bluuebunny/crossref_metadata_2025 huggingface dataset:
Racialization of Subaltern Populations across the Globe: The Politics of Difference
Authors: Pandey Gyanendra
Published: November 2015

The politics of difference - also named race or racism in various critical discourses - is the focus of this essay. The charge of being deviant, uncultured, “illegal” and out of place is leveled in a variety of ways, by those who claim the status of natural belonging, against subordinated and marginalized groups - from immigrants recently arrived in a place, to ancient inhabitants driven away from their lands and property and opportunities. The issue is not one of race but of racism, or what I describe as the deployment of difference. Whether grounded in genetic or biological condition, as it was in the 19th and early 20th centuries, or described more euphemistically as very deeply rooted (even if its sources supposedly lie in “history” and “culture”), the proposition commonly is that the difference at hand is not really bridgeable - at least in the foreseeable future. The deployment of such arguments of radical, incommensurable difference very often marks a shifting of weight from a barely acknowledged to a much more palpable prejudice and discrimination. A disdainful tolerance of groups that were generally ignored, that counted for little and sometimes remained literally uncounted, gives way to an increased marking and targeting of otherised communities.
Ego depletion: Applications and implications for auditing research
Authors: Hurley Patrick J.
Published: November 2015

In this paper, I synthesize the prior psychology literature on ego depletion and apply this literature to an auditing setting. Ego depletion refers to a reduced desire or ability to use self-control in task performance due to using self-control on prior tasks. I focus on the likely causes and consequences of depletion in an auditing setting, as well as means of mitigating depletion and recovering self-control resources. While ego depletion theory is prevalent in the psychology literature, little is known about whether or how ego depletion affects professionals on meaningful task performance. As a result, this synthesis is aimed at stimulating future ego depletion research in accounting, and specifically auditing, by surveying existing literature and applying this literature to an auditing setting. Further, I develop 13 questions for future research to investigate. My synthesis reveals that ego depletion likely has a pervasive effect in an auditing setting, and can hinder auditors’ judgment and decision-making (JDM) quality. Therefore, this synthesis helps to provide a greater understanding of the impact of auditing tasks on individuals, and refines both auditor JDM and ego depletion theories.
Brief report: Past, present, emergent and future identities of young inmates
Authors: Solomontos‐Kountouri Olga , Hatzittofi Panayiota
Published: November 2015

This study aims to investigate how young inmates integrate temporal and contextual elements of identity and what is the role of education in identity integration. Twenty‐six young inmates were interviewed. Thematic analysis revealed that inmates integrated the elements of four time identities using different mechanisms to deal with each identity: (a) Past identity (before imprisonment) is defined by cumulative risk factors, where detachment from family, society, and institutions prevails; (b) present identity is characterized by the engagement in prison's educational activities; (c) emergent identity (until their release) is characterized by their requests for a proper education and training and their commitment to acquire qualifications; (d) future identity (after their release) is characterized by the investment on future aims for personal growth, family, education/work and community. Inmates used the non‐formal educational program, which was offered in prison, as a vehicle towards positive identity contemplation.
Cystatin C attenuates insulin signaling transduction by promoting endoplasmic reticulum stress in hepatocytes
Authors: Ji Xiaolin , Yao Lili , Wang Meihong , Liu Xiaoyu , Peng Su , Li Kaixuan , Xu Muchen , Shen Ningmei , Luo Lan , Sun Cheng
Published: November 2015

It has been reported that cystatin c (Cys C) closely correlates with metabolic disorders such as obesity and diabetes. However, it is still unknown whether Cys C plays a role for these disorders. Our results showed that the insulin signal transduction was largely impaired by Cys C in hepatocytes. In myotubes, however, the insulin signal transduction was not affected. Following experiments revealed that Cys C could induce endoplasmic reticulum stress (ER stress) in hepatocytes, whereas Cys C had no such an effect in myotubes. The alleviation of ER stress by 4‐Phenyl butyric acid (4‐PBA) restored the impaired insulin signal transduction in Cys C‐treated hepatocytes. These results provided direct evidence that, by inducing ER stress, Cys C impairs insulin signal transduction in hepatocytes.
Specific mutations in mammalian P4‐ATPase ATP8A2 catalytic subunit entail differential glycosylation of the accessory CDC50A subunit
Authors: Vestergaard Anna L. , Mikkelsen Stine A. , Coleman Jonathan A. , Molday Robert S. , Vilsen Bente , Andersen Jens Peter
Published: November 2015

P4‐ATPases, or flippases, translocate phospholipids between the two leaflets of eukaryotic biological membranes. They are essential to the physiologically crucial phospholipid asymmetry and involved in severe diseases, but their molecular structure and mechanism are still unresolved. Here, we show that in an extensive mutational alanine screening of the mammalian flippase ATP8A2 catalytic subunit, five mutations stand out by leading to reduced glycosylation of the accessory subunit CDC50A. These mutations may disturb the interaction between the subunits.
The impact of antiphospholipid antibodies in children with lupus nephritis
Authors: Al-Mayouf Sulaiman M. , AlSaleem Alhanouf , Al-Hussain Turki , Al Sonbul Abdullah , AlMana Hadeel
Published: November 2015

Background and objectives:

To evaluate the frequency of antiphospholipid anti-bodies (APLa) among patients with childhood lupus nephritis (cLN) and to assess their impact on long-term renal outcomes.

