gebhart/patrepeval huggingface dataset:
Maturation of human oocytes in vitro and their developmental competence (2001)

Complete maturation of oocytes is essential for the developmental competence of embryos. Any interventions in the growth phase of the oocyte and the follicle in the ovary will affect oocyte maturation, fertilization and subsequent embryo development. Oocyte size is associated with maturation and embryo development in most species examined and this may indicate that a certain size is necessary to initiate the molecular cascade of normal nuclear and cytoplasmic maturation. The minimum size of follicle required for developmental competence in humans is 5-7 mm in diameter. Maturation in vitro can be accomplished in humans, but is associated with a loss of developmental competence unless the oocyte is near completion of its preovulatory growth phase. This loss of developmental competence is associated with the absence of specific proteins in oocytes cultured to metaphase II in vitro. The composition of culture medium used successfully for maturation of human oocytes is surprisingly similar to that originally developed for maturation of oocytes in follicle culture in vitro. The presence of follicle support cells in culture is necessary for the gonadotrophin-mediated response required to mature oocytes in vitro. Gonadotrophin concentration and the sequence of FSH and FSH-LH exposure may be important for human oocytes, particularly those not exposed to the gonadotrophin surge in vivo. More research is needed to describe the molecular and cellular events, the presence of checkpoints and the role of gene expression, translation and protein uptake on completing oocyte maturation in vitro and in vivo. In the meantime, there are very clear applications for maturing oocytes in human reproductive medicine and the success rates achieved in some of these special applications are clinically valuable.
Enhanced Certificate Revocation System (1995)

We apply off-line digital signatures to provide a novel approach to certificate revocation. Our approach dismisses with traditional CRLs and yields public-key infrastructures that are several-hundred times cheaper to run than traditional ones.
Use of biosensors to characterize recombinant proteins. (1994)

A new biosensor technology based on surface plasmon resonance (BIAcore, Pharmacia) is described which allows the surface and conformational integrity of a recombinant product to be monitored by measuring the binding characteristics of a panel of monoclonal antibodies. Interactions between the antibodies and the recombinant product are measured in real time in a quantitative and highly reproducible manner. This allows the association and dissociation kinetic rate constants of the antibodies to be calculated and not only the equilibrium binding constant. Besides using antibodies as conformational probes, the biosensor can also be used to measure directly the binding of a recombinant product to its natural biological ligand. Quantitative binding assays using biosensors are a powerful method for assessing the lot-to-lot consistency of recombinant products.
Structural analysis of oncogenic H-Ras mutants G12A and G13A (1999)

About 30% of human cancers are due to point mutations in one of the H-.K-, and N-Ras genes.These small GTPases act as early switch molecules tuming on and off cell proliferation processes in response to exocellular stimuli.Common mutations at Gly12, Gly13 and Gln61 prevent Ras fiom hydrolyzing GTP into GDP in the presence of a GAP (GTPase activating protein), prolonging the lifetime of the active state, therefore rendering the protein oncogenic.Frnm previous mutational and crystallographic studies, we know that too big a side chain at position 12 would stencally hinder the correct positioning of the Gln61 side chain for catalysis.To answer the questions why G12A is oncogenic while G12P is not and why a small change fkom a hydrogen to a methyl group at Gly13 also makes the protein transforming, we studied crystal structures of G12A and G13A H-Ras.Free G12NGDP was crystallized and subsequent modeling of its structure into the complex of H-Ras and p120GAPG~13 showed that Cp of Ala12 occupied the same position as that of ProlZ.The G13NGDP structure revealed no sign of involvernent of the 1 3 ' ~ residue with any other part of the molecule or with GAP.merelore, it appears that a hiIl understanding of the influences of amino acid changes at these positions will require cornplex structures of H-Ras mutants and the catalytic domain of GAP.1 am very gratefl to have had Dr. Young-Hwa Song constantly by my side when 1 took my fint steps in the world of protein biochemistry, and to have Wanda Gillon taking care of al1 things in the lab that I took for granted.In the two and half yean of rny study, many people, past and present members of the Pai lab have helped me on a great number of occasions.Particularly, 1 am thankful for the extensive computer knowledge of Dr. Rosi Hynes and Piotr Sliz, for Matthew Kimber's deep understanding of crystallography, and for Robert Garces' help in creating the beautiful slides and figures.Of course, 1 just have to mention my parents, the truly dearest people in the whole world.
Alkyl Monolayers on Silicon Prepared from 1-Alkenes and Hydrogen-Terminated Silicon (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkyl Monolayers on Silicon Prepared from 1-Alkenes and Hydrogen-Terminated SiliconMatthew R. Linford, Paul Fenter, Peter M. Eisenberger, and Christopher E. D. ChidseyCite this: J. Am. Chem. Soc. 1995, 117, 11, 3145–3155Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00116a019https://doi.org/10.1021/ja00116a019research-articleACS PublicationsRequest reuse permissionsArticle Views4953Altmetric-Citations1017LEARN 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
Ergebnisse (1989)

