bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of the 20‐week anomaly scan on prenatal diagnosis and management of fetal facial clefts
Authors: Ensing S. , Kleinrouweler C. E. , Maas S. M. , Bilardo C. M. , Van der Horst C. M. A. M. , Pajkrt E. 
Published: December 2013

ABSTRACTObjectiveTo investigate trends in prenatal diagnosis and termination of pregnancy rates in cases of fetal cleft lip with or without cleft palate (CL±P), before and after the introduction in The Netherlands of the 20‐week anomaly scan in 2007, and to assess the accuracy of this scan for the diagnosis of facial clefts.MethodsThis was a retrospective cohort study of consecutive cases of CL±P diagnosed in 2001–2010 in the referral region of the Academic Medical Centre. Cases diagnosed prenatally were identified from the hospital's database. These data, grouped according to the periods before and after the introduction of the routine 20‐week anomaly scan, were compared with data of all cases managed by the multidisciplinary cleft team, which services the same region, to identify cases of CL±P that were not seen prenatally.ResultsWe identified 123 cases of CL±P diagnosed prenatally, of which 76% (93/123) were diagnosed before 24 weeks. In one case, the CL±P was not confirmed after birth. There were 46 cases with associated structural anomalies and 76 isolated cases. The median gestational age at diagnosis decreased by 2 weeks after 2007 (P = 0.02). The proportion of isolated clefts detected prenatally increased significantly after 2007 (P < 0.0001), whereas the proportion of associated clefts remained stable over the years (P = 0.426). The overall detection rate of CL±P increased from 43% before 2007 to 86% after 2007 (P < 0.0001), without an increase in terminations of pregnancy.ConclusionIntroduction of the routine fetal anomaly scan has decreased the gestational age at diagnosis of CL±P and has increased the proportion diagnosed prenatally, without a significant change in the number of terminations of pregnancy. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd
Time to stop investing in carbon capture and storage and reduce government subsidies of fossil‐fuels
Authors: Stephens Jennie C. 
Published: December 2013

Government investment in carbon capture and storage (CCS) is a large and expensive fossil‐fuel subsidy with a low probability of eventual societal benefit. Within the tight resource constrained environments that almost all governments are currently operating in, it is irresponsible to sustain this type of subsidy. CCS has been promoted as a ‘bridging’ technology to provide CO2 reductions until non‐fossil‐fuel energy is ramped up. But the past decade of substantial government investment and slow progress suggests that the challenges are many, and it will take longer to build the CCS bridge than to shift away from fossil‐fuels. Optimism about the potential of CCS is based primarily on research on technical feasibility, but very little attention has been paid to the societal costs of governments perpetuating fossil‐fuels or to the sociopolitical requirements of long‐term regulation of CO2 stored underground. Deep systemic change is needed to alter the disastrous global fossil‐fuel trajectory. Government investment in CCS and other fossil‐fuel technologies must end so that the distraction and complacency of the false sense of security such investments provide are removed. Instead of continuing to invest billions in CCS, governments should invest more aggressively in technologies, policies, and initiatives that will accelerate a smooth transition to non‐fossil‐fuel‐based energy systems. We need to divest from perpetuating a fossil‐fuel infrastructure, and invest instead in social and technical changes that will help us prepare to be more resilient in an increasingly unstable and unpredictable future. WIREs Clim Change 2014, 5:169–173. doi: 10.1002/wcc.266This article is categorized under:

Climate Economics > Economics of Mitigation
The Carbon Economy and Climate Mitigation > Decarbonizing Energy and/or Reducing Demand
Financial modeling with heavy‐tailed stable distributions
Authors: Nolan John P. 
Published: December 2013

The aim of this article was to give an accessible introduction to stable distributions for financial modeling. There is a real need to use better models for financial returns because the normal (or bell curve/Gaussian) model does not capture the large fluctuations seen in real assets. Stable laws are a class of heavy‐tailed probability distributions that can model large fluctuations and allow more general dependence structures. WIREs Comput Stat 2014, 6:45–55. doi: 10.1002/wics.1286This article is categorized under:

Applications of Computational Statistics > Computational Finance
Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Statistical and Graphical Methods of Data Analysis > Robust Methods
The nature of friction: A critical assessment
Authors: Hsu Stephen , Ying Charles , Zhao Fei 
Published: December 2013

