bluuebunny/crossref_metadata_2025 huggingface dataset:
Why Women Request Labiaplasty
Authors: Sorice Sarah C. , Li Alexander Y. , Canales Francisco L. , Furnas Heather J.
Published: March 2017

Background:

In recent years, labiaplasty has jumped in popularity, despite opposition to the procedure. In 2007, the American College of Obstetricians and Gynecologists declared the recommendation of cosmetic vaginal procedures to be “untenable,” although in 2016 they allowed consideration of labiaplasty in adolescents if symptoms persist. The reasons for labiaplasty requests are not yet fully understood, and physician opposition limits patient access to surgical relief.

Methods:

In this prospective study, 50 consecutive patients consulting about labiaplasty were given a questionnaire assessing 11 physical and appearance-related symptoms associated with elongated labia.

Results:

The mean patient age was 33.5 years (range, 17 to 51 years). Fifty-eight percent of women had given birth, 52 percent noticed that their labia had become elongated as they got older, and 93 percent had bilateral elongation. When asked about physical symptoms, over half of patients experienced tugging during intercourse, found tight pants uncomfortable, experienced twisting of the labia, and noted labia visibility in yoga pants. Nearly half experienced pain during intercourse, and 40 percent said their labia could become exposed in bathing suits. Regarding appearance, almost all patients were self-conscious and over half felt less attractive to their partner, experienced restricted clothing choice, and noted a negative impact on self-esteem and intimacy. Nearly all patients experienced at least four symptoms.

Conclusions:

Most patients requesting labiaplasty experience both physical and appearance-related symptoms. Understanding this patient perspective is crucial in assessing surgical outcomes. Furthermore, the better all physicians understand labia symptomatology, the better supported patients will be in seeking surgical relief.
Evolution of a Surgical Philosophy in Orthognathic Surgery
Authors: Rosen Harvey M.
Published: March 2017

A surgical philosophy of orthognathic surgery is presented. It has evolved over an entire surgical career as orthognathic surgical goals have evolved to become primarily aesthetic. In this context, the occlusal result serves as a means of achieving the aesthetic ends. It relies on the physical examination, using qualitative concepts of facial appearance, to be the most important determinant of treatment plans. It makes a distinction between a quantitatively normal face and one that is visually well proportioned and emphasizes the attributes of the soft tissue. The emotional expression of the patient is also considered in treatment planning. By using surgical tactics that provide control of facial projection and height, this philosophy affords the surgeon an opportunity to manipulate the skeletal elements to the extent that one can simultaneously achieve a well-proportioned face and favorably influence the appearance of the soft tissues and facial countenance.
Top Surgery in Transgender Men: How Far Can You Push the Envelope?
Authors: Bluebond-Langner Rachel , Berli Jens U. , Sabino Jennifer , Chopra Karan , Singh Devinder , Fischer Beverly
Published: March 2017

Background:

The authors present their grading scale and the outcomes of the largest cohort of top surgery published to date. Application of this grading system can help determine which patients will benefit from a subcutaneous mastectomy with free nipple graft versus a circumareolar technique, with the primary endpoint being need for aesthetic revisions.

Methods:

The authors reviewed their database of transgender males who underwent bilateral mastectomy between 2006 and 2015. Data collected included age, body mass index, American Society of Anesthesiologists class, smoking, diabetes, testosterone use, months of social transition, technique used, postoperative complications, and need for revision. Two techniques were used, circumareolar incision and free nipple graft technique.

Results:

Between 2006 and 2015, 1686 consecutive mastectomies were performed on 843 patients. Of those, 548 patients were excluded because of inadequate follow-up. Of the 295 included, 109 were treated using a circumareolar incision and 186 were treated using a free nipple graft technique. There was no statistically significant difference in complications between the two groups; however, there was a statistically significant difference in the rate of aesthetic revisions in the grade 2B circumareolar incision group (34 percent versus 8.8 percent).

