gebhart/patrepeval huggingface dataset:
Quantitative Serum Nuclear Magnetic Resonance Metabolomics in Cardiovascular Epidemiology and Genetics (2015)

Metabolomics is becoming common in epidemiology due to recent developments in quantitative profiling technologies and appealing results from their applications for understanding health and disease. Our team has developed an automated high-throughput serum NMR metabolomics platform that provides quantitative molecular data on 14 lipoprotein subclasses, their lipid concentrations and composition, apolipoprotein A-I and B, multiple cholesterol and triglyceride measures, albumin, various fatty acids as well as on numerous low-molecular-weight metabolites, including amino acids, glycolysis related measures and ketone bodies. The molar concentrations of these measures are obtained from a single serum sample with costs comparable to standard lipid measurements. We have analyzed almost 250 000 samples from around 100 epidemiological cohorts and biobanks and the new international set-up of multiple platforms will allow an annual throughput of more than 250 000 samples. The molecular data have been used to study type 1 and type 2 diabetes etiology as well as to characterize the molecular reflections of the metabolic syndrome, long-term physical activity, diet and lipoprotein metabolism. The results have revealed new biomarkers for early atherosclerosis, type 2 diabetes, diabetic nephropathy, cardiovascular disease and all-cause mortality. We have also combined genomics and metabolomics in diverse studies. We envision that quantitative high-throughput NMR metabolomics will be incorporated as a routine in large biobanks; this would make perfect sense both from the biological research and cost point of view - the standard output of over 200 molecular measures would vastly extend the relevance of the sample collections and make many separate clinical chemistry assays redundant.
Kinetics of the Antibody Response to Tetanus-Diphtheria-Acellular Pertussis Vaccine in Women of Childbearing Age and Postpartum Women (2011)

(See the Editorial Commentary by Munoz and Englund, on pages 893–6.) Background. Because adolescents and adults act as a primary source of pertussis infection for infants, vaccination of mothers immediately postpartum is a potential strategy to reduce transmission (cocoon strategy). For this to be effective, high levels of antibodies must be achieved rapidly after vaccination. We sought to determine whether the antibody response to tetanus-diphtheria-acellular pertussis vaccine (Tdap) is sufficiently rapid to support the cocoon strategy. Methods. Two sequential studies were performed. The first was a nonrandomized, open study of a 5-pertussis-component Tdap vaccine (tetanus toxoid, diphtheria toxoid, pertussis toxoid [PT], filamentous hemagglutinin [FHA], fimbriae types 2 and 3 [FIM], and pertactin [PRN]) given to women of childbearing age; the second was a randomized, open study of Tdap or no vaccine in postpartum women. Serum levels of immunoglobin (Ig) G and IgA against pertussis antigens, serum levels of IgG against diphtheria and tetanus, and breast milk levels of IgA against pertussis antigens were measured at various times after vaccination. Results. In both studies, the antibody response was relatively rapid, with serum IgG and IgA levels beginning to increase noticeably by days 5–7 and approaching peak levels by day 14. Greater than 68% and 84.4% of IgG and IgA responders, respectively, achieved ≥90% of their maximum titer by day 14. The diphtheria and tetanus antibody kinetics followed a similar time course. Breast milk levels of IgA against PT, FHA, and FIM were first detectable at day 7, peaked by day 10, and then slowly decreased through day 28. Antibodies against PRN showed a similar response, although the peak occurred at day 14. There were no significant antibody responses in the control group. Conclusions. Although the antibody response to a dose of Tdap in healthy nonpregnant women of child-bearing age and postpartum women occurs by day 14 and is suggestive of an anamnestic immune response, it may not be sufficiently rapid to protect infants in the first weeks of life.
Usability of EFBs for viewing NOTAMs and AIS/MET data link messages (2013)

