bluuebunny/crossref_metadata_2025_split huggingface dataset:
PanViz: interactive visualization of the structure of functionally annotated pangenomes
Authors: Pedersen Thomas Lin , Nookaew Intawat , Wayne Ussery David , Månsson Maria 
Published: November 2016

Abstract

Summary
PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses.

Availability and Implementation
PanViz is written entirely in JavaScript and is available on https://github.com/thomasp85/PanViz. A companion R package that facilitates the creation of PanViz visualizations from a range of data formats is released through Bioconductor and is available at https://bioconductor.org/packages/PanVizGenerator.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting ecosystem responses to changes in fisheries catch, temperature, and primary productivity with a dynamic Bayesian network model
Authors: Trifonova Neda , Maxwell David , Pinnegar John , Kenny Andrew , Tucker Allan 
Published: November 2016

Abstract
The recent adoption of Bayesian networks (BNs) in ecology provides an opportunity to make advances because complex interactions can be recovered from field data and then used to predict the environmental response to changes in climate and biodiversity. In this study, we use a dynamic BN model with a hidden variable and spatial autocorrelation to explore the future of different fish and zooplankton species, given alternate scenarios, and across spatial scales within the North Sea. For most fish species, we were able to predict a trend of increase or decline in response to change in fisheries catch; however, this varied across the different areas, outlining the importance of trophic interactions and the spatial relationship between neighbouring areas. We were able to predict trends in zooplankton biomass in response to temperature change, with the spatial patterns of these effects varying by species. In contrast, there was high variability in terms of response to productivity changes and consequently knock-on effects on higher level trophic species. Finally, we were able to provide a new data-driven modelling approach that accounts for multispecies associations and interactions and their changes over space and time, which might be beneficial to give strategic advice on potential response of the system to pressure.
Five-year quality of life assessment after carbon ion radiotherapy for prostate cancer
Authors: Maruyama Katsuya , Tsuji Hiroshi , Nomiya Takuma , Katoh Hiroyuki , Ishikawa Hitoshi , Kamada Tadashi , Wakatsuki Masaru , Akakura Koichiro , Shimazaki Jun , Aoyama Hidefumi , Tsujii Hirohiko ,   the Working Group for Genitourinary Tumors
Published: November 2016

Abstract
The aim of this study was to prospectively assess 5-year health-related quality of life (HRQOL) of patients treated with carbon ion radiotherapy (C-ion RT) for clinically localized prostate cancer. A total of 417 patients received carbon ion radiotherapy at a total dose of 63–66 Gray-equivalents (GyE) in 20 fractions over 5 weeks, and neoadjuvant and adjuvant androgen deprivation therapy (ADT) were administered for intermediate and high-risk patients. A HRQOL assessment was performed at five time points (immediately before the initiation of C-ion RT, immediately after, and at 12, 36 and 60 months after completion of C-ion RT) using Functional Assessment of Cancer Therapy (FACT) questionnaires. FACT-G and FACT-P scores were significantly decreased; however, the absolute change after 60 months was minimal. The transient decreases in the Trial Outcome Index (TOI) score returned to their baseline levels. Use of ADT, presence of adverse events, and biochemical failure were related to lower scores. Scores of subdomains of FACT instruments indicated characteristic changes. The pattern of HRQOL change after C-ion RT was similar to that of other modalities. Further controlled studies focusing on a HRQOL in patients with prostate cancer are warranted.
On similarity of binary black hole gravitational-wave skymaps: to observe or to wait?
Authors: Vitale Salvatore , Essick Reed , Katsavounidis Erik , Klimenko Sergey , Vedovato Gabriele 
Published: November 2016

AbstractLocalization estimates for GW150914, the first binary black hole detected by the LIGO instruments, were shared with partner facilities for electromagnetic follow-up. While the source was a compact binary coalescence (CBC), it was first identified by algorithms that search for unmodelled signals, which produced the skymaps that directed electromagnetic observations. Later on, CBC-specific algorithms produced refined versions, which showed significant differences. In this Letter, we show that those differences were not accidental and that CBC and unmodelled skymaps for binary black holes will frequently be different; we thus provide a way to determine whether to observe electromagnetically as promptly as possible (following a gravitational-wave detection), or to wait until CBC skymaps become available, should they not be available in low latency. We also show that, unsurprisingly, CBC algorithms can yield much smaller searched areas.
Non-linear shrinkage estimation of large-scale structure covariance
Authors: Joachimi Benjamin 
Published: November 2016