Conclusions:

The authors’ outcomes are comparable to the literature, and demonstrate that these procedures can safely be performed in an outpatient setting. The authors’ grading scale classifies patients and helps the surgeon select a surgical technique. The authors show a statistical difference in rates of aesthetic revisions in Fischer grade 2B patients when a circumareolar incision is selected over a free nipple graft technique.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
A New Microtia Reconstruction Method Using Delayed Postauricular Skin Flap
Authors: Li Gaofeng , Zhang Fan , Ding Wei , Wu Zihan , Hu Yigao , Luo Tao , Zhang Bo , Jiang Xia
Published: March 2017

Background:

This article presents a new microtia reconstruction method using a delayed postauricular skin flap.

Methods:

The surgery is scheduled in three stages, the first of which delays the postauricular skin flap and deals with the remnant auricle. Three weeks later, the second stage is carried out. An erect, three-dimensional ear framework fabricated from autogenous rib cartilage is inserted between two flaps. The anterior auricular surface of the framework is draped with the delayed skin flap, and the postauricular surface is draped with postauricular fascia and overlying grafted skin. Six months later, the third stage reconstructs the tragus and shapes a hollow mimicking the external auditory meatus, and locally improves the reconstructed auricle.

Results:

Ninety-six cases of microtia were reconstructed using the delayed skin flap. All ear reconstructions were successful, with good locations, sizes, and shapes, with few complications.

Conclusions:

The authors’ method enables an adequately large, thin skin flap with sufficient blood supply, and also appropriately manages the remnant auricle. A delayed postauricular skin flap with a three-dimensional autologous costal cartilage framework represents a promising approach to microtia reconstruction.
Biological responses of sharks to ocean acidification
Authors: Rosa Rui , Rummer Jodie L. , Munday Philip L.
Published: March 2017

Sharks play a key role in the structure of marine food webs, but are facing major threats due to overfishing and habitat degradation. Although sharks are also assumed to be at relatively high risk from climate change due to a low intrinsic rate of population growth and slow rates of evolution, ocean acidification (OA) has not, until recently, been considered a direct threat. New studies have been evaluating the potential effects of end-of-century elevated CO2levels on sharks and their relatives' early development, physiology and behaviour. Here, we review those findings and use a meta-analysis approach to quantify the overall direction and magnitude of biological responses to OA in the species of sharks that have been investigated to date. While embryo survival and development time are mostly unaffected by elevated CO2, there are clear effects on body condition, growth, aerobic potential and behaviour (e.g. lateralization, hunting and prey detection). Furthermore, studies to date suggest that the effects of OA could be as substantial as those due to warming in some species. A major limitation is that all past studies have involved relatively sedentary, benthic sharks that are capable of buccal ventilation—no studies have investigated pelagic sharks that depend on ram ventilation. Future research should focus on species with different life strategies (e.g. pelagic, ram ventilators), climate zones (e.g. polar regions), habitats (e.g. open ocean), and distinct phases of ontogeny in order to fully predict how OA and climate change will impact higher-order predators and therefore marine ecosystem dynamics.
Population genetics of immune-related multilocus copy number variation in Native Americans
Authors: Zuccherato Luciana W. , Schneider Silvana , Tarazona-Santos Eduardo , Hardwick Robert J. , Berg Douglas E. , Bogle Helen , Gouveia Mateus H. , Machado Lee R. , Machado Moara , Rodrigues-Soares Fernanda , Soares-Souza Giordano B. , Togni Diego L. , Zamudio Roxana , Gilman Robert H. , Duarte Denise , Hollox Edward J. , Rodrigues Maíra R.
Published: March 2017

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameterf, which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins,CCL3L1/CCL4L1,FCGR3A,FCGR3BandFCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.
Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata
Authors: Hill A. A. , Crotta M. , Wall B. , Good L. , O'Brien S. J. , Guitian J.
Published: March 2017

Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
Shifts in rotifer life history in response to stable isotope enrichment: testing theories of isotope effects on organismal growth
Authors: Gorokhova Elena
Published: March 2017

