bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep apnoea and incident malignancy in type 2 diabetes
Authors: Driendl Sarah , Arzt Michael , Zimmermann Claudia S. , Jung Bettina , Pukrop Tobias , Böger Carsten A. , Haferkamp Sebastian , Zeman Florian , Heid Iris M. , Stadler Stefan 
Published: February 2021

BackgroundSleep apnoea and type 2 diabetes (T2D) have been linked to malignancy. The aim of the present study was to evaluate the association between sleep apnoea and incidence of malignancy in patients with T2D.MethodsThe DIACORE (DIAbetes COhoRtE) study is a prospective, population-based cohort study in T2D patients. In the sleep disordered breathing substudy, the apnoea–hypopnoea index (AHI), oxygen desaturation index (ODI) and percentage of night-time spent with a peripheral oxygen saturation of <90% (tsat90%) were assessed using a two-channel ambulatory monitoring device. Malignancy diagnoses were gathered using self-reported medical history data validated by medical records. Hazard ratios (HRs) for incident malignancy were derived by Cox regression adjusting for sex, age, body mass index, smoking status, alcohol intake, socioeconomic status and HbA1c.ResultsOf 1239 patients with T2D (mean age 67 years, 41% female, mean body mass index 30.9 kg·m−2), 79 (6.4%) were first-time diagnosed with a malignancy within a median follow-up period of 2.7 years (interquartile range 2.2–4.5 years). AHI, ODI andtsat90%were not associated with incident malignancy. In subgroup analysis, females showed increased cancer risk per AHI unit (adjusted HR 1.03 per AHI unit, 95% CI 1.00–1.06; p=0.028) and severe sleep apnoea (defined as AHI ≥30 events·h−1; adjusted HR 4.19, 95% CI 1.39–12.77; p=0.012). This was not seen in males, and a significant interaction was observed (interaction terms p=0.048 and p=0.033, respectively).ConclusionSleep apnoea was not associated with incident malignancy in T2D patients. However, stratified analysis revealed a significant association between sleep apnoea and incident malignancy in females, but not in males.
REINVENT: ERS International survey on REstrictive thoracic diseases IN long term home noninvasive VENTilation
Authors: Pierucci Paola , Crimi Claudia , Carlucci Annalisa , Carpagnano Giovanna E. , Janssens Jean-Paul , Lujan Manel , Noto Alberto , Wijkstra Peter J. , Windisch Wolfram , Scala Raffaele 
Published: February 2021

Background and aimLittle is known about the current use of long-term home noninvasive ventilation (LTHNIV) in restrictive thoracic diseases, including chest wall disorders and neuromuscular disorders (NMD). This study aimed to capture the pattern of LTHNIV in patients with restrictive thoracic diseasesviaa web-based international survey.MethodsThe survey involved European Respiratory Society (ERS) Assembly 2.02 (NIV-dedicated group), from October to December 2019.Results166 (22.2%) out of 748 members from 41 countries responded; 80% were physicians, of whom 43% worked in a respiratory intermediate intensive care unit. The ratio of NMD to chest wall disorders was 5:1, with amyotrophic lateral sclerosis the most frequent indication within NMD (78%). The main reason to initiate LTHNIV was diurnal hypercapnia (71%). Quality of life/sleep was the most important goal to achieve. In 25% of cases, clinicians based their choice of the ventilator on patients’ feedback. Among NIV modes, spontaneous-timed pressure support ventilation (ST-PSV) was the most frequently prescribed for day- and night-time. Mouthpieces were the preferred daytime NIV interface, whereas oro-nasal masks the first choice overnight. Heated humidification was frequently added to LTHNIV (72%). Single-limb circuits with intentional leaks (79%) were the most frequently prescribed. Follow-up was most often provided in an outpatient setting.ConclusionsThis ERS survey illustrates physicians’ practices of LTHNIV in patients with restrictive thoracic diseases. NMD and, specifically, amyotrophic lateral sclerosis were the main indications for LTHNIV. NIV was started mostly because of diurnal hypoventilation with a primary goal of patient-centred benefits. Bi-level ST-PSV and oro-nasal masks were more likely to be chosen for providing NIV. LTHNIV efficacy was assessed mainly in an outpatient setting.
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
Authors: Bokota Grzegorz , Sroka Jacek , Basu Subhadip , Das Nirmal , Trzaskoma Pawel , Yushkevich Yana , Grabowska Agnieszka , Magalska Adriana , Plewczynski Dariusz 
Published: February 2021

Abstract
Background
Bioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides access to an ever-increasing amount of high-quality images, there arises a need for their analysis in an automated, unbiased, and simple way. Segmentation of structures within the cell nucleus, which is the focus of this paper, presents a new layer of complexity in the form of dense packing and significant signal overlap. At the same time, the available segmentation tools provide a steep learning curve for new users with a limited technical background. This is especially apparent in the bulk processing of image sets, which requires the use of some form of programming notation.