Abstract
In many astrophysical settings, covariance matrices of large data sets have to be determined empirically from a finite number of mock realizations. The resulting noise degrades inference and precludes it completely if there are fewer realizations than data points. This work applies a recently proposed non-linear shrinkage estimator of covariance to a realistic example from large-scale structure cosmology. After optimizing its performance for the usage in likelihood expressions, the shrinkage estimator yields subdominant bias and variance comparable to that of the standard estimator with a factor of ∼50 less realizations. This is achieved without any prior information on the properties of the data or the structure of the covariance matrix, at a negligible computational cost.
Upper limits for mass and radius of objects around Proxima Cen from SPHERE/VLT
Authors: Mesa D. , Zurlo A. , Milli J. , Gratton R. , Desidera S. , Langlois M. , Vigan A. , Bonavita M. , Antichi J. , Avenhaus H. , Baruffolo A. , Biller B. , Boccaletti A. , Bruno P. , Cascone E. , Chauvin G. , Claudi R. U. , De Caprio V. , Fantinel D. , Farisato G. , Girard J. , Giro E. , Hagelberg J. , Incorvaia S. , Janson M. , Kral Q. , Lagadec E. , Lagrange A.-M. , Lessio L. , Meyer M. , Peretti S. , Perrot C. , Salasnich B. , Schlieder J. , Schmid H.-M. , Scuderi S. , Sissa E. , Thalmann C. , Turatto M. 
Published: November 2016

Abstract
The recent discovery of an earth-like planet around Proxima Centauri has drawn much attention to this star and its environment. We performed a series of observations of Proxima Centauri using Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE), the planet-finder instrument installed at the European Southern Observatory (ESO) Very Large Telescope (VLT) UT3, using its near-infrared modules, InfraRed Dual-band Imager and Spectrograph (IRDIS) and IFS. No planet was detected directly, but we set upper limits on the mass up to 7 au by exploiting the AMES-COND models. Our IFS observations reveal that no planet more massive than ∼6–7 MJup can be present within 1 au. The dual-band imaging camera IRDIS also enables us to probe larger separations than other techniques such as radial velocity or astrometry. We obtained mass limits of the order of 4 MJup at separations of 2 au or larger, representing the most stringent mass limits at separations larger than 5 au available at the moment. We also made an attempt to estimate the radius of possible planets around Proxima using the reflected light. Since the residual noise for the observations is dominated by photon noise and thermal background, longer exposures in good observing conditions could improve the achievable contrast limit further.
Pulmonary Signet-Ring Cell Adenocarcinoma Metastatic to the Skin
Authors: Boyd Alan S. 
Published: November 2016

Abstract:
Internal malignancies occasionally metastasize to the skin, usually imparting a poor prognosis. In men, pulmonary malignancies are the second most common offending tumor. Roughly, half such lesions are adenocarcinomas. A small subset of pulmonary adenocarcinomas exhibits signet-ring morphology. To date, a cutaneous metastasis arising from a pulmonary signet-ring cell adenocarcinoma has not been reported.
Pathogenesis and heterogeneity of ovarian cancer
Authors: Kroeger Paul T. , Drapkin Ronny 
Published: November 2016

Purpose of reviewThe most common type of ovarian cancer, high-grade serous ovarian carcinoma (HGSOC), was originally thought to develop from the ovarian surface epithelium. However, recent data suggest that the cells that undergo neoplastic transformation and give rise to the majority of HGSOC are from the fallopian tube. This development has impacted both translational research and clinical practice, revealing new opportunities for early detection, prevention, and treatment of ovarian cancer.Recent findingsGenomic studies indicate that approximately 50% of HGSOC are characterized by mutations in genes involved in the homologous recombination pathway of DNA repair, especiallyBRCA1andBRCA2. Clinical trials have demonstrated successful treatment of homologous recombination-defective cancers with poly-ribose polymerase inhibitors through synthetic lethality. Recently, amplification ofCCNE1was found to be another major factor in HGSOC tumorigenesis, accounting for approximately 20% of all cases. Interestingly, amplification ofCCNE1and mutation of homologous recombination repair genes are mutually exclusive in HGSOC.SummaryThe fallopian tube secretory cell is the cell of origin for the majority of ovarian cancers. Although it remains unclear what triggers neoplastic transformation of these cells, certain tumors exhibit loss ofBRCAfunction or amplification ofCCNE1. These alterations represent unique therapeutic opportunities in ovarian cancer.
Natural mineral-rich water ingestion by ovariectomized fructose-fed Sprague-Dawley rats: effects on sirtuin 1 and glucocorticoid signaling pathways
Authors: Das Jugal Kishore , Severo Milton , Pereira Cidália Dionísio , Patrício Emília , Magalhães José , Monteiro Rosário , Neves Delminda , Martins Maria João 
Published: November 2016

