bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geminiviruses for biotechnology: the art of parasite taming
Authors: Lozano‐Durán Rosa 
Published: July 2015

SummaryViruses are intracellular pathogens that have evolved efficient strategies for replication and expression of their proteins in the host cells. Geminiviruses – plant viruses with small circular single‐stranded DNA genomes – effectively manipulate plant cell processes for viral functions, entailing great potential for biotechnological applications. This potentiality has been realized in the form of protein expression and gene‐silencing vectors, and, more recently, vectors for genome editing – a technology that these viruses seem particularly well‐suited to facilitate. This insight offers an overview of the biological properties of geminiviruses, with emphasis on those leveraging development of geminivirus‐based replicons. It illustrates the basis for engineering geminivirus‐based replicons and their applications. Furthermore, it discusses the reported use and future perspectives of geminivirus‐based replicons for genome editing.

Contents

Summary
58

I.
Introduction
58

II.
Outsourcing DNA synthesis: geminiviral replication
59

III.
Geminivirus‐based replicons: all from one – and one for all
59

IV.
Genome editing in plants: how geminiviruses can help
60

V.
Conclusions and outlook
62

Acknowledgements
63

References
63
Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts
Authors: Bontemps Cyril , Rogel Marco Antonio , Wiechmann Anja , Mussabekova Assel , Moody Sarah , Simon Marcelo F. , Moulin Lionel , Elliott Geoffrey N. , Lacercat‐Didier Laurence , Dasilva Cindy , Grether Rosaura , Camargo‐Ricalde Sara L. , Chen Weimin , Sprent Janet I. , Martínez‐Romero Esperanza , Young J. Peter W. , James Euan K. 
Published: July 2015

Summary

The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species.

We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for betaproteobacteria using in situ immunolocalization. Rhizobia isolated from the nodules were genetically characterized and tested for their ability to nodulate Mimosa spp.

Immunological analysis of 25 host taxa suggested that most (including all the highland endemics) were not nodulated by betaproteobacteria. Phylogenetic analyses of 16S rRNA, recA, nodA, nodC and nifH genes from 87 strains isolated from 20 taxa confirmed that the endemic Mexican Mimosa species favoured alphaproteobacteria in the genera Rhizobium and Ensifer: this was confirmed by nodulation tests.

Host phylogeny, geographic isolation and coevolution with symbionts derived from very different soils have potentially contributed to the striking difference in the choice of symbiotic partners by Mexican and Brazilian Mimosa species.
Urinary L‐FABP as a mortality predictor in <5‐year‐old children with sepsis in Bangladesh
Authors: Yoshimatsu Shoji , Sugaya Takeshi , Hossain Md Iqbal , Islam M Munirul , Chisti Mohammod Jobayer , Kamoda Tomohiro , Fukushima Takashi , Wagatsuma Yukiko , Sumazaki Ryo , Ahmed Tahmeed 
Published: July 2015

AbstractBackgroundAlthough sepsis is often associated with high mortality in severely malnourished children, data are very limited on appropriate diagnostic tools to predict mortality. We examined the role of urinary liver‐type fatty acid‐binding protein (L‐FABP) in children <5 years old with sepsis who died.MethodsThis prospective observational study was conducted at the Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh. Children aged 6–59 months admitted with sepsis from April 2010 to December 2011 were enrolled. Comparison of clinical and laboratory characteristics was made between children who survived (n = 83) and those who did not survive (n = 22).ResultsOn multiple Poisson regression analysis, after adjusting for potential confounders such as mid‐upper arm circumference < 115 mm, plasma albumin < 2.5 g/dL, potassium > 5.0 mmol/L, and blood urea nitrogen > 20 mg/dL on admission, first urine L‐FABP ≥ 370 ng/mL (relative risk [RR], 2.76; 95%CI: 1.22–6.25), weight‐for‐length/height z score < –3 (RR, 2.54; 95%CI: 1.26–5.09), capillary refilling time > 2.0 s (RR, 5.16; 95%CI: 1.46–18.3), and sodium > 160 mmol/L (RR, 2.72; 95%CI: 1.07–6.90) were identified as significant risk factors of mortality in children with sepsis. Diagnostic performance of first urine L‐FABP was analyzed using receiver operating characteristic curve, and the area under the curve was 0.647 (95%CI: 0.500–0.795).ConclusionUrinary L‐FABP may be a useful predictor of mortality in septic children. Urinary examination is non‐invasive and easy to apply at the bedside.
Multidimensional Similarity Measuring for Semantic Trajectories
Authors: Furtado Andre Salvaro , Kopanaki Despina , Alvares Luis Otavio , Bogorny Vania 
Published: July 2015

