gebhart/patrepeval huggingface dataset:
Binding of Phosphorylated Sp1 Protein to Tandem Sp1 Binding Sites Regulates α2 Integrin Gene Core Promoter Activity (1997)

The alpha2beta1 integrin, a collagen/laminin receptor, is expressed by a variety of cell types, including epithelial cells, mesenchymal cells, and hematopoietic cells. To understand the molecular mechanisms that regulate expression of the alpha2beta1, integrin in cells with megakaryocytic differentiation, we characterized the 5' flanking region of the alpha2 integrin gene and identified three distinct regulatory regions, including a core promoter, a silencer, and megakaryocyte enhancers in the distal 5' flank (Zutter et al, Blood 96:3006, 1995 and Zutter et al, J Biol Chem 269:463, 1994). We now focus on the core promoter of the alpha2 integrin gene located between bp -30 and -92 that is required for transcriptional activity of the alpha2 integrin gene. Sequence analysis identified two Sp1 consensus sites and a potential AP2 site. Gel retardation assays showed that nuclear proteins from uninduced K562 cells and K562 cells induced to become megakaryocytic bound specifically to the core promoter region (bp -30 to bp -92) producing two DNA-protein complexes. In addition, nuclear extracts from cells induced along the megakaryocyte lineage produced a selective increase in the slower migrating complex. Site-directed mutagenesis of the 5', the 3', or both Sp1 binding sites suggested that both Sp1 binding sites are required for full promoter activity and for DNA-protein complex formation. DNA footprinting also showed specific protection of the 5' Sp1 site by nuclear extracts from uninduced K562 cells and protection of both the 5' and the 3' Sp1 sites by nuclear extracts from induced K562 cells. Sp1 protein-DNA complex formation was dependent on Sp1 phosphorylation. The faster migrating DNA-protein complex was enhanced by dephosphorylation; the slower migrating DNA-protein complex was diminished or lost.
Tubulointerstitial Nephritis with Uveitis in Chinese Adults (2013)

The diagnosis of TINU syndrome can be missed in a large fraction of patients with ATIN because uveitis can present well after the onset of tubulointerstitial nephritis. Elevated mCRP-Ab levels may be useful in predicting late-onset uveitis TINU syndrome. Unfortunately, patients with TINU tended to have frequent relapses and most patients had incomplete renal recovery. Long-term follow-up is needed to prevent misdiagnosis and properly manage TINU syndrome.
Vertex-Tracing - Interaktives Ray-Tracing durch adaptiv progressives Refinement im Objektraum (2004)

Abstract\n\nThis dissertation presents an approach for interactive, physically exact simulation of\nspecular reflections and specular refractions in virtual environments. The introduced\napproach is called Vertex Tracing and allows a hybrid rendering to add global\nillumination effects in traditional hardware rendering systems.\n\nThe core of the Vertex Tracing is an adaptive progressive ray tracing. In contrast to\nstandard ray tracing we use image coherence to compute only pixels (samples) that are\nessential for the final image reconstruction. The step by step adaption towards the final\nimage is performed by geometry refinement of chosen polyhedra. These are scene objects\nwith visual characteristics as specular reflections or refractions and should be handled\nparticularly for Vertex Tracing. The object vertices are the starting point of\ncomputation. First, primary rays are shot from the eye point to the object vertices and\nafter that, like in classical ray tracing approaches, a recursive ray shooting is\nperformed from each vertex. If needed new vertices are inserted and consequently a step\nby step refinement of the object geometry is done.\n\nThe reconstruction of the final image is performed by bilinear interpolation via graphics\nhardware. Beside the possibility of a combined rendering with OpenGL-objects, the use of\ngraphics hardware additionally allows an efficient handling of textures. In this context,\nwe introduce a defered texture lookup to prevent a costly sampling of high frequent\ntextures.\n\nIn addition, this thesis considers aspects of a distributed and parallel computation to\nspeed up Vertex Tracing. In detail we implemented a distributed Vertex Tracing for a\nheterogenous network as well as a parallel approach for shared memory machines. Despite\nthe adaptive progressive characteristic of the Vertex Tracing both techniques show that a\nsignificant speed-up can be achieved.
Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas (2019)

