gebhart/patrepeval huggingface dataset:
Amelioration of Ethanol‐Induced Neurotoxicity in the Neonatal Rat Central Nervous System by Antioxidant Therapy (2000)

These results suggest that ethanol-related cerebellar damage during this early postnatal period may be related to oxidative stress processes or the insufficiency of protective antioxidants. Thus, antioxidant treatment may represent a possible therapy for preventing or ameliorating the central nervous system (CNS) damage seen in the fetal alcohol syndrome.
Silica encapsulation of quantum dots and metal clusters (2000)

The use of nanometre thick silica shells as a means to stabilize metal clusters and semiconductor particles is discussed, and its potential advantages over conventional organic capping agents are presented. Shell deposition depends on control of the double layer potential, and requires priming of the core particle surface. Chemical reactions are possible within the core, via diffusion of reactants through the shell layer. Quantum dots can be stabilized against photochemical degradation through silica deposition, whilst retaining strong fluorescence quantum yields and their size dependent optical properties. Ordered 3D and 2D arrays of a macroscopic size with uniform particle spacing can be created. Thin colloid films can also be created with well-defined interparticle spacing, allowing controlled coupling of exciton and surface plasmon modes to be investigated. A number of future core–shell nanocomposite structures are postulated, including quantum bubbles and single electron capacitors based on Au@SiO2.
Insulin-Like Growth Factor-I Binds Selectively to Human Peripheral Blood Monocytes and B-Lymphocytes* (1991)

Insulin-like growth factor-I (IGF-I) is a potential modulator of responses to a variety of immunological challenges. Previous studies have suggested that specific IGF-I receptors are present on peripheral blood leukocytes, including polymorphonuclear leukocytes, lymphocytes, and monocytes. We sought to determine what type of IGF receptor was present on peripheral blood mononuclear cells and which types of cells possessed these receptors. Binding of [125I]IGF-I to mononuclear cells was inhibited by both unlabeled IGF-I and insulin, insulin being 200-fold less potent than IGF-I. Covalent affinity labeling with [125I]IGF-I, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography, revealed a specific binding species with an apparent mol wt of 130 kDa. Two color flow cytometric analysis of mononuclear cells stained with mouse monoclonal antibodies specific for the human IGF-I receptor, the human insulin receptor, and monoclonal antibodies directed against specific monocyte and lymphocyte subset cell surface antigens revealed that both IGF-I receptors and insulin receptors were present on nearly all monocytes and B-lymphocytes, but were present on only 2% of T-lymphocytes. We conclude from these data that among human peripheral blood nonactivated mononuclear cells, IGF-I binds to specific type I IGF receptors found predominantly on monocytes and B-lymphocytes.
Three-dimensional RNA structure refinement by hydroxyl radical probing (2020)

Molecular modeling guided by experimentally-derived structural information is an attractive approach for three-dimensional structure determination of complex RNAs that are not amenable to study by high-resolution methods. Hydroxyl radical probing (HRP), performed routinely in many laboratories, provides a measure of solvent accessibility at individual nucleotides. HRP measurements have, to date, only been used to evaluate RNA models qualitatively. Here, we report development of a quantitative structure refinement approach using HRP measurements to drive discrete molecular dynamics simulations for RNAs ranging in size from 80 to 230 nucleotides. HRP reactivities were first used to identify RNAs that form extensive helical packing interactions. For these RNAs, we achieved highly significant structure predictions, given inputs of RNA sequence and base pairing. This HRP-directed tertiary structure refinement approach generates robust structural hypotheses useful for guiding explorations of structure-function interrelationships in RNA.
Development of an aircraft wheel actuator for green taxiing (2014)

In this paper, the design and construction aspects of a wheel actuator to be used for aircraft taxiing on the ground and which will be located in the main landing gear are addressed. The main challenges with the application are the high torque density and fault tolerance requirements. This paper will look at all the different design aspects of the traction motor required for the actuator, including the electro-magnetic design and analysis, thermal management and mechanical analysis. The paper will then conclude with a brief overview of the construction aspects of the motor of the wheel actuator and experimental validation.
Efficient Multicistronic Expression of a Transgene in Human Embryonic Stem Cells (2007)

