gebhart/patrepeval huggingface dataset:
Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential (2014)

Pluripotency can be induced in somatic cells by overexpressing transcription factors, including POU class 5 homeobox 1 (OCT3/4), sex determining region Y-box 2 (SOX2), Krüppel-like factor 4 (KLF4), and myelocytomatosis oncogene (c-MYC). However, some induced pluripotent stem cells (iPSCs) exhibit defective differentiation and inappropriate maintenance of pluripotency features. Here we show that dynamic regulation of human endogenous retroviruses (HERVs) is important in the reprogramming process toward iPSCs, and in re-establishment of differentiation potential. During reprogramming, OCT3/4, SOX2, and KLF4 transiently hyperactivated LTR7s--the long-terminal repeats of HERV type-H (HERV-H)--to levels much higher than in embryonic stem cells by direct occupation of LTR7 sites genome-wide. Knocking down LTR7s or long intergenic non-protein coding RNA, regulator of reprogramming (lincRNA-RoR), a HERV-H-driven long noncoding RNA, early in reprogramming markedly reduced the efficiency of iPSC generation. KLF4 and LTR7 expression decreased to levels comparable with embryonic stem cells once reprogramming was complete, but failure to resuppress KLF4 and LTR7s resulted in defective differentiation. We also observed defective differentiation and LTR7 activation when iPSCs had forced expression of KLF4. However, when aberrantly expressed KLF4 or LTR7s were suppressed in defective iPSCs, normal differentiation was restored. Thus, a major mechanism by which OCT3/4, SOX2, and KLF4 promote human iPSC generation and reestablish potential for differentiation is by dynamically regulating HERV-H LTR7s.
When intracellular logistics fails - genetic defects in membrane trafficking (2006)

The number of human genetic disorders shown to be due to defects in membrane trafficking has greatly increased during the past five years. Defects have been identified in components involved in sorting of cargo into transport carriers, vesicle budding and scission, movement of vesicles along cytoskeletal tracks, as well as in vesicle tethering, docking and fusion at the target membrane. The nervous system is extremely sensitive to such disturbances of the membrane trafficking machinery, and the majority of these disorders display neurological defects--particularly diseases affecting the motility of transport carriers along cytoskeletal tracks. In several disorders, defects in a component that represents a fundamental part of the trafficking machinery fail to cause global transport defects but result in symptoms limited to specific cell types and transport events; this apparently reflects the redundancy of the transport apparatus. In groups of closely related diseases such as Hermansky-Pudlak and Griscelli syndromes, identification of the underlying gene defects has revealed groups of genes in which mutations lead to similar phenotypic consequences. New functionally linked trafficking components and regulatory mechanisms have thus been discovered. Studies of the gene defects in trafficking disorders therefore not only open avenues for new therapeutic approaches but also significantly contribute to our knowledge of the fundamental mechanisms of intracellular membrane transport.
Preparation of Macroporous Cellulose Beads through a Single-Step Non-Solvent Induced Phase Separation Method from a Cellulose Acetate Solution (2019)

Abstract Macroporous cellulose beads having a three-dimensionally interconnected porous structure have been economically prepared from a cellulose acetate solution in a single step at room temperature. The water absorbency and stiffness of the obtained macroporous beads could be controlled by changing the CA concentration.
366. Carbene chemistry. Part I. Reactions of fluoroalkyldiazo-compounds (1964)

R. Fields and R. N. Haszeldine, J. Chem. Soc., 1964, 1881 DOI: 10.1039/JR9640001881
Wearable conductive fiber sensors for measuring joint movements (2004)

This paper describes a technique that uses conductive fibers as part of a wearable sensor for continuous monitoring of joint movements. Conductive fibers are incorporated into flexible fabrics that fit tightly around a joint, and resistance changes in the fibers caused by skin extension can be measured, and related to joint motion. An overview of the sensor design, including functional requirements and design parameters, are presented, as well as preliminary results from a prototype sensor design. A single-axis joint model is also presented to illustrate the implementation of an extended Kalman filter to estimate joint angle. The Kalman filter also estimates parameters associated with misalignment errors that may be created every time the subject takes off and puts on the wearable sensor, allowing a sensor to be calibrated only once, with no need for re-calibration for all future uses.
Active Sites in Fe-exchanged Zeolites and Catalysis of Benzene Hydroxylation to Phenol (2014)

