gebhart/patrepeval huggingface dataset:
Mechanism of nanoelectronic switch based on telescoping carbon nanotubes (2006)

From ab initio calculations, a nanoelectronic switch is proposed based on telescoping double-walled carbon nanotubes (TDWCNTs), which can be conveniently turned on or off via the relative motion of tubes along the tube axis. It is found that the quantum conductance of switch periodically oscillates with the overlapping length of the two shells of the TDWCNT, which is mainly attributed to the variation of coupling effect between π electronic states of the two shells. The switching of TDWCNTs is determined by the distributions of delocalized frontier molecular orbitals of this system.
Activity-Guided Isolation of Antioxidative Constituents of<i>Cotinus</i><i>c</i><i>oggygria</i> (2000)

Six constituents (1-6) were isolated from EtOAc-soluble partitions of two separate collections of the whole plants of Cotinus coggygria, namely, disulfuretin ¿2,2'-[1,2-bis(3,4-dihydroxyphenyl)-1, 2-ethanedylidene]bis[6-hydroxy-3(2H)-benzofuranone] (1)¿, sulfuretin (2), sulfurein (3), gallic acid (4), methyl gallate (5), and pentagalloyl glucose (6). The structure of the novel biaurone 1 was determined by spectral and chemical methods. Compounds 1-6 were found to be potent antioxidants in a 1,1-diphenyl-2-picrylhydrazyl free-radical scavenging assay.
3D WLAN indoor positioning in multi-storey buildings (2009)

Many scenarios for indoor positioning require position estimation not only in two dimensions but in the third dimension as well. This paper presents the expansion of two two-dimensional WLAN fingerprinting localization algorithms based on received signal strength indication (RSSI) to the third dimension. The third dimension is regarded discretely as the floor level. Both algorithms were evaluated in two different test beds. Evaluation results will be presented and discussed.
Electrical Foot Stimulation and Implications for the Prevention of Venous Thromboembolic Disease (2002)

Mild electrical stimulation of the feet, as well as the calf, is a safe effective and convenient method for counteracting venous stasis and therefore has the potential to reduce the risk of deep vein thrombosis and pulmonary embolism for subjects who are immobilized.
Design and Property Analysis of the Metal Mesh Reinforced LVL (2010)

This study mainly analyzed the factors that affected the mechanical properties of laminated veneer lumber（LVL）. To increase the mechanical properties, metal mesh was inserted into LVL that made of fast-growing timber. Effects of different factors were evaluated on the mechanical properties of LVL, several enhancement modes of metal mesh were designed to reinforce the LVL. Then, the mechanical properties (modulus of rupture and modulus of elasticity) of the LVL specimens were measured by static bending test. The results of different enhancement modes were analyzed and compared to investigate the effects of different factors. The position of metal mesh and the mesh number of metal mesh make significant effects on the MOE; the type of metal mesh and the angle of metal mesh-wood grain do not have any obvious effects on the MOE. The type of metal mesh and the position of metal mesh make significant effects on the MOR; the mesh number of metal mesh and the angle of metal mesh-wood grain do not have any obvious effects on the MOR.
The 2006 NESCent Phyloinformatics Hackathon: A Field Report (2007)

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.
MISSING DATA IMPUTATION IN THE ELECTRONIC HEALTH RECORD USING DEEPLY LEARNED AUTOENCODERS (2016)

Electronic health records (EHRs) have become a vital source of patient outcome data but the widespread prevalence of missing data presents a major challenge. Different causes of missing data in the EHR data may introduce unintentional bias. Here, we compare the effectiveness of popular multiple imputation strategies with a deeply learned autoencoder using the Pooled Resource Open-Access ALS Clinical Trials Database (PRO-ACT). To evaluate performance, we examined imputation accuracy for known values simulated to be either missing completely at random or missing not at random. We also compared ALS disease progression prediction across different imputation models. Autoencoders showed strong performance for imputation accuracy and contributed to the strongest disease progression predictor. Finally, we show that despite clinical heterogeneity, ALS disease progression appears homogenous with time from onset being the most important predictor.
Absorbable Mesh Aids in Development of Discrete, Tissue-Engineered Constructs (2000)