In ecology, stable isotope labelling is commonly used for tracing material transfer in trophic interactions, nutrient budgets and biogeochemical processes. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism growth and metabolism. This assumption is, however, challenged by theoretical considerations and experimental studies on kinetic isotope effects
in vivo
. Here, I demonstrate profound changes in life histories of the rotifer
Brachionus plicatilis
fed
15
N-enriched algae (0.4–5.0 at%); i.e. at the enrichment levels commonly used in ecological studies. These findings support theoretically predicted effects of heavy isotope enrichment on growth, metabolism and ageing in biological systems and underline the importance of accounting for such effects when using stable isotope labelling in experimental studies.
An Integrative Framework for Detecting Structural Variations in Cancer Genomes
Authors: Dixon Jesse R. , Xu Jie , Dileep Vishnu , Zhan Ye , Song Fan , Le Victoria T. , Yardimci Galip Gürkan , Chakraborty Abhijit , Bann Darrin V. , Wang Yanli , Clark Royden , Zhang Lijun , Yang Hongbo , Liu Tingting , Iyyanki Sriranga , An Lin , Pool Christopher , Sasaki Takayo , Rivera Mulia Juan Carlos , Ozadam Hakan , Lajoie Bryan R. , Kaul Rajinder , Buckley Michael , Lee Kristen , Diegel Morgan , Pezic Dubravka , Ernst Christina , Hadjur Suzana , Odom Duncan T. , Stamatoyannopoulos John A. , Broach James R. , Hardison Ross , Ay Ferhat , Noble William Stafford , Dekker Job , Gilbert David M. , Yue Feng
Published: March 2017

Structural variants can contribute to oncogenesis through a variety of mechanisms, yet, despite their importance, the identification of structural variants in cancer genomes remains challenging. Here, we present an integrative framework for comprehensively identifying structural variation in cancer genomes. For the first time, we apply next-generation optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of cancer cells.

Using this approach, we identify and characterize structural variants in up to 29 commonly used normal and cancer cell lines. We find that each method has unique strengths in identifying different classes of structural variants and at different scales, suggesting that integrative approaches are likely the only way to comprehensively identify structural variants in the genome. Studying the impact of the structural variants in cancer cell lines, we identify widespread structural variation events affecting the functions of non-coding sequences in the genome, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel 3D chromatin structural domains.

These results underscore the importance of comprehensive structural variant identification and indicate that non-coding structural variation may be an underappreciated mutational process in cancer genomes.
The Cellular Expression and Genetics of Purple Body (Pb) inPoecilia reticulata, and its Interactions with Asian Blau (Ab) and Blond (bb) under Reflected and Transmitted Light
Authors: Bias Alan S. , Squire Richard D.
Published: March 2017

Mature Purple Body and Non-Purple Body male guppies differ from each other in several ways. Non-Purple males may have large numbers of xanthophores, erythrophores, and blue iridophores, in addition to the usual dendritic, corolla and punctate melanophores. Fewer violet iridophores are found. In contrast, homozygous Purple Body males lack collected and clustered xanthophores, although isolated single xanthophores remain. Violet iridophores and blue iridophores (violet-blue chromatophores units) abound. The dendrites of dendritic melanophores are finer and form chains with each other. Punctate and corolla melanophores in areas comprising orange ornaments are greatly reduced in number. The heterozygous Purple Body male has erythrophores similar to those of non-Purple males, but yellow pigment is reduced. The melanophores are not as greatly changed in orange ornaments. In Domestic Guppy strains, and at least in one suspected instance in wild-type, melanophore structure and populations may be further modified by one or more additional autosomal genes.
Use of Continuous Traits Can Improve Morphological Phylogenetics
Authors: Parins-Fukuchi Caroline
Published: March 2017

The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers’ subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximise phylogenetic information in morphological datasets by preserving larger variation in state space compared to many discretisation schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.
Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data
Authors: Zetner Adrian , Cabral Jennifer , Mataseje Laura , Knox Natalie C , Mabon Philip , Mulvey Michael , Van Domselaar Gary
Published: March 2017

Comparative analysis of bacterial plasmids from whole genome sequence (WGS) data generated from short read sequencing is challenging. This is due to the difficulty in identifying contigs harbouring plasmid sequence data, and further difficulty in assembling such contigs into a full plasmid. As such, few software programs and bioinformatics pipelines exist to perform comprehensive comparative analyses of plasmids within and amongst sequenced isolates. To address this gap, we have developed Plasmid Profiler, a pipeline to perform comparative plasmid content analysis without the need forde novoassembly. The pipeline is designed to rapidly identify plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. The pipeline allows users to query plasmids for genes or regions of interest and visualize results as an interactive heat map.

