gebhart/patrepeval huggingface dataset:
Arabidopsis Genes Involved in Acyl Lipid Metabolism. A 2003 Census of the Candidates, a Study of the Distribution of Expressed Sequence Tags in Organs, and a Web-Based Database (2003)

The genome of Arabidopsis has been searched for sequences of genes involved in acyl lipid metabolism. Over 600 encoded proteins have been identified, cataloged, and classified according to predicted function, subcellular location, and alternative splicing. At least one-third of these proteins were previously annotated as "unknown function" or with functions unrelated to acyl lipid metabolism; therefore, this study has improved the annotation of over 200 genes. In particular, annotation of the lipolytic enzyme group (at least 110 members total) has been improved by the critical examination of the biochemical literature and the sequences of the numerous proteins annotated as "lipases." In addition, expressed sequence tag (EST) data have been surveyed, and more than 3,700 ESTs associated with the genes were cataloged. Statistical analysis of the number of ESTs associated with specific cDNA libraries has allowed calculation of probabilities of differential expression between different organs. More than 130 genes have been identified with a statistical probability > 0.95 of preferential expression in seed, leaf, root, or flower. All the data are available as a Web-based database, the Arabidopsis Lipid Gene database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). The combination of the data of the Lipid Gene Catalog and the EST analysis can be used to gain insights into differential expression of gene family members and sets of pathway-specific genes, which in turn will guide studies to understand specific functions of individual genes.
1.3 &#x2013; 1.55 &#x00B5;m self-organized InAs quantum dot tube nanoscale lasers on silicon (2011)

We report on the design, fabrication, and characterization of rolled-up 1.3-1.5 μm InAs quantum dot tube nanoscale lasers and coherent light sources as well as their monolithic integration with Si waveguides on a Si platform.
Isolation and Characterization of Human Casein Kinase I∊ (CKI), a Novel Member of the CKI Gene Family (1995)

The casein kinase I (CKI) gene family is a rapidly enlarging group whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. We report here the cloning and characterization of a novel isoform of CKI from a human placental cDNA library. The cDNA for this isoform, hCKI epsilon, predicts a basic polypeptide of 416 amino acids and a molecular mass of 47.3 kDa. It encodes a core kinase domain of 285 amino acids and a carboxyl-terminal tail of 123 amino acids. The kinase domain is 53-98% identical to the kinase domains of other CKI family members and is most closely related to the delta isoform. Localization of the hCKI epsilon gene to chromosome 22q12-13 and the hCKI delta gene to chromosome 17q25 confirms that these are distinct genes in the CKI family. Northern blot analysis shows that hCKI epsilon is expressed in multiple human cell lines. Recombinant hCKI epsilon is an active enzyme that phosphorylates known CKI substrates including a CKI-specific peptide substrate and is inhibited by CKI-7, a CKI-specific inhibitor. A budding yeast isoform of CKI, HRR25, has been implicated in DNA repair responses. Expression of hCKI epsilon but not hCKI alpha rescued the slow-growth phenotype of a Saccharomyces cerevisiae strain with a deletion of HRR25. Human CKI epsilon is a novel CKI isoform with properties that overlap those of previously described CKI isoforms.
High sequence fidelity in a non-enzymatic DNA autoligation reaction (1999)

The success of oligonucleotide ligation assays in probing specific sequences of DNA arises in large part from high enzymatic selectivity against base mismatches at the ligation junction. We describe here a study of the effect of mismatches on a new non-enzymatic, reagent-free method for ligation of oligonucleotides. In this approach, two oligonucleotides bound at adjacent sites on a complementary strand undergo autoligation by displacement of a 5'-end iodide with a 3'-phosphorothioate group. The data show that this ligation proceeds somewhat more slowly than ligation by T4 ligase, but with substantial discrimination against single base mismatches both at either side of the junction and a few nucleotides away within one of the oligonucleotide binding sites. Selectivities of >100-fold against a single mismatch are observed in the latter case. Experiments at varied concentrations and temperatures are carried out both with the autoligation of two adjacent linear oligonucleotides and with intramolecular autoligation to yield circular 'padlock' DNAs. Application of optimized conditions to discrim-ination of an H- ras codon 12 point mutation is demonstrated with a single-stranded short DNA target.
2-Adic Complexity of a Sequence Obtained from a Periodic Binary Sequence by Either Inserting or Deleting k Symbols within One Period. (2008)

