bluuebunny/crossref_metadata_2025 huggingface dataset:
A progressively reduced pretension method to fabricate Bradbury-Nielsen gates with uniform tension
Authors: Ni Kai , Guo Jingran , Yu Zhou , Cao Like , Yu Quan , Qian Xiang , Wang Xiaohao
Published: November 2015

A Bradbury-Nielsen gate (BNG) is often used to modulate ion beams. It consists of two interleaved and electrically isolated sets of wires with uniform tension, which ideally keep parallel, equidistant, and coplanar over a wide temperature range, making the BNG reliable and robust. We have previously analyzed the non-uniformity problem of wire tensions with sequentially winding method and developed a template-based transfer method to solve this problem. In this paper, we introduced a progressively reduced pretension method, which allows directly and sequentially fixing wires onto the substrate without using a template. Theoretical analysis shows that by applying proper pretension to each wire when fixing it, the final wire tensions of all wires can be uniform. The algorithm and flowchart to calculate the pretension sequence are given, and the fabrication process is introduced in detail. Pretensions are generated by weight combination with a weaving device. A BNG with stainless steel wire and a printed circuit board substrate is constructed with this method. The non-uniformity of the final wire tensions is less than 2.5% in theory. The BNG is successfully employed in our ion mobility spectrometer, and the measured resolution is 33.5 at a gate opening time of 350 μs. Compared to the template-based method, this method is simpler, faster, and more flexible with comparable production quality when manufacturing BNGs with different configurations.
Distributed replica dynamics
Authors: Zhang Liang , Chill Samuel T. , Henkelman Graeme
Published: November 2015

A distributed replica dynamics (DRD) method is proposed to calculate rare-event molecular dynamics using distributed computational resources. Similar to Voter’s parallel replica dynamics (PRD) method, the dynamics of independent replicas of the system are calculated on different computational clients. In DRD, each replica runs molecular dynamics from an initial state for a fixed simulation time and then reports information about the trajectory back to the server. A simulation clock on the server accumulates the simulation time of each replica until one reports a transition to a new state. Subsequent calculations are initiated from within this new state and the process is repeated to follow the state-to-state evolution of the system. DRD is designed to work with asynchronous and distributed computing resources in which the clients may not be able to communicate with each other. Additionally, clients can be added or removed from the simulation at any point in the calculation. Even with heterogeneous computing clients, we prove that the DRD method reproduces the correct probability distribution of escape times. We also show this correspondence numerically; molecular dynamics simulations of Al(100) adatom diffusion using PRD and DRD give consistent exponential distributions of escape times. Finally, we discuss guidelines for choosing the optimal number of replicas and replica trajectory length for the DRD method.
Heat- and light-induced transformations of Yb trapping sites in an Ar matrix
Authors: Tao L.-G. , Kleshchina N. N. , Lambo R. , Buchachenko A. A. , Zhou X.-G. , Bezrukov D. S. , Hu S.-M.
Published: November 2015

The low-lying electronic states of Yb isolated in a solid Ar matrix grown at 4.2 K are characterized through absorption and emission spectroscopy. Yb atoms are found to occupy three distinct thermally stable trapping sites labeled “red,” “blue,” and “violet” according to the relative positions of the absorption features they produce. Classical simulations of the site structure and relative stability broadly reproduced the experimentally observed matrix-induced frequency shifts and thus identified the red, blue, and violet sites as due to respective single substitutional (ss), tetravacancy (tv), and hexavacancy (hv) occupation. Prolonged excitation of the 1S → 1P transition was found to transfer the Yb population from hv sites into tv and ss sites. The process showed reversibility in that annealing to 24 K predominantly transferred the tv population back into hv sites. Population kinetics were used to deduce the effective rate parameters for the site transformation processes. Experimental observations indicate that the blue and violet sites lie close in energy, whereas the red one is much less stable. Classical simulations identify the blue site as the most stable one.
Non-equilibrium theory of arrested spinodal decomposition
Authors: Olais-Govea José Manuel , López-Flores Leticia , Medina-Noyola Magdaleno
Published: November 2015

The non-equilibrium self-consistent generalized Langevin equation theory of irreversible relaxation [P. E. Ramŕez-González and M. Medina-Noyola, Phys. Rev. E 82, 061503 (2010); 82, 061504 (2010)] is applied to the description of the non-equilibrium processes involved in the spinodal decomposition of suddenly and deeply quenched simple liquids. For model liquids with hard-sphere plus attractive (Yukawa or square well) pair potential, the theory predicts that the spinodal curve, besides being the threshold of the thermodynamic stability of homogeneous states, is also the borderline between the regions of ergodic and non-ergodic homogeneous states. It also predicts that the high-density liquid-glass transition line, whose high-temperature limit corresponds to the well-known hard-sphere glass transition, at lower temperature intersects the spinodal curve and continues inside the spinodal region as a glass-glass transition line. Within the region bounded from below by this low-temperature glass-glass transition and from above by the spinodal dynamic arrest line, we can recognize two distinct domains with qualitatively different temperature dependence of various physical properties. We interpret these two domains as corresponding to full gas-liquid phase separation conditions and to the formation of physical gels by arrested spinodal decomposition. The resulting theoretical scenario is consistent with the corresponding experimental observations in a specific colloidal model system.
Minority carrier lifetime in iodine-doped molecular beam epitaxy-grown HgCdTe
Authors: Madni I. , Umana-Membreno G. A. , Lei W. , Gu R. , Antoszewski J. , Faraone L.
Published: November 2015

