bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of linked selective sweeps on demographic inference and model selection
Authors: Schrider Daniel R. , Shanku Alexander G. , Kern Andrew D. 
Published: April 2016

AbstractThe availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of datasets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models—often severely. Moreover, we find that selection can lead to incorrect inferences of population size changes when none have occurred. We argue that the amount of recent positive selection required to skew inferences may often be acting in natural populations. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.
The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective
Authors: Jacob Laurent , Speed Terence P. 
Published: April 2016

1AbstractIn a recent publication, Sood et al. [2015] presented a set of 150 probe-sets which could be used in a diagnosis of Alzheimer disease (AD) based on gene expression. We reproduce some of their experiments, and show that the performance of their particular set of 150 probe-sets does not stand out compared to that of randomly sampled sets of 150 probe-sets from the same array.
qpMerge: Merging different peptide isoforms using a motif centric strategy
Authors: Hindle Matthew M. , Le Bihan Thierry , Krahmer Johanna , Martin Sarah F. , Noordally Zeenat B. , Simpson T. Ian , Millar Andrew J. 
Published: April 2016

AbstractAccurate quantification and enumeration of peptide motifs is hampered by redundancy in peptide identification. A single phosphorylation motif may be split across charge states, alternative modifications (e.g.acetylation and oxidation), and multiple miss-cleavage sites which render the biological interpretation of MS data a challenge. In addition motif redundancy can affect quantitative and statistical analysis and prevent a realistic comparison of peptide numbers between datasets. In this study, we present a merging tool set developed for the Galaxy workflow environment to achieve a non-redundant set of quantifications for phospho-motifs. We present a Galaxy workflow to merge three exemplar dataset, and observe reduced phospho-motif redundancy and decreased replicate variation. The qpMerge tools provide a straightforward and reusable approach to facilitating phospho-motif analysis.The source-code and wiki documentation is publically available athttp://sourceforge.net/projects/ppmerge.The galaxy pipeline used in the exemplar analysis can be found athttp://www.myexperiment.org/workflows/4186.
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
Authors: Phuong Dao , Hoinka Jan , Wang Yijie , Takahashi Mayumi , Zhou Jiehua , Costa Fabrizio , Rossi John , Burnett John , Backofen Rolf , Przytycka Teresa M. 
Published: April 2016

AbstractAptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identifiedin vitrovia the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol. SELEX selects binders through an iterative process that, starting from a pool of random ssDNA/RNA sequences, amplifies target-affine species through a series of selection cycles. HT-SELEX, which combines SELEX with high throughput sequencing, has recently transformed aptamer development and has opened the field to even more applications. HT-SELEX is capable of generating over half a billion data points, challenging computational scientists with the task of identifying aptamer properties such as sequence structure motifs that determine binding. While currently available motif finding approaches suggest partial solutions to this question, none possess the generality or scalability required for HT-SELEX data, and they do not take advantage of important properties of the experimental procedure.We present AptaTRACE, a novel approach for the identification of sequence-structure binding motifs in HT-SELEX derived aptamers. Our approach leverages the experimental design of the SELEX protocol and identifies sequence-structure motifs that show a signature of selection. Because of its unique approach, AptaTRACE can uncover motifs even when these are present in only a minuscule fraction of the pool. Due to these features, our method can help to reduce the number of selection cycles required to produce aptamers with the desired properties, thus reducing cost and time of this rather expensive procedure. The performance of the method on simulated and real data indicates that AptaTRACE can detect sequence-structure motifs even in highly challenging data.
Developing a SEIL (Smart Enjoy Interact Light) bag utilizing LED display
Authors: Chun Jaehoon , Lee Myungsu 
Published: April 2016

Purpose
Bicycles are not only an environmentally friendly means of transportation but are also easily accessible exercise equipment for health. Thus the number of bicycles is gradually increasing. This study aims to develop a ‘Smart Enjoy Interact Light (SEIL)’ bag utilizing LED display and smartphone apps. By transmitting desired information or images with LEDs, a SEIL bag can protect bicyclists, and also allow wearers to communicate with others.

Design/methodology/approach
A SEIL built-in bag was developed in the form of a backpack to support all outdoor activities. It can show traffic signals using a wireless controller. Features of design are: ordinary fabric for IT devices; thick and stiff canvas fabric for flexible LEDs; a thin and air-permeable mesh for the LED light; a flexible PCB dashboard for absorbing various shocks; a PVC hard case for the LED display devices; UV coating for waterproofing and durability.

