bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh
Authors: Yulandi Adi , Suwanto Antonius , Waturangi Diana Elizabeth , Wahyudi Aris Tri 
Published: December 2020

Abstract
Objective
Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.

Results
Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.
High repetitive arginine in the anterior of PCV3 capsid protein is a severe obstacle for its expression in E. coli
Authors: Liu Bing Yan , Gao Bin , Liu Meng Zhi , Zhang Ting Ting , Liu Bao Shan , Chen Ze Liang 
Published: December 2020

AbstractPorcine circovirus type 3 (PCV3) is a novel circovirus identified in sows with PDNS-like clinical signs and reproductive failure. The capsid protein (CAP) of PCV3 is expected to be an effective vaccine candidate. Here, we expressed the original capsid protein, truncated capsid protein without anterior highly repetitive arginine (ΔCAP) and their codon-optimized counterparts in E. coli. These results showed that lots of repeated arginine could severely lower the expression of PCV3 capsid protein in E. coli. At the same time, the recombined truncated PCV3 capsid protein forms typic virions. The efficient expression of capsid protein is expected to serve the development of PCV3 vaccines and other studies of PCV3 capsid protein.
Unmanned aerial vehicles optimal airtime estimation for energy aware deployment in IoT-enabled fifth generation cellular networks
Authors: Majeed Saqib , Sohail Adnan , Qureshi Kashif Naseer , Kumar Arvind , Iqbal Saleem , Lloret Jaime 
Published: December 2020

AbstractCellular networks based on new generation standards are the major enabler for Internet of things (IoT) communication. Narrowband-IoT and Long Term Evolution for Machines are the newest wide area network-based cellular technologies for IoT applications. The deployment of unmanned aerial vehicles (UAVs) has gained the popularity in cellular networks by using temporary ubiquitous coverage in the areas where the infrastructure-based networks are either not available or have vanished due to some disasters. The major challenge in such networks is the efficient UAVs deployment that covers maximum users and area with the minimum number of UAVs. The performance and sustainability of UAVs is largely dependent upon the available residual energy especially in mission planning. Although energy harvesting techniques and efficient storage units are available, but these have their own constraints and the limited onboard energy still severely hinders the practical realization of UAVs. This paper employs neglected parameters of UAVs energy consumption in order to get actual status of available energy and proposed a solution that more accurately estimates the UAVs operational airtime. The proposed model is evaluated in test bed and simulation environment where the results show the consideration of such explicit usage parameters achieves significant improvement in airtime estimation.
Characterization and oncolytic virus targeting of FAP-expressing tumor-associated pericytes in glioblastoma
Authors: Li Ming , Li Guoping , Kiyokawa Juri , Tirmizi Zain , Richardson Leland G. , Ning Jianfang , Das Saumya , Martuza Robert L. , Stemmer-Rachamimov Anat , Rabkin Samuel D. , Wakimoto Hiroaki 
Published: December 2020

AbstractCancer-associated fibroblasts (CAFs) are activated fibroblasts constituting the major stromal components in many types of cancer. CAFs contribute to hallmarks of cancer such as proliferation, invasion and immunosuppressive tumor microenvironment, and are associated with poor prognosis of patients with cancer. However, in glioblastoma (GBM), the most common and aggressive primary malignant brain tumor, our knowledge about CAFs or CAF-like stromal cells is limited. Here, using commonly accepted CAF markers, we characterized CAF-like cell populations in clinical glioma specimens and datasets along with mouse models of GBM. We found that tumor-associated pericytes marked by co-expression of fibroblast activation protein α (FAP) and PDGFRβ represent major stromal cell subsets in both human GBM and mouse GBM models, while a fraction of mesenchymal neoplastic cells also express FAP in patient tumors. Since oncolytic viruses can kill cancer cells and simultaneously modulate the tumor microenvironment by impacting non-neoplastic populations such as immune cells and tumor vasculature, we further investigated the ability of oncolytic viruses to target GBM-associated stromal cells. An oncolytic adenovirus, ICOVIR15, carrying ∆24-E1A and an RGD-fiber, infects and depletes FAP+ pericytes as well as GBM cells in murine GBM. Our study thus identifies FAP+/PDGFRβ+ pericytes as a major CAF-like stromal cell population in GBM, and highlights the unique property of this oncolytic adenovirus to target both GBM cells and GBM-associated stromal FAP+ cells.
Ensuring competency in focused cardiac ultrasound: a systematic review of training programs
Authors: Gibson Lauren E. , White-Dzuro Gabrielle A. , Lindsay Patrick J. , Berg Sheri M. , Bittner Edward A. , Chang Marvin G. 
Published: December 2020