The minority carrier lifetime in molecular beam epitaxy grown layers of iodine-doped Hg1−xCdxTe (x ∼ 0.3) on CdZnTe substrates has been studied. The samples demonstrated extrinsic donor behavior for carrier concentrations in the range from 2 × 1016 cm−3 to 6 × 1017 cm−3 without any post-growth annealing. At a temperature of 77 K, the electron mobility was found to vary from 104 cm2/V s to 7 × 103 cm2/V s and minority carrier lifetime from 1.6 μs to 790 ns, respectively, as the carrier concentration was increased from 2 × 1016 cm−3 to 6 × 1017 cm−3. The diffusion of iodine is much lower than that of indium and hence a better alternative in heterostructures such as nBn devices. The influence of carrier concentration and temperature on the minority carrier lifetime was studied in order to characterize the carrier recombination mechanisms. Measured lifetimes were also analyzed and compared with the theoretical models of the various recombination processes occurring in these materials, indicating that Auger-1 recombination was predominant at higher doping levels. An increase in deep-level generation-recombination centers was observed with increasing doping level, which suggests that the increase in deep-level trap density is associated with the incorporation of higher concentrations of iodine into the HgCdTe.
Response to “Comment on ‘Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5”’ [J. Chem. Phys. 143, 177101 (2015)]
Authors: Harabuchi Yu , Ono Yuriko , Maeda Satoshi , Taketsugu Tetsuya
Published: November 2015

The existence of a valley-ridge transition (VRT) point along the intrinsic reaction coordinate does not always indicate the existence of two minima in the product side, but VRT is a sign of bifurcating nature of dynamical trajectories running on the potential energy surface. It is demonstrated by molecular dynamics simulations.
Multi-attribute integrated measurement of node importance in complex networks
Authors: Wang Shibo , Zhao Jinlou
Published: November 2015

The measure of node importance in complex networks is very important to the research of networks stability and robustness; it also can ensure the security of the whole network. Most researchers have used a single indicator to measure the networks node importance, so that the obtained measurement results only reflect certain aspects of the networks with a loss of information. Meanwhile, because of the difference of networks topology, the nodes' importance should be described by combining the character of the networks topology. Most of the existing evaluation algorithms cannot completely reflect the circumstances of complex networks, so this paper takes into account the degree of centrality, the relative closeness centrality, clustering coefficient, and topology potential and raises an integrated measuring method to measure the nodes' importance. This method can reflect nodes' internal and outside attributes and eliminate the influence of network structure on the node importance. The experiments of karate network and dolphin network show that networks topology structure integrated measure has smaller range of metrical result than a single indicator and more universal. Experiments show that attacking the North American power grid and the Internet network with the method has a faster convergence speed than other methods.
Ionization competition effects on population distribution and radiative opacity of mixture plasmas
Authors: Li Yongjun , Gao Cheng , Tian Qinyun , Zeng Jiaolong , Yuan Jianmin
Published: November 2015

Ionization competition arising from the electronic shell structures of various atomic species in the mixture plasmas was investigated, taking SiO2 as an example. Using a detailed-level-accounting approximation, we studied the competition effects on the charge state population distribution and spectrally resolved and Planck and Rosseland mean radiative opacities of mixture plasmas. A set of coupled equations for ionization equilibria that include all components of the mixture plasmas are solved to determine the population distributions. For a given plasma density, competition effects are found at three distinct temperature ranges, corresponding to the ionization of M-, L-, and K-shell electrons of Si. Taking the effects into account, the spectrally resolved and Planck and Rosseland mean opacities are systematically investigated over a wide range of plasma densities and temperatures. For a given mass density, the Rosseland mean decreases monotonically with plasma temperature, whereas Planck mean does not. Although the overall trend is a decrease, the Planck mean increases over a finite intermediate temperature regime. A comparison with the available experimental and theoretical results is made.
Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations
Authors: Rydzewski J. , Jakubowski R. , Nowak W.
Published: November 2015

This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads to an increase of the main- and side-chain entropies in proteins. We show that such over-minimization may diverge the protein structures from the near-native attraction basin which possesses a minimum of free energy. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein conformation. This measure may help in selection of adequate number of energy minimization steps in protein modelling and, thus, in preservation of the near-native protein conformation.
F-state quenching with CH4 for buffer-gas cooled 171Y b+ frequency standard
Authors: Jau Y.-Y. , Hunker J. D. , Schwindt P. D. D.
Published: November 2015