Abstract
Friction is an essential part of human experience. We need traction to walk, stand, work, and drive. At the same time, we need energy to overcome the resistance to motion, hence, too much friction costs excess energy to perform work, introducing inefficiencies. In the 21st century, we are facing the dual challenges of energy shortage and global warming from burning fossil fuels. Therefore, the ability to control friction has become a top priority in our world today. Yet our understanding of the fundamental nature of friction is still lacking.
Friction has always been a subject of curiosity. Intensive study of the origin of friction began in the 16th century, after the pioneering work by Leonardo da Vinci. Yet progress in understanding the nature of friction has been slow, hampered by the lack of instrument to measure friction precisely. Ingenious experiments performed by Amontons, Coulomb, and others have yielded important insights to build the foundation of our understanding. Beginning in the late 1800s and early 1900s, the advent of steam engines, locomotives, followed by the automobiles airplanes, and space exploration demands a clear understanding of friction and the ability to control it for the machinery to last. Significant progress on how to apply and control friction in engineering friction was made through trial and error. At the beginning of the 21st century, a new dimension of nanoscale friction came into the picture in conjunction with the arrival of nanotechnology. Our understanding of atomic and molecular friction has been expanding rapidly. However, integration of the new found knowledge of nanofriction into engineering practices has been elusive. Why? What is the scaling relationship between atomic friction and macro-friction? Is it possible to predict friction at the macro-level from nanoscale results? Why nanofriction values often do not agree with the macrofriction values given the same materials pair? Could it be there is a length scale dependent characteristic friction value?
In engineering practice, progress since the 1980s has been slow. Most of the effort has been focused on lubrication research such as elastohydrodynamic theories and solid lubricants. Friction mechanisms and failures have received relative little attention while nanofriction received much of the attention.
Today, energy efficiency and renewable energy generation demand our immediate attention while we seek reduction in carbon emission. The ability to control friction becomes an essential step in seeking sustainable technologies. Friction, after all, is an indicator of energy efficiency. If we can reduce the unnecessary parasitic energy losses and increase our current energy efficiency, it will give us time to develop alternative energy sources. This paper examines our current understanding of friction, filling some voids with experimental data, and attempts to integrate the various pieces to identify the gaps of our knowledge, hopefully to spark new avenues of investigations into this important area.
Effects of undernourishment, recurrent seizures and enriched environment during early life in hippocampal morphology
Authors: Alvarez Paula Steffen , Simão Fabrício , Hemb Marta , Xavier Léder Leal , Nunes Magda Lahorgue 
Published: December 2013

AbstractIt has been recently shown that enriched environment led to a significant benefit in learning and retention of visual–spatial memory, being able to reverse the cognitive impairment generated by undernourishment and recurrent seizures. We investigated the hippocampal morphological effects of recurrent seizures and undernourishment early in life in Wistar rats and the possible benefits produced by the enriched environment in these conditions. The morphological parameters stereologically evaluated were hippocampal volume, thickness of pyramidal stratum of the CA1 subfield and neuronal and glial densities in the same subfield. Male Wistar rats were divided into eight groups including nourished, nourished + enriched environment, nourished + recurrent seizures, nourished + recurrent seizures + enriched environment, undernourished, undernourished + enriched environment, undernourished + recurrent seizures and undernourished + recurrent seizures + enriched environment. Undernourishment model consisted in nutritional deprivation regimen from post‐natal day 2 (P2) to P15. From P8 to P10, recurrent seizures group were induced by flurothyl three times per day. Enriched environment groups were exposed between P21 and P51. Our main findings were: (1) animals submitted to the enriched environment showed an increased hippocampal volume; (2) enriched environment promotes increases in the thickness of the pyramidal layer in hippocampal CA1 subfield in animals nourished and undernourished with recurrent seizures; (3) undernourishment during early development decreased neuronal density in CA1 and CA3 subfields. Our findings show that these three conditions induces important changes in hippocampal morphology, the most deleterious changes are induced by undernourishment and recurrent seizures, while more beneficial morphological changes are produced by enriched environment.
SplicePlot: a utility for visualizing splicing quantitative trait loci
Authors: Wu Eric , Nance Tracy , Montgomery Stephen B. 
Published: December 2013

Abstract
Summary: RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure.
Availability and implementation: Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.
Contact: wu.eric.g@gmail.com or smontgom@stanford.edu
Efficient clustering of identity-by-descent between multiple individuals
Authors: Qian Yu , Browning Brian L. , Browning Sharon R. 
Published: December 2013