Abstract
Background
Focused cardiac ultrasound (FoCUS) is a valuable skill for rapid assessment of cardiac function and volume status. Despite recent widespread adoption among physicians, there is limited data on the optimal training methods for teaching FoCUS and metrics for determining competency. We conducted a systematic review to gain insight on the optimal training strategies, including type and duration, that would allow physicians to achieve basic competency in FoCUS.

Methods
Embase, PubMed, and Cochrane Library databases were searched from inception to June 2020. Included studies described standardized training programs for at least 5 medical students or physicians on adult FoCUS, followed by an assessment of competency relative to an expert. Data were extracted, and bias was assessed for each study.

Results
Data were extracted from 23 studies on 292 learners. Existing FoCUS training programs remain varied in duration and type of training. Learners achieved near perfect agreement (κ > 0.8) with expert echocardiographers on detecting left ventricular systolic dysfunction and pericardial effusion with 6 h each of didactics and hands-on training. Substantial agreement (κ > 0.6) on could be achieved in half this time.

Conclusion
A short training program will allow most learners to achieve competency in detecting left ventricular systolic dysfunction and pericardial effusion by FoCUS. Additional training is necessary to ensure skill retention, improve efficiency in image acquisition, and detect other pathologies.
Increasing levels of Parasutterella in the gut microbiome correlate with improving low-density lipoprotein levels in healthy adults consuming resistant potato starch during a randomised trial
Authors: Bush Jason R. , Alfa Michelle J. 
Published: December 2020

AbstractBackgroundPrebiotics, defined as a substrate that is selectively utilized by host microorganisms conferring a health benefit, present a potential option to optimize gut microbiome health. Elucidating the relationship between specific intestinal bacteria, prebiotic intake, and the health of the host remains a primary microbiome research goal.ObjectiveTo assess the correlations between gut microbiota, serum health parameters, and prebiotic consumption in healthy adults.MethodsWe performed ad hoc exploratory analysis of changes in abundance of genera in the gut microbiome of 75 participants from a randomized, placebo-controlled clinical trial that evaluated the effects of resistant potato starch (RPS; MSPrebiotic®,N = 38) intervention versus a fully digestible placebo (N = 37) for which primary and secondary outcomes have previously been published. Pearson correlation analysis was used to identify relationships between health parameters (ie. blood glucose and lipids) and populations of gut bacteria.ResultsAbundance ofParasutterella(phylum Proteobacteria) tended to increase in the gut microbiome of individuals consuming RPS and those increases inParasutterellawere correlated with reductions in low-density lipoprotein (LDL) levels in participants consuming RPS but not placebo. Segregating RPS-consuming individuals whose LDL levels decreased (ie “Responders”) from those who did not (ie. “Non-Responders”) revealed that LDL Responders had significantly higher levels ofParasutterellaboth at baseline and after 12 weeks of consuming RPS.ConclusionOur analyses suggest that RPS may help improve LDL levels depending upon the levels ofParasutterellain an individual’s gut microbiome.Trial registrationThis study protocol was reviewed and approved by Health Canada (Submission #188517; “Notice of Authorization” dated 06/05/13) and registered asNCT01977183(10/11/13) listed on NIH website: ClinicalTrials.gov. Data generated in this study have been submitted to NCBI (http://www.ncbi.nlm.nih.gov/bioproject/381931).FundingMSP Starch Products Inc.
Protective effect of Toxocara vitulorum extract against alpha-naphthylisothiocyanate-induced cholangitis in rat
Authors: Badr Abeer Mahmoud , Farid Mohamed , Biomy Ahmed Abdel Aziz , Mohamed Ayman Saber , Mahana Noha Ahmed , Fahmy Sohair Ramadan 
Published: December 2020

