bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate effects on the onset of flowering in the United Kingdom
Authors: Fox Nigel , Jönsson Anna Maria 
Published: November 2019

Abstract
Background
A warmer climate has consequences for the timing of phenological events, as temperature is a key factor controlling plant development and flowering. In this study, we analyse the effects of the long-term climate change and an extreme weather event on the first flowering day (FFD) of five spring-flowering wild plant species in the United Kingdom. Citizen science data from the UK Woodland Trust were obtained for five species: Tussilago farfara (coltsfoot), Anemone nemorosa (wood anemone), Hyacinthoides non-scripta (bluebell), Cardamine pratensis (cuckooflower) and Alliaria petiolate (garlic mustard).

Results
Out of the 351 site-specific time series (≥ 15-years of FFD records), 74.6% showed significant negative response rates, i.e. earlier flowering in warmer years, ranging from − 5.6 to − 7.7 days °C−1. 23.7% of the series had non-significant negative response rates, and 1.7% had non-significant positive response rates. For cuckooflower, the response rate was increasingly more negative with decreasing latitudes. The winter of 2007 reflects an extreme weather event, about 2 °C warmer compared to 2006, where the 2006 winter temperatures were similar to the 1961–1990 baseline average. The FFD of each species was compared between 2006 and 2007. The results showed that the mean FFD of all species significantly advanced between 13 and 18 days during the extreme warmer winter of 2007, confirming that FFD is affected by temperature.

Conclusion
Given that all species in the study significantly respond to ambient near-surface temperatures, they are suitable as climate-change indicators. However, the responses to a + 2 °C warmer winter were both more and less pronounced than expected from an analysis of ≥ 15-year time series. This may reflect non-linear responses, species-specific thresholds and cumulative temperature effects. It also indicates that knowledge on extreme weather events is needed for detailed projections of potential climate change effects.
Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis
Authors: Usai Mario Graziano , Casu Sara , Sechi Tiziana , Salaris Sotero L. , Miari Sabrina , Sechi Stefania , Carta Patrizia , Carta Antonello 
Published: November 2019

AbstractBackgroundThe detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by the high costs of large-scale phenotype and pedigree recording. QTL detection based on the combination of linkage disequilibrium and linkage analysis (LDLA) is the most suitable approach in family-structured populations. The main issue in performing LDLA mapping is the handling of the identity-by-descent (IBD) probability matrix. Here, we propose the use of principal component analysis (PCA) to perform LDLA mapping for milk traits in Sarda dairy sheep.MethodsA resource population of 3731 ewes belonging to 161 sire families and genotyped with the OvineSNP50 Beadchip was used to map genomic regions that affect five milk traits. The paternally and maternally inherited gametes of genotyped individuals were reconstructed and IBD probabilities between them were defined both at each SNP position and at the genome level. A QTL detection model fitting fixed effects of principal components that summarize IBD probabilities was tested at each SNP position. Genome-wide (GW) significance thresholds were determined by within-trait permutations.ResultsPCA resulted in substantial dimensionality reduction, in fact 137 and 32 (on average) principal components were able to capture 99% of the IBD variation at the locus and genome levels, respectively. Overall, 2563 positions exceeded the 0.05 GW significance threshold for at least one trait, which clustered into 75 QTL regions most of which affected more than one trait. The strongest signal was obtained for protein content onOvis aries(OAR) chromosome 6 and overlapped with the region that harbours the casein gene cluster. Additional interesting positions were identified on OAR4 for fat content and on OAR11 for the three yield traits.ConclusionsPCA is a good strategy to summarize IBD probabilities. A large number of regions associated to milk traits were identified. The outputs provided by the proposed method are useful for the selection of candidate genes, which need to be further investigated to identify causative mutations or markers in strong LD with them for application in selection programs assisted by molecular information.
Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
Authors: Wang Juan , Li Yuan , Li Chunjuan , Yan Caixia , Zhao Xiaobo , Yuan Cuiling , Sun Quanxi , Shi Chengren , Shan Shihua 
Published: November 2019

