gebhart/patrepeval huggingface dataset:
Role of the ribose 2'-hydroxyl groups for the stabilization of the ordered structures of ribonucleic acid (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of the ribose 2'-hydroxyl groups for the stabilization of the ordered structures of ribonucleic acidAlbert M. Bobst, Fritz Rottman, and Peter A. CeruttiCite this: J. Am. Chem. Soc. 1969, 91, 16, 4603–4604Publication Date (Print):July 1, 1969Publication History Published online1 May 2002Published inissue 1 July 1969https://pubs.acs.org/doi/10.1021/ja01044a081https://doi.org/10.1021/ja01044a081research-articleACS PublicationsRequest reuse permissionsArticle Views37Altmetric-Citations15LEARN 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
Structural and functional analysis of a yeast centromere (cen3) (1984)

Structure-function analysis of a yeast (Saccharomyces cerevisiae) centromere (CEN3) has been carried out by altering the nucleotide sequence of the DNA within and surrounding the centromere of yeast chromosome III, and observing the behaviour of the resulting altered chromosomes during mitotic and meiotic cell divisions. A centromere substitution vector (pJC3-13) was constructed, which contains in the proper orientation: the DNA sequences that normally flank the chromosome III centromere, a wild-type URA3 gene for selection, and a unique BamHI restriction site for insertion of various DNA sequences to be assayed for centromere activity. Cleavage of the plasmid DNA with EcoRI generates a linear DNA fragment whose ends are homologous with the regions flanking the centromere. Transformation of the appropriate homozygous ura3 diploid yeast strain with this linear DNA results in URA3+ transformants in which the CEN3 region on one copy of chromosome III has been replaced by the URA3 gene and the DNA sequence previously inserted into the vector. These studies identify a 289 base-pair (bp) DNA fragment from the CEN3 region that retains full centromere function when used to replace the normal CEN3 sequence. Centromeres function equally well in either orientation, and the chromosome XI centromere (CEN11) can be used to replace CEN3, with no observable effect on mitotic or meiotic chromosome segregation. Various DNA restriction fragments occurring within the CEN3 region were used alone or in combinations to replace the normal CEN3 sequence. Yeast centromeres contain a high A + T region about 82-89 bp in length (element II) flanked by a highly conserved 11 bp sequence (III) and a less-conserved 14 bp sequence (I). The experiments demonstrate that both regions II and III are necessary for normal centromere function, although centromeres containing III plus truncated or rearranged portions of the high A + T region II retain partial activity. Chromosomes of the latter type often give abnormal segregation patterns through meiosis, including separation and random segregation of sister chromatids during the first meiotic division.
Syndecan-4 Proteoglycan Regulates the Distribution and Activity of Protein Kinase C (1997)

During cell-matrix adhesion, both tyrosine and serine/threonine kinases are activated. Integrin ligation correlates with tyrosine phosphorylation, whereas the later stages of spreading and focal adhesion and stress fiber formation in primary fibroblasts requires interactions of cell surface proteoglycan with heparin-binding moieties. This correlates with protein kinase C (PKC) activation, and PKCalpha can become localized to focal adhesions in normal, but not transformed, cells. PKC activation has been thought to be downstream of initial receptor-ligand interactions. We now show, however, that syndecan-4 transmembrane heparan sulfate proteoglycan and PKC co-immunoprecipitate and co-patch in vivo. The core protein of syndecan-4 can directly bind the catalytic domain of PKCalpha and potentiate its activation by phospholipid mediators. It can also directly activate PKCalpha in the absence of other mediators. This activity resides in the sequence LGKKPIYKK in the center of the short cytoplasmic domain, and other syndecans lack this sequence and PKC regulatory properties. Syndecan-4 is a focal adhesion component, and this interaction may both localize PKC and amplify its activity at sites of forming adhesions. This represents the first report of direct transmembrane signaling through cell surface proteoglycans.
Scotty: Efficient Window Aggregation for Out-of-Order Stream Processing (2018)