We report that methane, CH4, can be used as an efficient F-state quenching gas for trapped ytterbium ions. The quenching rate coefficient is measured to be (2.8 ± 0.3) × 106 s−1 Torr−1. For applications that use microwave hyperfine transitions of the ground-state 171Y b ions, the CH4 induced frequency shift coefficient and the decoherence rate coefficient are measured as δν/ν = (−3.6 ± 0.1) × 10−6 Torr−1 and 1/T2 = (1.5 ± 0.2) × 105 s−1 Torr−1. In our buffer-gas cooled 171Y b+ microwave clock system, we find that only ≤10−8 Torr of CH4 is required under normal operating conditions to efficiently clear the F-state and maintain ≥85% of trapped ions in the ground state with insignificant pressure shift and collisional decoherence of the clock resonance.
A first principles study of iron doping in Ni2CoGa magnetic shape memory alloy
Authors: Tavana A. , Mikaeilzadeh L.
Published: November 2015

First principles calculations have been performed for the Ni2Co1-xFexGa Heusler compound in order to investigate the nature of structural instability and the effect of iron doping in enhancing the magneto-structural properties. Calculations show that the origin of structural instability is based on the Jahn-Teller mechanism. Based on the obtained results, the structural instability decreases by iron doping, nevertheless, it is expected that the structural phase transition temperature be always higher than the room temperature. Also, the results show that iron doping enhances the Curie temperature by enhancing the exchange interactions in these compounds. These suggest that the iron doping improves the overall magneto-mechanical properties of the Ni2CoGa Heusler compound.
A comparative account of the interpretation of temporal relations in narrative in Vietnamese and English
Authors: Ngo Thanh
Published: November 2015

This paper provides a comparative account of the interpretation of temporal relations in Vietnamese and English narrative, using a bi-directional corpus of 3,082 clauses of narrative passages originally written in Vietnamese and their English translations and 3,124 clauses of narrative passages originally written in English and their Vietnamese translations. It is shown that the principles for the interpretation of temporal relations between situations in narrative are similar for both English and Vietnamese despite the fact that English has a well-developed tense system, while Vietnamese is a widely-known tenseless language. The principles are based on the temporal properties of situation aspect and the discourse relations between the clauses, which are elicited from pragmatic inferences.
Reconstitution of biosynthetic machinery of fungal polyketides: unexpected oxidations of biosynthetic intermediates by expression host
Authors: Fujii Ryuya , Ugai Takahiro , Ichinose Hirofumi , Hatakeyama Mayumi , Kosaki Takuto , Gomi Katsuya , Fujii Isao , Minami Atsushi , Oikawa Hideaki
Published: November 2015

Reconstitution of whole biosynthetic genes in Aspergillus oryzae has successfully applied for total biosynthesis of various fungal natural products. Heterologous production of fungal metabolites sometimes suffers unexpected side reactions by host enzymes. In the studies on fungal polyketides solanapyrone and cytochalasin, unexpected oxidations of terminal olefin of biosynthetic intermediates were found to give one and four by-products by host enzymes of the transformants harboring biosynthetic genes. In this paper, we reported structure determination of by-products and described a simple solution to avoid the undesired reaction by introducing the downstream gene in the heterologous production of solanapyrone C.
Water-soluble ferulic acid derivatives improve amyloid-β-induced neuronal cell death and dysmnesia through inhibition of amyloid-β aggregation
Authors: Kikugawa Masaki , Tsutsuki Hiroyasu , Ida Tomoaki , Nakajima Hidemitsu , Ihara Hideshi , Sakamoto Tatsuji
Published: November 2015

Ferulic acid (FA) has been reported to exhibit protective effects against amyloid-β (Aβ)-induced neurodegeneration in vitro and in vivo. Recently, we developed two water-soluble FA derivatives: 1-feruloyl glycerol and 1-feruloyl diglycerol. In this study, we examined the neuroprotective effects of these water-soluble FA derivatives on Aβ-induced neurodegeneration both in vitro and in vivo. FA and water-soluble FA derivatives inhibited Aβ aggregation and destabilized pre-aggregated Aβ to a similar extent. Furthermore, water-soluble FA derivatives, as well as FA, inhibited Aβ-induced neuronal cell death in cultured neuronal cells. In in vivo experiments, oral administration of water-soluble FA derivatives to mice improved Aβ-induced dysmnesia assessed by contextual fear conditioning test and protected hippocampal neurons against Aβ-induced neurotoxicity. This study provides useful evidence suggesting that water-soluble FA derivatives are expected to be effective neuroprotective agents.
Heartwood extract of Rhus verniciflua Stokes and its active constituent fisetin attenuate vasoconstriction through calcium-dependent mechanism in rat aorta
Authors: Park Jung-Min , Lee Jun-Hyeong , Na Chun-Soo , Lee Dongho , Lee Jin-Yong , Satoh Masahiko , Lee Moo-Yeol
Published: November 2015

