gebhart/patrepeval huggingface dataset:
Valency Dependence of Polymorphism and Polyamorphism in DNA-Functionalized Nanoparticles (2009)

Nanoparticles (NP) functionalized with single-stranded DNA (ssDNA) offer a route to custom-designed, self-assembled nanomaterials with potentially unusual properties. The bonding selectivity of DNA guarantees one-to-one binding to form double-stranded DNA (dsDNA), and an appropriate base sequence results in head-to-tail binding linking NP into networks. We explore the phase behavior and structure of a model for NP functionalized with between 3 and 6 short ssDNA through simulations of a coarse-grained molecular model, allowing us to examine both the role of the number of attached strands (valency) and their relative orientations. The NP assemble into networks where the number of NP links is controlled by the number of attached strands. The large length scale of the DNA links relative to the core NP size opens the possibility for the formation of interpenetrating networks that give rise to multiple thermodynamically distinct states. We find that the 3-functionalized NP have only a single phase transition between a dilute solution of NPs and an assembled network state. 4-Functionalized NP (with tetrahedral symmetry) exhibit four amorphous phases, or polyamorphism, each higher density phase consisting of an additional interpenetrating network. The two investigated geometries of 5-functionalized NP both exhibit two phase transitions and three amorphous phases. Like the 4-functionalized NP, the highest density phase consists of interpenetrating networks, demonstrating that regular symmetry is not a prerequisite for interpenetration to produce thermodynamically distinct phases. The width of the coexistence regions for all phase transitions increases with increasing functionality. Finally, for 6-functionalized NP with octahedral symmetry, the possibility of observing disordered phases with significantly bonded particles is preempted by the formation of ordered crystal phases. Interestingly, the extreme softness of the potential combined with the directional interaction allows for the formation of (at least) six distinct crystalline structures (i.e., polymorphism) consisting of up to six interpenetrating simple cubic lattices.
High ambipolar carrier mobility in self-organizing terthiophene derivative (2000)

Dialkylterthiphene derivatives exhibiting self-organization of molecular alignment were synthesized and their electrical properties were studied. It was found that these materials exhibited very fast electron transport in smectic mesophases as well as hole transport, both of which were independent of electric field and temperature. The mobility for electrons and holes was 5×10−4 cm2/V s in smectic C (SmC) and was increased up to 2×10−3 cm2/V s and even more up to 1×10−2 cm2/V s in accompany with upgrade of molecular alignment from SmC to SmF and from SmF to SmG, respectively. This abrupt increase in the mobility to the extent of about one order of magnitude corresponds to that in 2-phenylnaphthalene derivatives at the phase transition from SmA to SmB and from SmB to SmE whose molecular alignments are in good correlation with those of SmC, SmF, and SmG, respectively.
Aberration-Reduced Holographic Concave Gratings for Seya–Namioka Monochromators (1975)

The theory of the holographic grating is applied to the design of aberration-reduced holographic concave gratings for use with Seya–Namioka monochromators. The proper recording parameters are determined for various types of aberration-reduced holographic concave gratings that have the effective grating constant of 1/1200 mm. The performance of the holographic gratings thus designed is evaluated in terms of the degree of spread in spot diagrams. The results show that coma-reduced holographic concave gratings are superior to conventionally ruled concave gratings and holographic concave gratings of Types I, II, and III, proving the usefulness of the design procedure adopted in the present study.
Electron-beam testing of VLSI circuits (1979)

The voltages at the internal voltage nodes of an IC have to be measured if the device operates imperfectly or the quality of a device or computer simulation have to be checked. Whereas the mechanical probe conventionally used for this purpose usually imposes such a large capacitive load on the specimen that its performance undergoes a change, the electron probe is both nonloading and nondestructive and can be used not only for quantitative waveform measurements on an IC but also for obtaining images of the logical states of relatively large portions of its circuit configuration. Since each type of configuration calls for a separate measuring technique, six different techniques are treated and their application and equipment needs described. The state of the art of electron-beam testing is demonstrated with reference to three typical applications, viz., checking a decoding schema, measuring the sense signal (approximately 300 mV) of a 16-kbit MOS RAM, and checking the operation of the timing circuitry of a 4-bit microprocessor. The present applicational limitations and future perspectives of electron-beam testing are discussed.
Antihyperglycemic and antihyperlipidemic effect of Uraria crinita water extract in diabetic mice induced by STZ and food (2010)