Absorbable mesh was investigated as a potential containment material in which to house discrete, small, tissue-engineered constructs. The mesh was fashioned into bags of varying shapes and consistent volumes. Cells were cultivated on porous, collagen beads, and the tissue constructs were placed into the bags. The mechanical integrity of the bags and feasibility of the design was tested in vitro. The bags successfully maintained their integrity as the cells developed on the collagen matrices. Furthermore, their porosity allowed access of nutrients and waste products to and from the developing tissue. Having demonstrated feasibility of processing, the next step is to optimize the cell culture specifications and materials design.
Large-Scale Code Reuse in Open Source Software (2007)

We are exploring the practice of large-scale reuse involving at least a group of source code files. Our research question is to determine the extent of such reuse occurring in open source projects, to identify the code that is reused the most, and to investigate patterns of large-scale reuse. We start by identifying a sample of projects involving all code in several large repositories of open source projects, all projects bundled with popular distributions of Linux and BSD, and several large individual projects. In the next step we obtain the source code and identify groups of files reused among projects and determine the code that is most widely reused in our sample. Our findings indicate that more than 50% of the files were used in more than one project. The most widely reused components were small and represented templates requiring major and minor modifications and a group of files reused without any change. Some widely reused components involved hundreds of files.
Elucidating the Effects of a Rare-Earth Oxide Shell on the Luminescence Dynamics of Er<sup>3+</sup>:Y<sub>2</sub>O<sub>3</sub>Nanoparticles (2012)

Rare-earth (RE) (Er3+ and Yb3+, Er3+)-doped yttrium oxide (Y2O3) core–shell particles were synthesized in this work using a two-step process where the cores were formed by molten salt synthesis while the shell was deposited by a sol–gel process. The cores were 100–150 nm, and a shell layer, up to 12 nm thick, was controllable based on the mass ratio between the RECl3 salts and the Er3+:Y2O3 (1 mol %) particles. A passive Y2O3 shell layer, at an optimal thickness around 8 nm, passivated the surface quenching sites and resulted in a 53% increase in photoluminescence lifetimes and visible separation in Stark splitting. Optically active shell layers, such as Yb2O3 and Yb3+:Y2O3, not only passivated the quenching sites but also facilitated energy transfer between the spatially controlled RE ions. Furthermore, the effect of surface passivation on the upconversion luminescence was determined through the purposed dynamic processes to corroborate the effect of the hydroxyl groups on energy dissipation. The addition of a passive shell layer or a sensitizer reduced the upconversion to a two-photon process due to a decreased branching ratio at the 4I11/2 energy level. Yb2O3 is deemed the most effective shell material due to the largest increase photoluminescence intensity at 1535 nm as a function of the pump power and the lifetime of the 4S3/2 radiative transition, important in upconversion luminescence. The increased lifetime and low pump power achieved with Er3+:Y2O3|Yb2O3 core–shell phosphors hold promise in lighting devices for improved overall device efficiency.
Influence of prestorage incubation on embryonic development, hatchability, and chick quality (2009)

Egg storage longer than 7 d is associated with a delay in hatch time and a decline in hatchability and chick quality. Prestorage incubation is suggested as a method to reduce the negative effects of prolonged storage times by altering the developmental stage of the embryo, but earlier research has shown that prestorage incubation can both be detrimental and beneficial for hatchability. The reason for these ambiguous results is not clear and the effect of prestorage incubation on chick quality is not studied extensively. The objective of this study was to investigate changes in developmental stage of embryos during prestorage incubation and the effect of prestorage incubation on hatchability and chick quality. Two experiments were conducted. In experiment I, eggs were stored for 3, 5, 8, or 12 d. In experiment II, eggs were stored for 5 or 11 d. Half of the eggs was stored immediately at 16 to 18 degrees C and the other half was exposed to prestorage incubation for 6 h in experiment I and for 4.5 h in experiment II. According to the classification table of Eyal-Giladi and Kochav (EG), embryonic development was advanced by prestorage incubation from developmental stage EG11.67 to developmental stage EG13.26 in experiment I (P = 0.02) and from developmental stage EG9.22 to developmental stage EG12.63 in experiment II (P < 0.0001). In experiment I, prestorage incubation reduced hatchability of set eggs from 59.3 to 51.5% when storage time was 12 d but did not reduce hatchability when storage time was 3, 5, or 8 d (interaction P = 0.02). Prestorage incubation increased chick length (P = 0.004). In experiment II, prestorage incubation increased hatchability of fertile eggs from 80.6 to 85.9% when storage time was 11 d but did not increase hatchability when storage time was 5 d (interaction P = 0.0009). Prestorage incubation increased percentage of second grade chicks (P = 0.0007). It seems that storage time, embryonic development at egg collection, and prestorage incubation duration determine the effect of prestorage incubation on hatchability and chick quality.
Rf liquid-level sensing technique (1966)

