bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds
Authors: Wang Zhandong , Popolan-Vaida Denisia M. , Chen Bingjie , Moshammer Kai , Mohamed Samah Y. , Wang Heng , Sioud Salim , Raji Misjudeen A. , Kohse-Höinghaus Katharina , Hansen Nils , Dagaut Philippe , Leone Stephen R. , Sarathy S. Mani 
Published: November 2017

SignificanceHighly oxygenated molecules are involved in autooxidation reactions leading to the formation of secondary organic aerosols (SOAs); they are also critical intermediates in autooxidation processes for liquid hydrogen degradation and the ignition of fuels in advanced combustion systems. However, these reactions are still poorly understood. In this study, we unveil a generalized reaction mechanism involving the autooxidation of peroxy radicals with at least three stages of sequential O2addition. We elucidate important underlying kinetics and structural characteristics of autooxidation processes used for developing new technologies including those aimed at reducing climatically active SOAs and pollutants from fuel combustion. We show that advances can be made by bridging experimental and theoretical methods used by atmospheric and combustion scientists.
Patterns of coevolving amino acids unveil structural and dynamical domains
Authors: Granata Daniele , Ponzoni Luca , Micheletti Cristian , Carnevale Vincenzo 
Published: November 2017

Significance
Patterns of pairwise correlations in sequence alignments can be used to reconstruct the network of residue-residue contacts and thus the three-dimensional structure of proteins. Less explored, and yet extremely intriguing, is the functional relevance of such coevolving networks: Do they encode for the collective motions occurring in proteins at thermal equilibrium? Here, by combining coevolutionary coupling analysis with a state-of-the-art dimensionality reduction approach, we show that the network of pairwise evolutionary couplings can be analyzed to reveal communities of amino acids, which we term “evolutionary domains,” that are in striking agreement with the quasi-rigid protein domains obtained from elastic network models and molecular dynamics simulations.
Relationship of tropospheric stability to climate sensitivity and Earth’s observed radiation budget
Authors: Ceppi Paulo , Gregory Jonathan M. 
Published: November 2017

Significance
In current climate models, the anticipated amount of warming under greenhouse gas forcing, quantified by the “effective climate sensitivity,” increases as time passes. Consequently, effective climate sensitivity values inferred from the historical record may underestimate the future warming. However, the mechanisms of this increase in effective climate sensitivity are not understood, limiting our confidence in climate model projections of future climate change. Here, we present observational and modeling evidence that the magnitude of effective climate sensitivity partly depends on the evolution of the vertical profile of atmospheric warming. In climate models, as the Earth warms overall, the warming becomes increasingly muted aloft, and this alters the strength of feedbacks controlling the radiative response to greenhouse gas forcing.
Robust zero resistance in a superconducting high-entropy alloy at pressures up to 190 GPa
Authors: Guo Jing , Wang Honghong , von Rohr Fabian , Wang Zhe , Cai Shu , Zhou Yazhou , Yang Ke , Li Aiguo , Jiang Sheng , Wu Qi , Cava Robert J. , Sun Liling 
Published: November 2017

Significance
High-entropy alloys (HEAs) are made from multiple transition-metal elements in equimolar or near-equimolar ratios. The elements in HEAs arrange themselves randomly on the crystallographic positions of a simple lattice. In addition to their excellent mechanical properties, one HEA has been reported to display superconductivity. In this work, we report that the Ta–Nb–Hf–Zr–Ti high-entropy alloy superconductor exhibits extraordinarily robust zero-resistance superconductivity under pressure up to 190.6 GPa. This is an observation of the zero-resistance state of a superconductor all the way from 1-bar pressure to the pressure of the earth’s outer core without structure phase transition, making the superconducting HEA a promising candidate for new application under extreme condition.
Vasopressin excites interneurons to suppress hippocampal network activity across a broad span of brain maturity at birth
Authors: Spoljaric Albert , Seja Patricia , Spoljaric Inkeri , Virtanen Mari A. , Lindfors Jenna , Uvarov Pavel , Summanen Milla , Crow Ailey K. , Hsueh Brian , Puskarjov Martin , Ruusuvuori Eva , Voipio Juha , Deisseroth Karl , Kaila Kai 
Published: November 2017

