gebhart/patrepeval huggingface dataset:
Parametric study on the interface pullout strength of the vertebral body replacement cage using FEM-based Taguchi methods (2008)

Improper design of vertebral body cages may seriously affect the interface strength and cause the lose of fixation for a vertebral body replacement. This research used a FEM-based Taguchi method to investigate the effects of various factors to find the robust design of the body cage. Three-dimensional finite element models with a nonlinear contact analysis have been developed to simulate the pullout strength of the body cage. Then, the Taguchi robust design method was used to evaluate the spike design. In a situation without bone fusion, the spike row, the spike oblique, and the spike height were especially important factors. The optimum combination has been found to be the pyramidal spike type, a spike height of 2mm, a spike diameter of 2.2mm, an oblique geometry, 11 rows per 28 mm, and an inner diameter of 10mm. In a situation with bone fusion, the spike row, the spike height, and the inner diameter were the most significant factors. Here, the optimum combination has been found to be the conical spike type, a spike height of 2mm, a spike diameter of 2.2mm, an oblique geometry, 11 rows per 28 mm, and an inner diameter of 20mm. The finite element analyses could be used to predict the interface stiffness of the body cages. The FEM-based Taguchi methods have effectively decreased the time and effort required for evaluating the design variables of implants and have fairly assessed the contribution of each design variable.
The Impact of Healing on the Growth of Christianity in Asia: An Empirical Investigation (2019)

This article explores the role healing has played in the expansion of Christianity throughout Asia. It documents stories from various regions of Asia to demonstrate that healing is an effective method for evangelism.
Cerebrospinal fluid levels of biotin in various neurological disorders (1999)

There is a significant reduction in cerebrospinal fluid biotin in epileptics and patients with multiple sclerosis compared to controls. In epileptics this may be related to competition between biotin and anticonvulsants bearing carbamide ring for absorption. Reduction of biotin levels in patients with multiple sclerosis could be attributed to intestinal malabsorption caused by the underlying disease or a biotin-binding immunoglobulin which may be involved in multiple sclerosis pathogenesis.
Neuroligin‐3 is a neuronal adhesion protein at GABAergic and glutamatergic synapses (2007)

Synaptic adhesion molecules are thought to play a critical role in the formation, function and plasticity of neuronal networks. Neuroligins (NL1-4) are a family of presumptive postsynaptic cell adhesion molecules. NL1 and NL2 isoforms are concentrated at glutamatergic and GABAergic synapses, respectively, but the cellular expression and synaptic localization of the endogenous NL3 and NL4 isoforms are unknown. We generated a panel of NL isoform-specific antibodies and examined the expression, developmental regulation and synaptic specificity of NL3. We found that NL3 was enriched in brain, where NL3 protein levels increased during postnatal development, coinciding with the peak of synaptogenesis. Subcellular fractionation revealed a concentration of NL3 in synaptic plasma membranes and postsynaptic densities. In cultured hippocampal neurons, endogenous NL3 was highly expressed and was localized at both glutamatergic and GABAergic synapses. Clustering of NL3 in hippocampal neurons by neurexin-expressing cells resulted in coaggregation of NL3 with glutamatergic and GABAergic scaffolding proteins. Finally, individual synapses contained colocalized NL2 and NL3 proteins, and coimmunoprecipitation studies revealed the presence of NL1-NL3 and NL2-NL3 complexes in brain extracts. These findings suggest that rodent NL3 is a synaptic adhesion molecule that is a shared component of glutamatergic and GABAergic synapses.
Biofilms in chronic wounds (2007)

Chronic wounds including diabetic foot ulcers, pressure ulcers, and venous leg ulcers are a worldwide health problem. It has been speculated that bacteria colonizing chronic wounds exist as highly persistent biofilm communities. This research examined chronic and acute wounds for biofilms and characterized microorganisms inhabiting these wounds. Chronic wound specimens were obtained from 77 subjects and acute wound specimens were obtained from 16 subjects. Culture data were collected using standard clinical techniques. Light and scanning electron microscopy techniques were used to analyze 50 of the chronic wound specimens and the 16 acute wound specimens. Molecular analyses were performed on the remaining 27 chronic wound specimens using denaturing gradient gel electrophoresis and sequence analysis. Of the 50 chronic wound specimens evaluated by microscopy, 30 were characterized as containing biofilm (60%), whereas only one of the 16 acute wound specimens was characterized as containing biofilm (6%). This was a statistically significant difference (p<0.001). Molecular analyses of chronic wound specimens revealed diverse polymicrobial communities and the presence of bacteria, including strictly anaerobic bacteria, not revealed by culture. Bacterial biofilm prevalence in specimens from chronic wounds relative to acute wounds observed in this study provides evidence that biofilms may be abundant in chronic wounds.
Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. (1994)

