bluuebunny/crossref_metadata_2025 huggingface dataset:
Reorganization of actin filaments by ADF/cofilin is involved in formation of microtubule structures duringXenopusoocyte maturation
Authors: Yamagishi Yuka , Abe Hiroshi
Published: October 2015

We examined the reorganization of actin filaments and microtubules during Xenopus oocyte maturation. Surrounding the germinal vesicle (GV) in immature oocytes, the cytoplasmic actin filaments reorganized to accumulate beneath the vegetal side of the GV, where the microtubule-organizing center and transient microtubule array (MTOC-TMA) assembled, just before GV breakdown (GVBD). Immediately after GVBD, both Xenopus ADF/cofilin (XAC) and its phosphatase Slingshot (XSSH) accumulated into the nuclei and intranuclear actin filaments disassembled from the vegetal side with the shrinkage of the GV. As the MTOC-TMA developed well, cytoplasmic actin filaments were retained at the MTOC-TMA base region. Suppression of XAC dephosphorylation by anti-XSSH antibody injection inhibited both actin filament reorganization and proper formation and localization of both the MTOC-TMA and meiotic spindles. Stabilization of actin filaments by phalloidin also inhibited formation of the MTOC-TMA and disassembly of intranuclear actin filaments without affecting nuclear shrinkage. Nocodazole also caused the MTOC-TMA and the cytoplasmic actin filaments at its base region to disappear, which further impeded disassembly of intranuclear actin filaments from the vegetal side. XAC appears to reorganize cytoplasmic actin filaments required for precise assembly of the MTOC and, together with the MTOC-TMA, regulate the intranuclear actin filament disassembly essential for meiotic spindle formation.
Intraflagellar transport is essential for mammalian spermiogenesis but is absent in mature sperm
Authors: San Agustin Jovenal T. , Pazour Gregory J. , Witman George B.
Published: October 2015

Drosophila sperm are unusual in that they do not require the intraflagellar transport (IFT) system for assembly of their flagella. In the mouse, the IFT proteins are very abundant in testis, but we here show that mature sperm are completely devoid of them, making the importance of IFT to mammalian sperm development unclear. To address this question, we characterized spermiogenesis and fertility in the Ift88Tg737Rpwmouse. This mouse has a hypomorphic mutation in the gene encoding the IFT88 subunit of the IFT particle. This mutation is highly disruptive to ciliary assembly in other organs. Ift88−/−mice are completely sterile. They produce ∼350-fold fewer sperm than wild-type mice, and the remaining sperm completely lack or have very short flagella. The short flagella rarely have axonemes but assemble ectopic microtubules and outer dense fibers and accumulate improperly assembled fibrous sheath proteins. Thus IFT is essential for the formation but not the maintenance of mammalian sperm flagella.
ANARCI: antigen receptor numbering and receptor classification
Authors: Dunbar James , Deane Charlotte M.
Published: October 2015

Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate residue positions, their definitions of position equivalence and their popularity within different scientific disciplines. However, currently no publicly available software exists that can apply all the most widely used schemes or for which an executable can be obtained under an open license.

Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences. It can annotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMGT and AHo.

Availability and implementation: ANARCI is available for download under GPLv3 license at opig.stats.ox.ac.uk/webapps/anarci. A web-interface to the program is available at the same address.

Contact:  deane@stats.ox.ac.uk
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis
Authors: Mahieu Nathaniel G. , Spalding Jonathan L. , Patti Gary J.
Published: October 2015

Motivation: Current informatic techniques for processing raw chromatography/mass spectrometry data break down under several common, non-ideal conditions. Importantly, hydrophilic liquid interaction chromatography (a key separation technology for metabolomics) produces data which are especially challenging to process. We identify three critical points of failure in current informatic workflows: compound specific drift, integration region variance, and naive missing value imputation. We implement the Warpgroup algorithm to address these challenges.

Results: Warpgroup adds peak subregion detection, consensus integration bound detection, and intelligent missing value imputation steps to the conventional informatic workflow. When compared with the conventional workflow, Warpgroup made major improvements to the processed data. The coefficient of variation for peaks detected in replicate injections of a complex Escherichia Coli extract were halved (a reduction of 19%). Integration regions across samples were much more robust. Additionally, many signals lost by the conventional workflow were ‘rescued’ by the Warpgroup refinement, thereby resulting in greater analyte coverage in the processed data.