Von den untersuchten deutschen Staatenl) führte Sachsen schon 1878 eine Einkommensteuer im engeren Sinne ein und machte sie zur Hauptsteuer seines direkten Steuersystems. Genau wie Sachsen einige Jahrzehnte zuvor brach dann Württemberg 1903 mit dem bisher die Staatsfinanzen stützenden System der Realsteuern und ging zur Einkommensteuer über, die auch dort bald zur aufkommenstärksten Steuer wurde. Im Gegensatz dazu gab es in Preußen eine kontinuierliche Entwicklung von der Klassen- und klassifizierten Einkommensteuer hin zum Einkommensteuergesetz von 1891.
with human papillomavirus-associated esophageal squamous cell carcinoma in Kazakh population (2016)

Background: p16 INK4A expression has been used as a surrogate marker for human papillomavirus (HPV) infection in cervical cancer and head and neck cancer. p53 has also been reported as a feasible marker to identify HPV-positive oropharyngeal carcinoma and penile lesions. This study aimed to investigate p16 INK4A and p53 expression levels and their correlation with HPV status and clinical parameters in Kazakh patients with esophageal squamous cell carcinoma. Methods: Immunohistochemical expression of p16 INK4A and p53 were evaluated in 163 cases of esophageal squamous cell carcinoma in Kazakh patients. The presence of HPV DNA was detected by polymerase chain reaction. Results: p16 INK4A -positive expression was detected in 19.0 % of patients, and its expression was significantly correlated with a lower frequency of lymph node metastasis (p= 0.038). By contrast no significant association was found between p16 INK4A -positive expression and HPV status (correlation coefficient =-0.062, p=0.499). p16 INK4A -positive expression did not affect the odds of tumors being HPV positive (odds ratio [OR] =0.727 with 95 % confidence interval [CI]=0.288– 1.836). The sensitivity of p16 INK4A -positive expression as an HPV marker was 0.164, with a specificity of 0.788 and a positive predictive value of 0.391. p53-positive expression was present in 88.3 % of all cases. Although no significant correlation with available clinical parameters was found, a significantly inverse correlation was observed between p53 expression and HPV status (correlation coefficient=-0.186, p=0.039). Moreover, p53-positive expression decreased the odds of tumors being HPV positive (OR= 0.292 with 95 % CI= 0.086–0.990). The sensitivity of p53-negative expression as an HPV marker was 0.179, with a specificity of 0.940 and a positive predictive value of 0.714. The overall HPV prevalence was high (45.5 %) in Kazakh patients, with no significant association between HPV positivity and available clinical parameters or combined p16 INK4A /p53 expression. Conclusions: p16 INK4A -positive expression was associated with lymph node metastasis. Results indicate that p53-negative expression and not p16 INK4A -positive expression may be used as a marker for HPV status in ESCC;
Defining Aggressive Prostate Cancer Using a 12-Gene Model (2006)

The critical clinical question in prostate cancer research is: How do we develop means of distinguishing aggressive disease from indolent disease? Using a combination of proteomic and expression array data, we identified a set of 36 genes with concordant dysregulation of protein products that could be evaluated in situ by quantitative immunohistochemistry. Another five prostate cancer biomarkers were included using linear discriminant analysis, we determined that the optimal model used to predict prostate cancer progression consisted of 12 proteins. Using a separate patient population, transcriptional levels of the 12 genes encoding for these proteins predicted prostate-specific antigen failure in 79 men following surgery for clinically localized prostate cancer (P = .0015). This study demonstrates that cross-platform models can lead to predictive models with the possible advantage of being more robust through this selection process.
Holographic photonic crystals with diamond symmetry (2003)

We explore the analytical design of high-symmetry photonic crystals made by holographic lithography. We show how holographic lithography may be used to produce diamond-like photonic crystals that have a full, three-dimensional photonic band gap at a refractive index contrast equal to the lowest yet published.
Profile of venetoclax and its potential in the context of treatment of relapsed or refractory chronic lymphocytic leukemia (2017)