Radio frequency liquid level sensing technique development for propellant tank applications
High Shear Rate Hemofiltration: Influence of Fiber Dimensions and Shear Rates (1989)

The variation of ultrafiltration flow rate (QF) at high transmembrane pressure with inlet wall shear rate (gamma w) was found to be proportional to gamma wn, with n ranging from 0.45 to 0.55, when gamma w increases up to 4,500 s-1. To test whether long filters operated at high shear rates were more efficient than shorter ones for the same inlet blood flow, we made experiments with 10- and 20-cm filters with same number of fibers (550) at various shear rates from 700 to 3,000 s-1. The filtration rates provided by the 20-cm filter were found to be 5-15% larger than those provided by two 10-cm filters arranged in parallel and 10-20% smaller than those provided by two 10-cm filters arranged in a series. The explanation lies in the rapid decay of QF with distance from the inlet due to the developing concentration boundary layer. When pulsations are imposed on the inlet blood flow, the filtration rate was seen to increase by 10-20%, and the effect of plugging was seen to decrease in small-area hemofilters.
Fenoxaprop Combined with Preemergence Herbicides for Crabgrass and Goosegrass Control in Turf (1988)

Abstract Fenoxaprop is an effective postemergence herbicide for summer annual grass weed control in cool-season turfgrasses. Following emergence of smooth crabgrass [ Digitarla ischaemum (Schreb.) Muhl.] and goosegrass [ Eleusine indica (L.) Gaertn.], fenoxaprop was applied alone or in combination with one of several preemergence herbicides. The objective of these field studies was to determine whether these herbicide combinations would provide both effective postemergence control of smooth crabgrass and goosegrass, as well as subsequent preemergence control of annual grass weed seed germinating thereafter. When fenoxaprop was applied alone in June or July to smooth crabgrass, the level of control ranged from poor (40%) to excellent (99%), depending on herbicide rate and timing of application. Smooth crabgrass control was erratic where plants had more than four tillers, particularly on a droughty site. When fenoxaprop (0.17, 0.20, or 0.39 kg·ha –1 ) was applied in combination with bensulide, benefin, DCPA, oxadiazon, pendimethalin, or prodiamine, excellent (90% to 100%) season-long smooth crabgrass control was achieved. Fenoxaprop + preemergence herbicide combinations exhibited complementary action, particularly in tank mixes applied to tillered smooth crabgrass. Fenoxaprop applied alone controlled goosegrass (two-leaf to three-tiller stage), but goosegrass reinfested treated plots from seed germinating after the herbicide application. When fenoxaprop (0.20 kg·ha –1 ) was applied with oxadiazon (2.2 kg·ha –1 ) to nontillered goosegrass, exceptional (99%) season-long goose-grass control was achieved. Chemical names used: (±)-ethyl 2-[4-[(6-chloro-2-benzoxazolyl)oxy]phenoxy] propanoate (fenoxaprop); N -butyl- N -ethyl-2,6-dinitro-4-trifluoromethyl)benzenamine (benefin); O,O -bis(l-methylethyl)- S -[2-[(phenylsulfonyl)amino]ethyl]phosphorodithioate (bensulide); dimethyl 2,3,5,6-tetrachloro-1,4-benzenedicarboxylate (DCPA); 3-[2,4-dichloro-5-(1-methylethoxy)phenyl]-5-(1,1-dimethylethyl)-l,3,4-oxadiazol-2-(3 H )-one (oxadiazon); N -(1-ethylpropyl)-3,4-dimethyl-2,6-dinitrobenzenamine (pendimethalin); 2,6-dinitro- N 1 , N 1 ,-dipropyl-6-(trifluoromethyl)-1,3-benzenediamine (prodiamine).
Method for Determining Kinematic Parameters of the<i>In Vivo</i>Thumb Carpometacarpal Joint (2008)