Uraria crinita (UC) is a traditional edible plant and has been used as herbal medicine for a long history in China. There is no report on its anti-diabetic activity. In the present study we evaluated anti-hyperglycemic and anti-hyperlipidemic effect of U. crinita water extract (UCWE) in diabetic mice. Type II diabetes was induced in mice by injection of streptozotocin (STZ) in combination with high fat and protein food. After 3 weeks, oral administration of UCWE significantly decreased the fasting blood glucose in oral glucose tolerance test (OGTT), as well as significantly suppressed the increase of blood glucose after glucose challenge. Plasma concentration of triglyceride (TG) and free fatty acids (FFAs) were also decreased. Furthermore, UCWE increased the concentration of plasma insulin. Taken together, UCWE exhibited hypoglycemic and hypolipidemic activity, indicating a beneficial effect in diabetes treatment.

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	Key words: Uraria crinita water extract (UCWE), diabetes, oral glucose tolerance test (OGTT), TG, FFAs, insulin.
A Method for Improving String Pattern Matching Machines (1984)

This correspondence describes an efficient string pattern matching machine to locate all occurrences of any of a finite number of keywords and phrases in an arbitrary text string. Some conditions are defined on the states of the machine in order to improve the speed and size of the machine by Aho and Corasick [1]. The pattern matching algorithm is partitioned into various cases by combining these conditions. Finally, the correspondence illustrates the proposed approach by applying it to the analysis of the machines for a simple search.
Pigeon-Inspired optimization approach to multiple UAVs formation reconfiguration controller design (2014)

This article introduces a controller for solving the problem of multiple unmanned aerial vehicles (UAVs) formation reconfiguration. Under the constraints of terminal status and of control action energy, the controller aims to find the best values of UAV's inputs (including thrust, load factor, bank angle) to accomplish the task. The basis of our controller is a method which combines PIO with CPTD. Pigeon-Inspired optimization (PIO) is a novel algorithm. It has been proposed and applied in engineering problems by following the inspirational precious works. CPTD is a method called control parameterization and time discretization. Besides, we use a mathematical model to get a function which can evaluate the reconfiguration effects. Finally, to verify the validity of our controller, comparative experiments between PIO and particle swarm optimization (PSO) are conducted. The comparative results demonstrate that our proposed controller embedded with PIO is much better than the one with PSO.
De Novo Biosynthesis of Volatiles Induced by Insect Herbivory in Cotton Plants (1997)

In response to insect feeding on the leaves, cotton (Gossypium hirsutum L.) plants release elevated levels of volatiles, which can serve as a chemical signal that attracts natural enemies of the herbivore to the damaged plant. Pulse-labeling experiments with [13C]CO2 demonstrated that many of the volatiles released, including the acyclic terpenes (E,E)-[alpha]-farnesene, (E)-[beta]-farnesene, (E)-[beta]-ocimene, linalool, (E)-4,8-dimethyl-1,3,7-nonatriene, and (E/E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene, as well as the shikimate pathway product indole, are biosynthesized de novo following insect damage. However, other volatile constituents, including several cyclic terpenes, butyrates, and green leaf volatiles of the lipoxygenase pathway are released from storage or synthesized from stored intermediates. Analysis of volatiles from artificially damaged plants, with and without beet armyworm (Spodoptera exigua Hubner) oral secretions exogenously applied to the leaves, as well as volatiles from beet armyworm-damaged and -undamaged control plants, demonstrated that the application of caterpillar oral secretions increased both the production and release of several volatiles that are synthesized de novo in response to insect feeding. These results establish that the plant plays an active and dynamic role in mediating the interaction between herbivores and natural enemies of herbivores.
A practical guide to membrane protein purification (1994)