Design and setting:

This is an observational hospital based study.

Patients and methods:

Patients with cLN diagnosed by renal biopsy seen between January 2002 and June 2014 were included. APLa positivity was defined if detection was positive on 2 occa-sions 6-12 weeks apart during their follow up. Demographic features, age at disease onset, disease duration, follow-up duration and clinical and laboratory variables at the time of renal biopsy were collected. The renal biopsy was reviewed for the nephritis class, microthrombi, activity and chronicity indices. Renal outcome measures included the serum creatinine levels, protein/creatinine ratio and end stage renal disease (ESRD).

Results:

Fifty-nine, (49 female) patients with a mean age of 19.8 years and mean disease dura-tion of 6.8 years were involved. APLa were detected in 46 (78%) patients. Twenty-two patients had class IV nephritis, which was more prevalent in APLa positive patients. The frequencies of class III and V nephritis was similar in 10 patients in each class (7 patients in each class with APLa). The presence of APLa did not correlate with nephritis activity or the chronicity indices. Microthrombosis was found in 10 patients, and 8 of them had APLa. Patients with APLa had a higher frequency of elevated serum creatinine and hypertension, 9 developed ESRD, and 7 had APLa. There was no statistically significant association between the presence of APLa and the accrual damage index and clinical manifestations. Furthermore, there was no association be-tween APLa and other autoantibodies.

Conclusion:

The frequency of APLa in cLN was high. While the association is not statistically significant, APLa positive patients tend to develop renal microthrombi and are probably at higher risk of ESRD.
Ellis van Creveld syndrome in a Tunisian child revealed by an Eisenmenger syndrome
Authors: Ajmi Houda , Ruiz Perez Victor L. , Hassayoun Saida , Mabrouk Sameh , Mahdoui Sana , Boughzela Essia , Zouari Noura , Abroug Saoussan
Published: November 2015

Ellis-van Creveld syndrome (EvC) is an autosomal recessive inherited disease result-ing from mutations in EVC1 or EVC2. Patients with this condition normally have chondrodyspla-sia, postaxial polydactyly, ectodermal dysplasia and congenital heart defects. We report the case of a 13-year-old Tunisian child who was admitted for cyanosis and acute heart failure. On clinical examination, he presented with typical features of EvC, cyanosis and dyspnea. EvC was confirmed by genetic tests, and echocardiography showed a partial atrioventricular canal defect with supra-systemic pulmonary artery pressure. The patient was treated; howev-er, the evolution was fatal.
The Effect of Body Mass Index on Fluoroscopic Time and Radiation Dose During Sacroiliac Joint Injections
Authors: Cushman Daniel , Flis Alexandra , Jensen Ben , McCormick Zachary
Published: November 2015

Background

Sacroiliac joint (SIJ) injections are commonly performed under fluoroscopic guidance. Radiation exposure to patients and providers has not been comprehensively studied, particularly the effect of body mass index (BMI).

Objective

To identify whether patients with a larger BMI require longer fluoroscopy time or a larger radiation dose during performance of an SIJ injection.

Design

Retrospective study of an academic institution database.

Setting

Academic outpatient musculoskeletal clinic.

Patients

All patients who underwent SIJ injections during a 10‐year period.

Main Outcome Measurements

Machine‐reported fluoroscopic time and machine‐reported radiation dose. A Bonferroni correction was implemented with P ≤ .01 as statistically significant.

Results

A total of 453 SIJ injections were performed in 359 patients. No statistically significant differences in fluoroscopy time were found between patients with BMI scores identified as normal, overweight, and obese (P = .054). However, the radiation doses were significantly greater for patients with higher BMI scores (χ2 [2, n = 441] = 62.4, P < .001); the median (interquartile range) doses were 1210 (839), 1671 (1240), and 2090 (2170) mGy‐cm2 for normal weight, overweight, and obese patients, respectively. Although longer needles were used more often in obese patients (χ2 [2, n = 452] = 31.5, P < .001), fluoroscopy time was not associated with needle length (P = .162). No relationships were identified between fluoroscopy time and first‐time (as opposed to repeat) injection (P = .123), trainee involvement (χ2 [1, n = 698] = 3.9, P = .049), or age (P = .337).

