bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adverse events reporting in stage III NSCLC trials investigating surgery and radiotherapy
Authors: Iseli Thomas , Berghmans Thierry , Glatzer Markus , Rittmeyer Achim , Massard Gilbert , Durieux Valérie , Buchsbaum Thomas , Putora Paul Martin 
Published: September 2020

BackgroundCurrent treatment options for stage III non-small cell lung cancer (NSCLC) consist of different combinations of chemotherapy, surgery, radiotherapy and immunotherapy. Treatment choices are highly individual decisions, in which adverse events (AEs) are relevant for decision-making. This study aims to analyse reporting of AEs in prospective stage III NSCLC trials, focussing on trials including radiotherapy and/or surgery.MethodsPubMed was searched for prospective studies dealing with stage III NSCLC from January 1987 to April 2019. Meta-analyses were screened as a positive control. Pearson's Chi-squared test and smooth kernel distribution were used to estimate distributions. Data was resampled using bootstrapping.ResultsOut of 1193 initially identified studies, 119 met the inclusion criteria. Of these, 31 had a surgical procedure in any study arm. Grade 3 and 4 AEs were reported in 94.12% and 92.44% of the included studies, respectively. Reporting of grade 5 AEs was provided in 87.39% of cases. Grade 1 and 2 AEs were less commonly reported at 53.78% and 63.03%, respectively. One study did not mention any AEs. Of the 31 treatment arms including any form of surgery, AEs were not reported in 10. Overall, 231 different AE items were reported, only 18 of them were included in at least 20% of the analysed studies.ConclusionOverall, AE reporting in stage III NSCLC was inconsistent and inhomogeneous. Studies including surgical study arms often reported only treatment-related deaths in regards of surgical AEs. Underreporting of AEs prohibits the extraction of patient-relevant information for decision-making and represents a suboptimal use of invested resources.
Mortality and morbidity in obstructive sleep apnoea–hypopnoea syndrome: results from a 30-year prospective cohort study
Authors: Dodds Sophie , Williams Linda J. , Roguski Amber , Vennelle Marjorie , Douglas Neil J. , Kotoulas Serafeim-Chrysovalantis , Riha Renata L. 
Published: September 2020

BackgroundObstructive sleep apnoea–hypopnoea syndrome (OSAHS) carries substantial negative health consequences. This study examines factors affecting mortality and morbidity according to continuous positive airway pressure (CPAP) use and predictors affecting CPAP adherence in a longitudinal cohort of OSAHS patients.Materials and methodsThis prospective, cohort study comprised 4502 patients who were diagnosed with OSAHS at a tertiary sleep disorders centre between 1982 and 2003. Of these, 1174 patients completed follow-up in 2012. Data collected included anthropometric, sleep and demographic characteristics, including comorbidities, ongoing medications and CPAP adherence. Patients were followed up for an average of 14.8±3.7 years.ResultsImputation analysis showed that long-term CPAP users (>5 years) were 5.63 times more likely to be alive at study end than non-CPAP users (95% CI: 4.83–6.58, p<0.001) and 1.74-times more likely than short-term CPAP users (≤5 years) (95% CI: 1.49–2.02, p<0.001). Females had a significantly higher mortality rate during the follow-up period (26.8%versus19.6%, p<0.001). Respiratory mortality was more common in patients with OSAHS, in particular those who did not use CPAP, compared to the general population (17.2%versus12.2%, p=0.002 respectively), whereas deaths from cancer were less common compared to the general population (16.2%versus25.6%, p<0.001). Compared to CPAP users, non-CPAP-users had a significantly increased incidence of type II diabetes mellitus (DMII) (27.9%versus18.7%, p=0.003), ischaemic heart disease (IHD) (25.5%versus12.7%, p<0.001) and myocardial infarction (MI) (14.7%versus4.2%, p<0.001) at long-term follow-up.ConclusionsLong-term CPAP use in men and women with OSAHS reduces mortality and decreases the incidence of DMII and cardiovascular disease.
Does an mHealth system reduce health service use for asthma?
Authors: To Teresa , Lougheed M. Diane , McGihon Rachel , Zhu Jingqin , Gupta Samir , Licskai Christopher 
Published: September 2020