In this paper, we propose a method to get the lower bounds of the 2-adic complexity of a sequence obtained from a periodic sequence over by either inserting or deleting symbols within one period. The results show the variation of the distribution of the 2-adic complexity becomes as increases. Particularly, we discuss the lower bounds when respectively. k (2) GF
Multi-projectors for arbitrary surfaces without explicit calibration nor reconstruction (2004)

We present a new approach allowing one or more projectors to display an undistorted image on a surface of unknown geometry. To achieve this, a single camera is used to capture the viewer's perspective of the projection surface. No explicit camera and projector calibration is required since only their relative geometries are computed using structured light patterns. There is no specific constraint on the position or the orientation of the projectors and the camera with respect to the projection surface, except that the area visible to the camera must be covered by the projectors. The procedure defines a function establishing the correspondence of each pixel of a projector image to a pixel of the camera image. After the mapping of each projector has been carried out, one can display an image corrected in real-time for the point of view of an observer, which takes into account his position, the surface distortion, and the projector position and orientation. This method automatically takes into account any distortion in the projector lenses. Typical applications of this method include projection in small rooms, shadow elimination and wide screen projection using multiple projectors. Intensity blending can be combined to our method to ensure minimal visual artifacts. The implementation has shown convincing results for many configurations.
Use of infliximab in patients with systemic juvenile idiopathic arthritis refractory to etanercept. (2005)

Most patients with SJIA who fail to respond to etanercept may not reach sustained improvement when switched to infliximab. The only patient in our group who improved sustainedly with infliximab did not show any systemic features at the beginning of therapy. Further controlled studies are needed in order to assess efficacy of infliximab in children with refractory SJIA.
A broad-host-range mobilizable shuttle vector for the construction of transcriptional fusions to β-galactosidase in Gram-positive bacteria (2006)

A low-copy-number vector designated pTCV-lac has been constructed to provide a convenient system to analyze regulatory elements in Gram-positive bacteria. The main components of this vector are: (i) the origins of replication of pACYC184 and of the broad-host-range enterococcal plasmid pAM beta 1, (ii) erythromycin- and kanamycin-resistance-encoding genes for selection in Gram-negative and Gram-positive bacteria, (iii) the transfer origin of the IncP plasmid RK2, and (iv) a promoterless beta-galactosidase-encoding lacZ gene with a Gram-positive ribosome binding site. This 12 kb plasmid is present in Gram-positive hosts in three to five copies per chromosome equivalent and contains three unique cloning sites (EcoRI, SmaI, BamHI) for cloning of DNA inserts upstream of the lacZ gene. Plasmid pTCV-lac and derivatives carrying different promoter fragments have been transferred by conjugation from an Escherichia coli IncP mobilizing donor strain to Bacillus subtilis, Listeria monocytogenes, Enterococcus faecalis, and Streptococcus agalactiae. These plasmids were structurally stable in these hosts and the corresponding promoter activities, quantitated by the determination of the beta-galactosidase specific activities, were found to cover at least a 100-fold range in beta-galactosidase values. These results indicate that pTCV-lac should be useful for analysis of gene regulation in a wide range of Gram-positive bacteria.
Three-Dimensional Graphene Nano-Networks with High Quality and Mass Production Capability via Precursor-Assisted Chemical Vapor Deposition (2013)

