bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell‐level anatomical characteristics explain high mesophyll conductance and photosynthetic capacity in sclerophyllous Mediterranean oaks
Authors: Peguero‐Pina José Javier , Sisó Sergio , Flexas Jaume , Galmés Jeroni , García‐Nogales Ana , Niinemets Ülo , Sancho‐Knapik Domingo , Saz Miguel Ángel , Gil‐Pelegrín Eustaquio 
Published: January 2017

Summary

Leaf mass per area (LMA) has been suggested to negatively affect the mesophyll conductance to CO2 (gm), which is the most limiting factor for area‐based photosynthesis (AN) in many Mediterranean sclerophyll species. However, despite their high LMA, these species have similar AN to plants from other biomes. Variations in other leaf anatomical traits, such as mesophyll and chloroplast surface area exposed to intercellular air space (Sm/S and Sc/S), may offset the restrictions imposed by high LMA in gm and AN in these species.

Seven sclerophyllous Mediterranean oaks from Europe/North Africa and North America with contrasting LMA were compared in terms of morphological, anatomical and photosynthetic traits.

Mediterranean oaks showed specific differences in AN that go beyond the common morphological leaf traits reported for these species (reduced leaf area and thick leaves). These variations resulted mainly from the differences in gm, the most limiting factor for carbon assimilation in these species.

Species with higher AN showed increased Sc/S, which implies increased gm without changes in stomatal conductance. The occurrence of this anatomical adaptation at the cell level allowed evergreen oaks to reach AN values comparable to congeneric deciduous species despite their higher LMA.
Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection
Authors: Kolawole Adesike O. , Menkir Abebe , Gedil Melaku , Blay Essie , Ofori Kwadwo , Kling Jennifer G. 
Published: January 2017

AbstractTwo tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S1 lines each from the original (C0) and advanced (C4) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C0 to C4, whereas those at intermediate frequencies increased at C4 in the two composites. More unique and other alleles were lost at C4 in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S1 lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.
Effects of iron deficiency on the growth and photosynthesis of three bloom‐forming cyanobacterial species isolated from Lake Taihu
Authors: Xu Kui , Li Zheng‐Ke , Liu Shu‐Wen , Qiu Bao‐Sheng 
Published: January 2017

SUMMARYCyanobacterial blooms are found in many freshwater ecosystems around the world, but the effect of environmental factors on their growth and the proportion of species still require more investigation. In this study, the physiological responses of bloom‐forming cyanobacteria
M

icrocystis aeruginosa FACHB912,
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icrocystis flos‐aquae FACHB1028 and
P

seudanabaena sp. FACHB1282 to iron deficiency were investigated. Their specific growth rates were found to decrease as the available iron concentration decreased. At low available iron concentrations of 1 × 10−7 M (pFe 21.3) and 5 × 10−8 M (pFe 21.6),
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. aeruginosa had the lowest specific growth rate among three studied species. The cell sizes of
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. flos‐aquae and Pseudanabaena sp. were significantly smaller under the lowest iron concentration. The chlorophyll a content of the three species decreased at the lowest iron concentration. The maximal relative electron transport rate, photosynthetic efficiency, and light‐saturation parameter of
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. aeruginosa were lower than the other two cyanobacteria at pFe 21.3. Therefore,
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. aeruginosa was the least able to adapt to iron deficiency. Under iron deficiency, the functional absorption cross‐section of PSII and electron transport rate on the acceptor side of PSII decreased in
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. aeruginosa, while the connectivity factor between individual photosynthetic units increased in
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. flos‐aquae, and the electron transport rate on the acceptor side of PSII and between PSII and PSI decreased in
P

seudanabaena sp. The ability to store iron was highest in
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. flos‐aquae, followed by
P

seudanabaena sp. and
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. aeruginosa. Thus, these results provide necessary information for detecting the role of iron in the succession of cyanobacterial species in Lake Taihu, the third largest freshwater lake in China, because all three species were isolated from this lake.
Complete Genome Sequences of 38
Gordonia
sp. Bacteriophages
Authors: Pope Welkin H. , Montgomery Matthew T. , Bonilla J. Alfred , Dejong Randall , Garlena Rebecca A. , Guerrero Bustamante Carlos , Klyczek Karen K. , Russell Daniel A. , Wertz John T. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: January 2017

ABSTRACT

We report here the genome sequences of 38 newly isolated bacteriophages using
Gordonia terrae
3612 (ATCC 25594) and
Gordonia neofelifaecis
NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.
Technical and scale efficiency in the delivery of child health services in Zambia: results from data envelopment analysis
Authors: Achoki Tom , Hovels Anke , Masiye Felix , Lesego Abaleng , Leufkens Hubert , Kinfu Yohannes 
Published: January 2017