BackgroundBreathe is a mobile health (mHealth) application developed for the self-management of asthma in adults. There is evidence to suggest that mHealth interventions can be used for asthma control; however, their effects on the use of health services remain poorly understood. We sought to determine whether Breathe reduces health services use amongst asthma patients who used the app compared to controls who did not.MethodsThe impact of Breathe on health services use was estimated using a quasi-experimental approach. Two groups of subjects who had participated in a previous randomised clinical trial were included: an intervention group of asthma patients who used the app for 12 months, and a group of controls who did not use the app but received equivalent quality asthma care. A third, external control group of asthma patients were matched to the intervention participants. Generalised linear mixed models were used to determine relative changes in rates of asthma hospitalisations, emergency department (ED) visits, outpatient physician visits and completion of pulmonary function tests (PFTs) over time.ResultsA total of 677 individuals with asthma were included in the study: 132 in the intervention group, and 149 and 396 in the internal and external control groups, respectively. There were no statistically significant differences in the change of asthma hospitalisations, ED visits, physician office visits or completion of PFTs between the intervention group and either control group.ConclusionsUse of the Breathe app is not associated with changes in health services use in adults with asthma.
Cigarette-related cadmium and environmental pollution exposure are reflected in airway ultrafine particle content
Authors: Fireman Einat Klein , Adir Yochai , Fireman Elizabeth , Kessel Aharon 
Published: September 2020

IntroductionParticulate matter (PM) and cigarette-related cadmium exposure increases inflammation and smokers' susceptibility to developing lung diseases. The majority of inhaled metals are attached to the surface of ultrafine particles (UFPs). A low inhaled UFP content in exhaled breath condensate (EBC) reflects a high inflammatory status of airways.MethodsEBC was collected from 58 COPD patients and 40 healthy smokers and nonsmokers. Participants underwent spirometry, diffusion capacity, EBC and blood sampling. Environmental pollution data were collected from monitoring stations. UFPs were measured in EBC and serum, and cadmium content was quantified.ResultsSubjects with low UFP concentrations in EBC (<0.18×108·mL−1) had been exposed to higher long-term PM2.5levelsversussubjects with high UFP concentrations in EBC (>0.18×108·mL−1) (21.9 µg·m−3versus17.4 µg·m−3, p≤0.001). Long-term PM2.5exposure levels correlated negatively with UFP concentrations in EBC and positively with UFP concentrations in serum (r=−0.54, p≤0.001 and r=0.23, p=0.04, respectively). Healthy smokers had higher cadmium levels in EBCversushealthy nonsmokers and COPD patients (25.2 ppmversus23.7 ppm and 23.3 ppm, p=0.02 and p=0.002, respectively). Subjects with low UFP concentrations in EBC also had low cadmium levels in EBCversussubjects with high UFP levels (22.8 ppmversus24.2 ppm, p=0.004)ConclusionsLow UFP concentration in EBC is an indicator of high-level PM exposure. High cadmium levels in EBC among smokers and the association between cadmium and UFP content in EBC among COPD patients indicate cadmium lung toxicity.
Impaired effective functional connectivity of the sensorimotor network in interictal episodic migraineurs without aura
Authors: Wei Heng-Le , Chen Jing , Chen Yu-Chen , Yu Yu-Sheng , Guo Xi , Zhou Gang-Ping , Zhou Qing-Qing , He Zhen-Zhen , Yang Lian , Yin Xindao , Li Junrong , Zhang Hong 
Published: September 2020

Abstract
Background
Resting-state functional magnetic resonance imaging (Rs-fMRI) has confirmed sensorimotor network (SMN) dysfunction in migraine without aura (MwoA). However, the underlying mechanisms of SMN effective functional connectivity in MwoA remain unclear. We aimed to explore the association between clinical characteristics and effective functional connectivity in SMN, in interictal patients who have MwoA.

Methods
We used Rs-fMRI to acquire imaging data in 40 episodic patients with MwoA in the interictal phase and 34 healthy controls (HCs). Independent component analysis was used to profile the distribution of SMN and calculate the different SMN activity between the two groups. Subsequently, Granger causality analysis was used to analyze the effective functional connectivity between the SMN and other brain regions.

Results
Compared to the HCs, MwoA patients showed higher activity in the bilateral postcentral gyri (PoCG), but lower activity in the left midcingulate cortex (MCC). Moreover, MwoA patients showed decreased effective functional connectivity from the SMN to left middle temporal gyrus, right putamen, left insula and bilateral precuneus, but increased effective functional connectivity to the right paracentral lobule. There was also significant effective functional connectivity from the primary visual cortex, right cuneus and right putamen to the SMN. In the interictal period, there was positive correlation between the activity of the right PoCG and the frequency of headache. The disease duration was positively correlated with abnormal effective functional connectivity from the left PoCG to right precuneus. In addition, the headache impact scores were negatively correlated with abnormal effective functional connectivity from the left MCC to right paracentral lobule, as well as from the right precuneus to left PoCG.