Findings
A SEIL bag for bicyclists can be useful in a variety of outdoor sports and in commercial applications as well, such as advertising or displaying products. The detachable part can be utilized as a hip sack or a pouch.

Originality/value
A SEIL bag not only protects bicyclists from traffic accidents, but with which they can express information or images in real time. A SEIL bag is interactive fashion item that emphases communication, thus it will contribute to development of smart-wear.
Research on the seam performance of waterproof clothing based on continuous ultrasonic welding technology
Authors: Shi Hui , Wang Jianping , Chen Xiaona , Luo Shunhua , Zhang Lingxi 
Published: April 2016

Purpose
An improved waterproof seam production technology (ultrasonic welding-thermo adhesive tape sealing (USW-TATS)) was developed in this study. The technology will improve the waterproof performance of seam which has problem resulted from needle holes and thread like seam leaking and excess shrinkage.

Design/methodology/approach
Threadless seams were produced by ultrasonic welding (USW) with coated and lamination fabric to replace the traditional sewing process in Sewing-thermo adhesive tape sealing (S-TATS). The process efficiency was evaluated by Methods-Time Measurement (MTM). Seam performance including hydrostatic pressure, shrinkage and tear force was compared among three technologies (USW, USW-TATS and S-TATS). The effect of ultrasonic welding parameters (amplitude, roller pressure and roller speed) on the USW-TATS seam performance was investigated.SEM analysis was carried out to examine the condition and morphology of the joints cross section.

Findings
It was found that waterproof performance and dimensional stability of USW-TATS seam were superior to that of S-TATS seam. Tear force and hydrostatic pressure increased firstly and then decreased with the increasing of USW parameters in UAW-TATS process. Binary regression relationships were found between the USW parameters and tear force or hydrostatic pressure. Shrinkage decreased with the increasing of roller pressure and speed.

Practical implications
Research results can be applied to predict seam performance of waterproof clothing, reduce equipment parameters setting time and enhance product quality in industry.

Originality/value
A threadless production technology (USW-TATS) was proposed to improve waterproof performance and dimensional stability of outdoor clothing seams.
Numerical simulation of top roller pressure and deformation in ring spinning with three draft zones using finite element method
Authors: Zhang Xiaojuan , Wu Juan , Xu Bojun , Liu Xinjin 
Published: April 2016

Purpose
This paper presented a new kind of ring spinning frame with four pairs of rollers, and they are the front roller and the front top roller, the first middle roller (FMR) and the first middle top roller (FMTR), the second middle roller and the second middle top roller, the back roller and the back top roller. The FMR is the front roller of middle draft zone, and the back roller of the front draft zone. Therefore, the deformation of FMTR during spinning is an important factor for yarn quality, which was studied in this paper.

Design/methodology/approach
In this paper, by finite element method (FEM), the pressure and deformation of FMTR were studied. FMTR made from steel and sleeved carbon fiber were compared. 5.8tex, 4.9tex and 3.9tex cotton yarns were spun, and corresponding numerical simulations of FMTR pressure and deformation were presented in ANSYS software and comparatively analyzed. Then, corresponding yarn qualities were compared.

Findings
The results indicate that pressure and deformation of FMTR have little effects on yarn tenacity and hairiness, while have great effects on yarn evenness. For 5.8tex and 4.9tex cotton yarn, yarns spun by FMTR made from sleeved carbon fiber have larger pressure and deformation at the middle of nipper bites of FMR and FMTR, and yarn evenness is better. For 3.9tex cotton yarns, at the middle of nipper bites of FMR and FMTR, FMTR made from steel has smaller pressure. But deformation of FMTR made from steel is larger, and yarn evenness is better.

Originality/value
This paper studied pressure and deformation of FMTR by finite element method (FEM), which serve as a theoretical underpinning for yarn spinning in three draft zones ring spinning machine.
Belief systems enforcing female genital mutilation in Europe
Authors: Alhassan Yussif Nagumse , Barrett Hazel , Brown Katherine E , Kwah Kayleigh 
Published: April 2016

Purpose
– Despite numerous studies on FGM, little is known about belief systems that support FGM in the EU. The purpose of this paper is to explore the dynamic nature of belief systems and enforcement mechanisms that perpetuate FGM among three African migrant communities in the EU.

Design/methodology/approach
– This paper is based on data collected through community-based participatory action research in three communities: Eritrean and Ethiopian community in Palermo, Italy; Guinea Bissauan community in Lisbon, Portugal; and Senegalese and Gambian community in Banyoles, Spain. A total of 24 FGDs and 70 in-depth narrative interviews were conducted for the research.