Conclusions

Patients with an elevated BMI score who are undergoing SIJ injection receive an increased radiation dose despite equivalent fluoroscopic time. This finding suggests that the increased dose is likely due to x‐ray output from the fluoroscope traversing a greater tissue mass, as opposed to the physician requiring more fluoroscopic images for proper needle placement. Fortunately, the increased radiation dose delivered to patients with a larger BMI score likely has negligible effects.
Who are Non-Resident Fathers?: A British Socio-Demographic Profile
Authors: POOLE ELOISE , SPEIGHT SVETLANA , O’BRIEN MARGARET , CONNOLLY SARA , ALDRICH MATTHEW
Published: November 2015

Despite international growth of, and policy interest in, divorce and separation since the 1970s, there is still surprisingly little known about non-residential fatherhood. This paper presents a ‘father-centric’ analysis and provides one of the first profiles of non-residential fatherhood in early millennium UK. Using data from Understanding Society Wave 1, a nationally representative survey of over 30,000 households in the UK, we found 1,070 men self-identifying as having a non-resident child under 16 years old (https://www.understandingsociety.ac.uk). We estimate a prevalence of 5 per cent of British men having a non-resident dependent child. Through latent class analysis, four distinct groups of non-resident fathers are identified: ‘Engaged’ fathers, ‘Less Engaged’ fathers, ‘Disengaged’ fathers and ‘Distance’ fathers. Our analysis finds that non-resident fathers form a heterogeneous group in terms of their socio-demographic profile and family behaviour. It is recommended that legislation and policy concerning fathers in post-separation families are sensitive to variation as well as commonality in socio-economic conditions and family lives and situations.
Good Holders, Bad Shufflers: An Examination of Working Memory Processes and Modalities in Children with and without Attention-Deficit/Hyperactivity Disorder
Authors: Simone Ashley N. , Bédard Anne-Claude V. , Marks David J. , Halperin Jeffrey M.
Published: November 2015

The aim of this study was to examine working memory (WM) modalities (visual-spatial and auditory-verbal) and processes (maintenance and manipulation) in children with and without attention-deficit/hyperactivity disorder (ADHD). The sample consisted of 63 8-year-old children with ADHD and an age- and sex-matched non-ADHD comparison group (N=51). Auditory-verbal and visual-spatial WM were assessed using the Digit Span and Spatial Span subtests from the Wechsler Intelligence Scale for Children Integrated - Fourth Edition. WM maintenance and manipulation were assessed via forward and backward span indices, respectively. Data were analyzed using a 3-way Group (ADHD vs. non-ADHD)×Modality (Auditory-Verbal vs. Visual-Spatial)×Condition (Forward vs. Backward) Analysis of Variance (ANOVA). Secondary analyses examined differences between Combined and Predominantly Inattentive ADHD presentations. Significant Group×Condition (p=.02) and Group×Modality (p=.03) interactions indicated differentially poorer performance by those with ADHD on backward relative to forward and visual-spatial relative to auditory-verbal tasks, respectively. The 3-way interaction was not significant. Analyses targeting ADHD presentations yielded a significant Group×Condition interaction (p=.009) such that children with ADHD-Predominantly Inattentive Presentation performed differentially poorer on backward relative to forward tasks compared to the children with ADHD-Combined Presentation. Findings indicate a specific pattern of WM weaknesses (i.e., WM manipulation and visual-spatial tasks) for children with ADHD. Furthermore, differential patterns of WM performance were found for children with ADHD-Predominantly Inattentive versus Combined Presentations. (JINS, 2016, 22, 1–11)
Slow-Moving Glide Avalanches Still Pack a Punch
Authors: McGuire Nancy
Published: November 2015

Predicting glide avalanches and explaining how they work are difficult tasks, but the forces they exert can be calculated fairly well.
Nucleotide-binding mechanisms in pseudokinases
Authors: Hammarén Henrik M. , Virtanen Anniina T. , Silvennoinen Olli
Published: November 2015

Pseudokinases are classified by the lack of one or several of the highly conserved motifs involved in nucleotide (nt) binding or catalytic activity of protein kinases (PKs). Pseudokinases represent ∼10% of the human kinome and they are found in all evolutionary classes of kinases. It has become evident that pseudokinases, which were initially considered somewhat peculiar dead kinases, are important components in several signalling cascades. Furthermore, several pseudokinases have been linked to human diseases, particularly cancer, which is raising interest for therapeutic approaches towards these proteins. The ATP-binding pocket is a well-established drug target and elucidation of the mechanism and properties of nt binding in pseudokinases is of significant interest and importance. Recent studies have demonstrated that members of the pseudokinase family are very diverse in structure as well as in their ability and mechanism to bind nts or perform phosphoryl transfer reactions. This diversity also precludes prediction of pseudokinase function, or the importance of nt binding for said function, based on primary sequence alone. Currently available data indicate that ∼40% of pseudokinases are able to bind nts, whereas only few are able to catalyse occasional phosphoryl transfer. Pseudokinases employ diverse mechanisms to bind nts, which usually occurs at low, but physiological, affinity. ATP binding serves often a structural role but in most cases the functional roles are not precisely known. In the present review, we discuss the various mechanisms that pseudokinases employ for nt binding and how this often low-affinity binding can be accurately analysed.
Glycogen synthase kinase-3-mediated phosphorylation of serine 73 targets sterol response element binding protein-1c (SREBP-1c) for proteasomal degradation
Authors: Dong Qingming , Giorgianni Francesco , Beranova-Giorgianni Sarka , Deng Xiong , O'Meally Robert N. , Bridges Dave , Park Edwards A. , Cole Robert N. , Elam Marshall B. , Raghow Rajendra
Published: November 2015

