gebhart/patrepeval huggingface dataset:
Angiogenesis: New insights and therapeutic potential (2000)

Angiogenesis, the formation of vessels from pre-existing vessels, is of critical importance not only during normal growth, but also in pathological situations. In the latter, some diseases are enhanced by excessive vascular growth (e.g., tumors), whereas in others inadequate vascular growth contributes to morbidity and mortality (e. g., ischemic heart disease). Our current state of knowledge makes it clear that the cascade of angiogenic events depends on complex processes that include cell-cell interactions, various intracellular signaling pathways, and the appropriate extracellular microenvironment. The literature regarding angiogenesis has increased exponentially during the last decade. Progress in this area is largely a consequence of advances in our understanding of angiogenic growth factor and cytokine function, in part due to the determination of their complete amino acid sequences and cloning of their genes. Other factors also play key roles in angiogenesis, including the extracellular matrix, adhesion molecules and their inhibitors, and metabolic and mechanical factors. The potential for developing therapeutic protocols has been enhanced by data from both in vitro and in vivo studies and has provided the rationale for clinic trials. Angiogenic therapy strategies include inhibition of aberrant angiogenesis, as seen in tumors or diabetes, as well as stimulation of angiogenesis in conditions of ischemia, such as ischemic heart or peripheral vascular disease. Anat Rec (New Anat) 261:126-135, 2000.
Compact single-channel rotary joint using ridged waveguide sections for phase adjustment (2003)

A new design for single-channel waveguide rotary joints for high-power applications is presented. In order to obtain correct signal phase conditions along the ring and, at the same time, reduce the diameter of the rotary joint, tapered ridged waveguide sections are introduced. Design guidelines with respect to general transmission characteristics, H-plane aperture couplers, and ridge waveguide analysis are presented. Measurements of a 9.05-GHz prototype show less than 1-dB insertion loss over a 250-MHz bandwidth and, hence, verify the design concept.
Learning for Dose Allocation in Adaptive Clinical Trials with Safety Constraints (2020)

Phase I dose-finding trials are increasingly challenging as the relationship between efficacy and toxicity of new compounds (or combination of them) becomes more complex. Despite this, most commonly used methods in practice focus on identifying a Maximum Tolerated Dose (MTD) by learning only from toxicity events. We present a novel adaptive clinical trial methodology, called Safe Efficacy Exploration Dose Allocation (SEEDA), that aims at maximizing the cumulative efficacies while satisfying the toxicity safety constraint with high probability. We evaluate performance objectives that have operational meanings in practical clinical trials, including cumulative efficacy, recommendation/allocation success probabilities, toxicity violation probability, and sample efficiency. An extended SEEDA-Plateau algorithm that is tailored for the increase-then-plateau efficacy behavior of molecularly targeted agents (MTA) is also presented. Through numerical experiments using both synthetic and real-world datasets, we show that SEEDA outperforms state-of-the-art clinical trial designs by finding the optimal dose with higher success rate and fewer patients.
Anionic tethered N-heterocyclic carbene chemistry (2007)

Since the discovery of a stable "bottleable" N-heterocyclic carbene (NHC), there has been a spectacular explosion of interest in this ligand class. This interest stems from a desire to understand the fundamentals of the structure and bonding of these systems, but also because of their numerous and emerging applications in small molecule activation, homogeneous catalysis and Lewis acid-catalysed reactions. In this Tutorial Review, we introduce the reader to NHCs, cover general synthetic methods to prepare anionic tethered NHCs and their metal complexes, and discuss emerging applications in reactivity and catalytic studies.
The Ensemble Kalman Filter in Reservoir Engineering--a Review (2009)