AbstractMost existing approaches aiming at measuring trajectory similarity are focused on two‐dimensional sequences of points, called raw trajectories. However, recent proposals have used background geographic information and social media data to enrich these trajectories with a semantic dimension, giving rise to the concept of semantic trajectories. Only a few works have proposed similarity measures for semantic trajectories or multidimensional sequences, having limitations such as predefined weight of the dimensions, sensitivity to noise, tolerance for gaps with different sizes, and the prevalence of the worst dimension similarity. In this article we propose MSM, a novel similarity measure for multidimensional sequences that overcomes the aforementioned limitations by considering and weighting the similarity in all dimensions. MSM is evaluated through an extensive experimental study that, based on a seed trajectory, creates sets of semantic trajectories with controlled transformations to introduce different kinds and levels of dissimilarity. For each set, we compute the similarity between the seed and the transformed trajectories, using different measures. The results showed that MSM was more robust and efficient than related approaches in the domain of semantic trajectories.
The network K‐function in context: examining the effects of network structure on the network K‐function
Authors: Lamb David S. , Downs Joni A. , Lee Chanyoung 
Published: July 2015

AbstractThe flaws of using traditional planar point‐pattern analysis techniques with network constrained points have been thoroughly explored in the literature. Because of this, new network‐based measures have been introduced for their planar analogues, including the network based K‐function. These new measures involve the calculation of network distances between point events rather than traditional Euclidean distances. Some have suggested that the underlying structure of a network, such as whether it includes directional constraints or speed limits, may be considered when applying these methods. How different network structures might affect the results of the network spatial statistics is not well understood. This article examines the results of network K‐functions when taking into consideration network distances for three different types of networks: the original road network, topologically correct networks, and directionally constrained networks. For this aim, four scenarios using road networks from Tampa, Florida and New York City, New York were used to test how network constraints affected the network K‐function. Depending on which network is under consideration, the underlying network structure could impact the interpretation. In particular, directional constraints showed reduced clustering across the different scenarios. Caution should be used when selecting the road network, and constraints, for a network K‐function analysis.
Effect of Sampling Frequency on Isometric Midthigh-Pull Kinetics
Authors: Dos’Santos Thomas , Jones Paul A. , Kelly Jonathan , McMahon John J. , Comfort Paul , Thomas Christopher 
Published: July 2015

Purpose:Skeletal-muscle function can be evaluated using force–times curves generated via the isometric midthigh pull (IMTP). Various sampling frequencies (500–1000 Hz) have been used for IMTP assessments; however, no research has investigated the influence of sampling frequency on IMTP kinetics. Therefore, the purpose of this study was to investigate the influence of sampling frequency on kinetic variables during the IMTP, including peak force, time-specific force values (100, 150, and 200 ms), and rate of force development (RFD) at 3 time bands (0–100, 0–150, 0–200 ms).Methods:Academy rugby league players (n = 30, age 17.5 ± 1.1 y, height 1.80 ± 0.06 m, mass 85.4 ± 10.3 kg) performed 3 IMTP trials on a force platform sampling at 2000 Hz, which was subsequently down-sampled to 1500, 1000, and 500 Hz for analysis.Results:Intraclass correlation coefficients (ICC) and coefficients of variation (CV) demonstrated high within-session reliability for all force and RFD variables across all sampling frequencies (ICC ≥ .80, CV ≤ 10.1%). Repeated-measures analysis of variance revealed no significant differences (P > .05, Cohen d ≤ 0.009) in kinetic variables between sampling frequencies. Overall, high reliability was observed across all sampling frequencies for all kinetic variables, with no significant differences (P > .05) for each kinetic variable across sampling frequencies.Conclusions:Practitioners and scientists may consider sampling as low as 500 Hz when measuring peak force, time-specific force values, and RFD at predetermined time bands during the IMTP for accurate and reliable data.
The Effect of Body Mass on the 30-15 Intermittent Fitness Test in Rugby Union Players
Authors: Darrall-Jones Joshua , Roe Gregory , Carney Shane , Clayton Ryan , Phibbs Padraic , Read Dale , Weakley Jonathon , Till Kevin , Jones Ben 
Published: July 2015