Rhus verniciflua Stokes (RVS) exert cardiovascular protective activity by promoting blood circulation, but its active ingredients and underlying mechanism have yet to be identified. This study investigated the vascular effects of RVS, focusing on vasoconstriction and smooth muscle Ca2+ signaling. RVS heartwood extract attenuated contraction of aortic rings induced by the vasoconstrictors serotonin and phenylephrine, and inhibited the Ca2+ signaling evoked by serotonin in vascular smooth muscle cells. Subsequent activity-guided fractionation identified fisetin as an active constituent exerting a Ca2+ inhibitory effect. Fisetin could inhibit major Ca2+ mobilization pathways including extracellular Ca2+ influx mediated by the L-type voltage-gated Ca2+ channel, Ca2+ release from the intracellular store and store-operated Ca2+ entry. In accordance with Ca2+ inhibitory effect, fisetin attenuated vasoconstriction by serotonin and phenylephrine. These results suggest that the anticontractile effect, which is presumably mediated by inhibition of Ca2+ signaling, may contribute to the improvement of blood circulation by RVS.
Quantifying Delayed Mortality from Barotrauma Impairment in Discarded Red Snapper Using Acoustic Telemetry
Authors: Curtis Judson M. , Johnson Matthew W. , Diamond Sandra L. , Stunz Gregory W.
Published: November 2015

Red Snapper Lutjanus campechanus is the most economically important reef fish in the Gulf of Mexico, and despite being intensively managed, the stock remains overfished. These fish are susceptible to pressure-related injuries (i.e., barotrauma) during fishing that compromise survival after catch and release. Barotrauma-afflicted fish may not only experience immediate mortality but also delayed mortality after returning to depth. This variability and unknown fate leads to uncertainty in stock assessment models and rebuilding plans. To generate better estimates of immediate and delayed mortality and postrelease behavior, Red Snapper were tagged with ultrasonic acoustic transmitters fitted with acceleration and depth sensors. Unique behavior profiles were generated for each fish using these sensor data that allowed the classification of survival and delayed mortality events. Using this information, we compared the survival of Red Snapper released using venting, nonventing, and descending treatments over three seasons and two depths. Red Snapper survival was highest at cooler temperatures and shallower depths. Fish released using venting and descender tools had similar survival, and both these groups of fish had higher survival than nonvented surface-released fish. Overall, Red Snapper had 72% survival, 15% immediate mortality, and 13% delayed mortality, and all fish suffering from delayed mortality perished within a 72-h period after release. Results from these field studies enhance the understanding of the delayed mortality and postrelease fate of Red Snapper regulatory discards. Moreover, these data support the practice of using venting or descender devices to increase the survival of discarded Red Snapper in the recreational fishery and show that acoustic telemetry can be a valuable tool in estimating delayed mortality.

Received March 6, 2015; accepted July 15, 2015
Functional Status and Antihypertensive Therapy in Older Adults: A New Perspective on Old Data
Authors: Charlesworth Christina J. , Peralta Carmen A. , Odden Michelle C.
Published: November 2015

BACKGROUND

Functional status may be useful for identifying older adults who benefit from lower blood pressure. We examined whether functional status modifies the effect of antihypertensive treatment among older adults.

METHODS

Post hoc analyses of the Systolic Hypertension in the Elderly Program (SHEP), a randomized trial of antihypertensive therapy vs. placebo (1985–1991) in 4,736 adults aged 60 years or older with isolated systolic hypertension. Outcomes were all-cause death, cardiovascular (CV) death, myocardial infarction (MI), stroke, falls, and symptoms of hypotension. The effect modifier of interest was functional status, assessed by self-reported physical ability limitation (PAL).

RESULTS

Among persons with no PAL, those receiving treatment had a lower rate of death, CV death, and MI compared with placebo (4.0, 2.9, and 4.2 per 1,000 person-years lower, respectively). In contrast, among persons with a PAL, those receiving treatment had a higher rate of death, CV death, and MI compared with placebo (8.6, 5.3, and 2.7 per 1,000 person-years higher, respectively). These patterns persisted in Cox models, although interaction terms did not reach statistical significance. Treatment remained protective for stroke regardless of functional status. The rate of falls associated with treatment differed by functional status; incidence-rate ratio = 0.81, 95% confidence interval (CI) = (0.66, 0.99), and 1.32, 95% CI = (0.87, 2.00) in participants without and with a PAL, respectively, in models adjusted for demographics and baseline blood pressure ( P -value for interaction, 0.04).

CONCLUSIONS

Functional status may modify the effect of antihypertensive treatment on MI, mortality, and falls, but not stroke, in older adults. Functional status should be examined in other trial settings.
Major Adverse Events and Relationship to Nil per Os Status in Pediatric Sedation/Anesthesia Outside the Operating Room
Authors: Beach Michael L. , Cohen Daniel M. , Gallagher Susan M. , Cravero Joseph P.
Published: November 2015

Background

Studies that have attempted to define the incidence of aspiration or pulmonary complications during sedation/anesthesia of children with respect to nil per os (NPO) status or other factors are difficult because of the relatively infrequent rate of these complications.