Introduction and Background There has been great progress in data assimilation within atmospheric and oceanographic sciences during the last couple of decades. In data assimilation, one aims at merging the information from observations into a numerical model, typically of a geophysical system. A typical example where data assimilation is needed is in weather forecasting. Here, the atmospheric models must take into account the most recent observations of variables such as temperature and atmospheric pressure for better forecasting of the weather in the next time period. A major challenge for these models is that they contain very large numbers of variables. The progress in data assimilation is because of both increased computational power and the introduction of techniques that are capable of handling large amounts of data and more severe nonlinearities. The aim of this paper is to focus on one of these techniques, the ensemble Kalman filter (EnKF). The EnKF has been introduced to petroleum science recently (Lorentzen et al. 2001a) and, in particular, has attracted attention as a promising method for solving the history matching problem. The literature available on the EnKF is now rather overwhelming. We hope that this review will help researchers (and students) working on adapting the EnKF to petroleum applications to find valuable references and ideas, although the number of papers discussing the EnKF is too large to give a complete review. For practitioners, we have cited critical EnKF papers from weather and oceanography. We have also tried to review most of the papers dealing with the EnKF and updating of reservoir models available to the authors by the beginning of 2008. The EnKF is based on the simpler Kalman filter (Kalman 1960). We will start by introducing the Kalman filter. The Kalman filter is an efficient recursive filter that estimates the state of a linear dynamical system from a series of noisy measurements. The Kalman filter is based on a model equation, where the current state of the system is associated with an uncertainty (expressed by a covariance matrix) and an observation equation that relates a linear combination of the states to measurements. The measurements are also associated with uncertainty. The model equations are used to compute a forward step (Eqs. 1 and 2) where the state variables are computed forward in time with the current estimate of the state as initial condition. The observation equations are used in the analysis step (Eqs. 3 through 5) where the estimated value of the state and its uncertainty are corrected to take into account the most recent measurements See, e.g., Cohn (1997), Maybeck (1979), or Stengel (1994) for an introduction to the Kalman filter.
Thrombosis and shock induced by activating antiplatelet antibodies in human FcγRIIA transgenic mice: the interplay among antibody, spleen, and Fc receptor (2000)

Transgenic mouse lines were created that express Fc gamma RIIA on platelets and macrophages at human physiologic levels, and they were used to explore the consequences in vivo of activating antiplatelet antibodies. Anti-CD9 antibody activated platelets of Fc gamma RIIA transgenic (tg) mice and, following injection in vivo, caused more rapid severe thrombocytopenia than nonactivating antiplatelet antibody. Anti-CD9 injected into Fc gamma RIIA tg crossed with FcR gamma-chain knockout (gamma-KO) mice caused thrombosis and shock in all mice, and death in 16 of 18 mice. The shock depended on platelet Fc receptor density and antibody dose. On histologic examination, the lung vasculature of anti-CD9-treated Fc gamma RIIA tg x gamma-KO mice contained extensive platelet-fibrin thrombi. Thrombosis and shock in Fc gamma RIIA tg mice in the context of the FcR gamma-chain knockout suggested the importance of the interplay of intravascular platelet activation and splenic clearance. Reduction of splenic clearance surgically (splenectomy) or functionally (monoclonal antibody treatment) also facilitated anti-CD9-mediated shock in Fc gamma RIIA tg mice. The spleen, which clears nonactivating antibody-coated platelets leading to thrombocytopenia, appears to play a protective role in the thrombosis and shock observed with activating antiplatelet antibody. The data indicate that antibodies, which activate platelets in an Fc gamma RIIA-dependent manner, can lead to thrombosis, shock, and death. Furthermore, antibody titer, platelet Fc receptor density, and splenic clearance are likely important determinants of the outcome. (Blood. 2000;96:4254-4260)
Immunochemical and genetic studies of Amb.t. V (Ra5G), an Ra5 homologue from giant ragweed pollen (1985)

Giant ragweed pollen allergen Amb.t. V (Ra5G), a homologue of short ragweed pollen Amb.a. V (Ra5S), was isolated in ultrapure form from a 16-min extract of ragweed pollen by a combination of molecular sieving through an Amicon hollow fiber cartridge (H1P5), cation-exchange chromatography, and gel filtration. The size was found to be 4400 daltons (D) by amino acid analysis and 6000 D by SDS-PAGE, and the pI was 8.3 as determined by isoelectric focusing. There was no cross-reactivity detected between the two Amb. V antigens by immunodiffusion and IEP with the use of hyperimmune antisera raised against crude or highly purified antigens. Cross-reactivity between the two Amb. V antigens was further investigated by inhibition double antibody radioimmunoassay by using the sera of nine selected ragweed-allergic patients who had recently been immunized with either mixed short-giant ragweed pollen extract or with short ragweed extract alone and who had IgG antibodies (Ab) to Amb.t. V and generally to Amb.a. V. Unlabeled Amb.t. V did not inhibit the binding of 125I-Amb.a. V to the IgG Ab in any of the sera tested. Conversely, unlabeled Amb.a. V produced some inhibition of the binding of 125I-Amb.t. V to the patients' IgG Ab, primarily in those patients who had received immunotherapy with short ragweed alone. This weak cross-reactivity was probably a result of the primary structural homology between the two protein allergens. The sera from two groups of ragweed-allergic individuals were investigated for the presence of IgG and IgE Ab to Amb.t. V. The presence of IgG Ab was found to be associated both with previous (or current) immunotherapy with giant ragweed extract and with HLA-Dw2. The HLA association is of interest in view of the previously established association between Dw2 and response toward the homologue Amb.a. V. The result suggests the existence of a similar genetic control at the primary level of antigenic recognition of the two Amb. V antigens.
Expression of Bcl-x in Erythroid Precursors from Patients with Polycythemia Vera (1998)

