bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caring for terminally ill Muslim patients: Lived experiences of non-Muslim nurses
Authors: Abudari Gassan , Hazeim Hassan , Ginete Gilda 
Published: April 2016

AbstractObjective:The nursing profession demands knowledge, awareness, and experience regarding the ethnic, religious, cultural, and social constructs involved in patient care. Non-Muslim nurses must have theoretical and empirical insights into treatment methods and caring for terminally ill Muslim patients. In particular, non-Muslim nurses should acquire knowledge of Islamic rules and regulations. They should also be familiar with the unique religious and sociocultural practices that pertain to healthcare practices. Our study aimed to explore non-Muslim nurses' experiences in caring for terminally ill Muslim patients and their families regarding physical, social, cultural, spiritual, and religious practices. The study also sought to investigate the context or situations that influence these experiences as described by the nurses.Method:In this qualitative descriptive study, 10 nurses working in medical, oncology, and oncology/palliative care units in a tertiary care hospital in Saudi Arabia were interviewed. A modified Stevick–Colaizzi–Keen method was employed for data analysis.Results:Three main themes constituted the nurses' lived experiences: family matters, end-of-life practices, and nurse challenges. Cultural values, religious practices, and a family approach to the process of care influenced nurses' experiences. Issues related to an absence of palliative care integration and the unavailability of members in the interdisciplinary team also influenced their experiences. Nurses showed a lack of cultural knowledge of some practices due to a lack of awareness of cultural diversity and the unavailability of formal cultural education.Significance of Results:Provision of culturally competent care at the end of life for Muslim patients in Saudi Arabia requires a thoughtful understanding of religious and cultural practices as well as knowledge of the role of the family throughout the care process. The introduction of a cultural care nursing delivery model that incorporates a cultural education program with Islamic teachings and practices at its core is recommended.
Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells
Authors: Bourseau-Guilmain E. , Menard J. A. , Lindqvist E. , Indira Chandran V. , Christianson H. C. , Cerezo Magaña M. , Lidfeldt J. , Marko-Varga G. , Welinder C. , Belting M. 
Published: April 2016

AbstractHypoxia promotes tumour aggressiveness and resistance of cancers to oncological treatment. The identification of cancer cell internalizing antigens for drug targeting to the hypoxic tumour niche remains a challenge of high clinical relevance. Here we show that hypoxia down-regulates the surface proteome at the global level and, more specifically, membrane proteome internalization. We find that hypoxic down-regulation of constitutive endocytosis is HIF-independent, and involves caveolin-1-mediated inhibition of dynamin-dependent, membrane raft endocytosis. Caveolin-1 overexpression inhibits protein internalization, suggesting a general negative regulatory role of caveolin-1 in endocytosis. In contrast to this global inhibitory effect, we identify several proteins that can override caveolin-1 negative regulation, exhibiting increased internalization at hypoxia. We demonstrate antibody-mediated cytotoxin delivery and killing specifically of hypoxic cells through one of these proteins, carbonic anhydrase IX. Our data reveal that caveolin-1 modulates cell-surface proteome turnover at hypoxia with potential implications for specific targeting of the hypoxic tumour microenvironment.
Non-equilibrium induction of tin in germanium: towards direct bandgap Ge1−xSnx nanowires
Authors: Biswas Subhajit , Doherty Jessica , Saladukha Dzianis , Ramasse Quentin , Majumdar Dipanwita , Upmanyu Moneesh , Singha Achintya , Ochalski Tomasz , Morris Michael A. , Holmes Justin D. 
Published: April 2016

AbstractThe development of non-equilibrium group IV nanoscale alloys is critical to achieving new functionalities, such as the formation of a direct bandgap in a conventional indirect bandgap elemental semiconductor. Here, we describe the fabrication of uniform diameter, direct bandgap Ge1−xSnx alloy nanowires, with a Sn incorporation up to 9.2 at.%, far in excess of the equilibrium solubility of Sn in bulk Ge, through a conventional catalytic bottom-up growth paradigm using noble metal and metal alloy catalysts. Metal alloy catalysts permitted a greater inclusion of Sn in Ge nanowires compared with conventional Au catalysts, when used during vapour–liquid–solid growth. The addition of an annealing step close to the Ge-Sn eutectic temperature (230 °C) during cool-down, further facilitated the excessive dissolution of Sn in the nanowires. Sn was distributed throughout the Ge nanowire lattice with no metallic Sn segregation or precipitation at the surface or within the bulk of the nanowires. The non-equilibrium incorporation of Sn into the Ge nanowires can be understood in terms of a kinetic trapping model for impurity incorporation at the triple-phase boundary during growth.
A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
Authors: Nguyen Nam-Phuong , Warnow Tandy , Pop Mihai , White Bryan 
Published: April 2016