Sterol regulatory element binding protein-1c (SREBP-1c) is a key transcription factor that regulates genes involved in the de novo lipid synthesis and glycolysis pathways. The structure, turnover and transactivation potential of SREBP-1c are regulated by macronutrients and hormones via a cascade of signalling kinases. Using MS, we have identified serine 73 as a novel glycogen synthase kinase-3 (GSK-3) phosphorylation site in the rat SREBP-1c purified from McA-RH7777 hepatoma cells. Our site-specific mutagenesis strategy revealed that the turnover of SREBP-1c, containing wild type, phospho-null (serine to alanine) or phospho-mimetic (serine to aspartic acid) substitutions, was differentially regulated. We show that the S73D mutant of pSREBP-1c, that mimicked a state of constitutive phosphorylation, dissociated from the SREBP-1c–SCAP complex more readily and underwent GSK-3-dependent proteasomal degradation via SCFFbw7 ubiquitin ligase pathway. Pharmacologic inhibition of GSK-3 or knockdown of GSK-3 by siRNA prevented accelerated degradation of SREBP-1c. As demonstrated by MS, SREBP-1c was phosphorylated in vitro by GSK-3β at serine 73. Phosphorylation of serine 73 also occurs in the intact liver. We propose that GSK-3-mediated phosphorylation of serine 73 in the rat SREBP-1c and its concomitant destabilization represents a novel mechanism involved in the inhibition of de novo lipid synthesis in the liver.
Intra-tumoral IFN-γ-producing Th22 cells correlate with TNM staging and the worst outcomes in pancreatic cancer
Authors: Niccolai Elena , Taddei Antonio , Ricci Federica , Rolla Simona , D'Elios Mario Milco , Benagiano Marisa , Bechi Paolo , Bencini Lapo , Ringressi Maria Novella , Pini Alessandro , Castiglione Francesca , Giordano Daniele , Satolli Maria Antonietta , Coratti Andrea , Cianchi Fabio , Bani Daniele , Prisco Domenico , Novelli Francesco , Amedei Amedeo
Published: November 2015

PDAC (pancreatic ductal adenocarcinoma) is the fifth leading cause of cancer-related death. The causes of this cancer remain unknown, but increasing evidence indicates a key role of the host immune response and cytokines in human carcinogenesis. Intra-tumoral IL (interleukin)-22 levels have been shown to be elevated in PDAC patients. However, little is known regarding the expression and clinical relevance of Th22 cells in human PDAC and, furthermore, which TILs (tumour-infiltrating lymphocytes) are the main producers of IL-22 is unknown. In the present study, we characterized the functional proprieties of the different subsets of IL-22-producing TILs and analysed their relationship with the TNM staging system and patient survival. We have demonstrated for the first time that, in PDAC patients, the T-cells co-producing IFN-γ (interferon γ) and exerting perforin-mediated cytotoxicity are the major intra-tumoral source of IL-22. In addition, isolated Th22 cells were able to induce apoptosis, which was antagonized by IL-22. Finally, we observed that the IL-22-producing T-cells were significantly increased in tumour tissue and that this increase was positively correlated with TNM staging of PDAC and poorer patient survival. These novel findings support the dual role of the anti-tumour immune system and that IL-22-producing cells may participate in PDAC pathogenesis. Therefore monitoring Th22 levels could be a good diagnostic parameter, and blocking IL-22 signalling may represent a viable method for anti-PDAC therapies.
Characterizing general scale-free networks by vertex-degree sequences
Authors: Xiao Wenjun , Lai Zhengwen , Chen Guanrong
Published: November 2015

Many complex networks possess a scale-free vertex-degree distribution in a power-law form of ck−γ, where k is the vertex-degree variable and c and γ are constants. To better understand the mechanism of the power-law formation in scale-free networks, it is important to understand and analyze their vertex-degree sequences. We had shown before that, for a scale-free network of size N, if its vertex-degree sequence is k1<k2<⋯1, then the length l of the vertex-degree sequence is of order log N. In the present paper, we further study complex networks with a more general vertex-degree distribution, not restricted to the power-law, and prove that the same conclusion holds as well. In addition, we verify the new result by real data from a large number of real-world examples. We finally discuss some potential applications of the new finding in various fields of science, technology, and society.
Signalling via glutamate and GLRs in Arabidopsis thaliana
Authors: Weiland Matthias , Mancuso Stefano , Baluska Frantisek
Published: November 2015