Conclusions
These differential, resting-state functional activities of the SMN in episodic MwoA may contribute to the understanding of migraine-related intra- and internetwork imbalances associated with nociceptive regulation and chronification.
Haemodynamic activity characterization of resting state networks by fractal analysis and thalamocortical morphofunctional integrity in chronic migraine
Authors: Porcaro Camillo , Di Renzo Antonio , Tinelli Emanuele , Di Lorenzo Giorgio , Parisi Vincenzo , Caramia Francesca , Fiorelli Marco , Di Piero Vittorio , Pierelli Francesco , Coppola Gianluca 
Published: September 2020

Abstract
Background
Chronic migraine (CM) can be associated with aberrant long-range connectivity of MRI-derived resting-state networks (RSNs). Here, we investigated how the fractal dimension (FD) of blood oxygenation level dependent (BOLD) activity may be used to estimate the complexity of RSNs, reflecting flexibility and/or efficiency in information processing in CM patients respect to healthy controls (HC).

Methods
Resting-state MRI data were collected from 20 untreated CM without history of medication overuse and 20 HC. On both groups, we estimated the Higuchi’s FD. On the same subjects, fractional anisotropy (FA) and mean diffusivity (MD) values of bilateral thalami were retrieved from diffusion tensor imaging and correlated with the FD values.

Results
CM showed higher FD values within dorsal attention system (DAS) and the anterior part of default-mode network (DMN), and lower FD values within the posterior DMN compared to HC. Although FA and MD were within the range of normality, both correlated with the FD values of DAS.

Conclusions
FD of DAS and DMN may reflect disruption of cognitive control of pain in CM. Since the normal microstructure of the thalamus and its positive connectivity with the cortical networking found in our CM patients reminds similar results obtained assessing the same structures but with the methods of neurophysiology, in episodic migraine during an attack, this may be yet another evidence in supporting CM as a never-ending migraine attack.
Social and family factors as determinants of exercise habits in Japanese elementary school children: a cross-sectional study from the Super Shokuiku School Project
Authors: Sawa Satomi , Sekine Michikazu , Yamada Masaaki , Fukazawa Yugo , Hiraku Yusuke 
Published: September 2020

Abstract
Background
Many studies have already reported on the relationship between exercise habits and health among schoolchildren. However, few have examined social and/or family factors as determinants of exercise habits.

Methods
This study’s participants included 1721 schoolchildren aged between 6 and 13 who were involved in the Super Shokuiku School Project in January 2016. A survey was conducted to assess gender, grade level, physical activity, lifestyle, overall health, enrichment of school life, social background, and parental lifestyles. Both dislike and lack of physical activity were used to measure poor exercise habits; correlates were analyzed using logistic regression.

Results
“Lack of close friends” had the strongest links with both dislike (adjusted odds ratio [OR] 5.30; 95% confidence interval [CI], 2.78–10.1) and lack of (adjusted OR 5.40; 95% CI, 2.81–10.4) physical activity. Further, children who engaged in long periods of screen time and lacked parental communication also tended to dislike and lack physical activity. Children with mothers who were unemployed (housewives) and had unhealthy lifestyles, as well as those with poor health, were also more likely to lack physical activity.

Conclusion
Social and family factors (e.g., having close friends) may be determinants of exercise habits among schoolchildren, independent of their own lifestyle factors. Although a longitudinal study is needed to determine causality, substantial attention may thus be required to these factors when promoting physical activity in children.
Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation
Authors: Martinsson Svante , Klinth Mårten , Erséus Christer 
Published: September 2020

AbstractBackgroundDeep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelidFridericia magna(Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species.ResultsA total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from otherFridericiaspecies.ConclusionWe show that the morphospeciesFridericia magnais a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.
The development of early pioneer neurons in the annelid Malacoceros fuliginosus
Authors: Kumar Suman , Tumu Sharat Chandra , Helm Conrad , Hausen Harald 
Published: September 2020

Abstract
Background
Nervous system development is an interplay of many processes: the formation of individual neurons, which depends on whole-body and local patterning processes, and the coordinated growth of neurites and synapse formation. While knowledge of neural patterning in several animal groups is increasing, data on pioneer neurons that create the early axonal scaffold are scarce. Here we studied the first steps of nervous system development in the annelid Malacoceros fuliginosus.