Over the last few years, dramatic changes have occurred in the treatment of chronic lymphocytic leukemia (CLL). The current standard for young and fit patients with CLL remains chemoimmunotherapy, namely the fludarabine, cyclophosphamide, and rituximab (FCR) regimen. However, novel oral therapies are presently being introduced and represent a considerable breakthrough concerning effectiveness and safety profile. In particular, the very high-risk group of CLL patients, defined by the genetic aberration del(17p) and/or <i>TP53</i> mutation, benefit from the new agents. These genetic abnormalities are the most relevant negative prognostic markers in the context of chemoimmunotherapy. New targeted therapies allow different approaches to improve outcomes.
Large-Scale Fe3O4Nanoparticles Soluble in Water Synthesized by a Facile Method (2008)

Large-scale hydrophilic Fe 3O 4 nanoparticles (NPs) were prepared in the presence of citrate and sodium nitrate via a facile method. The Fe 3O 4 NPs are quite stable and can be freely dispersed in water. The as-prepared magnetic nanoparticle solution can be stable for more than 1 month. The mean diameter of the Fe 3O 4 NPs can be controlled in the range of ∼20 to ∼40 nm in mean diameter. The NPs show superparamagnetic properties with a relatively high saturation magnetization moment 58 emu/mg at room temperature. Furthermore, a possible formation mechanism is proposed to explain why the magnetic nanoparticles are very well soluble in water.
A unified approach to statistical tomography using coordinate descent optimization (1996)

Over the past years there has been considerable interest in statistically optimal reconstruction of cross-sectional images from tomographic data. In particular, a variety of such algorithms have been proposed for maximum a posteriori (MAP) reconstruction from emission tomographic data. While MAP estimation requires the solution of an optimization problem, most existing reconstruction algorithms take an indirect approach based on the expectation maximization (EM) algorithm. We propose a new approach to statistically optimal image reconstruction based on direct optimization of the MAP criterion. The key to this direct optimization approach is greedy pixel-wise computations known as iterative coordinate decent (ICD). We propose a novel method for computing the ICD updates, which we call ICD/Newton-Raphson. We show that ICD/Newton-Raphson requires approximately the same amount of computation per iteration as EM-based approaches, but the new method converges much more rapidly (in our experiments, typically five to ten iterations). Other advantages of the ICD/Newton-Raphson method are that it is easily applied to MAP estimation of transmission tomograms, and typical convex constraints, such as positivity, are easily incorporated.
Learning to detect unseen object classes by between-class attribute transfer (2009)

We study the problem of object classification when training and test classes are disjoint, i.e. no training examples of the target classes are available. This setup has hardly been studied in computer vision research, but it is the rule rather than the exception, because the world contains tens of thousands of different object classes and for only a very few of them image, collections have been formed and annotated with suitable class labels. In this paper, we tackle the problem by introducing attribute-based classification. It performs object detection based on a human-specified high-level description of the target objects instead of training images. The description consists of arbitrary semantic attributes, like shape, color or even geographic information. Because such properties transcend the specific learning task at hand, they can be pre-learned, e.g. from image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In order to evaluate our method and to facilitate research in this area, we have assembled a new large-scale dataset, “Animals with Attributes”, of over 30,000 animal images that match the 50 classes in Osherson's classic table of how strongly humans associate 85 semantic attributes with animal classes. Our experiments show that by using an attribute layer it is indeed possible to build a learning object detection system that does not require any training images of the target classes.
Impact of Lactobacillus acidophilus Supplements on the Human Oropharyngeal and Intestinal Microflora (1987)

The influence of Lactobacillus acidophilus supplements on the oropharyngeal and intestinal microflora was studied before, during and after L. acidophilus administration. 10 healthy volunteers participated in the study. L. acidophilus was given as a fermented milk product containing 5 X 10(8)-2 X 10(9) CFU/ml in a dose of 250 ml twice a day for 7 days. Only minor changes in the number of aerobic and anaerobic microorganisms in the oropharynx were observed, with no increase in the number of lactobacilli. In the aerobic intestinal microflora a decrease in the number of Escherichia coli was observed in 6/10 subjects. Concerning the anaerobic intestinal microflora there was a significant increase in the number of lactobacilli in 9/10 subjects within 7 days of L. acidophilus administration. The increase in the number of lactobacilli remained as long as the subjects were consuming the L. acidophilus preparation. Lactobacilli returned to the same level as before the study 9 days after the L. acidophilus administration was stopped. Anaerobic cocci showed a decrease in 4/10 subjects, while the number of other anaerobic bacteria remained relatively constant throughout the observation time. These studies suggest that L. acidophilus in this type of preparation should be taken continuously in order to maintain high levels of lactobacilli in the intestine.
Regulation of microvascular permeability by vascular endothelial growth factors* (2002)