We report a novel approach to synthesize chemical vapor deposition-grown three-dimensional graphene nano-networks (3D-GNs) that can be mass produced with large-area coverage. Annealing of a PVA/iron precursor under a hydrogen environment, infiltrated into 3D-assembled-colloidal silicas reduces iron ions and generates few-layer graphene by precipitation of carbon on the iron surface. The 3D-GN can be grown on any electronic device-compatible substrate, such as Al2O3, Si, GaN, or Quartz. The conductivity and surface area of a 3D-GN are 52 S/cm and 1,025 m2/g, respectively, which are much better than the previously reported values. Furthermore, electrochemical double-layer capacitors based on the 3D-GN have superior supercapacitor performance with a specific capacitance of 245 F/g and 96.5% retention after 6,000 cycles due to the outstanding conductivity and large surface area. The excellent performance of the 3D-GN as an electrode for supercapacitors suggests the great potential of interconnected graphene networks in nano-electronic devices and energy-related materials.
Lenalidomide, Bortezomib, and Dexamethasone with Transplantation for Myeloma (2017)

Among adults with multiple myeloma, RVD therapy plus transplantation was associated with significantly longer progression-free survival than RVD therapy alone, but overall survival did not differ significantly between the two approaches. (Supported by Celgene and others; IFM 2009 Study ClinicalTrials.gov number, NCT01191060 .).
Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC (2004)

Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element composed of the mec gene complex, which encodes methicillin resistance, and the ccr gene complex, which encodes the recombinases responsible for its mobility. The mec gene complex has been classified into four classes, and the ccr gene complex has been classified into three allotypes. Different combinations of mec gene complex classes and ccr gene complex types have so far defined four types of SCCmec elements. Now we introduce the fifth allotype of SCCmec, which was found on the chromosome of a community-acquired methicillin-resistant Staphylococcus aureus strain (strain WIS [WBG8318]) isolated in Australia. The element shared the same chromosomal integration site with the four extant types of SCCmec and the characteristic nucleotide sequences at the chromosome-SCCmec junction regions. The novel SCCmec carried mecA bracketed by IS431 (IS431-mecA-DeltamecR1-IS431), which is designated the class C2 mec gene complex; and instead of ccrA and ccrB genes, it carried a single copy of a gene homologue that encoded cassette chromosome recombinase. Since the open reading frame (ORF) was found to encode an enzyme which catalyzes the precise excision as well as site- and orientation-specific integration of the element, we designated the ORF cassette chromosome recombinase C (ccrC), and we designated the element type V SCCmec. Type V SCCmec is a small SCCmec element (28 kb) and does not carry any antibiotic resistance genes besides mecA. Unlike the extant SCCmec types, it carries a set of foreign genes encoding a restriction-modification system that might play a role in the stabilization of the element on the chromosome.
Assessment of genetic risk for alzheimer's disease among first‐degree relatives (1989)

Life table methods were used to determine the relative risk of Alzheimer's disease (AD) in relatives of index cases with AD. Risk of AD was assessed in 967 first-degree relatives of 128 probands with clinically diagnosed AD and 572 first-degree relatives of a control group consisting of 84 subjects with Parkinson's disease (PD). Using a method that weights likelihood of correct diagnosis of AD, cumulative risk among AD relatives by age 93 was 24%, whereas relatives of the PD probands had a weighted risk of 16% by age 90. Overall, the total lifetime risk of developing dementia was similar among first-degree relatives of patients with AD and those of patients with PD. The age-specific risks were much different, however; from the age of 65 years to the age of 80 years, relatives of patients with AD had a twofold to fourfold increased risk of dementia. Equal risks were found for parents and siblings and for male and female relatives after adjustment for sex-specific patterns of survivorship. Relatives of probands with early-onset (less than or equal to 67 years) and late-onset (greater than 67 years) AD had equivalent risks of developing illness. Because onset age was found to cluster in families, the apparent increase in cumulative incidence for dementia in relatives of early-onset cases was likely due to relatives of the late-onset cases dying before developing illness.(ABSTRACT TRUNCATED AT 250 WORDS)
The Synthesis of Thienopyrroles (1985)

