gebhart/patrepeval huggingface dataset:
Cultivation-Independent Analysis of Changes in Bacterial Vaginosis Flora Following Metronidazole Treatment (2007)

PCR was used to survey bacterial vaginosis flora before and after metronidazole treatment. The species composition for pretreatment patients was variable. Lactobacillus iners was prominent in all patients posttreatment. Atopobium vaginae concentrations were highest for patients who failed or responded incompletely to treatment and lowest for patients who were cured.
Analysis of enzymatic DNA sequencing reactions by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (1995)

The products from base-specific, dideoxy-nucleotide chain-termination DNA sequencing reactions catalyzed by the modified T7 DNA polymerase have been analyzed by using the technique of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. Preliminary experiments were performed to determine detection limits for a synthetic mixture of mixed-base single-stranded DNA which contained a 14-mer, a 21-mer, and a 41-mer; acceptable spectra, showing peaks for each component, were obtainable for samples that contained as little as 5 fmol per component. Initial sequencing reactions were therefore carried out on 2-pmol amounts of a short synthetic template that was 45 nucleotides in length, employing 2 pmol of 12-mer as the primer strand. This provided readable sequence information out to the 19th base past the primer. Using a 21-mer primer, nearly the entire sequence of the template could be read.
Tumor Markers in Clinical Practice: A Review Focusing on Common Solid Cancers (2012)

Tumor markers are playing an increasingly important role in cancer detection and management. These laboratory-based tests are potentially useful in screening for early malignancy, aiding cancer diagnosis, determining prognosis, surveillance following curative surgery for cancer, up front predicting drug response or resistance, and monitoring therapy in advanced disease. Clinically useful markers include fecal occult blood testing in screening for early colorectal cancer, carcinoembryonic antigen in the management of patients with colorectal cancer, both α-fetoprotein and human chorionic gonadotrophin in the management of patients with non-seminomatous germ cell tumors, CA 125 for monitoring therapy in patients with ovarian cancer, estrogen receptors for predicting response to hormone therapy in breast cancer, human epidermal growth factor receptor 2 for the identification of women with breast cancer likely to respond to trastuzumab (Herceptin) and KRAS mutational status for identifying patients with advanced colorectal cancer likely to benefit from treatment with the anti-epidermal growth factor receptor antibodies, cetuximab and panitumumab. Although widely used, the value of prostate-specific antigen screening in reducing mortality from prostate cancer is unclear.
Model surfaces engineered with nanoscale roughness and RGD tripeptides promote osteoblast activity (2004)

Cell adhesion to biomaterials is a prerequisite for tissue integration with the implant surface. Herein, we show that we can generate a model silica surface that contains a minimal-length arginine-glycine-aspartic acid (RGD) peptide that maintains its biological activity. In the first part of this study, attachment of MC3T3-E1 osteoblast-like cells was investigated on silicon oxide, amine terminated substrates [i.e., 3-aminopropyl triethoxysilane (APTS)], grafted RGD, and physisorbed RGD control. The APTS layer exhibited nanoscale roughness and presented amine functional groups for grafting a minimal RGD tripeptide devoid of any flanking groups or spacers. Contact angle measurements indicated that the hydrophobicity of the APTS surface was significantly lower than that of the surface with grafted RGD (RGD-APTS). Atomic force microscopy showed that surfaces covered with RGD-APTS were smoother (Ra = 0.71 nm) than those covered with APTS alone (Ra = 1.59 nm). Focusing mainly on cell morphology, experiments showed that the RGD-APTS hybrid provided an optimum surface for cell adhesion, spreading, and cytoskeletal organization. Discrete focal adhesion plaques were also observed consistent with successful cell signaling events. In a second set of experiments, smooth, monolayers of APTS (Ra = 0.1 nm) were used to prepare arginine-glycine-aspartic acid-serine (RGDS)-APTS and arginine-glycine-glutamic acid-serine (RGES)-APTS (control) substrates. Focusing mainly on cell function, integrin and gene expression were all enhanced for rate osteosarcoma cells on surfaces containing grafted RGDS. Both sets of studies demonstrated that grafted molecules of RGD(S) enhance both osteoblast-like cell adhesion and function.
CD44 splice variants confer metastatic behavior in rats : homologous sequences are expressed in human tumor cell lines. (1991)

