gebhart/patrepeval huggingface dataset:
Automatic Algorithm for Generating Complex Polyhedral Scaffold Structures for Tissue Engineering (2004)

In this article, an approach for tissue-engineering (TE) scaffold fabrication by way of integrating computer-based medical imaging, computer graphics, data manipulation techniques, computer-aided design (CAD), and rapid prototyping (RP) technologies is introduced. The aim is to provide a generic solution for the production of scaffolds that can potentially meet the diverse requirements of TE applications. In the work presented, a novel parametric library of open polyhedral unit cells is developed to assist the user in designing the microarchitecture of the scaffold according to the requirements of its final TE application. Once an open polyhedral unit cell design is selected and sized, a specially developed algorithm is employed to assemble the microarchitecture of the scaffold while adhering to the external geometry of the patient's anatomy generated from medical imaging data. RP fabrication techniques are then employed to build the scaffolds according to the CAD-generated designs. The combined application of such technologies promises unprecedented scaffold qualities with spatially and anatomically accurate three-dimensional forms as well as highly consistent and reproducible microarchitectures. The integrated system also has great potential in providing new cost-effective and rapid solutions to customized made-to-order TE scaffold production.
Respiratory syncytial virus: A continuing culprit and conundrum. (1999)

For more than 4 decades, respiratory syncytial virus (RSV) has been recognized as a worldwide pathogen of import. In the United States alone, approximately 91,000 infants are hospitalized with RSV infections yearly, at an estimated annual cost of at least 300 million dollars. The burden of RSV infections is even greater if outpatient visits for children and adults and RSV morbidity in patients with underlying conditions are included. Obstacles to controlling RSV remain appreciable and challenging. The virus causes predictable, widespread outbreaks of illness each year and repeated infections throughout life. The most severe infections occur in the youngest infants, especially premature infants and those with bronchopulmonary dysplasia. Patients with chronic pulmonary and cardiac diseases and those with immunosuppression also are at high risk for severe RSV infection, and their risk may last well beyond infancy. Institutionalized adults, especially the elderly, also are at risk of complicated disease. To be effective, a vaccine against RSV must be administered shortly after birth and ideally should provide better immunity than natural disease, if reinfection is to be prevented. It must also be effective in the wide variety of populations at risk. Recently, several candidate vaccines for RSV have been developed. In the interim, RSV immune globulin and a monoclonal antibody to RSV have been approved for prophylaxis in infants at high risk. For therapy in immunocompromised patients, especially patients receiving transplants, a combination of RSV immune globulin and the antiviral ribavirin has been tried. Therapy for RSV, however, remains limited, controversial, and mostly supportive.
HeLa cells resistant to bromodeoxyuridine and deficient in thymidine kinase activity (1966)

Abstract Mutant sublines of HeLa S3 cells resistant to growth inhibition by bromodeoxyuridine (BUdR) have been isolated. The resistant cell lines (HeLa BU‐10, HeLa BU‐15, HeLa BU‐25, HeLa BU‐50, and HeLa BU‐100) proliferated in the presence of 10, 15, 25, 50, and 100 μg/ml BUdR, respectively. Extracts from HeLa BU‐25, HeLa BU‐50, and HeLa BU‐100 cells exhibited 2–5 per cent of the thymidine‐ 3 H, deoxyuridine‐ 3 H, and bromodeoxyuridine‐ 3 H phosphorylating activities of parental HeLa S3 cells. HeLa BU‐10 and HeLa BU‐15 cell extracts were also deficient in thymidine kinase activity, yielding approximately 43 per cent and 8 per cent, respectively, the thymidine kinase activity of parental HeLa S3 cells. The deficiency in thymidine kinase activity of HeLa BU‐100 cells was not due to negative feedback inhibition by high levels of BUdR or to interference with the thymidine kinase assay by inhibitors or competing enzymes in the HeLa BU‐100 cell extracts. Following 5 weekly passages in media lacking BUdR, the HeLa BU‐100 cells did not exhibit increased thymidine kinase activity. Moreover, mixtures of extracts from HeLa S3 and HeLa BU‐100 cells displayed a thymidine kinase activity equivalent to the sum of the activities of extracts prepared, respectively, from the HeLa S3 and HeLa BU‐100 cells. Radioautographic studies have shown that after HeLa S3 cells were incubated for 6 hours with thymidine‐ 3 H, 35–45 per cent of the nuclei were heavily labeled with radioactivity. However, fewer HeLa BU‐100 cells displayed labeled nuclei and the nuclei were only lightly labeled. HeLa BU‐100 cell extracts contained normal amounts of thymidylate synthetase, thymidylate kinase, and uridine kinase activities. Following infection by vaccinia virus, high levels of thymidine kinase activity were induced in HeLa BU‐100 cells.
Gastric inhibitory polypeptide links overnutrition to obesity (2003)