Methods for the preparation of thieno[2,3-b]-, -[3,2-b]-, -[3,4-b]-, -[2,3-c]-, and -[3,4-c]pyrroles are reviewed. The methods are classified according to the ring to be constructed: syntheses from thiophenes or syntheses from pyrroles, and according to starting materials. Finally, Tables of most of the compounds known are given. 1. Introduction 2. Syntheses from Thiophene Derivatives 3. Syntheses from Pyrrole Derivatives 4. Miscellaneous Syntheses 5. Tables of Thienopyrrole Derivatives
A Metalloporphyrin-Based Superoxide Dismutase Mimic Inhibits Adoptive Transfer of Autoimmune Diabetes by a Diabetogenic T-Cell Clone (2002)

We present here the first report of a metalloporphyrin-based antioxidant that can prevent or delay the onset of autoimmune diabetes. Type 1 diabetes is an autoimmune process whereby T-cells recognize pancreatic beta-cell antigens and initiate a leukocyte infiltrate that produces proinflammatory cytokines and reactive oxygen species (ROS), ultimately leading to beta-cell destruction. Because islet beta-cells have a reduced capacity to scavenge free radicals, they are very sensitive to ROS action. Metalloporphyrin-based superoxide dismutase (SOD) mimics scavenge ROS and protect cells from oxidative stress and apoptosis. To investigate the effect of SOD mimics and the role of oxidative stress in the development of autoimmune diabetes in vivo, we used a diabetogenic T-cell clone, BDC-2.5, to induce rapid onset of diabetes in young nonobese diabetic-severe combined immunodeficient mice (NOD.scid). Disease was significantly delayed or prevented altogether by treatment of recipient mice with an SOD mimic, AEOL-10113, before transfer of the BDC-2.5 clone. To investigate the mechanisms of protection, in vitro assays for T-cell proliferation and gamma-interferon (IFN-gamma) production were carried out using the T-cell clone BDC-2.5. We found that the SOD mimic significantly inhibited antigen-presenting cell-dependent T-cell proliferation and IFN-gamma production in vitro. In addition, pretreatment of lipopolysaccharide (LPS)-stimulated peritoneal macrophages with SOD mimic inhibited the LPS-dependent increase in TNF-alpha as well as the NADPH oxidase-dependent release of superoxide. Finally, this compound protected NIT-1 insulinoma cells from interleukin-1beta and alloxan cytotoxicity in vitro.
Synergistic, Additive, and Antagonistic Effects of Food Mixtures on Total Antioxidant Capacities (2011)

Different foods possess different bioactive compounds with varied antioxidant capacities. When foods are consumed together, the total antioxidant capacity of food mixtures may be modified via synergistic, additive, or antagonistic interactions among these components, which may in turn alter their physiological impacts. The main objective of this study was to investigate these interactions and identify any synergistic combinations. Eleven foods from three categories, including fruits (raspberry, blackberry, and apple), vegetables (broccoli, tomato, mushroom, and purple cauliflower), and legumes (soybean, adzuki bean, red kidney bean, and black bean) were combined in pairs. Four assays (total phenolic content, ferric reducing antioxidant power, 2,2-diphenyl-1-picrylhydrazyl, radical scavenging capacity, and oxygen radical absorbance capacity) were used to evaluate the antioxidant capacities of individual foods and their combinations. The results indicated that within the same food category, 13, 68, and 21% of the combinations produced synergistic, additive, and antagonistic interactions, respectively, while the combinations produced 21, 54, and 25% synergistic, additive, and antagonistic effects, respectively, across food categories. Combining specific foods across categories (e.g., fruit and legume) was more likely to result in synergistic antioxidant capacity than combinations within a food group. Combining raspberry and adzuki bean extracts demonstrated synergistic interactions in all four chemical-based assays. Compositional changes did not seem to have occurred in the mixture. Results in this study suggest the importance of strategically selecting foods or diets to maximum synergisms as well as to minimum antagonisms in antioxidant activity.
Molecular cloning and characterization of a Streptococcus sanguis DNase necessary for repair of DNA damage induced by UV light and methyl methanesulfonate (1987)