Availability and Implementation

Plasmid Profiler is freely available software released under the Apache 2.0 open source software license. A stand-alone version of the entire Plasmid Profiler pipeline is available as a Docker container athttps://hub.docker.com/r/phacnml/plasmidprofiler_0_1_6/.

The conda recipe for the Plasmid R package is available at:https://anaconda.org/bioconda/r-plasmidprofiler

The custom Plasmid Profiler R package is also available as a CRAN package athttps://cran.r-project.org/web/packages/Plasmidprofiler/index.html

Galaxy tools associated with the pipeline are available as a Galaxy tool suite athttps://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504

The source code is available at:https://github.com/phac-nml/plasmidprofiler

The Galaxy implementation is available at:https://github.com/phac-nml/plasmidprofiler-galaxy

Contact

Email:gary.vandomselaar@canada.ca

Address: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada

Supplementary information

Documentation:http://plasmid-profiler.readthedocs.io/en/latest/
RETA: An R package for whole exome and targeted region sequencing data analysis
Authors: Guo Mengbiao , Yang Jing , Lau Yu lung , Yang Wanling
Published: March 2017

Whole exome and targeted sequencing have been playing a major role in diagnoses of Mendelian diseases, but analysis of these data involves using many complicated tools and comprehensive understanding of the analysis results is difficult.Here, we report RETA, an R package to provide a one-stop analysis of these data and a comprehensive, interactive and easy-to-understand report with many advanced visualization features. It facilitates clinicians and scientists alike to better analyze and interpret this type of sequencing data for disease diagnoses.

Availability and implementation

https://github.com/reta-s/reta/releases

Contact

yangwl@hku.hk
Introgression makes waves in inferred histories of effective population size
Authors: Hawks John
Published: March 2017

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.
Glycosylation flux analysis reveals dynamic changes of intracellular glycosylation flux distribution in Chinese hamster ovary fed-batch cultures
Authors: Hutter Sandro , Villiger Thomas K. , Brühlmann David , Stettler Matthieu , Broly Hervé , Soos Miroslav , Gunawan Rudiyanto
Published: March 2017

N-linked glycosylation of proteins has both functional and structural significance. Importantly, the glycan structure of a therapeutic protein influences its efficacy, pharmacokinetics, pharmacodynamics and immunogenicity. In this work, we developed glycosylation flux analysis (GFA) for predicting intracellular production and consumption rates (fluxes) of glycoforms, and applied this method to CHO fed-batch monoclonal antibody (mAb) production using two different media compositions, with and without additional manganese feeding. The GFA is based on a constraint-based modelling of the glycosylation network, employing a pseudo steady state assumption. While the glycosylation fluxes in the network are balanced at each time point, the GFA allows the fluxes to vary with time by way of two scaling factors: (1) an enzyme-specific factor that captures the temporal changes among glycosylation reactions catalyzed by the same enzyme, and (2) the cell specific productivity factor that accounts for the dynamic changes in the mAb production rate. The GFA of the CHO fed-batch cultivations showed that regardless of the media composition, the fluxes of galactosylation decreased with the cultivation time in comparison to the other glycosylation reactions. Furthermore, the GFA showed that the addition of Mn, a cofactor of galactosyltransferase, has the effect of increasing the galactosylation fluxes but only during the beginning of the cultivation period. The results thus demonstrated the power of the GFA in delineating the dynamic alterations of the glycosylation fluxes by local (enzyme-specific) and global (cell specific productivity) factors.
Localised Dynactin protects growing microtubules to deliveroskarmRNA to the posterior cortex of theDrosophilaoocyte
Authors: Nieuwburg Ross , Nashchekin Dmitry , Jakobs Maximilian , Carter Andrew , Trong Philipp Khuc , Goldstein Raymond E. , Johnston Daniel St
Published: March 2017