Abstract
Motivation: Most existing identity-by-descent (IBD) detection methods only consider haplotype pairs; less attention has been paid to considering multiple haplotypes simultaneously, even though IBD is an equivalence relation on haplotypes that partitions a set of haplotypes into IBD clusters. Multiple-haplotype IBD clusters may have advantages over pairwise IBD in some applications, such as IBD mapping. Existing methods for detecting multiple-haplotype IBD clusters are often computationally expensive and unable to handle large samples with thousands of haplotypes.
Results: We present a clustering method, efficient multiple-IBD, which uses pairwise IBD segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome. Our method is an order of magnitude faster than existing methods and has comparable performance with respect to the quality of clusters it uncovers. We further investigate the potential application of multiple-haplotype IBD clusters in association studies by testing for association between multiple-haplotype IBD clusters and low-density lipoprotein cholesterol in the Northern Finland Birth Cohort. Using our multiple-haplotype IBD cluster approach, we found an association with a genomic interval covering the PCSK9 gene in these data that is missed by standard single-marker association tests. Previously published studies confirm association of PCSK9 with low-density lipoprotein.
Availability and implementation: Source code is available under the GNU Public License http://cs.au.dk/~qianyuxx/EMI/.
Contact: qianyuxx@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU
Authors: Su Xiaoquan , Wang Xuetao , Jing Gongchao , Ning Kang 
Published: December 2013

Abstract
Motivation: The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure.
Summary: We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of &gt;17 000 times compared with single-core CPU, and &gt;2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible.
Availability and implementation: GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.
Contact: ningkang@qibebt.ac.cn
Ondex Web: web-based visualization and exploration of heterogeneous biological networks
Authors: Taubert Jan , Hassani-Pak Keywan , Castells-Brooke Nathalie , Rawlings Christopher J. 
Published: December 2013

Abstract
Summary: Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL.
Availability and implementation: http://ondex.rothamsted.ac.uk/OndexWeb.
Contact: keywan.hassani-pak@rothamsted.ac.uk
Fast determination of displacement by PPP velocity estimation
Authors: Tu Rui 
Published: December 2013

Abstract
Global Positioning System (GPS) has been proven to be an effective tool to retrieve high-precision displacement for the natural hazard monitoring. The network positioning and Precise Point Positioning (PPP) are the two basic approaches for its data solution, but the former one can only get a relative displacement within the local reference frame and requires a complex and continuously linked infrastructure, and the latter one with a long convergence time to obtain the absolute displacements within the global reference frame. To overcome these drawbacks, this paper proposed a method of fast determining the displacement by PPP velocity estimation (PPPVE). The key of the approach is that the velocity vector parameters are not correlated with other unknown parameters, such as ambiguities and atmosphere, so they can be fast and accurately estimated and integrated into displacements. The validation shows that the displacement can be provided with a precision of 1–2 cm in 1 min by PPPVE. In additional, the Kalman smoothing estimation can be used to improve the PPP solution.
Found: the progenitors of AM CVn and supernovae .Ia
Authors: Kilic Mukremin , Hermes J. J. , Gianninas A. , Brown Warren R. , Heinke Craig O. , Agüeros M. A. , Chote Paul , Sullivan Denis J. , Bell Keaton J. , Harrold Samuel T. 
Published: December 2013

Abstract
We present optical and X-ray observations of two tidally distorted, extremely low-mass white dwarfs (WDs) with massive companions. There is no evidence of neutron stars in our Chandra and XMM observations of these objects. SDSS J075141.18−014120.9 (J0751) is an eclipsing double WD binary containing a 0.19 M⊙ WD with a 0.97 M⊙ companion in a 1.9 h orbit. J0751 becomes the fifth eclipsing double WD system currently known. SDSS J174140.49+652638.7 (J1741) is another binary containing a 0.17 M⊙ WD with an unseen M ≥ 1.11 M⊙ WD companion in a 1.5-h orbit. With a mass ratio of ≈0.1, J1741 will have stable mass transfer through an accretion disc and turn into an interacting AM Canum Venaticorum (AM CVn) system in the next ≈160 Myr. With a mass ratio of 0.2, J0751 is likely to follow a similar evolutionary path. These are the first known AM CVn progenitor binary systems and they provide important constraints on the initial conditions for AM CVn. Theoretical studies suggest that both J0751 and J1741 may create thermonuclear supernovae in ∼108 yr, either .Ia or Ia. Such explosions can account for ∼1 per cent of the Type Ia supernova rate.
The first month of evolution of the slow-rising Type IIP SN 2013ej in M74
Authors: Valenti S. , Sand D. , Pastorello A. , Graham M. L. , Howell D. A. , Parrent J. T. , Tomasella L. , Ochner P. , Fraser M. , Benetti S. , Yuan F. , Smartt S. J. , Maund J. R. , Arcavi I. , Gal-Yam A. , Inserra C. , Young D. 
Published: December 2013

