gebhart/patrepeval huggingface dataset:
Designing Mobile Interfaces (2011)

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.
Cross-Functionality of Nitrogenase Components NifH1 and VnfH in<i>Anabaena variabilis</i> (2006)

Anabaena variabilis fixes nitrogen under aerobic growth conditions in differentiated cells called heterocysts using either a Mo nitrogenase or a V nitrogenase. The nifH1 gene, which encodes the dinitrogenase reductase of the Mo nitrogenase that is expressed only in heterocysts, is cotranscribed with nifD1 and nifK1, which together encode the Mo dinitrogenase. These genes were expressed in the presence or absence of molybdate or vanadate. The vnfH gene, which encodes the dinitrogenase reductase of the V nitrogenase, was located about 23 kb from vnfDGK, which encodes the V dinitrogenase; however, like vnfDGK, vnfH was expressed only in the absence of molybdate, with or without vanadate. Like nifH1, the vnfH gene was expressed exclusively in heterocysts under either aerobic or anaerobic growth conditions and thus is under the control of developmental factors. The vnfH mutant was able to grow diazotrophically using the V nitrogenase, because NifH1, which was also made in cells starved for molybdate, could substitute for VnfH. Under oxic conditions, the nifH1 mutant grew in the absence of molybdate but not in its presence, using VnfH, while the nifH1 vnfH double mutant did not grow diazotrophically with or without molybdate or vanadate. A nifH1 mutant that expressed nifDK and vnfH but not vnfDGK was able to grow and fix nitrogen normally, indicating that VnfH could substitute for NifH in the Mo nitrogenase and that these dinitrogenase reductases are not involved in determining the metal specificity of the Mo nitrogenase or the V nitrogenase.
Using semicontrollable interfaces in testing army communications protocols: application to MIL-STD 188-220B (2003)

Testing army communications protocols is considered for a testing environment where the tester has limited degrees of controllability on applying inputs to an implementation under test. The inputs fall into three categories: directly controllable, semicontrollable, or uncontrollable. A graph conversion algorithm is presented to utilize the semicontrollable inputs, thereby increasing the number of testable transitions. The research was motivated while generating tests for MIL-STD 188-220B. The number of testable transitions for 188-220B Class A-Type 1 Datalink Service module is approximately 200 without utilizing semicontrollable inputs. These 200 account for only 30% of the transitions defined in the protocol specification. The presented methodology makes it possible to increase the number of testable transitions to over 700. Combined with our previous work on testing protocols with timing constraints, the methodology allows us to generate tests free of interruptions due to timeouts, and covering more than 95% of the defined transitions in 188-220B's Type 1 Datalink Layer.
Molecular Targeting in Pancreatic Cancer (2007)

The mortality and morbidity of tumors of the upper GI tract are formidable with incidence and mortality nearly the same. Therefore, better therapies are necessary, and these are generally molecularly targeted therapies. This chapter focuses on the treatment of pancreatic cancer with targeted therapy. Important cellular pathways are reviewed, including signal transduction, proteasome inhibition, cell cycle, anti-angiogenesis pathways, immunologic therapies, viral therapy, epigenetic therapies and microarray analysis. Signal transduction pathways include epidermal growth factor receptors, such as cetuximab and Tarceva, as well as other less well-defined pathways. Proteasome inhibition includes inhibition of the 26S proteasome with PS-341. Cell cycle therapies include inhibitors of all the proteins involved in pushing the cell through the cell cycle. Viral therapies mainly cover the adenoviruses, like ONYX-015, and Reolysin, a type 3 serotype Dearing strain with little pathogenicity. Immunological therapies include cytokines, vaccines and cell-based therapies. Epigenetic therapies are mainly centered around histone deacetylases. Microarray analysis analyzes expression of thousands of genes to create a tumor profile, mainly for prognosis or prediction. Various promising treatment strategies are reviewed in terms of treatment with molecularly-guided therapies. Complications of therapy, particularly rash and thrombosis are reviewed.
Predicting missing links in complex networks based on common neighbors and distance (2016)

The algorithms based on common neighbors metric to predict missing links in complex networks are very popular, but most of these algorithms do not account for missing links between nodes with no common neighbors. It is not accurate enough to reconstruct networks by using these methods in some cases especially when between nodes have less common neighbors. We proposed in this paper a new algorithm based on common neighbors and distance to improve accuracy of link prediction. Our proposed algorithm makes remarkable effect in predicting the missing links between nodes with no common neighbors and performs better than most existing currently used methods for a variety of real-world networks without increasing complexity.
Mechanical unloading of bone in microgravity reduces mesenchymal and hematopoietic stem cell-mediated tissue regeneration (2014)

