bluuebunny/crossref_metadata_2025 huggingface dataset:
Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking
Authors: Bezuglov Vitalik , Stupnikov Alexey , Skakov Ivan , Shtratnikova Victoria , Pilsner Jonathan Richard , Suvorov Alexander , Sergeyev Oleg
Published: February 2023

Expression analysis of small noncoding RNA (sRNA), including microRNA, piwi-interacting RNA, small rRNA-derived RNA, and tRNA-derived small RNA, is a novel and quickly developing field. Despite a range of proposed approaches, selecting and adapting a particular pipeline for transcriptomic analysis of sRNA remains a challenge. This paper focuses on the identification of the optimal pipeline configurations for each step of human sRNA analysis, including reads trimming, filtering, mapping, transcript abundance quantification and differential expression analysis. Based on our study, we suggest the following parameters for analysis of human sRNA in relation to categorical analyses with two groups of biosamples: (1) trimming with the lower length bound = 15 and the upper length bound = \(Read\ length - 40\% Adapter\ length\); (2) mapping on a reference genome with bowtie aligner with one mismatch allowed (-v 1 parameter); (3) filtering by mean threshold > 5; and (4) analyzing differential expression with DESeq2 with adjusted p-value < 0.05 or limma with p-value < 0.05 if there is very little signal and few transcripts.
Exploring the Potential of the Model Cyanobacteria Synecho-Coccus PCC 7002 and PCC 7942 for the Photoproduction of High-Value Terpenes: Comparison With Synechocystis PCC 6803
Authors: Chenebault Célia , Blanc-Garin Victoire , Vincent Marine , Diaz-Santos Encarnación , Goudet Amélie , Cassier-Chauvat Corinne , Chauvat Franck
Published: February 2023

We have performed the first comparative analysis of the potential of two physiologically-diverse model cyanobacteria, Synechococcus PCC 7002 (S.7002) and Synechococcus PCC 7942 (S.7942), for the photosynthetic production of four chemically-different high-value terpenes: two monoterpenes limonene and pinene, and two sesquiterpenes bisabolene and farnesene. We showed, for the first time, that S.7002 and S.7942 can produce farnesene and bisabolene, respectively. Both cyanobac-teria produced farnesene (S.7942 better than S.7002) more efficiently than the other tested terpenes (especially pinene the weakest produced terpene). S.7002 produced limonene better than bisabo-lene, whereas S.7942 produced bisabolene better than limonene. These findings suggest that S.7942 is better suited to produce sesquiterpenes than monoterpenes. Also interestingly, higher levels of terpenes were produced by S.7942 and S.7002 expressing a terpene-synthase gene from both a RSF1010-derived replicating plasmid and a neutral chromosomal site, as compared to ei-ther the plasmid alone or the chromosome alone. These results suggest that in both cyanobacteria the production of terpenes is more limited by the activity of terpene synthases than the abondance of terpene precursors. Finally, higher levels of terpenes were produced by S.7002 growing on urea (a frequent pollutant) as compared to nitrate (or ammonium) the standard nitrogen sources for cyanobacteria (more expensive than urea).
Atypical Neurogenesis, Astrogliosis, and Excessive Hilar Interneuron Loss Are Associated With the Development of Post-Traumatic Epilepsy
Authors: Gudenschwager-Basso Erwin Kristobal , Shandra Oleksii , Volanth Troy , Patel Dipankumar , Kelly Colin , Browning Jack L , Wei Xiaoran , Mahmutovic Dzenis , Kaloss Alexandra M , Correa Fernanda Guilhaume , Decker Jeremy , Maharathi Biswajit , Robel Stefanie , Sontheimer Harald , VandeVord Pamela J , Olsen Michelle L , Theus Michelle H
Published: February 2023

Background: Traumatic brain injury (TBI) remains a significant risk factor for post-traumatic epilepsy (PTE). The pathophysiological mechanisms underlying the injury-induced epileptogenesis are under under investigation. The dentate gyrus, a structure highly susceptible to injury, and has been implicated in the evolution of seizure development. Methods: Utilizing the murine unilateral focal control cortical impact (CCI) injury, we evaluated seizure onset using 24/7 EEG video analysis at 2-4 months post-injury. Cellular changes in the dentate gyrus and hilus of the hippocampus were quantified by non-biased stereology and Imaris image analysis to evaluate Prox1-positive cell migration, astrocyte branching and morphology, as well as neuronal loss at four months post-injury. Isolation of region-specific astrocytes and RNA-seq was performed to determine differential gene expression in PTE+ vs. PTE- that may comport with the epileptogenic process. Results: CCI injury resulted in 37% PTE+-incidence, which increased with injury severity and hippocampal damage. Histological assessments uncovered a significant loss of hilar interneurons that coincided with aberrant migration of Prox1-positive granule cells and reduced astroglial branching in PTE+ compared to PTE- mice. We uniquely identified Cst3 as a PTE+-specific gene signature in astrocytes across all brain regions. Conclusions: These findings suggest that epileptogenesis may emerge following TBI due to distinct aberrant cellular remodeling events and key molecular changes in the dentate gyrus of the hippocampus.
SFRRG: A Graph Neural Network Recommendation Model based on Feature and Structure Information
Authors: Patterson Devon , Wilson John , Forrow Michael , Wald Tereza
Published: February 2023

