gebhart/patrepeval huggingface dataset:
Multiple resolution segmentation of textured images (1991)

A multiple resolution algorithm is presented for segmenting images into regions with differing statistical behavior. In addition, an algorithm is developed for determining the number of statistically distinct regions in an image and estimating the parameters of those regions. Both algorithms use a causal Gaussian autoregressive model to describe the mean, variance, and spatial correlation of the image textures. Together, the algorithms can be used to perform unsupervised texture segmentation. The multiple resolution segmentation algorithm first segments images at coarse resolution and then progresses to finer resolutions until individual pixels are classified. This method results in accurate segmentations and requires significantly less computation than some previously known methods. The field containing the classification of each pixel in the image is modeled as a Markov random field. Segmentation at each resolution is then performed by maximizing the a posteriori probability of this field subject to the resolution constraint. At each resolution, the a posteriori probability is maximized by a deterministic greedy algorithm which iteratively chooses the classification of individual pixels or pixel blocks. The unsupervised parameter estimation algorithm determines both the number of textures and their parameters by minimizing a global criterion based on the AIC information criterion. Clusters corresponding to the individual textures are formed by alternately estimating the cluster parameters and repartitioning the data into those clusters. Concurrently, the number of distinct textures is estimated by combining clusters until a minimum of the criterion is reached.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis of the Methyl Glycosides of a Di- and Two Trisaccharide Fragments Specific for theShigella flexneriSerotype 2aO-Antigen (2000)

ABSTRACT The stereocontrolled synthesis of methyl α-D-glucopyranosyl-(1→4)-α-L-rhamnopyranoside (EC, 1), methyl α-L-rhamnopyranosyl-(1→3)-[α-D-glucopyranosyl-(1→4)]-α-L-rhamnopyranoside (B(E)C, 3) and methyl α-D-glucopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-2-acetamido-2-deoxy-β-D-glucopyranoside (ECD, 4) is described; these constitute the methyl glycosides of branched and linear fragments of the O-specific polysaccharide of Shigella flexneri serotype 2a. Emphasis was put on the construction of the 1,2-cis EC glycosidic linkage resulting in the selection of 2,3,4,6-tetra-O-benzyl-α-D-glucopyranosyl fluoride (8) as the donor. Condensation of methyl 2,3-O-isopropylidene-4-O-trimethylsilyl-α-L-rhamnopyranoside (11) and 8 afforded the fully protected αE-disaccharide 20, as a common intermediate in the synthesis of 1 and 3, together with the corresponding βE-anomer 21. Deacetalation and regioselective benzoylation of 20, followed by glycosylation with 2,3,4-tri-O-benzoyl-α-L-rhamnopyranosyl trichloroacetimidate (15) afforded the branched trisaccharide 25. Full deprotection of 20 and 25 afforded the targets 1 and 3, respectively. The corresponding βE-disaccharide, namely, methyl β-D-glucopyranosyl-(1→4)-α-L-rhamnopyranoside (βEC, 2) was prepared analogously from 21. Two routes to trisaccharide 4 were considered. Route 1 involved the coupling of a precursor to residue E and a disaccharide CD. Route 2 was based on the condensation of an appropriate EC donor and a precursor to residue D. The former route afforded a 1:2 mixture of the αE and βE condensation products which could not be separated, neither at this stage, nor after deacetalation. In route 2, the required αE-anomer was isolated at the disaccharide stage and transformed into 2,3,4,6-tetra-O-benzyl-α-D-glucopyranosyl-(1→4)-2,3-di-O-benzoyl-α-L-rhamnopyranosyl trichloroacetimidate (48) as the EC donor. Methyl 2-acetamido-2-deoxy-4,6-O-isopropylidene-β-D-glucopyran-oside (19) was preferred to its benzylidene analogue as the precursor to residue D. Condensation of 19 and 48 and stepwise deprotection of the glycosylation product afforded the target 4.
Effective view navigation (1997)

