gebhart/patrepeval huggingface dataset:
Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG{middle dot}C+ triplets (1998)

The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.
Osteogenic protein-1, a bone morphogenetic protein, induces angiogenesis in the chick chorioallantoic membrane and synergizes with basic fibroblast growth factor and transforming growth factor-β1 (2000)

Capillary invasion is a vital regulatory signal during bone morphogenesis that is influenced by angiogenic molecules such as fibroblast growth factor (FGF) and some members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-betas themselves. Bone morphogenetic proteins (BMPs), which are members of the TGF-beta superfamily, have previously not been shown to possess direct angiogenic properties. Osteogenic protein-1 (OP-1; BMP-7) is a potent regulator of cartilage and bone differentiation in vivo. The osteogenic and angiogenic properties of OP-1 at both ortho- and heterotopic sites in adult chacma baboons (Papio ursinus) are enhanced synergistically by the simultaneous application of relatively low doses of TGF-beta1. The single application of relatively high doses of TGF-beta1 (20 ng), and bFGF (500 ng) or relatively low (100 ng) and high (1,000 ng) doses of OP-1 in the chick chorioallantoic membrane (CAM) assay elicited a prominent and (for OP-1) dose-dependent angiogenic response. The binary application of a relatively low dose of OP-1 (100 ng) with a relatively low dose of bFGF (100 ng) or with a relatively low (5 ng) or high (20 ng) dose of TGF-beta1 resulted in a synergistic enhancement of the angiogenic response. The angiogenic effect of the relatively low doses of the combined morphogens was distinctly more pronounced than that of the single application of the relatively high doses of the respective factors. The present findings suggest that these morphogens may be deployed in binary combination in order to accentuate experimental angiogenesis. The cooperative interaction of the different morphogens in the CAM assay may provide important biological clues towards the control of clinical angiogenesis.
Computational modeling and analysis of thermoelectric properties of nanoporous silicon (2014)

In this paper, thermoelectric properties of nanoporous silicon are modeled and studied by using a computational approach. The computational approach combines a quantum non-equilibrium Green's function (NEGF) coupled with the Poisson equation for electrical transport analysis, a phonon Boltzmann transport equation (BTE) for phonon thermal transport analysis and the Wiedemann-Franz law for calculating the electronic thermal conductivity. By solving the NEGF/Poisson equations self-consistently using a finite difference method, the electrical conductivity σ and Seebeck coefficient S of the material are numerically computed. The BTE is solved by using a finite volume method to obtain the phonon thermal conductivity kp and the Wiedemann-Franz law is used to obtain the electronic thermal conductivity ke. The figure of merit of nanoporous silicon is calculated by ZT=S2σT/(kp+ke). The effects of doping density, porosity, temperature, and nanopore size on thermoelectric properties of nanoporous silicon are investigated. It is confirmed that nanoporous silicon has significantly higher thermoelectric energy conversion efficiency than its nonporous counterpart. Specifically, this study shows that, with a n-type doping density of 1020 cm–3, a porosity of 36% and nanopore size of 3 nm × 3 nm, the figure of merit ZT can reach 0.32 at 600 K. The results also show that the degradation of electrical conductivity of nanoporous Si due to the inclusion of nanopores is compensated by the large reduction in the phonon thermal conductivity and increase of absolute value of the Seebeck coefficient, resulting in a significantly improved ZT.
Novel Thrombotic Function of a Human SNP in STXBP5 Revealed by CRISPR/Cas9 Gene Editing in Mice (2016)

Using precise mammalian genome editing, we have identified a human nonsynonymous SNP rs1039084 in the STXBP5 locus as a causal variant for a decreased thrombotic phenotype. CRISPR/Cas9 genetic editing facilitates the rapid and efficient generation of animals to study the function of human genetic variation in vascular diseases.
Persistence of Fluridone in Five Georgia Soils (1986)