With the rapid development of the Internet industry, the problem of information overload has arisen due to the abundance of information available online. Recommendation algorithms, as the core of recommendation systems, have been attracting much attention and are a hot topic of research for many experts and scholars. The classical recommendation algorithms are mainly divided into three major categories: collaborative filtering recommendation algorithms, content-based recommendation algorithms, and hybrid-based recommendation algorithms. Although these algorithms are widely used in various fields, with the proliferation of information, these traditional recommendation algorithms are no longer able to meet the needs of the times. To address this issue, recommendation systems have been developed to provide users with personalized and relevant information or products. Despite the wide use of recommendation algorithms, such as collaborative filtering, content-based filtering, and hybrid approaches, traditional recommendation algorithms have limitations and are no longer suitable for meeting the demands of the times. This paper proposes a new recommendation algorithm, SFRRG, that fuses structure and feature information in graph neural networks to improve the performance of the recommendation system in rating prediction. The effectiveness of the proposed algorithm is demonstrated through experiments on various data sets and compared with existing recommendation algorithms.
Predictors of Engagement on Social Media and Instant Messaging Platforms during the COVID-19 Pandemic: Evidence from Romania
Authors: Corbu Nicoleta , Bârgăoanu Alina , Durach Flavia , Ștefăniță Oana
Published: February 2023

The COVID-19 pandemic raised important questions about news patterns of interaction on social network sites (SNS) and instant messaging platforms (IM), especially in the context of the massive replacement of face-to-face interactions with mediated interactions, due to the restrictive measures taken in many parts of the world. In this context, by means of a national survey conducted in Romania (N=1160), we investigated people’s willingness to engage on social media and instant messaging platforms about the topic of the COVID-19 pandemic. Results show that people are eager to share information about the topic on both SNS and IM, less interested in getting involved in debates, and even less in voluntary work. All these behaviors are predicted by trust of SNS and news consumption on these platforms, perceived size of the personal digital network, belief in conspiracy theories about the virus, uncertainty about the impact of the crisis, and level of education.
Knowledge user survey and Delphi process to inform development of a new risk of bias tool to assess systematic reviews with network meta-analysis (RoB NMA tool)
Authors: Lunny Carole , Veroniki Areti Angeliki , Hutton Brian , White Ian R , Higgins Julian PT , Wright James M , Kim Ji Yoon , Thirugnanasampanthar Sai Surabi , Siddiqui Shazia , Moja Lorenzo , Taske Nichole , Lorenz Robert , Gerrish Savannah , Straus Sharon , Minogue Virginia , Hu Franklin , Kapani Ayah , Nagi Samin , Chen Lillian , Akbar-nejad Mona , Tricco Andrea C.
Published: February 2023

