bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrode Array Displacement into the Fallopian Canal in Revisions of Long-standing Cochlear Implants
Authors: Alyono Jennifer , Locketz Garrett , Corrales Carleton Eduardo , Blevins Nikolas H. 
Published: March 2017

Objective:
To describe extracochlear extension of revision cochlear implant arrays into the Fallopian canal.

Patients:
Two adult patients with extension of revision cochlear implant arrays into the Fallopian canal.

Interventions:
Computed tomography (CT), selective deactivation of non-functional electrodes.

Main Outcome Measures:
Facial nerve function, facial nerve stimulation, cochlear implant electrode position, radiography, functional hearing.

Results:
Two patients presented with failure of their long-standing cochlear implants (CIs). One patient with presumed postviral hearing loss presented with declining function and increasing facial stimulation from an implant placed 30 years previous. A second with postmeningitic hearing loss presented with a draining mastoid fistula from an implant placed 7 years before. Both patients were reimplanted with minimal insertion resistance via the established electrode tract, yet demonstrated facial nerve stimulation during intraoperative telemetry and on device activation. Postoperative CTs of each patient showed exit of the electrode from the cochlea into the tympanic or labyrinthine Fallopian canal. Both patients can use their devices effectively with selective electrode deactivation.

Conclusions:
Our cases illustrate the potential association of long-standing electrodes with otic capsule changes, allowing extracochlear malposition of subsequent arrays. This can occur despite apparently uneventful reinsertion of a flexible array without undue force. Previously reported histopathology confirms the potential for a reactive osteitis from arrays that may contribute to this phenomenon. Intraoperative facial stimulation with neural telemetry testing can raise suspicion of a malpositioned array involving the Fallopian canal. Such cases can be effectively managed with selective deactivation of malpositioned electrode contacts.
Frontal Sinus Volume and Frontal Bar Position Are Associated in Unicoronal Craniosynostosis
Authors: Xu Wen , Gerety Patrick A. , Li Jing , Bartlett Scott P. , Taylor Jesse A. 
Published: March 2017

Background:
Frontal sinus pneumatization plays an important role in brow protrusion, and absence of frontal sinus development may be associated with brow retrusion. Using unicoronal craniosynostosis as a model, the authors studied the relationship among frontal sinus volume, supraorbital retrusion, and brow position.

Methods:
The authors conducted a retrospective review of unicoronal craniosynostosis patients with head computed tomographic scans and photographs taken from ages 5 to 18 years. Frontal sinus volume and supraorbital retrusion were calculated using three-dimensional computed tomographic reconstructions. A “brow score” from 0 to 3 was assigned to each patient’s photographs by a consensus of two craniofacial surgeons; sinus morphology and brow scores were compared.

Results:
The study included 20 unicoronal craniosynostosis patients. The affected side demonstrated increased retrusion (7.1 ± 3.7 mm versus 3.0 ± 3.1 mm; p < 0.001) and decreased frontal sinus volume (0.8 ± 0.9 cc versus 2.6 ± 1.8 cc; p < 0.001). Qualitative brow retrusion scores differed between affected and unaffected sides (score of 0, 17 percent affected versus 78 percent unaffected; score of 1, 28 percent versus 22 percent; score of 2, 39 percent versus 0 percent; and score of 3, 17 percent versus 0 percent; p < 0.001). Brow scores trended with retrusion measurements (score of 0, 2.7 ± 2.9 mm retrusion; score of 1, 6.1 ± 3.5 mm; score of 2, 8.9 ± 3.2 mm; and score of 3, 9.7 ± 2.8 mm; p < 0.001). Subjects with brow scores of 0 or 1 had larger frontal sinus volumes than subjects with brow scores of 2 or 3 (p = 0.018).

Conclusions:
Qualitative brow retrusion correlates strongly with both quantitative supraorbital retrusion and frontal sinus volume. Although this retrospective study cannot prove causality, which is likely multifactorial, its strong correlation with frontal sinus pneumatization highlights the importance of the frontal sinus in brow position in unicoronal craniosynostosis.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
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

Summary:
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.
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

AbstractStructural 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

AbstractMature 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

ABSTRACTThe 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

AbstractSummaryComparative 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 ImplementationPlasmid 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-plasmidprofilerThe custom Plasmid Profiler R package is also available as a CRAN package athttps://cran.r-project.org/web/packages/Plasmidprofiler/index.htmlGalaxy tools associated with the pipeline are available as a Galaxy tool suite athttps://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504The source code is available at:https://github.com/phac-nml/plasmidprofilerThe Galaxy implementation is available at:https://github.com/phac-nml/plasmidprofiler-galaxyContactEmail:gary.vandomselaar@canada.caAddress: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, CanadaSupplementary informationDocumentation: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

AbstractWhole 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 implementationhttps://github.com/reta-s/reta/releasesContactyangwl@hku.hk
Introgression makes waves in inferred histories of effective population size
Authors: Hawks John 
Published: March 2017

AbstractHuman 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

AbstractN-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.