Availability and  i  mplementation: Warpgroup is an open source R package available on GitHub at github.com/nathaniel-mahieu/warpgroup. The package includes example data and XCMS compatibility wrappers for ease of use.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  nathaniel.mahieu@wustl.edu or gjpattij@wustl.edu
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Authors: Okonechnikov Konstantin , Conesa Ana , García-Alcalde Fernando
Published: October 2015

Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.

Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.

Availability and implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.

Contact:  meyer@mpiib-berlin.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Child Abuse Mimic
Authors: Deutsch Stephanie Anne , Long Christopher J. , Srinivasan Arun K. , Wood Joanne N.
Published: October 2015

Sexual abuse of children is prevalent in today's society. In 2012, approximately 686,000 children (9.2 per 1000) in the United States were determined to be victims of substantiated child abuse and neglect, according to national data compiled by child protective service agencies; victimization rates were highest for children younger than 1 year. Nearly 9.3% of maltreated children were victims of sexual abuse, this finding was reported by US Department of Health and Human Services (http://www.acf.hhs.gov/programs/cb/research-data-technology/statistics-research/child-maltreatment). Previous research has shown that as many as 1 in 3 girls and 1 in 7 boys will be sexually abused during childhood (Child Abuse Negl. 2003;27:1205–1222). Although sexual abuse seems to be less common in boys than girls, this may be partly due to underdiagnosis and underreporting of sexual abuse in boys (Arch Dis Child. 2007;92:328–331). Clinicians should therefore consider the possibility of sexual abuse when boys present with genital injuries, because failing to recognize and diagnose sexual abuse can pose an ongoing safety risk to a child. However, an erroneous diagnosis of sexual abuse can have equally hazardous repercussions, including removal of a child from their caregivers or prosecution of an innocent individual. A number of medical conditions can mimic child sexual abuse injuries, including anal fissures, failure of midline fusion, perianal streptococcal dermatitis, and straddle injury (J Pediatr Health Care. 2009;23:283–288 and Acta Paediatr. 2011;100:590–593). The following case involves a 5-week-old male infant who presented to the pediatric emergency department with an avulsion injury to his penis concerning for sexual abuse. He was ultimately diagnosed with a relatively rare anatomic variant of the genitalia and determined to have sustained an accidental injury whose appearance mimicked abuse.
TRPA1 tunes mosquito thermotaxis to host temperatures
Authors: Corfas Román A. , Vosshall Leslie B.
Published: October 2015

While most ectotherms thermotax only to regulate their temperature, female mosquitoes are attracted to human body heat during pursuit of a blood meal. Here we elucidate the basic rules ofAedes aegyptithermotaxis and test the function of candidate thermoreceptors in this important behavior. We show that host-seeking mosquitoes are maximally attracted to thermal stimuli approximating host body temperatures, seeking relative warmth while avoiding both relative cooling and stimuli exceeding host body temperature. We found that the cation channelTRPA1,in addition to playing a conserved role in thermoregulation and chemosensation, is required for this specialized host-selective thermotaxis in mosquitoes. During host-seeking,AaegTRPA1-/-mutants failed to avoid stimuli exceeding host temperature, and were unable to discriminate between host-temperature and high-temperature stimuli.TRPA1-dependent tuning of thermotaxis is likely critical for mosquitoes host-seeking in a complex thermal environment in which humans are warmer than ambient air, but cooler than surrounding sun-warmed surfaces.
Modelling the role of immunity in reversion of viral antigenic sites
Authors: Chan Carmen H. S. , Sanders Lloyd P. , Tanaka Mark M.
Published: October 2015

Antigenic sites in viral pathogens exhibit distinctive evolutionary dynamics due to their role in evading recognition by host immunity. Antigenic selection is known to drive higher rates of non-synonymous substitution; less well understood is why differences are observed between viruses in their propensity to mutate to a novel or previously encountered amino acid. Here, we present a model to explain patterns of antigenic reversion and forward substitution in terms of the epidemiological and molecular processes of the viral population. We develop an analytical three-strain model and extend the analysis to a multi-site model to predict characteristics of observed sequence samples. Our model provides insight into how the balance between selection to escape immunity and to maintain viability is affected by the rate of mutational input. We also show that while low probabilities of reversion may be due to either a low cost of immune escape or slowly decaying host immunity, these two scenarios can be differentiated by the frequency patterns at antigenic sites. Comparison between frequency patterns of human influenza A (H3N2) and human RSV-A suggests that the increased rates of antigenic reversion in RSV-A is due to faster decaying immunity and not higher costs of escape.
Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
Authors: Mellis Ian A. , Raj Arjun
Published: October 2015

Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines.
The Mendelian disorders of the epigenetic machinery
Authors: Bjornsson Hans Tomas
Published: October 2015

The Mendelian disorders of the epigenetic machinery are genetic disorders that involve disruption of the various components of the epigenetic machinery (writers, erasers, readers, and remodelers) and are thus expected to have widespread downstream epigenetic consequences. Studying this group may offer a unique opportunity to learn about the role of epigenetics in health and disease. Among these patients, neurological dysfunction and, in particular, intellectual disability appears to be a common phenotype; however, this is often seen in association with other more specific features in respective disorders. The specificity of some of the clinical features raises the question whether specific cell types are particularly sensitive to the loss of these factors. Most of these disorders demonstrate dosage sensitivity as loss of a single allele appears to be sufficient to cause the observed phenotypes. Although the pathogenic sequence is unknown for most of these disorders, there are several examples where disrupted expression of downstream target genes accounts for a substantial portion of the phenotype; hence, it may be useful to systematically map such disease-relevant target genes. Finally, two of these disorders (Rubinstein-Taybi and Kabuki syndromes) have shown post-natal rescue of markers of the neurological dysfunction with drugs that lead to histone deacetylase inhibition, indicating that some of these disorders may be treatable causes of intellectual disability.
Biological data sciences in genome research
Authors: Schatz Michael C.
Published: October 2015

The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.
The Veiled Chameleon (Chamaeleo calyptratus Duméril and Duméril 1851): A Model for Studying Reptile Body Plan Development and Evolution
Authors: Diaz Raul E. , Anderson Christopher V. , Baumann Diana P. , Kupronis Richard , Jewell David , Piraquive Christina , Kupronis Jill , Winter Kristy , Bertocchini Federica , Trainor Paul A.
Published: October 2015

Vertebrate model organisms have facilitated the discovery and exploration of morphogenetic events and developmental pathways that underpin normal and pathological embryological events. In contrast to amniotes such as Mus musculus (Mammalia) and Gallus gallus (Aves), our understanding of early patterning and developmental events in reptiles (particularly nonavians) remains weak. Squamate reptiles (lizards, snakes, and amphisbaenians) comprise approximately one-third of all living amniotes. But studies of early squamate development have been limited because, in most members of this lineage, embryo development at the time of oviposition is very advanced (limb bud stages and older). In many cases, squamates give birth to fully developed offspring. However, in the veiled chameleon (Chamaeleo calyptratus), embryos have progressed only to a primitive pregastrula stage at the time of oviposition. Furthermore, the body plan of the veiled chameleon is highly specialized for climbing in an arboreal environment. It possesses an entire suite of skeletal and soft anatomical modifications, including cranioskeletal ornamentation, lingual anatomy and biomechanics for projection, autopodial clefting for grasping, adaptations for rapid integumental color changes, a prehensile tail with a lack of caudal autotomy, the loss of the tympanum in the middle ear, and the acquisition of turreted eyes. Thus, C. calyptratus is an important model organism for studying the role of ecological niche specialization, as well as genetic and morphological evolution within an adaptive framework. More importantly, this species is easily bred in captivity, with only a small colony (<10 individuals) needed to obtain hundreds of embryos every year.
Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years
Authors: Kemp Christopher J.
Published: October 2015

The identification of carcinogens in the workplace, diet, and environment through chemical carcinogenesis studies in animals has directly contributed to a reduction of cancer burden in the human population. Reduced exposure to these carcinogens through lifestyle changes, government regulation, or change in industry practices has reduced cancer incidence in exposed populations. In addition to providing the first experimental evidence for cancer's relationship to chemical and radiation exposure, animal models of environmentally induced cancer have and will continue to provide important insight into the causes, mechanisms, and conceptual frameworks of cancer. More recently, combining chemical carcinogens with genetically engineered mouse models has emerged as an invaluable approach to study the complex interaction between genotype and environment that contributes to cancer development. In the future, animal models of environmentally induced cancer are likely to provide insight into areas such as the epigenetic basis of cancer, genetic modifiers of cancer susceptibility, the systems biology of cancer, inflammation and cancer, and cancer prevention.
Improving the use of physical manipulatives in teaching science concepts through lesson study
Authors: Tan Rolando M.
Published: October 2015

Purpose

– The purpose of this paper is to present how lesson study can be instrumental in improving the use of physical manipulatives that are used in teaching elementary science topics.