Abstract

Objective:
Prevention or induction of metabolic disorders and obesity depend on estrogen signaling and/or exogenous factors, such as mineral content in diet. The protective effects of a Portuguese natural mineral-rich water against the induction of metabolic syndrome in fructose-fed male Sprague-Dawley rats have been reported. The present study was designed to assess the impact of this mineral-rich water on fructose-fed estrogen-deficient female Sprague-Dawley rats.

Methods:
Ovariectomized rats had access to tap (TWO) or mineral-rich (MWO) waters, with and without 10% fructose (10-wk treatment). A sham-operated (tap water supplied) group was included and each of the five groups included six rats. Plasma biochemical and metabolic parameters were evaluated by routine clinical measurements. Western blotting was used to assess hepatic protein expression of sirtuins (Sirt) 1 and 3, phosphorylated AMP-activated protein kinase-α (p-AMPKα), peroxisome proliferator-activated receptor gamma coactivator-1-α (PGC1α), glucocorticoid receptor, and 11beta-hydroxysteroid dehydrogenase type 1 (11βHSD1).

Results:
Ovariectomy increased plasma total cholesterol (46%/P < 0.05), but had no significant effects on hepatic protein expression. Fructose intake by ovariectomized rats increased PGC1α and 11βHSD1 (fructose in tap water [TWFO] vs TWO: 65%/P < 0.05 and 38%/P = 0.05, respectively) as well as glucocorticoid receptor (TWFO and fructose in natural mineral-rich water [MWFO] vs TWO and MWO: 107%/P = 0.05 and 182%/P < 0.05, respectively). Mineral-rich water ingestion exerted an increasing shape on Sirt1 (MWO vs TWO: 76%/P < 0.05; MWFO vs TWFO: 76%/P = 0.06), PGC1α (MWO vs TWO: 77%/P < 0.01), p-AMPKα (MWO vs TWO: 152%/P = 0.01; MWFO vs TWFO: 107%/P = 0.01), and 11βHSD1 (MWO vs TWO: 91%/P = 0.05; MWFO vs TWFO: 47%/P = 0.05).

Conclusions:
Mineral-rich water ingestion may have a prime role on the activation of Sirt1 signaling and the modulation of glucocorticoid signaling in the postmenopause.
Prevalence and correlates of vaginal estrogenization in postmenopausal women in the United States
Authors: Lindau Stacy Tessler , Dude Annie , Gavrilova Natalia , Hoffmann Joscelyn N. , Schumm L. Philip , McClintock Martha K. 
Published: November 2016

Abstract

Objective:
This work aims to establish current population-based vaginal estrogenization norms for postmenopausal US women.

Methods:
Using a US national probability sample of 868 postmenopausal women ages 57 to 85 years (mean age 67.6 ± 0.3 y, 21.6 ± 0.5 y since menopause), we calculated the epithelial maturation value (MV) generated from self-collected vaginal specimens and compared findings with historical clinical data. Linear and logistic regressions were used to describe the relationship between vaginal estrogenization and sociodemographic, physical, gynecologic, and sexual characteristics.

Results:
Among postmenopausal women, mean MV was 46.6 ± 0.8 (SD 17.4, range 2.5-100) and stable across age groups. In every age group, vaginal estrogenization was higher among postmenopausal nonusers of hormone therapy (HT) in the 2005-2006 US cohort than reported for the 1960s Canadian clinical cohort. MV was also higher among women who used postmenopausal HT in the prior 12 months compared with those who did not (55.1 ± 1.2 vs 44.4 ± 0.9, P < 0.001). In multivariate analyses, HT use, obesity and African American race were each independently associated with higher MV. Overall, MV was not associated with sexual activity, but low MV was associated with vaginal dryness during intercourse among sexually active women.

