bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)
Authors: HEENAN PETER B. , SMISSEN ROB D. 
Published: November 2013

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera. Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.
Interannual Variability of East Asian Summer Monsoon Simulated by CMIP3 and CMIP5 AGCMs: Skill Dependence on Indian Ocean–Western Pacific Anticyclone Teleconnection
Authors: Song Fengfei , Zhou Tianjun 
Published: November 2013

Abstract
The climatology and interannual variability of East Asian summer monsoon (EASM) are investigated by using 13 atmospheric general circulation models (AGCMs) from phase 3 of the Coupled Model Intercomparison Project (CMIP3) and 19 AGCMs from CMIP5. The mean low-level monsoon circulation is reasonably reproduced in the multimodel ensemble mean (MME) of CMIP3 and CMIP5 AGCMs, except for a northward shift of the western Pacific subtropical high. However, the monsoon rainband known as mei-yu/baiu/changma (28°–38°N, 105°–150°E) is poorly simulated, although a significant improvement is seen from CMIP3 to CMIP5. The interannual EASM pattern is obtained by regressing the precipitation and 850-hPa wind on the observed EASM index. The observed dipole rainfall pattern is partly reproduced in CMIP3 and CMIP5 MME but with two deficiencies: weaker magnitude and southward shift of the dipole rainfall pattern. These deficiencies are closely related to the weaker and southward shift of the western Pacific anticyclone (WPAC). The simulation skill of the interannual EASM pattern has been significantly improved from CMIP3 to CMIP5 MME accompanied by the enhanced dipole rainfall pattern and WPAC. Analyses demonstrate that the tropical eastern Indian Ocean (IO) rainfall response to local warm SST anomalies and the associated Kelvin wave response over the Indo–western Pacific region are important to maintain the WPAC. A successful reproduction of interannual EASM pattern depends highly on the IO–WPAC teleconnection. The significant improvement in the interannual EASM pattern from CMIP3 to CMIP5 MME is also due to a better reproduction of this teleconnection in CMIP5 models.
Time-Variable Refraction of the Internal Tide at the Hawaiian Ridge
Authors: Zaron Edward D. , Egbert Gary D. 
Published: November 2013

Abstract
The interaction of the dominant semidiurnal M2 internal tide with the large-scale subtidal flow is examined in an ocean model by propagating the tide through an ensemble of background fields in a domain centered on the Hawaiian Ridge. The background fields are taken from the Simple Ocean Data Assimilation (SODA) ocean analysis, at 2-month intervals from 1992 through 2001. Tides are computed with the Primitive Equation Z-coordinate Harmonic Analysis of Tides (PEZ-HAT) model by 14-day integrations using SODA initial conditions and M2 tidal forcing. Variability of the tide is found to occur primarily as the result of propagation through the nonstationary background fields, rather than via generation site variability. Generation of incoherent tidal variability is mapped and shown to occur mostly in association with waves generated at French Frigate Shoals scattering near the Musicians Seamounts to the north of the ridge. The phase-coherent internal tide loses energy at a domain-average rate of 2 mW m−2 by scattering into the nonstationary tide. Because of the interference of waves from multiple generation sites, variability of the internal tide is spatially inhomogeneous and values of the scattering rate 10 times larger occur in localized areas. It is estimated that 20% of the baroclinic tidal energy flux is lost by adiabatic scattering (refraction) within 250 km of the ridge, a value regarded as a lower bound because of the smoothed nature of the SODA fields used in this study.
Characteristics of Tropical Easterly Wave Pouches during Tropical Cyclone Formation
Authors: Wang Zhuo , Hankes Isaac 
Published: November 2013

Abstract
The pregenesis evolution of wave pouches was examined for 164 named tropical cyclones that originated from zonally propagating tropical easterly waves over the Atlantic during July–October 1989–2010 using the European Centre for Medium-Range Weather Forecasts (ECMWF) Interim Re-Analysis (ERA-Interim) and the Climate Prediction Center (CPC) morphing technique (CMORPH) precipitation. East of 60°W, most wave pouches (~80%) form at 700 hPa first, often extending down to 850 or 925 hPa off the coast of West Africa. By contrast, the majority of the wave pouches (~68%) over the west Atlantic (west of 60°W) form at 850 or 925 hPa first. Wave pouches become more vertically aligned approaching genesis. It was also found that vorticity at 925 hPa intensifies faster than that at 600 hPa. A warm-core structure forms at the meso-β scale near the pouch center prior to genesis but is less well defined at the meso-α pouch scale. The evolution of precipitation and the low-level convergence suggests that convection begins to organize near the pouch center about 1 day prior to genesis, along with the rapid intensification of vorticity in the inner pouch region. The composites derived from ERA-Interim show that the inner pouch region has higher specific humidity and equivalent potential temperature, especially in the middle troposphere within 1 day prior to genesis.
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
Authors: Guo Weilong , Fiziev Petko , Yan Weihong , Cokus Shawn , Sun Xueguang , Zhang Michael Q , Chen Pao-Yang , Pellegrini Matteo 
Published: November 2013