The localisation ofoskarmRNA to the posterior of theDrosophilaoocyte defines where the abdomen and germ cells form in the embryo. Kinesin 1 transportsoskarmRNA to the oocyte posterior along a polarised microtubule cytoskeleton that grows from non-centrosomal microtubule organising centres (ncMTOCs) along the anterior/lateral cortex. Here we show that the formation of this polarised microtubule network also requires the posterior regulation of microtubule growth. A mutation in the Dynactin Arp1 subunit causes mostoskarmRNA to localise in the posterior cytoplasm rather than cortically.oskarmRNA transport and anchoring are normal in this mutant, but the microtubules fail to reach the posterior pole. Thus, Dynactin acts as an anti-catastrophe factor that extends microtubule growth posteriorly. Kinesin 1 transports Dynactin to the oocyte posterior, creating a positive feedback loop that increases the length and persistence of the posterior microtubules that deliveroskarmRNA to the cortex.
Histologically resolved spatial multi-omics of human oral squamous cell carcinoma
Authors: Chen Tao , Cao Chen , Zhang Jianyun , Streets Aaron , Huang Yanyi , Li Tiejun
Published: March 2017

Both the composition of cell types and their spatial distribution in a tissue play a critical role in cellular function, organ development, and disease progression. For example, intratumor heterogeneity and the distribution of transcriptional and genetic events in single cells drive the genesis and development of cancer. However, it can be challenging to fully characterize the molecular profile of cells in a tissue with high spatial resolution because microscopy has limited ability to extract comprehensive genomic information, and the spatial resolution of genomic techniques tends to be limited by dissection. There is a growing need for tools that can be used to explore the relationship between histological features, gene expression patterns, and spatially correlated genomic alterations in healthy and diseased tissue samples. Here, we present a technique that combines label-free histology with spatially resolved multi-omics in un-fixed and unstained tissue sections. This approach leverages stimulated Raman scattering microscopy to provide chemical contrast that reveals histological tissue architecture, allowing for high-resolutionin situlaser micro-dissection of regions of interests. These micro-tissue samples are then processed for DNA and RNA sequencing to identify unique genetic profiles that correspond to distinct anatomical regions. We demonstrate the capabilities of this technique by mapping gene expression and copy number alterations to histologically defined regions in human squamous cell carcinoma (OSCC). Our approach provides complementary insights in tumorigenesis and offers an integrative tool for macroscale cancer tissues with spatial multi-omics assessments.
Predicting the impact of pneumococcal conjugate vaccine programme options in Vietnam: a dynamic transmission model
Authors: Le Polain De Waroux Olivier , Edmunds W. John , Takahashi Kensuke , Ariyoshi Koya , Mulholland E. Kim , Goldblatt David , Choi Yoon Hong , Dang Duc-Anh , Yoshida Lay Myint , Flasche Stefan
Published: March 2017

Background

Catch-up campaigns (CCs) at the introduction of the pneumococcal conjugate vaccines (PCVs) may accelerate the impact of PCVs. However, limited vaccine supplies may delay vaccine introduction if additional doses are needed for such campaigns. We studied the relative impact of introducing PCV13 with and without catch-up campaign, and the implications of potential introduction delays.

Methods

We used a dynamic transmission model applied to the population of Nha Trang in Sout central Vietnam. Four strategies were considered: routine vaccination (RV) only, and RV alongside catch-up campaigns among <1y olds (CC1), <2y olds (CC2) and <5y olds (CC5). The model was parameterised with local data on human social contact rates, and was fitted to local carriage data. Post-PCV predictions were based on best estimates of parameters governing post-PCV dynamics, including serotype competition, vaccine efficacy and duration of protection.

Results

Our model predicts elimination of vaccine-type (VT) carriage across all age groups within 10 years of introduction in all scenarios with near-complete replacement by non-VT. Most of the benefit of CCs is predicted to occur within the first 3 years after introduction, with the highest impact in the first year, when IPD incidence is predicted to be 11% (95%CrI 9 – 14%) lower than RV with CC1, 25% (21 – 30 %) lower with CC2 and 38% (32 – 46%) lower with CC5.

However, CCs would only prevent more cases of IPD insofar such campaigns do not delay introduction by more than 31 (95%CrI 30 – 32) weeks with CC1, 58 (53 – 63) weeks with CC2 and 89 (78 – 101) weeks for CC5.

