gebhart/patrepeval huggingface dataset:
ChemInform Abstract: TOTAL SYNTHESES OF 11‐DEOXY‐11‐ALPHA‐HYDROXYMETHYL PROSTAGLANDIN ES. SYNTHETIC STUDIES ON PROSTANOIDS PART 6 (1975)

Abstract Auf dem im Formelschema angegebenen Weg werden aus 3,4‐Dimethoxcarbonylcyclopentanon (I) die 11‐Desoxy‐11α‐hydroxymethylprostaglandine Es (XI) dargestellt.
Synthesis of Water-Soluble Self-Acid-Doped Polyaniline (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Water-Soluble Self-Acid-Doped PolyanilineShow-An Chen and Gue-Wuu HwangCite this: J. Am. Chem. Soc. 1994, 116, 17, 7939–7940Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ja00096a078https://doi.org/10.1021/ja00096a078research-articleACS PublicationsRequest reuse permissionsArticle Views1334Altmetric-Citations142LEARN 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
Characteristic changes in microbial community composition and expression of innate immune genes in acute appendicitis (2013)

Appendicitis represents a common and severe gastrointestinal illness in younger individuals worldwide. The disease is characterized by an excessive inflammatory response and it is believed that bacterial overgrowth due to blockage of the appendix lumen might be involved. Despite the high incidence, only limited data on the pathophysiological changes exist; in particular, the innate immune responses involved are largely unknown. Real-time PCR analysis of tissue samples from inflamed and normal appendices demonstrated differentially regulated expression patterns of epithelial-derived antimicrobial peptides (AMP). The α-defensins human neutrophil peptides 1-3, HD5 and HD6, as well as the two β-defensins, human β-defensins (hBD)-2 and hBD-3, were up-regulated, whereas hBD-1 was down-regulated in acute appendicitis. Expression of upstream regulators of AMP expression, NOD-2 and TLRs 1, 2, 4, 5, 7, 8 and 10 was significantly increased as detected by real-time PCR. Finally, we confirmed the involvement of the pro-inflammatory cytokines IL-1β and IL-8, and detected characteristic changes in microbial community composition in appendicitis tissue specimens by 16S rDNA based detection techniques. In this study, we demonstrate a differential regulation of the innate immune system along with an altered bacterial diversity in acute appendicitis.
Automatic fluorescent tag detection in 3D with super‐resolution: application to the analysis of chromosome movement (2002)

In this paper, we describe an algorithmic framework for the automatic detection of diffraction-limited fluorescent spots in 3D optical images at a separation below the Rayleigh limit, i.e. with super-resolution. We demonstrate the potential of super-resolution detection by tracking fluorescently tagged chromosomes during mitosis in budding yeast. Our biological objective is to identify and analyse the proteins responsible for the generation of tensile force during chromosome segregation. Dynamic measurements in living cells are made possible by green fluorescent protein (GFP)-tagging chromosomes and spindle pole bodies to generate cells carrying four fluorescent spots, and observe the motion of the spots over time using 3D-fluorescence microscopy. The central problem in spot detection arises with the partial or complete overlap of spots when tagged objects are separated by distances below the resolution of the optics. To detect multiple spots under these conditions, a set of candidate mixture models is built, and the best candidate is selected from the set based on chi2-statistics of the residuals in least-square fits of the models to the image data. Even with images having a signal-to-noise ratio (SNR) as low as 5-10, we are able to increase the resolution two-fold below the Rayleigh limit. In images with a SNR of 5-10, the accuracy with which isolated tags can be localized is less than 5 nm. For two tags separated by less than the Rayleigh limit, the localization accuracy is found to be between 10 and 20 nm, depending on the effective point-to-point distance. This indicates the intimate relationship between resolution and localization accuracy.
Efficient methods for attaching non-radioactive labels to the 5′ ends of synthetic oligodeoxyribonucleotides (1986)

The syntheses are described of two types of linker molecule useful for the specific attachment of non-radioactive labels such as biotin and fluorophores to the 5' terminus of synthetic oligodeoxyribonucleotides. The linkers are designed such that they can be coupled to the oligonucleotide as a final step in solid-phase synthesis using commercial DNA synthesis machines. Increased sensitivity of biotin detection was possible using an anti-biotin hybridoma/peroxidase detection system.
Clinicopathological significance of epidermal growth factor and its receptor in human pancreatic cancer. (1998)