Strategies and Techniques: G. von Jagow, T.A. Link, and H. Schagger, Purification Strategies for Membrane Proteins. H. Schagger, Chromatographic Techniques and Basic Operations in Membrane Protein Purification. H. Schagger, Denaturing Electrophoretic Techniques. H. Schagger, Native Gel Electrophresis. Discussion of Selected Isolation Protocols: H. Schagger, Isolation of Complex III, of Subcomplexes, and of Protein Subunits from Bovine Heart: Triton X-100/Hydroxylapatite. S.K. Buchanan and J.E. Walker, Chromatographic Purification of F1F0-ATPase and Complex I from Bovine Heart Mitochondria: FPLC-Anion Exchange and Dye-Ligand Chromatography. M. Bodicker and H. Weiss, Isolation of Ubiquinol: Cytochrome c Oxidoreductase (Complex III) from Fungal and Plant Mitochondria: Affinity Chromatography. A. Kroger, V. Geisler, and A. Duchene, Isolation of Wolinella succinogenes Hydrogenase: Chromatofocusing. G. Tsiotis, Photosystem I From Cyanobacteria Isolated in Crystallizing Form by Preparative Isoelectric Focusing. Subject Index.
Albumin-deficient mouse models for studying metabolism of human albumin and pharmacokinetics of albumin-based drugs (2015)

Serum albumin is the major determinant of blood colloidal osmotic pressure acting as a depot and distributor of compounds including drugs. In humans, serum albumin exhibits an unusually long half-life mainly due to protection from catabolism by neonatal Fc receptor (FcRn)-mediated recycling. These properties make albumin an attractive courier of therapeutically-active compounds. However, pharmaceutical research and development of albumin-based therapeutics has been hampered by the lack of appropriate preclinical animal models. To overcome this, we developed and describe the first mouse with a genetic deficiency in albumin and its incorporation into an existing humanized FcRn mouse model, B6.Cg-Fcgrt(tm1Dcr) Tg(FCGRT)32Dcr/DcrJ (Tg32). Albumin-deficient strains (Alb(-/-)) were created by TALEN-mediated disruption of the albumin (Alb) gene directly in fertilized oocytes derived from Tg32 mice and its non-transgenic background control, C57BL/6J (B6). The resulting Alb(-/-) strains are analbuminemic but healthy. Intravenous administration of human albumin to Tg32-Alb(-/-) mFcRn(-/-) hFcRn(Tg/Tg)) mice results in a remarkably extended human albumin serum half-life of ∼24 days, comparable to that found in humans, and in contrast to half-lives of 2.6-5.8 d observed in B6, B6-Alb(-/-) and Tg32 strains. This striking increase can be explained by the absence of competing endogenous mouse albumin and the presence of an active human FcRn. These novel albumin-deficient models provide unique tools for investigating the biology and pathobiology of serum albumin and are a more appropriate rodent surrogates for evaluating human serum albumin pharmacokinetics and albumin-based compounds.
De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple, Podophyllum hexandrum (2013)

The present data will help the identification of the potential genes and transcription factors involved in podophyllotoxin biosynthesis in P. hexandrum. The assembled transcripts could serve as potential candidates for marker discovery and conservation, which should form the foundations for future endeavors.
Bone marrow macrophages process exogenous Toxoplasma gondii polypeptides for recognition by parasite-specific cytolytic T lymphocytes (1993)

CD8+ T cells from mice vaccinated with an attenuated strain of Toxoplasma gondii have previously been shown to have cytolytic activity against bone marrow macrophages (BMM phi) preincubated with a soluble tachyzoite extract. In the present study, we show that class I-transfected L cells differ from BMM phi in that although both cell types are recognized CTL after infection, only BMM phi are killed after sensitization with soluble tachyzoite extract. Gel filtration studies indicated that the T. gondii Ag responsible for sensitization of BMM phi are macromolecules of M(r) > or = 12,000. In contrast, peptides derived by tryptic digestion of this material were found to sensitize both transfected L cells and BMM phi. Although exogenous beta 2-microglobulin markedly enhanced peptide sensitization of BMM phi, no such effect was observed using the macromolecular preparation. This result suggests a requirement for cellular internalization in the processing by BMM phi of soluble Ag for class I-restricted recognition. In related experiments, infected and Ag-sensitized BMM phi were found to express cross-reactive T. gondii epitopes, as determined by cold target inhibition studies. Supernatant derived by 100,000 x g centrifugation of tachyzoite extract had potent sensitizing activity, and after anion exchange chromatography most of the activity was associated with a single fraction. The p30 Ag was not detected by immunoblot analysis in the biologically active supernatant and chromatographic fractions. These findings establish the feasibility of identifying the parasite Ag recognized by CD8+ effectors by direct fractionation of T. gondii proteins coupled with sensitization of BMM phi targets.
Providing integrated toolkit-level support for ambiguity in recognition-based interfaces (2000)