AbstractBackgroundThe cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect.Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect.Arachisis the biggest taxonomic section within genusArachisand its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of theArachisspecies need first to be better understood.ResultsHere, in this study, we have sequenced and/or assembled twelveArachiscomplete chloroplast (cp) genomes (eleven from Sect.Arachis). These cp genome sequences enriched the publishedArachiscp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect.Arachisspecies into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts andA.monticolathat are the only tetraploid (AABB) species withinArachisare nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species.ConclusionIn summary, we have acquired sequences of twelve completeArachiscp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.
Accuracy in detecting inadequate research reporting by early career peer reviewers using an online CONSORT-based peer-review tool (COBPeer) versus the usual peer-review process: a cross-sectional diagnostic study
Authors: Chauvin Anthony , Ravaud Philippe , Moher David , Schriger David , Hopewell Sally , Shanahan Daniel , Alam Sabina , Baron Gabriel , Regnaux Jean-Philippe , Crequit Perrine , Martinez Valeria , Riveros Carolina , Le Cleach Laurence , Recchioni Alessandro , Altman Douglas G. , Boutron Isabelle 
Published: November 2019

Abstract
Background
The peer review process has been questioned as it may fail to allow the publication of high-quality articles. This study aimed to evaluate the accuracy in identifying inadequate reporting in RCT reports by early career researchers (ECRs) using an online CONSORT-based peer-review tool (COBPeer) versus the usual peer-review process.

Methods
We performed a cross-sectional diagnostic study of 119 manuscripts, from BMC series medical journals, BMJ, BMJ Open, and Annals of Emergency Medicine reporting the results of two-arm parallel-group RCTs. One hundred and nineteen ECRs who had never reviewed an RCT manuscript were recruited from December 2017 to January 2018. Each ECR assessed one manuscript. To assess accuracy in identifying inadequate reporting, we used two tests: (1) ECRs assessing a manuscript using the COBPeer tool (after completing an online training module) and (2) the usual peer-review process. The reference standard was the assessment of the manuscript by two systematic reviewers. Inadequate reporting was defined as incomplete reporting or a switch in primary outcome and considered nine domains: the eight most important CONSORT domains and a switch in primary outcome(s). The primary outcome was the mean number of domains accurately classified (scale from 0 to 9).

Results
The mean (SD) number of domains (0 to 9) accurately classified per manuscript was 6.39 (1.49) for ECRs using COBPeer versus 5.03 (1.84) for the journal’s usual peer-review process, with a mean difference [95% CI] of 1.36 [0.88–1.84] (p < 0.001). Concerning secondary outcomes, the sensitivity of ECRs using COBPeer versus the usual peer-review process in detecting incompletely reported CONSORT items was 86% [95% CI 82–89] versus 20% [16–24] and in identifying a switch in primary outcome 61% [44–77] versus 11% [3–26]. The specificity of ECRs using COBPeer versus the usual process to detect incompletely reported CONSORT domains was 61% [57–65] versus 77% [74–81] and to identify a switch in primary outcome 77% [67–86] versus 98% [92–100].

Conclusions
Trained ECRs using the COBPeer tool were more likely to detect inadequate reporting in RCTs than the usual peer review processes used by journals. Implementing a two-step peer-review process could help improve the quality of reporting.

Trial registration
Clinical.Trials.govNCT03119376 (Registered April, 18, 2017).
Comparison of Apolipoprotein B/A1 ratio, Framingham risk score and TC/HDL-c for predicting clinical outcomes in patients undergoing percutaneous coronary intervention
Authors: Tian Min , Li Rui , Shan Zhilei , Wang Dao Wen , Jiang Jiangang , Cui Guanglin 
Published: November 2019

Abstract
Background
Apolipoproteins (Apo) are known atherogenic factors that play important roles in many mechanisms related to coronary heart disease (CHD). However, it is unclear whether the apoB/apoA1 ratio is an equal or a better predictor than the Framingham Risk Score or TC/HDL-c for predicting clinical outcomes in patients undergoing percutaneous coronary intervention.