One of several splice variants of CD44 expressed in metastasizing cell lines of rat tumors has been shown to confer metastatic potential to the non-metastatic variant of a rat pancreatic carcinoma line (U. Günthert et al., Cell, 65: 13-24, 1991). The variant-specific rat CD44 sequences were used to detect RNA expression in human cell lines: in carcinoma lines from lung, breast and colon; and in keratinocyte lines. By polymerase chain reaction amplification, complementary DNAs encoding human homologues were isolated and sequenced. The largest splice variant has been found in a large cell lung carcinoma line and in keratinocyte cell lines. It carries at least 5 additional domains (exons) encoding a total of 338 amino acids in the membrane-proximal extracellular region of the standard CD44. Various alternative splice products have been detected in other human tumor cell lines. The distribution of CD44 splice variants is consistent with the speculation that they fulfill functions in only a few restricted differentiation pathways and that in tumor cells these pathways have been reactivated.
Human red cell aquaporin CHIP. I. Molecular characterization of ABH and Colton blood group antigens. (1994)

Blood group antigens are structural variants in surface carbohydrate or amino acid polymorphisms on extracellular domains of membrane proteins. The red cell water channel-forming integral protein (Aquaporin CHIP) is a homotetramer with only one N-glycosylated subunit, however no CHIP-associated blood group antigens have yet been identified. Immunoblotting, monosaccharide composition analysis, and selective glycosidase digestions revealed that the CHIP-associated oligosaccharide contains ABH determinants and resembles a band 3-type glycan that cannot be cleaved from intact membranes by Peptide:N-glycosidase F. The molecular structure of the Colton antigens was previously unknown, but CHIP was selectively immunoprecipitated with anti-Coa or anti-Co(b). The DNA sequence from Colton-typed individuals predicted that residue 45 is alanine in the Co(a+b-) phenotype and valine in the Co(a-b+) phenotype. The nucleotide polymorphism corresponds to a PflMI endonuclease digestion site in the DNA from Co(a-b+) individuals. These studies have defined antigens within two blood group systems on CHIP: (a) an ABH-bearing polylactosaminoglycan attached to a poorly accessible site in the native membrane; and (b) the Colton antigen polymorphism which may permit the identification of rare individuals with defective water channel expression.
Azimuthal Angle Dependence of Two and Three Particle Dynamical Correlation Among Target Fragments in 28Si-AgBr Interactions at 14.5 AGeV (2003)

I'his paper reports an investigation on the two particle and thiee particle short range dynamical angular correlation in emission yiifjlc -space among the target fragments produced in '''Si-AgBr interactions at 14.5 AGeV on different range of azimuthal angles 0" < 90"', 00" I80".180" 5 0 ^ 270" and 270" ^0 ^ 360" The expcnmcntal data have been compared with the Monte Carlo simulated events lo extract dynamical correlation.The analysis reveals that both two and three particle dynamical correlation among target fragments depend on (he a/imuthal angle space.
Axitinib: A Review of its Safety and Efficacy in the Treatment of Adults with Advanced Renal Cell Carcinoma (2013)

Over the last seven years, seven targeted agents have been approved in the treatment of advanced or metastatic renal cell cancer, changing the therapeutic approach and prognosis of the disease dramatically. The latest agent with demonstrated efficacy is axitinib (Inlyta(®)). This new generation of tyrosine kinase agent differs from previously existing agents by its greater activity potency of inhibition of vascular endothelial growth factor-receptor (VEGFR1-3). This efficacy has been tested in phase II and III clinical trials. Axitinib is the only targeted agent that benefits from recommended titration, with intra-patient dose escalation. The toxicity profile of the drug is tolerable. This paper reviews the mechanism of action of axitinib, its metabolism, and its pharmacokinetic profile. Clinical data of efficacy and safety is also detailed. The agent has been integrated in the international therapeutic guidelines, as a standard in treatment of renal cell cancer patients, previously treated through antiangiogenic therapy.
Fermentation properties and potential prebiotic activity of Bimuno®galacto-oligosaccharide (65 % galacto-oligosaccharide content) onin vitrogut microbiota parameters (2016)

