bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ventilator-associated pneumonia in critically ill patients with COVID-19
Authors: Maes Mailis , Higginson Ellen , Pereira-Dias Joana , Curran Martin D. , Parmar Surendra , Khokhar Fahad , Cuchet-Lourenço Delphine , Lux Janine , Sharma-Hajela Sapna , Ravenhill Benjamin , Hamed Islam , Heales Laura , Mahroof Razeen , Soderholm Amelia , Forrest Sally , Sridhar Sushmita , Brown Nicholas M. , Baker Stephen , Navapurkar Vilas , Dougan Gordon , Bartholdson Scott Josefin , Conway Morris Andrew 
Published: January 2021

Abstract
Background
Pandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP).

Objectives
To study the incidence of VAP and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients.

Methods
In this retrospective observational study, we compared the incidence of VAP and secondary infections using a combination of microbial culture and a TaqMan multi-pathogen array. In addition, we determined the lung microbiome composition using 16S RNA analysis in a subset of samples. The study involved 81 COVID-19 and 144 non-COVID-19 patients receiving invasive ventilation in a single University teaching hospital between March 15th 2020 and August 30th 2020.

Results
COVID-19 patients were significantly more likely to develop VAP than patients without COVID (Cox proportional hazard ratio 2.01 95% CI 1.14–3.54, p = 0.0015) with an incidence density of 28/1000 ventilator days versus 13/1000 for patients without COVID (p = 0.009). Although the distribution of organisms causing VAP was similar between the two groups, and the pulmonary microbiome was similar, we identified 3 cases of invasive aspergillosis amongst the patients with COVID-19 but none in the non-COVID-19 cohort. Herpesvirade activation was also numerically more frequent amongst patients with COVID-19.

Conclusion
COVID-19 is associated with an increased risk of VAP, which is not fully explained by the prolonged duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the causative organisms of secondary pneumonia observed are similar to that seen in critically ill patients ventilated for other reasons.
BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
Authors: Luhmann Nina , Holley Guillaume , Achtman Mark 
Published: January 2021

AbstractBlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. We show two examples using Salmonella genomes: finding within minutes the presence of genes in the SPI-2 pathogenicity island in a collection of 926 genomes and identifying single nucleotide polymorphisms associated with fluoroquinolone resistance in three genes among 190,209 genomes. BlastFrost is available at https://github.com/nluhmann/BlastFrost/tree/master/data.
The impact of computer-based cognitive training intervention on the quality of life among elderly people: a randomized clinical trial
Authors: kazazi Leila , Shati Mohsen , Mortazavi Seyede Salehe , Nejati Vahid , Foroughan Mahshid 
Published: January 2021

Abstract
Background
Through the process of normal aging, cognitive decline would cause a lower level of functioning in real life. This flow might interfere with health-related quality of life (QoL). The purpose of this study is to investigate the effect of computer-based cognitive intervention on increasing QoL of elderly people.

Methods
A total number of 52 community-dwelling older adults participated in this study. This community scored ≥ 21 in the Mini-Mental State Examination (MMSE) and a clock drawing test score ≥ 4 from health centers in Tehran, Iran. This study is a parallel group stratified randomized clinical trial. The intervention group received a 45-min cognitive training session twice a week for 10 sessions, using Attentive Rehabilitation of Attention and Memory (ARAM) software focusing on selective attention and working memory. QoL was evaluated as a primary outcome. The control group participated in educational workshops.

Results
From fifty-two persons, only one participant was excluded from the study in the intervention group during follow-up. Results revealed by increasing cognitive function, improvement occurred in QoL (F = 13.417, p value < 0.001, partial eta-squared = 0.324) as a primary outcome in the intervention group. Among eight domains of QoL, there was significant increasing in domain of role limitations due to emotional problems (F = 4.007, p value = 0.021, partial eta-squared = 0.059), social functioning (F = 2.423, p value = 0.044, partial eta-squared = 0.004), and role limitations due to physical health (F = 10.749, p value < 0.001, partial eta-squared = 0.026).

Conclusions
Based on the results, ARAM showed transition and long-term effects on QoL in elderly people by improving cognitive functions such as selective attention and working memory.