In view navigation a user moves about art information structure by selecting something in the current view of the structure. This paper explores the implications of rudimentary requirements for effective view navigation, namely that, despite the vastness of an information structure, the views must be small, moving around must not take too many steps and the route to any target be must be discoverable. The analyses help rationalize existing practice, give insight into the difficulties, and suggest strategies for design.
The Physical Biochemistry and Molecular Genetics of Sulfate Activation (1993)

This article is an overview of current research in the area of sulfate activation. Emphasis is placed on presenting unresolved issues in an appropriate context for critical evaluation by the reader. The energetics of sulfate activation is reevaluated in light of recent findings that demonstrate that the synthesis of activated sulfate is thermodynamically driven by GTP hydrolysis. The structural and functional bases of this GTPase activation are discussed in detail. The bonding and hydrolysis of the high-energy, phosphoric-sulfuric acid anhydride bond of activated sulfate are presented along with an analysis of the importance of the divalent cation and pyrophosphate protonation in the equilibria governing activated sulfate formation. The molecular genetics of sulfate assimilation in prokaryotes is reviewed with an emphasis on the regulation of the pathway. Recent discoveries connecting sulfate activation to plant/microbe symbiogenesis are presented, as are several examples of the importance of activated sulfate in human metabolism and disease.
FDA Approves New Drug for Advanced Ovarian Cancer (2015)

The FDA has approved olaparib, to be marketed under the name Lynparza, for the treatment of advanced ovarian cancer related to defective BRCA genes.
How Robert Burns Captured America (1998)

Before America discovered Robert Bums, Robert Bums had discovered America
Designing cell‐permeant phosphopeptides to modulate intracellular signaling pathways (2001)

A central theme in intracellular signaling is the regulatable interaction of proteins via the binding of specialized domains on one protein to short linear sequences on other molecules. The capability of these short sequences to mediate the required specificity and affinity for signal transduction allows for the rational design of peptide-based modulators of specific protein–protein interactions. Such inhibitors are valuable tools for elucidating the role of these interactions in cellular physiology and in targeting such interactions for potential therapeutic intervention. This approach is exemplified by the study of the role of phosphorylation of specific sites on signaling proteins. However, the difficulty of introducing large hydrophilic molecules such as phosphopeptides into cells has been a major drawback in this area. This review describes the application of recently developed cell-permeant peptide vectors in the introduction of biologically active peptides into cells, with particular emphasis on the antennapedia/penetratin, TAT, and signal-peptide based sequences. In addition, the modification of such peptides to increase uptake efficiency and affinity for their targets is discussed. Finally, the use of cell-permeant phosphopeptides to both inhibit and stimulate intracellular signaling mechanisms is described, by reference to the PLCγ, Grb2, and PI-3 kinase pathways. © 2001 John Wiley & Sons, Inc. Biopolymers (Pept Sci) 60: 45–60, 2001
THE DECADAL CLIMATE VARIABILITY AND THE ANOMALOUS ENSO DEVELOPMENTS IN 1990S (2002)

By using the wavelet transform method,the ENSO (2-7 a) signal and the decadal variability (8-20 a) are filtered out from the long-term SST data sets in order to investigate characteristics of the decadal variability and its impact on the ENSO.It is found that there are two different kinds of decadal SSTA modes-horseshoe and horse saddle patterns in the tropical Pacific.The horseshoe pattern represents that the decadal SSTA variability in the central Pacific is in phase with that in the eastern Pacific.The horse saddle pattern is named that they are out of phase.The former constituted the decadal variability before 1990s and the latter mainly prevailed during 1990s.As the response of atmosphere to the ocean,two decadal wind patterns appear in association with the SST decadal modes.One is characterized by anomalous development of the zonal wind,the other by anomalous development of the meridional wind.These two kinds of modes can also be regarded as different phases of the decadal oscillation.Further studies have shown that the influences of the two kinds of modes on the ENSO are different.The horse saddle mode has a stronger impact on the ENSO than the horseshoe mode.A possible mechanism for the influence of the decadal variability on the ENSO signal is presented.The central part of the thermocline along the equatorial Pacific moves up or down simultaneously with its eastern part while the decadal variability bears the horseshoe pattern.But the two segments of the thermocline in the central and eastern Pacific act oppositely while the decadal variability shows the horse saddle pattern.In this case it has an-influence on the individual ENSO'events by the superposition of the decadal variability.
Soft‐Templated Mesoporous Carbon‐Carbon Nanotube Composites for High Performance Lithium‐ion Batteries (2011)