Purpose:To evaluate the difference in performance of the 30-15 Intermittent Fitness Test (30–15IFT) across 4 squads in a professional rugby union club in the UK and consider body mass in the interpretation of the end velocity of the 30-15IFT (VIFT).Methods:One hundred fourteen rugby union players completed the 30-15IFT midseason.Results:VIFT demonstrated small and possibly lower (ES = –0.33; 4/29/67) values in the under 16s compared with the under 21s, with further comparisons unclear. With body mass included as a covariate, all differences were moderate to large and very likely to almost certainly lower in the squads with lower body mass, with the exception of comparisons between senior and under-21 squads.Conclusions:The data demonstrate that there appears to be a ceiling to the VIFT attained in rugby union players that does not increase from under-16 to senior level. However, the associated increases in body mass with increased playing level suggest that the ability to perform high-intensity running increases with age, although not translating into greater VIFT due to the detrimental effect of body mass on change of direction. Practitioners should be aware that VIFT is unlikely to improve, but it needs to be monitored during periods where increases in body mass are evident.
Effect of Different Repeated-High-Intensity-Effort Bouts on Subsequent Running, Skill Performance, and Neuromuscular Function
Authors: Johnston Rich D. , Gabbett Tim J. , Jenkins David G. , Speranza Michael J. 
Published: July 2015

Purpose:To assess the impact of different repeated-high-intensity-effort (RHIE) bouts on player activity profiles, skill involvements, and neuromuscular fatigue during small-sided games.Participants:22 semiprofessional rugby league players (age 24.0 ± 1.8 y, body mass 95.6 ± 7.4 kg).Methods:During 4 testing sessions, they performed RHIE bouts that each differed in the combination of contact and running efforts, followed by a 5-min off-side small-sided game before performing a second bout of RHIE activity and another 5-min small-sided game. Global positioning system microtechnology and video recordings provided information on activity profiles and skill involvements. A countermovement jump and a plyometric push-up assessed changes in lower- and upper-body neuromuscular function after each session.Results:After running-dominant RHIE bouts, players maintained running intensities during both games. In the contact-dominant RHIE bouts, reductions in moderate-speed activity were observed from game 1 to game 2 (ES = –0.71 to –1.06). There was also moderately lower disposal efficiency across both games after contact-dominant RHIE activity compared with running-dominant activity (ES = 0.62–1.02). Greater reductions in lower-body fatigue occurred as RHIE bouts became more running dominant (ES = –0.01 to –1.36), whereas upper-body fatigue increased as RHIE bouts became more contact dominant (ES = –0.07 to –1.55).Conclusions:Physical contact causes reductions in running intensity and the quality of skill involvements during game-based activities. In addition, the neuromuscular fatigue experienced by players is specific to the activities performed.
Lobular breast cancer - the most common special subtype or a most special common subtype?
Authors: Lehmann Ulrich 
Published: July 2015

AbstractLobular breast cancer is not only the second most common breast cancer subtype, known for decades, but also a tumour entity that still poses many unresolved questions. These include questions about the targets and cooperation partners of E-cadherin, the best model systems for translational research, and the best tools for detection, surveillance and therapy. Leading experts review the molecular and cellular bases, the model systems, the histopathology and profiling approaches, risk factors, imaging tools and therapeutic options for lobular breast cancer.
Laparoscopic splenectomy is emerging ‘gold standard’ treatment even for massive spleens
Authors: Somasundaram SK , Massey L , Gooch D , Reed J , Menzies D 
Published: July 2015