Field research was conducted in 1982 and 1983 to characterize the persistence of fluridone {1-methyl-3-phenyl-5-[3-(trifluoromethyl)phenyl]-4(1 H )pyridinone} in five Georgia soils. Fluridone persisted less than 365 days in all soils, with shorter persistence upon reapplication in 1983 which indicated the potential for enhanced microbial degradation. A significantly higher rate of loss in 1983 compared to 1982 was recorded in the Greenville sandy clay and Dothan loamy sand soils. A higher rate of loss was recorded for the 1.7 kg ai/ha than the 0.6 kg/ha treatment in the Bradson clay loam and Rome gravelly clay loam soils. No grain sorghum [ Sorghum bicolor (L.) Moench. ‘BR 64’) injury was observed in a field bio assay planted in the spring of 1984. Herbicide leaching did not appear to be an important method of loss.
The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region (1984)

The nucleotide sequence of 7200 bases of encephalomyocarditis (EMC) viral RNA, including the complete polyprotein-coding region, was determined. The polyprotein is encoded within a unique translational reading frame, 6870 bases in length. Protein synthesis begins with the sequence Met-Ala-Thr, and ends with the sequence Leu-Phe-Trp, 126 bases from the 3' end of the RNA. Viral capsid and noncapsid proteins were aligned with the deduced amino acid sequence of the polyprotein. The proteolytic processing map follows the standard 4-3-4 picornaviral pattern except for a short leader peptide (8 kd), which precedes the capsid proteins. Identification of the proteolytic cleavage sites showed that EMC viral protease, p22, has cleavage specificity for gln-gly or gln-ser sequences with adjacent proline residues. The cleavage specificity of the host-coded protease(s) includes both tyr-pro and gln-gly sequences.
Megestrol acetate for treatment of anorexia-cachexia syndrome (2005)

This review demonstrates that MA improves appetite and weight gain in patients with cancer. No overall conclusion about quality of life (QOL) could be drawn due to heterogeneity. The small number of patients, methodological shortcomings and poor reporting have not allowed us to recommend megestrol acetate in AIDS patients or with other underlying pathologies.
Cutting Edge: Anti-CD25 Monoclonal Antibody Injection Results in the Functional Inactivation, Not Depletion, of CD4+CD25+ T Regulatory Cells (2006)

CD4+CD25+ T regulatory (T(R)) cells are an important regulatory component of the adaptive immune system that limit autoreactive T cell responses in various models of autoimmunity. This knowledge was generated by previous studies from our lab and others using T(R) cell supplementation and depletion. Contrary to dogma, we report here that injection of anti-CD25 mAb results in the functional inactivation, not depletion, of T(R) cells, resulting in exacerbated autoimmune disease. Supporting this, mice receiving anti-CD25 mAb treatment display significantly lower numbers of CD4+CD25+ T cells but no change in the number of CD4+FoxP3+ T(R) cells. In addition, anti-CD25 mAb treatment fails to both reduce the number of Thy1.1+ congenic CD4+CD25+ T(R) cells or alter levels of CD25 mRNA expression in treatment recipients. Taken together, these findings have far-reaching implications for the interpretation of all previous studies forming conclusions about CD4+CD25+ T(R) cell depletion in vivo.
Synthesis and Structural Characterization of Stable Organogold(I) Compounds. Evidence for the Mechanism of Gold-Catalyzed Cyclizations (2008)

The vast majority of homogeneous Au-catalyzed reactions have exploited the propensity of Au to activate unsaturated carbon-carbon bonds as electrophiles. It is generally assumed that a nucleophile attacks a gold-activated carbon-carbon multiple bond to give an alkenyl Au intermediate, notwithstanding the fact that these intermediates are hitherto unknown. We have obtained room temperature stable gamma-lactone gold(I) complexes through the reaction of cationic Au(I) reagents with allenoates, under mild conditions. The reactions of one such complex with electrophiles yielded the expected products of Au-catalyzed cyclizations. These results furnish experimental evidence for the mechanism of Au-catalyzed cyclizations.
Distribution of Burkholderia cepacia Complex Species among Isolates Recovered from Persons with or without Cystic Fibrosis (2005)

