bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrocardiography-Gated Computed Tomography of the Bronchial Arteries With Iterative Image Reconstruction: Clinical Evaluation and Image Quality
Authors: Gang Qiangqiang , Xu Jun , Wang Junling , Hao Peng , Xu Yikai 
Published: April 2017

Background
The aim of this study was to apply electrocardiography (ECG)-gated prospective-triggered multidetector row computed tomography angiography with iterative model reconstruction (IMR) to optimize imaging of the bronchial arteries in patients with the chief complaint of hemoptysis.

Methods
This was a prospective observational study. Between August 2015 and June 2016, we enrolled 31 consecutive patients with the chief complaint of hemoptysis who were scheduled to undergo computed tomography of the bronchial artery. Patients were randomly divided into 3 groups: group A, with filtered back-projection reconstruction; group B, with iDose reconstruction; and group C, with ECG-gated prospective-triggered multidetector row computed tomography angiography with IMR. Image quality, visibility, and traceability were compared.

Results
Image quality, including signal-to-noise and contrast-to-noise ratios, visibility, and traceability, was best in group C.

Conclusions
With the help of IMR and ECG-synchronized prospective-triggered technology, the bronchial artery anatomy can be accurately depicted in patients with massive hemoptysis.
Iterative Reconstruction Designed for Brain CT: A Correlative Study With Filtered Back Projection for the Diagnosis of Acute Ischemic Stroke
Authors: Iyama Yuji , Nakaura Takeshi , Oda Seitaro , Kidoh Masafumi , Utsunomiya Daisuke , Yoshida Morikatsu , Yuki Hideaki , Hirata Kenichiro , Funama Yoshinori , Harada Kazunori , Awai Kazuo , Hirai Toshinori , Yamashita Yasuyuki 
Published: April 2017

Objectives
The objective of this study is to evaluate the usefulness of iterative model reconstruction designed for brain computed tomography (CT) (IMR-Neuro) for the diagnosis of acute ischemic stroke.

Methods
This retrospective study included 20 patients with acute middle cerebral artery infarction who have undergone brain CT and 20 nonstroke patients (control). We reconstructed axial images with filtered back projection (FBP) and IMR-Neuro (slice thickness, 1 and 5 mm). We compared the CT number of the infarcted area, the image noise, contrast, and the contrast to noise ratio of the infarcted and the noninfarcted areas between the different reconstruction methods. We compared the performance of 10 radiologists in the detection of parenchymal hypoattenuation between 2 techniques using the receiver operating characteristic (ROC) techniques with the jackknife method.

Results
The image noise was significantly lower with IMR-Neuro [5 mm: 2.5 Hounsfield units (HU) ± 0.5, 1 mm: 3.9 HU ± 0.5] than with FBP (5 mm: 4.9 HU ± 0.5, 1 mm: 10.1 HU ± 1.4) (P < 0.01). The contrast to noise ratio was significantly greater with IMR-Neuro (5 mm: 2.6 ± 2.1, 1 mm: 1.6 ± 1.3) than with FBP (5 mm: 1.2 ± 1.0; 1 mm: 0.6 ± 0.5) (P < 0.01). The value of the average area under the receiver operating curve was significantly higher with IMR-Neuro than FBP (5 mm: 0.79 vs 0.74, P = 0.04; 1 mm: 0.76 vs 0.69, P = 0.04).

Conclusions
Compared with FBP, IMR-Neuro improves the image quality and the performance for the detection of parenchymal hypoattenuation with acute ischemic stroke.
Extended Right Thoracic Approach Compared With Limited Left Thoracic Approach for Patients With Middle and Lower Esophageal Squamous Cell Carcinoma
Authors: Li Bin , Hu Hong , Zhang Yawei , Zhang Jie , Miao Longsheng , Ma Longfei , Luo Xiaoyang , Zhang Yiliang , Ye Ting , Li Hecheng , Zhou Jianhua , Li Yuan , Shen Lei , Zhao Kuaile , Fan Min , Zhu Zhengfei , Wang Jialei , Xu Jie , Deng Youjia , Lu Qiong , Jia Huixun , Cheng Xinghua , Li Hang , Zhang Yang , Li Chenguang , Pan Yunjian , Liu Shilei , Hu Haichuan , Shao Longlong , Sun Yihua , Xiang Jiaqing , Chen Haiquan 
Published: April 2017

Objective:
To investigate whether survival is improved by using the right thoracic approach (extended lymphadenectomy) compared with the left thoracic approach (limited lymphadenectomy) for esophageal cancer.