Mechanical loading of mammalian tissues is a potent promoter of tissue growth and regeneration, whilst unloading in microgravity can cause reduced tissue regeneration, possibly through effects on stem cell tissue progenitors. To test the specific hypothesis that mechanical unloading alters differentiation of bone marrow mesenchymal and hematopoietic stem cell lineages, we studied cellular and molecular aspects of how bone marrow in the mouse proximal femur responds to unloading in microgravity. Trabecular and cortical endosteal bone surfaces in the femoral head underwent significant bone resorption in microgravity, enlarging the marrow cavity. Cells isolated from the femoral head marrow compartment showed significant down-regulation of gene expression markers for early mesenchymal and hematopoietic differentiation, including FUT1(-6.72), CSF2(-3.30), CD90(-3.33), PTPRC(-2.79), and GDF15(-2.45), but not stem cell markers, such as SOX2. At the cellular level, in situ histological analysis revealed decreased megakaryocyte numbers whilst erythrocytes were increased 2.33 fold. Furthermore, erythrocytes displayed elevated fucosylation and clustering adjacent to sinuses forming the marrow-blood barrier, possibly providing a mechanistic basis for explaining spaceflight anemia. Culture of isolated bone marrow cells immediately after microgravity exposure increased the marrow progenitor's potential for mesenchymal differentiation into in-vitro mineralized bone nodules, and hematopoietic differentiation into osteoclasts, suggesting an accumulation of undifferentiated progenitors during exposure to microgravity. These results support the idea that mechanical unloading of mammalian tissues in microgravity is a strong inhibitor of tissue growth and regeneration mechanisms, acting at the level of early mesenchymal and hematopoietic stem cell differentiation.
Image-guided laser projection for port placement in minimally invasive surgery. (2006)

We present an application of an augmented reality laser projection system in which procedure-specific optimal incision sites, computed from pre-operative image acquisition, are superimposed on a patient to guide port placement in minimally invasive surgery. Tests were conducted to evaluate the fidelity of computed and measured port configurations, and to validate the accuracy with which a surgical tool-tip can be placed at an identified virtual target. A high resolution volumetric image of a thorax phantom was acquired using helical computed tomography imaging. Oriented within the thorax, a phantom organ with marked targets was visualized in a virtual environment. A graphical interface enabled marking the locations of target anatomy, and calculation of a grid of potential port locations along the intercostal rib lines. Optimal configurations of port positions and tool orientations were determined by an objective measure reflecting image-based indices of surgical dexterity, hand-eye alignment, and collision detection. Intra-operative registration of the computed virtual model and the phantom anatomy was performed using an optical tracking system. Initial trials demonstrated that computed and projected port placement provided direct access to target anatomy with an accuracy of 2 mm.
Synthesis and structure of tetrathiophene with a chiral 1,1′-binaphthyl kink (2001)

A chiral oligothiophene, possessing in-chain chirality, was prepared and its racemate was characterized by single crystal X-ray crystallography; the in-chain chiral 1,1′-binaphthyl moiety interrupts the π-conjugation and affects the solid state properties of the oligothiophene.
Biochemical consequences of sedlin mutations that cause spondyloepiphyseal dysplasia tarda (2009)

SEDT (spondyloepiphyseal dysplasia tarda) is a late-onset X-linked recessive skeletal dysplasia caused by mutations in the gene SEDL coding for sedlin. In the present paper, we investigated four missense mutations observed in SEDT and compare biochemical and cellular characteristics relative to the wild-type protein to address the mechanism of disease and to gain insight into the function of the sedlin protein. In situ hybridization and immunohistochemical experiments in mouse growth plates revealed sedlin to be predominantly expressed in proliferating and hypertrophic chondrocytes. Cell culture studies showed that the wild-type protein localized predominantly in the vicinity of the nucleus and the Golgi, with further localization around the cytoplasm, whereas mutation resulted in mislocalization. The D47Y mutant was expressed similarly to the wild-type, but the S73L, F83S and V130D mutants showed particularly low levels of expression that were rescued in the presence of the proteasome inhibitor MG132 (benzyloxycarbonyl-leucylleucylleucinal). Furthermore, whereas the D47Y mutant folded similarly and had similar stability to the wild-type sedlin as shown by CD and fluorescence, the S73L, F83S and V130D mutants all misfolded during expression. Two independent assays showed that the D47Y mutation resulted in an increased affinity for the transport protein particle component Bet3 compared with the wild-type sedlin. Our results suggest that the sedlin mutations S73L, F83S and V130D cause SEDT by sedlin misfolding, whereas the D47Y mutation may influence normal TRAPP (transport protein particle) dynamics.
Asymmetric cyanohydrin synthesis catalysed by a synthetic cyclic dipeptide (1981)

J. Oku and S. Inoue, J. Chem. Soc., Chem. Commun., 1981, 229 DOI: 10.1039/C39810000229
Gadolinium-148 production cross section measurements for 600-and 800-MEV protons. (2004)

