gebhart/patrepeval huggingface dataset:
Multiple protein structure alignment (1994)

A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core.
Secure Networking Protocol with Identity Protection for Cooperation of Unmanned Platforms (2014)

The cooperation of unmanned platforms needs dynamic networking for the secure group communication. Based on the different security domain of wireless environments, an secure networking protocol with identity protection for cooperation of unmanned platforms are proposed, which consists of a four-party security information exchange protocol for the data transmission between nodes in the dynamic network and an ID-based anonymous authentication scheme for the secure session keys of a node, which supports the combination of the decryption process and the identity protection. Finally, we show that the session key has the security characters of unforgeability, confidentiality and non-repudiation, and the new protocol has a secure, flexible and efficient method of key management for dynamic networking.
Long‐Living Holes in Grey Anatase TiO2 Enable Noble‐Metal‐Free and Sacrificial‐Agent‐Free Water Splitting (2020)

Abstract Titanium dioxide has been the benchmark semiconductor in photocatalysis for more than 40 years. Full water splitting, that is, decomposing water into H 2 and O 2 in stoichiometric amounts and with an acceptable activity, still remains a challenge, even when TiO 2 ‐based photocatalysts are used in combination with noble‐metal co‐catalysts. The bottleneck of anatase‐type TiO 2 remains the water oxidation, that is, the hole transfer reaction from pristine anatase to the aqueous environment. In this work, we report that “grey” (defect engineered) anatase can provide a drastically enhanced lifetime of photogenerated holes, which, in turn, enables an efficient oxidation reaction of water to peroxide via a two‐electron pathway. As a result, a Ni@grey anatase TiO 2 catalyst can be constructed with an impressive performance in terms of photocatalytic splitting of neutral water into H 2 and a stoichiometric amount of H 2 O 2 without the need of any noble metals or sacrificial agents. The finding of long hole lifetimes in grey anatase opens up a wide spectrum of further photocatalytic applications of this material.
Controlled semiconductor nanorodassembly from solution: influence of concentration, charge and solvent nature (2011)

Spontaneous supercrystal organisation of semiconductor nanorods (CdS and CdSe) of different aspect ratios into ordered superstructures was obtained by controlled evaporation of a nanorod solution. The rods either align into two dimensional close packed perpendicular arrays or into one dimensional rail tracks depending on the total interaction energy between the rods in solution. A detailed study has identified critical factors that affect this interaction energy such as nanorod concentration, surface charge, dipole moment and solvent nature (polarity and volatility), thereby allowing a general approach to control the nature of nanorod assembly (1D or 2D). Molecular dynamics (MD) of small charged nanorods showed that opposite dipolar alignment (antiferromagnetic) was the preferred rod orientation during self-assembly.
Evaluating Progress of a Social Venture in Wakiso District Uganda (2019)

Monitoring and evaluation (M&E) of funded projects is discussed. The goal is to determine an effective process with which IEEE Smart Village (ISV) can most easily collect the most valuable project data. The presentation begins with an operational definition of sustainable community development (SCD). The dichotomy between economic sustainability and charity is pointed out. A general model of SCD is discussed. Social Return on Investment (SRoI) is a number that is expected to reflect project efficacy. The process to determine SRoI scrutinizes a project under evaluation. The scrutiny uncovers data that becomes re-hidden in the single SRoI number. The authors of this paper took part in a SRoI process applied to an IEEE Smart Village funded non-profit, non-governmental organization, Africa Development Promise (ADP). The focus was to inform the ISV M&E process. Some salient features of the location (Wakiso District, Central Region, Uganda) are elucidated. Some detail of the sub-projects that are under valuation are given. Data collected from the SRoI process are used to determine what parts of the SRoI process are most relevant to M&E of the type of SCD projects that ISV is monitoring. An M&E process and its implementation are proposed and discussed.
In-gap states of an amorphous In–Ga–Zn–O thin film studied via high-sensitivity ultraviolet photoemission spectroscopy using low-energy photons (2021)