Introduction Since its first description by Delaitre and Maignien in 1991, laparoscopic splenectomy (LS) has evolved as treatment of choice for mild-to-moderately-enlarged spleens and for benign haematological disorders. LS is a challenge if massive spleens or malignant conditions necessitate treatment, but we report our method and its feasibility in this study. Methods We undertook a retrospective study of prospectively collected data of all elective splenectomies carried out in our firm of upper gastrointestinal surgeons from June 2003 to June 2012. Only patients opting for elective LS were included in this study. Results From June 2003 to June 2012, elective splenectomy was carried out in 80 patients. Sixty-seven patients underwent LS and 13 underwent open splenectomy (OS). In the LS group, there were 38 males and 29 females. Age ranged from 6 years to 82 years. Spleen size in the LS group ranged from ≤11cm to 27.6cm. Twelve patients had a spleen size of >20cm. Weight ranged from 35g to 2,400g. Eighteen patients had a spleen weight of 600–1,600g and eight had a spleen weight >1,600g. Operating times were available for 56 patients. Mean operating time for massive spleens was 129.73 min. There was no conversion to OS. There were no major complications. Conclusions With improved laparoscopic expertise and advancing technology, LS is safe and feasible even for massive spleens and splenic malignancies. It is the emerging ‘gold standard’ for all elective splenectomies and has very few contraindications.
Acute afferent loop syndrome in the early postoperative period following pancreaticoduodenectomy
Authors: Nageswaran H , Belgaumkar A , Kumar R , Riga A , Menezes N , Worthington T , Karanjia ND 
Published: July 2015

Introduction Afferent loop syndrome (ALS) is a recognised complication of foregut surgery caused by mechanical obstruction at the gastrojejunostomy anastomosis itself or at a point nearby. Acute ALS has only been reported following pancreaticoduodenectomy (PD) after several years due to recurrence of malignancy at the anastomotic site. We report five cases of acute ALS in the first postoperative week. Methods The presentation, clinical findings and successful management of the 5 patients with ALS were obtained from a prospectively collected database of 300 PDs. All five patients with early acute ALS presented with signs and symptoms of a bile leak. Since the fifth patient, the surgical technique has been modified with the creation of a larger window in the transverse mesocolon and a Braun enteroenterostomy. Results There have been no further incidents of ALS since the adoption of these modifications to the standard technique of PD and there has also been a reduction in postoperative bile leaks (6.4% vs 3.6%, p=0.416). Conclusions Acute ALS is a rare but important complication in the immediate postoperative period following PD and causes disruption to adjacent anastomoses, resulting in a bile leak. A prophylactic Braun anastomosis and wide mesocolic window may prevent this complication and subsequent deterioration.
The two-port laparoscopic retroperitoneal approach for minimal access pancreatic necrosectomy
Authors: Cresswell AB , Nageswaran H , Belgaumkar A , Kumar R , Menezes N , Riga A , Worthington TR , Karanjia ND 
Published: July 2015

Introduction Despite advances in surgery and critical care, severe pancreatitis continues to be associated with a high rate of mortality, which is increased significantly in the presence of infected pancreatic necrosis. Controversy persists around the optimal treatment for such cases, with specialist units variously advocating open necrosectomy, simple percutaneous drainage or one of several minimal access approaches. We describe our technique and outcomes with a two-port laparoscopic retroperitoneal necrosectomy (2P-LRN). Methods Thirteen consecutive patients with proven infected pancreatic necrosis were treated by 2P-LRN over a three-year period in the setting of a specialist hepatopancreatobiliary unit. The median patient age was 46 years (range: 28–87 years) and 10 of the patients were male. Results The median number of procedures required to clear the necrosis was 2 (range: 1–5), with a median time to discharge following the procedure of 44 days (range: 10–135 days). There was no 90-day mortality and the morbidity rate was 38%, consisting of pancreatic fistula (31%) and bleeding (23%). Conclusions Two-port laparoscopic retroperitoneal necrosectomy has been demonstrated to confer similar or better outcomes to other techniques for necrosectomy. It carries the additional advantages of better visualisation, leading to fewer procedures and the opportunity to deploy simple laparoscopic instruments such as diathermy or haemostatic clips.
A two-year follow-up observational study of the T-14 paediatric throat disorders outcome measure in tonsillectomy and adenotonsillectomy
Authors: Konieczny KM , Biggs TC , Pringle MB 
Published: July 2015