A gut derived peptide, gastric inhibitory polypeptide, directly links overnutrition to obesity and may be a potential
Structural basis of beta 1 integrin-mediated cell adhesion to a large heparan sulfate proteoglycan from basement membranes. (1993)

In a cell attachment assay, several cell lines were found to adhere and spread on heparan sulfate proteoglycan purified from a basement membrane-producing tumor. This adhesion was clearly distinct from that on laminin. Cell adhesion to the proteoglycan was completely inhibited by three different antibodies against integrin beta 1 subunit, while inhibitory antibodies against beta 3 and alpha 2 to alpha 6 subunits were without strong effects. Removal of heparan sulfate from the proteoglycan diminished cell attachment, but addition of heparin to the cells did not affect adhesion to the proteoglycan. This suggests that both the heparan sulfate side chains and core protein structures are required for efficient cell adhesion. Studies with proteolytic fragments and synthetic RGD peptides showed that the single RGD sequence of mouse proteoglycan is not involved in cellular recognition. Characterization of fragments also allowed to localize cell adhesion and heparan sulfate attachment sites to the same 160 kDa core protein structure but not to fragments derived from the N-terminal portion of the proteoglycan.
Aberrant methylation of the HPP1 gene in ulcerative colitis-associated colorectal carcinoma. (2002)

The HPP1 gene was cloned as a frequently methylated gene in hyperplastic polyps of the colon. It has been shown that HPP1 expression is silenced by HPP1 gene hypermethylation in sporadic colorectal cancers. To determine the role of HPP1 in ulcerative colitis (UC)-associated carcinogenesis, the prevalence of HPP1 methylation was investigated in three different histological stages of UC-associated carcinogenesis (non-neoplastic UC colon, dysplasia, and carcinoma). Quantitative methylation-specific PCR and quantitative reverse transcription-PCR were used to determine HPP1 gene methylation and expression levels, respectively. HPP1 methylation was observed in 24 of 48 (50%) adenocarcinomas and in 4 of 10 (40%) dysplasias. In contrast, no non-neoplastic UC mucosa showed HPP1 methylation. HPP1 expression in the HCT116 colon cancer cell line was restored after treatment with the demethylating agent 5-aza-2'-deoxycytidine. In conclusion, our data suggest that methylation of HPP1 is a relatively common early event in UC-associated carcinogenesis. HPP1 offers potential as a biomarker for the early detection of cancer or dysplasia in UC.
The divIVB region of the Bacillus subtilis chromosome encodes homologs of Escherichia coli septum placement (minCD) and cell shape (mreBCD) determinants (1992)