Methods
We investigated the association between Apolipoprotein B/A1 ratio and cardiovascular risk factors as well as the severity of CHD in 2256 Han Chinese patients. The potential of Apolipoprotein B/A1 ratio, Framingham Risk Score and TC/HDL-c were assessed as a marker to predict cardiovascular adverse events in a prospective subgroup of 1639 CHD patients during a 5-year follow-up.

Results
In the multivariate model, adjusted odds ratios (ORs) were significant for 3-VD vs. 1-VD (OR = 2.36; 95% CI: 1.65–3.38, for the fourth vs. first quartile; Ptrend < 0.001). The subgroup analysis showed that patients with a higher ApoB/ApoA1 ratio had an increased risk of developing multi-branch lesions and potentially suffer more cardiovascular adverse events (anginas, myocardial infarctions, heart failures, strokes, and cardiac deaths) in the future (adjusted HR =1.92; 95% CI: 1.10–3.13, for the fourth vs. first quartile). In the ROC analysis, the AUC for ApoB/A1 ratio was larger than that of Framingham Risk Score (0.604 vs. 0.543, p = 0.01) and TC/HDL-c (0.604 vs. 0.525, p < 0.01).

Conclusion
Our results suggest a significant association between ApoB/ApoA1 ratio and CHD severity and cardiovascular outcomes among patients with existing CHD and ApoB/A1 ratio demonstrated a better predictive accuracy for clinical outcomes compared with Framingham Risk Score and TC/HDL-c.
Incidence and risk factors of portomesenteric venous thrombosis after colorectal surgery for cancer in the elderly population
Authors: Manigrasso Michele , Milone Marco , Velotti Nunzio , Vertaldi Sara , Schettino Pietro , Musella Mario , Aprea Giovanni , Gennarelli Nicola , Maione Francesco , Sarnelli Giovanni , Venetucci Pietro , De Palma Giovanni Domenico , Milone Francesco 
Published: November 2019

Abstract
Background
Although it is known that portomesenteric venous thrombosis (PMVT) is associated with total colectomy and proctocolectomy in young patients with inflammatory bowel disease, little is known about incidence and risk factors of PMVT among the elderly population undergoing colorectal surgery for cancer.

Methods
Data of elderly patients (> 70 years) undergoing surgery for colorectal cancer were retrospectively registered. The occurrence of PMVT was correlated with the patients’ characteristics and operative variables. Data collected included age, sex, obesity, ASA score, tumor degree, type of surgical resection, surgical approach (laparoscopic or open), and duration of surgery (from skin incision to the application of dressings).

Results
A total of 137 patients > 70 years who underwent surgery for colorectal cancer and developed an acute intraabdominal process with suggestive symptoms, needing a CT scan, were included. Three of these patients (2.1%) had portomesenteric venous thrombosis during the study period, which was proved with CT scan. There were no significant patients’ characteristics or operative variables between patients with or without the occurrence of PMVT after surgery. Of interest, only operative time was significantly higher in patients with PMVT after surgery (256 ± 40 vs 140 ± 41, p < 0.001).

Conclusions
PMVT as a cause of abdominal pain after colorectal surgery for cancer in the elderly population is uncommon. An index of suspicion for PMVT in an elderly postoperative colorectal cancer patient with sudden onset of abdominal pain must be maintained.
TPP-related mitochondrial targeting copper (II) complex induces p53-dependent apoptosis in hepatoma cells through ROS-mediated activation of Drp1
Authors: Shao Jiangjuan , Li Mengmeng , Guo Zijian , Jin Chun , Zhang Feng , Ou Chunyan , Xie Yaochen , Tan Shanzhong , Wang Zhenyi , Zheng Shizhong , Wang Xiaoyong 
Published: November 2019

Abstract
Background
In recent years, copper complexes have gradually become the focus of potential anticancer drugs due to their available redox properties and low toxicity. In this study, a novel mitochondrion-targeting copper (II) complex, [Cu (ttpy-tpp)Br2] Br (simplified as CTB), is first synthesized by our group. CTB with tri-phenyl-phosphine (TPP), a targeting and lipophilic group, can cross the cytoplasmic and mitochondrial membranes of tumor cells. The present study aims to investigate how CTB affects mitochondrial functions and exerts its anti-tumor activity in hepatoma cells.

