bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of species boundaries in a Neotropical radiation of Begonia
Authors: Twyford Alex D. , Kidner Catherine A. , Ennos Richard A. 
Published: August 2015

AbstractA major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.
Evolution of complex symbiotic relationships in a morphologically derived family of lichen‐forming fungi
Authors: Divakar Pradeep K. , Crespo Ana , Wedin Mats , Leavitt Steven D. , Hawksworth David L. , Myllys Leena , McCune Bruce , Randlane Tiina , Bjerke Jarle W. , Ohmura Yoshihito , Schmitt Imke , Boluda Carlos G. , Alors David , Roca‐Valiente Beatriz , Del‐Prado Ruth , Ruibal Constantino , Buaruang Kawinnat , Núñez‐Zapata Jano , Amo de Paz Guillermo , Rico Víctor J. , Molina M. Carmen , Elix John A. , Esslinger Theodore L. , Tronstad Inger Kristin K. , Lindgren Hanna , Ertz Damien , Gueidan Cécile , Saag Lauri , Mark Kristiina , Singh Garima , Dal Grande Francesco , Parnmen Sittiporn , Beck Andreas , Benatti Michel Navarro , Blanchon Dan , Candan Mehmet , Clerc Philippe , Goward Trevor , Grube Martin , Hodkinson Brendan P. , Hur Jae‐Seoun , Kantvilas Gintaras , Kirika Paul M. , Lendemer James , Mattsson Jan‐Eric , Messuti María Inés , Miadlikowska Jolanta , Nelsen Matthew , Ohlson Jan I. , Pérez‐Ortega Sergio , Saag Andres , Sipman Harrie J. M. , Sohrabi Mohammad , Thell Arne , Thor Göran , Truong Camille , Yahr Rebecca , Upreti Dalip K. , Cubas Paloma , Lumbsch H. Thorsten 
Published: August 2015

Summary

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen‐forming fungi with complex and variable morphologies, also including several lichenicolous fungi.

We assembled a six‐locus data set including nuclear, mitochondrial and low‐copy protein‐coding genes from 293 operational taxonomic units (OTUs).

The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene.

Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene–Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen‐forming ascomycetes.
The functional relevance of somatic synonymous mutations in melanoma and other cancers
Authors: Gotea Valer , Gartner Jared J. , Qutob Nouar , Elnitski Laura , Samuels Yardena 
Published: August 2015

SummaryRecent technological advances in sequencing have flooded the field of cancer research with knowledge about somatic mutations for many different cancer types. Most cancer genomics studies focus on mutations that alter the amino acid sequence, ignoring the potential impact of synonymous mutations. However, accumulating experimental evidence has demonstrated clear consequences for gene function, leading to a widespread recognition of the functional role of synonymous mutations and their causal connection to various diseases. Here, we review the evidence supporting the direct impact of synonymous mutations on gene function via gene splicing; mRNA stability, folding, and translation; protein folding; and miRNA‐based regulation of expression. These results highlight the functional contribution of synonymous mutations to oncogenesis and the need to further investigate their detection and prioritization for experimental assessment.
Putting laughter in context: Shared laughter as behavioral indicator of relationship well‐being
Authors: KURTZ LAURA E. , ALGOE SARA B. 
Published: August 2015

AbstractLaughter is a pervasive human behavior that most frequently happens in a social context. However, data linking the behavior of laughter with psychological or social outcomes are exceptionally rare. Here, the authors draw attention toshared laughteras a useful objective marker of relationship well‐being. Spontaneously generated laughs of 71 heterosexual romantic couples were coded from a videorecorded conversation about how the couple first met. Multilevel models revealed that while controlling for all other laughter present, the proportion of the conversation spent laughing simultaneously with the romantic partner was uniquely positively associated with global evaluations of relationship quality, closeness, and social support. Results are discussed with respect to methodological considerations and theoretical implications for relationships and behavioral research more broadly.
Host‐induced gene silencing in the necrotrophic fungal pathogen Sclerotinia sclerotiorum
Authors: Andrade C. M. , Tinoco M. L. P. , Rieth A. F. , Maia F. C. O. , Aragão F. J. L. 
Published: August 2015