To maintain genomic integrity, double-strand breaks (DSBs) in chromosomal DNA must be repaired. In mammalian systems, the analysis of the repair of chromosomal DSBs has been limited by the inability to introduce well-defined DSBs in genomic DNA. In this study, we created specific DSBs in mouse chromosomes for the first time, using an expression system for a rare-cutting endonuclease, I-SceI. A genetic assay has been devised to monitor the repair of DSBs, whereby cleavage sites for I-SceI have been integrated into the mouse genome in two tandem neomycin phosphotransferase genes. We find that cleavage of the I-SceI sites is very efficient, with at least 12% of stably transfected cells having at least one cleavage event and, of these, more than 70% have undergone cleavage at both I-SceI sites. Cleavage of both sites in a fraction of clones deletes 3.8 kb of intervening chromosomal sequences. We find that the DSBs are repaired by both homologous and nonhomologous mechanisms. Nonhomologous repair events frequently result in small deletions after rejoining of the two DNA ends. Some of these appear to occur by simple blunt-ended ligation, whereas several others may occur through annealing of short regions of terminal homology. The DSBs are apparently recombinogenic, stimulating gene targeting of a homologous fragment by more than 2 orders of magnitude. Whereas gene-targeted clones are nearly undetectable without endonuclease expression, they represent approximately 10% of cells transfected with the I-SceI expression vector. Gene targeted clones are of two major types, those that occur by two-sided homologous recombination with the homologous fragment and those that occur by one-sided homologous recombination. Our results are expected to impact a number of areas in the study of mammalian genome dynamics, including the analysis of the repair of DSBs and homologous recombination and, potentially, molecular genetic analyses of mammalian genomes.
Life Events and Depressive Disorder Reviewed (1980)

I reviewed studies examining the hypothesis that life events may precipitate a depressive disorder. Although some contradictory results exist, the majority of studies demonstrate that depressed patients experience more stressful events in the months that precede the onset of their disorder than do normal controls or schizophrenics. In calculating relative risk figures, it seems that depressive risk is increased by a factor of about 5 or 6 for the six months after an event. Certain events, such as undesirable, loss, or severely threatening events, are particularly likely to precede a depression. These results suggest that stressful events can bring about depressive episodes, but most of the evidence that supports this conclusion emanates from retrospective studies, and corroborating prospective studies are definitely needed. Furthermore, not all depressives report precipitating events, so other causal factors are also operative.
Frequent Amplification of CENPF, GMNN and CDK13 Genes in Hepatocellular Carcinomas (2012)

Genomic changes frequently occur in cancer cells during tumorigenesis from normal cells. Using the Illumina Human NS-12 single-nucleotide polymorphism (SNP) chip to screen for gene copy number changes in primary hepatocellular carcinomas (HCCs), we initially detected amplification of 35 genes from four genomic regions (1q21-41, 6p21.2-24.1, 7p13 and 8q13-23). By integrated screening of these genes for both DNA copy number and gene expression in HCC and colorectal cancer, we selected CENPF (centromere protein F/mitosin), GMNN (geminin, DNA replication inhibitor), CDK13 (cyclin-dependent kinase 13), and FAM82B (family with sequence similarity 82, member B) as common cancer genes. Each gene exhibited an amplification frequency of ~30% (range, 20-50%) in primary HCC (n = 57) and colorectal cancer (n = 12), as well as in a panel of human cancer cell lines (n = 70). Clonogenic and invasion assays of NIH3T3 cells transfected with each of the four amplified genes showed that CENPF, GMNN, and CDK13 were highly oncogenic whereas FAM82B was not. Interestingly, the oncogenic activity of these genes (excluding FAM82B) was highly correlated with gene-copy numbers in tumor samples (correlation coefficient, r>0.423), indicating that amplifications of CENPF, GMNN, and CDK13 genes are tightly linked and coincident in tumors. Furthermore, we confirmed that CDK13 gene copy number was significantly associated with clinical onset age in patients with HCC (P = 0.0037). Taken together, our results suggest that coincidently amplified CDK13, GMNN, and CENPF genes can play a role as common cancer-driver genes in human cancers.
Fast, Cell‐Compatible Click Chemistry with Copper‐Chelating Azides for Biomolecular Labeling (2012)