Conclusion

CCs are predicted to offer a substantial additional reduction in pneumococcal disease burden over RV alone, if their implementation does not result in much introduction delay. Those findings are important to help guide vaccine introduction in countries that have not yet introduced PCV, particularly in Asia.
Interaction of N-3-oxododecanoyl homoserine lactone with transcriptional regulator LasR ofPseudomonas aeruginosa: Insights from molecular docking and dynamics simulations
Authors: Grabski Hovakim , Hunanyan Lernik , Tiratsuyan Susanna , Vardapetyan Hrachik
Published: March 2017

Background

In 2017 World Health Organization announced the list of the most dangerous superbugs and among them isPseudomonas aeruginosa,which is an antibiotic resistant opportunistic human pathogen as well as one of the ‘SKAPE’ pathogens. The central problem is that it affects patients suffering from AIDS, cystic fibrosis, cancer, burn victims etc.P. aeruginosacreates and inhabits surface-associated biofilms. Biofilms increase resistance to antibiotics and host immune responses, because of those current treatments are not effective. It is imperative to find new antibacterial treatment strategies againstP. aeruginosa,but detailed molecular properties of the LasR protein are not clearly known to date. In the present study, we tried to analyse the molecular properties of the LasR protein as well as the mode of its interactions with autoinducer (AI) the N-3-oxododecanoyl homoserine lactone (3-0-C12-HSL).

Results

We performed docking and molecular dynamics (MD) simulations of the LasR protein ofP. aeruginosawith the 3-0-C12-HSL ligand. We assessed the conformational changes of the interaction and analysed the molecular details of the binding of the 3-0-C12-HSL with LasR. A new interaction site of the 3-0-C12-HSL with LasR protein was found, which involves interaction with conservative residues from ligand binding domain (LBD), beta turns in the short linker region (SLR) and DNA binding domain (DBD). It will be referenced as the LBD-SLR-DBD bridge interaction or “the bridge”. We have also performed LasR monomer protein docking and found a new form of dimerization.

Conclusions

This study may offer new insights for future experimental studies to detect the interaction of the autoinducer with “the bridge” of LasR protein and a new interaction site for drug design.
Modelling firing regularity in the ventral cochlear nucleus: mechanisms, and effects of stimulus level and synaptopathy
Authors: Goodman Dan F. M. , Winter Ian M. , Léger Agnès C. , de Cheveigné Alain , Lorenzi Christian
Published: March 2017

The auditory system processes temporal information at multiple scales, and disruptions to this temporal processing may lead to deficits in auditory tasks such as detecting and discriminating sounds in a noisy environment. Here, a modelling approach is used to study the temporal regularity of firing by chopper cells in the ventral cochlear nucleus, in both the normal and impaired auditory system. Chopper cells, which have a strikingly regular firing response, divide into two classes, sustained and transient, based on the time course of this regularity. Several hypotheses have been proposed to explain the behaviour of chopper cells, and the difference between sustained and transient cells in particular. However, there is no conclusive evidence so far. Here, a reduced mathematical model is developed and used to compare and test a wide range of hypotheses with a limited number of parameters. Simulation results show a continuum of cell types and behaviours: chopper-like behaviour arises for a wide range of parameters, suggesting that multiple mechanisms may underlie this behaviour. The model accounts for systematic trends in regularity as a function of stimulus level that have previously only been reported anecdotally. Finally, the model is used to predict the effects of a reduction in the number of auditory nerve fibres (deafferentation due to, for example, cochlear synaptopathy). An interactive version of this paper in which all the model parameters can be changed is available online.

Highlights

A low parameter model reproduces chopper cell firing regularity

Multiple factors can account for sustained vs transient chopper cell response

The model explains stimulus level dependence of firing regularity

The model predicts chopper cells fire more irregularly after deafferentation

An interactive version of the paper allows readers to change parameters
Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments
Authors: Bowler Michael G. , Bowler David R. , Bowler Matthew W.
Published: March 2017

The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012).Acta Cryst.F68, 111–114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.
The perforated borders of labour migration and the formal state
Authors: Portes Virginio Francis Vinicius , Garvey Brian , Stewart Paul
Published: March 2017

Purpose

The purpose of this paper is to explore the variation in migrant labour market regimes and what these reveal about variant patterns of state and extra state regulation in two contemporary political economies.