Methods

The Pediatric Sedation Research Consortium consists of 42 participating institutions with elective sedation services that submit consecutive patient encounter information to a central database. The authors evaluated aspiration episodes and a combined outcome of major adverse events (defined as aspiration, death, cardiac arrest, or unplanned hospital admission) with respect to NPO status, American Society of Anesthesiologists physical status, age, propofol use, procedure types, and urgency of the procedure.

Results

A total of 139,142 procedural sedation/anesthesia encounters were collected between September 2, 2007 and November 9, 2011. There were 0 deaths, 10 aspirations, and 75 major complications. NPO status was known for 107,947 patients, of whom 25,401 (23.5 %) were not NPO. Aspiration occurred in 8 of 82,546 (0.97 events per 10,000) versus 2 of 25,401 (0.79 events per 10,000) patients who were NPO and not NPO, respectively (odds ratio, 0.81; 95% CI, 0.08 to 4.08; P = 0.79). Major complications occurred in 46 of 82,546 (5.57 events per 10,000) versus 15 of 25,401 (5.91 events per 10,000) (odds ratio, 1.06; 95% CI, 0.55 to 1.93; P = 0.88). Multivariate adjustment did not appreciably impact the effect of NPO status.

Conclusions

The analysis suggests that aspiration is uncommon. NPO status for liquids and solids is not an independent predictor of major complications or aspiration in this sedation/anesthesia data set.
Effects of a Structured Discharge Planning Program on Perceived Functional Status, Cardiac Self-efficacy, Patient Satisfaction, and Unexpected Hospital Revisits Among Filipino Cardiac Patients
Authors: Cajanding Ruff Joseph
Published: November 2015

Background:

Cardiovascular diseases remain the leading cause of morbidity and mortality among Filipinos and are responsible for a very large number of hospital readmissions. Comprehensive discharge planning programs have demonstrated positive benefits among various populations of patients with cardiovascular disease, but the clinical and psychosocial effects of such intervention among Filipino patients with acute myocardial infarction (AMI) have not been studied.

Aims/Objectives:

In this study we aimed to determine the effectiveness of a nurse-led structured discharge planning program on perceived functional status, cardiac self-efficacy, patient satisfaction, and unexpected hospital revisits among Filipino patients with AMI.

Methods:

A true experimental (randomized control) 2-group design with repeated measures and data collected before and after intervention and at 1-month follow-up was used in this study. Participants were assigned to either the control (n = 68) or the intervention group (n = 75). Intervention participants underwent a 3-day structured discharge planning program implemented by a cardiovascular nurse practitioner, which is comprised of a series of individualized lecture-discussion, provision of feedback, integrative problem solving, goal setting, and action planning. Control participants received standard routine care. Measures of functional status, cardiac self-efficacy, and patient satisfaction were measured at baseline; cardiac self-efficacy and patient satisfaction scores were measured prior to discharge, and perceived functional status and number of revisits were measured 1 month after discharge.

Results:

Participants in the intervention group had significant improvement in functional status, cardiac self-efficacy, and patient satisfaction scores at baseline and at follow-up compared with the control participants. Furthermore, participants in the intervention group had significantly fewer hospital revisits compared with those who received only standard care.

Conclusion:

The results demonstrate that a nurse-led structured discharge planning program is an effective intervention in improving perceived functional health status, cardiac self-efficacy, and patient satisfaction, while reducing the number of unexpected hospital revisits, among Filipino patients with AMI. It is recommended that this intervention be incorporated in the optimal care of patients being discharged with an AMI.
Micronutrient Deficiency Independently Predicts Adverse Health Outcomes in Patients With Heart Failure
Authors: Song Eun Kyeung , Kang Seok-Min
Published: November 2015

Background:

Despite growing evidence on the important role of micronutrients in prognosis of heart failure (HF), there has been limited research that micronutrient deficiency predicts health outcomes in patients with HF.

Purpose:

The aim of this study was to determine whether micronutrient deficiency independently predicts adverse health outcomes.

Methods:

A total of 113 consecutive outpatients with HF completed a 3-day food diary to measure intake of 15 micronutrients. The Computer Aided Nutrition Analysis Program for Professionals was used to analyze the food diaries and determine dietary micronutrient deficiencies. Patients completed the Minnesota Living With HF Questionnaire to assess health-related quality of life (HRQoL) and were followed up for 1 year to determine cardiac-related hospitalization or cardiac death. Hierarchical multiple linear regressions and Cox proportional hazard regressions were used to determine whether micronutrient deficiencies predicted health outcomes.

Results:

Fifty-eight patients (51%) had at least 3 micronutrient deficiencies (range, 0–14). Calcium, magnesium, and vitamin D were the most common micronutrient deficiencies. Micronutrient deficiency was independently associated with worse HRQoL (β = .187, P = .025) in hierarchical multiple linear regression. Thirty-nine patients were hospitalized or died during 1-year follow-up because of cardiac problems. The number of micronutrient deficiencies independently predicted cardiac event–free survival (hazard ratio, 1.14; 95% confidence interval, 1.02–1.28).