Findings
– The research finds that belief systems supporting the practice of FGM among African migrants in the European diaspora are similar to those in their home countries. Beliefs structured around religion, sexuality, decency, marriage and socialisation are particularly significant in perpetuating FGM in the study migrant communities. These are enforced through sanctions and social expectations from the migrants’ home and host communities.

Research limitations/implications
– Members of the migrant communities that were the focus of this research are ethnically diverse; therefore it is possible that differences in the practice of and views on FGM by various ethnicities may have been masked. Also, due to close linkages between the migrants and their home countries it was hard to delineate beliefs that are specific to the host countries. In addition, it was difficult to assess the level of education of the migrants and how this may have impacted on their beliefs due to their contrasting and inconsistent educational backgrounds.

Originality/value
– This paper provides evidence to show that the practice of FGM among migrants in the EU is driven by both social norms and individual (parent) behaviour and therefore there is a need for interventions to focus on individual behaviour change and social norm transformation techniques. It also suggests that beliefs around FGM have remained socially significant among migrants despite their exposure to European culture because such beliefs are used to promote the moral standards of girls, marriageability of women, respectability of families, and the assertion of cultural and religious identity in the migrants’ new environment. The paper further underscores the role of migrants’ European context as well as the home country in strengthening beliefs that perpetuate FGM in the EU.
Male perspectives on FGM among communities of African heritage in Italy
Authors: Catania Lucrezia , Mastrullo Rosaria , Caselli Angela , Cecere Rosa , Abdulcadir Omar , Abdulcadir Jasmine 
Published: April 2016

Purpose– The purpose of this paper is to investigate the attitudes, knowledge and beliefs regarding female genital mutilation/cutting (FGM/C) of six groups of immigrant men from countries where FGM/C is practiced and to identify their role in the decision-making process of circumcising their daughters.Design/methodology/approach– The study took the form of qualitative action research with seven focus groups of 50 men coming from Somalia, Eritrea, Ethiopia, Benin, Egypt and Nigeria, living in Florence, Italy.Findings– Different conceptions, cultures and attitudes about FGM/C exist among men coming from different countries, but also within the same community. The participants expressed positions both in favor and against the maintenance of the practice. There were opposite beliefs about the religious motivations invoked.Research limitations/implications– The study is qualitative and the non-probability sample and the small number of participants are important limitations.Practical implications– The study improves current knowledge on men’s role and attitude in FGM/C and gives important information for the prevention of future activities that could include both men and women of the community.Social implications– The need to involve men in preventive actions against FGM/C has been underlined by the World Health Organization. The involvement of men and leaders of the communities could facilitate cultural changes toward the abandoning of these practices. FGM/C is often considered as a phenomenon concerning only women, who are frequently left alone to face the decision of whether to abandon the ritual.Originality/value– The great advantage of conducting such a study in a country of migration is the presence of different communities, with different cultural views, in the same area.
Time trends in educational inequalities in cancer mortality in Colombia, 1998–2012
Authors: de Vries Esther , Arroyave Ivan , Pardo Constanza 
Published: April 2016

ObjectivesTo evaluate trends in premature cancer mortality in Colombia by educational level in three periods: 1998–2002 with low healthcare insurance coverage, 2003–2007 with rapidly increasing coverage and finally 2008–2012 with almost universal coverage (2008–2012).SettingColombian population-based, national secondary mortality data.ParticipantsWe included all (n=188 091) cancer deaths occurring in the age group 20–64 years between 1998 and 2012, excluding only cases with low levels of quality of registration (n=2902, 1.5%).Primary and secondary outcome measuresIn this descriptive study, we linked mortality data of ages 20–64 years to census data to obtain age-standardised cancer mortality rates by educational level. Using Poisson regression, we modelled premature mortality by educational level estimating rate ratios (RR), relative index of inequality (RII) and the Slope Index of Inequality (SII).ResultsRelative measures showed increased risks of dying among the lower educated compared to the highest educated; this tendency was stronger in women (RRprimary1.49; RRsecondary1.22, both p<0.0001) than in men (RRprimary1.35; RRsecondary1.11, both p<0.0001). In absolute terms (SII), cancer caused a difference per 100 000 deaths between the highest and lowest educated of 20.5 in males and 28.5 in females. RII was significantly higher among women and the younger age categories. RII decreased between the first and second periods; afterwards (2008–2012), it increased significantly back to their previous levels. Among women, no significant increases or declines in cancer mortality over time were observed in recent periods in the lowest educated group, whereas strong recent declines were observed in those with secondary education or higher.ConclusionsEducational inequalities in cancer mortality in Colombia are increasing in absolute and relative terms, and are concentrated in young age categories. This trend was not curbed by increases in healthcare insurance coverage. Policymakers should focus on improving equal access to prevention, early detection, diagnostic and treatment facilities.
Improving referrals for tilt table testing in patients with transient loss of consciousness
Authors: Thornton Luke , Rahunathan Nithusa , Verma Narain , Wong Kenneth 
Published: April 2016