We have established a glioma-specific cancer panel. GliomaSCAN highly excelled in capturing somatic variations in terms of both sensitivity and specificity and provided potential clinical implication in facilitating genome-based clinical trials. Our results could provide conceptual advance towards improving the response of genomically guided molecularly targeted therapy in glioma patients.
A Foreign Protein Incorporated on the Tip of T3 Pili in <i>Lactococcus lactis</i> Elicits Systemic and Mucosal Immunity (2009)

The use of Lactococcus lactis to deliver a chosen antigen to the mucosal surface has been shown to elicit an immune response in mice and is a possible method of vaccination in humans. The recent discovery on Gram-positive bacteria of pili that are covalently attached to the bacterial surface and the elucidation of the residues linking the major and minor subunits of such pili suggests that the presentation of an antigen on the tip of pili external to the surface of L. lactis might constitute a successful vaccine strategy. As a proof of principle, we have fused a foreign protein (the Escherichia coli maltose-binding protein) to the C-terminal region of the native tip protein (Cpa) of the T3 pilus derived from Streptococcus pyogenes and expressed this fusion protein (MBP*) in L. lactis. We find that MBP* is incorporated into pili in this foreign host, as shown by Western blot analyses of cell wall proteins and by immunogold electron microscopy. Furthermore, since the MBP* on these pili retains its native biological activity, it appears to retain its native structure. Mucosal immunization of mice with this L. lactis strain expressing pilus-linked MBP* results in production of both a systemic and a mucosal response (IgG and IgA antibodies) against the MBP antigen. We suggest that this type of mucosal vaccine delivery system, which we term UPTOP (for unhindered presentation on tips of pili), may provide an inexpensive and stable alternative to current mechanisms of immunization for many serious human pathogens.
Plastic Optical Fibre Sensors for Structural Health Monitoring: A Review of Recent Progress (2009)

While a number of literature reviews have been published in recent times on the applications of optical fibre sensors in smart structures research, these have mainly focused on the use of conventional glass‐based fibres. The availability of inexpensive, rugged, and large‐core plastic‐based optical fibres has resulted in growing interest amongst researchers in their use as low‐cost sensors in a variety of areas including chemical sensing, biomedicine, and the measurement of a range of physical parameters. The sensing principles used in plastic optical fibres are often similar to those developed in glass‐based fibres, but the advantages associated with plastic fibres render them attractive as an alternative to conventional glass fibres, and their ability to detect and measure physical parameters such as strain, stress, load, temperature, displacement, and pressure makes them suitable for structural health monitoring (SHM) applications. Increasingly their applications as sensors in the field of structural engineering are being studied and reported in literature. This article will provide a concise review of the applications of plastic optical fibre sensors for monitoring the integrity of engineering structures in the context of SHM.
Phenotypic Characterization of Lymphocyte Subpopulations in Horses Affected with Chronic Obstructive Pulmonary Disease and in Normal Controls (1997)

The alterations in lymphocyte subsets in chronic obstructive pulmonary disease (COPD) in the horse were investigated by using monoclonal antibodies to identify CD3+, CD4+, CD8+, and surface immunoglobulin positive (sIg+) lymphocytes in peripheral blood, bronchoalveolar lavage fluid (BALF), and pulmonary biopsy frozen tissue sections. COPD-affected horses (n = 5) and normal controls (n = 5) were sampled prestabling and 14 days poststabling, at which time the COPD-affected horses wee exhibiting clinical signs of COPD. The peripheral blood absolute CD4+ lymphocyte count was significantly elevated in the COPD-affected horses pre- and poststabling. The CD4:CD8 ratio in peripheral blood of COPD-affect horses was unaffected by stabling, but the same ratio in the control horses was significantly decreased. These findings support a hypothesis of deficient regulation of a systemic immune response to indoor air in the COPD-affected horses. A large population of leukocytes in pulmonary biopsy immunohistochemical sections from both groups of horses appeared to be CD3+ CD4- CD8-, an uncommon phenotype in both the peripheral blood and BALF.
Processing and characterisation of PECVD silicon nitride films (1996)