Background:
The optimal surgical technique for esophageal cancer remains unclear.

Methods:
Between May 2010 and July 2012, 300 patients with middle and lower thoracic esophageal carcinoma were randomized to receive esophagectomy through either the right or left thoracic approach. Of these, 286 patients with squamous cell carcinoma determined by postoperative pathology were included in this analysis. Disease-free survival (DFS) and overall survival (OS) were compared between the right (n = 146) and left thoracic groups (n = 140).

Results:
The median follow-up was 55.9 months [95% confidence interval (CI): 53.1–58.6]. The 3-year DFS rates were 62% and 52% in the right and left thoracic arms, respectively [hazard ratio (HR) 0.709; 95% CI, 0.506–0.995; P = 0.047, log-rank test]. The 3-year OS rates were 74% and 60%, respectively (HR, 0.663; 95% CI, 0.457–0.961; P = 0.029). Subgroup analyses revealed longer DFS in the right thoracic arm (vs left thoracic arm) in patients with lymph node involvement (HR, 0.632; 95% CI, 0.412–0.969, P = 0.034), but not in patients without lymph node involvement (HR, 0.757; 95% CI, 0.434–1.320, P = 0.325), and in patients with R1–2 resection margins (HR, 0.495; 95% CI, 0.290–0.848, P = 0.009), but not R0 margins (HR, 0.944; 95% CI, 0.603–1.477, P = 0.801).

Conclusions:
Compared with the left thoracic approach, the right thoracic approach associated with increased DFS and OS in esophageal squamous cell carcinoma patients, particularly in those with lymph node involvement and/or R1–2 resection margins.
A Placebo-Controlled Crossover Trial of Gastrin-Releasing Peptide in Childhood Autism
Authors: Marchezan Josemar , Becker Michele , Schwartsmann Gilberto , Ohlweiler Lygia , Roesler Rafael , Renck Luiza Brusius , Gonçalves Marcela Matos Monteiro , Ranzan Josiane , Riesgo Rudimar dos Santos 
Published: April 2017

Objectives
The aim of this study was to evaluate the efficacy, safety, and tolerability of gastrin-releasing peptide (GRP) compared with placebo in autism spectrum disorder symptoms.

Methodology
This is a randomized, double-blind, placebo-controlled crossover trial using GRP 160 pmol/kg for 4 consecutive days in 10 children with autism. Outcomes were measured by the Aberrant Behavior Checklist (ABC) scale.

Results
All participants were boys, aged between 4 and 9 years. There was a reduction in the scores of the ABC range and its subscales after use GRP and placebo. The reduction was more prominent with GRP, particularly in the subscale “hyperactivity and noncompliance,” but there was no statistical difference between the results (P = 0.334). After a week of infusion, 5 children showed improvement of 25% or greater in the total score of the ABC scale with GRP use and 2 with placebo use; however, there was no statistical difference (P = 0.375). There were no adverse effects, changes in vital signs, or laboratory abnormalities associated with the use of GRP.