Prebiotic oligosaccharides have the ability to generate important changes in the gut microbiota composition that may confer health benefits to the host. Reducing the impurities in prebiotic mixtures could expand their applications in food industries and improve their selectivity and prebiotic effect on the potential beneficial bacteria such as bifidobacteria and lactobacilli. This study aimed to determine the in vitro potential fermentation properties of a 65 % galacto-oligosaccharide (GOS) content Bimuno® GOS (B-GOS) on gut microbiota composition and their metabolites. Fermentation of 65 % B-GOS was compared with 52 % B-GOS in pH- and volume-controlled dose-response anaerobic batch culture experiments. In total, three different doses (1, 0·5 and 0·33 g equivalent to 0·1, 0·05 and 0·033 g/l) were tested. Changes in the gut microbiota during a time course were identified by fluorescence in situ hybridisation, whereas small molecular weight metabolomics profiles and SCFA were determined by 1H-NMR analysis and GC, respectively. The 65 % B-GOS showed positive modulation of the microbiota composition during the first 8 h of fermentation with all doses. Administration of the specific doses of B-GOS induced a significant increase in acetate as the major SCFA synthesised compared with propionate and butyrate concentrations, but there were no significant differences between substrates. The 65 % B-GOS in syrup format seems to have, in all the analysis, an efficient prebiotic effect. However, the applicability of such changes remains to be shown in an in vivo trial.
Strategies to overcoming rituximab-chemotherapy resistance by targeting the autophagy pathway using bortezomib in combination with the Bcl-2 inhibitor obatoclax in non-Hodgkin's lymphomas (NHL) (2009)

8543 We found that repeated rituximab exposure leads to deregulation of Bcl-2 proteins and concomitant chemotherapy resistance. We demonstrated that obatoclax (O), a potent Bcl-2 inhibitor, enhanced the anti-tumor activity of rituximab or chemotherapy agents. The proteasome is known to regulate Bcl-2 family members expression. In the current work we study the interactions between bortezomib (B) and O against B-cell NHL. Studies were conducted in rituximab sensitive (RSCL) and resistant cell lines (RRCL), as well as in malignant B-cells derived from patients with NHL (n = 20). Cells were exposed in vitro to escalating doses of O with/without B. Cell death was determined by the Cell glow luminescent assay and DNA synthesis by [ 3 H]-Thymidine incorporation. To further study the mechanisms of O and/or B action, RSCL or RRCL were exposed to O or B with or without caspase inhibitors; viability was evaluated as above and apoptosis by flow cytometry and PARP cleavage. Autophagy was detected by LC3 conversion and electron microscopy (EM). Changes in p53 or BH3 domain proteins were evaluated by Western blot. To determine the role of p53 and/or autophagy in O or B activity, SiRNA assays were performed. O or B monotherapy induced time- and dose-dependent cell death of all cells tested. In vitro exposure of RRCL, RSCL and lymphoma specimens to O and B resulted in significant synergistic activity. In vitro exposure of NHL cells to O lead to p53 degradation and Noxa or PUMA induction; while exposure to B resulted in Bax upregulation and Mcl-1 downregulation. The ability of O or B to induce PARP cleavage varied between patient samples and was not observed in RRCL. Inhibition of caspase activity did not affect the ability of O or B to kill NHL cells. Induction of autophagy was detected by LC3 conversion and EM not only in RSCL or RRCL but also in patient-derived tumor cells. Additionally, cell death induced by O could be inhibited by knock-down of Beclin-1 or p53. Our data suggest that O and B have a dual mechanism of action. We also provide data suggesting that both p53 and Beclin-1 have a pivotal role in response to O. Our findings strongly suggest that O added to B may result in a novel and potent therapeutic strategy against aggressive NHL. No significant financial relationships to disclose.
IMU Preintegration on Manifold for Efficient Visual-Inertial Maximum-a-Posteriori Estimation (2015)