The expression of epidermal growth factor (EGF) and its receptor (EGF-R) was examined immunohistochemically in 60 primary and 26 metastatic lesions of pancreatic carcinoma. EGF was stained mainly in the cytoplasm of tumor cells, and EGF-R was stained mainly on the surface of cells. The expression rates of EGF and EGF-R were 28% and 43% for primary lesions, and 46% and 46% for metastatic lesions, respectively. The expression of EGF and EGF-R alone did not correlate with any clinicopathological factors such as clinical stage, tumor size, nodal involvement, histology, etc. The median survival period after pancreatectomy was 21.4 months for patients with EGF(+) cancers and 25.1 months for those with EGF (-) ones. On the other hand, the median survival period was 22.7 months for patients with EGF-R (+) cancers and 25.0 months for those with EGF-R (-) cancers. There were no significant differences in survival between groups of patients differing in EGF or EGF-R expression. When the expression of EGF and EGF-R was analysed in combination, the survival curve of patients with EGF(+) and EGF-R(+) cancers was found to be lower than that of the rest of the patients (p = 0.07), and especially the survival curve of patients with EGF(+)EGF-R(+) cancers was significantly lower than that of patients with EGF(+)EGF-R(-) cancers (p = 0.02), and EGF(-)EGF-R(+) cancers (p = 0.06). These results indicate that the expression of EGF or EGF-R alone in pancreatic cancer does not reflect the prognosis of patients; however the coexpression of EGF and EGF-R may be a beneficial prognostic factor for pancreatic cancer.
Antibody microarray‐based profiling of complex specimens: systematic evaluation of labeling strategies (2007)

Antibody microarrays have often had limited success in detection of low abundant proteins in complex specimens. Signal amplification systems improve this situation, but still are quite laborious and expensive. However, the issue of sensitivity is more likely a matter of kinetically appropriate microarray design as demonstrated previously. Hence, we re-examined in this study the suitability of simple and inexpensive detection approaches for highly sensitive antibody microarray analysis. N-hydroxysuccinimidyl ester (NHS)- and Universal Linkage System (ULS)-based fluorescein and biotin labels used as tags for subsequent detection with anti-fluorescein and extravidin, respectively, as well as fluorescent dyes were applied for analysis of blood plasma. Parameters modifying strongly the performance of microarray detection such as labeling conditions, incubation time, concentrations of anti-fluorescein and extravidin and extent of protein labeling were analyzed and optimized in this study. Indirect detection strategies whether based on NHS- or ULS-chemistries strongly outperformed direct fluorescent labeling and enabled detection of low abundant cytokines with many dozen-fold signal-to-noise ratios. Finally, particularly sensitive detection chemistry was applied to monitoring cytokine production of stimulated peripheral T cells. Microarray data were in accord with quantitative cytokine levels measured by ELISA and Luminex, demonstrating comparable reliability and femtomolar range sensitivity of the established microarray approach.
WHAT MATTERS FOR PREDICTING THE OCCURRENCES OF TREES: TECHNIQUES, DATA, OR SPECIES' CHARACTERISTICS? (2007)

Data characteristics and species traits are expected to influence the accuracy with which species' distributions can be modeled and predicted. We compare 10 modeling techniques in terms of predictive power and sensitivity to location error, change in map resolution, and sample size, and assess whether some species traits can explain variation in model performance. We focused on 30 native tree species in Switzerland and used presence-only data to model current distribution, which we evaluated against independent presence–absence data. While there are important differences between the predictive performance of modeling methods, the variance in model performance is greater among species than among techniques. Within the range of data perturbations in this study, some extrinsic parameters of data affect model performance more than others: location error and sample size reduced performance of many techniques, whereas grain had little effect on most techniques. No technique can rescue species that are difficult to predict. The predictive power of species-distribution models can partly be predicted from a series of species characteristics and traits based on growth rate, elevational distribution range, and maximum elevation. Slow-growing species or species with narrow and specialized niches tend to be better modeled. The Swiss presence-only tree data produce models that are reliable enough to be useful in planning and management applications.
A counterselection for the tryptophan pathway in yeast: 5‐fluoroanthranilic acid resistance (2000)

