bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole exome sequencing of suspected mitochondrial patients in clinical practice
Authors: Wortmann Saskia B. , Koolen David A. , Smeitink Jan A. , den van Heuvel Lambert , Rodenburg Richard J. 
Published: March 2015

AbstractMitochondrial disorders are characterized by a broad clinical spectrum. Identical clinical signs and symptoms can be caused by mutations in different mitochondrial or nuclear genes. Vice versa, the same mutation can lead to different phenotypes. Genetic syndromes and neuromuscular disorders mimicking mitochondrial disorders further complicate the diagnostic process. Whole exome sequencing (WES) is the state of the art next generation sequencing technique to identify genetic defects in mitochondrial disorders. Until recently it has mainly been used as a research tool. In this study, the use of WES in routine diagnostics is described. The WES data of 109 patients, referred under the suspicion of a mitochondrial disorder, were examined in two steps. First, the data were filtered using a virtual gene panel of genes known to be associated with mitochondrial disease. If negative, the entire exome was examined. A molecular diagnosis was achieved in 39 % of the heterogeneous cohort, and in 57 % of the subgroup of 42 patients with the highest suspicion for a mitochondrial disease. In addition to mutations in genes known to be associated with mitochondrial disorders (e.g. TUFM, MTFMT, FBXL4), in the subgroup of patients with the lowest suspicion for a mitochondrial disorder we found mutations in several genes associated with neuromuscular disorders (e.g. SEPN1, ACTA1) and genetic syndrome (e.g. SETBP1, ARID1B). Our results show that WES technology has been successfully implemented as a state‐of‐the‐art, molecular diagnostic test for mitochondrial disorders as well as for the mimicking disorders in daily clinical practice. It also illustrates that clinical and biochemical phenotyping is essential for successful application of WES to diagnose individual patients.
Synthesis of steel slag ceramics: chemical composition and crystalline phases of raw materials
Authors: Zhao Li-hua , Wei Wei , Bai Hao , Zhang Xu , Cang Da-qiang 
Published: March 2015

Abstract
Two types of porcelain tiles with steel slag as the main raw material (steel slag ceramics) were synthesized based on the CaO-Al2O3-SiO2 and CaO-MgO-SiO2 systems, and their bending strengths up to 53.47 MPa and 99.84 MPa, respectively, were obtained. The presence of anorthite, α-quartz, magnetite, and pyroxene crystals (augite and diopside) in the steel slag ceramics were very different from the composition of traditional ceramics. X-ray diffraction (XRD) and electron probe X-ray microanalysis (EPMA) results illustrated that the addition of steel slag reduced the temperature of extensive liquid generation and further decreased the firing temperature. The considerable contents of glass-modifying oxide liquids with rather low viscosities at high temperature in the steel slag ceramic adobes promoted element diffusion and crystallization. The results of this study demonstrated a new approach for extensive and effective recycling of steel slag.
Impact of Medicare’s Hospital-Acquired Condition Policy on Infections in Safety Net and Non–Safety Net Hospitals
Authors: Vaz Louise Elaine , Kleinman Kenneth P. , Kawai Alison Tse , Jin Robert , Kassler William J. , Grant Patricia S. , Rett Melisa D. , Goldmann Donald A. , Calderwood Michael S. , Soumerai Stephen B. , Lee Grace M. 
Published: March 2015

BACKGROUNDPolicymakers may wish to align healthcare payment and quality of care while minimizing unintended consequences, particularly for safety net hospitals.OBJECTIVETo determine whether the 2008 Centers for Medicare and Medicaid Services Hospital-Acquired Conditions policy had a differential impact on targeted healthcare-associated infection rates in safety net compared with non–safety net hospitals.DESIGNInterrupted time-series design.SETTING AND PARTICIPANTSNonfederal acute care hospitals that reported central line–associated bloodstream infection and ventilator-associated pneumonia rates to the Centers for Disease Control and Prevention’s National Health Safety Network from July 1, 2007, through December 31, 2013.RESULTSWe did not observe changes in the slope of targeted infection rates in the postpolicy period compared with the prepolicy period for either safety net (postpolicy vs prepolicy ratio, 0.96 [95% CI, 0.84–1.09]) or non–safety net (0.99 [0.90–1.10]) hospitals. Controlling for prepolicy secular trends, we did not detect differences in an immediate change at the time of the policy between safety net and non–safety net hospitals (P for 2-way interaction, .87).CONCLUSIONSThe Centers for Medicare and Medicaid Services Hospital-Acquired Conditions policy did not have an impact, either positive or negative, on already declining rates of central line–associated bloodstream infection in safety net or non–safety net hospitals. Continued evaluations of the broad impact of payment policies on safety net hospitals will remain important as the use of financial incentives and penalties continues to expand in the United States.Infect Control Hosp Epidemiol 2015;00(0): 1–7
The development of the causative construction in Persian child language
Authors: FAMILY NEILOUFAR , ALLEN SHANLEY E. M. 
Published: March 2015