The applicability of human embryonic stem cells (hESCs) will be greatly enhanced by techniques that permit efficient genetic modification with multiple transgenes. We report here on single-promoter-driven foot-and-mouth disease virus segment 2A-mediated multicistronic expression of a transgene in hESCs. Efficient multicistronic expression of the transgene was permitted by 2A-mediated separation with almost the same amounts of encoded proteins in hESC. In addition, the multicistronic protein expression was successful in hESC-derived differentiated cells in in vivo and in vitro differentiation assays. This technology may be a significant advance in the genetic engineering of hESCs and hESC-derived cells for purposes that require the reliable expression of multiple transgenes. Disclosure of potential conflicts of interest is found at the end of this article.
Targeting Vascular NADPH Oxidase 1 Blocks Tumor Angiogenesis through a PPARα Mediated Mechanism (2011)

Reactive oxygen species, ROS, are regulators of endothelial cell migration, proliferation and survival, events critically involved in angiogenesis. Different isoforms of ROS-generating NOX enzymes are expressed in the vasculature and provide distinct signaling cues through differential localization and activation. We show that mice deficient in NOX1, but not NOX2 or NOX4, have impaired angiogenesis. NOX1 expression and activity is increased in primary mouse and human endothelial cells upon angiogenic stimulation. NOX1 silencing decreases endothelial cell migration and tube-like structure formation, through the inhibition of PPARα, a regulator of NF-κB. Administration of a novel NOX-specific inhibitor reduced angiogenesis and tumor growth in vivo in a PPARα dependent manner. In conclusion, vascular NOX1 is a critical mediator of angiogenesis and an attractive target for anti-angiogenic therapies.
When ribosomes go bad: diseases of ribosome biogenesis (2010)

Ribosomes are vital for cell growth and survival. Until recently, it was believed that mutations in ribosomes or ribosome biogenesis factors would be lethal, due to the essential nature of these complexes. However, in the last few decades, a number of diseases of ribosome biogenesis have been discovered. It remains a challenge in the field to elucidate the molecular mechanisms underlying them.
Regulation of Serine Biosynthesis in Arabidopsis (1999)

In plants, Ser is synthesized through a couple of pathways. 3-Phosphoglycerate dehydrogenase (PGDH), the first enzyme that is involved in the phosphorylated pathway of Ser biosynthesis, is responsible for the oxidation of 3-phosphoglycerate to phosphohydroxypyruvate. Here we report the first molecular cloning and characterization of PGDH from Arabidopsis thaliana. Sequence analysis of cDNA and a genomic clone revealed that the PGDH gene is composed of three exons, encoding a 623-amino acid polypeptide (66, 453 Da). The deduced protein, containing three of the most conserved regions in the NAD-dependent 2-hydroxyacid dehydrogenase family, has 38-39% identity to its animal and bacterial counterparts. The presence of an N-terminal signal sequence for translocation into plastids was confirmed by particle-gun bombardment experiments using green fluorescence protein as a reporter protein for subcellular localization. Southern hybridization analysis and restriction fragment length polymorphism mapping indicated that PGDH is a single-copy gene that is mapped to the upper arm of chromosome 1. Northern hybridization analysis indicated preferential expression of PGDH mRNA in root tissues of light-grown plants, suggesting that the phosphorylated pathway of Ser biosynthesis plays an important role in supplying Ser to non-photosynthetic tissues. The recombinant enzyme overproduced in Escherichia coli displayed hyperbolic kinetics with respect to 3-phosphoglycerate and NAD+.
Monitoring Aircraft Cabin Particulate Matter Using a Wireless Sensor Network (2013)

The semi-enclosed and pressurized nature of the aircraft cabin results in a highly dynamic environment. The dynamic conditions establish spatiotemporal dependent environmental characteristics. Characterization of aircraft cabin environmental and bleed-air conditions have traditionally been done with stand-alone measurement systems which, by their very nature, cannot provide the necessary sensor coverage in such an environment. To this purpose, a prototype wireless sensor network system has been developed that can be deployed in the aircraft cabin environment. Each sensor node in the system incorporates the ability to measure common aircraft contaminants such as particulate matter and carbon dioxide, along with other key environmental factors such as temperature, air pressure, humidity, and sound pressure level. The wireless sensor network enables the collection of time-correlated results from the aircraft cabin, passing sensor data to a central collection point for storage or real-time monitoring. This paper discusses the results of testing this sensor system in a mockup of the Boeing 767 aircraft cabin environment. In this series of tests, both particulate matter and carbon dioxide were introduced into the simulated aircraft environment and measured using an array of 16 wirelessly connected sensor nodes. Two different arrangements of sensor nodes targeted both a two-dimensional plane across the aircraft cabin space and a localized three-dimensional space centered on two rows of the cabin. The test results show successful simultaneous tracking of the particulate matter and carbon dioxide concentrations as they disperse over time.
Parallelism and its price (1995)