Design/methodology/approach

– Objectives are achieved through the following means: first, planning a research lesson in the workshop; second, presentation and critiquing in a seminar workshop; third, implementing the research lesson with observation of co-teachers and knowledgeable other; fourth, post lesson discussion; and fifth, revising the research lesson.

Findings

– The research lesson improved significantly after the first post lesson discussion as the concrete to abstract approach was used and the defect of the physical manipulative (eardrum model) was addressed to avoid possible misconceptions from pupils during discussions as part of the formative assessment portion of the lesson.

Research limitations/implications

– The lesson study process was not further extended to the third and fourth implementation to see other problems in the use of their physical manipulative (eardrum) model.

Practical implications

– The need for teachers to use the physical manipulative as an analogical model in teaching science concepts.

Originality/value

– The paper shows the effectiveness of lesson study in the development of manipulative models in instruction.
Peer-learning between pre-service teachers: embracing Lesson Study
Authors: Lamb Penny
Published: October 2015

Purpose

– The purpose of this paper is to explore a model of Lesson Study owned entirely by pre-service teachers (PSTs), conveying its potential to facilitate mutual spaces of learning between peers beyond formal hierarchical relationships with expert teachers. Fuller’s (1969) conceptual framework of teacher development informed the study, consisting of self, task and impact “phases of concern”.

Design/methodology/approach

– Participants were secondary physical education PSTs (n=17), completing a university-led postgraduate certificate in education course. Action research methodology was adopted during school placements, when PSTs engaged in Lesson Study with peers. Data obtained through a group discussion board, individual questionnaires and interviews, were subjected to inductive analysis, with key patterns compared to locate themes.

Findings

– All PSTs felt Lesson Study contributed positively to their training, reinforcing perceived benefits of cycles of action for planning, observing a lesson, reviewing and adapting the plan before re-teaching the revised plan. Findings reveal increased confidence in reducing self and task concerns through four emergent themes: acquiring content and pedagogical knowledge; developing the planning process; understanding individual learners’ needs; and embedding reflective practice. Mutually supportive peer-learning environments created pedagogic space beyond formal mentoring processes, augmenting learning to teach and the understanding of learners’ needs.

Research limitations/implications

– Endorsement of Lesson Study by PSTs as a method of engaging in a positive peer-learning climate suggests the workability of this model.

Originality/value

– Findings contribute to existing literature exploring the effectiveness and impact of Lesson Study within initial teacher education.
Smart city intellectual capital: an emerging view of territorial systems innovation management
Authors: Dameri Renata P. , Ricciardi Francesca
Published: October 2015

Purpose

– The purpose of this paper is to explore whether and how the intellectual capital (IC) approach and concepts could be fruitfully adapted to study the smart city phenomenon from a managerial point of view.

Design/methodology/approach

– This study is based on a long-term, in-depth ethnographic exploration of the vast global community, which is created around the smart city movement.

Findings

– The analysis suggests that, in order to effectively analyse a smart city context through the IC lens, the traditional IC framework needs to be extended for: expected outcomes, which should also include sustainability, resilience and quality of life; categories of key resources, which should also include institutional capital and environmental capital; units of analysis, which should also include territorial systems, such as transportation or waste; and key managerial challenges implied. As a final result, a smart city intellectual capital (SC-IC) framework is proposed.

Research limitations/implications

– Most of the cases analysed in this study are European; further studies are advisable to better investigate non-European smart city contexts.

Practical implications

– The paper suggests that the knowledge management, project portfolio management and network management approaches are crucial to better support managerial practices in smart city organizations.

Originality/value

– The SC-IC framework allows for a clear definition of the smart city organization, as a new knowledge-based, project-oriented, network-shaped type of organization. Therefore, the SC-IC framework provides smart city research with a consistent rooting in management studies. Further, this paper contributes to the fourth stage of IC research.
The relational capital of the IT department
Authors: Zardini Alessandro , Ricciardi Francesca , Rossignoli Cecilia
Published: October 2015

Purpose

– The purpose of this paper is to shed light on how the relational capital of the information technology (IT) department creates value in organizations. In addition, the paper presents a multi-dimensional scale to measure and manage relational capital in the IT department.

Design/methodology/approach

– In the first, explorative phase of the study, interviews and focus groups were conducted in order to develop a new measurement scale, which was subsequently tested through a survey questionnaire (212 respondents).

Findings

– This research suggests that the relational capital of the IT department is a very important resource for the creation of strategic value. The statistical analysis conducted for this study confirmed the validity and reliability of the novel scale developed to measure this resource. Finally, thanks to factor analysis, five dimensions for the scale were identified.