Abstract

Background
DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data.

Results
We have developed BS-Seeker2, an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes. BS-Seeker2 improves mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy. Moreover, BS-Seeker2 provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing the overestimation of DNA methylation levels. We also defined CGmap and ATCGmap file formats for full representations of DNA methylomes, as part of the outputs of BS-Seeker2 pipeline together with BAM and WIG files.

Conclusions
Our evaluations on the performance show that BS-Seeker2 works efficiently and accurately for both WGBS data and RRBS data. BS-Seeker2 is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ and the Galaxy server.
A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton
Authors: Said Joseph I , Lin Zhongxu , Zhang Xianlong , Song Mingzhou , Zhang Jinfa 
Published: November 2013

Abstract

Background
The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and pest resistance, branch number, seed quality and yield and yield related traits, drought tolerance, and morphological traits. However, results among these studies differed due to the use of different genetic populations, markers and marker densities, and testing environments. Since two previous meta-QTL analyses were performed on fiber traits, a number of papers on QTL mapping of fiber quality, yield traits, morphological traits, and disease resistance have been published. To obtain a better insight into the genome-wide distribution of QTL and to identify consistent QTL for marker assisted breeding in cotton, an updated comparative QTL analysis is needed.

Results
In this study, a total of 1,223 QTL from 42 different QTL studies in Gossypium were surveyed and mapped using Biomercator V3 based on the Gossypium consensus map from the Cotton Marker Database. A meta-analysis was first performed using manual inference and confirmed by Biomercator V3 to identify possible QTL clusters and hotspots. QTL clusters are composed of QTL of various traits which are concentrated in a specific region on a chromosome, whereas hotspots are composed of only one trait type. QTL were not evenly distributed along the cotton genome and were concentrated in specific regions on each chromosome. QTL hotspots for fiber quality traits were found in the same regions as the clusters, indicating that clusters may also form hotspots.

Conclusions
Putative QTL clusters were identified via meta-analysis and will be useful for breeding programs and future studies involving Gossypium QTL. The presence of QTL clusters and hotspots indicates consensus regions across cultivated tetraploid Gossypium species, environments, and populations which contain large numbers of QTL, and in some cases multiple QTL associated with the same trait termed a hotspot. This study combines two previous meta-analysis studies and adds all other currently available QTL studies, making it the most comprehensive meta-analysis study in cotton to date.
Comfort, safety and quality of upper gastrointestinal endoscopy after 2 hours fasting: a randomized controlled trial
Authors: Koeppe Angélica Terezinha , Lubini Marcio , Bonadeo Nilton Maiolini , Moraes Iran , Fornari Fernando 
Published: November 2013

Abstract

Background
Upper gastrointestinal endoscopy has been performed after fasting 8 or more hours, which can be harmful to the patients. We assessed comfort, safety and quality of endoscopy under moderate sedation after 2 hours fasting for clear liquids.

Methods
In this clinical trial, patients referred for elective endoscopy were randomly assigned to a fasting period of 8 hours (F8) or a shorter fasting (F2), in which 200 ml of clear liquids were ingested 2 hours before the procedure. Endoscopists blinded to patients fasting status carried out the endoscopies. Comfort was rated by the patients, whereas safety and quality were determined by the endoscopists.

Results
Ninety-eight patients were studied (aging 48.5 ± 16.5 years, 60% women): 50 patients (51%) in F2 and 48 in F8. Comfort was higher in F2 than F8 in regard to anxiety (8% vs. 25%; P = 0.029), general discomfort (18% vs. 42%; P = 0.010), hunger (44% vs. 67%; P = 0.024), and weakness (22% vs. 42%; P = 0.034). Regurgitation of gastric contents into the esophagus after endoscopic intubation did not differ between F2 and F8 (26% vs. 19%; P = 0.471). There was no case of pulmonary aspiration. Gastric mucosal visibility was normal in most patients either in F2 or F8 (96% vs. 98%; P = 0.999).