Methods
Multiple molecular experiments including Flow cytometry, Western blot, Immunofluorescence, Tracker staining, Transmission Electron Microscopy and Molecular docking simulation were used to elucidate the underlying mechanisms. Human hepatoma cells were subcutaneously injected into right armpit of male nude mice for evaluating the effects of CTB in vivo.

Results
CTB induced apoptosis via collapse of mitochondrial membrane potential (MMP), ROS production, Bax mitochondrial aggregation as well as cytochrome c release, indicating that CTB-induced apoptosis was associated with mitochondrial pathway in human hepatoma cells. Mechanistic study revealed that ROS-related mitochondrial translocation of p53 was involved in CTB-mediated apoptosis. Simultaneously, elevated mitochondrial Drp1 levels were also observed, and interruption of Drp1 activation played critical role in p53-dependent apoptosis. CTB also strongly suppressed the growth of liver cancer xenografts in vivo.

Conclusion
In human hepatoma cells, CTB primarily induces mitochondrial dysfunction and promotes accumulation of ROS, leading to activation of Drp1. These stimulation signals accelerate mitochondrial accumulation of p53 and lead to the eventual apoptosis. Our research shows that CTB merits further evaluation as a chemotherapeutic agent for the treatment of Hepatocellular carcinoma (HCC).
Correction to: Inhibition of the key metabolic pathways, glycolysis and lipogenesis, of oral cancer by bitter melon extract
Authors: Sur Subhayan , Nakanishi Hiroshi , Flaveny Colin , Ippolito Joseph E. , McHowat Jane , Ford David A. , Ray Ratna B. 
Published: November 2019

Following publication of the original article [1], it was reported that Fig. 1c was not entirely readable due to overlapping Fig. 1d. The publishers apologise for this error.
Optimising the use of caesarean section: a generic formative research protocol for implementation preparation
Authors: Bohren Meghan A. , Opiyo Newton , Kingdon Carol , Downe Soo , Betrán Ana Pilar 
Published: November 2019

Abstract
Background
Caesarean section rates are rising across all geographical regions. Very high rates for some groups of women co-occur with very low rates for others. Both extremes are associated with short and longer term harms. This is a major public health concern. Making the most effective use of caesarean section is a critical component of good quality, sustainable maternity care. In 2018, the World Health Organization published evidence-based recommendations on non-clinical interventions to reduce unnecessary caesarean section. The guideline identified critical research gaps and called for formative research to be conducted ahead of any interventional research to define locally relevant determinants of caesarean birth and factors that may affect implementation of multifaceted optimisation strategies. This generic formative research protocol is designed as a guide for contextual assessment and understanding for anyone planning to take action to optimise the use of caesarean section.

Methods
This formative protocol has three main components: (1) document review; (2) readiness assessment; and (3) primary qualitative research with women, healthcare providers and administrators. The document review and readiness assessment include tools for local mapping of policies, protocols, practices and organisation of care to describe and assess the service context ahead of implementation. The qualitative research is organized according to twelve identified interventions that may optimise use of caesarean section. Each intervention is designed as a “module” and includes a description of the intervention, supporting evidence, theory of change, and in-depth interview/focus group discussion guides. All study instruments are included in this protocol.