Design/methodology/approach

Research based upon a participatory action research agenda in Mexico and the north of Ireland. Migrant workers and their families where involved in the project and its development. This included participation in the research design, its focus and purpose.

Findings

Migrant workers experiences of labour market subordination are part of wider processes of subordination and exclusion involving both the state, but also wider, often meta- and para-state, agents. In different locations, states and contexts, the precarity experienced by migrant workers and their families highlights the porosity of the formal rational legal state and moreover, in the current economic context, the compatibility of illegality and state sponsored neoliberal economic policies.

Research limitations/implications

It is important to extend this study to other geographic and political economy spaces.

Practical implications

The study challenges the limits of state agency suggesting the need for extra state, i.e. civil society, participation to support and defend migrant workers.

Originality/value

Notwithstanding the two very different socio-economic contexts, the paper reveals that the interaction, dependence and restructuring of migrant labour markets can be understood within the context of meta- and para-state activities that link neoliberal employment insecurities. Migrants’ experiences illustrate the extent to which even formal legal employment relations can also be sustained by para- and meta- (illegal and alegal) actions and institutions.
All precarious? Institutional change and turning points in labour market trajectories in Spain
Authors: López Andreu Martí
Published: March 2017

Purpose

The purpose of this paper is to explore the effects of changes in employment regulation in Spain on individual labour market trajectories. It is well known that the Spanish labour market has been strongly hit by the 2007 recession. Furthermore, after 2010 and in the benchmark of “austerity”, several reforms were implemented to further flexibilise employment regulation. At the same time, public sector budgets suffered severe cutbacks, that impacted working conditions and prospects of public sector workers. These reforms were implemented by different governments and substantially changed previous existing patterns of employment. This paper explains how these reforms have reinforced previous existing trends towards greater flexibility and weaker employment protection and how they lead to a shift in the position of work in society.

Design/methodology/approach

The emerging patterns that these changes provoked are illustrated thorough data from narrative biographies of workers affected by a job loss or a downgrading of working conditions. The workers of the sample had relatively stable positions and careers and were affected by changes that substantially modified their paths.

Findings

The paper shows how reforms have expanded work and employment insecurities and have broken career paths. It demonstrates how the reforms have weakened the position of work and organised labour in society and how, when institutional supports are jeopardised, the capacity to plan and act is harassed by the traditional social inequalities.

Originality/value

The paper enhances the knowledge about the impact of institutional changes by analysing their effects in individual working lives by means of narrative biographies.
Re-evaluating work-based learning pedagogy
Authors: Nottingham Paula McIver
Published: March 2017

Purpose

The purpose of this paper is to examine work-based learning (WBL) pedagogy within higher education (HE) related to the use of the “field of study” concept.

Design/methodology/approach

This paper reviews WBL literature to discuss the original context of the concept and relates this to current pedagogic approaches through qualitative interviews and written explanations.

Findings

WBL pedagogy continues to use the concepts from field of study WBL but the study also indicates that academic practitioners are developing pedagogy to meet the needs of current workplace and educational policy.

Research limitations/implications

This paper is limited in its scope due to the small number of respondents but there are potential implications about emerging directions for this pedagogic range.

Practical implications

The paper argues that field of study WBL is still relevant to existing practice but further engagement and research surrounding WBL pedagogy is needed to examine this range of HE.

Originality/value

The added value is the evidence of evolving WBL pedagogy that can inform issues of flexibility within HE provision.
Leaving fingerprints: principals’ considerations while implementing education reforms
Authors: Schechter Chen , Shaked Haim
Published: March 2017

Purpose

Turning an education reform program into school reality greatly depends on the principal. In certain cases, principals choose to implement reform instructions only partially. The purpose of this paper is to explore school principals’ considerations leading to their decisions not to fulfill a national reform’s guidelines in a full and complete way.

Design/methodology/approach

This qualitative study is based on interviews with 59 school principals. Generating themes was an inductive process, grounded in the various perspectives articulated by principals.