Electronic Flight Bags (EFB) are increasingly integral to flight deck information management. A piloted simulation study was conducted at NASA Langley Research Center, one aspect of which was to evaluate the usability and acceptability of EFBs for viewing and managing Notices to Airmen (NOTAMs) and data linked aeronautical information services (AIS) and meteorological information (MET). The study simulated approaches and landings at Memphis International Airport (KMEM) using various flight scenarios and weather conditions. Ten two-pilot commercial airline crews participated, utilizing the Cockpit Motion Facility's Research Flight Deck (CMF/RFD) simulator. Each crew completed approximately two dozen flights over a two day period. Two EFBs were installed, one for each pilot. Study data were collected in the form of questionnaire/interview responses, audio/video recordings, oculometer recordings, and aircraft/system state data. Preliminary usability results are reported primarily based on pilot interviews and responses to questions focused on ease of learning, ease of use, usefulness, satisfaction, and acceptability. Analysis of the data from the other objective measures (e.g., oculometer) is ongoing and will be reported in a future publication. This paper covers how the EFB functionality was set up for the study; the NOTAM, AIS/MET data link, and weather messages that were presented; questionnaire results; selected pilot observations; and conclusions.
Molecular and biochemical basis of intermediate maple syrup urine disease. Occurrence of homozygous G245R and F364C mutations at the E1 alpha locus of Hispanic-Mexican patients. (1995)

Maple syrup urine disease (MSUD) is caused by a deficiency of the mitochondrial branched-chain alpha-keta acid dehydrogenase (BCKAD) complex. The multienzyme complex comprises five enzyme components, including the E1 decarboxylase with a heterotetrameric (alpha 2 beta 2) structure. Four unrelated Hispanic-Mexican MSUD patients with the intermediate clinical phenotype were diagnosed 7 to 22 mo after birth during evaluation for developmental delay. Three of the four patients were found homozygous for G to A transition at base 895 (exon 7) of the E1 alpha locus, which changes Gly-245 to Arg (G245R) in that subunit. The remaining patient was homozygous for T to G transversion at base 1,253 in the E1 alpha gene, which converts Phe-364 to Cys (F364C) in the gene product. Transfection studies in E1 alpha-deficient lymphoblasts indicate that both G245R and F364C mutant E1 alpha subunits were unable to significantly reconstitute BCKAD activity. Western blotting showed that both mutant E1 alpha subunits in transfected cells failed to efficiently rescue the normal E1 beta through assembly. The putative assembly defect was confirmed by pulse-chase labeling of E1 subunits in a chaperone-augmented bacterial overexpression system. The kinetics of initial assembly of the G245R E1 alpha subunit with the normal E1 beta was shown to be slower than the normal E1 alpha. No detectable assembly of the F364C E1 alpha with normal E1 beta was observed during the 2 h chase. Small amounts of recombinant mutant E1 proteins were produced after 15 h induction with isopropyl thiogalactoside and exhibited very low or no E1 activity. Our study establishes that G245R and F364C mutations in the E1 alpha subunit disrupt both the E1 heterotetrameric assembly and function of the BCKAD complex. Moreover, the results suggest that the G245R mutant E1 alpha allele may be important in the Hispanic-Mexican population.
Small Interfering RNA Targeting 14-3-3ζ Increases Efficacy of Chemotherapeutic Agents in Head and Neck Cancer Cells (2010)

Patients diagnosed in advanced stages of head and neck squamous cell carcinoma often show limited response to chemotherapeutic agents. Recently, we reported the overexpression of 14-3-3ζ protein in head and neck premalignant and cancer tissues using liquid chromatography-tandem mass spectrometry with isotopic labeling and revealed its significance as a prognostic marker using immunohistochemical analysis. In this study, we determined the potential of 14-3-3ζ as a therapeutic target for head and neck cancer. Small interfering RNA (siRNA) targeting 14-3-3ζ was used to downregulate its expression in head and neck cancer cells in culture. Cell cycle analysis showed that head and neck cancer cells transfected with siRNA targeting 14-3-3ζ showed G(2)-M arrest. These siRNA transfectants also showed increased cell death on treatment with any one of the following chemotherapeutic agents: cisplatin, 5-fluorouracil, paclitaxel, or doxorubicin in comparison with the no transfection controls. Flow cytometric analysis using propidium iodide staining showed increased sub-G(0) fraction in siRNA-transfected cells treated with any of these chemotherapeutic agents, suggesting cell death; in addition, Annexin V staining and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling assay revealed increased apoptosis. Taken together, our results strongly showed that downregulation of 14-3-3ζ expression may serve to improve the sensitivity of head and neck cancer cells to chemotherapeutic agents.
Advances in fusion of high resolution underwater optical and acoustic data (2002)