Mesoporous carbon with homogeneously dispersed multi-walled carbon nanotubes (MWNTs) are synthesized via a one-step “brick and mortar” soft-templating approach. Nanocomposites exhibit a reversible lithium storage capacity of 900 mA h g−1 and a good rate performance. Such homogeneous nanocomposites are ideal candidates for electric vehicle applications where high power and energy density are primary requirements.
Characterisation of the conformational changes in platelet factor 4 induced by polyanions: towards in vitro prediction of antigenicity (2014)

Heparin-induced thrombocytopenia (HIT) is the most frequent drug-induced immune reaction affecting blood cells. Its antigen is formed when the chemokine platelet factor 4 (PF4) complexes with polyanions. By assessing polyanions of varying length and degree of sulfation using immunoassay and circular dichroism (CD)-spectroscopy, we show that PF4 structural changes resulting in antiparallel β-sheet content >30% make PF4/polyanion complexes antigenic. Further, we found that polyphosphates (polyP-55) induce antigenic changes on PF4, whereas fondaparinux does not. We provide a model suggesting that conformational changes exposing antigens on PF4/polyanion complexes occur in the hairpin involving AA 32-38, which form together with C-terminal AA (66-70) of the adjacent PF4 monomer a continuous patch on the PF4 tetramer surface, explaining why only tetrameric PF4 molecules express "HIT antigens". The correlation of antibody binding in immunoassays with PF4 structural changes provides the intriguing possibility that CD-spectroscopy could become the first antibody-independent, in vitro method to predict potential immunogenicity of drugs. CD-spectroscopy could identify compounds during preclinical drug development that induce PF4 structural changes correlated with antigenicity. The clinical relevance can then be specifically addressed during clinical trials. Whether these findings can be transferred to other endogenous proteins requires further studies.
Encoded combinatorial peptide libraries containing non-natural amino acids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEncoded combinatorial peptide libraries containing non-natural amino acidsJanice M. Kerr, Steven C. Banville, and Ronald N. ZuckermannCite this: J. Am. Chem. Soc. 1993, 115, 6, 2529–2531Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ja00059a070https://doi.org/10.1021/ja00059a070research-articleACS PublicationsRequest reuse permissionsArticle Views624Altmetric-Citations168LEARN 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
Adipose-derived stem cells for clinical applications: a review (2010)

The use of stem cells derived from adipose tissue as an autologous and self-replenishing source for a variety of differentiated cell phenotypes, provides a great deal of promise for reconstructive surgery. In this article, we review available literature encompassing methods of extraction of pluripotent adipose stem cells (ASCs) from lipoaspirate locations, their storage, options for culture, growth and differentiation, cryopreservation and its effect on stem cell survival and proliferation, and new technologies involving biomaterials and scaffolds. We will conclude by assessing potential avenues for developing this incredibly promising field.
High amounts of circulating interleukin (IL)‐6 in the form of monomeric immune complexes during anti‐IL‐6 therapy. Towards a new methodology for measuring overall cytokine production in human in vivo (1992)

A patient with plasma cell leukemia was treated with anti-interleukin (IL)-6 monoclonal antibodies (mAb) for 2 months. Using chromatography on protein A-Sepharose, anti-murine-IgG-Sepharose, anti-IL-6-mAb-Sepharose and gel filtration at pH 2.3, we have demonstrated that the anti-IL-6 mAb, by preventing the binding of IL-6 to its cell membrane receptor and its renal elimination, has induced huge amounts of IL-6 to circulate in the form of monomeric immune complexes. By using this observation, we have developed a mathematical modelling that allows the determination of the overall daily production of IL-6 in this patient, which was in the range of 15 micrograms per day. Overall in vivo production of cytokines has never been evaluated in animals or in humans before.
Evaluation of automated COBAS AMPLICOR PCR system for detection of several infectious agents and its impact on laboratory management (1996)