Significance
The transition from placental to lung-based oxygen supply at mammalian birth involves an obligatory period of asphyxia, which is further aggravated by complications during delivery. This oxygen deprivation is a major threat to the fetal brain, and, under such conditions, hormonal and cardiovascular mechanisms are activated to enhance brain perfusion. Our work now demonstrates an intrinsic mechanism in the fetal brain whereby vasopressin activates hippocampal interneurons, leading to desynchronization and suppression of neuronal network activity in species (rat and guinea pig) that are born at widely different stages of brain maturation. Silencing of synchronous neuronal activity by vasopressin is expected to decrease neuronal energy demand and prevent maladaptive synaptic plasticity, thus acting as a pan-mammalian neuroprotective mechanism during birth.
High-resolution mapping ofcis-regulatory variation in budding yeast
Authors: Kita Ryosuke , Venkataram Sandeep , Zhou Yiqi , Fraser Hunter B. 
Published: November 2017

SignificanceGenetic variants affecting gene-expression levels are a major source of phenotypic variation. Using 85 diverse isolates ofSaccharomyces cerevisiae, we mapped genetic variants that affect gene expression with 50-fold higher resolution than previously possible. By doing so, we were able to pinpoint likely causal variants and investigate their molecular mechanisms. We found that these genetic variants are generally under negative selection, but also that clinical yeast isolates have undergone positive selection for up-regulation of genes involved in biofilm suppression. Altogether, our results demonstrate the power of high-resolution mapping of genetic variants that affect gene expression, particularly in understanding the molecular mechanisms of regulatory variation and the natural selection acting on this variation.
iDINGO—integrative differential network analysis in genomics with Shiny application
Authors: Class Caleb A , Ha Min Jin , Baladandayuthapani Veerabhadran , Do Kim-Anh 
Published: November 2017

Abstract

Motivation
Differential network analysis is an important way to understand network rewiring involved in disease progression and development. Building differential networks from multiple ‘omics data provides insight into the holistic differences of the interactive system under different patient-specific groups. DINGO was developed to infer group-specific dependencies and build differential networks. However, DINGO and other existing tools are limited to analyze data arising from a single platform, and modeling each of the multiple ‘omics data independently does not account for the hierarchical structure of the data.

Results
We developed the iDINGO R package to estimate group-specific dependencies and make inferences on the integrative differential networks, considering the biological hierarchy among the platforms. A Shiny application has also been developed to facilitate easier analysis and visualization of results, including integrative differential networks and hub gene identification across platforms.

Availability and implementation
R package is available on CRAN (https://cran.r-project.org/web/packages/iDINGO) and Shiny application at https://github.com/MinJinHa/iDINGO.

Supplementary information
Supplementary data are available at Bioinformatics online.
bioBakery: a meta’omic analysis environment
Authors: McIver Lauren J , Abu-Ali Galeb , Franzosa Eric A , Schwager Randall , Morgan Xochitl C , Waldron Levi , Segata Nicola , Huttenhower Curtis 
Published: November 2017

Abstract

Summary
bioBakery is a meta’omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.

Availability and implementation
bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.

Supplementary information
Supplementary data are available at Bioinformatics online.
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
Authors: Cleary Alan , Farmer Andrew 
Published: November 2017

Abstract

Summary
The Genome Context Viewer is a visual data-mining tool that allows users to search across multiple providers of genome data for regions with similarly annotated content that may be aligned and visualized at the level of their shared functional elements. By handling ordered sequences of gene family memberships as a unit of search and comparison, the user interface enables quick and intuitive assessment of the degree of gene content divergence and the presence of various types of structural events within syntenic contexts. Insights into functionally significant differences seen at this level of abstraction can then serve to direct the user to more detailed explorations of the underlying data in other interconnected, provider-specific tools.