Mutation of the divIVB locus in Bacillus subtilis causes frequent misplacement of the division septum, resulting in circular minicells, short rods, and filaments of various sizes. The divIVB1 mutant allele maps to a region of the chromosome also known to encode sporulation (spo0B, spoIVF, spoIIB) and cell shape (rodB) determinants. This study reports the cloning and sequence analysis of 4.4 kb of the B. subtilis chromosome encompassing the divIVB locus. This region contains five open reading frames (ORFs) arranged in two functionally distinct gene clusters (mre and min) and transcribed colinearly with the direction of replication. Although sequence analysis reveals potential promoters preceding each gene cluster, studies with integrational plasmids suggest that all five ORFs are part of a single transcription unit. The first gene cluster contains three ORFs (mreBCD) homologous to the mre genes of Escherichia coli. We show that rodB1 is allelic to mreD and identify the rodB1 mutation. The second gene cluster contains two ORFs (minCD) homologous to minC and minD of E. coli but lacks a minE homolog. We show that divIVB1 is allelic to minD and identify two mutations in the divIVB1 allele. Insertional inactivation of either minC or minD or the presence of the divIVB region on plasmids produces a severe minicell phenotype in wild-type cells. Moreover, E. coli cells carrying the divIVB region on a low-copy-number plasmid produce minicells, suggesting that a product of this locus may retain some function across species boundaries.
Cyclins and cyclin-dependent kinases: a biochemical view (1995)

Research Article| June 15 1995 Cyclins and cyclin-dependent kinases: a biochemical view J Pines J Pines 1Wellcome/CRC Institute, and Department of Zoology, Tennis Court Road, Cambridge CB2 1QR, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8728 Print ISSN: 0264-6021 © 1995 The Biochemical Society, London1995 Biochem J (1995) 308 (3): 697–711. https://doi.org/10.1042/bj3080697 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J Pines; Cyclins and cyclin-dependent kinases: a biochemical view. Biochem J 15 June 1995; 308 (3): 697–711. doi: https://doi.org/10.1042/bj3080697 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1995 The Biochemical Society, London1995 Article PDF first page preview Close Modal You do not currently have access to this content.
Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains (2020)

Low-density lipoprotein receptor-related protein 6 (LRP6) is a coreceptor of the β-catenin-dependent Wnt signaling pathway. The LRP6 ectodomain binds Wnt proteins, as well as Wnt inhibitors such as sclerostin (SOST), which negatively regulates Wnt signaling in osteocytes. Although LRP6 ectodomain 1 (E1) is known to interact with SOST, several unresolved questions remain, such as the reason why SOST binds to LRP6 E1E2 with higher affinity than to the E1 domain alone. Here, we present the crystal structure of the LRP6 E1E2-SOST complex with two interaction sites in tandem. The unexpected additional binding site was identified between the C-terminus of SOST and the LRP6 E2 domain. This interaction was confirmed by in vitro binding and cell-based signaling assays. Its functional significance was further demonstrated in vivo using Xenopus laevis embryos. Our results provide insights into the inhibitory mechanism of SOST on Wnt signaling.
Sterol Regulatory Element-binding Protein-1 Is Regulated by Glucose at the Transcriptional Level (2000)

In vivo studies suggest that sterol regulatory element-binding protein (SREBP)-1 plays a key role in the up-regulation of lipogenic genes in the livers of animals that have consumed excess amounts of carbohydrates. In light of this, we sought to use an established mouse hepatocyte cell line, H2-35, to further define the mechanism by which glucose regulates nuclear SREBP-1 levels. First, we show that these cells transcribe high levels of SREBP-1c that are increased 4-fold upon differentiation from a prehepatocyte to a hepatocyte phenotype, making them an ideal cell culture model for the study of SREBP-1c induction. Second, we demonstrate that the presence of precursor and mature forms of SREBP-1 protein are positively regulated by medium glucose concentrations ranging from 5. 5 to 25 mm and are also regulated by insulin, with the amount of insulin in the fetal bovine serum being sufficient for maximal stimulation of SREBP-1 expression. Third, we show that the increase in SREBP-1 protein is due to an increase in SREBP-1 mRNA. Reporter gene analysis of the SREBP-1c promoter demonstrated a glucose-dependent induction of transcription. In contrast, expression of a fixed amount of the precursor form of SREBP-1c protein showed that glucose does not influence its cleavage. Fourth, we demonstrate that the glucose induction of SREBP could not be reproduced by fructose, xylose, or galactose nor by glucose analogs 2-deoxy glucose and 3-O-methyl glucopyranose. These data provide strong evidence for the induction of SREBP-1c mRNA by glucose leading to increased mature protein in the nucleus, thus providing a potential mechanism for the up-regulation of lipogenic genes by glucose in vivo.
Application of a simple resist model to fast optical proximity correction (1997)