Background: Network meta-analysis (NMA) is increasingly used in guideline development and other aspects of evidence-based decision-making. We aimed to develop a risk of bias (RoB) tool to assess NMAs (RoB NMA tool). An international steering committee intended the RoB NMA tool to be used in combination with ROBIS (recommend as it was designed to assess biases only) or other similar quality appraisal tools (e.g., AMSTAR 2) to assess quality of systematic reviews. The RoB NMA tool will assess NMA biases and limitations regarding how the analysis was planned, data were analysed, and results were presented, including the way in which the evidence was assembled and interpreted.
Objectives: Conduct (a) a Delphi process to determine expert opinion on an item’s inclusion, and (b) a knowledge user survey to widen its impact.
Design: Cross sectional survey and Delphi process
Methods: Delphi panellists were asked to rate whether items should be included. All agreed-upon item were included in a second round of the survey (defined as 70% agreement). We surveyed knowledge users’ views and preferences about the importance, utility, and willingness to use the RoB NMA tool to evaluate evidence in practice and in policymaking. We included 12 closed and 10 open-ended questions, and we followed a knowledge translation plan to disseminate the survey through social media and professional networks.
Results: 22 items were entered into a Delphi survey of which 28 respondents completed round 1, and 22 completed round 2.Seven items did not reach consensus in round 2. A total of 298 knowledge users participated in the survey (14% respondent rate). 75% indicated that their organization produced NMAs, and 78% showedhigh interest in the tool, especially if they had received adequate training (84%). Most knowledge users and Delphi panellists preferred a tool to assess both bias in individual NMA results and authors’ conclusions. Response bias in our sample is a major limitation as knowledge users working in higher income countries were more represented. One of the limitations of the Delphi process is that it depends on the purposive selection of experts and their availability, thus limiting the variability in perspectives and scientific disciplines.
Conclusions: This Delphi process and knowledge user survey informs the development of the RoB NMA tool.
Registration: We uploaded our study protocol on the Open Science Framework at https://osf.io/da4uy/
Transcriptome research on differentially expressed genes in a thermotolerant yeast strain from Daqu of Luzhou-flavor liquors
Authors: Liu Yanbo , Gu Wenning , Li Haideng , Zhao Zhijun , Han Suna , Wang Xian , Sun Xiyu , Pan Chunmei
Published: February 2023

Yeast is one of the microorganisms widely used in fermentation industry, and its high temperature resistance plays an important role in fermentation. However, the complex regulatory process of cell tolerance to heat stress has not been fully understood. Therefore, this study carried out basic research on high temperature resistant yeast at 28℃, 37℃ and 43℃, including morphological observation, determination of trehalose content and cell membrane permeability, and combined with RNA-seq technology to screen differentially expressed genes in yeast responding to high temperature stress at the transcriptome level. The results showed that under heat treatment conditions, the macroscopic and microscopic morphology of yeast cells were changed, the selective permeability of cell membrane was changed, and the intracellular trehalose was accumulated. Different nitrogen sources and inorganic salt ions can improve the high temperature tolerance of yeast ZG-3. In addition, a total of 517 differentially expressed genes were screened by comparing the temperature resistant yeast at 28℃ with that at 37℃, among which 435 genes were up-regulated and 82 genes were down-regulated. A total of 632 differentially expressed genes were screened at 37℃ compared with that at 43℃, among which 393 genes were up-regulated and 239 genes were down-regulated. Among them, SSA3, SSA4, HSP82, SSE1, KAR2, FES1, HSP26, HSP42 genes of the heat shock protein family were significantly up-regulated, which improved the basic and acquired heat tolerance of yeast. This study combined physical and chemical properties analysis and transcriptome analysis to preliminarily explore the differentially expressed genes in yeast in response to high temperature stress, which provides a theoretical basis for further study of yeast high temperature tolerance.
Second order blind identification of event related potentials sources
Authors: Ponomarev Valery A. , Kropotov Jury D.
Published: February 2023

Event-related potentials (ERPs) recorded on the surface of the head are a mixture of signals from many sources in the brain due to volume conductions. As a result, the spatial resolution of the ERPs is quite low. Blind source separation can help to recover source signals from multichannel ERP records. In this study, we present a novel implementation of a method for decomposing multi-channel ERP into components, which is based on the modeling of second-order statistics of ERPs. We also report a new implementation of Bayesian Information Criteria (BIC), which is used to select the optimal number of hidden signals (components) in the original ERPs. We tested these methods using both synthetic datasets and real ERPs data arrays. Testing has shown that the ERP decomposition method can reconstruct the source signals from their mixture with acceptable accuracy even when these signals overlap significantly in time and the presence of noise. The use of BIC allows us to determine the correct number of source signals at the signal-to-noise ratio commonly observed in ERP studies. The proposed approach was compared with conventionally used methods for the analysis of ERPs. It turned out that the use of this new method makes it possible to observe such phenomena that are hidden by other signals in the original ERPs. The proposed method for decomposing a multichannel ERP into components can be useful for studying cognitive processes in laboratory settings, as well as in clinical studies.
Media screen time use and mental health in school aged children during the pandemic
Authors: Hmidan Amira , Seguin Diane , Duerden Emma G.
Published: February 2023