We evaluated the COBAS AMPLICOR (CA) PCR system (Roche Diagnostic Systems) designed for automated PCR amplification and detection of nucleic acids from infectious agents in clinical samples. The Roche AMPLICOR microwell plate (MWP) PCR was the reference method. CA amplifies target nucleic acid, captures the biotinylated amplification products by using magnetic particles coated with specific oligonucleotide probes, and detects the bound products colorimetrically. For Mycobacterium tuberculosis, the correlation of the results of CA tests with those of MWP tests was 100% with 230 samples, including 20 culture-positive samples. For hepatitis C virus, the correlation was 100% with 214 samples, including 60 positive samples. MultiPlex CA analysis of 199 cervical specimens for Chlamydia trachomatis, Neisseria gonorrhoeae, and the internal control gave 100% concordance. These samples included 19 C. trachomatis and 3 N. gonorrhoeae culture-positive samples. Overall, the agreement between PCR methods for all 842 comparisons was 100%. Compared with culture, the sensitivities of the assays for C. trachomatis and M tuberculosis were > or = 95%. After spiking alternating amplification tubes in the CA system with 10(14) copies of the Chlamydia amplicon per ml, we were unable to demonstrate any carryover cross-contamination of negative samples. Using the criteria of the College of American Pathologists workload recording method, we found that the total hands-on time to produce CA PCR results was 4.4, 7.9, and 3.3 min for M. tuberculosis, hepatis C virus, and the MultiPlexed assay for chlamydia plus gonorrhea and an internal control, respectively. The CA system brings true PCR automation to laboratories. In addition to the accuracy of automated results, the CA system provides labor savings, provides containment of the amplification and detection components of PCR, and supports both MultiPlex amplification and sequential algorithm (ReFlex) detection of analytes.
Endothelial-cell-specific regulation of von Willebrand factor gene expression. (1994)

In both tissue sections and cell culture, the endothelial nature of a cell is most commonly determined by demonstration of its expression of von Willebrand factor (vWf) protein and/or mRNA. Thus, the mechanism of cell-type-specific transcriptional regulation of the vWf gene is central to studying the basis of endothelial-cell-specific gene expression. In this study, deletion analyses were carried out to identify the region of the vWf gene which regulates its endothelial-cell-specific expression. A 734-bp fragment which spans the sequence from -487 to +247 relative to the transcription start site was identified as the cell-type-specific promoter. It consists of a minimal core promoter located between -90 and +22, a strong negative regulatory element located upstream of the core promoter (ca. -500 to -300), and a positive regulatory region located downstream of the core promoter in the first exon. The activity of the core promoter is not cell type specific, and the negative regulatory region is required to inhibit its activity in all cell types. The positive regulatory region relieves this inhibition only in endothelial cells and results in endothelial-cell-specific gene expression. The positive regulatory region contains sequences predicting possible SP1, GATA, and octamer binding sites. Mutations in either the SP1 or octamer sequence have no effect on transcriptional activity, while mutation in the GATA binding element totally abolishes the promoter activity. Evidence that a GATA factor is involved in this interaction is presented. Thus, the positive regulatory region with an intact GATA binding site is required to overcome the inhibitory effect of the negative regulatory element and activate vWf gene expression in an endothelial-cell-specific manner.
A structural equation model of physician productivity. (1988)

The understanding of physicians' practicing behaviors can enhance the development of active marketing strategies. The authors investigate the effects of physician characteristics on physician productivity in a hospital setting. Use of admission records, coupled with data from a survey of physicians' perceptions of hospital operations and their commitment to the study hospital, provides useful results for determining the most effective means for promoting physician satisfaction. Information from the survey can be used to forecast both the demand for various services and the likely physician response to the improvement of services and communications between physicians and administrative staff.
Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1 (2008)