We report efforts to merge data from the complementary modalities of optical and acoustic sensing for obtaining more accurate representations of the seafloor. We show that the principal obstacles to merging the acoustic and optical imaging modalities are the distortions inherent to each modality. The construction of geometrically accurate photomosaics is dominated by incremental errors arising as individual images are scaled and warped to form the photomosaic. For microbathymetric mapping, principal errors arise from sensor position and orientation calibration parameters that affect our ability to construct maps from sonar data that are commensurate with sensor and navigation resolution. We show that photomosaics can be combined with microbathymetry through simple, locally defined, finite element warps. An error analysis quantitatively evaluating photomosaic geometric distortions is reported. This technique is shown to be successful in providing opto-acoustic high resolution three dimensional perspectives of large areas of unstructured seafloor features. These issues are evaluated with a combined optical and acoustic survey data set obtained from a 675 kHz pencil-beam sonar and electronic still camera survey of a 4th century B.C. Roman shipwreck. This survey was conducted by the authors with the Jason ROV in the Mediterranean Sea in 800 meters of water depth.
AN UNFOLDING OF DEGENERATE EQUILIBRIA WITH LINEAR PART $\chi$'v= y, y' = 0 (1997)

In this paper, we study the dynamics of a two-parameter unfolding system ' = y, y' = y＋f(＋yg(), where f(,) is a second order polynomial in and g() is strictly nonlinear in . We show that the higher order term yg() in the system does not change qulitative structure of the Hopf bifurcations near the fixed points for small and if the nontrivial fixed point approaches to the origin as approaches zero.
Simultaneous bidirectional fiber-optic transmission using a single source (1986)

We have demonstrated simultaneous bidirectional transmission of signals over a 2-km monomode fiber link utilizing only a single light source. This is potentially significant for subscriber loops and local area networks wherein a major part of the cost may be contained within semiconductor lasers used as the source elements. In the system described here, one source is used both to provide data transmission in one direction and as a light source for transmission in the other direction, the encoding being achieved in the latter case by means of an integrated optic modulator in a reflecting configuration. The data rates employed in our demonstration system are 565 Mbit/s (forward direction) and 34 Mbit/s (reverse direction). Both signals are carried simultaneously by a single monomode fiber.
Impact of Cloudlets on Interactive Mobile Cloud Applications (2012)

In this paper we analyze and study the impact of cloudlets in interactive mobile cloud applications. To study the impact we propose the design of cloudlet network and service architectures. Our study focuses on file editing, video streaming and collaborative chatting which are representative enterprise application scenarios. Initial simulation results show the performance gains of using cloudlets over using clouds in terms of data transfer delay and system throughput. When not more than two cloudlet wireless hops are used to transfer data, the cloudlet-based approach outperforms the cloud-based approach for all three application scenarios. With more cloudlet wireless hops under mobility, the cloud-based approach can give a better performance for some of the data transfers even though the cloudlet-based can outperform the cloud-based approach for most of the flows. In such scenarios, we suggest that an adaptive scheme should be used. For example, a scheme making an intelligent decision on either the cloudlet network or the cloud network, whichever gives minimum delay, can be used.
Selective Recognition of Phosphatidylinositol 3,4,5-Trisphosphate by a Synthetic Peptide (1997)