The implementation of a simple, semi-empirical resist model into an OPC algorithm, which up to now uses aerial image simulation, is described. The model assumes that the main component of proximity effects comes from the aerial image. It uses two pattern density functions to describe the shift in edge placement due to resist and etching processes. Besides the parameters for the aerial image (numerical aperture, coherence, wavelength, lens aberrations, defocus, etc.), the model needs only four additional parameters. The model is tested using resist simulation and electrical linewidth measurement data from fully processed testwafers. For linewidths of 350 nm and larger, printed with i-line lithography into a standard i-line resist, the OPC algorithm with the implemented model reduces proximity effects to less than 10 nm. A similar performance is indicated by preliminary data of electrical linewidth measurements.
Cinematic Visual Discourse: Representation, Generation, and Evaluation (2010)

In this paper, we present the design, implementation, and evaluation of an end-to-end camera planning system called Darshak. Darshak automatically constructs cinematic narrative discourse of a given story in a 3-D virtual environment. It utilizes a hierarchical partial-order causal link (POCL) planning algorithm to generate narrative plans that contain story events and camera directives for filming them. Dramatic situation patterns, commonly used by writers of fictional narratives, are formalized as communicative plan operators that provide a basis for structuring the cinematic content of the story's visualization. The dramatic patterns are realized through abstract communicative operators that represent operations on a viewer's beliefs about the story and its telling. Camera shot compositions and transitions are defined in this plan-based framework as execution primitives. Darshak's performance is evaluated through a novel user study based on techniques used to evaluate existing cognitive models of narrative comprehension. Initial study reveals significant effect of the choice of visualization strategies on measured viewer comprehension. It further shows significant effect of Darshak's choice of visualization strategy on comprehension.
Dual fluorescence of p,p'-disubstituted 1,6-diphenyl-1,3,5-hexatrienes: evidence of a twisted intramolecular charge-transfer state (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDual fluorescence of p,p'-disubstituted 1,6-diphenyl-1,3,5-hexatrienes: evidence of a twisted intramolecular charge-transfer stateC. T. Lin, H. W. Guan, R. K. McCoy, and C. W. SpanglerCite this: J. Phys. Chem. 1989, 93, 1, 39–43Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/j100338a013https://doi.org/10.1021/j100338a013research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations19LEARN 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 options Get e-Alerts
KIDS:K-anonymization data stream base on sliding window (2010)

In a wide range of fields, data arrive in the form of high speed and huge data streams, and accompanying risks of disclosure of privacy. Most of previous studies about privacy preserving, such as k-anonymity methods, are excellent and effective, however, focus on static data sets. In this paper, we study a novel framework KIDS (K-anonymIzation Data Stream base on sliding window) to solve this problem by continuously k-anonymity on the sliding window. KIDS protects privacy of data stream well and considers the distribute density of data in data stream, thereby improve usefulness of data largely. Our theoretical analysis and experimental results show that we can receive more accurate data mining results by KIDS with high efficiency.
Learning symbolic representations of hybrid dynamical systems (2012)

A hybrid dynamical system is a mathematical model suitable for describing an extensive spectrum of multi-modal, time-series behaviors, ranging from bouncing balls to air traffic controllers. This paper describes multi-modal symbolic regression (MMSR): a learning algorithm to construct non-linear symbolic representations of discrete dynamical systems with continuous mappings from unlabeled, time-series data. MMSR consists of two subalgorithms--clustered symbolic regression, a method to simultaneously identify distinct behaviors while formulating their mathematical expressions, and transition modeling, an algorithm to infer symbolic inequalities that describe binary classification boundaries. These subalgorithms are combined to infer hybrid dynamical systems as a collection of apt, mathematical expressions. MMSR is evaluated on a collection of four synthetic data sets and outperforms other multi-modal machine learning approaches in both accuracy and interpretability, even in the presence of noise. Furthermore, the versatility of MMSR is demonstrated by identifying and inferring classical expressions of transistor modes from recorded measurements.
Sensitivity of Multiple Damage Parameters to Compressive Overload in Cortical Bone (2005)