AbstractThe standard pipeline for 16S amplicon analysis starts by clustering sequences within a percent sequence similarity threshold (typically 97%) into ‘Operational Taxonomic Units’ (OTUs). From each OTU, a single sequence is selected as a representative. This representative sequence is annotated, and that annotation is applied to all remaining sequences within that OTU. This perspective paper will discuss the known shortcomings of this standard approach using results obtained from the Human Microbiome Project. In particular, we will show that the traditional approach of using pairwise sequence alignments to compute sequence similarity can result in poorly clustered OTUs. As OTUs are typically annotated based upon a single representative sequence, poorly clustered OTUs can have significant impact on downstream analyses. These results suggest that we need to move beyond simple clustering techniques for 16S analysis.
Medically induced amenorrhea in female astronauts
Authors: Jain Varsha , Wotring Virginia E 
Published: April 2016

AbstractMedically induced amenorrhea can be achieved through alterations in the normal regulatory hormones via the adoption of a therapeutic agent, which prevents menstrual flow. Spaceflight-related advantages for medically induced amenorrhea differ according to the time point in the astronaut’s training schedule. Pregnancy is contraindicated for many pre-flight training activities as well as spaceflight, therefore effective contraception is essential. In addition, the practicalities of menstruating during pre-flight training or spaceflight can be challenging. During long-duration missions, female astronauts have often continuously taken the combined oral contraceptive pill to induce amenorrhea. Long-acting reversible contraceptives (LARCs) are safe and reliable methods used to medically induce amenorrhea terrestrially but as of yet, not extensively used by female astronauts. If LARCs were used, daily compliance with an oral pill is not required and no upmass or trash would need disposal. Military studies have shown that high proportions of female personnel desire amenorrhea during deployment; better education has been recommended at recruitment to improve uptake and autonomous decision-making. Astronauts are exposed to similar austere conditions as military personnel and parallels can be drawn with these results. Offering female astronauts up-to-date, evidence-based, comprehensive education, in view of the environment in which they work, would empower them to make informed decisions regarding menstrual suppression while respecting their autonomy.
Spin-orbital effects in metal-dichalcogenide semiconducting monolayers
Authors: Reyes-Retana J. A. , Cervantes-Sodi F. 
Published: April 2016

AbstractMetal-dioxide & metal-dichalcogenide monolayers are studied by means of Density Functional Theory. For an accurate reproduction of the electronic structure of transition metal systems, the spin orbit interaction is considered by using fully relativistic pseudopotentials (FRUP). The electronic and spin properties of MX2 (M = Sc, Cr, Mn, Ni, Mo & W and X = O, S, Se & Te) were obtained with FRUP, compared with the scalar relativistic pseudopotentials (SRUP) and with the available experimental results. Among the differences between FRUP and SRUP calculations are giant splittings of the valence band, substantial band gap reductions and semiconductor to metal or non-magnetic to magnetic “transitions”. MoO2, MoS2, MoSe2, MoTe2, WO2, WS2 and WSe2 are proposed as candidates for spintronics, while CrTe2, with μ ~ 1.59 μB, is a magnetic metal to be experimentally explored.
Characterization of the resistance to Vip3Aa in Helicoverpa armigera from Australia and the role of midgut processing and receptor binding
Authors: Chakroun Maissa , Banyuls Núria , Walsh Tom , Downes Sharon , James Bill , Ferré Juan 
Published: April 2016