Trial registration
Iranian Registry of Clinical Trials IRCT2016122731602N1. Registered on June 21, 2017
Characterization of polysaccharides from different species of brown seaweed using saccharide mapping and chromatographic analysis
Authors: Chen Shengqin , Sathuvan Malairaj , Zhang Xiao , Zhang Wancong , Tang Shijie , Liu Yang , Cheong Kit-Leong 
Published: January 2021

AbstractBrown seaweed polysaccharides (BSPs) are one of the primary active components from brown seaweed that has a range of pharmaceutical and biomedical applications. However, the quality control of BSPs is a challenge due to their complicated structure and macromolecule. In this study, saccharide mapping based on high-performance liquid chromatography (HPLC), multi-angle laser light scattering, viscometer, and refractive index detector (HPSEC-MALLS-Vis-RID), and Fourier transform infrared (FT-IR) were used to discriminate the polysaccharides from nine different species of brown algae (BA1-9). The results showed that BSPs were composed of β-D-glucans and β-1,3−1,4-glucan linkages. The molecular weight, radius of gyration, and intrinsic viscosity of BSPs were ranging from 1.718 × 105 Da to 6.630 × 105 Da, 30.2 nm to 51.5 nm, and 360.99 mL/g to 865.52 mL/g, respectively. Moreover, α values of BSPs were in the range of 0.635 to 0.971, which indicated a rigid rod chain conformation. The antioxidant activities of BSPs exhibited substantial radical scavenging activities against DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS (2, 2’-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) radicals, which indicated that the use of BSPs might be a potential approach for antioxidant supplements. Thus, this study gives insights about the structure-function relationship of BSPs, which will be beneficial to improve the quality of polysaccharides derived from marine algae.
Spatio-temporal analysis of the main dengue vector populations in Singapore
Authors: Sun Haoyang , Dickens Borame L , Richards Daniel , Ong Janet , Rajarethinam Jayanthi , Hassim Muhammad E. E. , Lim Jue Tao , Carrasco L. Roman , Aik Joel , Yap Grace , Cook Alex R. , Ng Lee Ching 
Published: January 2021

Abstract
Background
Despite the licensure of the world’s first dengue vaccine and the current development of additional vaccine candidates, successful Aedes control remains critical to the reduction of dengue virus transmission. To date, there is still limited literature that attempts to explain the spatio-temporal population dynamics of Aedes mosquitoes within a single city, which hinders the development of more effective citywide vector control strategies. Narrowing this knowledge gap requires consistent and longitudinal measurement of Aedes abundance across the city as well as examination of relationships between variables on a much finer scale.

Methods
We utilized a high-resolution longitudinal dataset generated from Singapore’s islandwide Gravitrap surveillance system over a 2-year period and built a Bayesian hierarchical model to explain the spatio-temporal dynamics of Aedes aegypti and Aedes albopictus in relation to a wide range of environmental and anthropogenic variables. We also created a baseline during our model assessment to serve as a benchmark to be compared with the model’s out-of-sample prediction/forecast accuracy as measured by the mean absolute error.

Results
For both Aedes species, building age and nearby managed vegetation cover were found to have a significant positive association with the mean mosquito abundance, with the former being the strongest predictor. We also observed substantial evidence of a nonlinear effect of weekly maximum temperature on the Aedes abundance. Our models generally yielded modest but statistically significant reductions in the out-of-sample prediction/forecast error relative to the baseline.

Conclusions
Our findings suggest that public residential estates with older buildings and more nearby managed vegetation should be prioritized for vector control inspections and community advocacy to reduce the abundance of Aedes mosquitoes and the risk of dengue transmission.

Graphical Abstract
Evaluating putative repellent ‘push’ and attractive ‘pull’ components for manipulating the odour orientation of host-seeking malaria vectors in the peri-domestic space
Authors: Njoroge Margaret Mendi , Fillinger Ulrike , Saddler Adam , Moore Sarah , Takken Willem , van Loon Joop J. A. , Hiscox Alexandra 
Published: January 2021

AbstractBackgroundNovel malaria vector control approaches aim to combine tools for maximum protection. This study aimed to evaluate novel and re-evaluate existing putative repellent ‘push’ and attractive ‘pull’ components for manipulating the odour orientation of malaria vectors in the peri-domestic space.MethodsAnopheles arabiensisoutdoor human landing catches and trap comparisons were implemented in large semi-field systems to (i) test the efficacy of Citriodiol®or transfluthrin-treated fabric strips positioned in house eave gaps as push components for preventing bites; (ii) understand the efficacy of MB5-baited Suna-traps in attracting vectors in the presence of a human being; (iii) assess 2-butanone as a CO2replacement for trapping; (iv) determine the protection provided by a full push-pull set up. The air concentrations of the chemical constituents of the push–pull set-up were quantified.ResultsMicroencapsulated Citriodiol®eave strips did not provide outdoor protection against host-seekingAn. arabiensis. Transfluthrin-treated strips reduced the odds of a mosquito landing on the human volunteer (OR 0.17; 95% CI 0.12–0.23). This impact was lower (OR 0.59; 95% CI 0.52–0.66) during the push-pull experiment, which was associated with low nighttime temperatures likely affecting the transfluthrin vaporisation. The MB5-baited Suna trap supplemented with CO2attracted only a third of the released mosquitoes in the absence of a human being; however, with a human volunteer in the same system, the trap caught < 1% of all released mosquitoes. The volunteer consistently attracted over two-thirds of all mosquitoes released. This was the case in the absence (‘pull’ only) and in the presence of a spatial repellent (‘push-pull’), indicating that in its current configuration the tested ‘pull’ does not provide a valuable addition to a spatial repellent. The chemical 2-butanone was ineffective in replacing CO2. Transfluthrin was detectable in the air space but with a strong linear reduction in concentrations over 5 m from release. The MB5 constituent chemicals were only irregularly detected, potentially suggesting insufficient release and concentration in the air for attraction.ConclusionThis step-by-step evaluation of the selected ‘push’ and ‘pull’ components led to a better understanding of their ability to affect host-seeking behaviours of the malaria vectorAn. arabiensisin the peri-domestic space and helps to gauge the impact such tools would have when used in the field for monitoring or control.Graphical Abstract
Heart rate tracking in photoplethysmography signals affected by motion artifacts: a review
Authors: Ismail Shahid , Akram Usman , Siddiqi Imran 
Published: January 2021