Results
In this paper, we present PartSeg, a tool for segmentation and reconstruction of 3D microscopy images, optimised for the study of the cell nucleus. PartSeg integrates refined versions of several state-of-the-art algorithms, including a new multi-scale approach for segmentation and quantitative analysis of 3D microscopy images. The features and user-friendly interface of PartSeg were carefully planned with biologists in mind, based on analysis of multiple use cases and difficulties encountered with other tools, to offer an ergonomic interface with a minimal entry barrier. Bulk processing in an ad-hoc manner is possible without the need for programmer support. As the size of datasets of interest grows, such bulk processing solutions become essential for proper statistical analysis of results. Advanced users can use PartSeg components as a library within Python data processing and visualisation pipelines, for example within Jupyter notebooks. The tool is extensible so that new functionality and algorithms can be added by the use of plugins. For biologists, the utility of PartSeg is presented in several scenarios, showing the quantitative analysis of nuclear structures.

Conclusions
In this paper, we have presented PartSeg which is a tool for precise and verifiable segmentation and reconstruction of 3D microscopy images. PartSeg is optimised for cell nucleus analysis and offers multi-scale segmentation algorithms best-suited for this task. PartSeg can also be used for the bulk processing of multiple images and its components can be reused in other systems or computational experiments.
Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress
Authors: Wang Huan , Ding Zhaotang , Gou Mengjie , Hu Jianhui , Wang Yu , Wang Lu , Wang Yuchun , Di Taimei , Zhang Xinfu , Hao Xinyuan , Wang Xinchao , Yang Yajun , Qian Wenjun 
Published: February 2021

Abstract
Background
Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.

Results
In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.

Conclusions
We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus
Authors: Li Yisong , Sun Zhong-Zhi , Rong Jin-Cheng , Xie Bin-Bin 
Published: February 2021

Abstract
Background
Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.

Results
High-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pan-genome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis further suggested the existence of an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role in the evolutionary process of the species, with upto two-thirds of the core genes having been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association analysis revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats.

Conclusions
These results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.
Family medicine residents’ skill levels in emergency chest X-ray interpretation
Authors: Al Shammari Malak , Hassan Ali , AlShamlan Nouf , Alotaibi Sarah , Bamashmoos Manar , Hakami Amani , Althunyan Abdullatif , Basager Shymaa , Motabgani Sameerah , Aljubran Sawsan , Alsaif Hind S. 
Published: February 2021

Abstract
Background
Family medicine physicians may encounter a wide variety of conditions, including acute and urgent cases. Considering the limited access to diagnostic investigations in primary care practice, chest X-ray remains the imaging modality of choice. The current study assessed the competency of family medicine residents in the interpretation of chest X-rays for emergency conditions and to compare it with that of diagnostic radiology residents, general practitioners, and medical interns.

Methods
An online survey was distributed to 600 physicians, including family medicine residents, medical interns, general practitioners, and diagnostic radiology residents. The study included some background information such as gender, years in practice, training type, interest in pulmonary medicine and diagnostic radiology, and having adequate training on the interpretation of chest X-rays. The survey had 10 chest X-ray cases with brief clinical information. Participants were asked to choose the most likely diagnosis and to rate their degree of confidence in the interpretation of the chest X-ray for each case.

Results
The survey was completed by 205 physicians (response rate = 34.2%). The overall diagnostic accuracy was 63.1% with a significant difference between family medicine and radiology residents (58.0% vs. 90.5%; P < 0.001). The COVID-19 pneumonia (85.4%) and pneumoperitoneum (80.5%) cases had the highest diagnostic accuracy scores. There was a significant correlation between the diagnostic confidence and accuracy (rs = 0.39; P < 0.001). Multivariable regression analysis revealed that being diagnostic radiology residents (odds ratio [OR]: 13.0; 95% confidence interval [CI]: 2.5–67.7) and having higher diagnostic confidence (OR: 2.2; 95% CI: 1.3–3.8) were the only independent predictors of achieving high diagnostic accuracy.