The genome of Arabidopsis thaliana (L. Heynh.) contains 20 coding sequences for homologues of animal ionotropic glutamate receptors. These glutamate receptor-like receptors act as sensors and mediators of a multitude of exogenous as well as endogenous signals and are found in all analysed plant species. Their molecular structure clearly indicates a function as integral membrane proteins with a ligand-gated ion channel activity. Altered gene expressions and the occurrence of mRNA splice variants confer a high flexibility on the gene as well as on the RNA level. An individual glutamate receptor of A. thaliana is able to bind two different ligands (most probable amino acids and their derivatives), whereas a functional receptor complex is likely to consist of four single proteins. These features enable an immense number of sensitivities against various local and temporal stimuli. This review encompasses the last 15 years of research concerning glutamate signalling and glutamate receptors in plants. It is aimed at summarising their major characteristics and involvements to obtain a broader and farer reaching perspective of these fundamental components of plant signal transduction.
Prescription rates of the contraceptive implant in Australia 2008–2012: impact of patient age and area of residence
Authors: Bingham Amie L. , Garrett Cameryn C. , Kavanagh Anne M. , Keogh Louise A. , Bentley Rebecca J. , Hocking Jane S.
Published: November 2015

Background
Long-acting reversible contraceptives are an effective means of preventing unwanted pregnancies and associated negative consequences. The Sexual Health and Family Planning Association of Australia has called for efforts to address barriers to the uptake of long-acting reversible contraceptives (LARCs) in Australia, where LARC uptake is thought to be low, though comprehensive data describing use and associated factors is scarce. The aims of this study were to describe patterns of prescriptions for the etonogestrel-releasing subdermal implant (SDI) in Australia, 2008–2012, and associated factors. Methods: Records of prescriptions written through Australia’s Pharmaceutical Benefits Scheme from 2008 to 2012 were obtained, including patient age and geographic location. Direct, age-standardised rates (ASR) of prescriptions were calculated for each year and location, with multivariate analysis used to examine associations between prescription rates and patient age, location and proximity to family planning clinics (FPC) or Aboriginal Medical Services (AMS). Results: ASR of prescriptions rose ~6% per year (OR 1.06, 95%CI: 1.05–1.06) from 13.05 per 1000 (2008) to 15.76 per 1000 (2012; P < 0.01). Rates were highest among 15- to 19-year-olds, increasing from 20.81 (2008) to 29.09 per 1000 (2012: P < 0.01) and lowest among 45- to 49-year-olds, increasing from 3.37 to 3.73 per 1000 (P < 0.01). ASR by location were significantly higher in regional than metropolitan areas. Conclusions:This is the first analysis of SDI prescriptions across all ages and regions of Australia. Uptake of SDI in Australia is increasing but remains low. Significant associations were found between prescription rates and patient age and residence in regional/remote areas.
Reliable ABC model choice via random forests
Authors: Pudlo Pierre , Marin Jean-Michel , Estoup Arnaud , Cornuet Jean-Marie , Gautier Mathieu , Robert Christian P.
Published: November 2015

Motivation: Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques.

Results: We propose a novel approach based on a machine learning tool named random forests (RF) to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with RF and postponing the approximation of the posterior probability of the selected model for a second stage also relying on RF. Compared with earlier implementations of ABC model choice, the ABC RF approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least 50) and (iv) it includes an approximation of the posterior probability of the selected model. The call to RF will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets.

Availability and implementation: The proposed methodology is implemented in the R package abcrf available on the CRAN.

Contact:  jean-michel.marin@umontpellier.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
hybridSPAdes: an algorithm for hybrid assembly of short and long reads
Authors: Antipov Dmitry , Korobeynikov Anton , McLean Jeffrey S. , Pevzner Pavel A.
Published: November 2015

Motivation: Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.

Results: We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.

Availability and implementation:  hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades

Contact:  d.antipov@spbu.ru

Supplementary information:  supplementary data are available at Bioinformatics online.
ParTIES: a toolbox for Paramecium interspersed DNA elimination studies
Authors: Denby Wilkes Cyril , Arnaiz Olivier , Sperling Linda
Published: November 2015

Motivation: Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.

Results: We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.

Availability and implementation: ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.

Contact:  linda.sperling@i2bc.paris-saclay.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effects of elevated CO2 on early life history development of the yellowtail kingfish, Seriola lalandi, a large pelagic fish
Authors: Munday Philip L. , Watson Sue-Ann , Parsons Darren M. , King Alicia , Barr Neill G. , Mcleod Ian M. , Allan Bridie J. M. , Pether Steve M. J.
Published: November 2015