Tilt table testing has been used for over twenty years in the investigation of patients with transient loss of consciousness. The European Society of Cardiology (ESC) recently recommended new guidance regarding indications for tilt table testing. We conducted an educational intervention and produced a new referral proforma that referring clinicians are expected to fill in for all patients referred for tilt table testing. At baseline, 76% (n=84) of referrals for tilt table testing were made in accordance to ESC guidance.Following a simple educational intervention, 100% (n=6) were in line with ESC guidance. After the introduction of the referral proforma, 92% (n=12) of referrals followed ESC guidance. At final data collection, 100% (n=11) of referrals followed ESC guidance. In conclusion, a simple educational intervention and the use of a referral proforma in this quality improvement project have made a sustained difference in improving the appropriateness of referrals for tilt table testing. This has the potential to optimise the efficient use of resources and improve patient care through avoiding unnecessary investigation.
Three-dimensional image fusion of CTA and angiography for real-time guidance during neurointerventional procedures
Authors: Zhang Qiang , Sun Qi , Zhang Yiqi , Zhang Hao , Shan Tonghui , Han Jingfeng , Pan Wenlong , Gu Chuanqi , Xu Ruxiang 
Published: April 2016

AimTo evaluate the accuracy of three-dimensional (3D) images from two modalities—CT angiography (CTA) and digital subtraction angiography (DSA). Additionally, to explore the value of using preprocedural CTA for real-time guidance during neurointerventional procedures.Materials and methods25 patients with CTA-confirmed cerebral arterial lesions were enrolled. For 12 of these patients, 3D DSA images of the contrast medium-enhanced target vessel were acquired during the intervention and registered with the preprocedurally acquired CTA images for evaluation of the accuracy of image fusion, focusing on the target vessel and the lesion. For the other 13 patients, a low-dose non-contrast 3D angiographic scan was performed. The preprocedurally acquired CTA image was then registered with the coordinate of angiography and overlaid onto the live fluoroscopic image to provide interventional guidance.ResultsBased on visual inspection by two experienced physicians and quantitative evaluation, excellent accuracy in the 3D registration of the CTA and DSA was achieved for all 12 patients examined. Additionally, CTA could be used successfully to guide the interventional procedures, including both diagnostic DSA and stent treatment. The radiation dose and contrast medium use were compared with those used by conventional interventional procedures and both were found to be significantly reduced.Conclusions3D CTA and angiographic image fusion was approved as highly accurate for neurovasculature. Additionally, using the fusion technique to guide interventional procedures enhanced the workflow, and required much less radiation exposure and contrast medium use, thus helping to reduce potential risks and increase treatment safety.
Elemental analysis of erythrocytes in patients with chronic liver diseases positive for hepatitis C virus
Authors: Nagamine Takeaki , Kasamatsu Tetsuhiro , Murakami Kazuhiro , Kohka Masashi , Satoh Takahiro , Tomihiro Takahiro , Goto Shoko , Sera Koichiro 
Published: April 2016

The present study aimed to evaluate the relationship between elemental changes in erythrocytes and hepatogenous anemia. Five chronic hepatitis C, five liver cirrhosis (HCV positive) and three healthy controls were enrolled in this study. Using in-air micro-PIXE, we determined that K rods formed small nodule and Cl rods distributed diffusely in all over erythrocytes, resulting in disappearance of the donut-like pattern of erythrocytes. These findings may reect the alternation of ery- throcyte membrane structures. Fe dots were divided into two to four compartments in erythrocytes of control group, and the similar distribution of Fe rods was shown in those of chronic hepatitis and liver cirrhosis. Na concentrations analyzed by in-vacuum PIXE were significantly higher in liver cirrhosis than in chronic hepatitis and control, possibly because of the disturbance of Na–K pump. Present study suggests that the alternation of erythrocyte membrane and Na–K pump failure may participate in hepatogenous anemia accompanied with liver cirrhosis.