Availability and implementation
GCV is provided under the GNU General Public License version 3 (GPL-3.0). Source code is available at https://github.com/legumeinfo/lis_context_viewer.

Supplementary information
Supplementary data are available at Bioinformatics online.
Intradermal Proliferative Fasciitis Occurring With Chondrodermatitis Nodularis Helicis
Authors: Elsensohn Ashley , Getty Sasha , Shiu Jessica , de Feraudy Sébastien 
Published: November 2017

Abstract:
Nodular fasciitis is a benign myofibroblastic tumor. Its uncommon variant, proliferative fasciitis (PF), can present in an even less common intradermal form. We report a case of intradermal PF of the ear in a 45-year-old man who presented with recurrent episodes of pain and swelling of the lesion. Histologic examination showed a dermal, nodular proliferation of ganglion-like basophilic fibroblasts with prominent nuclei and nucleoli, admixed with foamy histiocytes and areas of spindle cells arranged in intersecting fascicles in a fibromyxoid background. Lesional cells stained positive for smooth muscle actin and were negative for AE1/AE3, p63, and Melan-A. CD68 highlighted intervening histiocytes. We postulate that the underlying chondrodermatitis nodularis helicis was a triggering etiology, consistent with the current speculation that intradermal PF results from trauma.
Fractional Carbon Dioxide Laser Resurfacing in Combination With Potent Topical Corticosteroids for Hypertrophic Burn Scars in the Pediatric Age Group: An Open Label Study
Authors: Majid Imran , Imran Saher 
Published: November 2017

BACKGROUND
Lasers and potent topical corticosteroids are used as therapeutic options in hypertrophic burn scars.

OBJECTIVE
To assess the therapeutic effect of fractional CO2 laser resurfacing in combination with potent topical corticosteroids on hypertrophic burn scars in pediatric age group.

METHODS
Ten children (5–12 years) with postburn hypertrophic scars were treated with 3 to 5 sessions of fractional CO2 laser resurfacing at 1-month intervals, and triamcinolone suspension was applied immediately after each laser session. Patients were also instructed to apply clobetasol propionate gel for 1 week after each laser session. Response to treatment was assessed using Vancouver Scar Scale (VSS) and Physician Global Assessment (PGA). Tolerability for the procedure and adverse effects were also assessed.

RESULTS
Laser sessions were well tolerated under the effect of topical or local anesthesia. At the time of final assessment, there was mean reduction of 4.2 (range: 2.8–7) in VSS. Reduction of VSS by ≥4 points was observed in 8 of 10 cases, whereas PGA revealed excellent response in 6 of 10 cases. No significant adverse effects were reported by any patient.

CONCLUSION
Fractional CO2 laser resurfacing in combination with potent topical steroids leads to significant therapeutic benefits in children with postburn hypertrophic scars.
Dynamic Model of Applied Facial Anatomy with Emphasis on Teaching of Botulinum Toxin A
Authors: Boggio Ricardo Frota 
Published: November 2017

Background:The use of botulinum toxin type A is considered one of the most revolutionary and promising face rejuvenation methods. Although rare, most of the complications secondary to the use of botulinum toxin A are technician dependent. Among the major shortcomings identified in the toxin administration education is unfamiliarity with applied anatomy. This article proposes the use of body painting as an innovative method of teaching the application of botulinum toxin A.Methods:Using the body painting technique, facial anatomy was represented on the face of a model showing the major muscle groups of botulinum toxin A targets. Photographic records and films were made for documentation of represented muscles at rest and contraction.Results:Using the body painting technique, each of the muscles involved in facial expression and generation of hyperkinetic wrinkles can be faithfully reproduced on the model’s face. The documentation of the exact position of the points of application, the distribution of the feature points in the muscular area, the proper angulation and syringe grip, as well as the correlation of the points of application with the presence of hyperkinetic wrinkles, could be properly registered, providing professional training with information of great practical importance, development of highly effective treatments, and low complication rates.Conclusion:By making it possible to interrelate anatomy of a function, body painting is proposed in the present study as an innovative method, which in a demonstrative and highly didactic manner presents great potential as a teaching tool in the application of botulinum toxin A.
AFLIBERCEPT AFTER RANIBIZUMAB INTRAVITREAL INJECTIONS IN EXUDATIVE AGE–RELATED MACULAR DEGENERATION
Authors: Blanco-Garavito Rocio , Jung Camille , Uzzan Joel , Quaranta-ElMaftouhi Maddalena , Coscas Florence , Sahel Jose , Korobelnik Jean-Francois , Béchet Stéphane , Querques Giuseppe , Souied Eric H. 
Published: November 2017