The ability to counterselect, as well as to select for, a genetic marker has numerous applications in microbial genetics. Described here is the use of 5-fluoroanthranilic acid for the counterselection of TRP1, a commonly used genetic marker in the yeast Saccharomyces cerevisiae. Counterselection using 5-fluoroanthranilic acid involves antimetabolism by the enzymes of the tryptophan biosynthetic pathway, such that trp1, trp3, trp4 or trp5 strains, which lack enzymes required for the conversion of anthranilic acid to tryptophan, are resistant to 5-fluoroanthranilic acid. Commonly used genetic procedures, such as selection for loss of a chromosomally integrated plasmid, and a replica-plating method to rapidly assess genetic linkage in self-replicating shuttle vectors, can now be carried out using the TRP1 marker gene. In addition, novel tryptophan auxotrophs can be selected using 5-fluoroanthranilic acid. Copyright © 2000 John Wiley & Sons, Ltd.
Coordination chemistry and biology of chelators for the treatment of iron overload disorders (2007)

Treatment of the medical condition generally referred to as iron overload through the delivery of chelators has recently received a major boost. In 2005 Novartis gained FDA approval for the drug deferasirox, which may be taken orally. Until this time most patients with Fe overload have had to endure long periods of subcutaneous infusions of the orally ineffective drug desferrioxamine (desferal) which has led to major problems with patient compliance. An effective Fe chelator must possess a number of properties for it to be able to complex Fe in vivo and be excreted intact. This Perspective will provide an overview of the current state of chelators for Fe overload; both those currently approved and those undergoing preclinical development.
The t(14;18) Chromosome Translocations Involved in B-Cell Neoplasms Result from Mistakes in VDJ Joining (1985)

In this study, the joining sequences between chromosomes 14 and 18 on the 14q+ chromosomes of a patient with pre-B-cell leukemia and four patients with follicular lymphoma carrying a t(14;18) chromosome translocation were analyzed. In each case, the involved segment of chromosome 18 has recombined with the immunoglobulin heavy-chain joining segment (JH) on chromosome 14. The sites of the recombination on chromosome 14 are located close to the 5' end of the involved JH segment, where the diversity (D) regions are rearranged with the JH segments in the production of active heavy-chain genes. As extraneous nucleotides (N regions) were observed at joining sites and specific signal-like sequences were detected on chromosome 18 in close proximity to the breakpoints, it is concluded that the t(14;18) chromosome translocation is the result of a mistake during the process of VDJ joining at the pre-B-cell stage of differentiation. The putative recombinase joins separated DNA segments on two different chromosomes instead of joining separated segments on the same chromosome, causing a t(14;18) chromosome translocation in the involved B cells.
Vascular Endothelial Growth Factor Is Sufficient to Produce Iris Neovascularization and Neovascular Glaucoma in a Nonhuman Primate (1996)

Intravitreal injections of recombinant human VEGF165 in amounts comparable with those measured in eyes with active neovascularization are sufficient to produce noninflammatory iris neovascularization in a nonhuman primate. Prolonged exposure to VEGF165 can produce ectropion uveae and neovascular glaucoma.
Genetically optimized all-dielectric metasurfaces (2017)

We present and study theoretically a new design approach for obtaining wide angle, highly efficient, all-dielectric metasurfaces. As a concrete example we focus on optimizing flat beam deflector for both the infra-red and visible spectral regions. Transmission efficiencies of up to 87.2% are obtained theoretically for deflection angle of 65° in visible (580nm) spectrum and up to 82% for deflection angle of 30.5° at telecom wavelength (1550nm). The enhanced efficiencies at wide deflection angles are obtained by genetic optimization of the nano-structures comprising the metasurface. Compared to previously employed design approaches, our approach enhances the transmission efficiency substantially without sacrificing rectangular grid arrangement and facilitates the realization of wide angle flat deflectors and holograms/lenses.
Development of passive CLARITY and immunofluorescent labelling of multiple proteins in human cerebellum: understanding mechanisms of neurodegeneration in mitochondrial disease (2016)