In a series of experiments at LANSCE's WNR facility, {sup 148}Gd production was measured for 600- and 800-MeV protons on tungsten, tantalum, and gold. These experiments used 3 {mu}m thin W, Ta, and Au foils and 10 {mu}m thin Al activation foils. Gadolinium spallation yields were determined from these foils using alpha spectroscopy and compared with the LANL codes CEM2k+GEM2 and MCNPX. When heavy metal targets, such as tungsten, are bombarded with protons greater than a few hundred MeV many different nuclides are produced. These nuclides are both stable and radioactive and are created by spallation, proton activation, or secondary reactions with neutrons and other nuclear particles made in the target. These products are distributed somewhat heterogeneously throughout a thick target because of the energy dependence of the cross sections and energy loss of the proton beam within the target. From this standpoint, it is difficult to measure nuclide production cross sections for a given energy proton in a thick target. At the Los Alamos Neutron Science Center (LANSCE) accelerator complex, protons are accelerated to 800 MeV and directed to two tungsten targets, Target 4 at the Weapons Neutron Research (WNR) facility and 1L target at the Manuel Lujan Jr. Neutron Scattering Center. DOE requires hazard classification analyses to be performed on these targets and places limits on radionuclide inventories in the target as a means of determining the 'nuclear facility' category level. Presently, WNR's Target 4 is a non-nuclear facility while the Lujan 1L target is classified as a Category 3 nuclear facility. Gadolinium-148 is a radionuclide created from the spallation of tungsten and other heavy elements. Allowable isotopic inventories are particularly low for this isotope because it is an alpha-particle emitter with a 75-year half-life. The activity level of {sup 148}Gd is generally low, but it encompasses almost two-thirds of the total inhalation dose burden in an accident scenario for the two tungsten targets at LANSCE based on present yield estimates. From a hazard classification standpoint, this severely limits the irradiation lifetime of these tungsten targets. As 800-MeV protons pass through the tungsten targets at WNR and the Lujan Center, the proton energy is degraded to 600 MeV upon exiting the target. Since the facility classification is partly driven by the inventory of {sup 148}Gd, a better estimate of the true production rate in tungsten targets is needed.
Structural genomics target selection for the New York consortium on membrane protein structure (2009)

The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at least two predicted transmembrane helices, no predicted long disordered regions and, except for community nominated targets, no significant sequence similarity in the predicted transmembrane region to any known protein structure. Proteins that feed our experimental pipeline are selected by defining a protein seed and searching the set of all valid targets for proteins that are likely to have a transmembrane region structurally similar to that of the seed. We require sequence similarity aligning at least half of the predicted transmembrane region of seed and target. Seeds are selected according to their feasibility and/or biological interest, and they include both centrally selected targets and community nominated targets. As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space.
Iron Sources Used by the Nonpathogenic Lactic Acid Bacterium <i>Lactobacillus sakei</i> as Revealed by Electron Energy Loss Spectroscopy and Secondary-Ion Mass Spectrometry (2009)

Lactobacillus sakei is a lactic acid bacterium naturally found on meat. Although it is generally acknowledged that lactic acid bacteria are rare species in the microbial world which do not have iron requirements, the genome sequence of L. sakei 23K has revealed quite complete genetic equipment dedicated to transport and use of this metal. Here, we aimed to investigate which iron sources could be used by this species as well as their role in the bacterium's physiology. Therefore, we developed a microscopy approach based on electron energy loss spectroscopy (EELS) analysis and nano-scale secondary-ion mass spectrometry (SIMS) in order to analyze the iron content of L. sakei cells. This revealed that L. sakei can use iron sources found in its natural ecosystem, myoglobin, hemoglobin, hematin, and transferrin, to ensure long-term survival during stationary phase. This study reveals that analytical image methods (EELS and SIMS) are powerful complementary tools for investigation of metal utilization by bacteria.
Use of ATP-MgCl2 in the evaluation and treatment of children with pulmonary hypertension secondary to congenital heart defects. (1994)

ATP-MgCl2 is a safe, effective, and preferential pulmonary vasodilator in children with pulmonary hypertension secondary to congenital heart defects. It is useful for evaluating pulmonary vasoreactivity during cardiac catheterization and for treating pulmonary hypertension after cardiac surgery.
Effect of Cationic Surfactant on Deposition Behaviour in Electroless Ni-P-PTFE Composite Plating (1994)

SUMMARYThis paper describes the effects of the presence of cationic surfactants upon the deposition behaviour of electrolessly deposited composite films. Polytetrafluoroethylene (PTFE) particles were codeposited in electroless nickel phosphorus plated films. In this study, it was found that the zeta potential of the particle surface in the plating solutions and the content of the particles in the films both depend upon the surfactant type, with a specific correlation also observed between the PTFE content in the film and the zeta potential.
Near-Infrared Fluorescent Oligodeoxyribonucleotide Reporters for Sensing NF-κB DNA Interactions <i>In Vitro</i> (2008)