Conclusions:

These findings show that micronutrient deficiency independently predicted poor HRQoL and earlier cardiac event–free survival in patients with HF. Further research is needed to provide for specific dietary guidelines for better health outcomes in HF patients.
Practical Use of Infliximab Concentration Monitoring in Pediatric Crohn Disease
Authors: Minar Phillip , Saeed Shehzad A. , Afreen Mahrukh , Kim Mi‐Ok , Denson Lee A.
Published: November 2015

Objectives:

Therapeutic drug monitoring (TDM) that guides infliximab (IFX) intensification strategies has been shown to improve IFX efficacy. We conducted a review to evaluate the utility of TDM in the assessment and subsequent management of IFX loss of response in our pediatric population with Crohn disease (CD).

Methods:

Single‐center retrospective study of patients with CD receiving IFX that had TDM from December 2009 to September 2013. We defined subtherapeutic trough as a drug level below the detection limit of the Prometheus enzyme‐linked immunoabsorbant assay and AnserTM reference values (1.4 and 1 μg/mL, respectively) or a mid‐interval level <12 μg/mL.

Results:

One hundred ninety‐one IFX concentration tests were performed on 72 patients with CD with loss of response to therapy as the primary indication (72%). 34% of all TDM were subtherapeutic. After initial TDM, 25 of the 72 patients received regimen intensification with 72% in clinical remission at 6 months. Including all of the TDM that resulted in IFX dose intensification, we found a significant improvement in 6‐month remission rates whether intensification followed mid‐interval (88% remission) or trough (56% remission) testing (P = 0.026). Antibody to infliximab was found in 14 patients with 5 occurring in the first year of therapy. Furthermore, 71% of patients with antibody to infliximab that were switched to an alternative anti‐tumor necrosis factor achieved clinical remission at six months. In multivariable regression analysis, we found IFX dose (mg/kg), IFX dosing frequency (weeks), and the erythrocyte sedimentation rate at the previous infusion were significantly associated with the IFX concentration.

Conclusions:

TDM in our pediatric population with CD led to informed clinical decisions and improved rates of clinical remission.
ADAGE analysis of publicly available gene expression data collections illuminatesPseudomonas aeruginosa-hostinteractions
Authors: Tan Jie , Hammond John H. , Hogan Deborah A. , Greene Casey S.
Published: November 2015

The growth in genome-scale assays of gene expression for different species in publicly available databases presents new opportunities for computational methods that aid in hypothesis generation and biological interpretation of these data. Here, we present an unsupervised machine-learning approach, ADAGE (Analysis usingDenoisingAutoencoders ofGeneExpression) and apply it to the interpretation of all of the publicly available gene expression data forPseudomonas aeruginosa,an important opportunistic bacterial pathogen. In post-hoc positive control analyses using curated knowledge, theP. aeruginosaADAGE model found that co-operonic genes often participated in similar processes and accurately predicted which genes had similar functions. By analyzing newly generated data and previously published microarray and RNA-seq data, the ADAGE model identified gene expression differences between strains, modeled the cellular response to low oxygen, and predicted the involvement of biological processes despite low level expression differences in directly involved genes. Comparison of ADAGE with PCA and ICA revealed that ADAGE extracts distinct signals. We provide the ADAGE model with analysis of all publicly availableP. aeruginosaGeneChip experiments, and we provide open source code for use in other species and settings.
Transcription and imprinting dynamics in developing postnatal male germline stem cells
Authors: Hammoud Saher Sue , Low Diana H.P. , Yi Chongil , Lee Chee Leng , Oatley Jon M. , Payne Christopher J. , Carrell Douglas T. , Guccione Ernesto , Cairns Bradley R.
Published: November 2015

Postnatal spermatogonial stem cells (SSCs) progress through proliferative and developmental stages to populate the testicular niche prior to productive spermatogenesis. To better understand, we conducted extensive genomic profiling at multiple postnatal stages on subpopulations enriched for particular markers (THY1, KIT, OCT4, ID4, or GFRa1). Overall, our profiles suggest three broad populations of spermatogonia in juveniles: (1) epithelial-like spermatogonia (THY1+; high OCT4, ID4, and GFRa1), (2) more abundant mesenchymal-like spermatogonia (THY1+; moderate OCT4 and ID4; high mesenchymal markers), and (3) (in older juveniles) abundant spermatogonia committing to gametogenesis (high KIT+). Epithelial-like spermatogonia displayed the expected imprinting patterns, but, surprisingly, mesenchymal-like spermatogonia lacked imprinting specifically at paternally imprinted loci but fully restored imprinting prior to puberty. Furthermore, mesenchymal-like spermatogonia also displayed developmentally linked DNA demethylation at meiotic genes and also at certain monoallelic neural genes (e.g., protocadherins and olfactory receptors). We also reveal novel candidate receptor–ligand networks involving SSCs and the developing niche. Taken together, neonates/juveniles contain heterogeneous epithelial-like or mesenchymal-like spermatogonial populations, with the latter displaying extensive DNA methylation/chromatin dynamics. We speculate that this plasticity helps SSCs proliferate and migrate within the developing seminiferous tubule, with proper niche interaction and membrane attachment reverting mesenchymal-like spermatogonial subtype cells back to an epithelial-like state with normal imprinting profiles.
Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer
Authors: Horan Lucas , Yasuhara Jiro C. , Kohlstaedt Lori A. , Rio Donald C.
Published: November 2015

Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5′ exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5′ exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites.
A novel one-dimensional metal–organic framework with a μ-cyanido-argentate group:catena-poly[[(5,5′-dimethyl-2,2′-bipyridyl-κ2N,N′)silver(I)]-μ-cyanido-κ2N:C]
Authors: Piromchom Jureepan , Othong Jintana , Boonmak Jaursup , Mutikainen Ilpo , Youngme Sujittra
Published: November 2015

The design and synthesis of metal coordination and supramolecular frameworks containingN-donor ligands and dicyanidoargentate units is of interest due to their potential applications in the fields of molecular magnetism, catalysis, nonlinear optics and luminescence. In the design and synthesis of extended frameworks, supramolecular interactions, such as hydrogen bonding, π–π stacking and van der Waals interactions, have been exploited for molecular recognition associated with biological activity and for the engineering of molecular solids.The title compound, [Ag(CN)(C12H12N2)]n, crystallizes with the AgIcation on a twofold axis, half a cyanide ligand disordered about a centre of inversion and half a twofold-symmetric 5,5′-dimethyl-2,2′-bipyridine (5,5′-dmbpy) ligand in the asymmetric unit. Each AgIcation exhibits a distorted tetrahedral geometry; the coordination environment comprises one C(N) atom and one N(C) atom from substitutionally disordered cyanide bridging ligands, and two N atoms from a bidentate chelating 5,5′-dmbpy ligand. The cyanide ligand links adjacent AgIcations to generate a one-dimensional zigzag chain. These chains are linked togetherviaweak nonclassical intermolecular interactions, generating a two-dimensional supramolecular network.
Bis(2-{1-[(2,4,6-trimethylphenyl)imino]ethyl}pyrrol-1-ido-κ2N,N′)nickel(II): a supramolecular structure formed by C—H...π(arene) hydrogen bonds
Authors: Su Bi-Yun , Li Xiao-Teng , Wang Jia-Xiang , Wang Xu-Dong
Published: November 2015

Nitrogen-based polydentate ligands are of interest owing to their flexible complexation to transition metal atoms. For the title compound, [Ni(C15H17N2)2], a transition metal complex formed by the coordination of two identicalN,N′-bidentate mono(imino)pyrrolyl ligands to an NiIIcentre, an X-ray crystal diffraction study indicates that the two ligands show an inverted arrangement with respect to one another around the NiIIcentre, which is located on a crystallographic inversion centre. The planes of the aromatic substituents at the imine N atoms of the ligands show dihedral angles of 85.91 (5)° with respect to the NiN4plane. The Ni—N bond lengths are in the range 1.9072 (15)–1.9330 (15) Å and the Nimino—Ni—Npyrrolebite angles are 83.18 (6)°. The Ni—Npyrrolebond is substantially shorter than the Ni—Niminobond. Molecules are linked into an extensive network by means of intermolecular C—H...π(arene) hydrogen bonds in which every molecule acts both as hydrogen-bond donor and acceptor. The supramolecular assembly takes the form of an infinite two-dimensional sheet.
From exclusion to inclusion
Authors: Workman-Stark Angela
Published: November 2015

Purpose

– The purpose of this paper is to examine the cultural aspect of policing, particularly as it relates to the role of gender, and proposes an alternative approach to addressing the culture of masculinity within policing.

Design/methodology/approach

– First, the author provides a brief overview of the nature of policing. This is followed by a review of the relevant literature on policing and gender and the implications for men, women, and police organizations of adhering to a militarized or hegemonic form of masculinity. Finally, the author discusses Ely and Myerson’s proposed theory for “undoing gender” and its relevance for policing.

Findings

– The findings of this paper suggest that the police culture continues to reinforce the masculine image of policing, thereby representing a significant barrier to the advancement of women. The findings also suggest that this barrier may be overcome through shared goals that advance collective well-being, definitions of competence linked to task requirements, and a learning orientation toward work.

Originality/value

– This paper makes an important contribution to the existing literature on gender and policing, as it specifically focusses on the cultural influences of masculinity and considers the structural, behavioral, and cultural changes required to create margins of safety for police officers to experiment with new behaviors.
Gender, gender identification and perceived gender discrimination
Authors: Foley Sharon , Ngo Hang-yue , Loi Raymond , Zheng Xiaoming
Published: November 2015

Purpose

– The purpose of this paper is to examine the effects of gender and strength of gender identification on employees’ perception of gender discrimination. It also explores whether gender comparison and perceived gender bias against women act as mediators in the above relationships. It aims to advance the understanding of the processes leading to individual’s perception of gender discrimination in the Chinese workplace.