Interfaces based on recognition technologies are used extensively in both the commercial and research worlds. But recognizers are still error-prone, and this results in human performance problems, brittle dialogues, and other barriers to acceptance and utility of recognition systems. Interface techniques specialized to recognition systems can help reduce the burden of recognition errors, but building these interfaces depends on knowledge about the ambiguity inherent in recognition. We have extended a user interface toolkit in order to model and to provide structured support for ambiguity at the input event level. This makes it possible to build re-usable interface components for resolving ambiguity and dealing with recognition errors. These interfaces can help to reduce the negative effects of recognition errors. By providing these components at a toolkit level, we make it easier for application writers to provide good support for error handling. Further, with this robust support, we are able to explore new types of interfaces for resolving a more varied range of ambiguity.
Developmental Typology of Trajectories to Nighttime Bladder Control: Epidemiologic Application of Longitudinal Latent Class Analysis (2003)

The authors aimed to characterize developmental trajectories to nighttime continence by applying two latent class models-longitudinal latent class analysis (LLCA) and latent class growth analysis (LCGA)-to data on nighttime bed-wetting from a population-based birth cohort, the Medical Research Council 1946 National Survey of Health and Development cohort. Data on a binary outcome (wetting in the past month vs. not wetting) were available for children at six ages (4, 6, 8, 9, 11, and 15 years) assessed in 1950, 1952, 1954, 1955, 1957, and 1961. For 3,272 children with complete data (62.5% of the cohort), results of sequential model comparisons (T classes vs. T + 1 classes) and chi-square goodness-of-fit tests were evaluated using parametric bootstrapping. At least four trajectory classes (LLCA and LCGA) were identified. Associations between class membership and the prevalence of related measures were examined using a confirmatory latent class analysis approach. Inclusion of 1,483 children with partially incomplete data (n = 4,755; 90.9% of the cohort) enabled the authors to refine trajectories further: normal development (prevalence = 84.0%); delayed acquisition of bladder control ("transient" (8.7%) and "persistent" (1.8%)), capturing primary enuresis; chronic bed-wetting (2.6%), or experiencing night wetting until age 15 years; and a final trajectory (relapse = 2.9%) capturing secondary or onset enuresis. This empirically based, typologic approach to analysis of extensive longitudinal data in a general population sample provides an alternative perspective to that offered by traditional diagnostic criteria.
Sulfobutylether‐β‐cyclodextrin‐mediated capillary electrophoresis for separation of chlorinated and substituted phenols (1997)

Cyclodextrin-mediated capillary electrophoresis has been developed for separation and analysis of chlorinated as well as substituted phenolic compounds. The procedure used a negatively charged sulfobutylether-beta-cyclodextrin (SB-betaCD) to effect differential partitioning of the phenols between the buffer and CD phases. In 50 mM phosphate buffer containing as low as 1 mM SB-betaCD, 25 phenolic compounds including 11 Environmental Protection Agency (EPA) priority phenols were separated with theoretical plate numbers well above 100,000, for 50 cm of effective length in most cases. An equilibrium complexation model was used for investigating the effect of pH as well as different cyclodextrin concentrations on the electrophoretic mobility. The cyclodextrin-mediated capillary electrophoresis system was also applicable for separating and quantifying the level of pentachlorophenol in contaminated soil samples.
Energy-optimal path planning for six-rotors on multi-target missions (2015)