The mobility of the thumb carpometacarpal (CMC) joint is critical for functional grasping and manipulation tasks. We present an optimization technique for determining from surface marker measurements a subject-specific kinematic model of the in vivo CMC joint that is suitable for measuring mobility. Our anatomy-based cost metric scores a candidate joint model by the plausibility of the corresponding joint angle values and kinematic parameters rather than only the marker trajectory reconstruction error. The proposed method repeatably determines CMC joint models with anatomically-plausible directions for the two dominant rotational axes and a lesser range of motion (RoM) for the third rotational axis. We formulate a low-dimensional parameterization of the optimization domain by first solving for joint axis orientation variables that then constrain the search for the joint axis location variables. Individual CMC joint models were determined for 24 subjects. The directions of the flexion--extension (FE) axis and adduction--abduction (AA) axis deviated on average by 9 degrees and 22 degrees , respectively, from the mean axis direction. The average RoM for FE, AA, and pronation--supination (PS) joint angles were 76 degrees , 43 degrees , and 23 degrees for active CMC movement. The mean separation distance between the FE and AA axes was 4.6 mm, and the mean skew angle was 87 degrees from the positive flexion axis to the positive abduction axis.
Dielectric microconcentrators for efficiency enhancement in concentrator solar cells (2007)

Metal fingers typically cover more than 10% of the active area of concentrator solar cells. Microfabricated dielectric optical designs that can completely eliminate front contact shading losses are explored. Essentially no microconcentrator optical losses need be incurred, series resistance losses can be reduced, and net efficiency gains of roughly 15% (relative) are realistic.
Novel iron uptake system specified by ColV plasmids: an important component in the virulence of invasive strains of Escherichia coli (1979)

The enhanced virulence of invasive strains of Escherichia coli carrying ColV plasmids was shown to be due to a novel plasmid-mediated iron uptake system. Possession of a ColV plasmid conferred strong selective advantage on the host bacterial strain in experimental infections unless excess iron was administered in the inoculum. Moreover, supplementation of defined minimal medium with transferrin to complex available iron caused marked limitation of the growth of plasmid-free strains but had no effect on strains carrying a ColV plasmid. The activity of an efficient iron uptake process was clearly shown by experiments with a mutant of E. coli deficient in enterochelin biosynthesis. Although the mutant was dependent on the presence of citrate in the growth medium to facilitate iron transport, colicinogenic derivatives did not require added citrate for growth. Radioactive iron was shown to be taken up rapidly by nongrowing cells of the plasmid-carrying strain. Furthermore, it was observed that repression of the synthesis of specific outer membrane proteins normally induced by conditions of iron deficit was maintained after a shift of the colicinogenic strains from a rich medium to a medium low in iron. The ColV plasmid-mediated iron uptake system was independent of the active iron transport mechanisms known in E. coli, but like them it required tonB activity as a source of energy.
Characterization of the Inflammatory Response to Severe COVID-19 Illness (2020)