An increasing number of studies have examined the effects of elevated carbon dioxide (CO2) and ocean acidification on marine fish, yet little is known about the effects on large pelagic fish. We tested the effects of elevated CO2 on the early life history development and behaviour of yellowtail kingfish, Seriola lalandi. Eggs and larvae were reared in current day control (450 µatm) and two elevated CO2 treatments for a total of 6 d, from 12 h post-fertilization until 3 d post-hatching (dph). Elevated CO2 treatments matched projections for the open ocean by the year 2100 under RCP 8.5 (880 µatm CO2) and a higher level (1700 µatm CO2) relevant to upwelling zones where pelagic fish often spawn. There was no effect of elevated CO2 on survival to hatching or 3 dph. Oil globule diameter decreased with an increasing CO2 level, indicating potential effects of elevated CO2 on energy utilization of newly hatched larvae, but other morphometric traits did not differ among treatments. Contrary to expectations, there were no effects of elevated CO2 on larval behaviour. Activity level, startle response, and phototaxis did not differ among treatments. Our results contrast with findings for reef fish, where a wide range of sensory and behavioural effects have been reported. We hypothesize that the absence of behavioural effects in 3 dph yellowtail kingfish is due to the early developmental state of newly hatched pelagic fish. Behavioural effects of high CO2 may not occur until larvae commence branchial acid–base regulation when the gills develop; however, further studies are required to test this hypothesis. Our results suggest that the early stages of kingfish development are tolerant to rising CO2 levels in the ocean.
Geographic variation in subantarctic fur seal pup growth: linkages with environmental variability and population density
Authors: Oosthuizen W. Chris , de Bruyn P. J. Nico , Wege Mia , Bester Marthán N.
Published: November 2015

Marine predator populations are sensitive to temporal variation in prey availability, but prey dynamics are often difficult to quantify. Long-term measures of offspring growth is a useful performance attribute to gauge the potential demographic direction for such predator populations, especially where other metrics (e.g., population size estimates) are lacking. Subantarctic fur seal ( Arctocephalus tropicalis ) females are central place foragers during a protracted lactation period, and their foraging success determines the growth and vitality of their offspring. Using data spanning over 2 decades, we assessed geographic and temporal variation in growth rates and weaning mass of subantarctic fur seal pups at 2 of the species’ principal populations (Gough and Marion islands) and identified environmental conditions that may, through assumed bottom-up mechanisms, affect body mass at weaning. While Marion Island pups grew at an average rate of between 0.040 and 0.067kg/day early in lactation (comparable to conspecific growth at Amsterdam Island), the mean growth rate at Gough Island (approximately 0.030kg/day) was lower than the growth rate represented by the bottom 5% of the body mass distribution at Marion Island. Notwithstanding substantial interannual variability, we found support for a negative trend in weaning mass at both populations, suggesting a rise in limiting factors that is hypothesized to relate to concurrent local population size increases. Weaning mass tended to be higher when sea surface temperatures were warmer (with a stronger positive effect at Gough Island) and during positive phases of the Southern Oscillation Index (La Niña events), with a stronger positive effect in males. Given the low weaning mass of Gough Island fur seal pups, continued population growth here seems unlikely. While density-dependent regulation appears to have increased in strength at Marion Island, terminating rapid population growth, current weaning weights remain above the physiological limits of growth in subantarctic fur seals.
On the use of the number count of blue horizontal branch stars to infer the dominant building blocks of the Milky Way halo
Authors: Chung Chul , Lee Young-Wook , Pasquato Mario
Published: November 2015

The formation of the Milky Way stellar halo is thought to be the result of merging and accretion of building blocks such as dwarf galaxies and massive globular clusters. Recently, Deason et al. suggested that the Milky Way outer halo formed mostly from big building blocks, such as dwarf spheroidal galaxies, based on the similar number ratio of blue straggler (BS) stars to blue horizontal branch (BHB) stars. Here we demonstrate, however, that this result is seriously biased by not taking into detailed consideration on the formation mechanism of BHB stars from helium-enhanced second-generation population. In particular, the high BS-to-BHB ratio observed in the outer halo fields is most likely due to a small number of BHB stars provided by globular clusters (GCs) rather than to a large number of BS stars. This is supported by our dynamical evolution model of GCs which shows preferential removal of first-generation stars in GCs. Moreover, there are a sufficient number of outer halo GCs which show very high BS-to-BHB ratio. Therefore, the BS-to-BHB number ratio is not a good indicator to use in arguing that more massive dwarf galaxies are the main building blocks of the Milky Way outer halo. Several lines of evidence still suggest that GCs can contribute a significant fraction of the outer halo stars.
Carbon production on accreting neutron stars in a new regime of stable nuclear burning
Authors: Keek L. , Heger A.
Published: November 2015

Accreting neutron stars exhibit Type I X-ray bursts from both frequent hydrogen/helium flashes as well as rare carbon flashes. The latter (superbursts) ignite in the ashes of the former. Hydrogen/helium bursts, however, are thought to produce insufficient carbon to power superbursts. Stable burning could create the required carbon, but this was predicted to only occur at much larger accretion rates than where superbursts are observed. We present models of a new steady-state regime of stable hydrogen and helium burning that produces pure carbon ashes. Hot CNO burning of hydrogen heats the neutron star envelope and causes helium to burn before the conditions of a helium flash are reached. This takes place when the mass accretion rate is around 10  per cent of the Eddington limit: close to the rate where most superbursts occur. We find that increased heating at the base of the envelope sustains steady-state burning by steepening the temperature profile, which increases the amount of helium that burns before a runaway can ensue.
The disappearance of the progenitor of SN 2012aw in late-time imaging
Authors: Fraser Morgan
Published: November 2015