Introduction The T-14 questionnaire is a validated patient reported outcome measure used to assess the value of paediatric tonsillectomy from the patient’s perspective. There are currently limited data revealing the long-term postoperative effects of tonsillectomy on quality of life in the paediatric population. A previously published study was therefore extended to provide additional data at 12 and 24 months following surgery. Methods A prospective uncontrolled observational study was undertaken examining 54 paediatric patients undergoing tonsillectomy at Portsmouth Hospitals NHS Trust. Parents of children having surgery were invited to complete a T-14 questionnaire preoperatively as well as at 3, 6 (previously published), 12 and 24 months postoperatively. Results The questionnaire was completed for 50 of the 54 patients preoperatively as well as at 3, 6 and 12 months postoperatively, with 44 being completed at 24 months. The mean difference between the preoperative T-14 scores and the scores at 3, 6, 12 and 24 months following surgery were highly statistically significant (p<0.001). Conclusions This is the first study published in the literature to assess the T-14 questionnaire at 12 and 24 months following paediatric tonsillectomy, providing evidence of the ongoing benefit of patient reported outcome measures. This further confirms the value of tonsillectomy in the paediatric population and demonstrates its ongoing positive effects on quality of life.
The Emergency Surgical Team – The Way Forward in Emergency Care?
Authors: Tincknell Laura , Burton Sarah , Cooke Claire , Black Stephen , Andreani Stefano , Jourdan Iain , Gudgeon Mark 
Published: July 2015

INTRODUCTION With reduced working hours and shift patterns, surgical training and continuity of patient care is being put at risk. We have devised a system for managing the emergency surgical patients in an effort to counteract these perceived problems. This study describes the emergency surgical team and audits its activity. PATIENTS AND METHODS The emergency surgery team concept is described in detail. Over a 2-week period, general surgical referral data, patient management and operative activity were audited. RESULTS A total of 229 patients were referred to the emergency surgical team with 159 treated conservatively, 45 underwent operative intervention and 25 were discharged without admission. Of the emergency surgical team referrals, 58% had gallstone pathology, appendicitis or constipation/non-specific abdominal pain. Average daily number of patients under the care of the emergency surgical team was 26 (range, 10–40). CONCLUTIONS The consultant-led emergency surgical team look after many of the acutely sick surgical patients. Our system not only provides good teaching opportunities but ensures optimal continuity of patient care in a busy district general hospital. Such an approach to emergency surgical care has been successfully developed to optimise training opportunities and improve patient care in a setting of reduced working hours and shift systems in our hospital.
An assessment of fine-needle sampling techniques
Authors: Titoria Puneet , Siva Thiru M , Malik Tass 
Published: July 2015

INTRODUCTION Fine-needle cytology sampling, when adequate, is highly sensitive and specific for tissue-type diagnosis, with figures of 94% and 88%, respectively. This study explores the technique of sampling to reduce interoperator variability and ensure maximal tissue yield. MATERIALS AND METHODS Apple cortical tissue was sampled as a proxy of human lymph node. A total of 200 samples, by four methods, with 50 by each sampling method, were taken using blue venepuncture needles and weighed to assess tissue yield. Results were analysed using one-way analysis of variance and Tukey's HSD test. Comparable yields, by mass, were achieved by both straight lance and coring techniques (P > 0.05). Significantly greater yield was achieved with a multiplanar technique (P < 0.05). CONCLUSIONS Multiplanar sampling increases mass yield of tissue in fine-needle sampling. Coring appears to have little bearing on yield.