Deregulated expression of Bcl-x may contribute to the erythropoietin-independent survival of erythroid-lineage cells in polycythemia vera and thereby contribute to the pathogenesis of this disease.
Two New Pimelic Diphenylamide HDAC Inhibitors Induce Sustained Frataxin Upregulation in Cells from Friedreich's Ataxia Patients and in a Mouse Model (2010)

Our results support the pre-clinical development of a therapeutic approach based on pimelic diphenylamide HDACIs for FRDA and provide information for the design of future human trials of these drugs, suggesting an intermittent administration of the drug.
Continuous nonlinear dimensionality reduction by kernel eigenmaps (2003)

We equate nonlinear dimensionality reduction (NLDR) to graph embedding with side information about the vertices, and derive a solution to either problem in the form of a kernel-based mixture of affine maps from the ambient space to the target space. Unlike most spectral NLDR methods, the central eigenproblem can be made relatively small, and the result is a continuous mapping defined over the entire space, not just the datapoints. A demonstration is made to visualizing the distribution of word usages (as a proxy to word meanings) in a sample of the machine learning literature. 1 Background: Graph embcddings Consider a connected graph with weighted undirected edges specified by edge matrix W. Let be the positive edge weight between connected vertices i and j zero otherwise. Let D = diag(Wl) be a diagonal matrix where the cumulative edge weights into vertex /. The following points are well known or easily derived in spectral
Characterization of a basement membrane protein (BM180) using capillary electrophoresis. (1999)

Coeliac disease (gluten intolerance) is a genetically based autoimmune disease that becomes evident following ingestion of cereal prolamins such as the wheat gliadins. The process of this disease is not yet thoroughly understood. Purification of basement membrane protein-180 (BM180) (a basement membrane protein with a potential autoantigen role) and multiple analysis of the purified protein can lead to a better understanding of this disorder, which affects millions of people worldwide. Our preliminary work on the purification and characterization of this protein is presented in this paper. BM180 proteins were expressed in mouse EHS (Engelberth-Holm-Swarm) tumor cells. A crude purification process (see "Methods") was performed and the purified fractions were analyzed by capillary gel electrophoresis (CGE) for determination of the apparent molecular weight of the protein components in each fraction. The fractions, which contained compounds of the expected molecular weight, were further analyzed using a capillary zone electrophoresis (CZE) method developed for the routine analysis of wheat gliadins. Using the two CE methods, we were able to compare BM180 with certain gliadin fractions. Additional information on the protein stability was also obtained.
A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease (2003)

The diagnosis of Alzheimer's disease (AD), the most common form of dementia in the general population, usually relies upon the presence of typical clinical features and structural changes on brain magnetic resonance imaging. Over the last decade, a number of biological abnormalities have been reported in the cerebrospinal fluid (CSF) of AD patients, in particular altered levels of the tau protein and the 1-42 fragment of the amyloid precursor protein. These, however, have not yet proved sensitive and specific enough to be included in the diagnostic criteria for AD, leaving plenty of room for the search of novel biomarkers. The present study describes the analysis of CSF polypeptides by a protein-chip array technology called surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS). Using this approach, we detected statistically significant quantitative differences (p < 0.05) regarding four overexpressed and one underexpressed polypeptides in the CSF of AD patients as compared to healthy controls. Four of them were further purified by strong anionic exchange chromatography (SAX) and identified by MS analysis as cystatin C, two beta-2-microglobulin isoforms, an unknown 7.7 kDa polypeptide, and a 4.8 kDa VGF polypeptide. The combination of the five polypeptides for the diagnosis of AD allowed to classified six AD patients out of the nine included in this study and all the ten controls, which means in this small cohort that the specificity and sensitivity are 100% and 66%, respectively. This study, based on the protein-chip array technology, demonstrates the presence in the CSF of novel potential biomarkers for AD, which may be used for the diagnosis and perhaps the assessment of the severity and progression of the disease.
Stable Peptides Instead of Stapled Peptides: Highly Potent αvβ6‐Selective Integrin Ligands (2015)

The αvβ6 integrin binds the RGD-containing peptide of the foot and mouth disease virus with high selectivity. In this study, the long binding helix of this ligand was downsized to an enzymatically stable cyclic peptide endowed with sub-nanomolar binding affinity toward the αvβ6 receptor and remarkable selectivity against other integrins. Computational studies were performed to disclose the molecular bases underlying the high binding affinity and receptor subtype selectivity of this peptide. Finally, the utility of the ligand for use in biomedical studies was also demonstrated here.
Next-Generation Securities Market Systems: An Experimental Investigation of Quote-Driven and Order-Driven Trading (1997)