Research limitations/implications

– Data were collected in northern Italy only. Further studies are advisable to confirm the validity of the constructs and scale.

Practical implications

– The questionnaire presented in this study can be used to monitor the effectiveness of the interactions between the IT department and the other key actors involved in IT-enabled innovation. The adoption of this scale and its possible adaptation to specific, evolving business contexts may enhance the practitioner’s understanding of the role of relational capital in the value creation process.

Originality/value

– The paper contributes to the “third stage” of intellectual capital research by concentrating on an intra-organizational level of analysis, which has been overlooked in the literature to date.
Understanding the importance of small patches of habitat for conservation
Authors: Tulloch Ayesha I. T. , Barnes Megan D. , Ringma Jeremy , Fuller Richard A. , Watson James E. M.
Published: October 2015

Conservation activities in fragmented landscapes have largely focused on keeping remaining large patches intact, often disregarding the increasingly important role of smaller patches in the conservation of remaining vegetation. As habitat loss proceeds in fragmented landscapes, there is an increasing need to measure the relative contribution of all patches (large and small) to overall ecosystem persistence, in a way that helps deliver effective conservation strategies aimed at preventing the death of ecosystems by a thousand cuts.

Using Australian vegetation communities as a case study, we calculated the historical change in the contribution of patches below different sized thresholds to overall extent. We introduced a new patch assessment metric based on the Gini coefficient that indicates how unequal the distribution of patch sizes is relative to historical distributions.

At least 22% of major vegetation communities in Australia have >50% of their remaining extent in patches <1000 ha. Loss does not always match fragmentation status: though some vegetation communities are exposed to the double jeopardy of high loss and high fragmentation, others are far more affected by fragmentation than loss of extent.

For some communities, actions focused on protecting large patches are critical but for many others, protecting and managing small patches is crucial for community persistence.

Synthesis and applications. Arbitrary patch size thresholds for permitting native vegetation clearing are dangerous for ecosystems whose distribution is now restricted to small patches. We recommend that clearing thresholds be scaled to reflect the fact that some ecosystems are more dominated by small patches than others. With a renewed focus on formally assessing the threat status of ecosystems as well as species, ecosystem accounts such as those demonstrated in this study are the first step to reliably assessing vulnerability. Measures of ecosystem vulnerability that only consider the extent of vegetation loss and not the size of remaining patches are likely to be ineffective for impact assessment, conservation planning and preventing ecosystem loss.
Europe's refugee crisis
Authors: Albahari Maurizio
Published: October 2015

In this guest editorial Maurizio Albahari considers the refugee crisis, Europe's worst since WWII. Does this crisis represent a critical turning point?
Restrictions on Foreign Investments and the Relocation of Firms
Authors: Dong Quan , Bárcena‐Ruiz Juan Carlos , Garzón María Begoña
Published: October 2015

We analyse why the Chinese government sets restrictions on foreign direct investment (FDI). We focus our analysis on the percentage of shares in relocated firms that the government allows to be foreign‐owned. The government's decision on this percentage depends on the entry cost, the number of firms that relocate and the weight of the consumer surplus in the objective function of the government. We show that by its choice of this percentage, the Chinese government may restrict or encourage FDI to its country. We also find that if the government may subsidise the fixed entry cost, it provides a subsidy only when the producer surplus has a greater weight than the consumer surplus in weighted welfare. In that case, the subsidy encourages relocation by both firms and permits the government to allow a lower percentage of shares to be foreign‐owned in relocated firms.
A 3–year follow‐up after anterior colporrhaphy compared with collagen‐coated transvaginal mesh for anterior vaginal wall prolapse: a randomised controlled trial
Authors: Rudnicki M , Laurikainen E , Pogosean R , Kinne I , Jakobsson U , Teleman P
Published: September 2015

Objective

To compare the 1–year (previously published) and 3–year objective and subjective cure rates, and complications, related to the use of a collagen‐coated transvaginal mesh for anterior vaginal wall prolapse against a conventional anterior repair.

Design

Randomised controlled study.

Setting

Six departments of obstetrics and gynaecology in Norway, Sweden, Finland, and Denmark.

Population

A total of 138 women, of 55 years of age or older, admitted for stage ≥2 anterior vaginal wall prolapse.

Methods

The women scheduled for primary anterior vaginal wall prolapse surgery were randomised between conventional anterior colporrhaphy and surgery with a collagen‐coated prolene mesh. All patients were evaluated using the Pelvic Organ Prolapse Quantification (POP–Q) assessment before and after surgery. Symptoms related to pelvic organ prolapse were evaluated using the Pelvic Floor Impact Questionnaire (PFIQ–7) and the Pelvic Floor Distress Inventory (PFDI–20).