Low-density electronic states in the energy gap of an amorphous In–Ga–Zn–O film control device performance. Herein, density of states (DOS) distribution from valence band to the in-gap states of 1014 cm−3 eV−1 level was determined using high-sensitivity UV photoemission spectroscopy. Exponential tail states accompanying two energetically-localized states were directly observed as reported previously. The observed slope of the exponential tail state was different from the Urbach energy derived using photothermal deflection spectroscopy, indicating the importance of directly observing the DOS of in-gap states.
Changes in c-Fos Expression in the Forced Swimming Test: Common and Distinct Modulation in Rat Brain by Desipramine and Citalopram (2013)

Rodents exposed to a 15-min pretest swim in the forced swimming test (FST) exhibit prolonged immobility in a subsequent 5-min test swim, and antidepressant treatment before the test swim reduces immobility. At present, neuronal circuits recruited by antidepressant before the test swim remain unclear, and also less is known about whether antidepressants with different mechanisms of action could influence neural circuits differentially. To reveal the neural circuits associated with antidepressant effect in the FST, we injected desipramine or citalopram 0.5 h, 19 h, and 23 h after the pretest swim and observed changes in c-Fos expression in rats before the test swim, namely 24 h after the pretest swim. Desipramine treatment alone in the absence of pretest swim was without effect, whereas citalopram treatment alone significantly increased the number of c-Fos-like immunoreactive cells in the central nucleus of the amygdala and bed nucleus of the stria terminalis, where this pattern of increase appears to be maintained after the pretest swim. Both desipramine and citalopram treatment after the pretest swim significantly increased the number of c-Fos-like immunoreactive cells in the ventral lateral septum and ventrolateral periaqueductal gray before the test swim. These results suggest that citalopram may affect c-Fos expression in the central nucleus of the amygdala and bed nucleus of the stria terminalis distinctively and raise the possibility that upregulation of c-Fos in the ventral lateral septum and ventrolateral periaqueductal gray before the test swim may be one of the probable common mechanisms underlying antidepressant effect in the FST.
A Decremental PEEP Trial Identifies the PEEP Level That Maintains Oxygenation After Lung Recruitment (2006)

OBJECTIVE:To assess the ability of a decremental trial of positive end-expiratory pressure (PEEP) to identify an optimal PEEP level that maintains oxygenation after a lung-recruitment maneuver. PATIENTS:Twenty sedated patients with acute lung injury and/or acute respiratory distress syndrome, ventilated for 1.2 ± 0.4 d. INTERVENTION:Each patient received up to 3 lung-recruitment maneuvers with continuous positive airway pressure of 40 cm H2O sustained for 40 s to increase the ratio of PaO2 to FIO2 by > 20%. Following the lung-recruitment maneuver, PEEP was set at 20 cm H2O and then the FIO2 was decreased until the oxygen saturation (measured via pulse oximetry [SpO2]) was 90–94%. PEEP was then decreased in 2-cm H2O steps until the SpO2 dropped below 90%. The step preceding the drop to below 90% was considered the optimal PEEP. The lung was then re-recruited and PEEP and FIO2 were set at the identified levels. The patients were followed for 4 h after the PEEP trial and the setting of PEEP and FIO2. RESULTS:After the lung-recruitment maneuver, all the patients' PaO2/FIO2 increased > 50%. The mean ± SD PaO2/FIO2 on the optimal decremental trial PEEP was 211 ± 79 mm Hg, versus 135 ± 37 mm Hg at baseline (p < 0.001), and was sustained at that level for the 4-h study period (227 ± 81 mm Hg at 4 h). FIO2 at baseline was 0.54 ± 0.12 versus 0.38 ± 0.12 (p < 0.001) at 4 h. PEEP was 11.9 ± 3.0 cm H2O at baseline and 9.1 ± 4.7 cm H2O (p = 0.011) at 4 h. CONCLUSION:A decremental PEEP trial identifies a PEEP setting that sustains for 4 h the oxygenation benefit of a 40-cm H2O, 40-s lung-recruitment maneuver.
Dynamic, electronically controlled angle steering of spatial solitons for a 1×4 optical interconnect (2003)