We analyzed Burkholderia cepacia complex isolates recovered from 1,218 cystic fibrosis (CF) patients and 90 patients without CF. Although all B. cepacia complex species were found, some were rarely identified. The distribution of species differed between the CF and non-CF populations and appears to be changing over time among CF patients.
Survival of Donor Leukocyte Subpopulations in Immunocompetent Transfusion Recipients: Frequent Long-Term Microchimerism in Severe Trauma Patients (1999)

We recently reported detection of a transient increase in circulating donor leukocytes (WBCs) in immunocompetent recipients 3 to 5 days posttransfusion (tx) (Blood 85:1207, 1995). We have now characterized survival kinetics of specific donor WBC subsets in additional tx populations. Eight female elective surgery patients (pts) were sampled pre-tx and on days 1, 3, 5, 7, and 14 post-tx. Ten female trauma pts transfused with a total of 4 to 18 U of relatively fresh red blood cells were sampled up to 1.5 years post-tx. WBC subsets from frozen whole blood were isolated using CD4, CD8 (T cell), CD15 (myeloid), and CD19 (B cell) antibody-coated magnetic beads. Donor WBCs were counted by quantitative polymerase chain reaction (PCR) of male-specific sex determining region (SRY) sequences. PCR HLA typing and mixed leukocyte reaction (MLR) between recipient and donor WBCs were performed on two of the trauma tx recipients who had long-term chimerism of donor cells post-tx. In 6 of 8 female surgery pts, circulating CD4(+) male donor cells peaked at day 3 or 5 (0.01 to 1 cell/microL), followed by clearance by day 14. In 7 of 10 female trauma pts, we observed multilineage persistence of male donor WBCs (CD4, CD8, CD15, CD19) for 6 months to 1.5 years post-tx at concentrations of 10 to 100 cells/microL. In 2 trauma recipients studied, MLR showed no, or very low, response to WBC of the single donor implicated as the source of microchimerism by HLA typing. Establishment of long-term multilineage chimerism in trauma recipients is probably caused by engraftment of donor stem cells and mutual tolerance between recipient and donor leukocytes. A better understanding of factors determining clearance versus chimerism of transfused leukocytes is critical to prevention of alloimmunization and transfusion-induced graft-versus-host disease, and, potentially, to induction of tolerance for transplantation.
Composition of tall oil pitch (1978)

Abstract Compositions of six grades of tall oil pitch (TOP), four of finnish and two of U.S. origin were investigated. The pitch samples contained 34.6–51.6% free acids, 23.2–37.8% esterified acids, and 25.3–34.4% unsaponifiable neutral compounds. Each of the above fractions was analyzed by high resolution gas chromatography‐mass spectrometry. Approximately 60% of the weight fraction in TOP consisted of high molecular components of which about half were acidic compounds. The low molecular free acids were mainly dehydroabietic, abietic, and other resin acids. The esterified acids consisted chiefly of oleic and linoleic acids. Unsaponifiable fractions were composed of diterpene alcohols, fatty alcohols, sterols, and dehydrated sterols. The alcohol components were almost completely esterified.
Efficient face detection for multimedia applications (2000)