Abstract
Background
Cholestasis is the major cause of bile acid accumulation leading to liver damage. Chronic infection of worms can modulate the immune response towards T helper (Th)2-related cytokines. The present study aims to evaluate the protective impact of an ascarid nematode Toxocara vitulorum extract (TvE) against alpha-naphthylisothiocyanate (ANIT)-induced cholangitis male wistar rat model compared to ursodeoxycholic acid (UDCA) as a standard drug.

Results
Pretreatment with TvE and/or UDCA induced a marked reduction in the levels of liver function tests and malondialdehyde, while antioxidant markers were increased compared to cholestatic rats. Pretreatment with either TvE or combination before cholangitis induction attenuated the predominant Th1-related cytokines (IFN-γ and TNF-α) to Th2 (IL-13 and IL-10). TvE administration promoted higher expression levels of Bcl-2 protein and lower levels of caspase-3 compared to cholestatic rats.

Conclusions
Treatment with TvE has improved the liver functions and elevated the levels of oxidative stress markers. The upregulation of Th2-related cytokines and suppression of apoptosis through caspase-3 might be considered as a potential mechanism of TvE. Thereby, this natural extract revealed an opportunity for use in treatment of cholangitis disease.
Association between microstructural white matter abnormalities and cognitive functioning in patients with type 2 diabetes mellitus: a diffusion tensor imaging study
Authors: Osama Ahmed , Khalil Tarek Hassan , Negm Mohamed , AbdEl-Razek Reda , AbouElhamd Hend 
Published: December 2020

AbstractBackgroundDiffusion tensor imaging (DTI) technique is important for exploring more sensitive imaging-based biomarkers in prevention and early treatment of cognitive dysfunction induced by type 2 diabetes mellitus (DM).ObjectivesTo predict early cognitive dysfunction and detection of microstructural white matter changes in patients with type 2 DM by diffusion tensor imaging.Patients and methodsA case-control study included thirty patients aged ≥ 18 years old of both sexes with type 2 DM and 30 controls. All subjects underwent to Montreal Cognitive Assessment (MoCA) “Arabic version”: to detect mild cognitive impairment (MCI) and diffusion tensor imaging study (DTI).ResultsMild cognitive impairment is related to type 2 DM (56.7% of diabetic group), reduced fractional anisotropy (FA) values, and elevated mean diffusivity (MD) values were related to cognitive impairment evaluated through Montreal Cognitive Assessment (MoCA) in patients with type 2 DM.ConclusionThe integrity of the white matter measured using DTI vary in MCI diabetics compared with non-MCI diabetics. Such changes have major implications on the cognitive function.
Matrix stiffness regulates α-TAT1-mediated acetylation of α-tubulin and promotes silica-induced epithelial–mesenchymal transition via DNA damage
Authors: Li Gengxu , Chen Si , Zhang Yi , Xu Hong , Xu Dingjie , Wei Zhongqiu , Gao Xuemin , Cai Wenchen , Mao Na , Zhang Lijuan , Li Shumin , Yang Fang , Liu Heliang , Li Shifeng 
Published: December 2020