Bring your own copper: Copper-chelating azides undergo much faster click reactions (CuAAC) than nonchelating azides under a variety of biocompatible conditions. This kinetic enhancement allows site-specific protein labeling to be performed on the surface of living cells with only 10–40 μM CuI/CuII (see scheme). Detection sensitivity was also increased for CuAAC detection of alkyne-modified proteins and RNA.
Cellular uptake, evolution, and excretion of silica nanoparticles in human cells (2011)

A systematic study on the interaction of silica nanoparticles (NPs) with human cells has been carried out in the present work. Endocytosis and exocytosis are identified as major pathways for NPs entering, and exiting the cells, respectively. Most of the NPs are found to be enclosed in membrane bounded organelles, which are fairly stable (against rupture) as very few NPs are released into the cytoplasm. The nanoparticle-cell interaction is a dynamic process, and the amount of NPs inside the cells is affected by both the amount and morphology (degree of aggregation) of NPs in the medium. These interaction characteristics determine the low cytotoxicity of SiO(2) NPs at low feeding concentration.
Multitouch Gestures for Constrained Transformation of 3D Objects (2012)

Abstract 3D transformation widgets allow constrained manipulations of 3D objects and are commonly used in many 3D applications for fine‐grained manipulations. Since traditional transformation widgets have been mainly designed for mouse‐based systems, they are not user friendly for multitouch screens. There is little research on how to use the extra input bandwidth of multitouch screens to ease constrained transformation of 3D objects. This paper presents a small set of multitouch gestures which offers a seamless control of manipulation constraints (i.e., axis or plane) and modes (i.e., translation, rotation or scaling). Our technique does not require any complex manipulation widgets but candidate axes, which are for visualization rather than direct manipulation. Such design not only minimizes visual clutter but also tolerates imprecise touch‐based inputs. To further expand our axis‐based interaction vocabulary, we introduce intuitive touch gestures for relative manipulations, including snapping and borrowing axes of another object. A preliminary evaluation shows that our technique is more effective than a direct adaption of standard transformation widgets to the tactile paradigm.
An overview of sigma-delta converters (1996)

Using sigma-delta A/D methods, high resolution can be obtained for only low to medium signal bandwidths. This article describes conventional A/D conversion, as well as its performance modeling. We then look at the technique of oversampling, which can be used to improve the resolution of classical A/D methods. We discuss how sigma-delta converters use the technique of noise shaping in addition to oversampling to allow high resolution conversion of relatively low bandwidth signals. We examine the use of sigma-delta converters to convert narrowband bandpass signals with high resolution. Several parallel sigma-delta converters, which offer the potential of extending high resolution conversion to signals with higher bandwidths, are also described.
REMOVED: Aquaporin-based Biomimetic Membranes for Desalination (2012)

This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been removed at the request of the Executive Publisher. This article has been removed because it was published without the permission of the author(s).
Branched-chain sugar nucleosides. V. Synthesis and antiviral properties of several branched-chain sugar nucleosides (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBranched-chain sugar nucleosides. V. Synthesis and antiviral properties of several branched-chain sugar nucleosidesEdward Walton, Susan R. Jenkins, Ruth F. Nutt, Frederick W. Holly, and Marjorie NemesCite this: J. Med. Chem. 1969, 12, 2, 306–309Publication Date (Print):March 1, 1969Publication History Published online1 May 2002Published inissue 1 March 1969https://pubs.acs.org/doi/10.1021/jm00302a025https://doi.org/10.1021/jm00302a025research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations62LEARN 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
Synthesis and Biological Effects of Hydrogen Sulfide (H2S): Development of H2S-Releasing Drugs as Pharmaceuticals (2010)

ADVERTISEMENT RETURN TO ISSUEPREVPerspectiveNEXTSynthesis and Biological Effects of Hydrogen Sulfide (H2S): Development of H2S-Releasing Drugs as PharmaceuticalsGiuseppe Caliendo*†, Giuseppe Cirino‡, Vincenzo Santagada†, and John L. Wallace§View Author Information† Dipartimento di Chimica Farmaceutica e Tossicologica‡ Dipartimento di Farmacologia Sperimentale Università degli Studi di Napoli Federico II, Via Domenico Montesano, 49, 80131 Napoli, Italy§ Farncombe Family Digestive Health Research Institute, McMaster University, 1200 Main Street West, Room HSC-3N9, Hamilton, Ontario, L8N 3Z5, Canada*To whom correspondence should be addressed. Phone: +39081678649. Fax: +39081678649. E-mail: [email protected]Cite this: J. Med. Chem. 2010, 53, 17, 6275–6286Publication Date (Web):May 12, 2010Publication History Received5 November 2009Published online12 May 2010Published inissue 9 September 2010https://pubs.acs.org/doi/10.1021/jm901638jhttps://doi.org/10.1021/jm901638jreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views6080Altmetric-Citations223LEARN 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 SUBJECTS:Anatomy,Central nervous system,Hydrogen sulfide,Peptides and proteins,Rodent models Get e-Alerts
The neighbor-joining method: a new method for reconstructing phylogenetic trees. (1987)