AbstractThe acquisition of systematic patterns and exceptions in different languages can be readily examined using the causative construction. Persian allows four types of causative structures, including one productive multiword structure (i.e. the light verb construction). In this study, we examine the development of all four structures in Persian child speech between the ages of 1;11 and 6;7, in correspondence with their caregivers’ speech. We define developmental stages based on dendrograms derived from variability clustering (Gries & Stoll, 2009). These stages are further substantiated by qualitative data, including overgeneralization errors and alternating structures. We find that Persian-speaking children learn to exploit two (i.e. lexical and light verb construction causatives) of the four constructions. They go from relying on lexical causatives to forming progressively constrained templates for the more complex light verb construction. This first study of the development of Persian causatives supports a usage-based account of verb-by-verb learning in child language development.
ROC Working Party: Towards the Optimal Reserving Process. The Fast Close process
Authors: Bruce Neil , Lauder Alastair , Heath Cameron , Bennett Camilla , Wong Chi , Overton Gregory , Ryan Joe , Laidlar Katherine , Taylor Keith , Jenkins Tim 
Published: March 2015

AbstractOur principal focus in this paper is on ways that a Fast Close process (or indeed any reserving process) can be structured to maximise the value added within the process given the time and resource available. This builds on the use of actual vs. expected techniques investigated in our previous paper, and also looks at forces external to the reserving function that may derail smooth progress. We highlight a number of practical ways that the balance can be restored in favour of adding value rather than crunching numbers. This paper forms the second in the TORP series.
Is increased time to diagnosis and treatment in symptomatic cancer associated with poorer outcomes? Systematic review
Authors: Neal R D , Tharmanathan P , France B , Din N U , Cotton S , Fallon-Ferguson J , Hamilton W , Hendry A , Hendry M , Lewis R , Macleod U , Mitchell E D , Pickett M , Rai T , Shaw K , Stuart N , Tørring M L , Wilkinson C , Williams B , Williams N , Emery J 
Published: March 2015

AbstractBackground:It is unclear whether more timely cancer diagnosis brings favourable outcomes, with much of the previous evidence, in some cancers, being equivocal. We set out to determine whether there is an association between time to diagnosis, treatment and clinical outcomes, across all cancers for symptomatic presentations.Methods:Systematic review of the literature and narrative synthesis.Results:We included 177 articles reporting 209 studies. These studies varied in study design, the time intervals assessed and the outcomes reported. Study quality was variable, with a small number of higher-quality studies. Heterogeneity precluded definitive findings. The cancers with more reports of an association between shorter times to diagnosis and more favourable outcomes were breast, colorectal, head and neck, testicular and melanoma.Conclusions:This is the first review encompassing many cancer types, and we have demonstrated those cancers in which more evidence of an association between shorter times to diagnosis and more favourable outcomes exists, and where it is lacking. We believe that it is reasonable to assume that efforts to expedite the diagnosis of symptomatic cancer are likely to have benefits for patients in terms of improved survival, earlier-stage diagnosis and improved quality of life, although these benefits vary between cancers.
Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples
Authors: Tan Boonfei , Jane Fowler S , Laban Nidal Abu , Dong Xiaoli , Sensen Christoph W , Foght Julia , Gieg Lisa M 
Published: March 2015

Abstract
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.
Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae
Authors: Begg Stephanie L. , Eijkelkamp Bart A. , Luo Zhenyao , Couñago Rafael M. , Morey Jacqueline R. , Maher Megan J. , Ong Cheryl-lynn Y. , McEwan Alastair G. , Kobe Bostjan , O’Mara Megan L. , Paton James C. , McDevitt Christopher A. 
Published: March 2015

AbstractCadmium is a transition metal ion that is highly toxic in biological systems. Although relatively rare in the Earth’s crust, anthropogenic release of cadmium since industrialization has increased biogeochemical cycling and the abundance of the ion in the biosphere. Despite this, the molecular basis of its toxicity remains unclear. Here we combine metal-accumulation assays, high-resolution structural data and biochemical analyses to show that cadmium toxicity, in Streptococcus pneumoniae, occurs via perturbation of first row transition metal ion homeostasis. We show that cadmium uptake reduces the millimolar cellular accumulation of manganese and zinc, and thereby increases sensitivity to oxidative stress. Despite this, high cellular concentrations of cadmium (~17 mM) are tolerated, with negligible impact on growth or sensitivity to oxidative stress, when manganese and glutathione are abundant. Collectively, this work provides insight into the molecular basis of cadmium toxicity in prokaryotes, and the connection between cadmium accumulation and oxidative stress.
Molecular magnetic switch for a metallofullerene
Authors: Wu Bo , Wang Taishan , Feng Yongqiang , Zhang Zhuxia , Jiang Li , Wang Chunru 
Published: March 2015