Main outcome measures

Objective cure, defined as POP–Q stage <2 prolapse at the 1‐ and 3–year follow‐ups. Furthermore, mesh exposure and dyspareunia were also recorded.

Results

In total, 138 patients (70 from the mesh group versus 68 from the conventional anterior colporrhaphy group) out of 160 (86.3%) participated in the 3–year follow‐up. POP–Q revealed an objective anatomic cure for 88.1 and 91.4%, respectively, in the mesh group at the 1‐ and 3–year follow‐ups, compared with 39.9 and 41.2% in the colporrhaphy group. No difference between the groups was observed regarding PFIQ–7, PFDI–20, and Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ–12) scores. The number of mesh exposures did not change during the study period and all exposures were minor.

Conclusion

Our study demonstrates that although the objective outcome was superior in the mesh group, the use of mesh had no impact on the subjective outcome.

Tweetable abstract

POP–Q deteriorates after anterior prolapse surgery but remains stable in women with mesh implantation.
Appropriateness of Prostate Cancer Imaging among Veterans in a Delivery System without Incentives for Overutilization
Authors: Makarov Danil V. , Hu Elaine Y. C. , Walter Dawn , Braithwaite R. Scott , Sherman Scott , Gold Heather T. , Zhou Xiao‐Hua Andrew , Gross Cary P. , Zeliadt Steven B.
Published: October 2015

Objective

To determine the frequency of appropriate and inappropriate prostate cancer imaging in an integrated health care system.

Data Sources/Study Setting

Veterans Health Administration Central Cancer Registry linked to VA electronic medical records and Medicare claims (2004–2008).

Study Design

We performed a retrospective cohort study of VA patients diagnosed with prostate cancer (N = 45,084). Imaging (CT, MRI, bone scan, PET) use was assessed among patients with low‐risk disease, for whom guidelines recommend against advanced imaging, and among high‐risk patients for whom guidelines recommend it.

Principal Findings

We found high rates of inappropriate imaging among men with low‐risk prostate cancer (41 percent) and suboptimal rates of appropriate imaging among men with high‐risk disease (70 percent). Veterans utilizing Medicare‐reimbursed care had higher rates of inappropriate imaging [OR: 1.09 (1.03–1.16)] but not higher rates of appropriate imaging. Veterans treated in middle [OR: 0.51 (0.47–0.56)] and higher [OR: 0.50 (0.46–0.55)] volume medical centers were less likely to undergo inappropriate imaging without compromising appropriate imaging.

Conclusions

Our results highlight the overutilization of imaging, even in an integrated health care system without financial incentives encouraging provision of health care services. Paradoxically, imaging remains underutilized among high‐risk patients who could potentially benefit from it most.
The Effect of Mortgage Payment Reduction on Default: Evidence from the Home Affordable Refinance Program
Authors: Zhu Jun , Janowiak Jared , Ji Lu , Karamon Kadiri , McManus Douglas
Published: October 2015

This article evaluates the effect of payment reduction on mortgage default within the context of the Home Affordable Refinance Program. We find that mortgage default is sensitive to payment reduction using univariate, duration and hazard modeling approaches. A relative risk Cox model of default with time‐varying covariates estimates that a 10% reduction in mortgage payment is associated with about a 10–11% reduction in monthly default hazard for loans. This finding is robust to the inclusion of empirically important mortgage risk drivers (such as current loan‐to‐value and FICO score) as well as controlling for selection effects based on observables.
The Cost of Foreclosure Delay
Authors: Cordell Larry , Geng Liang , Goodman Laurie S. , Yang Lidan
Published: October 2015

We measure the cost of foreclosure delay by estimating time‐related foreclosure costs using a large national sample of residential mortgages before, during, and after the recent U.S. housing crisis. The large volume of foreclosures, coupled with an unprecedented series of government interventions in mortgage servicing practices, significantly extended foreclosure timelines during and after the crisis.  Costs were especially pronounced in judicial review states, which saw average foreclosure costs go up 15 percentage points, 24 percentage points in the highest cost state.  Cost increases of this magnitude are likely to have consequences for servicing practices and mortgage credit availability.
Mitochondrial capture enriches mito‐DNA 100 fold, enabling PCR‐free mitogenomics biodiversity analysis
Authors: Liu Shanlin , Wang Xin , Xie Lin , Tan Meihua , Li Zhenyu , Su Xu , Zhang Hao , Misof Bernhard , Kjer Karl M. , Tang Min , Niehuis Oliver , Jiang Hui , Zhou Xin
Published: October 2015