Computing aggregates over windows is at the core of virtually every stream processing job. Typical stream processing applications involve overlapping windows and, therefore, cause redundant computations. Several techniques prevent this redundancy by sharing partial aggregates among windows. However, these techniques do not support out-of-order processing and session windows. Out-of-order processing is a key requirement to deal with delayed tuples in case of source failures such as temporary sensor outages. Session windows are widely used to separate different periods of user activity from each other. In this paper, we present Scotty, a high throughput operator for window discretization and aggregation. Scotty splits streams into non-overlapping slices and computes partial aggregates per slice. These partial aggregates are shared among all concurrent queries with arbitrary combinations of tumbling, sliding, and session windows. Scotty introduces the first slicing technique which (1) enables stream slicing for session windows in addition to tumbling and sliding windows and (2) processes out-of-order tuples efficiently. Our technique is generally applicable to a broad group of dataflow systems which use a unified batch and stream processing model. Our experiments show that we achieve a throughput an order of magnitude higher than alternative state-of-the-art solutions.
<title>Counter sniper: a small projectile and gunfire localization system</title> (2001)

This paper describes a prototype sensor system for detection and 3D tracking of bullets and other small projectiles. The intended purpose of the system is to rapidly locate a sniper to a few meters accuracy at ranges to 1 km in three dimensions. The system detects and tracks a single bullet, and based on the measured 3D trajectory, backtracks to the sniper location. Details of the system are describe including optics, infrared camera, scanning system, laser ranging system, computer control and electronics, and data reduction algorithm. The system has been field tested against bullets, and has been shown to locate a sniper to a few meters accuracy at 500 meters range. Plans for improving tracking performance are also described.
Blue-light generation by frequency doubling of a laser diode in a periodically domain-inverted LiTaO/sub 3/ waveguide (1992)

The authors report quasi-phase matched second-harmonic generation by frequency doubling of a laser diode in LiTaO/sub 3/ having a first-order periodically domain-inverted region and proton-exchanged channel waveguide. A deep domain-inverted region and a low-loss channel waveguide with strong confinement are formed by using proton-exchange and quick heat treatment techniques. Utilizing this structure, a high normalized conversion efficiency of 157%/W is obtained with a Ti:Al/sub 2/O/sub 3/ laser. Using a temperature-controlled laser diode and AR coating on the input and output facet of the waveguide, the laser diode maintains single-mode oscillation without any mode hopping. Consequently, 1.1 mW of blue light is obtained at a wavelength of 436.5 nm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DisProt: the Database of Disordered Proteins (2006)

The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs). Intrinsically disordered proteins do not form a fixed three-dimensional structure under physiological conditions, either in their entireties or in segments or regions. We define IDP as a protein that contains at least one experimentally determined disordered region. Although lacking fixed structure, IDPs and regions carry out important biological functions, being typically involved in regulation, signaling and control. Such functions can involve high-specificity low-affinity interactions, the multiple binding of one protein to many partners and the multiple binding of many proteins to one partner. These three features are all enabled and enhanced by protein intrinsic disorder. One of the major hindrances in the study of IDPs has been the lack of organized information. DisProt was developed to enable IDP research by collecting and organizing knowledge regarding the experimental characterization and the functional associations of IDPs. In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at http://www.disprot.org.
Development and Comparison of Automated Classifiers for Glaucoma Diagnosis Using Stratus Optical Coherence Tomography (2005)

With Stratus OCT parameters used as input, automated classifiers show promise for discriminating between glaucomatous and normal eyes. MD measured from multivariate data can predict the severity of glaucoma through the construction of a measurement space. After PCA, implementation results show that the Mahalanobis space created by MD surpasses LDA and ANN in diagnosing glaucoma.
MicroRNA-29 overexpression by adeno-associated virus suppresses fibrosis and restores muscle function in combination with micro-dystrophin (2017)