We developed a method for cloning cellular nucleases from streptococci. Recombinant lambda gt11 bacteriophage containing streptococcal nuclease determinants were identified by the production of pink plaques on toluidine blue O DNase plates. We used this technique to clone a 3.2-kilobase-pair EcoRI fragment with DNase activity from the chromosome of Streptococcus sanguis. The locus was designated don (DNase one) and could be subcloned and stably maintained on plasmid vectors in Escherichia coli. Minicell analyses of various subclones of the don locus allowed us to determine the coding region and size of the Don nuclease in E. coli. The don gene product had an apparent molecular mass of 34 kilodaltons and degraded native DNA most efficiently, with lesser activity against denatured DNA and no detectable activity against RNA. S. sanguis don deletion mutants were constructed by transformation of competent cells with in vitro-prepared plasmid constructs. S. sanguis don deletion mutants retained normal transformation frequencies for exogenously added donor DNA. However, when compared with Don+ wild-type cells, these mutants were hypersensitive to DNA damage induced by UV light and methyl methanesulfonate. An S. sanguis don-specific DNA probe detected homology to chromosomal DNA isolated from Streptococcus pneumoniae and Streptococcus mutans Bratthall serogroups d and g. Our results suggested that the don locus was the S. sanguis allele of the previously described S. pneumoniae major exonuclease and was involved in repair of DNA damage. Furthermore, hybridization studies suggested that the don locus was conserved among species of oral streptococci.
The Impact of Charging Plug-In Hybrid Electric Vehicles on a Residential Distribution Grid (2009)

Alternative vehicles, such as plug-in hybrid electric vehicles, are becoming more popular. The batteries of these plug-in hybrid electric vehicles are to be charged at home from a standard outlet or on a corporate car park. These extra electrical loads have an impact on the distribution grid which is analyzed in terms of power losses and voltage deviations. Without coordination of the charging, the vehicles are charged instantaneously when they are plugged in or after a fixed start delay. This uncoordinated power consumption on a local scale can lead to grid problems. Therefore, coordinated charging is proposed to minimize the power losses and to maximize the main grid load factor. The optimal charging profile of the plug-in hybrid electric vehicles is computed by minimizing the power losses. As the exact forecasting of household loads is not possible, stochastic programming is introduced. Two main techniques are analyzed: quadratic and dynamic programming.
Single nucleotide polymorphism seeking long term association with complex disease (2002)

Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required. A plethora of suitable and reliable methods have been developed, each of which has its own unique advantage. The characteristics of the most promising genotyping and polymorphism scanning technologies are presented. These technologies are examined both in the context of complex disease investigation and in their capacity to face the unique physical and molecular challenges (allele amplification, loss of heterozygosity and stromal contamination) of solid tumor research.
The -Adrenergic Receptors and the Control of Adipose Tissue Metabolism and Thermogenesis (2001)

The beta-adrenergic receptors (betaARs) are members of the large family of G protein-coupled receptors. There are three betaAR subtypes (beta1AR, beta2AR beta3AR), each of which is coupled to Galphas and the stimulation of intracellular cAMP levels. While beta1AR and beta2AR are broadly expressed throughout tissues of the body, beta3AR is found predominantly in adipocytes. Stimulation of the betaARs leads to lipolysis in white adipocytes and nonshivering thermogenesis in brown fat. However, in essentially all animal models of obesity, the betaAR system is dysfunctional and the ability to stimulate lipolysis and thermogenesis is impaired. Nevertheless, we and others have shown that selective beta3AR agonists are able to prevent or reverse obesity and the loss of betaAR expression and to stimulate thermogenesis. This chapter will review the current understanding of the role of the sympathetic nervous system and the adipocyte betaARs in models of obesity; the physiologic impact of changes in betaAR expression on body composition and thermogenesis; and the regulation and unique properties of betaAR subtypes in brown and white adipocytes. The latter includes our recent discovery of novel signal transduction mechanisms utilized by beta3AR to activate simultaneously the protein kinase A and MAP kinase pathways. The impact of understanding these pathways and their potential role in modulating adaptive thermogenesis is discussed.