Conclusions
The results of this study, despite the small sample size, reinforce previous data on the safety of the GRP in short-term use. There is a need for further research with other designs and a larger sample size to evaluate the efficacy and safety of GRP in children with autism.
A Systematic Nomenclature for theDrosophilaVentral Nervous System
Authors: Court Robert , Namiki Shigehiro , Armstrong J Douglas , Börner Jana , Card Gwyneth , Costa Marta , Dickinson Michael , Duch Carsten , Korff Wyatt , Mann Richard , Merritt David , Murphey Rod K , Seeds Andrew , Shirangi Troy , Simpson Julie H. , Truman James W , Tuthill John , Williams Darren , Shepherd David 
Published: April 2017

AbstractThe fruit fly,Drosophila melanogaster, is an established and powerful model system for neuroscience research with wide relevance in biology and medicine. Until recently, research on theDrosophilabrain was hindered by the lack of a complete and uniform nomenclature. Recognising this problem, the Insect Brain Name Working Group produced an authoritative hierarchical nomenclature system for the adult insect brain, usingDrosophila melanogasteras the reference framework, with other taxa considered to ensure greater consistency and expandability (Ito et al., 2014). Here, we extend this nomenclature system to the sub-gnathal regions of the adultDrosophilanervous system, thus providing a systematic anatomical description of the ventral nervous system (VNS). This portion of the nervous system includes the thoracic and abdominal neuromeres that were not included in the original work and contains the motor circuits that play essential roles in most fly behaviours.
Photoacoustic molecular rulers based on DNA nanostructures
Authors: Joseph James , Koehler Philipp , Zuehlsdorff Tim J. , Cole Daniel J. , Baumann Kevin N. , Weber Judith , Bohndiek Sarah E. , Hernández-Ainsa Silvia 
Published: April 2017

ABSTRACTMolecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality forin vivoimaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths. Using DNA nanotechnology we created several nanostructures with precisely positioned fluorophore-quencher pairs over a range of nanoscale separation distances. PAT of the DNA nanostructures showed distance-dependent photoacoustic signal generation and experimentally demonstrated the ability of PAT to reveal the FRET process deep within tissue mimicking phantoms. Further, we experimentally validated these DNA nanostructures as providing a novel and biocompatible strategy to augment the intrinsic photoacoustic signal generation capabilities of small molecule fluorescent dyes.
Ecological Network Metrics: Opportunities for Synthesis
Authors: Lau Matthew K. , Borrett Stuart R. , Baiser Benjamin , Gotelli Nicholas J. , Ellison Aaron M. 
Published: April 2017

AbstractNetwork ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ecosystems, and long-term ecological dynamics (e.g., stability). Whereas the introduction of network theory has enabled ecologists to quantify not only the degree, but also the architecture of ecological complexity, these advances have come at the cost of introducing new challenges, including new theoretical concepts and metrics, and increased data complexity and computational intensity. Synthesizing recent developments in the network ecology literature, we point to several potential solutions to these issues: integrating network metrics and their terminology across sub-disciplines; benchmarking new network algorithms and models to increase mechanistic understanding; and improving tools for sharing ecological network research, in particular “model” data provenance, to increase the reproducibility of network models and analyses. We propose that applying these solutions will aid in synthesizing ecological subdisciplines and allied fields by improving the accessibility of network methods and models.
Demographic consequences of climate variation along an elevational gradient for a montane terrestrial salamander
Authors: Caruso Nicholas M. , Rissler Leslie J. 
Published: April 2017

AbstractClimate change represents a significant threat to amphibians, which are already imperiled. However, for many species, the relationship between demographic vital rates (survival and growth) and climate is unknown, which limits predictive models. Here we describe the life history variation ofPlethodon montanususing capture-recapture data over a period of four years, at five sites along an elevational gradient to determine how survival and growth vary with temperature, precipitation, and how these relationships vary with elevation. We used a hierarchical model to estimate asymptotic size and growth rate, and used a spatial Cormack-Jolly-Seber model to estimate probability of capture and survival, as well as dispersal variance. Our results show that during the active season, growth and survival rates are both positively affected by precipitation, while survival was positively affected by temperature at all elevations, the relationship between growth rates and temperature varied along the elevational gradient. Generally at lower elevations, higher temperatures led to a decrease in growth while at higher elevations the opposite was true. During the inactive season we found elevational variation in the relationship between survival and the amount of snow; at low elevations snowfall was low but survival decreased with increasing snowfall while at higher elevations increasing snowfall lead to higher survival. Our results demonstrate that understanding how the environment can affect salamander demography to develop mechanistic models, will require knowledge of the actual environmental conditions experienced by a given population as well as an understanding of the overall differences in climate at a given site.
Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids
Authors: Hashemi Abolfazl , Zhu Banghua , Vikalo Haris 
Published: April 2017