Purpose:
To analyze the efficacy of aflibercept switch treatment for regression of pigment epithelial detachment (PED) in patients previously treated with ranibizumab.

Methods:
Multicenter, prospective, nonrandomized clinical trial. One eye of patients presenting neovascular age–related macular degeneration with PED of more than 250 μm in height, with persistent fluid, was included. Patients had to have received at least six ranibizumab intravitreal injections during the 12 months before enrollment. Patients were switched from ranibizumab pro re nata to aflibercept (fixed regimen, 3 monthly intravitreal injections, and then Q6). Main outcome measure was change in PED height from baseline to Week 12 after switch. Secondary outcomes were best-corrected visual acuity and PED volume changes.

Results:
Eighty four patients were included. Mean delay between last ranibizumab intravitreal injection and switch was 44.7 days. Mean maximal PED height at baseline visit was 347 μm (±109) and reduced to a mean of 266 μm (±114) at Week 12 (P < 0.001) and 288.2 μm at Week 32 (P < 0.001). Mean PED volume was reduced from 1.3 mm3 to 0.98 mm3 at Week 12 (P < 0.001). Best-corrected visual acuity improved by 3.3 Early Treatment Diabetic Retinopathy Study letters at Week 32 (P = 0.003).

Conclusion:
Aflibercept switch therapy seems to be effective on large PED in patients previously treated with pro re nata ranibizumab.
EVALUATION OF OBSTRUCTIVE SLEEP APNEA SYNDROME AS A RISK FACTOR FOR DIABETIC MACULAR EDEMA IN PATIENTS WITH TYPE II DIABETES
Authors: Vié Anne-Laure , Kodjikian Laurent , Agard Emilie , Voirin Nicolas , El Chehab Hussam , Denis Philippe , Coste Olivier , Dot Corinne 
Published: November 2017

Purpose:
To evaluate the association between obstructive sleep apnea and diabetic macular edema (DME) in patients with Type II diabetes, using the apnea–hypopnea index and other nocturnal hypoxemia parameters.

Methods:
This cross-sectional, case–control study included 99 patients with Type II diabetes: the first group included patients with DME (DME+ group) and the second patients without DME (DME− group). Polysomnography was performed in all patients. The two groups were compared, and the risk factors were studied using logistic regression.

Results:
The DME+ group comprised 38 patients, and the DME− group comprised 61 patients, aged a mean 68.8 years and 66.3 years (P = 0.27), respectively; mean body mass index was 29.7 and 30.9 (P = 0.16), respectively. The mean apnea–hypopnea index was significantly higher in the DME+ group (43.95 [13.5–87.3]) than in the DME− group (35.18 [3.55–90.7]) (P = 0.034). Patients with DME had more severe obstructive sleep apnea (apnea–hypopnea index >30) than the others: 71% versus 50.8% (P = 0.049). Cumulative time of SPO2 below 90% (CT90%) was independently associated with DME after adjusting for confounding factors, whereas there was no difference between the oxygen desaturation index and minimum O2 saturation.