Sclerotinia sclerotiorum is a necrotrophic fungus that causes a devastating disease called white mould, infecting more than 450 plant species worldwide. Control of this disease with fungicides is limited, so host plant resistance is the preferred alternative for disease management. However, due to the nature of the disease, breeding programmes have had limited success. A potential alternative to developing necrotrophic fungal resistance is the use of host‐induced gene silencing (HIGS) methods, which involves host expression of dsRNA‐generating constructs directed against genes in the pathogen. In this study, the target gene chosen was chitin synthase (chs), which commands the synthesis of chitin, the polysaccharide that is a crucial structural component of the cell walls of many fungi. Tobacco plants were transformed with an interfering intron‐containing hairpin RNA construct for silencing the fungal chs gene. Seventy‐two hours after inoculation, five transgenic lines showed a reduction in disease severity ranging from 55·5 to 86·7% compared with the non‐transgenic lines. The lesion area did not show extensive progress over this time (up to 120 h). Disease resistance and silencing of the fungal chs gene was positively correlated with the presence of detectable siRNA in the transgenic lines. It was demonstrated that expression of endogenous genes from the very aggressive necrotrophic fungus S. sclerotiorum could be prevented by host induced silencing. HIGS of the fungal chitin synthase gene can generate white mould‐tolerant plants. From a biotechnological perspective, these results open new prospects for the development of transgenic plants resistant to necrotrophic fungal pathogens.
Post‐radiotherapy hypothyroidism in dogs treated for thyroid carcinomas
Authors: Amores‐Fuster I. , Cripps P. , Blackwood L. 
Published: August 2015

AbstractHypothyroidism is a common adverse event after head and neck radiotherapy in human medicine, but uncommonly reported in canine patients. Records of 21 dogs with histologically or cytologically confirmed thyroid carcinoma receiving definitive or hypofractionated radiotherapy were reviewed. Nine cases received48 Gyin 12 fractions, 10 received36 Gyin 4 fractions and 2 received32 Gyin 4 fractions. Seventeen cases had radiotherapy in a post‐operative setting. Ten cases developed hypothyroidism (47.6%) after radiotherapy. The development of hypothyroidism was not associated with the radiotherapy protocol used. Median time to diagnosis of hypothyroidism was 6 months (range, 1–13 months). Hypothyroidism is a common side effect following radiotherapy for thyroid carcinomas. Monitoring of thyroid function following radiotherapy is recommended. No specific risk factors have been identified.
Negative pressure and nanocrystalline silver dressings for nonhealing ulcer: A randomized pilot study
Authors: Sáez‐Martín Luis C. , García‐Martínez Lourdes , Román‐Curto Concepción , Sánchez‐Hernández Miguel V. , Suárez‐Fernández Ricardo M. 
Published: August 2015

ABSTRACTChronic wounds have a high prevalence and wound care, treatment, and prevention consume large quantities of resources. Chronic wounds are a growing challenge for clinicians. A prospective randomized pilot study was conducted to assess the effectiveness in terms of reduction in area and safety of the combined use of negative‐pressure wound therapy and nanocrystalline silver dressings as compared to negative pressure wound therapy (NPWT) alone in the management of outpatients with chronic wounds. A total of 17 patients were included in the study, 10 were treated with the combined method and 7 with NPWT. Patients were followed for 6 weeks, with a final assessment at 3 months. Clinical improvement, microbiologic data, and toxicity of silver were evaluated. The antibacterial effects of ionic silver together with the development of granulation tissue promoted by NPWT reduced significantly the median extension of the wound between weeks 3 and 6 of treatment. The combination with silver also reduced bacterial colonization with Pseudomonas aeruginosa and the bacterial load on the surface of the wound. The silver levels correlated positively with the extension of the wound, although in none of the patients’ toxic levels were reached. The combination of NPWT with nanocrystalline silver dressings was safe and as effective as NPWT alone.
Automated quantitative 3D analysis of aorta size, morphology, and mural calcification distributions
Authors: Kurugol Sila , Come Carolyn E. , Diaz Alejandro A. , Ross James C. , Kinney Greg L. , Black‐Shinn Jennifer L. , Hokanson John E. , Budoff Matthew J. , Washko George R. , San Jose Estepar Raul 
Published: August 2015

Purpose:The purpose of this work is to develop a fully automated pipeline to compute aorta morphology and calcification measures in large cohorts of CT scans that can be used to investigate the potential of these measures as imaging biomarkers of cardiovascular disease.Methods:The first step of the automated pipeline is aorta segmentation. The algorithm the authors propose first detects an initial aorta boundary by exploiting cross‐sectional circularity of aorta in axial slices and aortic arch in reformatted oblique slices. This boundary is then refined by a 3D level‐set segmentation that evolves the boundary to the location of nearby edges. The authors then detect the aortic calcifications with thresholding and filter out the false positive regions due to nearby high intensity structures based on their anatomical location. The authors extract the centerline and oblique cross sections of the segmented aortas and compute the aorta morphology and calcification measures of the first 2500 subjects from COPDGene study. These measures include volume and number of calcified plaques and measures of vessel morphology such as average cross‐sectional area, tortuosity, and arch width.Results:The authors computed the agreement between the algorithm and expert segmentations on 45 CT scans and obtained a closest point mean error of 0.62 ± 0.09 mm and a Dice coefficient of 0.92 ± 0.01. The calcification detection algorithm resulted in an improved true positive detection rate of 0.96 compared to previous work. The measurements of aorta size agreed with the measurements reported in previous work. The initial results showed associations of aorta morphology with calcification and with aging. These results may indicate aorta stiffening and unwrapping with calcification and aging.Conclusions:The authors have developed an objective tool to assess aorta morphology and aortic calcium plaques on CT scans that may be used to provide information about the presence of cardiovascular disease and its clinical impact in smokers.
Local curvature analysis for classifying breast tumors: Preliminary analysis in dedicated breast CT
Authors: Lee Juhun , Nishikawa Robert M. , Reiser Ingrid , Boone John M. , Lindfors Karen K. 
Published: August 2015