Amorphous Si-N films are synthesised from an NH3/SiH4 gas mixture by plasma-enhanced chemical vapour deposition (PECVD) at fixed radio frequency (13.56 MHz) and total gas pressure (34 ± 4 Torr). The variable process parameters and their ranges are: (i) substrate temperature, 200–400°C; (ii) RF power density, 0.08–0.35 W cm−2; (iii) NH3/SiH4 flow ratio, 40:400–40: 1200 ml min−1. Fundamental properties of the Si-N films are characterised through elemental composition, chemical speciation, optical and electrical properties, all of which are dependent on the process parameters.
Geostatistical Modeling of Complex Deltaic Reservoirs Integrating Production Data through Optimized History Matching (2015)

Abstract Reservoir modeling involves the characterization of the internal gridded petrophysical properties distribution and the simulation of fluid production. However, a common problem associated with reservoir modeling is the highly non-linear relationship between the distribution of the petrophysical parameters (frequently with a non-stationary character) and the fluid production. To tackle this problem, this paper presents a new methodology for integrated reservoir modeling by addressing a multiscale optimization approach applied for non-stationary geostatistical history matching of complex connectivity hydrocarbon reservoirs. The methodology comprises a two staged procedure for multiscale optimization, which includes a global optimization stage followed by a local refining stage. The former consists of optimizing the geological spatial anisotropy trend by coupling the stochastic optimization over the anisotropy multiparameter space with an image generation algorithm - direct sequential simulation with local anisotropy correction. The latter aims at refining the small scale heterogeneity by performing the local optimization based on a regional image perturbation method. The local refining optimization is achieved by taking into account the best individual well production matches. A complex deltaic reservoir case study is presented to illustrate the applicability of the proposed methodology. An ensemble of multiple optimized history matched models is obtained respecting both the production data and the geological settings. The results show that the deltaic complex channelized pattern is well reproduced and also that the multiscale optimization improves the match between the simulated fluid profiles and the observed production data. As such, optimization is performed at multiple scales: the anisotropy trend model accounts for larger scale variability of the structures, while consecutive local refining improves convergence to dynamic response around individual wells. The contribution of this work to petroleum technology is the implementation of a novel methodology for the reproduction of the fluids production profiles through the perturbation of the subsurface petrophysical models while honoring complex geological constrains.
Excited-state absorption spectrum of cresyl violet perchlorate (1974)

Measurements of excited singlet state absorption in the laser dye cresyl violet perchlorate (CVP) are described. The influence of this process on the efficiency of longitudinally pumped dye lasers can be significant and is discussed.
The gounders and the congress: Political recruitment in South India, 1920–1937 (1974)

(1974). The gounders and the congress: Political recruitment in South India, 1920–1937. South Asia: Journal of South Asian Studies: Vol. 4, No. 1, pp. 1-20.
Functional Cooperation among Human IgG-Specific Murine Monoclonal Antibodies for the Detection of Weak Blood Group Antibodies in Routine Agglutination Tests (1993)

Seven monoclonal antibodies (MAbs) selected from a large panel of human IgG-specific murine MAbs were characterized serologically and studied for their ability to cooperate in routine antihuman globulin agglutination tests. In binding inhibition experiments, three of these MAbs were shown to bind simultaneously to immobilized human IgG molecules. Cooperation among these MAbs increased significantly the capacity of the individual MAbs to agglutinate red cells sensitized with weak blood group antibodies. These results demonstrate the usefulness of selected MAb blending for the preparation of potent antihuman IgG reagents from murine monoclonal antibodies.
Logical Reversibility of Computation (1973)