Design/methodology/approach

– Data were collected from 362 workers via an employee survey in three large companies in China. The human resource staff helped us to distribute a self-administered questionnaire to the employees, and the authors assured them of confidentiality and protected their anonymity. To test the hypotheses, the authors employed structural equation modeling. The authors first conducted confirmatory factor analysis on the measurement model, and then the authors estimated three nested structural models to test the mediating hypotheses.

Findings

– The results reveal that gender and strength of gender identification are related to perceived gender discrimination. The authors further found that gender comparison and perceived gender bias against women partially mediated the relationship between gender and perceived gender discrimination, while gender comparison fully mediated the relationship between strength of gender identification and perceived gender discrimination.

Practical implications

– The study helps managers understand why and how their subordinates form perceptions of gender discrimination. Given the findings, they should be aware of the importance of gender identity, gender comparison, and gender bias in organizational practices in affecting such perceptions.

Originality/value

– This study is the first exploration of the complex relationships among gender, gender identification, gender comparison, perceived gender bias against women, and perceived gender discrimination. It shows the salient role of gender comparison and gender bias against women in shaping employees’ perceptions of gender discrimination, apart from the direct effects of gender and strength of gender identification.
The impact of climate change on road and building infrastructure: a four-country study
Authors: Chinowsky Paul , Schweikert Amy , Hughes Gordon , Hayles Carolyn S. , Strzepek Niko , Strzepek Kenneth , Westphal Michael
Published: November 2015

Purpose

– The purpose of this study is to examine the potential impact of climate change on the built environment in four Northern Asian countries. The impact on roads and buildings infrastructure in China, Japan, South Korea and Mongolia were considered during the decades 2030, 2050 and 2090.

Design/methodology/approach

– The study is based on a stressor-response approach, where using the analysis of 17 Intergovernmental Panel on Climate Change (IPCC) approved Global Circulation Model (GCM) scenarios, projections for impacts from flooding events, precipitation amounts and temperature were determined. The cost of the impacts, based on both maintenance and new construction considerations, were then determined. “Adapt” and “No Adapt” scenarios were incorporated to predict potential costs in each era.

Findings

– Mongolia is vulnerable under the majority of scenarios and faces the greatest opportunity cost in terms of potential loss to enhancing the road stock. China is also vulnerable, but the extent of this vulnerability varies widely based on the climate scenarios. Japan is primarily vulnerable to road stock impacts, although some scenarios indicate buildings vulnerability. South Korea appears to have the least vulnerability but could still face $1 billion annual costs from climate change impacts.

Practical implications

– Results indicate the need for proactive policy planning to avoid costly impacts later in the century.

Originality/value

– The study illustrates the diverse affects that may occur under climate change scenarios and the potential benefit gained from understanding and planning for the projected climate impacts on the built environment.
A framework to improve the resilience of critical infrastructures
Authors: Labaka Leire , Hernantes Josune , Sarriegi Jose Mari
Published: November 2015

Purpose

– This study aims to present a resilience framework for critical infrastructures (CIs) taking into account internal and external stakeholders involved in a crisis situation and covering the four resilience dimensions defined in the literature, as well as providing practical policies to facilitate their implementation in practice.

Design/methodology/approach

– The research methodology consists of an iterative process in which different research methods such as group model building, multiple case study and Delphi method are applied to gather knowledge from experts in the field.

Findings

– This study presents a holistic and easily applicable framework for CIs where: first, a list of resilience policies is defined and second, the influence of each resilience policy in the three resilience life-cycle stages is assessed.

Originality/value

– This study overcomes three of the main limitations that current resilience building frameworks have: some of them only focus on one resilience dimension without covering the four resilience dimensions of resilience, most of them only focus on internal stakeholders without taking into account external stakeholders, and finally, most frameworks limit to describe the framework theoretically without explaining how it can be implemented in practice.
Priority-based task scheduling on heterogeneous resources in the Expert Cloud
Authors: Ashouraie Mehran , Jafari Navimipour Nima
Published: November 2015

Purpose

– Expert Cloud as a new class of Cloud systems provides the knowledge and skills of human resources (HRs) as a service using Cloud concepts. Task scheduling in the Expert Cloud is a vital part that assigns tasks to suitable resources for execution. The purpose of this paper is to propose a method based on genetic algorithm to consider the priority of arriving tasks and the heterogeneity of HRs. Also, to simulate a real world situation, the authors consider the human-based features of resources like trust, reputation and etc.

Design/methodology/approach

– As it is NP-Complete to schedule tasks to obtain the minimum makespan and the success of genetic algorithm in optimization and NP-Complete problems, the authors used a genetic algorithm to schedule the tasks on HRs in the Expert Cloud. In this method, chromosome or candidate solutions are represented by a vector; fitness function is calculated based on several factors; one point cross-over and swap mutation are also used.

Findings

– The obtained results demonstrated the efficiency of the proposed algorithm in terms of time complexity, task fail rate and HRs utilization.

Originality/value

– In this paper the task scheduling issue in the Expert Cloud and improving pervious algorithm are pointed out and the approach to resolve the problem is applied into a practical example.