ObjectiveDespite tremendous efforts to scale up key maternal and child health interventions in Zambia, progress has not been uniform across the country. This raises fundamental health system performance questions that require further investigation. Our study investigates technical and scale efficiency (SE) in the delivery of maternal and child health services in the country.SettingThe study focused on all 72 health districts of Zambia.MethodsWe compiled a district-level database comprising health outcomes (measured by the probability of survival to 5 years of age), health outputs (measured by coverage of key health interventions) and a set of health system inputs, namely, financial resources and human resources for health, for the year 2010. We used data envelopment analysis to assess the performance of subnational units across Zambia with respect to technical and SE, controlling for environmental factors that are beyond the control of health system decision makers.ResultsNationally, average technical efficiency with respect to improving child survival was 61.5% (95% CI 58.2% to 64.8%), which suggests that there is a huge inefficiency in resource use in the country and the potential to expand services without injecting additional resources into the system. Districts that were more urbanised and had a higher proportion of educated women were more technically efficient. Improved cooking methods and donor funding had no significant effect on efficiency.ConclusionsWith the pressing need to accelerate progress in population health, decision makers must seek efficient ways to deliver services to achieve universal health coverage. Understanding the factors that drive performance and seeking ways to enhance efficiency offer a practical pathway through which low-income countries could improve population health without necessarily seeking additional resources.
Efficacy of interventions to improve physical activity levels in individuals with stroke: a systematic review protocol
Authors: Aguiar Larissa Tavares , Martins Júlia Caetano , Nadeau Sylvie , Britto Raquel Rodrigues , Teixeira-Salmela Luci F , Faria Christina D C M 
Published: January 2017

IntroductionStroke is a leading health problem worldwide and an important cause of disability. Stroke survivors show low levels of physical activity, and increases in physical activity levels may improve function and health status. Therefore, the aims are to identify which interventions that have been employed to increase physical activity levels with stroke survivors, to verify their efficacy and to identify the gaps in the literature.Methods and analysisA systematic review of randomised controlled trials that investigated the efficacy of interventions aiming at increasing physical activity levels of stroke survivors will be conducted. Electronic searches will be performed in the MEDLINE, Physiotherapy Evidence Database (PEDro), Excerpta Medica (EMBASE), Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS) and Scientific Electronic Library Online (SCIELO) databases. Hand searches of the reference lists of the included studies or relevant reviews will also be employed. Two independent reviewers will screen all the retrieved titles, abstracts and full texts. A third reviewer will be referred to solve any disagreements. The quality of the included studies will be assessed by the PEDro Rating Scale. This systematic review will also include a qualitative synthesis. Meta-analyses will be performed, if the studies are sufficiently homogeneous. This review will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement. The quality of the evidence regarding physical activity will be assessed, according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE).DiscussionThis systematic review will provide information on which interventions are effective for increasing physical activity levels of stroke survivors. This evidence may be important for clinical decision-making and will allow the identification of gaps in the literature that may be useful for the definition of future research goals and the planning of new trials.Trial registration numberCRD42016037750.
Study protocol for a randomised controlled multicentre study: the Foraminotomy ACDF Cost-Effectiveness Trial (FACET) in patients with cervical radiculopathy
Authors: Broekema A E H , Kuijlen J M A , Lesman-Leegte G A T , Bartels R H M A , van Asselt A D I , Vroomen P C A J , van Dijk J M C , Reneman M F , Soer R , Groen R J M 
Published: January 2017

IntroductionCervical radiculopathy due to discogenic or spondylotic stenosis of the neuroforamen can be surgically treated by an anterior discectomy with fusion (ACDF) or a posterior foraminotomy (FOR). Most surgeons prefer ACDF, although there are indications that FOR is as effective as ACDF, has a lower complication rate and is less expensive. A head-to-head comparison of the 2 surgical techniques in a randomised controlled trial has not yet been performed. The study objectives of the Foraminotomy ACDF Cost-Effectiveness Trial (FACET) study are to compare clinical outcomes, complication rates and cost-effectiveness of FOR to ACDF.Methods and analysisThe FACET study is a prospective randomised controlled trial conducted in 7 medical centres in the Netherlands. The follow-up period is 2 years. The main inclusion criterion is a radiculopathy of the C4, C5, C6 or C7 nerve root, due to a single-level isolated cervical foraminal stenosis caused by a soft disc and/or osteophytic component, requiring operative decompression. A sample size of 308 patients is required to test the hypothesis of clinical non-inferiority of FOR versus ACDF. Primary outcomes are: ‘operative success’, the measured decrease in radiculopathy assessed by the visual analogue scale and ‘patient success’, assessed by the modified Odom's criteria. Secondary outcomes are: Work Ability Index (single-item WAI), quality of life (EuroQol 5 Dimensions 5 level Survey, EQ-5D-5L), Neck Disability Index (NDI) and complications. An economic evaluation will assess cost-effectiveness. In addition, a budget impact analysis will be performed.Ethics and disseminationEthical approval was obtained from the Institutional Ethics Committee of the University Medical Center Groningen. Results of this study will be disseminated through national and international papers. The participants and relevant patient support groups will be informed about the results of the study.Trial registration numberNTR5536, pre-results.
Hospitalisation with community-acquired pneumonia among patients with type 2 diabetes: an observational population-based study in Spain from 2004 to 2013
Authors: López-de-Andrés Ana , de Miguel-Díez Javier , Jiménez-Trujillo Isabel , Hernández-Barrera Valentín , de Miguel-Yanes José M , Méndez-Bailón Manuel , Pérez-Farinós Napoleón , Salinero-Fort Miguel Á ngel , Jiménez-García Rodrigo 
Published: January 2017