Two types of reporters for optical sensing of NF-kappaB p50 protein-oligodeoxyribonucleotide (ODN) duplex interactions were designed and compared in vitro. The reporters were based on the effect of fluorescence resonance energy transfer (FRET) between the pair donor Cy5.5 near-infrared (NIR) fluorochrome and either 800CW emitting fluorescence dye acceptor (800CW-Cy), or a nonemitting QSY 21 dye quencher (QSY-Cy). The donor and the acceptor dyes were covalently linked to the complementary oligonucleotides, respectively: Cy dye was conjugated to 3'-thiol, whereas 800CW or QSY21 were conjugated to a hydrophilic internucleoside phosphate amino linker. The reporters were tested initially using recombinant NF-kappaB p50 protein binding assays. Both reporters were binding p50 protein, which protected oligonucleotide duplex from degradation in the presence of exonuclease.The incubation of 800CW-Cy reporter in the presence of control or IL-1beta treated human endothelial cells showed the uptake of the reporter in the cytoplasm and the nucleus. The measurement of NIR fluorescence ratio (i.e. Cy5.5/800CW) showed a partial loss of FRET and the increased Cy5.5 fluorescence in nontreated, control cells. Thus, the specific p50 binding to ODN duplex reporters affected the donor-acceptor fluorochrome pair. NF-kappaB p50 exhibited the protective effect on FRET between NIR fluorochromes linked to the complementary strands of the reporter duplex.
Development of Pushrim-Activated Power-Assisted Wheelchair (2015)

Recent studies have focused on power-assisted wheelchairs because they have several advantages related to both manual and electric powered wheelchairs. They provide users with exercise for rehabilitation and reduce the user’s physical fatigue by providing electric assistance. However, if the assist function is too strong, the effect of exercise may be decreased, and it may cause the weight heavy. Conversely, if it is too weak, the effect of the physical assistance may be insufficient. In this study, the wheelchair driving mechanism is modeled, and the appropriate motor power is chosen based on the computer simulation. For the driving experiments, the wheelchair is developed with in-wheel type electric assist wheels, which can be detached from the wheelchair body, and supports the manual driving mode with a clutch unit. In the experiments, the performance of the developed pushrim-activated power-assisted wheelchair is shown to be close to the proposed design specifications.
Uplink DPCCH Gating of Inactive UEs in Continuous Packet Connectivity Mode for HSUPA (2007)

In order to further improve the packet performance in the UMTS FDD system, uplink dedicated physical control channel (DPCCH) gating as a scheme is proposed in 3GPP under the work item "continuous connectivity for packet data users". In this paper, the uplink DPCCH gating concept is described and analyzed on both a qualitative and a quantitative level. And the system performance of different gating patterns used in the scheme was investigated by analytical prediction and system level simulations with different channel profiles. As shown, the selection of the gating pattern has a significant influence on the system performance, which is correlated with the uplink data transmission activity and the uplink power control. This contributes to a better understanding of the effects involved with uplink DPCCH gating where the biggest potential for performance optimizations can be found. In summary, the scheme of the uplink DPCCH gating is promising to improve the packet performance.
Toxin-Coupled MHC Class I Tetramers Can Specifically Ablate Autoreactive CD8+ T Cells and Delay Diabetes in Nonobese Diabetic Mice (2010)

There is compelling evidence that self-reactive CD8(+) T cells are a major factor in development and progression of type 1 diabetes in animals and humans. Hence, great effort has been expended to define the specificity of autoimmune CD8(+) T cells and to alter their responses. Much work has focused on tolerization of T cells using proteins or peptides. A weakness in this approach is that residual autoreactive T cells may be activated and exacerbate disease. In this report, we use a novel approach, toxin-coupled MHC class I tetramers. Used for some time to identify Ag-specific cells, in this study, we use that same property to delete the Ag-specific cells. We show that saporin-coupled tetramers can delete islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)-reactive T cells in vitro and in vivo. Sequence analysis of TCRbeta-chains of IGRP(+) cells reveals the repertoire complexity in the islets is markedly decreased as NOD mice age and significantly altered in toxic tetramer-treated NOD mice. Further tetramer(+) T cells in the islets are almost completely deleted, and, surprisingly, loss of tetramer(+) T cells in the islets is long lasting. Finally, we show deletion at 8 wk of age of IGRP(+) CD8(+) T cells, but not dystophia myotonica kinase- or insulin B-reactive cells, significantly delays diabetes in NOD mice.
Albuterol as an adjunctive treatment to enzyme replacement therapy in infantile-onset Pompe disease (2017)

The results of our study suggest that albuterol showed a good safety profile as an adjunctive treatment in our IOPD cohort, although the benefits are limited.