Purpose:The purpose of this study is to measure the effectiveness of local curvature measures as novel image features for classifying breast tumors.Methods:A total of 119 breast lesions from 104 noncontrast dedicated breast computed tomography images of women were used in this study. Volumetric segmentation was done using a seed‐based segmentation algorithm and then a triangulated surface was extracted from the resulting segmentation. Total, mean, and Gaussian curvatures were then computed. Normalized curvatures were used as classification features. In addition, traditional image features were also extracted and a forward feature selection scheme was used to select the optimal feature set. Logistic regression was used as a classifier and leave‐one‐out cross‐validation was utilized to evaluate the classification performances of the features. The area under the receiver operating characteristic curve (AUC, area under curve) was used as a figure of merit.Results:Among curvature measures, the normalized total curvature (CT) showed the best classification performance (AUC of 0.74), while the others showed no classification power individually. Five traditional image features (two shape, two margin, and one texture descriptors) were selected via the feature selection scheme and its resulting classifier achieved an AUC of 0.83. Among those five features, the radial gradient index (RGI), which is a margin descriptor, showed the best classification performance (AUC of 0.73). A classifier combining RGI and CT yielded an AUC of 0.81, which showed similar performance (i.e., no statistically significant difference) to the classifier with the above five traditional image features. Additional comparisons in AUC values between classifiers using different combinations of traditional image features and CT were conducted. The results showed that CT was able to replace the other four image features for the classification task.Conclusions:The normalized curvature measure contains useful information in classifying breast tumors. Using this, one can reduce the number of features in a classifier, which may result in more robust classifiers for different datasets.
SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine
Authors: Yang Jianfeng , Ding Xiaofan , Sun Xing , Tsang Shui-Ying , Xue Hong 
Published: August 2015

Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078–2079, 2009.] have taken on a main role in bioinformatics since the development of massive parallel sequencing. However, because misalignment of sequences poses a significant problem in analysis of sequencing data that could lead to false positives in variant calling, the exclusion of misaligned reads is a necessity in analysis. In this regard, the multiple features of SAM-formatted sequences can be treated as vectors in a multi-dimension space to allow the application of a support vector machine (SVM). Applying the LIBSVM tools developed by Chang and Lin [Chang C-C, Lin C-J, ACM Trans Intell Syst Technol 2:1–27, 2011.] as a simple interface for support vector classification, the SAMSVM package has been developed in this study to enable misalignment filtration of SAM-formatted sequences. Cross-validation between two simulated datasets processed with SAMSVM yielded accuracies that ranged from 0.89 to 0.97 with F-scores ranging from 0.77 to 0.94 in 14 groups characterized by different mutation rates from 0.001 to 0.1, indicating that the model built using SAMSVM was accurate in misalignment detection. Application of SAMSVM to actual sequencing data resulted in filtration of misaligned reads and correction of variant calling.
Teaching Mathematical Reasoning Principles for Software Correctness and Its Assessment
Authors: Drachova Svetlana V. , Hallstrom Jason O. , Hollingsworth Joseph E. , Krone Joan , Pak Rich , Sitaraman Murali 
Published: August 2015

Undergraduate computer science students need to learn analytical reasoning skills to develop high-quality software and to understand why the software they develop works as specified. To accomplish this central educational objective, this article describes a systematic process of introducing reasoning skills into the curriculum and assessing how well students have learned those skills. To facilitate assessment, a comprehensive inventory of principles for reasoning about correctness that captures the finer details of basic skills that students need to learn has been defined and used. The principles can be taught at various levels of depth across the curriculum in a variety of courses.
The use of a particular instructional process is illustrated to inculcate reasoning principles across several iterations of a sophomore-level development foundations course and a junior-level software engineering course. The article summarizes how learning outcomes motivated by the inventory of reasoning principles lead to questions that in turn form the basis for a careful analysis of student understanding and for fine-tuning teaching interventions that together facilitate continuous improvements to instruction.
Information-Theoretical Quantifier of Brain Rhythm Based on Data-Driven Multiscale Representation
Authors: Choi Young-Seok 
Published: August 2015