Fe-exchanged zeolites show great promise for the direct benzene hydroxylation to phenol, one of the most important industrial chemicals. In this review, the recent achievements on the active sites and benzene hydroxylation have been summarized and discussed. Firstly, the catalytic results that are assumed in absence of Fe ions are given; secondly, the indispensible role of Fe ions has been revealed. Four types of Fe-involved active sites reported so far have been elaborated, and each type may correpond to a variety of active-site structures. Then the catalytic mechanisms of the mono- and binuclear-Fe sites are sucessively exploited, which are found to be quite similar. The comprising Fe<sup>3+</sup> ions are catalytically unfavorable owing to the formation of specailly stable phenolate intermediates that result in deactivation to the catalysts. The Fe<sup>2+</sup> ions, whether in the mononuclear or binuclear sites, are potentially active for the catalytic reaction. Finally, a brief concluding remark is presented listing some unresolved problems that may seriously impede this catalytic reaction on an industrial scale.
Conformationally Altered p53: A Putative Peripheral Marker for Alzheimer’s Disease (2008)

The identification of biological markers of Alzheimer's disease (AD) can be extremely useful to improve diagnostic accuracy and/or to monitor the efficacy of putative therapies. In this regard, peripheral cells may be of great importance because of their easy accessibility. After subjects were grouped according to diagnosis, the expression of conformational mutant p53 in blood cells was compared by immunoprecipitation or by a cytofluorimetric assay. One hundred and four patients with AD, 92 age-matched controls, 15 patients with Parkinson's disease, and 9 with other types of dementia were analyzed. Two independent methods to evaluate the differential expression of a conformational mutant p53 were developed. Mononuclear cells were analyzed by immunoprecipitation or by flow cytometric analysis, following incubation with a conformation-specific p53 antibody, which discriminates unfolded p53 tertiary structure. Mononuclear cells from AD patients express a statistically significantly higher amount of mutant-like p53 compared to mononuclear cells from non-AD subjects, thus supporting the study of conformational mutant p53 as a new putative marker to discriminate AD from non-AD patients. We also observed a strong positive correlation between the expression of p53 and the age of patients. The expression of mutant p53 did not correlate with the duration of illness and the Mini Mental State Examination scores.
Genes of the GadX-GadW Regulon in<i>Escherichia coli</i> (2003)

Acid in the stomach is thought to be a barrier to bacterial colonization of the intestine. Escherichia coli, however, has three systems for acid resistance, which overcome this barrier. The most effective of these systems is dependent on transport and decarboxylation of glutamate. GadX regulates two genes that encode isoforms of glutamate decarboxylase critical to this system, but additional genes associated with the glutamate-dependent acid resistance system remained to be identified. The gadX gene and a second downstream araC-like transcription factor gene, gadW, were mutated separately and in combination, and the gene expression profiles of the mutants were compared to those of the wild-type strain grown in neutral and acidified media under conditions favoring induction of glutamate-dependent acid resistance. Cluster and principal-component analyses identified 15 GadX-regulated, acid-inducible genes. Reverse transcriptase mapping demonstrated that these genes are organized in 10 operons. Analysis of the strain lacking GadX but possessing GadW confirmed that GadX is a transcriptional activator under acidic growth conditions. Analysis of the strain lacking GadW but possessing GadX indicated that GadW exerts negative control over three GadX target genes. The strain lacking both GadX and GadW was defective in acid induction of most but not all GadX target genes, consistent with the roles of GadW as an inhibitor of GadX-dependent activation of some genes and an activator of other genes. Resistance to acid was decreased under certain conditions in a gadX mutant and even more so by combined mutation of gadX and gadW. However, there was no defect in colonization of the streptomycin-treated mouse model by the gadX mutant in competition with the wild type, and the gadX gadW mutant was a better colonizer than the wild type. Thus, E. coli colonization of the mouse does not appear to require glutamate-dependent acid resistance.
Prevalence of Childhood and Adult Obesity in the United States, 2011-2012 (2014)