The present study takes a novel approach to explore the mode of action of phosphoinositide 3-kinase lipid products by identifying a synthetic peptide W-NG(28-43) (WAAKIQASFRGHMARKK) that displays discriminative affinity with phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). This PtdIns(3,4,5)P3-binding peptide was discovered by a gel filtration-based binding assay and exhibits a high degree of stereochemical selectivity in phosphoinositide recognition. It forms a 1:1 complex with PtdIns(3,4,5)P3 with Kd of 2 microM, but binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) with substantially lower affinity (5- and 40-fold, respectively) despite the largely shared structural motifs with PtdIns(3,4,5)P3. Other phospholipids examined, including phosphatidylserine, phosphatidylcholine, phosphatidylinositol, and phosphatidylethanolamine, show low or negligible affinity with the peptide. Several lines of evidence indicate that this phosphoinositide-peptide interaction is not due to nonspecific electrostatic interactions or phospholipid aggregation, and requires a cooperative action among the hydrophobic and basic residues to exert the selective recognition. CD data suggest that the peptide acquires an ordered structure upon binding to PtdIns(3,4,5)P3. Further, we demonstrate that PtdIns(3,4,5)P3 enhances the phosphorylation rate of this binding peptide by protein kinase C (PKC)-alpha in a dose-dependent manner. In view of the findings that this stimulatory effect is not noted with other PKC peptide substrates lacking affinity with PtdIns(3,4,5)P3 and that PKC-alpha is not susceptible to PtdIns(3,4,5)P3 activation, the activity enhancement is thought to result from the substrate-concentrating effect of the D-3 phosphoinositide, i.e. the presence of PtdIns(3,4,5)P3 allows the peptide to bind to the same vesicles/micelles to which PKC is bound. Moreover, it is noteworthy that neurogranin, the full-length protein of W-NG(28-43) and a relevant PKC substrate in the forebrain, binds PtdIns(3,4,5)P3 with high affinity. Taken together, it is plausible that, in addition to PKC activation, PtdIns(3,4,5)P3 provides an alternative mechanism to regulate PKC activity in vivo by recruiting and concentrating its target proteins at the interface to facilitate the subsequent PKC phosphorylation.
All-laser-driven, MeV-energy X-ray source for detection of SNM (2008)

A quasi-monoenergetic MeV X-ray source based on laser-driven electron acceleration and Thomson scattering is under development at the Extreme Light Laboratory at the University of Nebraska, Lincoln. Reported are experimental results on the generation of high- brightness, nearly monoenergetic 300-MeV energy electron beams with the high power, short-pulse DIOCLES laser system. The laser system produces > 100 TW of maximum peak power per pulse. The maximum pulse energy is 3.5 J with a temporal duration of 30 fs. Energetic electron beams are produced by focusing a laser pulse with 40-50-TW peak-power on a supersonic helium nozzle to drive a relativistic plasma wave (laser wakefield). Electron beams with energies of 320 + 2.0 MeV are accelerated over a distance of 3 mm. The beam has an angular spread of 5 mrad with a charge of 100 pC. The use of a stable and well-characterized laser system - in conjunction with high temporal contrast and adaptive optics correction on the amplified beam (to obtain ideal focal spots) - has enabled generation of very reproducible electron beams, both in terms of energy and pointing stability. It is found that electron acceleration is most efficient, beam brightness is highest and reproducibility is best in the resonant regime, where the temporal duration of the laser pulse equals the plasma period. A beamsplitter is used after compression to generate two pulses in the ratio of 80% to 20%. The higher power pulse drives the laser wakefield to produce the energetic electron beams while the lower power pulse is transported through an independent line and focused on the electron beam to generate X-rays. Experiments are currently in progress to observe and characterize the X-ray beam. Theoretical predictions indicate that 1~2 plusmn 10% - MeV X-ray photons can be produced in a well-collimated beam. The expected photon flux is 10 photons per laser shot. Characterization of such a high-flux high energy X-ray beam is in progress. Quasi-monoenergetic X-rays offer significant advantages for the detection of sensitive nuclear materials using techniques such as nuclear resonance fluorescence. A systematic effort is also in progress to further improve the characteristics of laser produced electron beams with regard to monochromaticity, divergence and stability and also permit easy tunability of the X-ray source. The design of a compact system capable of being deployed in the field will also be discussed as part of a long-term solution to the critical requirement for an efficient cargo-scanning system.
Tunable far infrared laser spectrometers (1991)