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Characterization of PEGylated Factor VIII Molecules. (2006)

Abstract Patients with hemophilia A typically require frequent treatment with replacement Factor VIII (FVIII) products due to the relatively short circulating half-life of FVIII. Increasing the half-life of FVIII would profound impact the lives of patients with hemophilia A, especially children, by reducing the frequency of infusions. The addition of polyethylene glutamate (PEG) to therapeutic molecules or their carriers has been demonstrated to increase the survival of such molecules in the circulation. To create a longer circulating product, we have developed novel FVIII molecules using site specific PEGylation techniques. We present a characterization of these PEGylated FVIII molecules in terms of the site of PEGylation, the binding of von Willebrand Factor (vWF), and the effect of PEGylation on thrombin digestion, and we compare the one-stage and chromogenic potency test results. The site of PEGylation was determined using MALDI-mass spectrometry. A vWF binding assay was developed using surface plasmon resonance technology (Biacore). The effect of PEGylation on thrombin digestion of the novel constructs was evaluated using MALDI-mass spectrometry, thrombin activation, and potency decay curves following thrombin activation. All novel constructs were PEGylated on the expected target site based on the site of introduced mutation. PEGylation of FVIII appeared to have a slight reduction on vWF-binding capability. The site of PEGylation reduced the ability of thrombin to digest FVIII, as assayed by MALDI-mass spectrometry analysis and by thrombin digestion and decay curves. The size and position of the PEG molecule influenced the extent of FVIII thrombin sensitivity. The one-stage potency assay was more sensitive to the size and position of the attached PEG molecule than the chromogenic potency assay. We report that some PEGylated FVIII molecules are less sensitive to thrombin activation than unmodified FVIII, and that the size and position of the PEG molecule can significantly affect the potency of FVIII. The findings of this study suggest that site-directed PEGylation of FVIII may be a useful technique for the development of FVIII molecules with extended activity in circulation and that careful choice of size and position of the PEG molecule is critical.
The Development of Tissue Around Various Prosthetic Implants Used as Replacements for Ligaments and Tendons (1985)

Currently, no ideal prosthesis is available for the repair or replacement of tendons and ligaments. Although filamentous carbon is a useful fibrogenic material, it does not fulfill the ideal requirements of a soft-tissue prosthesis. A number of other synthetic fibers were examined for biocompatibility and fibrogenic properties in both cell culture and in vivo implantation. It was found that the less extensible materials could adversely affect the normal morphology of the induced collagen. None of the materials examined exhibited mechanical properties similar to those of collagen; therefore, a composite prosthesis was designed to incorporate three criteria: mechanical characteristics similar to those of the normal tissue, fibrogenic capability to induce replacement collagen, and replacement collagen developing with normal morphologic characteristics. A prototype prosthesis for the Achilles tendon in rabbits, evaluated by mechanical and histologic methods, shows that these criteria can be fulfilled and thus form the basis for future prosthetic tendon and ligament research.
Scorpion (2013)

Database users commonly explore large data sets by running aggregate queries that project the data down to a smaller number of points and dimensions, and visualizing the results. Often, such visualizations will reveal outliers that correspond to errors or surprising features of the input data set. Unfortunately, databases and visualization systems do not provide a way to work backwards from an outlier point to the common properties of the (possibly many) unaggregated input tuples that correspond to that outlier. We propose Scorpion, a system that takes a set of user-specified outlier points in an aggregate query result as input and finds predicates that explain the outliers in terms of properties of the input tuples that are used to compute the selected outlier results. Specifically, this explanation identifies predicates that, when applied to the input data, cause the outliers to disappear from the output. To find such predicates, we develop a notion of influence of a predicate on a given output, and design several algorithms that efficiently search for maximum influence predicates over the input data. We show that these algorithms can quickly find outliers in two real data sets (from a sensor deployment and a campaign finance data set), and run orders of magnitude faster than a naive search algorithm while providing comparable quality on a synthetic data set.