Overall, there have been no significant changes in obesity prevalence in youth or adults between 2003-2004 and 2011-2012. Obesity prevalence remains high and thus it is important to continue surveillance.
Self-organized structures in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mtext>CoCr</mml:mtext></mml:mrow><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>4</mml:mn></mml:msub><mml:mo>(</mml:mo><mml:mn>001</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:math>thin films: Tunable growth from pyramidal clusters to a<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mrow><mml:mo>{</mml:mo><mml:mrow><mml:mn>111</mml:mn></mml:mrow><mml:mo>}</mml:mo></mml:mrow></mml:mrow></mml:math>fully faceted surface (2004)

Self-organized pyramidal structures (quadratic or hut-cluster type) of ferrimagnetic spinel ${\text{CoCr}}_{2}{\mathrm{O}}_{4}$ (CCO) are grown by deposition from vapor phase on ${\text{MgAl}}_{2}{\mathrm{O}}_{4}(001)$ substrates. The surfaces of the structures, forming an angle $\ensuremath{\Theta}\ensuremath{\approx}50--55\ifmmode^\circ\else\textdegree\fi{}$ with the (001) surface, are identified as the spinel ${111}$ facets, so the pyramids can be considered as true three-dimensional objects. Important characteristics of the structures can be tuned by varying the deposition time and/or growth temperature. It allows one to obtain isolated ${111}$ pyramids self-ordered in arrays along $⟨110⟩$ directions or fully ${111}$ faceted surfaces. The size and size distribution of the objects can be controlled by varying the fabrication conditions: the observed bimodal distribution obtained at low temperatures transforms into a single-modal one in films grown at high temperature. Moreover, the equilibrium shape of CCO islands is pyramidal for any object size, which is key for the controlled fabrication of nano-objects. The driving forces for the observed ${111}$ faceted objects and surfaces, bimodal size distributions and long range order are discussed. We end by discussing the (dis)similarities of the growth of the spinel CCO structures with that of the widely studied of silicon-germanium semiconductor dots and underlining prospects for new functionalities of self-ordered growth of complex oxides.
ERRORS INVOLVED IN RADIOLOGICAL HEART VOLUME DETERMINATION BY THE ELLIPSOID-APPROXIMATION TECHNIQUE (1965)

The radiological measurement of the heart's volume during life has been attempted by modelmaking The latter depend upon the assumption that the shape of the heart approximates to that of some regular figure, estimates of its volume then being obtainable from measurements of the heart's shadows in orthodiagraphic or teleradiographic projections. The simplest such assumption is that which considers the heart as a sphere, and on this basis volume estimates can be made from measure- ment of a single projection of the heart (Geigel, 1914). These estimates are-unsatisfactory, however, chiefly because the heart's depth bears no constant relation to the dimensions of its postero-anterior projection
A Bregman Divergence Optimization Framework for Ranking on Data Manifold and Its New Extensions (2021)

Recently, graph-based ranking algorithms have received considerable interests in machine learning, computer vision and information retrieval communities. Ranking on data manifold (or manifold ranking, MR) is one of the representative approaches. One of the limitations of manifold ranking is its high computational complexity (O(n3), where n is the number of samples in database). In this paper, we cast the manifold ranking into a Bregman divergence optimization framework under which we transform the original MR to an equivalent optimal kernel matrix learning problem.With this new formulation, two effective and efficient extensions are proposed to enhance the ranking performance. Extensive experimental results on two real world image databases show the effectiveness of the proposed approach.
Capillary affinophoresis of pea lectin with polyliganded affinophores: A model study of divalent‐polyvalent interactions (1998)

Affinophoresis is a type of affinity electrophoresis using an affinophore, a soluble ionic carrier bearing affinity ligand(s). It was reported previously that an affinophore, prepared by coupling multiple p-aminophenyl alpha-D-mannoside ligands to a part of the carboxyl groups of succinylated polylysine, specifically changed the mobility of pea lectin in agarose gel. The affinophoresis of this divalent lectin with the polyliganded affinophore was investigated by using capillary electrophoresis. Analysis of the mobility change of the lectin in the presence of differently modified affinophores showed that the affinity was larger for affinophores having higher ligand density. Analysis of the inhibition of the mobility change by a neutral ligand, with a known affinity constant for the lectin, allowed estimation of the contributions of monovalent and divalent interactions to the binding in the lectin-affinophore complex. The proportion of divalent complexes was greater for affinophores having higher ligand density. This approach to estimate the contribution of divalency in complex formation should be generally applicable to the analysis of divalent interactions with different techniques other than electrophoresis.
Selection in a Database: A Complete Discussion (1986)