Conclusion
The competency of family medicine residents in the interpretation of chest X-ray for emergency conditions was far from optimal. The introduction of radiology training courses on emergency conditions seems imperative. Alternatively, the use of tele-radiology in primary healthcare centers should be considered.
Comparing mortality between positive and negative blood culture results: an inverse probability of treatment weighting analysis of a multicenter cohort
Authors: Liu Aibo , Yo Chia-Hung , Nie Lu , Yu Hua , Wu Kuihai , Tong Hoi Sin , Hsu Tzu-Chun , Hsu Wan-Ting , Lee Chien-Chang 
Published: February 2021

Abstract
Background
The association between blood culture status and mortality among sepsis patients remains controversial hence we conducted a tri-center retrospective cohort study to compare the early and late mortality of culture-negative versus culture-positive sepsis using the inverse probability of treatment weighting (IPTW) method.

Methods
Adult patients with suspected sepsis who completed the blood culture and procalcitonin tests in the emergency department or hospital floor were eligible for inclusion. Early mortality was defined as 30-day mortality, and late mortality was defined as 30- to 90-day mortality. IPTW was calculated from propensity score and was employed to create two equal-sized hypothetical cohorts with similar covariates for outcome comparison.

Results
A total of 1405 patients met the inclusion criteria, of which 216 (15.4%) yielded positive culture results and 46 (21.3%) died before hospital discharge. The propensity score model showed that diabetes mellitus, urinary tract infection, and hepatobiliary infection were independently associated with positive blood culture results. There was no significant difference in early mortality between patients with positive or negative blood culture results. However, culture-positive patients had increased late mortality as compared with culture-negative patients in the full cohort (IPTW-OR, 1.95, 95%CI: 1.14–3.32) and in patients with severe sepsis or septic shock (IPTW-OR, 1.92, 95%CI: 1.10–3.33). After excluding Staphylococcal bacteremia patients, late mortality difference became nonsignificant (IPTW-OR, 1.78, 95%CI: 0.87–3.62).

Conclusions
Culture-positive sepsis patients had comparable early mortality but worse late mortality than culture-negative sepsis patients in this cohort. Persistent Staphylococcal bacteremia may have contributed to the increased late mortality.
Following cytotoxic nanoconjugates from injection to halting the cell cycle machinery and its therapeutic implications in oral cancer
Authors: Abdel Hamid Hend M. , Darwish Zeinab E. , Elsheikh Sahar M. , Mourad Ghada M. , Donia Hanaa M. , Afifi Marwa M. 
Published: February 2021

Abstract
Background
The concept of personalized therapy has been proven to be a promising approach. A popular technique is to utilize gold nanoparticles (AuNPs) as drug delivery vectors for cytotoxic drugs and small molecule inhibitors to target and eradicate oral cancer cells in vitro and in vivo. Both drug and nanocarrier designs play important roles in the treatment efficacy. In our study, we standardized the nanosystem regarding NPs type, size, surface ligands and coverage percentage leaving only the drugs mode of action as the confounding variable. We propose that similarly constructed nanoparticles (NPs) can selectively leverage different conjugated drugs irrelevant to their original mode of action. If proven, AuNPs may have a secondary role beyond bypassing cancer cell membrane and delivering their loaded drugs.

Methods
We conjugated 5- fluorouracil (5Fu), camptothecin (CPT), and a fibroblast growth factor receptor1-inhibitor (FGFR1i) to gold nanospheres (AuNSs). We followed their trajectories in Syrian hamsters with chemically induced buccal carcinomas.

Results
Flow cytometry and cell cycle data shows that 5Fu- and CPT- induced a similar ratio of S-phase cell cycle arrest as nanoconjugates and in their free forms. On the other hand, FGFR1i-AuNSs induced significant sub-G1 cell population compared with its free form. Despite cell cycle dynamics variability, there was no significant difference in tumor cells’ proliferation rate between CPT-, 5Fu- and FGFR1i- AuNSs treated groups. In our in vivo model, FGFR1i-AuNSs induced the highest tumor reduction rates followed by 5Fu- AuNSs. CPT-AuNSs induced significantly lower tumor reduction rates compared with the 5Fu- and FGFR1i- AuNSs despite showing similar proliferative rates in tumor cells.