CLARITY enables immunofluorescent labelling and imaging of large volumes of tissue to provide a better insight into the three dimensional relationship between cellular morphology and spatial interactions between different cell types. In the current study, we optimise passive CLARITY and immunofluorescent labelling of neurons and mitochondrial proteins in mouse and human brain tissues to gain further insights into mechanisms of neurodegeneration occurring in mitochondrial disease. This is the first study to utilise human cerebellum fixed in paraformaldehyde and cryoprotected in conjunction with formalin-fixed tissues opening up further avenues for use of archived tissue. We optimised hydrogel-embedding and passive clearance of lipids from both mouse (n = 5) and human (n = 9) cerebellum as well as developing an immunofluorescent protocol that consistently labels different neuronal domains as well as blood vessels. In addition to visualising large structures, we were able to visualise mitochondrial proteins in passively cleared tissues to reveal respiratory chain deficiency associated with mitochondrial disease. We also demonstrate multiple use of tissues by stripping antibodies and re-probing the cerebellum. This technique allows interrogation of large volumes intact brain samples for better understanding of the complex pathological changes taking place in mitochondrial disease.
Sparse Representation for Signal Classification (2007)

In this paper, application of sparse representation (factorization) of signals over an overcomplete basis (dictionary) for signal classification is discussed.Searching for the sparse representation of a signal over an overcomplete dictionary is achieved by optimizing an objective function that includes two terms: one that measures the signal reconstruction error and another that measures the sparsity.This objective function works well in applications where signals need to be reconstructed, like coding and denoising.On the other hand, discriminative methods, such as linear discriminative analysis (LDA), are better suited for classification tasks.However, discriminative methods are usually sensitive to corruption in signals due to lacking crucial properties for signal reconstruction.In this paper, we present a theoretical framework for signal classification with sparse representation.The approach combines the discrimination power of the discriminative methods with the reconstruction property and the sparsity of the sparse representation that enables one to deal with signal corruptions: noise, missing data and outliers.The proposed approach is therefore capable of robust classification with a sparse representation of signals.The theoretical results are demonstrated with signal classification tasks, showing that the proposed approach outperforms the standard discriminative methods and the standard sparse representation in the case of corrupted signals.
Issues of controlling public kiosks and other self service machines using gesture recognition (2002)

We discuss the issues involved in controlling self service machines via gestures composed of both static symbols and dynamic motions. Each gesture is modeled from either static model information or a linear-in-parameters dynamic system. Recognition occurs in a real-time environment using a small amount of processing time and memory. We will examine which gestures are appropriate, how the gestures can be recognized, and which commands the gestures should control.
Polymeric nanoparticles for cancer therapy (2008)

Cancer is an ever-increasing menace that needs to be curbed soon. Though chemotherapy is successful to some extent, the main drawbacks of chemotherapy is the limited accessibility of drugs to the tumor tissues requiring high doses, their intolerable toxicity, development of multiple drug resistance and their non-specific targeting. Nanoparticles (NPs), an evolution of nanotechnology, have the potential to successfully address these problems related to drug delivery and retention and are considered potential candidates to carry drugs to the desired site of therapeutic action. In this review, we give an overview of the use of clinically applicable NPs mainly for cancer therapy. We also focus on the different types of nanoscale polymer carriers used for the delivery of chemotherapeutic agents and the mechanisms that facilitate their targeted delivery to tumor cells.
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria (2014)

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.
Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations (1988)

A new hybrid distance space-real space method for determining three-dimensional structures of proteins on the basis of interproton distance restraints is presented. It involves the following steps: (i) the approximate polypeptide fold is obtained by generating a set of substructures comprising only a small subset of atoms by projection from multi-dimensional distance space into three-dimensional cartesian coordinate space using a procedure known as 'embedding'; (ii) all remaining atoms are then added by best fitting extended amino acids one residue at a time to the substructures; (iii) the resulting structures are used as the starting point for real space dynamical simulated annealing calculations. The latter involve heating the system to a high temperature followed by slow cooling in order to overcome potential barriers along the pathway towards the global minimum region. This is carried out by solving Newton's equations of motion. Unlike conventional restrained molecular dynamics, however, the non-bonded interactions are represented by a simple van der Waals repulsion term. The method is illustrated by calculations on crambin (46 residues) and the globular domain of histone H5 (79 residues). It is shown that the hybrid method is more efficient computationally and samples a larger region of conformational space consistent with the experimental data than full metric matrix distance geometry calculations alone, particularly for large systems.
A Quantitative Analysis of Sensory Function in Lumbar Radiculopathy Using Current Perception Threshold Testing (2002)

Current perception threshold testing showed that the functions of A-beta, A-delta, and C fibers deteriorated in patients with lumbar radiculopathy. This technique may be useful for quantifying sensory nerve dysfunction in patients with radiculopathy.