AbstractThe endohedral fullerenes lead to well-protected internal species by the fullerene cages, and even highly reactive radicals can be stabilized. However, the manipulation of the magnetic properties of these radicals from outside remains challenging. Here we report a system of a paramagnetic metallofullerene Sc3C2@C80connected to a nitroxide radical, to achieve the remote control of the magnetic properties of the metallofullerene. The remote nitroxide group serves as a magnetic switch for the electronic spin resonance (ESR) signals of Sc3C2@C80via spin–spin interactions. Briefly, the nitroxide radical group can ‘switch off’ the ESR signals of the Sc3C2@C80moiety. Moreover, the strength of spin–spin interactions between Sc3C2@C80and the nitroxide group can be manipulated by changing the distance between these two spin centres. In addition, the ESR signals of the Sc3C2@C80moiety can be switched on at low temperatures through weakened spin–lattice interactions.
All-optical broadband ultrasonography of single cells
Authors: Dehoux T. , Ghanem M. Abi , Zouani O. F. , Rampnoux J.-M. , Guillet Y. , Dilhaire S. , Durrieu M.-C. , Audoin B. 
Published: March 2015

AbstractCell mechanics play a key role in several fundamental biological processes, such as migration, proliferation, differentiation and tissue morphogenesis. In addition, many diseased conditions of the cell are correlated with altered cell mechanics, as in the case of cancer progression. For this there is much interest in methods that can map mechanical properties with a sub-cell resolution. Here, we demonstrate an inverted pulsed opto-acoustic microscope (iPOM) that operates in the 10 to 100 GHz range. These frequencies allow mapping quantitatively cell structures as thin as 10 nm and resolving the fibrillar details of cells. Using this non-invasive all-optical system, we produce high-resolution images based on mechanical properties as the contrast mechanisms and we can observe the stiffness and adhesion of single migrating stem cells. The technique should allow transferring the diagnostic and imaging abilities of ultrasonic imaging to the single-cell scale, thus opening new avenues for cell biology and biomaterial sciences.
A practical topological insulator saturable absorber for mode-locked fiber laser
Authors: Yan Peiguang , Lin Rongyong , Ruan Shuangchen , Liu Aijiang , Chen Hao , Zheng Yuequn , Chen Sifan , Guo Chunyu , Hu Juguang 
Published: March 2015

AbstractA novel saturable absorber (SA) was fabricated by coating the topological insulator (TI) film on microfiber using pulsed laser deposition (PLD) method. The TISA device had an insertion loss of ~1.25 dB, a saturable intensity of 26.7 MW/cm2, a modulation depth of ~5.7% and a nonsaturable loss of 20.5%. Upon employing this SA device, we established a passively mode-locked EDFL and achieved nearly free-chirped soliton pulse with 286 fs of pulse duration and >73 dB of signal to noise ratio (SNR). This result clearly evidences that the PLD is an effective scheme for practical SA device fabrication.
Distance-dependent patterns of molecular divergences in tuatara mitogenomes
Authors: Subramanian Sankar , Mohandesan Elmira , Millar Craig D. , Lambert David M. 
Published: March 2015

AbstractPopulation genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
Nitroxyl: a vasodilator of human vessels that is not susceptible to tolerance
Authors: Andrews Karen L. , Lumsden Natalie G. , Farry Julie , Jefferis Ann-Maree , Kemp-Harper Barbara K. , Chin-Dusting Jaye P. F. 
Published: March 2015