ObjectivesTo describe trends in the incidence and outcomes of community-acquired pneumonia (CAP) hospitalisations among patients with or without diabetes in Spain (2004–2013).DesignRetrospective, observational study using the Spanish National Hospital Discharge Database (Conjunto Mínimo Básico de Datos (CMBD)).SettingSpain.ParticipantsWe used national hospital discharge data to select all hospital admissions for CAP.Main outcome measuresIncidence was calculated overall and stratified by diabetes status: type 2 diabetes mellitus (T2DM) and no diabetes.ResultsWe identified 901 136 admissions for CAP (24.8% with T2DM). Incidence rates of CAP increased significantly in patients with T2DM over time. The incidence was higher among people with T2DM for all time periods. Patients with T2DM were older and had higher comorbidity index than non-diabetics.Streptococcus pneumoniaedecreased over time for both groups. Time trend analyses showed significant decreases in mortality during admission for CAP for patients with and without T2DM. Factors associated with higher mortality in both groups included: older age, higher comorbidity, mechanical ventilation, red cell transfusion, readmission andStaphylococcus aureusdetection.Diabetes was associated with a lower in-hospital mortality (OR 0.92, 95% CI 0.91 to 0.94) after a CAP hospitalisation.ConclusionsCAP incidence rates were higher and increased over time at a higher rate among patients with T2DM. Mortality decreased over time in all groups. The presence of diabetes is not a risk factor for death during admission for CAP.
Protocol for a prospective, controlled, observational study to evaluate the influence of hypoxia on healthy volunteers and patients with inflammatory bowel disease: the Altitude IBD Study
Authors: Vavricka Stephan , Ruiz Pedro A , Scharl Sylvie , Biedermann Luc , Scharl Michael , de Vallière Cheryl , Lundby Carsten , Wenger Roland H , Held Leonhard , Merz Tobias M , Gassmann Max , Lutz Thomas , Kunz Andres , Bron Denis , Fontana Adriano , Strauss Laura , Weber Achim , Fried Michael , Rogler Gerhard , Zeitz Jonas 
Published: January 2017

IntroductionInflammatory bowel disease (IBD) is a chronic intestinal disorder, often leading to an impaired quality of life in affected patients. The importance of environmental factors in the pathogenesis of IBD, including their disease-modifying potential, is increasingly recognised. Hypoxia seems to be an important driver of inflammation, as has been reported by our group and others. The aim of the study is to evaluate if hypoxia can alter disease activity of IBD measured by Harvey-Bradshaw Activity Index in Crohn's disease (increase to ≥5 points) and the partial Mayo Score for ulcerative colitis (increase to ≥2 points). To test the effects of hypoxia under standardised conditions, we designed a prospective and controlled investigation in healthy controls and patients with IBD in stable remission.Methods and analysisThis is a prospective, controlled and observational study. Participants undergo a 3-hour exposure to hypoxic conditions simulating an altitude of 4000 metres above sea level (m.a.s.l.) in a hypobaric pressure chamber. Clinical parameters, as well as blood and stool samples and biopsies from the sigmoid colon are collected at subsequent time points.Ethics and disseminationThe study protocol was approved by the Ethics Committee of the Kanton Zurich (reference KEK-ZH-number 2013-0284). The results will be published in a peer-reviewed journal and shared with the worldwide medical community.Trials registration numberNCT02849821; Pre-results.
Pioglitazone and cardiovascular outcomes in patients with insulin resistance, pre-diabetes and type 2 diabetes: a systematic review and meta-analysis
Authors: Liao Hung-Wei , Saver Jeffrey L , Wu Yi-Ling , Chen Tso-Hsiao , Lee Meng , Ovbiagele Bruce 
Published: January 2017