Recent results in monocular visual-inertial navigation (VIN) have shown that optimization-based approaches outperform filtering methods in terms of accuracy due to their capability to relinearize past states. However, the improvement comes at the cost of increased computational complexity. In this paper, we address this issue by preintegrating inertial measurements between selected keyframes. The preintegration allows us to accurately summarize hundreds of inertial measurements into a single relative motion constraint. Our first contribution is a preintegration theory that properly addresses the manifold structure of the rotation group and carefully deals with uncertainty propagation. The measurements are integrated in a local frame, which eliminates the need to repeat the integration when the linearization point changes while leaving the opportunity for belated bias corrections. The second contribution is to show that the preintegrated IMU model can be seamlessly integrated in a visual-inertial pipeline under the unifying framework of factor graphs. This enables the use of a structureless model for visual measurements, further accelerating the computation. The third contribution is an extensive evaluation of our monocular VIN pipeline: experimental results confirm that our system is very fast and demonstrates superior accuracy with respect to competitive state-of-the-art filtering and optimization algorithms, including off-the-shelf systems such as Google Tango [1].
Effects of fluorine implantation on the kinetics of dry oxidation of silicon (1986)

Kinetics of dry oxidation of silicon after implantation of fluorine in the oxide layer are investigated. It appeared that implanted fluorine can result in negative values of the linear oxidation rate constant. Fluorine profiles obtained by the nuclear reaction analysis (NRA) method using a resonant 19F(α, p)22Ne nuclear reaction will be presented. At 1200 °C the fluorine moves to the interface of Si and SiO2, both in dry oxidizing and inert atmospheres. Based on these findings, a model is presented that explains quantitatively the observed anomalous behavior of the linear oxidation rate constant.
An internal-coordinate Monte Carlo method for searching conformational space (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn internal-coordinate Monte Carlo method for searching conformational spaceGeorge Chang, Wayne C. Guida, and W. Clark StillCite this: J. Am. Chem. Soc. 1989, 111, 12, 4379–4386Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/ja00194a035https://doi.org/10.1021/ja00194a035research-articleACS PublicationsRequest reuse permissionsArticle Views1875Altmetric-Citations1004LEARN 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
The Genome-wide Transcriptional Responses of Saccharomyces cerevisiae Grown on Glucose in Aerobic Chemostat Cultures Limited for Carbon, Nitrogen, Phosphorus, or Sulfur (2003)

Profiles of genome-wide transcriptional events for a given environmental condition can be of importance in the diagnosis of poorly defined environments. To identify clusters of genes constituting such diagnostic profiles, we characterized the specific transcriptional responses of Saccharomyces cerevisiae to growth limitation by carbon, nitrogen, phosphorus, or sulfur. Microarray experiments were performed using cells growing in steady-state conditions in chemostat cultures at the same dilution rate. This enabled us to study the effects of one particular limitation while other growth parameters (pH, temperature, dissolved oxygen tension) remained constant. Furthermore, the composition of the media fed to the cultures was altered so that the concentrations of excess nutrients were comparable between experimental conditions. In total, 1881 transcripts (31% of the annotated genome) were significantly changed between at least two growth conditions. Of those, 484 were significantly higher or lower in one limitation only. The functional annotations of these genes indicated cellular metabolism was altered to meet the growth requirements for nutrient-limited growth. Furthermore, we identified responses for several active transcription factors with a role in nutrient assimilation. Finally, 51 genes were identified that showed 10-fold higher or lower expression in a single condition only. The transcription of these genes can be used as indicators for the characterization of nutrient-limited growth conditions and provide information for metabolic engineering strategies.
The prevalence of celiac disease in Europe: Results of a centralized, international mass screening project (2010)

CD is common in Europe. CD prevalence shows large unexplained differences in adult age across different European countries.
Campath-1H monoclonal antibody therapy (2000)