Pre-clinical studies have identified nitroxyl (HNO), the reduced congener of nitric oxide (NO•), as a potent vasodilator which is resistant to tolerance development. The present study explores the efficacy of HNO in human blood vessels and describes, for the first time, a vasodilator for humans that is not susceptible to tolerance. Human radial arteries and saphenous veins were obtained from patients undergoing coronary artery graft surgery and mounted in organ baths. Repeated vasodilator responses to the HNO donor Angeli's salt (AS) and NO• donor glyceryl trinitrate (GTN) were determined. AS- and GTN-induced concentration-dependent vasorelaxation of both human radial arteries (AS pEC50: 6.5±0.2; −log M) and saphenous veins (pEC50: 6.7±0.1) with similar potency. In human radial arteries, GTN-induced relaxation was reduced by the NO• scavenger hydroxocobalamin (HXC; P&lt;0.05) but was unaffected by the HNO scavenger L-cysteine. Alternately, AS was unaffected by HXC but was reduced by L-cysteine (5-fold shift, P&lt;0.05). The sGC (soluble guanylate cyclase) inhibitor ODQ abolished responses to both AS and GTN in arteries and veins (P&lt;0.05). Inhibition of voltage-dependent potassium channels (Kv channels) with 4-AP also significantly reduced responses to AS (pEC50: 5.5) and GTN, suggesting that the relaxation to both redox congeners is cGMP- and Kv channel-dependent. Critically, a concentration-dependent development of tolerance to GTN (1 and 10 μM; P&lt;0.05), but not to AS, was observed in both saphenous veins and radial arteries. Like GTN, the HNO donor AS causes vasorelaxation of human blood vessels via activation of a cGMP-dependent pathway. Unlike GTN, however, it does not develop tolerance in human blood vessels.
Breaking up of prolonged sitting over three days sustains, but does not enhance, lowering of postprandial plasma glucose and insulin in overweight and obese adults
Authors: Larsen Robyn N. , Kingwell Bronwyn A. , Robinson Carol , Hammond Louise , Cerin Ester , Shaw Jonathan E. , Healy Genevieve N. , Hamilton Marc T. , Owen Neville , Dunstan David W. 
Published: March 2015

To compare the cumulative (3-day) effect of prolonged sitting on metabolic responses during a mixed meal tolerance test (MTT), with sitting that is regularly interrupted with brief bouts of light-intensity walking. Overweight/obese adults (n=19) were recruited for a randomized, 3-day, outpatient, cross-over trial involving: (1) 7-h days of uninterrupted sitting (SIT); and (2) 7-h days of sitting with light-intensity activity breaks [BREAKS; 2-min of treadmill walking (3.2 km/h) every 20 min (total: 17 breaks/day)]. On days 1 and 3, participants underwent a MTT (75 g of carbohydrate, 50 g of fat) and the incremental area under the curve (iAUC) was calculated from hourly blood samples. Generalized estimating equation (GEE) models were adjusted for gender, body mass index (BMI), energy intake, treatment order and pre-prandial values to determine effects of time, condition and time × condition. The glucose iAUC was 1.3±0.5 and 1.5±0.5 mmol·h·l−1 (mean differences ± S.E.M.) higher in SIT compared with BREAKS on days 1 and 3 respectively (condition effect: P=0.001), with no effect of time (P=0.48) or time × condition (P=0.8). The insulin iAUC was also higher on both days in SIT (day 1: ∆151±73, day 3: ∆91±73 pmol·h·l−1, P=0.01), with no effect of time (P=0.52) or time × condition (P=0.71). There was no between-treatment difference in triglycerides (triacylglycerols) iAUC. There were significant between-condition effects but no temporal change in metabolic responses to MTT, indicating that breaking up of sitting over 3 days sustains, but does not enhance, the lowering of postprandial glucose and insulin.
Investigation of a cross‐gain modulation in a semiconductor optical amplifier based on a quantum dot‐in‐a‐well structure
Authors: Ben Ezra Yosef , Lembrikov Boris I. 
Published: March 2015

The authors theoretically investigated the cross‐gain modulation and the related cross‐phase modulation in a travelling wave quantum dot‐in‐a‐well (QDWELL) semiconductor optical amplifier (SOA). They show that the strong enough pumping wave with an optical power in the range of 1 mW up to several milliwatts synchronises the carrier dynamics in the QDWELL SOA, increasing its operation rate to the frequency of 240 Gb/s and decreasing the patterning effect and chirp.
Observation of Au nanoparticles on the surface of silicon nanowire grown by rapid thermal chemical vapour deposition
Authors: Kwak Dong Wook , Lee Dong Wha , Cho Hoon Young 
Published: March 2015

The size evolution of gold (Au) nanoparticles (NPs) on the sidewall surface of silicon (Si) nanowires (NWs) has been investigated by thermal treatments, using high‐angle annular dark field scanning transmission electron microscopy. The Si NWs grown at 550°C by rapid thermal chemical vapour deposition have been observed to be surrounded by Au NPs with less than 5 nm diameter and ∼1012 cm−2 density on the whole Si NW surface. To explore the size change of Au NPs, the Au NPs on the Si NW were annealed ex situ at the temperature range of 700–900°C for 20 min. The sizes of NPs for samples annealed at 700, 800 and 900°C represent Gaussian distribution with the average size of 4, 6 and 7 nm, respectively, while at high temperatures above 900°C, they change to a bimodal distribution. It is suggested that the surface diffusion rate of Au NPs on Si NW is much lower than that on the Si substrate because of the substitutional diffusion mechanism.