Results
We performed a dense expression profiling of a broad set of neural genes. We found that SoxB expression begins at 4 h postfertilization, and shortly later, the neuronal progenitors can be identified at the anterior and the posterior pole by the transient and dynamic expression of proneural genes. At 9 hpf, the first neuronal cells start differentiating, and we provide a detailed description of axonal outgrowth of the pioneer neurons that create the primary neuronal scaffold. Tracing back the clonal origin of the ventral nerve cord pioneer neuron revealed that it is a descendant of the blastomere 2d (2d221), which after 7 cleavages starts expressing Neurogenin, Acheate-Scute and NeuroD.

Conclusions
We propose that an anterior and posterior origin of the nervous system is ancestral in annelids. We suggest that closer examination of the first pioneer neurons will be valuable in better understanding of nervous system development in spirally cleaving animals, to determine the potential role of cell-intrinsic properties in neuronal specification and to resolve the evolution of nervous systems.
Overexpression of transcription factor SlWRKY28 improved the tolerance of Populus davidiana × P. bolleana to alkaline salt stress
Authors: Wang Xin , Ajab Zainab , Liu Chenxi , Hu Songmiao , Liu Jiali , Guan Qingjie 
Published: September 2020

Abstract
Background
WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene.

Results
In this study, we cloned a WRKY gene (SlWRKY28) from the Salix linearistipularis and then transferred to the Populus davidiana × P. bolleana for expression. Sequence analysis on the transcriptome of Salix linearistipular showed the significant up-regulation of WRKY gene expression in response to salt-alkali stress in seedlings. Our data showed that SlWRKY28 localized to the nucleus. Furthermore, the expression of the SlWRKY28 from female plants increased with saline-alkali stress according to the northern blot analysis results. The results of 3,3′-Diaminobenzidine (DAB) staining showed that hydrogen peroxide (H2O2) concentration was lower under stress, but ascorbate peroxidase (APX) enzyme activity was significantly higher in the overexpressed plants than that in non-transgenic (NT) plants.

Conclusions
We found out the SlWRKY28 induced regulation of the enzyme gene in the reactive oxygen species (ROS) scavenging pathway is a potential mechanism for transgenic lines to improve their resistance to alkaline salt. This study shows theoretical and practical significance in determining SlWRKY28 transcription factors involved in the regulation of alkaline salt tolerance.
Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach
Authors: Parreira José Ricardo , Hernández-Castellano Lorenzo Enrique , Argüello Anastasio , Capote Juan , Castro Noemí , de Sousa Araújo Susana , de Almeida André Martinho 
Published: September 2020

AbstractBackgroundSeasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance:Majorera(tolerant) andPalmera(susceptible). NineMajoreraand tenPalmeragoats were randomly distributed in a control and a restricted group:MajoreraControl (adequately fed; MC;n = 4),PalmeraControl (adequately fed; PC;n = 6),MajoreraRestricted (feed restricted; ME;n = 5) andPalmeraRestricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis.ResultsFrom these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups.ConclusionsFeed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction.This research also highlights the importance or involvement of the genes in tolerance (ENPP1,S-LZ,MT2AandGPNB) and susceptibility (GPD1,CTPS1,ELOVL6andNR4A1) to SWL with respectively higher expression in theMajorerarestriced group and thePalmerarestricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.
CrustyBase: an interactive online database for crustacean transcriptomes
Authors: Hyde Cameron J. , Fitzgibbon Quinn P. , Elizur Abigail , Smith Gregory G. , Ventura Tomer 
Published: September 2020

AbstractTranscriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets are a rich source of information that can be mined for many years into the future, with each dataset providing a unique angle on a specific context in biology. Maintaining accessibility to this accumulation of data presents quite a challenge for researchers.The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or individual. The addition of expression data adds a new dimension to this paradigm – the sampling context. Does gene expression describe different tissues, a temporal distribution or an experimental treatment? These data not only describe an individual, but the biological context surrounding that individual. The structure and utility of a transcriptome database must therefore reflect these attributes. We present an online database which has been designed to maximise the accessibility of crustacean transcriptome data by providing intuitive navigation within and between datasets and instant visualization of gene expression and protein structure.The site is accessible at https://crustybase.org and currently holds 10 datasets from a range of crustacean species. It also allows for upload of novel transcriptome datasets through a simple web interface, allowing the research community to contribute their own data to a pool of shared knowledge.