ABSTRACTA framework that formulates haplotype assembly as sparse tensor decomposition is proposed. The problem is cast as that of decomposing a tensor having special structural constraints and missing a large fraction of its entries into a product of two factors, U and; tensorreveals haplotype information while U is a sparse matrix encoding the origin of erroneous sequencing reads. An algorithm, AltHap, which reconstructs haplotypes of either diploid or poly-ploid organisms by solving this decomposition problem is proposed. Starting from a judiciously selected initial point, AltHap alternates between two optimization tasks to recover U andby relying on a modified gradient descent search that exploits salient structural properties of U and. The performance and convergence properties of AltHap are theoretically analyzed and, in doing so, guarantees on the achievable minimum error correction scores and correct phasing rate are established. AltHap was tested in a number of different scenarios and was shown to compare favorably to state-of-the-art methods in applications to haplotype assembly of diploids, and significantly outperform existing techniques when applied to haplotype assembly of polyploids.
apterous Aspecifies dorsal wing patterns and sexual traits in butterflies
Authors: Prakash Anupama , Monteiro Antónia 
Published: April 2017

AbstractButterflies have evolved different color patterns on their dorsal and ventral wing surfaces to serve different signaling functions, yet the developmental mechanisms controlling surface-specific patterning are still unknown. Here, we mutate both copies of the transcription factorapterousinBicyclus anynanabutterflies using CRISPR/Cas9 and show thatapterous Afunctions both as a repressor and modifier of ventral wing color patterns, as well as a promoter of dorsal sexual ornaments in males. We propose that the surface-specific diversification of wing patterns in butterflies proceeded via the co-option ofapterous Ainto various gene regulatory networks involved in the differentiation of discrete wing traits. Further, interactions betweenapterousand sex-specific factors such asdoublesexmay have contributed to the origin of sexually dimorphic surface-specific patterns. Finally, we discuss the evolution of eyespot pattern diversity in the family Nymphalidae within the context of developmental constraints due toapterousregulation.Significance statementButterflies have evolved different wing patterns on their dorsal and ventral wing surfaces that serve different signaling functions. We identify the transcription factor,apterous A, as a key regulator of this surface-specific differentiation in butterflies. We also show a role forapterous Ain restricting the developmental origin of a novel trait, eyespots, to just the ventral wing surface. Dorsal-ventral differentiation of tissues is not just restricted to butterfly wings but occurs in many other organs and organisms from arthropods to humans. Thus, we believe that our work will be of interest to a diverse group of biologists and layman alike interested in the role of development in shaping biodiversity.
Faster growth with shorter antigens explains a VSG hierarchy during African trypanosome infections: a feint attack by parasites
Authors: Liu Dianbo , Albergante Luca , Horn David , Newman Timothy 
Published: April 2017