This paper presents a data-driven multiscale entropy measure to reveal the scale dependent information quantity of electroencephalogram (EEG) recordings. This work is motivated by the previous observations on the nonlinear and nonstationary nature of EEG over multiple time scales. Here, a new framework of entropy measures considering changing dynamics over multiple oscillatory scales is presented. First, to deal with nonstationarity over multiple scales, EEG recording is decomposed by applying the empirical mode decomposition (EMD) which is known to be effective for extracting the constituent narrowband components without a predetermined basis. Following calculation of Renyi entropy of the probability distributions of the intrinsic mode functions extracted by EMD leads to a data-driven multiscale Renyi entropy. To validate the performance of the proposed entropy measure, actual EEG recordings from ratsn=9experiencing 7 min cardiac arrest followed by resuscitation were analyzed. Simulation and experimental results demonstrate that the use of the multiscale Renyi entropy leads to better discriminative capability of the injury levels and improved correlations with the neurological deficit evaluation after 72 hours after cardiac arrest, thus suggesting an effective diagnostic and prognostic tool.Corrigendum to “Information-Theoretical Quantifier of Brain Rhythm Based on Data-Driven Multiscale Representation”
The Capability of ENSEMBLES Models in Predicting the Principal Modes of Pan-Asian Monsoon Precipitation
Authors: Gao Ya , Wang Huijun , Chen Dong 
Published: August 2015

AbstractThe predictability of the dominant modes of summer (June–September) precipitation in the pan-Asian monsoon region is evaluated based on 1-month-lead retrospective forecasts in five state-of-the-art coupled models from the ENSEMBLES project for the period 1979–2005. The results show that the models and their multimodel ensemble mean (MME) perform well in reproducing the interannual variability of the climatology and the spatiotemporal distribution of the first mode of summer precipitation in the pan-Asian monsoon region. The associated oceanic and atmospheric circulation indicators are also well captured, such as the spatiotemporal structures of the simultaneous El Niño–Southern Oscillation (ENSO) and Antarctic Oscillation in the Pacific Ocean (AAOSP). Moreover, the interannual variation of the preceding AAOSP can also be captured by some of the coupled models. For individual models, the ECMWF, Météo-France, and Met Office models exhibit better skill with respect to the first mode of summer precipitation in the pan-Asian monsoon region, which displays a tripole pattern from north to south over 80°–140°E. In addition, these models can successfully predict the intensity and location of the associated ENSO, as well as the simultaneous summer AAOSP distributions. By contrast, the prediction capabilities of the Leibniz Institute of Marine Sciences (IFM-GEOMAR) and Euro-Mediterranean Center for Climate Change (CMCC-INGV) models are relatively weaker. Furthermore, the predictions of the second mode of the summer precipitation in the pan-Asian monsoon region are investigated. Some of the ENSEMBLES models show good capability in predicting the spatiotemporal distribution of the second mode, owing to the successful prediction of the atmospheric convection activities over the tropical Indian Ocean.
The West African Monsoon Onset: A Concise Comparison of Definitions
Authors: Fitzpatrick Rory G. J. , Bain Caroline L. , Knippertz Peter , Marsham John H. , Parker Douglas J. 
Published: August 2015

Abstract
The onset of the West African monsoon (WAM) marks a vital time for local and regional stakeholders. While the seasonal progression of monsoon winds and the related migration of precipitation from the Guinea Coast toward the Sudan/Sahel is apparent, there exist contrasting man-made definitions of what the WAM onset means. Broadly speaking, onset can be analyzed regionally, locally, or over a designated intermediate scale. There are at least 18 distinct definitions of the WAM onset in publication, with little work done on comparing observed onset from different definitions or comparing onset realizations across different datasets and resolutions. Here, nine definitions have been calculated using multiple datasets of different metrics at different resolutions. It is found that mean regional onset dates are consistent across multiple datasets and different definitions. There is low interannual variability in regional onset, suggesting that regional seasonal forecasting of the onset provides few benefits over climatology. In contrast, local onsets show high spatial, interannual, and interdefinition variability. Furthermore, it is found that there is little correlation between local onset dates and regional onset dates across West Africa, implying a disharmony between regional measures of onset and the experience on a local scale. The results of this study show that evaluation of seasonal monsoon onset forecasts is far from straightforward. Given a seasonal forecasting model, it is possible to simultaneously have a good and a bad prediction of monsoon onset simply through selection of the onset definition and observational dataset used for comparison.