Conclusions:
Compared to 1960s clinical data, current population estimates revealed higher vaginal estrogenization across all age groups and no decline with age. The strongest independent correlates of vaginal estrogenization in postmenopausal US women were current HT use, obesity, and African American race. Postmenopause, half of all women exhibit low vaginal estrogenization.
Primary Fat Grafting to the Pectoralis Muscle during Latissimus Dorsi Breast Reconstruction
Authors: Niddam Jeremy , Vidal Luciano , Hersant Barbara , Meningaud Jean Paul 
Published: November 2016

Background:
Latissimus dorsi flap is one of the best options for immediate and delayed breast reconstruction. However, this technique is limited by the tissue volume provided by the flap. To improve breast volume while reducing complications, fat grafting is now very often used in addition to latissimus dorsi flap. To the best of our knowledge, fat grafting was always performed as a second-line surgery, at least a few months after the flap procedure. We aimed to report our experience with an associated breast reconstruction technique combining musculocutaneous latissimus dorsi flap with intrapectoral lipofilling for totally autologous breast reconstruction.

Methods:
Between September 2014 and January 2015, 20 patients underwent this technique for unilateral autologous breast reconstruction (14 delayed and 6 immediate breast reconstructions). A mean harvested fat volume of 278 ml (range: 190–350 ml) and a mean injected fat volume of 228 ml (range: 170–280 ml) were used.

Results:
None of the patients experienced complications, such as flap necrosis, breast skin necrosis, hematomas, or infection. One of the patients developed a seroma, which was treated with 3 drainage punctions. Only 2 patients underwent delayed fat grafting procedure.

Conclusion:
Totally autologous breast reconstruction combining latissimus dorsi flap and intrapectoral fat grafting in the same procedure is a new technique allowing increased breast volume in a single surgery.
Nasal Reshaping with Hyaluronic Acid: An Alternative or Complement to Surgery
Authors: Hedén Per 
Published: November 2016

Background:
Rhinoplasty has traditionally been preferred for correction of nasal defects. Long-term clinical experience with hyaluronic acid (HA) injection as an alternative or complement to rhinoplasty is presented.

Methods:
A retrospective review of the author’s clinical experience with HA gel for nasal reshaping from 1997 to 2012 was conducted, with treatments performed during 1998, 2005, and 2012 selected for detailed review.

Results:
More than 250 patients were treated for nasal reshaping with HA since 1997. In addition to being a complement to surgery, HA injection successfully addressed nasal defects that would have been difficult to correct surgically. The effect persisted for >1 year in most patients (>5 y in some patients), with individual variations. No serious complications occurred. When comparing the 3 years reviewed in detail, new indications for nasal reshaping with HA gel became evident over time, which was also reflected by the increase in number of patients treated (1998: n = 2; 2005: n = 22; 2012: n = 51). Of these patients, 55 (73%) received HA injection instead of rhinoplasty, 20 (27%) received HA injection after rhinoplasty, and 5 (7%) underwent rhinoplasty after HA injection. The mean injection volume was 0.4 mL HA gel/treatment. All patients were satisfied with the primary outcome of treatment. Retreatment was performed in 32 patients (43%).

Conclusions:
Injection of HA gel is a valuable tool for nasal reshaping. It can also be used for correction of minor postrhinoplasty defects in appropriate patients.
Examination of Epithelial Mesenchymal Transition in Keloid Tissues and Possibility of Keloid Therapy Target
Authors: Kuwahara Hiroaki , Tosa Mamiko , Egawa Seiko , Murakami Masahiro , Mohammad Ghazizadeh , Ogawa Rei 
Published: November 2016

Background:
Keloid is a fibroproliferative skin disorder that is characterized by collagen accumulation and blood vessel proliferation in the reticular layer of the dermis. It is caused by prolonged inflammation after cutaneous injury. Several studies suggested recently that epithelial mesenchymal transition (EMT) is involved in the development of fibrosis. This study assessed whether EMT also participates in keloid development and/or aggravation.