Conclusion:
Severe obstructive sleep apnea (apnea–hypopnea index >30) and parameters of nocturnal hypoxemia (cumulative time of SPO2 below 90%) are associated with DME.
COMPARING MICROPERIMETRIC AND STRUCTURAL FINDINGS IN PATIENTS WITH BRANCH RETINAL VEIN OCCLUSION AND DIABETIC MACULAR EDEMA
Authors: Sachdev Amun , Edington Magdalena , Morjaria Rupal , Chong Victor 
Published: November 2017

Purpose:
To compare retinal sensitivity and central retinal thickness in patients with focal diabetic macular edema (DME) and edema secondary to branch retinal vein occlusion (BRVO).

Methods:
In this consecutive, cross-sectional, observational study, patients with either DME or BRVO underwent measurements for best-corrected visual acuity, microperimetry, and spectral domain optical coherence tomography. Retinal thickness and sensitivity were measured using Optos Spectral optical coherence tomography/scanning laser ophthalmoscopy (Optos plc, Dunfermline, Scotland, United Kingdom). Areas defined as abnormal demonstrated edema with clearly defined cystic spaces. Abnormal and control areas were compared in mean retinal sensitivity and mean retinal thickness for both conditions.

Results:
Twenty eyes with focal DME and nine eyes with BRVO were included. In DME, mean retinal thickness was 413.6 ± 84.5 μm and 291.7 ± 36.7 μm in abnormal and control areas, respectively. Mean retinal sensitivity was 10.22 ± 4.23 dB and 12.25 ± 3.57 dB, respectively. In BRVO, mean retinal thickness was 491.4 ± 102.9 μm and 315.9 ± 29.9 μm in abnormal and control areas, respectively. Mean retinal sensitivity was 6.36 ± 5.47 dB and 13.05 ± 2.28 dB. In DME, a decrease in retinal thickness of 0.341 μm correlated with 1 dB reduction of retinal sensitivity, although this was not statistically significant (P = 0.717). In BRVO, however, an increase in retinal thickness of 9.702 μm correlated with 1 dB reduction of retinal sensitivity (P = 0.001).

Conclusion:
In BRVO, an increase in retinal thickness corresponded with a significant reduction in retinal sensitivity; in DME, however, there was no significant correlation between retinal thickness and retinal sensitivity. Further study is required to assess why this is the case. The Optos Spectral optical coherence tomography/scanning laser ophthalmoscopy allows for a reliable point-to-point correlation, as microperimetry and spectral domain optical coherence tomography can be performed in the same device.
EFFICACY OF DOUBLE DOSE PHOTODYNAMIC THERAPY FOR CIRCUMSCRIBED CHOROIDAL HEMANGIOMA
Authors: Lee Ji Hwan , Lee Christopher Seungkyu , Lee Sung Chul 
Published: November 2017

Purpose:
To evaluate the efficacy of photodynamic therapy using a double dose of verteporfin for patients with circumscribed choroidal hemangioma.

Methods:
This retrospective comparative case series evaluated data from 10 patients who were treated using double dose photodynamic therapy (12 mg/m2) and seven patients who were treated using the standard dose (6 mg/m2). A laser was applied with a radiant exposure of 50 J/cm2. The ophthalmologic examinations were performed at baseline and 1 year after the treatment and included best-corrected visual acuity, slit-lamp biomicroscopy, fundus examination, spectral domain optical coherence tomography, and B-scan ultrasonography.

Results:
The mean age in the double dose group was 51.60 years, compared with 50.57 years in the standard-dose group. The only significant difference between the two groups' baseline characteristics was observed in their initial tumor heights. Foveal center thickness, subretinal fluid, and subfoveal choroidal thickness decreased significantly at 1 year after treatment in both groups. Tumor height and the greatest linear dimension of the tumor's base only decreased significantly in the double dose group (P = 0.031). Both groups did not experience significant visual improvements.

Conclusion:
Double dose photodynamic therapy was effective and safe for treating circumscribed choroidal hemangioma and provided better tumor regression with similar resorption of subretinal fluid, compared with standard-dose photodynamic therapy.