Conclusions
Elective upper GI endoscopy after 2 hours fasting for clear liquids was more comfortable and equally safe compared to conventional fasting. This preparation might be cautiously applied for patients in regular clinical conditions referred for elective endoscopy.

Trial registration
SAMMPRIS ClinicalTrial.gov number, NCT01492296
Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity
Authors: DaRe Jeana T , Vasta Valeria , Penn John , Tran Nguyen-Thao B , Hahn Si Houn 
Published: November 2013

Abstract

Background
Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities.

Methods
We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested.

Results
We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders.

Conclusions
Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here.
Wnt signaling in triple negative breast cancer is associated with metastasis
Authors: Dey Nandini , Barwick Benjamin G , Moreno Carlos S , Ordanic-Kodani Maja , Chen Zhengjia , Oprea-Ilies Gabriella , Tang Weining , Catzavelos Charles , Kerstann Kimberly F , Sledge George W , Abramovitz Mark , Bouzyk Mark , De Pradip , Leyland-Jones Brian R 
Published: November 2013

Abstract

Background
Triple Negative subset of (TN) Breast Cancers (BC), a close associate of the basal-like subtype (with limited discordance) is an aggressive form of the disease which convey unpredictable, and poor prognosis due to limited treatment options and lack of proven effective targeted therapies.

Methods
We conducted an expression study of 240 formalin-fixed, paraffin-embedded (FFPE) primary biopsies from two cohorts, including 130 TN tumors, to identify molecular mechanisms of TN disease.

Results
The annotation of differentially expressed genes in TN tumors contained an overrepresentation of canonical Wnt signaling components in our cohort and others. These observations were supported by upregulation of experimentally induced oncogenic Wnt/β-catenin genes in TN tumors, recapitulated using targets induced by Wnt3A. A functional blockade of Wnt/β-catenin pathway by either a pharmacological Wnt-antagonist, WntC59, sulidac sulfide, or β-catenin (functional read out of Wnt/β-catenin pathway) SiRNA mediated genetic manipulation demonstrated that a functional perturbation of the pathway is causal to the metastasis- associated phenotypes including fibronectin-directed migration, F-actin organization, and invasion in TNBC cells. A classifier, trained on microarray data from β-catenin transfected mammary cells, identified a disproportionate number of TNBC breast tumors as compared to other breast cancer subtypes in a meta-analysis of 11 studies and 1,878 breast cancer patients, including the two cohorts published here. Patients identified by the Wnt/β-catenin classifier had a greater risk of lung and brain, but not bone metastases.

Conclusion
These data implicate transcriptional Wnt signaling as a hallmark of TNBC disease associated with specific metastatic pathways.
A feasibility study of expert patient and community mental health team led bipolar psychoeducation groups: implementing an evidence based practice
Authors: Coulthard Katharine , Patel Dipty , Brizzolara Clare , Morriss Richard , Watson Stuart 
Published: November 2013

Abstract

Background
Group psychoeducation is a cost effective intervention which reduces relapse and improves functioning in bipolar disorder but is rarely implemented. The aim of this study was to identify the acceptability and feasibility of a group psychoeducation programme delivered by community mental health teams (CMHTs) and peer specialist (PS) facilitators. Organisational learning was used to identify and address systematically barriers and enablers, at organisational, health professional and patient levels, to its implementation into a routine service.

Methods
A systematic examination of barriers and enablers to a three day training process informed the delivery of a first treatment group and a similar process informed the delivery of the second treatment group. Triangulation of research methods improved its internal validity: direct observation of training, self-rated surveys of participant experiences, group discussion, and thematically analysed individual participant and facilitator interviews were employed.

Results
Barriers and enablers were identified at organisational, educational, treatment content, facilitator and patient levels. All barriers under the control of the research team were addressed with subsequent improvements in patient knowledge about the condition and about local service. In addition, self-management, agency and altruism were enhanced. Barriers that could not be addressed required senior clinical and education leadership outside the research team’s control. PS and professional facilitators were successfully trained and worked together to deliver groups which were generally reported as being beneficial.