Face detection is becoming an important tool in the framework of many multimedia applications. Several face detection algorithms based on skin color characteristics have appeared in the literature. Most of them have generalization problems due to the skin color model they use. We present a study which attempts to minimize the generalization problem by combining the M-RSST color segmentation algorithm
Site-specific modulation of c-Myc cotransformation by residues phosphorylated in vivo. (1994)

c-Myc is a nuclear phosphoprotein which binds DNA as a heterodimer with Max. We have identified two in vivo phosphorylation sites, Thr58 and Ser62, within a domain highly conserved among all Myc family members. Thr58 is mutated in several viral forms of the protein and constitutes a mutational hot-spot in Burkitt's lymphoma. Members of the GSK-3 and MAP kinase families, but not CKII, specifically phosphorylated these sites in vitro. The effect of these phosphorylation sites on Myc function was assessed by cotransformation of primary rat embryo fibroblasts with Ras. Mutagenesis of Thr58 to alanine potentiated focus formation, whereas substitution of Ser62 severely inhibited transformation. Mutation of both residues restored wild-type activity. These data suggest acute, post-translational modulation of Myc via phosphorylation of a conserved region previously implicated in transactivation, transformation and autorepression.
Shape google (2011)

The computer vision and pattern recognition communities have recently witnessed a surge of feature-based methods in object recognition and image retrieval applications. These methods allow representing images as collections of “visual words” and treat them using text search approaches following the “bag of features” paradigm. In this article, we explore analogous approaches in the 3D world applied to the problem of nonrigid shape retrieval in large databases. Using multiscale diffusion heat kernels as “geometric words,” we construct compact and informative shape descriptors by means of the “bag of features” approach. We also show that considering pairs of “geometric words” (“geometric expressions”) allows creating spatially sensitive bags of features with better discriminative power. Finally, adopting metric learning approaches, we show that shapes can be efficiently represented as binary codes. Our approach achieves state-of-the-art results on the SHREC 2010 large-scale shape retrieval benchmark.
Comparison of Antiarrhythmic Drug Therapy and Radiofrequency Catheter Ablation in Patients With Paroxysmal Atrial Fibrillation (2010)

clinicaltrials.gov Identifier: NCT00116428.
Function of FGF‐4 in limb development (1994)

The apical ectodermal ridge plays a central role in limb development through its interactions with the underlying mesenchyme. Removal of the AER results in cessation of limb outgrowth and leads to truncation of the limb along the proximo-distal axis. The many functions attributed to the ridge include maintenance of the progress zone mesenchyme. Here, cells are stimulated to proliferate, are maintained in an undifferentiated state, and are assigned progressively more distal positional values as the limb grows. The AER also functions to maintain the activity of the polarizing region, a region of mesenchyme which is thought to provide the primary signal for patterning along the antero-posterior axis. We have begun to explore the function of fibroblast growth factor-4 (FGF-4) during limb development. FGF-4, which encodes an efficiently secreted protein, is expressed in the AER. We have previously demonstrated that FGF-4 protein can stimulate limb mesenchyme proliferation and can induce the expression of a downstream homeobox gene, Evx-1 (homologue of the Drosophila even-skipped gene), that is normally regulated by a signal from the AER. To determine to what extent FGF-4 protein can substitute for the AER to allow normal limb outgrowth, we performed experiments on the developing chick limb in ovo. Remarkably, we find that after AER removal, the FGF-4 protein can provide all the signals required for virtually normal outgrowth and patterning of the limb.(ABSTRACT TRUNCATED AT 250 WORDS)
Stimulus waveforms for selective neural stimulation (1995)

The authors review recent efforts to design stimulus waveforms for selective electrical stimulation of the nervous system. Two types of selectivity are considered. Fiber diameter selectivity refers to the ability to activate one group of nerve fibers having a common diameter without activating nerve fibers having different diameters. Spatial selectivity refers to the ability to activate nerve fibers in a localized region without activating nerve fibers in neighboring regions. The fundamental principles governing the response of excitable nerve fibers to imposed stimuli are reviewed and used to design waveforms. The emphasis of the presentation is on excitation of peripheral myelinated nerve fibers, The underlying principles, however, are broadly applicable to all excitable membranes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional group analysis (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFunctional group analysisWalter T. Smith and John M. PattersonCite this: Anal. Chem. 1974, 46, 5, 394–398Publication Date (Print):April 1, 1974Publication History Published online1 May 2002Published inissue 1 April 1974https://pubs.acs.org/doi/10.1021/ac60341a022https://doi.org/10.1021/ac60341a022research-articleACS PublicationsRequest reuse permissionsArticle Views104Altmetric-Citations1LEARN 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
Evidence for a Substrate Specific and Inhibitable Drug Efflux System in Chloroquine Resistant Plasmodium falciparum Strains (2004)