Discussion
This generic protocol is designed to underpin the formative stage of implementation research relating to optimal use of caesarean section. We encourage researchers, policy-makers and ministries of health to adapt and adopt this design to their context, and share their findings as a catalyst for rapid uptake of what works.
JNER at 15 years: analysis of the state of neuroengineering and rehabilitation
Authors: Reinkensmeyer David J. 
Published: November 2019

Abstract
On JNER’s 15th anniversary, this editorial analyzes the state of the field of neuroengineering and rehabilitation. I first discuss some ways that the nature of neurorehabilitation research has evolved in the past 15 years based on my perspective as editor-in-chief of JNER and a researcher in the field. I highlight increasing reliance on advanced technologies, improved rigor and openness of research, and three, related, new paradigms – wearable devices, the Cybathlon competition, and human augmentation studies – indicators that neurorehabilitation is squarely in the age of wearability. Then, I briefly speculate on how the field might make progress going forward, highlighting the need for new models of training and learning driven by big data, better personalization and targeting, and an increase in the quantity and quality of usability and uptake studies to improve translation.
Potential risk factors and triggers for back pain in children and young adults. A scoping review, part II: unclear or mixed types of back pain
Authors: Beynon Amber M , Hebert Jeffrey J , Lebouef-Yde Charlotte , Walker Bruce F 
Published: November 2019

AbstractBackgroundBack pain is a global problem in terms of disability and financially, with a large burden both to the individual and to society. Back pain was previously believed to be uncommon in children. However, there is a growing body of evidence that this is not the case.ObjectivePart I of this scoping review studied risk factors of incident and episodic back pain. In this part II we aimed to identify all risk factors and triggers with unclear or mixed type back pain in young people and to identify any gaps in the literature.MethodsA scoping review design was selected to summarise the evidence, as there are many studies on “risk factors” for back pain. The scoping review followed the PRISMSA-ScR guidelines. We considered all studies that tested potential risk factors and triggers for thoracic and/or lumbar spine pain, in children, adolescents, and young adults (≤ 24 years). PubMed and Cochrane databases were searched from inception to September 2018, to identify relevant English language articles. The results regarding potential risk factors were separated into temporal precursors and bidirectional risk factors and the studies were classified by study design.ResultsOur comprehensive search strategy identified 7356 articles, of which 83 articles were considered eligible for this review (part II). There were 53 cross-sectional studies and 30 cohort studies. Potential risk factors for back pain were: female sex, older age, later pubertal status, positive family history of back pain, increased growth, and a history of back pain, most of which are temporal precursor variables. There was limited research for the illness factors, spinal posture, and muscle endurance in the development of back pain.ConclusionMany of the included studies approached risk factors in similar ways and found factors that were associated with back pain but were not obvious risk factors as causality was uncertain. Future research should be more rigorous and innovative in the way that risk factors are considered. This could be through statistical approaches including cumulative exposures, or longitudinal approaches including multi-trajectory methods. Additionally, data on proposed risk factors should be collected before the onset of back pain.
Genetic dynamics in untreated CLL patients with either stable or progressive disease: a longitudinal study
Authors: Ramassone Alice , D’Argenio Andrea , Veronese Angelo , Basti Alessio , Soliman Shimaa Hassan AbdelAziz , Volinia Stefano , Bassi Cristian , Pagotto Sara , Ferracin Manuela , Lupini Laura , Saccenti Elena , Balatti Veronica , Pepe Felice , Rassenti Laura Z. , Innocenti Idanna , Autore Francesco , Marzetti Laura , Mariani-Costantini Renato , Kipps Thomas J. , Negrini Massimo , Laurenti Luca , Visone Rosa 
Published: November 2019

AbstractClonal evolution of chronic lymphocytic leukemia (CLL) often follows chemotherapy and is associated with adverse outcome, but also occurs in untreated patients, in which case its predictive role is debated. We investigated whether the selection and expansion of CLL clone(s) precede an aggressive disease shift. We found that clonal evolution occurs in all CLL patients, irrespective of the clinical outcome, but is faster during disease progression. In particular, changes in the frequency of nucleotide variants (NVs) in specific CLL-related genes may represent an indicator of poor clinical outcome.