AbstractThe parasitic African trypanosome,Trypanosoma brucei, evades the adaptive host immune response by a process of antigenic variation that involves the clonal switching of variant surface glycoproteins (VSGs). The VSGs that periodically come to dominatein vivodisplay a hierarchy, but how this hierarchy arises is not well-understood. Combining publicly available genetic data with mathematical modelling, we report a VSG-length-dependent hierarchical timing of clonal VSG dominance in a mouse model, revealing an inverse correlation between VSG length and trypanosome growth-rate. Our analysis indicates that, among parasites switching to new VSGs, those expressing shorter VSGs preferentially accumulate to a detectable level that is sufficient to trigger an effective immune response. Subsequent elimination of faster-growing parasites then allows slower parasites with longer VSGs to accumulate. This interaction between the host and parasite is able by itself to explain the temporal distribution of VSGs observedin vivo. Thus, our findings reveal a length-dependent hierarchy that operates duringT. bruceiinfection, representing a ‘feint attack’ diversion tactic utilised during infection by these persistent parasites to out-maneuver the host immune system.Significance StatementThe protozoan parasiteTrypanosoma bruceicauses devastating and lethal diseases in humans and livestock. This parasite continuously evades the host adaptive immune response by drawing on a library of variant surface proteins but the mechanisms determining the timing of surface protein – host interactions are not understood. We report a simple mechanism, based on differential growth of parasites with surface proteins of different lengths, which can explain the hierarchy of variants over time. This allows parasites to evade host immune responses for extended timeframes using limited cohorts of surface proteins. We liken this strategy to a military ‘feint attack’, that enhances the parasites ability to evade the host immune response. A similar mechanism may also operate in other important pathogens.
Spatially explicit approach to population abundance estimation in field surveys
Authors: Takashina Nao , Kusumoto Buntarou , Beger Maria , Rathnayake Suren , Possingham Hugh P. 
Published: April 2017

AbstractThe abundance of species is a fundamental consideration in ecology and conservation biology. Although broad models have been proposed to estimate the population abundance using existing data, available data is often limited. With no information available, a population estimation will rely on time consuming field surveys. Typically, time is a critical constraint in conservation and often management decisions must be made quickly under the data limited situation. Depending on time and budgetary constraints, the required accuracy of field survey changes significantly. Hence, it is desirable to set up an effective survey design to minimize time and effort of sampling given required accuracy. We examine a spatially-explicit approach to population estimation using spatial point processes, enabling us to explicitly and consistently discuss various sampling designs. We find that the accuracy of abundance estimation varies with both ecological factors and survey design. Although the spatial scale of sampling does not affect estimation accuracy when the underlying individual distribution is random, it decreases with the sampled unit size if individuals tend to form clusters. These results are derived analytically and checked numerically. Obtained insights provide a benchmark to predict the quality of population estimation, and improve survey designs for ecological studies and conservation.
The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals
Authors: Shaw Liam , Ribeiro Andre L. R. , Levine Adam P. , Pontikos Nikolas , Balloux Francois , Segal Anthony W. , Roberts Adam P. , Smith Andrew M. 
Published: April 2017

AbstractThe human microbiome is affected by multiple factors, including the environment and host genetics. In this study, we analyzed the oral microbiome of an extended family of Ashkenazi Jewish individuals living in several cities and investigated associations with both shared household and host genetic similarities. We found that environmental effects dominated over genetic ones. While there was weak evidence of geographic structuring at the level of cities, we observed a large and significant effect of shared household on microbiome composition, supporting the role of immediate shared environment in dictating the presence or absence of taxa. This effect was also seen when including adults who had grown up in the same household but moved out prior to the time of sampling, suggesting that the establishment of the oral microbiome earlier in life may affect its long-term composition. We found weak associations between host genetic relatedness and microbiome dissimilarity when using family pedigrees as proxies for genetic similarity. However this association disappeared when using more accurate measures of kinship based on genome-wide genetic markers, indicating that environment rather than host genetics is the dominant factor affecting the composition of the oral microbiome in closely-related individuals. Our results support the concept that there is a consistent core microbiome conserved across global scales, but that small-scale effects due to shared living environment significantly affect microbial community composition.IMPORTANCEPrevious research shows that relatives have a more similar oral microbiome composition than non-relatives, but it remains difficult to distinguish the effects of relatedness and shared household environment. Furthermore, pedigree measures may not accurately measure host genetic similarity. In this study, we include genetic relatedness based on genome-wide SNPs (rather than pedigree measures) and shared environment in the same analysis. We quantify the relative importance of these factors by studying the oral microbiome in members of a large extended Ashkenazi Jewish family who share a similar diet and lifestyle despite living in different locations. We find that host genetics plays no significant role and that the dominant factor is shared environment at the household level. We also find that this effect appears to persist in individuals who have moved out of the parental household, suggesting that the oral microbiome established earlier in life persists long-term.