We describe the use of parallel execution techniques and measure the price of parallel execution in NonStop SQL/MP, a commercial parallel database system from Tandem Computers. Non-Stop SQL uses intra-operator parallelism to parallelize joins, groupings and scans. Parallel execution consists of starting up several processes and communicating data between them. Our measurements show (a) Startup costs are negligible when processes are reused rather than created afresh (b) Communication costs are significant — they may exceed the costs of operators such as scan, grouping or join. We also show two counter-examples to the common intuition that parallel execution reduces response time at the expense of increased work — parallel execution may reduce work or may increase response time depending on communication costs.
Resonant leaky-wave coupling in linear arrays of antiguides (1988)

In a uniform array of antiguides, when codirectional leaky waves from adjacent elements add in phase each element equally couples to all others, causing the fundamental-mode near field to become uniform. The resonance condition is derived. When codirectional leaky waves are out of phase, coupling is only nearest-neighbour, causing the fundamentalmode near-field intensity envelope to be cosine-like. The consequences are discussed.
Permeation of Gases through Solids (1957)

The permeation process consists of the steps: adsorption, solution, diffusion, and desorption. These are discussed for glasses, polymers, and metals. There are two generalizations: (1) All gases go through all polymers. (2) No rare gas permeates any metal. Criteria are given for measurements of the permeation process. In glasses the permeation rate depends on atomic size and glass composition. Some special processes which may simulate permeation in vacuum devices are discussed: oxide dissociation, electrolysis in ceramic materials, nuclear reactions, and ionic impact.
Characterization of KIF12 gene in silico. (2005)

Kinesin family (KIF) proteins with Kinesin motor catalytic (KISc) domain and Coiled-coil domain are micro-tubule-dependent molecular motors. KIF proteins produce forces by using the energy from ATP hydrolysis within the KISc domain. We have recently identified that KIF27 is one of mammalian orthologs for Drosophila Costal-2 (Cos2), functioning as regulator of Hedgehog signaling pathway. Mouse Kif12 RefSeq (NM_010616.1) contains the complete coding sequence (CDS); however, human KIF12 Refseq (NM_138424.1) encodes an N-terminally truncated KIF12 protein corresponding to codon 134-642 of mouse Kif12. Here, we characterized the human KIF12 gene by using bioinformatics. Complete CDS of human KIF12 was determined by assembling nucleotide sequences of BQ129377.1 EST, CD358781.1 EST and NM_138424.1 RefSeq. KIF12 gene at human chromosome 9q32 consists of 19 exons. NM_138424.1 RefSeq was a variant KIF12 cDNA with alternative transcription start site (TSS) and skipping of exon 4. NM_138424.1 RefSeq encoded a 513-amino-acid aberrant KIF7 protein with N-terminal-truncation, while KIF12 complete CDS encoded a 651-amino-acid full-length KIF12 protein. Representative human KIF12 and mouse Kif12 proteins with 80.8% total-amino-acid identity shared the common domain architecture, consisting of KISc domain, Coiled-coil domain with internal hinge region, and C-terminal tail domain. KIF12 mRNA was expressed in fetal liver, adult brain and pancreatic islet as well as in kidney tumors, uterus cancer and pancreatic cancer. This is the first report on comprehensive characterization of the human KIF12 gene.
Sphingosine 1-phosphate receptor expression profile and regulation of migration in human thyroid cancer cells (2006)