AbstractCrops expressing genes from Bacillus thuringiensis (Bt crops) are among the most successful technologies developed for the control of pests but the evolution of resistance to them remains a challenge. Insect resistant cotton and maize expressing the Bt Vip3Aa protein were recently commercialized, though not yet in Australia. We found that, although relatively high, the frequency of alleles for resistance to Vip3Aa in field populations of H. armigera in Australia did not increase over the past four seasons until 2014/15. Three new isofemale lines were determined to be allelic with previously isolated lines, suggesting that they belong to one common gene and this mechanism is relatively frequent. Vip3Aa-resistance does not confer cross-resistance to Cry1Ac or Cry2Ab. Vip3Aa was labeled with 125I and used to show specific binding to H. armigera brush-border membrane vesicles (BBMV). Binding was of high affinity (Kd = 25 and 19 nM for susceptible and resistant insects, respectively) and the concentration of binding sites was high (Rt = 140 pmol/mg for both). Despite the narrow-spectrum resistance, binding of 125I-labeled Vip3Aa to BBMV of resistant and susceptible insects was not significantly different. Proteolytic conversion of Vip3Aa protoxin into the activated toxin rendered the same products, though it was significantly slower in resistant insects.
Ultrafast charge separation dynamics in opaque, operational dye-sensitized solar cells revealed by femtosecond diffuse reflectance spectroscopy
Authors: Ghadiri Elham , Zakeeruddin Shaik M. , Hagfeldt Anders , Grätzel Michael , Moser Jacques-E. 
Published: April 2016

AbstractEfficient dye-sensitized solar cells are based on highly diffusive mesoscopic layers that render these devices opaque and unsuitable for ultrafast transient absorption spectroscopy measurements in transmission mode. We developed a novel sub-200 femtosecond time-resolved diffuse reflectance spectroscopy scheme combined with potentiostatic control to study various solar cells in fully operational condition. We studied performance optimized devices based on liquid redox electrolytes and opaque TiO2 films, as well as other morphologies, such as TiO2 fibers and nanotubes. Charge injection from the Z907 dye in all TiO2 morphologies was observed to take place in the sub-200 fs time scale. The kinetics of electron-hole back recombination has features in the picosecond to nanosecond time scale. This observation is significantly different from what was reported in the literature where the electron-hole back recombination for transparent films of small particles is generally accepted to occur on a longer time scale of microseconds. The kinetics of the ultrafast electron injection remained unchanged for voltages between +500 mV and –690 mV, where the injection yield eventually drops steeply. The primary charge separation in Y123 organic dye based devices was clearly slower occurring in two picoseconds and no kinetic component on the shorter femtosecond time scale was recorded.
Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport
Authors: Gruss Daniel , Velizhanin Kirill A. , Zwolak Michael 
Published: April 2016

AbstractLandauer’s formula is the standard theoretical tool to examine ballistic transport in nano- and meso-scale junctions, but it necessitates that any variation of the junction with time must be slow compared to characteristic times of the system, e.g., the relaxation time of local excitations. Transport through structurally dynamic junctions is, however, increasingly of interest for sensing, harnessing fluctuations and real-time control. Here, we calculate the steady-state current when relaxation of electrons in the reservoirs is present and demonstrate that it gives rise to three regimes of behavior: weak relaxation gives a contact-limited current; strong relaxation localizes electrons, distorting their natural dynamics and reducing the current; and in an intermediate regime the Landauer view of the system only is recovered. We also demonstrate that a simple equation of motion emerges, which is suitable for efficiently simulating time-dependent transport.
Receptor residence time trumps drug-likeness and oral bioavailability in determining efficacy of complement C5a antagonists
Authors: Seow Vernon , Lim Junxian , Cotterell Adam J. , Yau Mei-Kwan , Xu Weijun , Lohman Rink-Jan , Kok W. Mei , Stoermer Martin J. , Sweet Matthew J. , Reid Robert C. , Suen Jacky Y. , Fairlie David P. 
Published: April 2016