AbstractNon-invasive photoplethysmography (PPG) technology was developed to track heart rate during motion. Automated analysis of PPG has made it useful in both clinical and non-clinical applications. However, PPG-based heart rate tracking is a challenging problem due to motion artifacts (MAs) which are main contributors towards signal degradation as they mask the location of heart rate peak in the spectra. A practical analysis system must have good performance in MA removal as well as in tracking. In this article, we have presented state-of-art techniques in both areas of the automated analysis, i.e., MA removal and heart rate tracking, and have concluded that adaptive filtering and multi-resolution decomposition techniques are better for MA removal and machine learning-based approaches are future perspective of heart rate tracking. Hence, future systems will be composed of machine learning-based trackers fed with either empirically decomposed signal or from output of adaptive filter.
Prevalence, risk factors, and interventions for chronic obstructive pulmonary disease in South Asia: a scoping review protocol
Authors: Islam Rafiqul , Hossain Md. Tarek , Chakma Nantu , Khanom Afroza , Mazumder Tapas , Islam Md. Tauhidul 
Published: January 2021

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is increasingly contributing to the disease burden in South Asia. This review will summarize the prevalence and risk factors of COPD in South Asia and the interventions regarding COPD that have been introduced in South Asian countries.

Method
This scoping review will primarily follow Arksey and O’Malley’s six steps of scoping review methodology. Additionally, it will follow the recent upgradation of the scoping review methodology by Levac et al., and the Joanna Briggs Institute. Research questions were already identified at the beginning of the proposed scoping review. Electronic databases will be searched (PubMed, Web of Science, and ProQuest) using search terms. Studies will be screened independently by two reviewers through a two-stage screening process using pre-developed inclusion criteria for this scoping review. Eligible studies will be abstracted and charted in a standardised form. Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) will be used to report the result. Additionally, feedback from South Asia’s experienced COPD researchers on the final literature list will be collected for gap identification in literature search. Two independent reviewers will assess the quality of each included study’s design using the Joanna Briggs Institute’s tool.

Discussion
The proposed scoping review will map the evidence on COPD in South Asia through literature review, and it will focus on prevalence, risk factors, and interventions. This review will contribute to the advancement of research on COPD and will be beneficial for policy-makers, public health specialists, and clinicians.
Existence and Ulam–Hyers stability of a kind of fractional-order multiple point BVP involving noninstantaneous impulses and abstract bounded operator
Authors: Zhao Kaihong , Deng Shoukai 
Published: January 2021

AbstractIn this paper, we mainly study a kind of fractional-order multiple point boundary value problem involving noninstantaneous impulse and abstract bounded operator. The existence and uniqueness is obtained by the Banach contraction principle. And by applying direct analysis methods, we establish some conditions of the Ulam–Hyers stability for this problem. Finally, an interesting application example is given to illustrate the validity of the results.
Innovation strategy on the example of companies using bamboo
Authors: Borowski Piotr F. 
Published: January 2021

AbstractInnovations and new technologies allow companies to function, work, and develop in an ever-changing environment. The article discusses the importance of innovative strategies and presents the results of research carried out on the role of each employee group (CEO, R+D department, other workers) in implementing innovations, depending on the size of the enterprise: micro company, mini company, medium company, and large company. A look not only through the prism of the size of the organization, but also by the groups of people (knowledge group) responsible for innovation is a novelty of the research and fills the gap in research on innovation of enterprises. Moreover, as an exemplification of theory which is used in practice, the article also presents innovations related to bamboo use in many enterprises from different sectors of the economy (energy, automobile, and textile). Bamboo, thanks to its mechanical and chemical properties, can become an innovative material widely used by various companies. Innovations based on the use of bamboo become eco-innovations that support eco-efficiency and the circular economy. The cognitive and utilitarian value of completed research lies in the possibility of a broad look at the innovation strategy (including bamboo as an innovative material) and in the possibility of its implementation and application in various enterprises operating on the market.
The role of lactose in weanling pig nutrition: a literature and meta-analysis review
Authors: Zhao Jinbiao , Zhang Zeyu , Zhang Shuai , Page Greg , Jaworski Neil W. 
Published: January 2021