S1P (sphingosine 1-phosphate) receptor expression and the effects of S1P on migration were studied in one papillary (NPA), two follicular (ML-1, WRO) and two anaplastic (FRO, ARO) thyroid cancer cell lines, as well as in human thyroid cells in primary culture. Additionally, the effects of S1P on proliferation, adhesion and calcium signalling were addressed in ML-1 and FRO cells. All cell types expressed multiple S1P receptors. S1P evoked intracellular calcium signalling in primary cultures, ML-1 cells and FRO cells. Neither proliferation nor migration was affected in primary cultures, whereas S1P partly inhibited proliferation in ML-1 and FRO cells. Low nanomolar concentrations of S1P inhibited migration in FRO, WRO and ARO cells, but stimulated ML-1 cell migration. Consistently, S1P1 and S1P3, which mediate migratory responses, were strongly expressed in ML-1 cells, and S1P2, which inhibits migration, was the dominating receptor in the other cell lines. The migratory effect in ML-1 cells was mediated by G(i) and phosphatidylinositol 3-kinase. Both S1P and the S1P1-specific agonist SEW-2871 induced Akt phosphorylation at Ser473. However, SEW-2871 failed to stimulate migration, whereas the S1P1/S1P3 antagonist VPC 23019 inhibited S1P-induced migration. The results suggest that aberrant S1P receptor expression may enhance thyroid cancer cell migration and thus contribute to the metastatic behaviour of some thyroid tumours.
Basal and Stimulated Protein S-Nitrosylation in Multiple Cell Types and Tissues (2002)

There is substantial evidence that protein S-nitrosylation provides a significant route through which nitric oxide (NO)-derived bioactivity is conveyed. However, most examples of S-nitrosylation have been characterized on the basis of analysis in vitro, and relatively little progress has been made in assessing the participant forms of nitric-oxide synthase (NOS) or the dynamics of protein S-nitrosylation in situ. Here we utilize antibodies specific for the nitrosothiol (SNO) moiety to provide an immunohistochemical demonstration that protein S-nitrosylation is coupled to the activity of each of the major forms of NOS. In cultured endothelial cells, SNO-protein immunoreactivity increases in response to Ca(2+)-stimulated endothelial NOS (eNOS) activity, and in aortic rings, endothelium-derived and eNOS-mediated relaxation (EDRF) is coupled to increased protein S-nitrosylation in both endothelial and associated smooth muscle cells. In cultured macrophages, SNO-protein levels increase upon cytokine induction of induced NOS (iNOS), and in PC12 cells, increased protein S-nitrosylation is linked to nerve growth factor induction of neuronal NOS (nNOS). In addition, we describe developmental and pathophysiological increases in SNO-protein immunoreactivity within human lung. These results, which demonstrate Ca(2+), neurohumoral, growth factor, cytokine, and developmental regulation of protein S-nitrosylation that is coupled to NOS expression and activity, provide unique evidence for the proposition that this ubiquitous NO-derived post-translational protein modification serves as a major effector of NO-related bioactivity.
The TEL/ETV6 gene is required specifically for hematopoiesis in the bone marrow (1998)

The TEL (translocation-Ets-leukemia or ETV6) locus, which encodes an Ets family transcription factor, is frequently rearranged in human leukemias of myeloid or lymphoid origins. By gene targeting in mice, we previously showed that TEL-/- mice are embryonic lethal because of a yolk sac angiogenic defect. TEL also appears essential for the survival of selected neural and mesenchymal populations within the embryo proper. Here, we have generated mouse chimeras with TEL-/- ES cells to examine a possible requirement in adult hematopoiesis. Although not required for the intrinsic proliferation and/or differentiation of adult-type hematopoietic lineages in the yolk sac and fetal liver, TEL function is essential for the establishment of hematopoiesis of all lineages in the bone marrow. This defect is manifest within the first week of postnatal life. Our data pinpoint a critical role for TEL in the normal transition of hematopoietic activity from fetal liver to bone marrow. This might reflect an inability of TEL-/- hematopoietic stem cells or progenitors to migrate or home to the bone marrow or, more likely, the failure of these cells to respond appropriately and/or survive within the bone marrow microenvironment. These data establish TEL as the first transcription factor required specifically for hematopoiesis within the bone marrow, as opposed to other sites of hematopoietic activity during development.
Bioinformatics Approach Reveals Evidence for Impaired Endometrial Maturation Before and During Early Pregnancy in Women Who Developed Preeclampsia (2014)