Methods:
Resected keloid (n = 19) and normal skin (n = 13) samples were subjected to immunohistochemical, immunofluorescent, and Western blot analyses of their expression of epidermal (E-cadherin) and mesenchymal (vimentin) proteins.

Results:
Immunohistochemical analysis showed that the keloid tissues had more vimentin-positive cells in the epidermis than the normal tissues. When normal primary keratinocytes were cultured with proinflammatory cytokines, the cobblestone-shaped cells changed to a spindle shape and many vimentin-positive cells were detected. When immortalized HaCaT keratinocytes were cocultured in split-well plates with normal or keloid-derived fibroblasts, they also underwent EMT, as indicated by their greater vimentin expression on Western blot analysis compared with HaCaT cells that were cultured alone.

Conclusions:
EMT was observed in keloid specimens. EMT was induced by inflammatory cytokines and fibroblasts. EMT may be involved in keloid generation and/or aggravation and may have potential as a keloid treatment target.
Conditioned pain modulation in patients with nonspecific chronic back pain with chronic local pain, chronic widespread pain, and fibromyalgia
Authors: Gerhardt Andreas , Eich Wolfgang , Treede Rolf-Detlef , Tesarz Jonas 
Published: November 2016

Abstract
Findings considering conditioned pain modulation (CPM) in chronic back pain (CBP) are contradictory. This might be because many patients with CBP report pain in further areas of the body, and altered CPM might influence spatial extent of pain rather than CBP per se. Therefore, we compared CPM in patients with CBP with different pain extent. Patients with fibromyalgia syndrome (FMS), for whom CPM impairment is reported most consistently, were measured for comparison. Based on clinical evaluation and pain drawings, patients were categorized into chronic local back pain (CLP; n = 53), chronic widespread back pain (CWP; n = 32), and FMS (n = 92). Conditioned pain modulation was measured by the difference in pressure pain threshold (test stimuli) at the lower back before and after tonic heat pain (conditioning stimulus). We also measured psychosocial variables. Pressure pain threshold was significantly increased in CLP patients after tonic heat pain (P < 0.001) indicating induction of CPM. Conditioned pain modulation in CLP was significantly higher than that in CWP and FMS (P < 0.001), but CPM in CWP and FMS did not differ. Interestingly, a higher number of painful areas (0-10) were associated with lower CPM (r = 0.346, P = 0.001) in CBP but not in FMS (r = −0.013, P = 0.903). Anxiety and depression were more pronounced in FMS than in CLP or CWP (P values <0.01). Our findings suggest that CPM dysfunction is associated with CWP and not with FMS as suggested previously. FMS seems to differ from CWP without FMS by higher psychosocial burden. Moreover, patients with CBP should be stratified into CLP and CWP, and centrally acting treatments targeting endogenous pain inhibition seem to be more indicated the higher the pain extent.
Dental Trauma in a Pediatric Emergency Department Referral Center
Authors: Hall Emily , Hickey Patricia , Nguyen-Tran Thuy , Louie Jeff 
Published: November 2016

Objective
The purpose of this study was to describe dental and associated oral injuries in a pediatric population that presents to an emergency department.

Methods
We performed a retrospective study and identified children from January 2007 to September 2011. Charts were reviewed for any subject, age from newborn to younger than 19 years, based on International Classification of Diseases, Ninth Revision codes for any dental or oral injury. Data abstraction included demographics, time of day of presentation, location and identification of tooth (s) injured, management, and disposition.

Results
We identified 108 children with dental and if present, associated oral injuries. The median age was 12.3 years, the most common tooth injured were the primary (25.9%) or permanent (62%) upper central incisors, and the majority of subjects presented in the afternoon (mean time was 3:50 pm, SD ±24 minutes). A large proportion of dental injuries occurred in patients with permanent dentation (62%) and half of all children had more than 1 tooth injury. The majority of children (75%) were evaluated by either pediatric dental, oral surgery, or otolaryngology services, whereas 3.7% of the cases required multiple services. Twenty-five percent of children had an associated jaw fracture. Eighty-three percent of children were discharged home, of those, 49.1% were prescribed opioids, and 38.3% oral antibiotics.

Conclusions
Emergency departments are often relied upon to evaluate and treat simple and complex dental and oral injuries. The ability to use a multidisciplinary team to manage pediatric oral and dental trauma is essential for care.