Damage accumulation plays a key role in weakening bones prior to complete fracture and in stimulating bone remodeling. The goal of this study was to characterize the degradation in the mechanical properties of cortical bone following a compressive overload. Longitudinally oriented, low-aspect ratio specimens (n=24) of bovine cortical bone were mechanically tested using an overload-hold-reload protocol. No modulus reductions greater than 5% were observed following overload magnitudes less than 0.73% strain. For each specimen, changes in strength and Poisson's ratio were greater (p=0.02) than that in modulus by 10.8- and 26.6-fold, respectively, indicating that, for the specimen configuration used in this study, longitudinal elastic modulus is one of the least sensitive properties to a compressive overload. Residual strains were also proportionately greater by 6.4-fold (p=0.01) in the transverse than axial direction. These results suggest that efforts to relate microcrack density and morphology to changes in compressive mechanical properties of cortical bone may benefit from considering alternative parameters to modulus reductions.
Specific induction of pp125 focal adhesion kinase in human breast cancer (2005)

The pp125 focal adhesion kinase (FAK) is involved in integrin-mediated cell signalling and overexpressed in a variety of solid tumours. Focal adhesion kinase expression has been correlated to invasion and metastasis, but the data on breast cancer are inconclusive. We analysed FAK mRNA, protein levels and expression patterns in primary breast cancer and normal breast tissue. FAK expression on the functional protein level and mRNA was determined in 55 matched pairs of breast cancer and corresponding normal tissue by Western blot, immunohistochemistry and RT-PCR. Using a score ranging from 0 to +5 for Western blots, we determined in normal breast tissue a score of 1.51+/-0.84 (mean+/-standard deviation), which was strongly induced to 2.91 (+/-1.22) in breast cancers (P<0.001). Overall, 45 out of 55 tissue pairs (81.8%) showed this upregulation of FAK protein in tumours in comparison to normal tissue. Immunohistochemistry confirmed these findings with a significant higher score for tumours vs physiological tissue (1.0+/-0.63 vs 2.27+/-0.91; P=0.001). Interestingly, no overall significant difference in the mRNA levels (P=0.359) was observed. In conclusion, expression levels of the FAK protein are specifically upregulated in breast cancer in comparison to matched normal breast tissue supporting its pivotal role in neoplastic signal transduction and representing a potential marker for malignant transformation.
Pathological role of interleukin 17 in mice subjected to repeated BCG vaccination after infection with Mycobacterium tuberculosis (2010)

Infection usually leads to the development of acquired immune responses associated with clearance or control of the infecting organism. However, if not adequately regulated, immune-mediated pathology can result. Tuberculosis is a worldwide threat, and development of an effective vaccine requires that the protective immune response to Mycobacterium tuberculosis (Mtb) be dissected from the pathological immune response. This distinction is particularly important if new vaccines are to be delivered to Mtb-exposed individuals, as repeated antigenic exposure can lead to pathological complications. Using a model wherein mice are vaccinated with bacille Calmette-Guérin after Mtb infection, we show that repeated vaccination results in increased IL-17, tumor necrosis factor, IL-6, and MIP-2 expression, influx of granulocytes/neutrophils, and lung tissue damage. This pathological response is abrogated in mice deficient in the gene encoding IL-23p19 or in the presence of IL-17-blocking antibody. This finding that repeated exposure to mycobacterial antigen promotes enhanced IL-17-dependent pathological consequences has important implications for the design of effective vaccines against Mtb.