Summary form only given. We have recently demonstrated measurable steering of spatial solitons and the weak signal beams guided within by means of an electronically induced prism in AlGaAs slab waveguides. Here we report on further development of this work, showing the feasibility of an 1 X 4 interconnect based on soliton steering.
Gene Transfer into Mammalian Cells Using Targeted Filamentous Bacteriophage (2011)

INTRODUCTION Phage vectors, because of their genetic simplicity, are uniquely suited to methods that use directed evolution to genetically optimize vectors for therapeutic gene delivery. Moreover, because phage production is restricted to strain-specific bacteria, the hosts are equally amenable to genetic engineering, modification, and even genetic selections to optimize yield, genetic stability, manufacture, and cost. The choice of targeting ligand determines the specificity of targeted phage transduction. Genetic targeting is limited to proteins that can be efficiently expressed and biologically active following secretion into the periplasmic space of the bacteria and subsequent incorporation into the phage particle. The capacity of phage to display a chosen targeting ligand must be determined empirically and optimized. Alternatively, the targeting ligand can be selected after display in a phage library. The orientation of the reporter gene relative to the phage structural genes can affect vector transduction efficiency. We have also targeted phage particles for gene delivery using an avidin-biotin linkage. This allows selection of ligands without concern for their ability to be displayed genetically. This protocol describes the use of targeted filamentous phage for gene delivery to mammalian cells. The final vector, although of low efficiency, is meant to serve as a starting point for a vector development platform that can use in vitro and in vivo techniques of combinatorial display to direct its evolution to high efficiency, high specificity, and eventually, safety in humans.
Evaluation of indoxyl-beta-D-glucuronide as a chromogen in media specific for Escherichia coli (1993)

Indoxyl-beta-D-glucuronide (indoxyl) was evaluated as a specific chromogen for detection of Escherichia coli by the membrane filter method. In all, 413 colonies were tested from the indoxyl-supplemented media, yielding 93.3% confirmation, as E. coli. Compared with the indoxyl medium, other media gave either much lower recovery with high verification or equal recovery with poor verification.
In vivoantimalarial efficacy of acetogenins, alkaloids and flavonoids enriched fractions fromAnnona crassifloraMart. (2014)

Annona crassiflora and Annonaceae plants are known to be used to treat malaria by traditional healers. In this work, the antimalarial efficacy of different fractions of A. crassiflora, particularly acetogenin, alkaloids and flavonoid-rich fractions, was determined in vivo using Plasmodium berghei-infected mice model and toxicity was accessed by brine shrimp assay. The A. crassiflora fractions were administered at doses of 12.5 mg/kg/day in a 4-day test protocol. The results showed that some fractions from woods were rich in acetogenins, alkaloids and terpenes, and other fractions from leaves were rich in alkaloids and flavonoids. The parasitaemia was significantly (p < 0.05, p < 0.001) reduced (57-75%) with flavonoid and alkaloid-rich leaf fractions, which also increased mean survival time of mice after treatment. Our results confirm the usage of this plant in folk medicine as an antimalarial remedy.
Wind turbine control applications of turbine-mounted LIDAR (2014)

In recent years there has been much interest in the possible use of LIDAR systems for improving the performance of wind turbine controllers, by providing preview information about the approaching wind field. Various potential benefits have been suggested, and experimental measurements have sometimes been used to claim surprising gains in performance. This paper reports on an independent study which has used detailed analytical methods for two main purposes: firstly to try to evaluate the likely benefits of LIDAR-assisted control objectively, and secondly to provide advice to LIDAR manufacturers about the characteristics of LIDAR systems which are most likely to be of value for this application. Many different LIDAR configurations were compared: as a general conclusion, systems should be able to sample at least 10 points every second, reasonably distributed around the swept area, and allowing a look-ahead time of a few seconds. An important conclusion is that the main benefit of the LIDAR will be to enhance of collective pitch control to reduce thrust-related fatigue loads; there is some indication that extreme loads can also be reduced, but this depends on other considerations which are discussed in the paper. LIDAR-assisted individual pitch control, optimal Cp tracking and yaw control were also investigated, but the benefits over conventional methods are less clear.
Study on Passive, Wide Area and Multi-State Parameter Monitoring and Diagnosis for Power Transmission Lines (2018)