This chapter contains sections titled: Problem Summary, Selection Constraints, Horizontal Constraints, Vertical Constraints, Selection Using Relational Algebra, Pattern Recognition
Failure Analysis Techniques for Microsystems-Enabled Photovoltaics (2013)

Microsystems-enabled photovoltaics (MEPV) has great potential to meet the increasing demands for light-weight, photovoltaic solutions with high power density and efficiency. This paper describes effective failure analysis techniques to localize and characterize nonfunctional or underperforming MEPV cells. The defect localization methods such as electroluminescence under forward and reverse bias, as well as optical beam induced current using wavelengths above and below the device band gap, are presented. The current results also show that the MEPV has good resilience against degradation caused by reverse bias stresses.
Bangladesh: An Overview of Open Access (OA) Initiatives (2014)

The present paper describes about the universal access to knowledge and information in the network and digital environment. The paper discusses the Open Access (OA) and Institutional Repositories (IR) initiatives for global access, repository, preservation, and organized management of networked information services in an environment where both the users and resources are at varied locations. The paper highlights the importance of open access and Institutional Repositories initiatives to the system of scholarly communication in Bangladesh. The paper explains research communities’ benefits of open access, salient features of ICT in Bangladesh, initiatives of institutional repositories in Bangladesh, open access movement in Bangladesh. Open Access Movement and IR could contribute significantly to economic, scientific and research growth of the respective country by providing access to scholarly materials without the economic barriers that currently exist in scholarly publishing.
Characterization of antibodies elicited by XMRV infection and development of immunoassays useful for epidemiologic studies (2010)

This study provides the first demonstration of seroconversion patterns elicited by XMRV infection. The nature and kinetics of antibody responses to XMRV in primates were fully characterized. Moreover, key serologic markers useful for detection of XMRV infection were identified. Three prototype immunoassays were developed to detect XMRV-specific antibodies. These assays demonstrated good sensitivity and specificity; thus, they will facilitate large scale epidemiologic studies of XMRV infection in humans.
Epigenetic Gene Regulation in the Bacterial World (2006)

Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.
Emulation of floating memcapacitors and meminductors using current conveyors (2011)

Suggested are circuit realisations of emulators transforming memristive devices into effective floating memcapacitive and meminductive systems. The emulator's circuits are based on second generation current conveyors and involve either four single-output or two dual-output current conveyors. The equations governing the resulting memcapactive and meminductive systems are presented.
Plasmin cleaves Aβ42 in vitro and prevents its aggregation into β-pleated sheet structures (2001)

The formation, aggregation and deposition of amyloid beta peptide (Abeta) is implicated in the aetiology of Alzheimer's disease. Impairment of proteolytic degradation of Abeta may be a key factor in the progression of the disease. We have used RP-HPLC and thioflavin T fluorescence to demonstrate that Abeta42 is rapidly cleaved by the protease plasmin and that cleavage prevented the aggregation of Abeta42, and its cleavage products, into beta-pleated sheet structures. Plasmin may fulfil a similar role in vivo.
Synthesis and pharmacological properties of substituted cinnamohydroxamic acids (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and pharmacological properties of substituted cinnamohydroxamic acidsN. P. Buu-Hoi, Claude L. Gillet, Georges E. Lambelin, Jose L. Roba, and Jacques E. ThiriauxCite this: J. Med. Chem. 1970, 13, 2, 211–213Publication Date (Print):March 1, 1970Publication History Published online1 May 2002Published inissue 1 March 1970https://pubs.acs.org/doi/10.1021/jm00296a010https://doi.org/10.1021/jm00296a010research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations5LEARN 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
High Pressure Behavior of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi>ZrW</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>O</mml:mi></mml:mrow><mml:mrow><mml:mn>8</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>: Grüneisen Parameter and Thermal Properties (2000)

High pressure Raman spectroscopic studies are carried out on negative thermal expansion material ZrW2O8. The system exhibits amorphization at 2.2+/-0.3 GPa via an intermediate orthorhombic phase. In the cubic phase most modes below 50 meV are found to have negative Gruneisen parameter. Using the reported phonon density of states thermal properties are calculated and compared with the reported results. In contrast to the earlier belief, the present results show that modes of energies much higher than 10 meV also contribute substantially to the negative thermal expansion.