Findings

Data analysis yielded three major considerations: adjusting to school reality; caring for teachers; and using discretion.

Research limitations/implications

Longitudinal studies in order to explore how principals’ considerations and mediation strategies evolve and unfold throughout the reform implementation would be useful. The authors suggest complementing principals’ verbally expressed perceptions with more objective measures such as direct observations (recorded on video and then reflected upon), to evaluate their considerations and mediating strategies.

Practical implications

Providing prospective and in-service principals with leadership education programs in order to develop an upgraded understanding of their role as mediating agents between the inner and outer spheres of school-life.

Originality/value

As principals serve as mid-level policymakers who leave their “fingerprints” on policies received from the authorities, exploring these considerations may contribute to both the scholarship and the practice of the leadership role in times of education reforms.
Concentration and financial stability in the property-liability insurance sector: global evidence
Authors: Altuntas Muhammed , Rauch Jannes
Published: March 2017

Purpose

This paper aims to examine the effect of concentration in the insurance sector on insurer stability for a large set of developed and developing countries. In particular, the authors test whether concentration reduces financial fragility in the insurance sector (“concentration-stability view”) or decreases stability in the insurance sector (“concentration-fragility view”).

Design/methodology/approach

The authors use a data set of 14,402 firm-year observations of property-liability insurers who appear in A.M. Best’s Statement File Global database during the period 2004-2012. They use regression analyses to examine the effect of concentration on the stability of insurance firms and apply different measures of concentration.

Findings

The results provide empirical support for the “concentration- fragility view”; that is, higher levels of concentration are associated with decreases in the insurance sector’s financial stability.

Research limitations/implications

The results have important policy implications, given that a primary purpose of insurance regulation is to protect policyholders against insurance firm defaults.

Originality/value

No previous research analyzes how recent trends in competition and consolidation, which have led to changes in insurance market concentration, affect the stability of insurance firms around the world. This research is the first paper that provides evidence on the relation between concentration and stability in the insurance sector.
Five years investigation of female and male genotypes in périgord black truffle (Tuber melanosporum Vittad.) revealed contrasted reproduction strategies
Authors: De la Varga Herminia , Le Tacon François , Lagoguet Mélanie , Todesco Flora , Varga Torda , Miquel Igor , Barry‐Etienne Dominique , Robin Christophe , Halkett Fabien , Martin Francis , Murat Claude
Published: March 2017

The Périgord black truffle (Tuber melanosporum Vittad.) is a heterothallic ascomycete that establishes ectomycorrhizal symbiosis with trees and shrubs. Small‐scale genetic structures of female genotypes in truffle orchards are known, but it has not yet been studied in male genotypes. In this study, our aim was to characterize the small‐scale genetic structure of both male and female genotypes over five years in an orchard to better understand the T. melanosporum sexual reproduction strategy, male genotype dynamics, and origins. Two‐hundred forty‐one ascocarps, 475 ectomycorrhizas, and 20 soil cores were harvested and genotyped using microsatellites and mating type genes. Isolation by distance analysis revealed pronounced small‐scale genetic structures for both female and male genotypes. The genotypic diversity was higher for male than female genotypes with numerous small size genotypes suggesting an important turnover due to ascospore recruitment. Larger and perennial female and male genotypes were also detected. Only three genotypes (1.5%) were found as both female and male genotypes (hermaphrodites) while most were detected only as female or male genotype (dioecy). Our results suggest that germinating ascospores act as male genotypes, but we also proposed that soil mycelium could be a reservoir of male genotypes.
Gregarious cyanobacteria
Authors: Stal Lucas J.
Published: March 2017

Huber and collaborators reported in this issue of Environmental Microbiology about freshwater picocyanobacteria that showed phenotypic plasticity in the sense that they appeared as single cells as well as in aggregates. The authors suggested that aggregation might be an inducible defense as a response to the presence of grazers. This has been described for eukaryotic phytoplankton and for the cyanobacterium Microcystis but thus far not for picocyanobacteria. Although inducible defense as an explanation is an attractive possibility, it is also problematic. Aggregation is common among cyanobacteria and it offers many advantages as compared with a free‐living lifestyle. Here these advantages are highlighted and the possibility of inducible defense is critically assessed.