Duchenne muscular dystrophy (DMD) is caused by dystrophin deficiency resulting in progressive muscle weakness and fibrotic scarring. Muscle fibrosis impairs blood flow, hampering muscle repair and regeneration. Irrespective of the success of gene restoration, functional improvement is limited without reducing fibrosis. The levels of miR-29c, a known regulator of collagen, are reduced in DMD. Our goal is to develop translational, antifibrotic therapy by overexpressing miR-29c. We injected the gastrocnemius muscle with either self-complementary AAV.CMV.miR-29c or single-stranded AAV.MCK.micro-dystrophin alone or in combination in the mdx/utrn+/- mouse, a DMD mouse model. Treatment of 3-month-old mdx/utrn+/- mice with AAV.miR-29c showed a reduction in collagen and increased absolute and specific force compared with untreated animals, but neither parameter reached WT levels. Combinatorial gene delivery in 3-month-old mdx/utrn+/- mice further decreased fibrosis, and showed a reduction of transcript levels for Col1A, Col3A, fibronectin, and Tgfb1. In addition, absolute and specific force was normalized and equivalent to WT. However, protection against eccentric contraction fell short of WT levels at this time point. When this same mouse model was treated with miR-29c/micro-dystrophin combinatorial therapy at 1 month of age, there was complete normalization of specific and absolute force and protection against eccentric contraction-induced injury was comparable to WT. These findings highlight the potential for miR-29c as an important addition to the armamentarium for translational gene therapy, especially when used in combination with micro-dystrophin in DMD.
Transforming growth factor beta is a bifunctional regulator of replication and collagen synthesis in osteoblast-enriched cell cultures from fetal rat bone. (1987)

Transforming growth factor beta (TGF beta) stimulates cell replication in fetal rat calvariae, and studies with isolated bone cells suggest that the primary mitogenically responsive cell is of the osteoblast lineage. The effect of TGF beta on bone cell replication is biphasic and depends on both the TGF beta concentration and cell density in monolayer culture. After 23 h of treatment, DNA synthesis in confluent cells is progressively enhanced by 0.15-15 ng/ml TGF beta; but in subconfluent cells, 15 ng/ml is less than maximal; and in sparse cell cultures, it is inhibitory. At all cell densities, however, 15 ng/ml TGF beta stimulates collagen synthesis, an effect which is more pronounced when DNA synthesis rates are declining. Furthermore, 1 mM hydroxyurea, which blocks the mitogenic effect of TGF beta by 85%, only minimally influences the increase in collagen synthesis. Cytoplasmic slot blot analysis reveals alterations in the amount of type I collagen mRNA in TGF beta-treated cells, suggesting that control is exerted, at least in part, at the transcriptional level. Since TGF beta is found in culture medium conditioned by bone explants and in bone tissue extracts, these results support that TGF beta is an important and multifunctional autocrine regulator of bone formation.
Expression of hepatitis B surface antigen gene in yeast. (1983)

The DNA sequence coding for hepatitis B virus surface antigen (HBsAg) was placed under control of the repressible acid phosphatase promoter of the yeast Saccharomyces cerevisiae in a plasmid capable of autonomous replication in both yeast and Escherichia coli. Yeast transformed by this plasmid synthesized up to 5 X 10(5) molecules per cell of immunologically active HBsAg polypeptide in phosphate-free medium. The HBsAg polypeptides produced in the yeast cells were assembled into 20- to 22-nm spherical or oval particles and were immunogenic.
Ice Adhesion on Lubricant-Impregnated Textured Surfaces (2013)

Ice accretion is an important problem and passive approaches for reducing ice-adhesion are of great interest in various systems such as aircrafts, power lines, wind turbines, and oil platforms. Here, we study the ice-adhesion properties of lubricant-impregnated textured surfaces. Force measurements show ice adhesion strength on textured surfaces impregnated with thermodynamically stable lubricant films to be higher than that on surfaces with excess lubricant. Systematic ice-adhesion measurements indicate that the ice-adhesion strength is dependent on texture and decreases with increasing texture density. Direct cryogenic SEM imaging of the fractured ice surface and the interface between ice and lubricant-impregnated textured surface reveal stress concentrators and crack initiation sites that can increase with texture density and result in lowering adhesion strength. Thus, lubricant-impregnated surfaces have to be optimized to outperform state-of-the-art icephobic treatments.
Initiation of Metastatic Breast Carcinoma by Targeting of the Ductal Epithelium with Adenovirus-Cre: A Novel Transgenic Mouse Model of Breast Cancer (2014)