We present new late-time near-infrared imaging of the site of the nearby core-collapse supernova SN 2012aw, confirming the disappearance of the point source identified by Fraser et al. and Van Dyk et al. as a candidate progenitor in both J and Ks filters. We remeasure the progenitor photometry, and find that both the J and Ks magnitudes of the source are consistent with those quoted in the literature. We also recover a marginal detection of the progenitor in H-band, for which we measure H = 19.67 ± 0.40 mag. Comparing the luminosity of the progenitor to stellar evolutionary models, SN 2012aw appears to have resulted from the explosion of a 12.5 ± 1.5 M⊙ red supergiant.
West Nile Virus Population Structure, Injury, and Interferon-Stimulated Gene Expression in the Brain From a Fatal Case of Encephalitis
Authors: Grubaugh Nathan D. , Massey Aaron , Shives Katherine D. , Stenglein Mark D. , Ebel Gregory D. , Beckham J. David
Published: November 2015

Background.  West Nile virus (WNV) infection in humans can result in severe, acute encephalitis typically involving subcortical gray matter brain regions. West Nile virus replication within specific human brain regions from a human case of acute encephalitis has not been studied.

Methods.  We describe a fatal case of WNV encephalitis in which we obtained tissue from specific brain regions at autopsy to evaluate viral-host interactions using next-generation sequencing and immunohistochemistry analysis.

Results.  We found that WNV populations in the injured subcortical brain regions exhibited increased amino acid variation and increased expression of specific interferon genes compared with cortical tissues despite similar viral burden.

Conclusions.  These observational, patient-based data suggest that neuronal injury and the strength of viral selection pressure may be associated with the level of the innate immune responses. Further studies in human and animal models evaluating the role of innate immune responses on injury patterns and viral selection pressure are needed.
Three-dimensional distribution of the ISM in the Milky Way galaxy. III. The total neutral gas disk
Authors: Nakanishi Hiroyuki , Sofue Yoshiaki
Published: November 2015

We present newly obtained three-dimensional gaseous maps of the Milky Way Galaxy: H i, H2, and total-gas (H i plus H2) maps, which were derived from the H i and 12CO(J = 1–0) survey data and rotation curves based on the kinematic distance. The H i and H2 face-on maps show that the H i disk is extended to a radius of 15–20 kpc and its outskirts are asymmetric to the Galactic center, while most of the H2 gas is distributed inside the solar circle. The total gas mass within a radius of 30 kpc amounts to 8.0 × 109 M⊙, 89% and 11% of which are H i and H2, respectively. The vertical slices show that the outer H i disk is strongly warped and the inner H i and H2 disks are corrugated. The total gas map is advantageous for tracing spiral structures from the inner to outer disk. Spiral structures such as the Norma–Cygnus, the Perseus, the Sagittarius–Carina, the Scutum–Crux, and the Orion arms are more clearly traced in the total gas map than ever. All the spiral arms are well explained by logarithmic spiral arms with pitch angles of 11°–15°. The molecular fraction of the total gas is high near the Galactic center and decreases with Galactocentric distance. The molecular fraction is also locally enhanced at the spiral arms compared with the inter-arm regions.
Signs of active galactic nucleus quenching in a merger remnant with radio jets
Authors: Ichikawa Kohei , Ueda Junko , Shidatsu Megumi , Kawamuro Taiki , Matsuoka Kenta
Published: November 2015

We investigate optical, infrared, and radio active galactic nucleus (AGN) signs in the merger remnant Arp 187, which hosts luminous jets launched in the order of 105 yr ago but whose present-day AGN activity is still unknown. We find AGN signs from the optical Baldwin–Phillips–Telervich diagram and infrared [O iv] 25.89 μm line, originating from the narrow line regions of AGN. On the other hand, Spitzer/IRS show host galaxy dominated spectra, suggesting that the thermal emission from the AGN torus is considerably small or already diminished. Combining the black hole mass, the upper limit of radio luminosity of the core, and the fundamental plane of the black hole enables us to estimate X-ray luminosity, which gives <1040 erg s−1. Those results suggest that the AGN activity of Arp 187 has already been quenched, but the narrow line region is still alive owing to the time delay of emission from the past AGN activity.
An Expanded Theoretical Framework of Care Coordination Across Transitions in Care Settings
Authors: Radwin Laurel E. , Castonguay Denise , Keenan Carolyn B. , Hermann Cherice
Published: November 2015

For many patients, high-quality, patient-centered, and cost-effective health care requires coordination among multiple clinicians and settings. Ensuring optimal care coordination requires a clear understanding of how clinician activities and continuity during transitions affect patient-centeredness and quality outcomes. This article describes an expanded theoretical framework to better understand care coordination. The framework provides clear articulation of concepts. Examples are provided of ways to measure the concepts.
Frequency-dependent representation of reinforcement-related information in the human medial and lateral prefrontal cortex
Authors: Smith Elliot , Banks Garrett , Mikell Charles , Patel Shaun , Cash Sydney , Eskandar Emad , Sheth Sameer
Published: November 2015