Previously, several individuals with X-linked SCID (SCID-X1) were treated by gene therapy to restore the missing IL-2 receptor gamma (IL2RG) gene to CD34+ BM precursor cells using gammaretroviral vectors. While 9 of 10 patients were successfully treated, 4 of the 9 developed T cell leukemia 31-68 months after gene therapy. In 2 of these cases, blast cells contained activating vector insertions near the LIM domain-only 2 (LMO2) proto-oncogene. Here, we report data on the 2 most recent adverse events, which occurred in patients 7 and 10. In patient 10, blast cells contained an integrated vector near LMO2 and a second integrated vector near the proto-oncogene BMI1. In patient 7, blast cells contained an integrated vector near a third proto-oncogene,CCND2. Additional genetic abnormalities in the patients' blast cells included chromosomal translocations, gain-of-function mutations activating NOTCH1, and copy number changes, including deletion of tumor suppressor gene CDKN2A, 6q interstitial losses, and SIL-TAL1 rearrangement. These findings functionally specify a genetic network that controls growth in T cell progenitors. Chemotherapy led to sustained remission in 3 of the 4 cases of T cell leukemia, but failed in the fourth. Successful chemotherapy was associated with restoration of polyclonal transduced T cell populations. As a result, the treated patients continued to benefit from therapeutic gene transfer.
Inhibition of fatty acid synthesis delays disease progression in a xenograft model of ovarian cancer. (1996)

One of the key limiting factors in the treatment of advanced stage human epithelial malignancies is the lack of selective molecular targets for antineoplastic therapy. A substantial subset of human ovarian, endometrial, breast, colorectal, and prostatic cancers exhibit increased endogenous fatty acid biosynthesis and overexpress certain enzymes in the pathway. Cell lines derived from these tumors use endogenously synthesized fatty acids for cellular functions, whereas normal cells and tissues appear to utilize dietary lipids preferentially. We have previously shown that the difference in fatty acid biosynthesis between cancer and normal cells is an exploitable target for metabolic inhibitors in vitro. Here, we report observations in vivo using the i.p. model of the multiply drug-resistant OVCAR-3 human ovarian carcinoma in nude mice which demonstrate that: (a) fatty acid synthase overexpression in OVCAR-3 is comparable to levels in primary human tumors assessed by immunohistochemistry; (b) fatty acid synthetic activity of OVCAR-3 is comparably elevated in vitro and in vivo and is 4 to >20-fold higher than normal murine tissues; (c) treatment with the specific fatty acid synthase inhibitor, cerulenin, markedly reduces tumor cell fatty acid biosynthesis in vivo; (d) fatty acid synthase inhibition produces regression of established ascites tumor; and (e) treatment with cerulenin causes reduction in ascites incidence, delay in onset of ascites, and significantly increased survival (P<0.04).
SYSTEMIC AND REGIONAL EFFECTS OF ENDOTHELIN IN RABBITS: EFFECTS OF ENDOTHELIN ANTIBODY (1990)

1. The effects of porcine endothelin-1 (10(-12)-5 x 10(-10) mol/kg) on arterial blood pressure (BP) and the renal, mesenteric and carotid blood flow (BF), and the effects of endothelin-1 antibody were studied in rabbits. 2. Endothelin-1 caused a sustained increase in BP. The renal, mesenteric and carotid BF were decreased dose-dependently by endothelin-1. The approximate half-maximal effective values (ED50) were 5.5 x 10(-11), 8.6 x 10(-11) and 2.0 x 10(-10) mol/kg for renal, mesenteric and carotid BF respectively. Compared with carotid BF, the renal and mesenteric BF responses were significantly more sensitive to endothelin-1. 3. Combined administration of endothelin-1 and its antibody showed a significant inhibition of the BP and renal BF responses. However, endothelin-1 antibody alone did not change either BP, renal BF, mesenteric BF or carotid BF in vivo. 4. The present results demonstrate that endothelin is a potent vasoconstrictor in vivo. However, circulating endothelin may not contribute to the control of BF and BP. The role of endothelin as a local modulator of the vascular tone remains to be investigated.