Breast cancer is a heterogeneous disease involving complex cellular interactions between the developing tumor and immune system, eventually resulting in exponential tumor growth and metastasis to distal tissues and the collapse of anti-tumor immunity. Many useful animal models exist to study breast cancer, but none completely recapitulate the disease progression that occurs in humans. In order to gain a better understanding of the cellular interactions that result in the formation of latent metastasis and decreased survival, we have generated an inducible transgenic mouse model of YFP-expressing ductal carcinoma that develops after sexual maturity in immune-competent mice and is driven by consistent, endocrine-independent oncogene expression. Activation of YFP, ablation of p53, and expression of an oncogenic form of K-ras was achieved by the delivery of an adenovirus expressing Cre-recombinase into the mammary duct of sexually mature, virgin female mice. Tumors begin to appear 6 weeks after the initiation of oncogenic events. After tumors become apparent, they progress slowly for approximately two weeks before they begin to grow exponentially. After 7-8 weeks post-adenovirus injection, vasculature is observed connecting the tumor mass to distal lymph nodes, with eventual lymphovascular invasion of YFP+ tumor cells to the distal axillary lymph nodes. Infiltrating leukocyte populations are similar to those found in human breast carcinomas, including the presence of αβ and γδ T cells, macrophages and MDSCs. This unique model will facilitate the study of cellular and immunological mechanisms involved in latent metastasis and dormancy in addition to being useful for designing novel immunotherapeutic interventions to treat invasive breast cancer.
Polyvalent Oligonucleotide Gold Nanoparticle Conjugates as Delivery Vehicles for Platinum(IV) Warheads (2009)

Amine-functionalized polyvalent oligonucleotide gold nanoparticles (DNA-Au NPs) were derivatized with a cisplatin prodrug, and the resulting DNA-Au NP conjugates were used to internalize multiple platinum centers. A platinum(IV) complex, c,c,t-[Pt(NH(3))(2)Cl(2)(OH)(O(2)CCH(2)CH(2)CO(2)H)], was tethered to the surface of DNA-Au NPs through amide linkages. The platinum-tethered gold nanoparticles were taken into several cancer cells. The drop in intracellular pH facilitated reductive release of cisplatin from the prodrug, which then formed 1,2-d(GpG) intrastrand cross-links in the cell nuclei, as confirmed by an antibody specific for this adduct. The cytotoxicity of the platinum(IV) complex increases significantly in several cancer cell lines when the complex is attached to the surface of the DNA-Au NPs and in some instances exceeds that of cisplatin.
Purification of granulocyte chemotactic peptide/interleukin‐8 reveals N‐terminal sequence heterogeneity similar to that of β‐thromboglobulin (1989)

Stimulated human peripheral blood leukocytes produce a chemotactic factor for granulocytes (granulocyte chemotactic peptide/interleukin-8; GCP/IL-8), which is structurally related to platelet-derived beta-thromboglobulin. Analytically pure CGP/IL-8 and beta-thromboglobulin could be obtained after three purification steps, comprising adsorption to silicic acid, heparin-Sepharose chromatography and ion-exchange chromatography. Although GCP/IL-8 and beta-thromboglobulin had a similar affinity for heparin, they could be separated on a cation-exchange column. Both molecules were heterogeneous in that 6-7-kDa protein doublets were detected upon SDS/PAGE. N-terminal amino acid sequence analysis revealed the presence of six immunologically related but differently truncated polypeptides of beta-thromboglobulin, of which only two corresponded to previously described forms. Similarly, apart from a major polypeptide, five minor species of GCP/IL-8 were detected that also differed by N-terminal truncation. The most processed forms of beta-thromboglobulin and GCP/IL-8 were found to have their N-terminus in that region of the primary structure where a significant similarity between the two molecules starts. GCP/IL-8 was found to be chemotactic for granulocytes with a specific activity of 10(5) units/mg, whereas none of the beta-thromboglobulin species possessed detectable chemotactic activity.
Origins and patterning of avian outflow tract endocardium (1991)