Abstract
We present early photometric and spectroscopic observations of SN 2013ej, a bright Type IIP supernova (SN) in M74. SN 2013ej is one of the closest SNe ever discovered. The available archive images and the early discovery help to constrain the nature of its progenitor. The earliest detection of this explosion was on 2013 July 24.125 ut and our spectroscopic monitoring with the FLOYDS spectrographs began on July 27.7 ut, continuing almost daily for two weeks. Daily optical photometric monitoring was achieved with the 1 m telescopes of the Las Cumbres Observatory Global Telescope (LCOGT) network, and was complemented by UV data from Swift and near-infrared spectra from Public ESO Spectroscopic Survey of Transient Objects and Infrared Telescope Facility. The data from our monitoring campaign show that SN 2013ej experienced a 10 d rise before entering into a well-defined plateau phase. This unusually long rise time for a Type IIP has been seen previously in SN 2006bp and SN 2009bw. A relatively rare strong absorption blueward of Hα is present since our earliest spectrum. We identify this feature as Si ii, rather than high-velocity Hα as sometimes reported in the literature.
Hawkish but helpful: When cultural group selection favors within-group aggression
Authors: Hanowell Ben 
Published: December 2013

AbstractThe origin of cooperation is a central problem in evolutionary biology and social science. Cultural group selection and parochial altruism are popular but controversial evolutionary explanations for large-scale cooperation. Proponents of the cultural group selection hypothesis argue that the human tendency to conform—a consequence of our reliance on social learning—maintained sufficient between-group variation to allow group selection (which favors altruism) to overpower individual selection (which favors selfishness), whereupon large-scale altruism could emerge. Proponents of the parochial altruism hypothesis argue that altruism could emerge in tandem with hostility toward other groups if the combination of the two traits increased success in inter-group contests. Proponents of both hypotheses assume that cooperation is altruistic and that within-group conflict is antithetical to cooperation, implying that group selection for cooperation reduces within-group conflict. Yet within-group conflict need not be antithetical to cooperation. This essay uses a mathematical model to show that selection between groups can lead to greater within-group aggression if within-group aggression enhances the value of individually costly public goods contributions. This model may help to explain cross-cultural associations between warfare, socialization for aggression, aggressive sports, and interpersonal violence among humans. It may also apply to other forms of inter-group conflict among humans. Finally, the model suggests that group selection can lead to disharmony within groups, a caveat to the use of group selection models to inform social policy.
ArabidopsisChlorophyll Biosynthesis: An Essential Balance between the Methylerythritol Phosphate and Tetrapyrrole Pathways
Authors: Kim Se , Schlicke Hagen , Van Ree Kalie , Karvonen Kristine , Subramaniam Anant , Richter Andreas , Grimm Bernhard , Braam Janet 
Published: December 2013

AbstractChlorophyll, essential for photosynthesis, is composed of a chlorin ring and a geranylgeranyl diphosphate (GGPP)–derived isoprenoid, which are generated by the tetrapyrrole and methylerythritol phosphate (MEP) biosynthesis pathways, respectively. Although a functional MEP pathway is essential for plant viability, the underlying basis of the requirement has been unclear. We hypothesized that MEP pathway inhibition is lethal because a reduction in GGPP availability results in a stoichiometric imbalance in tetrapyrrolic chlorophyll precursors, which can cause deadly photooxidative stress. Consistent with this hypothesis, lethality of MEP pathway inhibition in Arabidopsis thaliana by fosmidomycin (FSM) is light dependent, and toxicity of MEP pathway inhibition is reduced by genetic and chemical impairment of the tetrapyrrole pathway. In addition, FSM treatment causes a transient accumulation of chlorophyllide and transcripts associated with singlet oxygen-induced stress. Furthermore, exogenous provision of the phytol molecule reduces FSM toxicity when the phytol can be modified for chlorophyll incorporation. These data provide an explanation for FSM toxicity and thereby provide enhanced understanding of the mechanisms of FSM resistance. This insight into MEP pathway inhibition consequences underlines the risk plants undertake to synthesize chlorophyll and suggests the existence of regulation, possibly involving chloroplast-to-nucleus retrograde signaling, that may monitor and maintain balance of chlorophyll precursor synthesis.