:Several major securities markets including Nasdaq in the United States and the London Stock Exchange’s SEAQ are organized as dealer markets that use computer screen displays of competitive dealer quotes to establish fair trade prices. To improve their markets and to reduce investors’ trading costs, these exchanges are introducing new rules and systems for handling investors’ orders. The redesign of a market structure raises important strategic issues for exchanges; more attractive trading mechanisms will increase order flow and improve liquidity, but margins and total profits earned by traditional exchange intermediaries may be reduced. To examine the consequences of market structure changes, we conducted experimental tests of the integration of an order-driven trading system into a dealer/quote-driven market. Using computer-based simulations of a stock market, experimental subjects traded using a traditional dealer quote screen to which a public limit order facility was added. Data captured on subjects’ trading decisions revealed that the limit order system was used by the subjects, attracting some orders that would have otherwise gone to dealers, and lowered investor trading costs. The integration of limit orders reduced dealers’ activities as a percentage of total market volume and lowered dealers’ trading margins, except in a special “informed dealer” case.
Prolonged hybridization with a cRNA probe improves the signal to noise ratio for in-tube in situ hybridization for quantification of mRNA after fluorescence-activated cell sorting (2012)

We developed an in-tube in situ hybridization method for mRNA quantification after fluorescence-activated cell sorting (FACS-mQ). A specific RNA in a particular cell type is stained with a cRNA probe and a fluorescent dye, which allows the stained cells to be selected by FACS without excessive RNA degradation. Our previous protocol required 4 h for hybridization with a cRNA probe, which might not produce enough fluorescence signal for sorting genes with low expressions. We determined the effect of prolonged hybridization for in-tube in situ hybridization on quantitative measurement of intracellular RNAs. During the hybridization step, the quantity of ACTB mRNA decreased gradually until 4 h, but remained constant from 4 to 16 h below 63.6° C. For flow cytometry, cells hybridization with cRNA probes for TG mRNA at 60° C for 16 h showed both increased signal and decreased background fluorescence compared to those hybridized for 4 h. These results indicate that when performing in-tube in situ hybridization, hybridization temperature can be raised to 63.6° C and the hybridization step can be extended up to 16 h without excessive intracellular RNA degradation.
Organic Laboratory Techniques, 3rd Edition (Fessenden, Ralph J.; Fessenden, Joan S.; Feist, Patty) (2001)

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewNEXTOrganic Laboratory Techniques, 3rd Edition (Fessenden, Ralph J.; Fessenden, Joan S.; Feist, Patty)Daniel Berger View Author Information Department of Chemistry, Bluffton College, Bluffton, OH 45817-1196Cite this: J. Chem. Educ. 2001, 78, 10, 1336Publication Date (Web):October 1, 2001Publication History Received3 August 2009Published online1 October 2001Published inissue 1 October 2001https://doi.org/10.1021/ed078p1336.2RIGHTS & PERMISSIONSArticle Views4730Altmetric-Citations-LEARN 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 InReddit PDF (59 KB) Get e-Alerts Get e-Alerts
Challenges faced in the implementation of localised advanced level geography syllabus: a case of Harare high schools (2008)

The paper examines the challenges met in implementing the Localized A Level Geography Syllabus. The study was conducted at 2006 in 52 Harare High Schools offering the localized A Level Geography syllabus. The sample for the study consisted of108 A Level Geography students, 54 A Level Geography teachers, 3 education officers and14 former Geography ' Level students already enrolled at the University of Zimbabwe. The research used both qualitative and quantitative aspects of research. Data was analysed using the manual sort and count, grouping, coding, classifying and categorizing to identify trends and patterns as they were emerging. Thick description was also employed using information and excerpts from
questionnaires, interviews, observations and document analysis. The major findings were that teachers are not using the new 'A Level Geography syllabus in planning their lessons. Teachers are still using notes that they made from the previous syllabus and students' exercises, which are derived from the old syllabus. Teachers are not confident when teaching the new syllabus and in planning their lessons. The content in
available textbooks is largely not relevant to the new A Level Geography syllabus as some case studies are out-dated and that the textbooks do not have local and regional examples. Teachers are having problems in implementing the new A Level syllabus as intended by the curriculum planners. The study recommends that teachers, as classroom practitioners, should discuss approaches in their districts or cluster workshops, seminars and staff developments on how to improve the implementation of this new A Level Geography syllabus with a view to making them feel more confident in the teaching and learning of Geography