Conclusions
Our data indicates that the cellular biological events do not predict the outcome seen in our in vivo model. Furthermore, our results suggest that AuNSs selectively enhance the therapeutic effect of small molecule inhibitors such as FGFR1i than potent anticancer drugs. Future studies are required to better understand the underlying mechanism.
Preliminary evidence for an influence of exposure to polycyclic aromatic hydrocarbons on the composition of the gut microbiota and neurodevelopment in three-year-old healthy children
Authors: Zhang Wei , Sun Zhongqing , Zhang Qian , Sun Zhitao , Su Ya , Song Jiahui , Wang Bingling , Gao Ruqin 
Published: February 2021

Abstract
Background
During the second and third year after birth the gut microbiota (GM) is subjected to important development. The polycyclic aromatic hydrocarbon (PAH) exposure could influence the GM in animal and early postnatal exposure is associated with neurodevelopment disorder in children. This study was designed to explore the possible influence of the polycyclic aromatic hydrocarbons (PAHs) on the composition of the gut microbiota (GM) and neurodevelopment in a sample of 38 healthy children at the age of 3 years.

Methods
A brief development (Gesell Development Inventory, GDI) and behavior test (Child Behavior Checklist, CBCL) were completed on 3-yr-olds and stool samples were collected for 16S rRNA V4-V5 sequencing. The PAH-DNA adduct in the umbilical cord blood and the urinary hydroxyl PAHs (OH-PAHs) at the age of 12 months were measured as pre- and postnatal PAH exposure, respectively.

Results
The most abundant two phyla were Bacteroidetes (68.6%) and Firmicutes (24.2%). The phyla Firmicutes, Actinobacteria, Proteobacteria, Tenericutes, and Lentisphaerae were positively correlated with most domain behaviors of the GDI, whereas the Bacteroidetes, Cyanobacteria, and Fusobacteria were negatively correlated. Correspondingly, the phyla Bacteroidetes, Actinobacteria, and Fusobacteria showed positive correlations with most CBCL core and broadband syndromes, whereas the Firmicutes, Verrucomicrobia, Synergistetes, Proteobacteria and Tenericules were negatively correlated. The OH-PAH levels were not significantly associated with the Firmicutes phylum whereas the Bacteroidetes, Bacteroidia, and Bacteroidales all showed significant negative association with the OH-PAH levels.

Conclusion
The current findings suggest that composition of the GM is associated with neurodevelopment of the child. PAHs seem to change the relative abundance of some taxa (some deleted and some recruited) to counteract the negative effects of the PAHs.
Image classification of osteoporotic vertebral fracture with endplate-disc complex Injury
Authors: Zhang Shuai , Wang Song , Wang Qing , Yang Jin , Xu Shuang 
Published: February 2021

Abstract
Background
The purpose of this study was to use MRI and CT to observe osteoporosis vertebral fracture (OVF) combined with endplate-disc complex (EDC) injury and to classify the degree of EDC injury according to the changes in EDC signal intensity and morphology on the images.

Methods
We investigated the incidence of EDC injury, observed the morphology and signal intensity changes of EDC injury using MRI and CT, and graded the injuries from 0 to 4 according to their severity. We compared whether there were differences in the degree of EDC injury among different vertebral fractures, bone mineral density(BMD), and severity of vertebral fractures.

Results
A total of 479 patients were included in this study, of whom 321 had EDC injury adjacent to the fractured vertebral body. Among those, 158 cases were grade 0, 66 cases were grade 1, 72 cases were grade 2, 78 cases were grade 3, and 92 cases were grade 4. The degree of EDC injury associated with thoracolumbar vertebral fractures was more serious than that of EDC injuries associated with thoracic and lumbar vertebral body fractures. Vertebral fractures with severe osteoporosis were associated with more severe EDC injury. Additionally, the more severe the vertebral fracture, the more severe was the combined EDC injury.

Conclusion
This study found that the incidence rate of EDC injury reached 67.0%. Among patients with OVF, severe osteoporosis and severe fractures in the thoracolumbar segments were often associated with more severe EDC injury.