ObjectivesTo evaluate the effect of pioglitazone in people with insulin resistance, pre-diabetes and type 2 diabetes.Design and settingSystematic review and meta-analysis of randomised, controlled trials.Data sourcesLiterature searches were performed across PubMed, EMBASE, MEDLINE and Cochrane Central Register of Controlled Trials from 1966 to May 2016 to identify randomised, controlled trials with more than 1 year follow-up.Outcome measuresRelative risk (RR) with 95% CI was used to evaluate the association between pioglitazone and the risk of major adverse cardiovascular events (MACE: composite of non-fatal myocardial infarction, non-fatal stroke and cardiovascular death) and safety outcomes, after pooling data across trials in a fixed-effects model.ResultsNine trials with 12 026 participants were enrolled in the current meta-analysis. Pioglitazone therapy was associated with a lower risk of MACE in patients with pre-diabetes or insulin resistance (RR 0.77, 95% CI 0.64 to 0.93), and diabetes (RR 0.83, 95% CI 0.72 to 0.97). Risks of heart failure (RR 1.32; CI 1.14 to 1.54), bone fracture (RR 1.52, 95% CI 1.17 to 1.99), oedema (RR, 1.63; CI 1.52 to 1.75) and weight gain (RR 1.60; CI 1.50 to 1.72) increased in pioglitazone group.ConclusionsPioglitazone was associated with reduced risk of MACE in people with insulin resistance, pre-diabetes and diabetes mellitus. However, the risks of heart failure, bone fracture, oedema and weight gain were increased.
Protocol for intraoperative assessment of the human cerebrovascular glycocalyx
Authors: Haeren R H L , Vink H , Staals J , van Zandvoort M A M J , Dings J , van Overbeeke J J , Hoogland G , Rijkers K , Schijns O E M G 
Published: January 2017

IntroductionAdequate functioning of the blood–brain barrier (BBB) is important for brain homoeostasis and normal neuronal function. Disruption of the BBB has been described in several neurological diseases. Recent reports suggest that an increased permeability of the BBB also contributes to increased seizure susceptibility in patients with epilepsy. The endothelial glycocalyx is coating the luminal side of the endothelium and can be considered as the first barrier of the BBB. We hypothesise that an altered glycocalyx thickness plays a role in the aetiology of temporal lobe epilepsy (TLE), the most common type of epilepsy. Here, we propose a protocol that allows intraoperative assessment of the cerebrovascular glycocalyx thickness in patients with TLE and assess whether its thickness is decreased in patients with TLE when compared with controls.Methods and analysisThis protocol is designed as a prospective observational case–control study in patients who undergo resective brain surgery as treatment for TLE. Control subjects are patients without a history of epileptic seizures, who undergo a craniotomy or burr hole surgery for other indications. Intraoperative glycocalyx thickness measurements of sublingual, cortical and hippocampal microcirculation are performed by video microscopy using sidestream dark-field imaging. Demographic details, seizure characteristics, epilepsy risk factors, intraoperative haemodynamic parameters and histopathological evaluation are additionally recorded.Ethics and disseminationThis protocol has been ethically approved by the local medical ethical committee (ID: NL51594.068.14) and complies with the Declaration of Helsinki and principles of Good Clinical Practice. Informed consent is obtained before study enrolment and only coded data will be stored in a secured database, enabling an audit trail. Results will be submitted to international peer-reviewed journals and presented at international conferences.Trial registration numberNTR5568.
Exploring Underdetermined Specifications using Java PathFinder
Authors: Gyori Alex , Lambeth Ben , Khurshid Sarfraz , Marinov Darko 
Published: January 2017

Some Java libraries have underdetermined specifications that allow more than one correct output for the same input, e.g., an output array may have its elements in any order. While such specifications have a number of advantages (e.g., a library can change while still satisfying the specification), the non-determinism inherent in underdetermined specifications can lead to failures in client code that erroneously assumes behaviors based on the library implementation instead of only the specification. Our recent work introduced the NonDex approach for detecting such erroneous assumptions by checking client code against models of library methods, which encode all behaviors allowed by the specifications
We present NonDex for JPF, which includes JPF models for 11 methods from the Java standard library (i.e., all methods that JPF supports from the current methods in Non-Dex). We use these models to systematically explore state spaces of 46 tests from student homework submissions. Our experiments show several interesting results, which provide new insights into the complexity of exploring the behaviors of code that uses underdetermined APIs and the structure of state spaces that arise in the exploration, and provide basis for future work on better detecting faults in tests that invoke underdetermined APIs as well as developing tool support for writing and maintaining more robust test suites