Outflow tract endocardium links the atrioventricular lining, which develops from cardiogenic plate mesoderm, with aortic arches, whose lining forms collectively from splanchnopleuric endothelial channels, local endothelial vesicles, and invasive angioblasts. At two discrete sites, outflow tract endocardial cells participate in morphogenetic events not within the repertoire of neighboring endocardium: they form mesenchymal precursors of endocardial cushions. The objectives of this research were to document the history of outflow tract endocardium in the avian embryo immediately prior to development of the heart, and to ascertain which, if any, aspects of this history are necessary to acquire cushion-forming potential. Paraxial and lateral mesodermal tissues from between somitomere 3 (midbrain level) and somite 5 were grafted from quail into chick embryos at 3-10 somite stages and, after 2-5 days incubation, survivors were fixed and sectioned. Tissues were stained with the Feulgen reaction to visualize the quail nuclear marker or with antibodies (monoclonal QH1 or polyclonals) that recognize quail but not chick cells. Many quail endothelial cells lose the characteristic nuclear heterochromatin marker, but they retain the species-specific epitope recognized by these antibodies. Precursors of outflow tract but not atrioventricular endocardium are present in cephalic paraxial and lateral mesoderm, with their greatest concentration at the level of the otic placode. Furthermore, the ventral movement of individual angiogenic cells is a normal antecedent to outflow tract formation. Cardiac myocytes were never derived from grafted head mesoderm. Thus, unlike the atrioventricular regions of the heart, outflow tract endocardial and myocardial precursors do not share a congruent embryonic history. The results of heterotopic transplantation, in which trunk paraxial or lateral mesoderm was grafted into the head, were identical, including the formation of cushion mesenchyme. This means that cushion positioning and inductive influences must operate locally within the developing heart tubes.
Production of therapeutic antibodies in plants (2003)

Antibodies are versatile tools for the diagnosis and treatment of many diseases. Their use has increased dramatically with the advent of recombinant antibody (rAb) technology, allowing the production of immunological reagents with improved and novel properties. The main challenge now lies in achieving cost-effective production on a large scale. Over the past 15 years, the potential of plants for the production of pharmaceutical proteins has become well-established. Plants represent an inexpensive, efficient and safe alternative to traditional systems used for the commercial-scale synthesis of rAbs. This review describes the current status of antibody production in plants, focusing on their advantages compared with other expression systems and the remaining obstacles to widespread acceptance.
Epidermal ornithine decarboxylase activity and thymidine incorporation following treatment with ultraviolet A combined with topical 8-methoxy-psoralen or anthracene in the hairless mouse (1981)

Epidermal thymidine incorporation, as a measure of DNA synthesis, and ornithine decarboxylase activity were estimated in hairless albino mice following phototoxic reactions induced by topical anthracene + UV-A, and topical 8-methoxypsoralen (8-MOP) + UV-A. Both treatments caused depression of epidermal thymidine incorporation to 26% of control values at 4 h; this depression persisted through 24 h following 8-MOP + UV-A. Animals treated with anthracene + UV-A showed a fourfold increase in thymidine incorporation at 48 h, declining at 72 and 96 h; after 8-MOP + UV-A increased thymidine incorporation was observed between 4 and 10 days, when a plateau of 96 h duration was observed. After treatment with anthracene + UV-A, epidermal ornithine decarboxylase activity (ODC) was maximal at 4 h, and exhibited a rapid decline, with normal levels at 48 h. Following 8-MOP, UV-A dose-dependent ODC induction occurred: this was later than that induced by anthracene + UV-A with no detectable activity at 4 or 12 h, and maximum activity at 24 h, the elevation persisting through 96 h. The relationship between ODC induction and epidermal hyperproliferation following these treatments is discussed.