The usual general-purpose computing automaton (e.g., a Turing machine) is logically irreversible—its transition function lacks a single-valued inverse. Here it is shown that such machines may be made logically reversible at every step, while retaining their simplicity and their ability to do general computations. This result is of great physical interest because it makes plausible the existence of thermodynamically reversible computers which could perform useful computations at useful speed while dissipating considerably less than kT of energy per logical step. In the first stage of its computation the logically reversible automaton parallels the corresponding irreversible automaton, except that it saves all intermediate results, thereby avoiding the irreversible operation of erasure. The second stage consists of printing out the desired output. The third stage then reversibly disposes of all the undesired intermediate results by retracing the steps of the first stage in backward order (a process which is only possible because the first stage has been carried out reversibly), thereby restoring the machine (except for the now-written output tape) to its original condition. The final machine configuration thus contains the desired output and a reconstructed copy of the input, but no other undesired data. The foregoing results are demonstrated explicitly using a type of three-tape Turing machine. The biosynthesis of messenger RNA is discussed as a physical example of reversible computation.
The Complete Nucleotide Sequence of a Pathogenic Molecular Clone of Simian Immunodeficiency Virus (1990)

The complete nucleotide sequence of an infectious clone of simian immunodeficiency virus of macaques, SIVmac239, has been determined. Virus produced from this molecular clone causes AIDS in rhesus monkeys in a time frame suitable for laboratory investigation. The proviral genome including both long terminal repeats is 10,279 base pairs in length and contains open reading frames for gag, pol, vif, vpr, vpx, tat, rev, and env. The nef gene contains an in-frame premature stop after the 92nd codon. At the nucleotide level, SIVmac239 is closely related to SIVmac251 (98%) and SIVmac142 (96%). It will not be possible to test which features of the viral sequence are critical molecular determinants for the pathogenesis of AIDS.
Observation of histidine residues in proteins by nuclear magnetic resonance spectroscopy (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleObservation of histidine residues in proteins by nuclear magnetic resonance spectroscopyJohn L. MarkleyCite this: Acc. Chem. Res. 1975, 8, 2, 70–80Publication Date (Print):February 1, 1975Publication History Published online1 May 2002Published inissue 1 February 1975https://pubs.acs.org/doi/10.1021/ar50086a004https://doi.org/10.1021/ar50086a004research-articleACS PublicationsRequest reuse permissionsArticle Views1021Altmetric-Citations395LEARN 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
Birefringent Lens Polarizer for the Vacuum Ultraviolet (1971)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text V. Chandrasekharan and H. Damany, "Birefringent Lens Polarizer for the Vacuum Ultraviolet," Appl. Opt. 10, 681_1-682 (1971) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Advances in superconducting quantum electronic microcircuit fabrication (1975)

Standard microelectronic fabrication techniques have been utilized to produce batch quantities of superconducting quantum electronic devices and circuits. The overall goal is a fabrication technology yielding circuits that are rugged and stable and capable of being fabricated controllably and reproducibly in sizeable quantities. Our progress toward this goal is presented, with primary emphasis on the most recent work, which includes the use of electron-beam lithography and techniques of hybrid microelectronics. Several prototype microcircuits have been successfully fabricated. These microcircuits are formed in a thin-film parent material consisting of layers of superconducting and normal metals, and use proximity-effect structures as the active circuit elements.
Joint Calibration for Semantic Segmentation (2015)

Semantic segmentation is the task of assigning a class-label to each pixel in an image. We propose a region-based semantic segmentation framework which handles both full and weak supervision, and addresses three common problems: (1) Objects occur at multiple scales and therefore we should use regions at multiple scales. However, these regions are overlapping which creates conflicting class predictions at the pixel-level. (2) Class frequencies are highly imbalanced in realistic datasets. (3) Each pixel can only be assigned to a single class, which creates competition between classes. We address all three problems with a joint calibration method which optimizes a multi-class loss defined over the final pixel-level output labeling, as opposed to simply region classification. Our method outperforms the state-of-the-art on the popular SIFT Flow [18] dataset in both the fully and weakly supervised setting by a considerably margin (+6% and +10%, respectively).
The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea (2016)