ABSTRACT
Silicosis is characterized by silica exposure-induced lung interstitial fibrosis and formation of silicotic nodules, resulting in lung stiffening. The acetylation of microtubules mediated by α-tubulin N-acetyltransferase 1 (α-TAT1) is a posttranslational modification that promotes microtubule stability in response to mechanical stimulation. α-TAT1 and downstream acetylated α-tubulin (Ac-α-Tub) are decreased in silicosis, promoting the epithelial–mesenchymal transition (EMT); however, the underlying mechanisms are unknown. We found that silica, matrix stiffening or their combination triggered Ac-α-Tub downregulation in alveolar epithelial cells, followed by DNA damage and replication stress. α-TAT1 elevated Ac-α-Tub to limit replication stress and the EMT via trafficking of p53-binding protein 1 (53BP1, also known as TP53BP1). The results provide evidence that α-TAT1 and Ac-α-Tub inhibit the EMT and silicosis fibrosis by preventing 53BP1 mislocalization and relieving DNA damage. This study provides insight into how the cell cycle is regulated during the EMT and why the decrease in α-TAT1 and Ac-α-Tub promotes silicosis fibrosis.
This article has an associated First Person interview with the first authors of the paper.
Methods used to meta-analyse results from interrupted time series studies: A methodological systematic review protocol
Authors: Korevaar Elizabeth , Karahalios Amalia , Forbes Andrew B. , Turner Simon L. , McDonald Steve , Taljaard Monica , Grimshaw Jeremy M. , Cheng Allen C. , Bero Lisa , McKenzie Joanne E. 
Published: December 2020

Background: Systematic reviews are used to inform healthcare decision making. In reviews that aim to examine the effects of organisational, policy change or public health interventions, or exposures, evidence from interrupted time series (ITS) studies may be included. A core component of many systematic reviews is meta-analysis, which is the statistical synthesis of results across studies. There is currently a lack of guidance informing the choice of meta-analysis methods for combining results from ITS studies, and there have been no studies examining the meta-analysis methods used in practice. This study therefore aims to describe current meta-analysis methods used in a cohort of reviews of ITS studies. Methods: We will identify the 100 most recent reviews (published between 1 January 2000 and 11 October 2019) that include meta-analyses of ITS studies from a search of eight electronic databases covering several disciplines (public health, psychology, education, economics). Study selection will be undertaken independently by two authors. Data extraction will be undertaken by one author, and for a random sample of the reviews, two authors. From eligible reviews we will extract details at the review level including discipline, type of interruption and any tools used to assess the risk of bias / methodological quality of included ITS studies; at the meta-analytic level we will extract type of outcome, effect measure(s), meta-analytic methods, and any methods used to re-analyse the individual ITS studies. Descriptive statistics will be used to summarise the data. Conclusions: This review will describe the methods used to meta-analyse results from ITS studies. Results from this review will inform future methods research examining how different meta-analysis methods perform, and ultimately, the development of guidance.
All-polymeric high-Q optofluidic Fabry–Perot resonator
Authors: Testa Genni , Persichetti Gianluca , Bernini Romeo 
Published: December 2020

A full polymeric optofluidic Fabry–Perot (FP) resonator with a high quality factor (Q) is proposed and tested. The device is based on multilayer optical polymeric films that act as high reflectivity interference mirrors. The all-polymeric laminated structure avoids any deposition or etching process, simplifying the fabrication procedure while retaining a high quality optical surface. The measured quality factor of the FP resonator is

3.03

×

10

4

, and the finesse is 91 around 700 nm. The refractometric sensing properties have been measured, and a sensitivity of 314 nm/RIU with a limit of detection of

2.55

×

10

−
5

R
I
U

could be achieved. The device exhibits a very high figure of merit of

1.36

×

10

4

R
I
U

−
1

that is comparable with the performance attainable with sensors based on photonic crystal and whispering gallery mode resonators.
Low-power and high-speed 2 × 2 thermo-optic MMI-MZI switch with suspended phase arms and heater-on-slab structure
Authors: Duan Fei , Chen Kai , Chen Da , Yu Yonglin 
Published: December 2020

We propose a

thermo-optic switch with high switching performance. The switch is based on multimode interferometer (MMI) couplers and a Mach–Zehnder interferometer (MZI) structure, where the phase arms are designed as laterally supported suspended ridge waveguides (LSSRWs) with a metallic heater placed on the slab. It is experimentally demonstrated that this switch has a power consumption of 1.07 mW, a thermal time constant