The state of the art in far infrared (FIR) spectroscopy is reviewed. The development of tunable, coherent FIR radiation sources is discussed. Applications of tunable FIR laser spectrometers for measurement of rotational spectra and dipole moments of molecular ions and free radicals, vibration-rotation-tunneling (VRT) spectra of weakly bound complexes, and vibration-rotation spectra of linear carbon clusters are presented. A detailed description of the Berkeley tunable FIR laser spectrometers is presented in the following article.
Isothermal phase transition of liquid crystals induced by photoisomerization of doped spiropyrans (1991)

The phase-transition behaviour of mixtures of liquid crystals (LCs) and photochromic spiropyran derivatives, induced by isomerization of the guest molecules, has been investigated. Two types of spiropyran derivatives were employed: normal spiropyrans which are stable in the closed form (spiropyran form; SPF) and open-form (merocyanine form; MCF) stabilized derivatives. These spiropyran derivatives were doped into two LC compounds: 5-cyanobiphenyl (5CB) and 4-butoxyphenyl-4′-ethylcyclohexanecarboxylate (ECH 204). SPF-Stabilized derivatives exhibited photoisomerization behaviour from SPF to MCF in LC media which was accompanied by an isotropic (I) to nematic (N) phase transition of the mixtures. On the other hand, an N → I phase transition of the mixtures was observed when the MCF-stabilized spiropyran doped in both LCs was photoisomerized from MCF to SPF. The result was interpreted in terms of shape anisotropy of the guest molecule associated with each isomer of the spiropyrans.
A graph-based friend recommendation system using Genetic Algorithm (2010)

A social network is composed by communities of individuals or organizations that are connected by a common interest. Online social networking sites like Twitter, Facebook and Orkut are among the most visited sites in the Internet. Presently, there is a great interest in trying to understand the complexities of this type of network from both theoretical and applied point of view. The understanding of these social network graphs is important to improve the current social network systems, and also to develop new applications. Here, we propose a friend recommendation system for social network based on the topology of the network graphs. The topology of network that connects a user to his friends is examined and a local social network called Oro-Aro is used in the experiments. We developed an algorithm that analyses the sub-graph composed by a user and all the others connected people separately by three degree of separation. However, only users separated by two degree of separation are candidates to be suggested as a friend. The algorithm uses the patterns defined by their connections to find those users who have similar behavior as the root user. The recommendation mechanism was developed based on the characterization and analyses of the network formed by the user's friends and friends-of-friends (FOF).
The Cyclin-Dependent Kinase Inhibitor Orysa;KRP1 Plays an Important Role in Seed Development of Rice (2006)

Kip-related proteins (KRPs) play a major role in the regulation of the plant cell cycle. We report the identification of five putative rice (Oryza sativa) proteins that share characteristic motifs with previously described plant KRPs. To investigate the function of KRPs in rice development, we generated transgenic plants overexpressing the Orysa;KRP1 gene. Phenotypic analysis revealed that overexpressed KRP1 reduced cell production during leaf development. The reduced cell production in the leaf meristem was partly compensated by an increased cell size, demonstrating the existence of a compensatory mechanism in monocot species by which growth rate is less reduced than cell production, through cell expansion. Furthermore, Orysa;KRP1 overexpression dramatically reduced seed filling. Sectioning through the overexpressed KRP1 seeds showed that KRP overproduction disturbed the production of endosperm cells. The decrease in the number of fully formed seeds was accompanied by a drop in the endoreduplication of endosperm cells, pointing toward a role of KRP1 in connecting endocycle with endosperm development. Also, spatial and temporal transcript detection in developing seeds suggests that Orysa;KRP1 plays an important role in the exit from the mitotic cell cycle during rice grain formation.