Biodiversity analyses based on next‐generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR‐free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR‐free methods will inevitably result in a huge excess of data (>99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www.1kite.org). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by approximately 100‐fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias in abundance. However, the frequencies of input taxa were largely maintained after capture (R2 = 0.81). We suggest that our mitogenome capture approach coupled with PCR‐free shotgun sequencing could provide ecological researchers an efficient NGS method to deliver reliable biodiversity assessment.
DNA barcodes from century‐old type specimens using next‐generation sequencing
Authors: Prosser Sean W. J. , deWaard Jeremy R. , Miller Scott E. , Hebert Paul D. N.
Published: October 2015

Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next‐generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century‐old type specimens of Lepidoptera by attempting to recover 164‐bp and 94‐bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164‐bp sequence), medium (94‐bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR‐based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
Type 5 adenylyl cyclase disruption leads to enhanced exercise performance
Authors: Vatner Dorothy E. , Yan Lin , Lai Lo , Yuan Chujun , Mouchiroud Laurent , Pachon Ronald E. , Zhang Jie , Dillinger Jean‐Guillaume , Houtkooper Riekelt H. , Auwerx Johan , Vatner Stephen F.
Published: October 2015

The most important physiological mechanism mediating enhanced exercise performance is increased sympathetic, beta adrenergic receptor (β‐AR), and adenylyl cyclase (AC) activity. This is the first report of decreased AC activity mediating increased exercise performance. We demonstrated that AC5 disruption, that is, knock out (KO) mice, a longevity model, increases exercise performance. Importantly for its relation to longevity, exercise was also improved in old AC5 KO. The mechanism resided in skeletal muscle rather than in the heart, as confirmed by cardiac‐ and skeletal muscle‐specific AC5 KO's, where exercise performance was no longer improved by the cardiac‐specific AC5 KO, but was by the skeletal muscle‐specific AC5 KO, and there was no difference in cardiac output during exercise in AC5 KO vs. WT. Mitochondrial biogenesis was a major mechanism mediating the enhanced exercise. SIRT1, FoxO3a, MEK, and the anti‐oxidant, MnSOD were upregulated in AC5 KO mice. The improved exercise in the AC5 KO was blocked with either a SIRT1 inhibitor, MEK inhibitor, or by mating the AC5 KO with MnSOD hetero KO mice, confirming the role of SIRT1, MEK, and oxidative stress mechanisms. The Caenorhabditis elegans worm AC5 ortholog, acy‐3 by RNAi, also improved fitness, mitochondrial function, antioxidant defense, and lifespan, attesting to the evolutionary conservation of this pathway. Thus, decreasing sympathetic signaling through loss of AC5 is not only a mechanism to improve exercise performance, but is also a mechanism to improve healthful aging, as exercise also protects against diabetes, obesity, and cardiovascular disease, which all limit healthful aging.
Interactions Between Chronic Ethanol Consumption and Thiamine Deficiency on Neural Plasticity, Spatial Memory, and Cognitive Flexibility
Authors: Vedder Lindsey C. , Hall Joseph M. , Jabrouin Kimberly R. , Savage Lisa M.
Published: September 2015

Background

Many alcoholics display moderate to severe cognitive dysfunction accompanied by brain pathology. A factor confounded with prolonged heavy alcohol consumption is poor nutrition, and many alcoholics are thiamine deficient. Thus, thiamine deficiency (TD) has emerged as a key factor underlying alcohol‐related brain damage (ARBD). TD in humans can lead to Wernicke Encephalitis that can progress into Wernicke–Korsakoff syndrome and these disorders have a high prevalence among alcoholics. Animal models are critical for determining the exact contributions of ethanol (EtOH)‐ and TD‐induced neurotoxicity, as well as the interactions of those factors to brain and cognitive dysfunction.

Methods

Adult rats were randomly assigned to 1 of 6 treatment conditions: chronic EtOH treatment (CET) where rats consumed a 20% v/v solution of EtOH over 6 months; severe pyrithiamine‐induced TD (PTD‐moderate acute stage); moderate PTD (PTD‐early acute stage); moderate PTD followed by CET (PTD‐CET); moderate PTD during CET (CET‐PTD); and pair‐fed (PF) control. After recovery from treatment, all rats were tested on spontaneous alternation and attentional set‐shifting. After behavioral testing, brains were harvested for determination of mature brain‐derived neurotrophic factor (BDNF) and thalamic pathology.