Monoclonal antibodies are receiving ever-increasing utilization in the treatment of hematologic malignancies. Campath-1 antibodies are directed against the surface antigen CD52 that is expressed on virtually all lymphocytes and monocytes. Murine forms, Campath-1G and Campath-1M, have been utilized extensively in allogeneic bone marrow transplants in order to purge the allograft of lymphocytes. The humanized form, Campath-1H, is currently the focus of many clinical trials in hematologic malignancies and autoimmune diseases. The genetically engineered Campath-1H has been utilized in the treatment of lymphomas and lymphoid leukemias with impressive results. T-cell prolymphocytic leukemia, chronic lymphocytic leukemia, and non-Hodgkin lymphomas appear to be particularly good targets for this agent. Campath-1H may be administered intravenously or subcutaneously. Infectious complications are the most significant side effect associated with its usage, with fevers, chills, nausea, and vomiting most common. Antibiotic prophylaxis has made the infectious morbidity associated with Campath-1H more manageable. The efficacy demonstrated in clinical trials and manageable toxicities make Campath-1H an appealing agent in the treatment of hematologic malignancies.
Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis (2013)

We conducted an analysis integrating multiple genomic features including mutations, copy number alterations, gene expression and methylation. This integrated approach in which one considers all of these genomic features performs better than any individual genomic assay. We identified multiple genes that robustly delineate advanced clinical stage, suggesting their possible role in colorectal cancer metastatic progression.
Regulation of Intracellular Cholesterol Distribution by Na/K-ATPase (2009)

Recent studies have ascribed many non-pumping functions to the Na/K-ATPase. We show here that graded knockdown of cellular Na/K-ATPase alpha1 subunit produces a parallel decrease in both caveolin-1 and cholesterol in light fractions of LLC-PK1 cell lysates. This observation is further substantiated by imaging analyses, showing redistribution of cholesterol from the plasma membrane to intracellular compartments in the knockdown cells. Moreover, this regulation is confirmed in alpha1(+/-) mouse liver. Functionally, the knockdown-induced redistribution appears to affect the cholesterol sensing in the endoplasmic reticulum, because it activates the sterol regulatory element-binding protein pathway and increases expression of hydroxymethylglutaryl-CoA reductase and low density lipoprotein receptor in the liver. Consistently, we detect a modest increase in hepatic cholesterol as well as a reduction in the plasma cholesterol. Mechanistically, alpha1(+/-) livers show increases in cellular Src and ERK activity and redistribution of caveolin-1. Although activation of Src is not required in Na/K-ATPase-mediated regulation of cholesterol distribution, the interaction between the Na/K-ATPase and caveolin-1 is important for this regulation. Taken together, our new findings demonstrate a novel function of the Na/K-ATPase in control of the plasma membrane cholesterol distribution. Moreover, the data also suggest that the plasma membrane Na/K-ATPase-caveolin-1 interaction may represent an important sensing mechanism by which the cells regulate the sterol regulatory element-binding protein pathway.
Deoxyadenosine triphosphate as a potentially toxic metabolite in adenosine deaminase deficiency. (1978)

The inherited deficiency of adenosine deaminase (adenosine aminohydrolase; EC 3.5.4.4) activity in humans is associated with an immunodeficiency. Some of the immunodeficient and enzyme-deficient patients respond immunologically to periodic infusions of irradiated erythrocytes containing adenosine deaminase. It has been previously reported that erythrocytes and lymphocytes from immunodeficient ane enzyme-deficient children contained increased concentrations of ATP, and in the one child studied after erythrocyte infusion therapy, the intracellular level of ATP diminished. Using high-pressure liquid chromatography that resolves ATP and 2'-dATP, we have observed greater than 50-fold elevations of dATP in the erythrocytes of immunodeficient, adenosine deaminase-deficient patients but not in the erythrocytes of an immunocompetent adenosine deaminase-deficient patient. The erythrocyte dATP in two unrelated adenosine deaminase-deficient, immunodeficient patients disappeared after infusion of normal erythrocytes. We propose that deoxyadenosine, a substrate of adenosine deaminase, is the potentially toxic substrate in adenosine deaminase deficiency, and that the mediator of the toxic effect is dATP, a recognized potent inhibitor of ribonucleotide reductase.