AbstractDrug discovery and translation are normally based on optimizing efficacy by increasing receptor affinity, functional potency, drug-likeness (rule-of-five compliance) and oral bioavailability. Here we demonstrate that residence time of a compound on its receptor has an overriding influence on efficacy, exemplified for antagonists of inflammatory protein complement C5a that activates immune cells and promotes disease. Three equipotent antagonists (3D53, W54011, JJ47) of inflammatory responses to C5a (3nM) were compared for drug-likeness, receptor affinity and antagonist potency in human macrophages, and anti-inflammatory efficacy in rats. Only the least drug-like antagonist (3D53) maintained potency in cells against higher C5a concentrations and had a much longer duration of action (t1/2 ~ 20 h) than W54011 or JJ47 (t1/2 ~ 1–3 h) in inhibiting macrophage responses. The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor. Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h. Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.
A somatic reference standard for cancer genome sequencing
Authors: Craig David W. , Nasser Sara , Corbett Richard , Chan Simon K. , Murray Lisa , Legendre Christophe , Tembe Waibhav , Adkins Jonathan , Kim Nancy , Wong Shukmei , Baker Angela , Enriquez Daniel , Pond Stephanie , Pleasance Erin , Mungall Andrew J. , Moore Richard A. , McDaniel Timothy , Ma Yussanne , Jones Steven J. M. , Marra Marco A. , Carpten John D. , Liang Winnie S. 
Published: April 2016

AbstractLarge-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.
Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics
Authors: Francoz Edith , Ranocha Philippe , Pernot Clémentine , Ru Aurélie Le , Pacquit Valérie , Dunand Christophe , Burlat Vincent 
Published: April 2016

AbstractThe rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.
Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems
Authors: Noyes Noelle R. , Yang Xiang , Linke Lyndsey M. , Magnuson Roberta J. , Cook Shaun R. , Zaheer Rahat , Yang Hua , Woerner Dale R. , Geornaras Ifigenia , McArt Jessica A. , Gow Sheryl P. , Ruiz Jaime , Jones Kenneth L. , Boucher Christina A. , McAllister Tim A. , Belk Keith E. , Morley Paul S. 
Published: April 2016

AbstractIt has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.
Bio-inspired dewetted surfaces based on SiC/Si interlocked structures for enhanced-underwater stability and regenerative-drag reduction capability
Authors: Lee By Junghan , Zhang Zhuo , Baek Seunghyun , Kim Sangkuk , Kim Donghyung , Yong Kijung 
Published: April 2016

AbstractDrag reduction has become a serious issue in recent years in terms of energy conservation and environmental protection. Among diverse approaches for drag reduction, superhydrophobic surfaces have been mainly researched due to their high drag reducing efficiency. However, due to limited lifetime of plastron (i.e., air pockets) on superhydrophobic surfaces in underwater, the instability of dewetted surfaces has been a sticking point for practical applications. This work presents a breakthrough in improving the underwater stability of superhydrophobic surfaces by optimizing nanoscale surface structures using SiC/Si interlocked structures. These structures have an unequaled stability of underwater superhydrophobicity and enhance drag reduction capabilities,with a lifetime of plastron over 18 days and maximum velocity reduction ratio of 56%. Furthermore, through photoelectrochemical water splitting on a hierarchical SiC/Si nanostructure surface, the limited lifetime problem of air pockets was overcome by refilling the escaping gas layer, which also provides continuous drag reduction effects.
Microbiota-based Signature of Gingivitis Treatments: A Randomized Study
Authors: Huang Shi , Li Zhen , He Tao , Bo Cunpei , Chang Jinlan , Li Lin , He Yanyan , Liu Jiquan , Charbonneau Duane , Li Rui , Xu Jian 
Published: April 2016

AbstractPlaque-induced gingivitis can be alleviated by various treatment regimens. To probe the impacts of various anti-gingivitis treatments on plaque microflora, here a double blinded, randomized controlled trial of 91 adults with moderate gingivitis was designed with two anti-gingivitis regimens: the brush-alone treatment and the brush-plus-rinse treatment. In the later group, more reduction in both Plaque Index (TMQHI) and Gingival Index (mean MGI) at Day 3, Day 11 and Day 27 was evident, and more dramatic changes were found between baseline and other time points for both supragingival plaque microbiota structure and salivary metabonomic profiles. A comparison of plaque microbiota changes was also performed between these two treatments and a third dataset where 50 subjects received regimen of dental scaling. Only Actinobaculum, TM7 and Leptotrichia were consistently reduced by all the three treatments, whereas the different microbial signatures of the three treatments during gingivitis relieve indicate distinct mechanisms of action. Our study suggests that microbiota based signatures can serve as a valuable approach for understanding and potentially comparing the modes of action for clinical treatments and oral-care products in the future.