Smart grid has put forward a very high request to the sensor technology and the comprehensive data analysis ability of sensing parameters. To monitor the infrastructures with multi-state parameters in power grid by use of the common communication fiber in electric power cables, such as OPGW / ADSS / OPPC etc.), or other kinds of optical fibers will help to improve the level of data collection, extraction and comprehensive analysis for power facility state information. The multi-parameter coherent distributed optical fiber sensing apparatus is proposed and developed for power grid application. It is excellent for fiber fault location, and it is both sensitive to the temperature and stress, and can capture the mechanical characteristics of power transmission line, so by combination with the stress feature that the stress caused by the covered ice on power transmission line focuses on the fixed two points that hold the power transmission line, it can be used to warn the icing state. And by considering the characteristics of temperature transient increase and short-duration at the lightning position caused by lightning strike, the lightning strike identification and location on OPGW can be feasible. Furthermore, the temperature information along the power transmission line can be obtained in real time, so that the temperature data needed for the microclimate along the transmission line can be obtained and then combining with the heat dissipation conditions such as wind speed and humidity, it can be used to guide the dynamic capacity increase for the power transmission line.
Detachment of CHO cells adhered on DLC-treated dish using acoustic pressure (2017)

The mass cell culture is an inevitable process for tissue engineering and regenerative medicine, because the therapies are requited a lot of cells. However, the process has not been optimized for maintaining cell activity. Especially, cell detachment using trypsin causes a damage of cells, because surface proteins of cells are degraded. Hence, a novel process to replace trypsinization has been required. In this research, the detachment method—combination of DLC-treated dish and acoustic pressure exposure is developed. The DLC-treated dish has 50 nm DLC layer and the intensity ratio of ID/IG is 0.70. In order to generate acoustic pressure, a piezoelectric ceramic plate is glued on a glass plate to configure an ultrasonic transducer. The glass plate and a polycarbonate wall compose a chamber in which a DLC-treated dish is placed via glycerol. Glycerol transmits acoustic pressure to cells that adhere on the DLC-treated dish. In the results of cell culture experiment, the number of detached cells by using proposed method is equivalent to that by using conventional method (trypsinization). Additionally, initial adhesion of cells detached by the proposed method is improved compared with the cells detached by the conventional method. Moreover, cells detached by the proposed method had surface proteins richly, while cells detached by the conventional method decreased them. The proposed method provides a cell detachment method to keep cell viability so that it may be used in future clinical applications instead of trypsinization.
Influence of the C rc regulator on the hierarchical use of carbon sources from a complete medium in P seudomonas (2015)

The Crc protein, together with the Hfq protein, participates in catabolite repression in pseudomonads, helping to coordinate metabolism. Little is known about how Crc affects the hierarchy of metabolite assimilation from complex mixtures. Using proton Nuclear Magnetic Resonance (NMR) spectroscopy, we carried out comprehensive metabolite profiling of culture supernatants (metabolic footprinting) over the course of growth of both Pseudomonas putida and P. aeruginosa, and compared the wild-type strains with deletion mutants for crc. A complex metabolite consumption hierarchy was observed, which was broadly similar between the two species, although with some important differences, for example in sugar utilization. The order of metabolite utilization changed upon inactivation of the crc gene, but even in the Crc-null strains some compounds were completely consumed before late metabolites were taken up. This suggests the presence of additional regulatory elements that determine the time and order of consumption of compounds. Unexpectedly, the loss of Crc led both species to excrete acetate and pyruvate as a result of unbalanced growth during exponential phase, compounds that were later consumed in stationary phase. This loss of carbon during growth helps to explain the contribution of the Crc/Hfq regulatory system to evolutionary fitness of pseudomonads.
Vanadium Complexes as Insulin Mimetic Agents:  Coordination Chemistry and in Vivo Studies of Oxovanadium(IV) and Dioxovanadate(V) Complexes Formed from Naturally Occurring Chelating Oxazolinate, Thiazolinate, or Picolinate Units (1999)