Conclusion
Psychoeducation groups involving CMHT and PS facilitators is acceptable and feasible but their sustainment requires senior leadership within and outside the organisation that control finance and education services.
Inactivated autograft–prosthesis composite have a role for grade III giant cell tumor of bone around the knee
Authors: Xu SongFeng , Yu XiuChun , Xu Ming , Fu ZhiHou 
Published: November 2013

AbstractBackgroundGiant cell tumors (GCT) around the knee are common and pose a special problem of reconstruction after tumor excision, especially for grade III GCT. We questioned whether en bloc resection and reconstruction with alcohol inactivated autograft-prosthesis composite would provide (1) local control and long-term survival and (2) useful limb function in patients who had grade III GCT around the knee.MethodsWe retrospectively reviewed eight patients (5 males and 3 females) treated with this procedure with mean age of 31 years (range 20 to 43 years) from Jan 2007 to Oct 2008. 5 lesions were located in distal femur and 3 in proximal tibia. 4 patients were with primary tumor and the other 4 with recurrence. 2 patients showed pathological fracture.ResultsMean Follow-up is 54 months ranging from 38 to 47 months. No recurrence, metastasis, prosthesis loosening were found. The mean healing time between autograft and host bone was 5.5 months. The mean MSTS score was 26.3 (88%) ranging from 25 to 29. The mean ISOLS composite graft score was 32.8 (88.5%) ranging from 28 to 35. Creeping substitution is possibly the main way in bony junction. The healing time in femoral lesion is faster than that in tibial lesion.ConclusionsThe technique of alcohol inactivated autograft-prosthesis composite could be able to achieve satisfactory oncological and functional outcomes in Grade III GCT.
Evaluation of ranges of motion of a new constrained acetabular prosthesis for canine total hip replacement
Authors: Wu Ching-Ho , Lin Cheng-Chung , Lu Tung-Wu , Hou Sheng-Mao , Hu Chih-Chung , Yeh Lih-Seng 
Published: November 2013

AbstractBackgroundTotal hip replacement (THR) is considered to be the most effective treatment option for advanced osteoarthritis of the hip in large breed dogs. However, a proportion of post-THR patients suffer prosthesis dislocation for various reasons, which may be addressed by a constrained acetabular prosthesis design. The study proposed a new THR with constrained acetabular component that aimed to decrease the incidence of postoperative dislocation while maintaining the necessary range of motion (ROM); and, through computer-simulated implantations, evaluated the ROM of the THR with and without malpositioning of the acetabular component.MethodsA new THR with a constrained acetabular component that had an inward eccentric lining and a 60° cut-out on the dorsal side was designed, and its computer-aided design models were implanted into the pelvic and femoral models reconstructed from the computed tomography data of six healthy Labrador Retriever dogs. The allowable and functional ROM of the implanted THR were determined via computer simulations. The contact patterns between the bone or the prosthetic components at extreme positions of the THR were analyzed. Influence of malpositioning of the acetabular component on the ROM was assessed.ResultsThe means (SD) of the functional ranges for flexion, extension, adduction, abduction, internal rotation and external rotation were 51.8° (6.6°), 163.3° (7.3°), 33.5° (5.7°), 74.0° (3.7°), 41.5° (8.3°) and 65.2° (9.9°), respectively. Malpositioning of the acetabular component by 20° in one direction was found to reduce ROM in other directions (reducing lateral opening: flexion: 12°, adduction: 20°, internal/external rotations: < 20°; increasing lateral opening: extension and abduction: < 16°; reducing retroversion: extension: < 20°, abduction: 15°, external rotation: < 20°; increasing retroversion: flexion: < 20°, abduction, adduction and internal rotation: 20°).ConclusionsFrom the computer-aided surgical simulations, the new THR was found to have sufficient functional ranges for flexion, extension, abduction, adduction and external rotation for Labrador Retrievers. Analysis of the malpositioning of the acetabular component suggests that accurate placement of the acetabular component is critical for achieving desirable ROM for daily activities.
Massive hemoptysis controlled with transection of a pulmonary vein and bronchus-a case report
Authors: Ho Hui-Ju , Cheng Ching-Yuan , Wang Bing-Yen 
Published: November 2013

Abstract
Massive hemoptysis caused by bronchiectasis in which bronchial artery embolization does not control the bleeding is not rare. Traditional surgical intervention is anatomical lung resection. We present a case of a patient with bronchiectasis and massive hemoptysis in which the bleeding was controlled with transection of a pulmonary vein and bronchus with preservation of the pulmonary artery.