The feedback-related negativity (FRN) is a commonly observed potential in scalp electroencephalography (EEG) studies related to the valence of feedback about a subject's performance. This potential classically manifests as a negative deflection in medial frontocentral EEG contacts following negative feedback. Recent work has shown prominence of theta power in the spectral composition of the FRN, placing it within the larger class of 'frontal midline theta' cognitive control signals. Although the dorsal anterior cingulate cortex (dACC) is thought to be the cortical generator of the FRN, conclusive data regarding its origin and propagation are lacking. Here we examine intracranial electrophysiology from the human medial and lateral prefrontal cortex (PFC) in order to better understand the anatomical localization and communication patterns of the FRN. We show that the FRN is evident in both low- and high-frequency local field potentials (LFPs) recorded on electrocorticography. The FRN is larger in medial compared to lateral PFC, and coupling between theta band phase and high frequency LFP power is also greater in medial PFC. Using Granger causality and conditional mutual information analyses, we provide evidence that feedback-related information propagates from medial to lateral PFC, and that this information transfer oscillates with theta-range periodicity. These results provide evidence for the dACC as the cortical source of the FRN, provide insight into the local computation of frontal midline theta, and have implications for reinforcement learning models of cognitive control.
Polarized Cortical Tension drives Zebrafish Epiboly Movements
Authors: Hernández-Vega Amayra , Marsal María , Pouille Philippe-Alexandre , Tosi Sebastien , Colombelli Julien , Luque Tomás , Navajas Daniel , Pagonabarraga Ignacio , Martín-Blanco Enrique
Published: November 2015

The physical principles underlying the biomechanics of morphogenetic processes are largely unknown. Epiboly is an essential embryonic event in which three distinct tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly and how these are globally coupled remains elusive. Here we first develop a method, Hydrodynamic Regression (HR), to infer 3D dynamic pressure fields, mechanical power densities and cortical surface tension profiles within living organisms. HR is based on velocity measurements retrieved from 2D+T microscopy time-lapses and their hydrodynamic modeling. We then applied this method to identify biomechanically active structures during epiboly in the zebrafish and the changes in the distribution of cortex local tension as epiboly progresses. Based on these results, we propose a novel simple physical description for epiboly, where tissue movements are directed by a polarized gradient of cortical tension. We found that this tensional gradient relies on local contractile forces at the cortex, differences in the elastic properties of cortex components and force passive transmission within the incompressible yolk cell. All in all, our work identifies a novel way to physically regulate concerted cellular movements that will be fundamental for the mechanical control of many morphogenetic processes.
Conjecture: Some auto-immune diseases are caused by the tissue, not a problem with the immune system
Authors: Robins Harlan
Published: November 2015

Applying highly sensitive modern immune profiling techniques to the blood or inflamed tissue of auto-immune patients with one of the common T-cell mediated diseases fails to detect large clonal expansions or other signs of a dysregulated immune system. Additionally, these new methods have shown that self-reactive T-cells are found in the periphery (and are not completely negatively selected in the thymus as previously believed). Combining these new data with well-established studies in auto-immunity leads to the conjecture that certain auto-immune diseases are likely to be caused by defects in tissue, not by dysregulation of the adaptive immune system. In particular, one hypothesis is that specific tissues up-regulate HLA class 2 genes, presenting epitopes that are bound by CD4+helper T cells, which facilitates an immune response against the tissue specific cells.
Genome-wide analysis of microRNA signature in lung adenocarcinoma with EGFR exon 19 deletion
Authors: Ju Lixia , Han Mingquan , Li Xuefei , Zhao Chao
Published: November 2015

Purpose

The findings of EGFR mutations and the development of targeted therapies have significantly improved the overall survival of lung cancer patients. Still, the prognosis remains poor, so we need to know more about the genetic alterations in lung cancer. MicroRNAs are dysregulated in lung cancer, and microRNAs can regulate EGFR. So it is very important to predict the candidate microRNAs that target mutated EGFR and to investigate the role of these candidate microRNAs in lung cancer.

Materials and methods

In this study, we investigated the difference of microRNAs expression between lung adenocarcinoma cell lines with EGFR exon 19 deletion (H1650 and PC9) and its wild-type (H1299 and A549) using the Phalanx Human Whole Genome Microarray. Then the expression of individual microRNAs was validated by qRT-PCR assays. Moreover, we have detected the microRNAs expression in serum of lung adenocarcinoma patients with EGFR exon 19 deletion and wild-type.

Results

The expression of 1,732 microRNAs was evaluated, and we found that microRNAs expression was different between these two groups. Hsa-miR-141-3p, hsa-miR-200c-3p, hsa-miR-203, hsa-miR-3182, hsa-miR-934 were up-regulated and hsa-miR-3196 was down-regulated in the EGFR exon 19 deletion group compared with wild-type group. The detection of circulating microRNAs showed that miR-3196 was down-regulated in lung adenocarcinoma patients with EGFR exon 19 deletion compared with wild-type.

Conclusions

It is suggested that microRNAs associate with EGFR exon 19 deletion and miR-3196 can be further explored for potential predictor and targeted biomarker when it is difficult to get the tumors.