Results

Moderate TD combined with CET, regardless of treatment order, produced significant impairments in spatial memory, cognitive flexibility, and reductions in brain plasticity as measured by BDNF levels in the frontal cortex and hippocampus. These alterations are greater than those seen in moderate TD alone, and the synergistic effects of moderate TD with CET lead to a unique cognitive profile. However, CET did not exacerbate thalamic pathology seen after moderate TD.

Conclusions

These data support the emerging theory that subclinical TD during chronic heavy alcohol consumption is critical for the development of significant cognitive impairment associated with ARBD.
Segregation and Inequality in Public Goods
Authors: Trounstine Jessica
Published: October 2015

Many U.S. cities function without regular problems. They have well‐kept roads, sewers that never overflow, and public parks with swing sets and restrooms. Others struggle to maintain balanced budgets, fail to adequately equip or staff their police forces, and offer little assistance to residents of limited means. What explains these differences? I argue that segregation along racial lines contributes to public goods inequalities. Racially segregated cities are also politically polarized cities, making collective investment more challenging and public goods expenditures lower. I provide evidence for this argument using election data from 25 large cities and demographic data matched to city finances in more than 2,600 places. To handle the problem of endogeneity, I instrument for segregation using the number of waterways in a city. I find that segregated municipalities are more politically polarized and spend less on a wide range of public goods.
Unfree Radicals: Geoscientists, the Anthropocene, and Left Politics
Authors: Castree Noel
Published: October 2015

Neil Smith's writings about capitalism and what we call “nature” were insightful and influential. This paper asks what Smith would make of the “radical turn” today occurring in the world of international geoscience. If we “think with” Smith, how should we view Naomi Klein's recent statement that geoscientists can act as fifth columnists calling the capitalist way of life into question? In the first half of the essay I address these questions. I summarise and apply the insights of Smith's writings to recent developments in international geoscience. Smith wrote about science in most of his published statements about capitalist ecology and I show that he would ultimately have regarded Klein as hopeful, even naïve. I then go on, in the second half of the essay, to “think against” Smith. I suggest his views on science bespeak a wider, unhelpful separation between Left scholarship in the social sciences and humanities and the STEM subjects (science, technology, engineering, and medicine). Recalling earlier attempts to radicalise science politically, and highlighting the radical potentials of geoscience today, I make the case for forms of interdisciplinarity that might render geoscience more political. Though this case opens space for perspectives beyond the Marxism Smith did so much to develop, he would—I hope—see it as a legitimate part of the Left's long war against capitalism's rule over society and environment.
Colectomy for constipation: time trends and impact based on the US Nationwide Inpatient Sample, 1998–2011
Authors: Dudekula A. , Huftless S. , Bielefeldt K.
Published: October 2015

Background

Current guidelines include subtotal colectomy as treatment for refractory slow transit constipation.

Aim

To use the US Nationwide Inpatient Sample (NIS) (1998–2011) and longitudinal data from the State Inpatient Database (2005–2011), comparable to NIS, to examine colectomy rates, in‐hospital morbidity and emergency department (ED) visits or readmissions among patients treated for constipation.

Methods

Colectomies for any reason were identified based on the primary procedural code (ICD‐9‐CM 45.8x). Index hospitalisations were defined by the primary diagnosis of constipation (ICD‐9‐CM 564.x) associated with the primary procedural code for colectomy (ICD‐9‐CM45.8x) after exclusion of other diseases associated with colectomy. Demographic variables, comorbidities, complications and adverse events during the hospitalisation were captured, and ED visits and admissions were recorded for periods before and after colectomy.

Results

Nationally, colectomies for constipation rose from 104 procedures in 1998 (1.2% of annual colectomies) to 311 in 2011 (2.4% of annual colectomies). While there were no perioperative deaths, perioperative complications occurred in 42.7% of patients during the index hospitalisation. Longitudinal data were analysed for 181 patients, with similar perioperative complications and a readmission rate of 28.9% within the first 30 days after the index hospitalisation. Resource utilisation was tracked for a median time of 630 (0–2386) before and 463 (0–2204) days after colectomy with unchanged ED visits (median: 2 vs. 2, P = 0.21), but increased hospitalisations (median: 1 vs. 2, P = 0.003).

Conclusions

Colectomy rates for constipation are rising, are associated with significant morbidity and do not decrease resource utilisation, raising questions about the true benefit of surgery for slow transit constipation.