Impaired uterine invasion by extravillous trophoblast in early gestation is implicated in the genesis of preeclampsia, a potentially lethal malady of human pregnancy. However, reasons for extravillous trophoblast dysfunction remain unclear because of virtual inaccessibility of early placental and uterine tissues from women who develop preeclampsia, and the absence of animal models in which the disease spontaneously occurs. Consequently, the possibility that deficient or defective maturation of the endometrium (decidualization) may compromise extravillous trophoblast invasion in preeclampsia remains unexplored. Using a bioinformatics approach, we tested this hypothesis identifying 396 differentially expressed genes (DEG) in chorionic villous samples from women at ≈11.5 gestational weeks who developed severe preeclampsia symptoms 6 months later compared with chorionic villous samples from normal pregnancies. A large number, 154 or 40%, overlapped with DEG associated with various stages of normal endometrial maturation before and after implantation as identified by other microarray data sets (P=4.7×10(-14)). One-hundred and sixteen of the 154 DEG or 75% overlapped with DEG associated with normal decidualization in the absence of extravillous trophoblast, ie, late-secretory endometrium (LSE) and endometrium from tubal ectopic pregnancy (EP; P=4.2×10(-9)). Finally, 112 of these 154 DEG or 73% changed in the opposite direction in microarray data sets related to normal endometrial maturation (P=0.01), including 16 DEG upregulated in decidual (relative to peripheral blood) natural killer cells that were downregulated in chorionic villous samples from women who developed preeclampsia (P<0.0001). Taken together, these results suggest that insufficient or defective maturation of endometrium and decidual natural killer cells during the secretory phase and early pregnancy preceded the development of preeclampsia.
Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile (2015)

Clostridium difficile is the major cause of nosocomial infections associated with antibiotic therapy worldwide. To survive in bacteriophage-rich gut communities, enteropathogens must develop efficient systems for defense against foreign DNA elements. CRISPR-Cas systems have recently taken center stage among various anti-invader bacterial defense systems. We provide experimental evidence for the function of the C. difficile CRISPR system against plasmid DNA and bacteriophages. These data demonstrate the original features of active C. difficile CRISPR system and bring important insights into the interactions of this major enteropathogen with foreign DNA invaders during its infection cycle.
Skeleton-Based Edge Bundling for Graph Visualization (2011)

In this paper, we present a novel approach for constructing bundled layouts of general graphs. As layout cues for bundles, we use medial axes, or skeletons, of edges which are similar in terms of position information. We combine edge clustering, distance fields, and 2D skeletonization to construct progressively bundled layouts for general graphs by iteratively attracting edges towards the centerlines of level sets of their distance fields. Apart from clustering, our entire pipeline is image-based with an efficient implementation in graphics hardware. Besides speed and implementation simplicity, our method allows explicit control of the emphasis on structure of the bundled layout, i.e. the creation of strongly branching (organic-like) or smooth bundles. We demonstrate our method on several large real-world graphs.
Signal dynamics in Sonic hedgehog tissue patterning (2006)

During development, secreted signaling factors, called morphogens, instruct cells to adopt specific mature phenotypes. However, the mechanisms that morphogen systems employ to establish a precise concentration gradient for patterning tissue architecture are highly complex and are typically analyzed only at long times after secretion (i.e. steady state). We have developed a theoretical model that analyzes dynamically how the intricate transport and signal transduction mechanisms of a model morphogen, Sonic hedgehog (Shh), cooperate in modular fashion to regulate tissue patterning in the neural tube. Consistent with numerous recent studies, the model elucidates how the dynamics of gradient formation can be a key determinant of cell response. In addition, this work yields several novel insights into how different transport mechanisms or ;modules' control pattern formation. The model predicts that slowing the transport of a morphogen, such as by lipid modification of the ligand Shh, by ligand binding to proteoglycans, or by the moderate upregulation of dedicated transport molecules like Dispatched, can actually increase the signaling range of the morphogen by concentrating it near the secretion source. Furthermore, several transcriptional targets of Shh, such as Patched and Hedgehog-interacting protein, significantly limit its signaling range by slowing transport and promoting ligand degradation. This modeling approach elucidates how individual modular elements that operate dynamically at various times during patterning can shape a tissue pattern.