to increased carbonaceous materials deposited on the bed materials. The activated clay held two or more times the amounts of carbonaceous materials than porous silica did, although the specific surface areas were almost the same. Carbonaceous materials deposited on FCC particle in 923 K were easily gasified at temperatures greater than 973 K. Following up on these results, wood biomass gasification experiments were carried out at 923–1023 K for 90 min in activated clay or silica sand beds. Activated clay showed significantly high energy conversion to gas by gasification of captured carbonaceous materials.
Understanding Evolution of Lithium Trivanadate Cathodes During Cycling via Reformulated Physics-Based Models and Experiments (2021)

Degradation of lithium trivanadate ( Li x V 3 O 8 ) cathodes has been widely reported in the literature, but studies have offered little insight towards developing a detailed understanding of the evolution of the active material, and have been inconclusive as to the root cause of degradation. Here, we refit a validated physics-based model to discharge curves over the course of cycling at C/5, and use the evolution of the model parameters to track evolution of the cathode. A regularization penalty for adjusting model parameters from the validated model is introduced as a framework to identify which model parameters can explain a significant portion of the observed change in the voltage profile over the course of cycling. SEM reveals that lithium trivandate particles fracture upon cycling at C/5, consistent with the results of the parameter estimation, deactivation of lithium trivanadate and faster diffusion of lithium within the active particles. The physics-based model is then used to design modified cycling protocols which identify the phase transformation during discharge of lithium trivanadate as the driver of the particle fracture and capacity fade.
Anti-viral actions and viral dynamics in the early phase of three different regimens of interferon treatment for chronic hepatitis C: differences between the twice-daily administration of interferon-beta treatment and the combination therapy with interferon-alpha plus ribavirin. (2003)

To improve the efficacy of interferon (IFN) treatment for chronic hepatitis C, we have proposed the twice-daily administration of IFN-beta as a promising induction therapy. In this study, we demonstrated differences between the clearance of circulating HCV-RNA and the induction of anti-viral actions during the first 2 weeks of treatment. Nine patients with a high viral load and genotype 1b were randomly assigned to 3 groups: group A received 3MU of IFN-beta twice a day at intervals of 5 and 19 h; group B received 3MU of IFN-beta twice a day at intervals of 10 and 14 h; group C received 6MU of IFN-alpha once a day with ribavirin. The expression of OAS2, PKR, and MxA in peripheral blood mononuclear cells (PBMCs) were quantified by real-time polymerase chain reaction method. The viral clearance showed a bi-phasic pattern, and those in the second phase of groups A and B were significantly steeper than that of group C. The peak level of OAS2 during the first phase was correlated with the first phase decay. The MxA expression tended to be higher in group A and B than in group C. The expression of these 3 proteins tended to decrease at day 6 in group C, but increase in groups A and B. These might make differences in the viral decay during the second phase
Iron biofortification and homeostasis in transgenic cassava roots expressing the algal iron assimilatory gene, FEA1 (2012)

We have engineered the tropical root crop cassava (Manihot esculenta) to express the Chlamydomonas reinhardtii iron assimilatory gene, FEA1, in its storage roots with the objective of enhancing the root nutritional qualities. Iron levels in mature cassava storage roots were increased from 10 to 36 ppm in the highest iron accumulating transgenic lines. These iron levels are sufficient to meet the minimum daily requirement for iron in a 500 g meal. Significantly, the expression of the FEA1 gene in storage roots did not alter iron levels in leaves. Transgenic plants also had normal levels of zinc in leaves and roots consistent with the specific uptake of ferrous iron mediated by the FEA1 protein. Relative to wild-type plants, fibrous roots of FEA1 expressing plants had reduced Fe (III) chelate reductase activity consistent with the more efficient uptake of iron in the transgenic plants. We also show that multiple cassava genes involved in iron homeostasis have altered tissue-specific patterns of expression in leaves, stems, and roots of transgenic plants consistent with increased iron sink strength in transgenic roots. These results are discussed in terms of strategies for the iron biofortification of plants.
Corneal Healing After Excimer Laser Surface Ablation (1988)

The special properties of far-uv light sources include tissue removal without major temperature rise and preparation of a surface well suited for cell locomotion and adherence. We have evaluated the use of the 193 nm excimer laser for large area surface ablation of the cornea. We have found that tissue removal can be accomplished with successful wound healing and corneal function by selecting the proper laser parameters. Available data suggest that an ablative excimer laser of uniform and predictable beam power can supplant existing procedures for treating some corneal dystrophies, and preparing graft beds. The natural healing properties of the cornea aid in such procedures yet may make minor refractive change difficult to accomplish.
Grid-based Gaussian Processes Factorization Machine for Recommender Systems (2017)

Matrix Factorization (MF) is an effective approach to Collaborative Filtering (CF) in the field of recommender systems. However, the traditional Matrix Factorization method can only model the linear interaction of latent features between users and items, which is not convincing in reality. In addition, when only sparse dataset of small size is available and the historic behavior logs of most users are scarce, the traditional Matrix Factorization method behaves badly. In this paper, we propose a new model called Grid-based Gaussian Processes Factorization Machine (GGPFM), which is based on Gaussian Processes (GP), to capture the nonlinear relationship between users and items. The generic inference and learning algorithms for GP regression have cubic complexity with respect to the size of dataset. Rather than using off-the-shelf GP model, we endow the latent features with grid structures in order to decrease the model's complexity. Finally, we empirically show that our approach outperforms the state of the art method Gaussian Processes Factorization Machine (GPFM) and the traditional MF method significantly in cases where the data is sparse and most users are inactive.
Physical Exercise Induces Significant Changes in Immunoglobulin G N-Glycan Composition in a Previously Inactive, Overweight Population (2023)

Regular exercise improves health, modulating the immune system and impacting inflammatory status. Immunoglobulin G (IgG) N-glycosylation reflects changes in inflammatory status; thus, we investigated the impact of regular exercise on overall inflammatory status by monitoring IgG N-glycosylation in a previously inactive, middle-aged, overweight and obese population (50.30 ± 9.23 years, BMI 30.57 ± 4.81). Study participants (<i>N</i> = 397) underwent one of three different exercise programs lasting three months with blood samples collected at baseline and at the end of intervention. After chromatographically profiling IgG N-glycans, linear mixed models with age and sex adjustment were used to investigate exercise effects on IgG glycosylation. Exercise intervention induced significant changes in IgG N-glycome composition. We observed an increase in agalactosylated, monogalctosylated, asialylated and core-fucosylated N-glycans (padj = 1.00 × 10<sup>-4</sup>, 2.41 × 10<sup>-25</sup>, 1.51 × 10<sup>-21</sup> and 3.38 × 10<sup>-30</sup>, respectively) and a decrease in digalactosylated, mono- and di-sialylated N-glycans (padj = 4.93 × 10<sup>-12</sup>, 7.61 × 10<sup>-9</sup> and 1.09 × 10<sup>-28</sup>, respectively). We also observed a significant increase in GP9 (glycan structure FA2[3]G1, β = 0.126, padj = 2.05 × 10<sup>-16</sup>), previously reported to have a protective cardiovascular role in women, highlighting the importance of regular exercise for cardiovascular health. Other alterations in IgG N-glycosylation reflect an increased pro-inflammatory IgG potential, expected in a previously inactive and overweight population, where metabolic remodeling is in the early stages due to exercise introduction.