AbstractLactose plays a crucial role in the growth performance of pigs at weaning because it is a palatable and easily digestible energy source that eases the transition from milk to solid feed. However, the digestibility of lactose declines after weaning due to a reduction in endogenous lactase activity in piglets. As a result, some lactose may be fermented in the gastrointestinal tract of pigs. Fermentation of lactose by intestinal microbiota yields lactic acid and volatile fatty acids, which may positively regulate the intestinal environment and microbiome, resulting in improved gastrointestinal health of weanling pigs. We hypothesize that the prebiotic effect of lactose may play a larger role in weanling pig nutrition as the global feed industry strives to reduce antibiotic usage and pharmacological levels of zinc oxide and supra-nutritional levels of copper. Evidence presented in this review indicates that high dietary lactose improves growth performance of piglets, as well as the growth of beneficial bacteria, particularlyLactobacillus, with the positive effects being more pronounced in the first 2 weeks after weaning. However, the risk of post-weaning diarrhea may increase as pigs get older due to reduced lactase activity, high dietary lactose concentrations, and larger feed intakes, all of which may lead to excessive lactose fermentation in the intestine of the pig. Therefore, dietary lactose levels exert different effects on growth performance and gastrointestinal physiological functions in different feeding phases of weanling pigs. However, no formal recommendation of lactose for weanling pigs has been reported. A meta-analysis approach was used to determine that diets fed to swine should include 20%, 15%, and 0 lactose from d 0–7, d 7–14, and d 14–35 post-weaning, respectively. However, sustainable swine production demands that economics must also be taken into account as lactose and lactose containing ingredients are expensive. Therefore, alternatives to lactose, so called “lactose equivalents” have also been studied in an effort to decrease feed cost while maintaining piglet performance with lower dietary lactose inclusions. In summary, the present review investigated dose-response effects of dietary lactose supplementation to exert positive responses and begin to elucidate its mechanisms of action in post-weaning pig diets. The results may help to replace some or all lactose in the diet of weanling pigs, while improving production economics given the high cost of lactose and availability in some swine production markets.
Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients
Authors: Lin Peng-Chan , Chen Hui-O , Lee Chih-Jung , Yeh Yu-Min , Shen Meng-Ru , Chiang Jung-Hsien 
Published: January 2021

Abstract
Background
Functional disruptions by large germline genomic structural variants in susceptible genes are known risks for cancer. We used deletion structural variants (DSVs) generated from germline whole-genome sequencing (WGS) and DSV immune-related association tumor microenvironment (TME) to predict cancer risk and prognosis.

Methods
We investigated the contribution of germline DSVs to cancer susceptibility and prognosis by silicon and causal inference models. DSVs in germline WGS data were generated from the blood samples of 192 cancer and 499 non-cancer subjects. Clinical information, including family cancer history (FCH), was obtained from the National Cheng Kung University Hospital and Taiwan Biobank. Ninety-nine colorectal cancer (CRC) patients had immune response gene expression data. We used joint calling tools and an attention-weighted model to build the cancer risk predictive model and identify DSVs in familial cancer. The survival support vector machine (survival-SVM) was used to select prognostic DSVs.

Results
We identified 671 DSVs that could predict cancer risk. The area under the curve (AUC) of the receiver operating characteristic curve (ROC) of the attention-weighted model was 0.71. The 3 most frequent DSV genes observed in cancer patients were identified as ADCY9, AURKAPS1, and RAB3GAP2 (p < 0.05). The DSVs in SGSM2 and LHFPL3 were relevant to colorectal cancer. We found a higher incidence of FCH in cancer patients than in non-cancer subjects (p < 0.05). SMYD3 and NKD2DSV genes were associated with cancer patients with FCH (p < 0.05). We identified 65 immune-associated DSV markers for assessing cancer prognosis (p < 0.05). The functional protein of MUC4 DSV gene interacted with MAGE1 expression, according to the STRING database. The causal inference model showed that deleting the CEP72 DSV gene affect the recurrence-free survival (RFS) of IFIT1 expression.

Conclusions
We established an explainable attention-weighted model for cancer risk prediction and used the survival-SVM for prognostic stratification by using germline DSVs and immune gene expression datasets. Comprehensive assessments of germline DSVs can predict the cancer risk and clinical outcome of colon cancer patients.