The synthesis and characterization of four complexes containing naturally occurring binding groups are reported: VO(pic)2·H2O (Hpic = picolinic or pyridine-2-carboxylic acid), NH4[VO2(pic)2]·2H2O, VO(oz)2 (Hoz = 2-(2‘-hydroxyphenyl)-2-oxazoline), and VO(thoz)2 (Hthoz = 2-(2‘-hydroxyphenyl)-2-thiazoline). The X-ray structures of NH4[VO2(pic)2]·2H2O, VO(oz)2, and VO(thoz)2 have been determined. Crystals of NH4[VO2(pic)2]·2H2O (C12H12N3O6V·2H2O) are monoclinic, space group Cc, a = 10.347(2) Å, b = 26.318(2) Å, c = 7.247(1) Å, β = 128.37(1)°, V = 1547.3(5) Å3, Z = 4; those of VO(oz)2 (C18H16N2O5V) are triclinic, P1̄, a = 10.408(1) Å, b = 11.282(1) Å, c = 7.666(1) Å, α = 103.78(1)°, β = 109.64(1)°, γ = 84.75(1)°, V = 823.3(2) Å3, Z = 2; and those of VO(thoz)2 (C18H16N2O3S2V) are orthorhombic, Pbca, a = 12.331(2) Å, b = 26.090(2) Å, c = 11.125(2) Å, V = 3579.3(9) Å3, Z = 4. The structures of NH4[VO2(pic)2]·2H2O and VO(oz)2 were solved by direct methods and that of VO(thoz)2 by the Patterson method. The structures were refined by full-matrix least-squares procedures to R = 0.034, 0.035, and 0.034 (Rw = 0.031, 0.030, and 0.035) for 2428, 1672, and 4595 reflections with I ≥ 3σ(I), respectively. In the case of NH4[VO2(pic)2]·2H2O, the [VO2(pic)2]- anion consists of a cis-VO2+ center with the two picolinate ligands bound with an interplanar angle of 97.25°. Both VO(oz)2 and VO(thoz)2 demonstrate the common distorted square pyramidal geometry, with bidentate oxazolinate or thiazolinate ligands bound to the vanadium center through trans phenolate oxygens and trans oxazoline or thiazoline ring nitrogens giving anti arrangements for the two ligands in each compound. The vanadium atoms in these complexes are elevated by approximately 0.6 Å from the basal square planes defined by the two pairs of ligand O and N donors. Of the four complexes, VO(pic)2·H2O, on the basis of solubility and stability, was selected as the most appropriate for in vivo testing. VO(pic)2·H2O was administered in drinking water for 6 weeks to control−treated (CT) and streptozotocin-induced diabetic−treated (DT) male Wistar rats. Treatment in drinking water resulted in 38% of diabetic−treated animals responding with significant lowering of plasma glucose levels at an initial concentration of 1.52 mM; a subsequent increase to 2.28 mM resulted in 50% response. Lowering of plasma glucose in treated animals was not accompanied by any increase in plasma insulin levels. Intraperitoneal treatment with VO(pic)2·H2O at an acute dose of 0.06 mmol kg-1 produced significant lowering of plasma glucose within 2 h of administration with a peak lowering effect at 8 h. Chronic intraperitoneal administration of VO(pic)2·H2O at a dose of 0.03 mmol kg-1 d-1 for 3 weeks resulted in significant lowering of fasted plasma glucose without any increase in insulin output.