Generation of new blood vessels from pre-existing vasculature (angiogenesis) is accompanied in almost all states by increased vascular permeability. This is true in physiological as well as pathological angiogenesis, but is more marked during disease states. Physiological angiogenesis occurs during tissue growth and repair in adult tissues, as well as during development. Pathological angiogenesis is seen in a wide variety of diseases, which include all the major causes of mortality in the west: heart disease, cancer, stroke, vascular disease and diabetes. Angiogenesis is regulated by vascular growth factors, particularly the vascular endothelial growth factor family of proteins (VEGF). These act on two specific receptors in the vascular system (VEGF-R1 and 2) to stimulate new vessel growth. VEGFs also directly stimulate increased vascular permeability to water and large-molecular-weight proteins. We have shown that VEGFs increase vascular permeability in mesenteric microvessels by stimulation of tyrosine auto-phosphorylation of VEGF-R2 on endothelial cells, and subsequent activation of phospholipase C (PLC). This in turn causes increased production of diacylglycerol (DAG) that results in influx of calcium across the plasma membrane through store-independent cation channels. We have proposed that this influx is through DAG-mediated TRP channels. It is not known how this results in increased vascular permeability in endothelial cells in vivo. It has been shown, however, that VEGF can stimulate formation of a variety of pathways through the endothelial cell, including transcellular gaps, vesiculovacuolar organelle formation, and fenestrations. A hypothesis is outlined that suggests that these all may be part of the same process.
Inhibition of NFkappaB-mediated interleukin-1beta-stimulated prostaglandin E2 formation by the marine natural product hymenialdisine. (1997)

Exposure of human rheumatoid synovial fibroblasts (RSF) to interleukin 1beta (IL-1beta) results in the coordinate up-regulation of 85-kDa phospholipase A2 (PLA2) and mitogen-inducible cyclooxygenase (COX II) and subsequent biosynthesis of prostaglandin E2 (PGE2). We have recently demonstrated, through the use of oligonucleotide decoys and antisense, the participation of the proinflammatory transcription factor, nuclear factor kappaB (NFkappaB), in the regulation of the prostanoid-metabolizing enzymes. Hymenialdisine, a marine natural product has recently been characterized as an inhibitor of NFkappaB activation and exposure of IL-1-stimulated RSF-inhibited PGE2 production in a concentration-dependent manner (IC50 approximately 1 microM). Alternatively, both an analog, aldisine, and the protein kinase C inhibitor, RO 32-0432, were without affect. Direct action of hymenialdisine on IL-1-induced NFkappaB activation was demonstrated by a significant reduction (approximately 80%) in NFkappaB binding to the classical kappaB consensus motif (as assessed by electrophoretic mobility shift assay) and inhibition of stimulated p65 migration from the cytosol of treated cells (as assessed by Western analysis). Consistent with the role of NFkappaB in the transcriptional regulation of COX II and 85-kDa PLA2, hymenialdisine-treated RSF did not transcribe the respective mRNAs in response to IL-1. This led to reductions in their respective protein levels and subsequent reductions in the ability to produce PGE2. Specificity of action is suggested as IL-1-stimulated interleukin-8 (IL-8) production, which is known to be an NFkappaB-regulated event, was also inhibited by hymenialdisine, whereas IL-1-induced production of vascular endothelial growth factor, a non-NFkappaB-regulated gene, was not affected by exposure to hymenialdisine. Taken together, hymenialdisine inhibits IL-1-stimulated-RSF PGE2 formation acting predominately through modulation of NFkappaB activation and offers an interesting novel tool to evaluate the role of NFkappaB in inflammatory disease.
Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast (2002)

Methylation of histone H3 at lysine 4 (H3 Lys-4) or lysine 9 (H3 Lys-9) is known to define active and silent chromosomal domains respectively from fission yeast to humans. However, in budding yeast, H3 Lys-4 methylation is also necessary for silent chromatin assembly at telomeres and ribosomal DNA. Here we demonstrate that deletion of set1, which encodes a protein containing an RNA recognition motif at its amino terminus and a SET domain at the carboxy terminus, abolishes H3 Lys-4 methylation in fission yeast. Unlike in budding yeast, Set1-mediated H3 Lys-4 methylation is not required for heterochromatin assembly at the silent mating-type region and centromeres in fission yeast. Our analysis suggests that H3 Lys-4 methylation is a stable histone modification present throughout the cell cycle, including mitosis. The loss of H3 Lys-4 methylation in set1Delta cells is correlated with a decrease in histone H3 acetylation levels, suggesting a mechanistic link between H3 Lys-4 methylation and acetylation of the H3 tail. We suggest that methylation of H3 Lys-4 primarily acts in the maintenance of transcriptionally poised euchromatic domains, and that this modification is dispensable for heterochromatin formation in fission yeast, which instead utilizes H3 Lys-9 methylation.