The mechanism underpinning chloroquine drug resistance in the human malarial parasite Plasmodium falciparum remains controversial. By investigating the kinetics of chloroquine accumulation under varying-trans conditions, we recently presented evidence for a saturable and energy-dependent chloroquine efflux system present in chloroquine resistant P. falciparum strains. Here, we further characterize the putative chloroquine efflux system by investigating its substrate specificity using a broad range of different antimalarial drugs. Our data show that preloading cells with amodiaquine, primaquine, quinacrine, quinine, and quinidine stimulates labeled chloroquine accumulation under varying-trans conditions, while mefloquine, halofantrine, artemisinin, and pyrimethamine do not induce this effect. In the reverse of the varying-trans procedure, we show that preloaded cold chloroquine can stimulate quinine accumulation. On the basis of these findings, we propose that the putative chloroquine efflux system is capable of transporting, in addition to chloroquine, structurally related quinoline and methoxyacridine antimalarial drugs. Verapamil and the calcium/calmodulin antagonist W7 abrogate stimulated chloroquine accumulation and energy-dependent chloroquine extrusion. Our data are consistent with a substrate specific and inhibitible drug efflux system being present in chloroquine resistant P. falciparum strains.
Long wavelength red fluorescent dyes from 3,5-diiodo-BODIPYs (2010)

Amphiphilic and long wavelength red fluorescent dyes (4 and 7) were prepared from the Sonogashira coupling reactions of 3,5-diiodo-BODIPYs (1 and 6). One of these compounds, BODIPY 7, readily accumulated within human carcinoma HEp2 cells and was found to localize mainly within the endoplasmic reticulum (ER).
Anaerobiosis, type 1 fimbriae, and growth phase are factors that affect invasion of HEp-2 cells by Salmonella typhimurium (1990)

The invasion of HEp-2 cells by Salmonella typhimurium was studied under various conditions. Anaerobiosis was shown to markedly affect the internalization of bacterial cells by HEp-2 cells. Anaerobically grown bacteria incubated with HEp-2 cells under anaerobic conditions markedly stimulated the rate of invasion. Anaerobiosis may therefore be a controlling factor in the invasion process. Cells obtained during the logarithmic phase of growth invaded at much higher rates than cells obtained during the stationary phase of growth. The presence of mannose-sensitive type 1 fimbriae on the bacterial surface also promoted invasion, and these fimbriae appear to play a role as an accessory virulence factor.
BALI: A solution for high-speed CDMA data (2002)

Existing standards-based code division multiple access (CDMA) systems support circuit-mode and packet-mode data services at an effective rate limited to 8 to 13 kb/s. Lucent Technologies has taken the lead in addressing this limitation. Lucent's phase 1 solution offers the highest possible performance while conforming to current IS-95-A air interface design characteristics and thereby maintaining strict compatibility with existing base station hardware. The proposed standard will support a high data rate (64 kb/s) both to and from the mobile device. This paper describes the architecture, design, and performance of the Burst Admission based on Load and Interference (BALI) high-speed data solution for CDMA. High-speed service is provided through the aggregation of multiple codes. A new burst-mode capability is defined to allow better interference management and capacity utilization. In the burst mode, the number of codes that may be used by a mobile on the forward or reverse link for the duration of a burst is controlled by the infrastructure. Static allocation of multiple codes to a small number of users can result in inefficient use of CDMA air interface capacity. Dynamic infrastructure-controlled burst allocation makes it possible to share the bandwidth efficiently among several high-speed packet data mobiles.