Often times in multi-target, Unmanned Aerial System (UAS) applications, minimizing energy consumption is a common goal. In simplified cases, this problem can be solved by minimizing the path length between targets using the Traveling Salesman Problem with Neighborhoods (TSPN). However, this method does not take into account the attitude of the UAS. In addition, minimum path length does not always correlate to minimum energy consumption. This research proposes an approach to both problems. A method is proposed to more accurately model multi-target, six-rotor aircraft missions using the Generalized TSPN (GTSPN), which can account for the non-convex characteristics of the neighborhoods created by accounting for variable attitude. To address the energy consumption problem, a heuristic procedure is proposed to solve GTSPN instances using a genetic algorithm approach that incorporates a fine-tuned, dynamic model of a six-rotor to simulate energy consumption. Numerical simulations are performed on randomly generated instances with up to 50 targets to show that the proposed procedure determines tours for a given instance within a 1% standard deviation error from the best-known tour and on average improves the results obtained with the TSPN formulation up to 11.4%.
Unmanned Aerial Vehicle Meets Vehicle-to-Everything in Secure Communications (2019)

Enabling vehicles to communicate with other vehicles, infrastructure, pedestrians, and everything for use cases such as road safety, automatic driving, and infotainment is important for the future cellular networks. However, some vehicle-to-everything (V2X) services need secure transmissions and should be prevented from eavesdropping. Physical layer security, an information- theoretical framework, utilizes the randomness of underlying channels to ensure secrecy in the physical layer. Different from ground communications, unmanned aerial vehicles (UAVs) create line-of-sight connections to vehicles and mobile users making them an ideal platform to conduct physical layer security strategies. In this article, we embrace UAV to V2X communications to enhance the V2X security from the physical layer security's perspective. To be specific, we present security problems in V2X systems, highlight security threats in V2X networks, and illustrate some potential applications of UAVs in V2X security. Open problems for UAV-assisted V2X secure communications are also discussed.
Genome-wide expression analysis detects eight genes with robust alterations specific to bipolar I disorder: relevance to neuronal network perturbation (2006)

The limited number of genome-wide transcriptome analyses using the postmortem brains of bipolar disorder sufferers has not produced a clear consensus on the molecular pathways affected by the disorder. To expand the knowledge in this area, we examined the expression levels of more than 12 000 genes in Brodmann's Area (BA), 46 (dorsolateral prefrontal cortex) from bipolar I disorder and control samples using Affymetrix GeneChips. This analysis detected 108 differentially expressed genes in bipolar brains. Validation studies using quantitative RT-PCR on the two original diagnostic cohorts plus tissue from schizophrenic subjects, confirmed the differential expressions of eight genes (RAP1GA1, SST, HLA-DRA, KATNB1, PURA, NDUFV2, STAR and PAFAH1B3) in a bipolar-specific manner and one gene (CCL3) which was downregulated in both bipolar and schizophrenic brains. Of these, protein levels of RAP1GA1 (RAP1 GTPase activating protein 1) showed a trend of increase in BA46 from bipolar brains, in keeping with mRNA transcript levels. Transmission disequilibrium analysis of the nine genes using 43 single nucleotide polymorphisms (SNPs) in 229 National Institute of Mental Health bipolar trios exposed nominal SNP association and modest empirical haplotypic association (P=0.033) between SST (somatostatin) and disease. Finally, gene network analysis using the currently obtained expression data highlighted cellular growth and nervous system development pathways as potential targets in the molecular pathophysiology of bipolar disorder.
Establishment of a Gene Expression System in <i>Ochrobactrum anthropi</i> (2006)

Genetic studies of Ochrobactrum anthropi are hindered by the lack of a suitable gene expression system. We constructed a set of vectors containing several promoters and a His tag fusion in the N terminus to facilitate protein detection and purification. The new vectors should significantly enhance the genetic manipulation and characterization of O. anthropi.
Low profile wide band VHF/UHF antenna (2014)

Summary form only given. Many applications in communications and radar require antennas that conform to the surface of the supporting structure. Whenever applicable, the antenna aperture is approximated by a plane with the requirement that the dimension normal to the aperture (“profile”) be minimized. Low profile antennas are of special importance within the VHF/UHF bands where they are used as communications antennas on airborne platforms. In addition to low profiles, these antennas also require wide bandwidths. Meeting both requirements at the long wavelengths involved poses special difficulties. Although the subject of profile reduction for flush mounted antennas is not new, the number of papers dealing specifically with VHF/UHF band designs is surprisingly small. Two recently proposed designs employ variants of a discone antenna.