Enzymes for making (or breaking) methane The last enzymatic step of microbial methanogenesis, and the first step of microbial methane oxidation, relies on the nickel-containing tetrapyrrole coenzyme F430. The successful metabolic engineering of any organism to enzymatically consume methane thus also needs the appropriate machinery to synthesize this compound. Using comparative genomics, Zheng et al. identified several candidate genes responsible for coenzyme F430 biosynthesis. Cloning and expression of all the subsequent proteins in Escherichia coli confirmed the complete in vitro conversion of sirohydrochlorin into mature F430. Science , this issue p. 339
Elevated precursor 16S rRNA levels suggest the presence of growth inhibitors in wastewater (2003)

Conventional activated sludge systems require bacteria to grow to avoid washout through decay and routine solids wasting. Recently we developed a procedure targeting precursor 16S ribosomal RNA to measure the in situ growth activity of phylogenetically defined microbial populations, and this procedure was used to study the growth of bacteria in activated sludge systems. The current study significantly expands this previous work by quantifying levels of precursor 16S ribosomal RNA within individual cells of pure cultures of bacteria exposed to various culture conditions. Initially, three ranges (Type I, Type II, and Type III) of precursor 16S ribosomal RNA levels were defined by whole cell fluorescence in situ hybridization of a pure culture of Acinetobacter calcoaceticusT prepared in three culture conditions. Low levels of precursor 16S ribosomal RNA (Type I) corresponded to a stationary phase culture prepared overnight in Luria-Bertani medium. Intermediate levels of precursor 16S ribosomal RNA (Type II) corresponded to a culture transferred into fresh Luria-Bertani medium, and high levels of precursor 16S ribosomal RNA (Type III) corresponded to a culture treated with the growth inhibiting antibiotic chloramphenicol. Subsequently, the abundance of individual cells of each Type were measured in four different pure cultures after exposure to 0.45-microm filtered primary effluent collected from four different conventional activated sludge treatment plants in Cincinnati, OH, USA. Individual cells of each Type were observed in the culture of A. calcoaceticusT exposed to each of the four primary effluents. Only Type I cells were observed in cultures of A. johnsoniiT, A. johnsonii strain 210a, and Escherichia coliT exposed to each of the four primary effluents. These results suggest that the growth of A. calcoaceticusT was inhibited by an unidentified component of filtered primary effluent present in each of the four wastewaters; whereas the growth of A. johnsoniiT, A. johnsonii strain 210a, and E. coliT were not inhibited. These results have significance for understanding the growth of phylogenetically defined microbial populations within activated sludge treatment systems. If the pattern of elevated p16S rRNA levels observed in A. calcoaceticusT is prevalent in many microbial populations in activated sludge systems, this may have implications for preventing washout of critical microbial populations that may be experiencing growth inhibition.
Detection of the<i>Escherichia coli</i>Group 2 Polysaccharide Capsule Synthesis Gene<i>kpsM</i>by a Rapid and Specific PCR-Based Assay (2004)

A rapid and simple PCR-based assay for detection of the group 2 capsule synthesis gene kpsM of Escherichia coli was designed and validated. When combined with the published group 2 primers (kpsIIf, 5'-GCGCATTTGCTGATACTGTTG-3'; kpsIIr, 5'-CATCCAGACGATAAGCATGAGCA-3'), the new primers (the kpsIIf primer and a new reverse primer K2r, 5'-AGGTAGTTCAGACTCACACCT-3') allowed specific identification by exclusion of the heretofore elusive K2 kpsM variant. The primers yielded the predicted amplicon when multiplexed with other primers and used under varied assay conditions, including a range of concentrations of individual reaction mixture ingredients and of annealing temperatures (from 54 to 64 degrees C).