, an extinction ratio

, and an insertion loss

. Particularly, the corresponding figure of merit (FOM) has been improved by 1 order magnitude compared with general thermo-optic switches. This

thermo-optic MMI-MZI switch may find potential application for network reconfiguration and on-chip optical information processing.
Factors associated with chronic energy malnutrition among reproductive-age women in Ethiopia: An analysis of the 2016 Ethiopia demographic and health survey data
Authors: Dagnew Gizachew Worku , Asresie Melash Belachew 
Published: December 2020

Background
Women with chronic-energy malnutrition persists in many developing countries, including Ethiopia. To avert this problem identifying the predictor variables for a high magnitude of underweight is paramount. Consequently, this study aimed to assess the factors associated with chronic energy malnutrition among reproductive-age women in Ethiopia.

Methods
We used the 2016 Ethiopia demographic health survey data. The survey was a community-based cross-sectional study conducted from January 18 to June 27, 2016. A two-stage stratified cluster sampling technique was employed to select Participants. A total of 13,451 reproductive-age group women (age 15–49 years and who were not pregnant and < 2 months of postpartum) were included in the analysis. Both descriptive and analytical analyses were performed. A P-value of less than 0.05 was used to declare statistical significance.

Results
About 22.6% (95%CI: 21.5%-23.6%) of reproductive-age women were underweight. The magnitude of underweight is highest in the Afar region (39.6%) and lowest in Addis Ababa city administration (13.5%). Women who lived in the rural area (AOR = 1.59; 95%CI: 1.19–2.12), those who did not attend formal education (AOR = 1.23; 95%CI: 1.01–1.50), unemployed women (AOR = 1.28; 95%CI:1.13–1.44), women who belong to the poorest household wealth index (AOR = 1.42; 95%CI:1.04–1.94), women who were not married (AOR = 1.41; 95%CI: 1.18–2.69), women who lived in Tigray and the pastoral regions have higher odds of underweight. On the other hand, women who lived in southern nations nationalities and people’s region, and women whose age group 25–34 years had lower odds of underweight.

Conclusions
Chronic-energy malnutrition among reproductive-age women is high in Ethiopia. Improving the food security of rural, never married, and unemployed women would reduce the magnitude of underweight. Moreover, strengthening girls’ education, creating employment opportunities for women, and enhancing household income can further reduce the problem of chronic energy malnutrition.
Health, educational and employment outcomes among children treated for a skin disorder: Scotland-wide retrospective record linkage cohort study of 766,244 children
Authors: Fleming Michael , McLay James S. , Clark David , King Albert , Mackay Daniel F. , Pell Jill P. 
Published: December 2020

Background
To compare health, educational and employment outcomes of schoolchildren receiving medication for a skin disorder with peers.

Methods
This retrospective population cohort study linked eight Scotland-wide databases, covering dispensed prescriptions, hospital admissions, maternity records, death certificates, annual pupil census, school examinations, school absences/exclusions and unemployment to investigate educational (absence, exclusion, special educational need, academic attainment), employment, and health (admissions and mortality) outcomes of 766,244 children attending local authority run primary, secondary and special schools in Scotland between 2009 and 2013.

Results
After adjusting for sociodemographic and maternity confounders the 130,087 (17.0%) children treated for a skin disorder had increased hospitalisation, particularly within one year of commencing treatment (IRR 1.38, 95% CI 1.35–1.41, p<0.001) and mortality (HR 1.50, 95% CI 1.18–1.90, p<0.001). They had greater special educational need (OR 1.19, 95% CI 1.17–1.21, p<0.001) and more frequent absences from school (IRR 1.07, 95% CI 1.06–1.08, p<0.001) but did not exhibit poorer exam attainment or increased post-school unemployment. The associations remained after further adjustment for comorbid chronic conditions.

Conclusions
Despite increased hospitalisation, school absenteeism, and special educational need, children treated for a skin disorder did not have poorer exam attainment or employment outcomes. Whilst findings relating to educational and employment outcomes are reassuring, the association with increased risk of mortality is alarming and merits further investigation.