<b>Rationale:</b> Coronavirus disease (COVID-19) is a global threat to health. Its inflammatory characteristics are incompletely understood.<b>Objectives:</b> To define the cytokine profile of COVID-19 and to identify evidence of immunometabolic alterations in those with severe illness.<b>Methods:</b> Levels of IL-1β, IL-6, IL-8, IL-10, and sTNFR1 (soluble tumor necrosis factor receptor 1) were assessed in plasma from healthy volunteers, hospitalized but stable patients with COVID-19 (COVID<sub>stable</sub> patients), patients with COVID-19 requiring ICU admission (COVID<sub>ICU</sub> patients), and patients with severe community-acquired pneumonia requiring ICU support (CAP<sub>ICU</sub> patients). Immunometabolic markers were measured in circulating neutrophils from patients with severe COVID-19. The acute phase response of AAT (alpha-1 antitrypsin) to COVID-19 was also evaluated.<b>Measurements and Main Results:</b> IL-1β, IL-6, IL-8, and sTNFR1 were all increased in patients with COVID-19. COVID<sub>ICU</sub> patients could be clearly differentiated from COVID<sub>stable</sub> patients, and demonstrated higher levels of IL-1β, IL-6, and sTNFR1 but lower IL-10 than CAP<sub>ICU</sub> patients. COVID-19 neutrophils displayed altered immunometabolism, with increased cytosolic PKM2 (pyruvate kinase M2), phosphorylated PKM2, HIF-1α (hypoxia-inducible factor-1α), and lactate. The production and sialylation of AAT increased in COVID-19, but this antiinflammatory response was overwhelmed in severe illness, with the IL-6:AAT ratio markedly higher in patients requiring ICU admission (<i>P</i> < 0.0001). In critically unwell patients with COVID-19, increases in IL-6:AAT predicted prolonged ICU stay and mortality, whereas improvement in IL-6:AAT was associated with clinical resolution (<i>P</i> < 0.0001).<b>Conclusions:</b> The COVID-19 cytokinemia is distinct from that of other types of pneumonia, leading to organ failure and ICU need. Neutrophils undergo immunometabolic reprogramming in severe COVID-19 illness. Cytokine ratios may predict outcomes in this population.
Thymic Stromal Lymphopoietin Interferes with Airway Tolerance by Suppressing the Generation of Antigen-Specific Regulatory T Cells (2011)

Thymic stromal lymphopoietin (TSLP) is an essential cytokine for the initiation and development of allergic inflammation. In this study, we have investigated the role of TSLP in the breakdown of immune tolerance and generation of inducible regulatory T cells (iTregs). Our results demonstrated that TSLP diverted airway tolerance against OVA to Th2 sensitization and inhibited the generation of OVA-specific iTregs. TSLP exerted a direct inhibitory effect on both human and mouse iTreg development in vitro. Low doses of TSLP were capable of inhibiting iTreg induction without significantly promoting Th2 development, indicating that these two functions of TSLP are separable. Moreover, the TSLP-mediated inhibition of iTreg generation was only partially dependent on IL-4 and Stat6, and was effective when TSLP was present for the first 24 h of T cell activation. These results define a novel role for TSLP in regulating the balance of airway tolerance and allergic inflammation.
Therapeutic potential of glutathione. (2000)

Reactive oxygen species, formed in various biochemical reactions, are normally scavenged by antioxidants. Glutathione in its reduced form (GSH) is the most powerful intracellular antioxidant, and the ratio of reduced to oxidised glutathione (GSH:GSSG) serves as a representative marker of the antioxidative capacity of the cell. Several clinical conditions are associated with reduced GSH levels which as a consequence can result in a lowered cellular redox potential. GSH and the redox potential of the cell are components of the cell signaling system influencing the translocation of the transcription factor NF kappa B which regulates the synthesis of cytokines and adhesion molecules. Therefore, one possibility to protect cells from damage caused by reactive oxygen species is to restore the intracellular glutathione levels. Cellular GSH concentration can be influenced by exogenous administration of GSH (as intravenous infusion or as aerosol), of glutathione esters or of GSH precursors such as glutamine or cysteine (in form of N-acetyl-L-cysteine, alpha-lipoic acid). The modulation of GSH metabolism might present a useful adjuvant therapy in many pathologies such as intoxication, diabetes, uremia, sepsis, inflammatory lung processes, coronary disease, cancer and immunodeficiency states.
Hydrogen-Bonded Arrays Coupled by Cross-Metathesis (2008)

Recently, supramolecular assemblies have been created as responsive, reversible, and dynamic materials. By a modular approach, we discuss the reversible cross-metathesis of terminal olefins containing self-complementary hydrogen-bond donor and acceptor arrays. These compounds are readily constructed from 2,6-diaminotriazines or cytosine and chiral elements can be installed from modified amino acids. Dynamic combinatorial libraries should be accessible via this approach.