Background
Children’s screen time activity has increased significantly during the pandemic. Extended school closures and heightened parent stress are associated with children’s behavioural difficulties and time spent watching screens. The primary aim of this study was to determine which school and household factors were associated with challenging behaviours in Canadian schoolchildren during the COVID-19 pandemic.
Methods
This longitudinal survey study examined the association amongst screen time, internalizing and externalizing behaviours in school-aged children at two time points over the 2020-2021 academic school year. Parents completed survey measures on their parental involvement, stress levels, and their child’s screen time use as well as their emotional and behavioural difficulties.
Results
Children’s average daily screen time was 4.40 hours (SE=18.45) at baseline and 3.89 hours (SE=16.70) at 1-year follow up, with no significant change across the school year (p=.316). Increased screen time was associated with a greater incidence of internalizing behaviours in children (p=.03). Children who spent more time on screens and who were in households with parents reporting higher stress levels had increased internalizing behaviours (p=.001). No association between screen time use and externalizing behaviours was evident; however, parent stress was positively associated with children’s externalizing behaviours (p< .001).
Conclusions
Children’s screen time use has remained high during the pandemic and is associated with anxious and depressive symptoms. Children who spent more time on screens and who were in households with parents reporting higher stress levels had increased internalizing behaviours. Parent stress was positively associated with children’s externalizing behaviours. Targeted family intervention plans focused on reducing parent stress and screen time use may aid in improving children’s mental health during the ongoing pandemic.
Inclination controls CO2 and N2O fluxes, but not CH4 uptake, from a temperate upland forest soil
Authors: Gillespie Lauren Michelle , Triches Nathalie Ylenia , Abalos Diego , Finke Peter , Zechmeister-Boltenstern Sophie , Glatzel Stephan , Díaz-Pinés Eugenio
Published: February 2023

Inclination and spatial variability in soil and litter properties influence soil greenhouse gas (GHG) fluxes, and thus on-going climate change, but their relationship in forest ecosystems is poorly understood. To elucidate this, we explored the effect of inclination, distance to a stream, soil moisture, soil temperature, and other soil and litter properties on soil-atmosphere fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) with automated static chambers in a temperate upland forest in Eastern Austria. We hypothesised that soil CO2 emissions and CH4 uptake are higher in sloped locations with lower soil moisture content, whereas soil N2O emissions are higher in flat, wetter locations. During the measurement period, soil CO2 emissions were significantly higher on flat locations (p < 0.05), and increased with increasing soil temperature (p < 0.001) and decreasing soil moisture (p < 0.001). The soil acted as a CH4 sink, and CH4 uptake was not significantly related to inclination. However, CH4 uptake was significantly higher at locations furthest away from the stream compared to at the stream (p < 0.001), and positively related to litter weight and soil C content (p < 0.01). N2O fluxes were significantly higher on flat locations and further away from the stream (p < 0.05), and increased with increasing soil moisture (p < 0.001), soil temperature (p < 0.001) and litter depth (p < 0.05). Overall, this study underlines the importance of inclination and the resulting soil and litter properties in predicting GHG fluxes from forest soils and therefore their potential source-sink balance.
Healthy City: Global Systematic Scoping Review of City Initiatives to Improve Health with Policy Recommendations
Authors: danielli shaun , Ashrafian Hutan , Darzi Ara
Published: February 2023

Background
Global health will increasingly be determined by cities. Currently over half of the world’s population, over 4 billion people, live in cities. This systematic scoping review has been conducted to understand what cities are doing to improve health and healthcare for their populations.
Methods
We conducted a systematic search to identify literature on city-wide initiatives to improve health. The study was conducted in accordance with PRISMA and the protocol was registered with PROSPERO (CRD42020166210).
Results
The search identified 42,137 original citations, yielding 1,614 papers across 227 cities meeting the inclusion criteria. The results show the majority of initiatives were targeted at non-communicable diseases. City health departments are making an increasing contribution however the role of mayors appears to be limited.
Conclusion
The collective body of evidence identified in this review, built up over the last 130 years, has hitherto been poorly documented and characterised. Cities are a meta-system with population health dictated by multiple interactions and multidirectional feedback loops. Improving health in cities requires multiple actions, by multiple actors, at every level. The authors use the term ‘The Vital 5’. They are the 5 most important health risk factors; tobacco use; harmful alcohol use; physical-inactivity, unhealthy diet and planetary health. These ‘Vital 5’ are most concentrated in deprived areas and show the greatest increase is in low and middle income countries. Every city should develop a comprehensive strategy and action plan to address these ‘Vital 5’
A Partitioned Vibration Absorber with Acoustic Black Hole Features
Authors: Zhao Xiaoning , Ji Hongli , Qiu Jinhao , Cheng Li
Published: February 2023

Previous efforts in developing acoustic black hole (ABH) based add-on dynamic vibration absorbers (DVA) show promise as well as unresolved challenges, especially in terms of ensuring effective coupling with host structures under control. In this study, a partitioned ABH-featured dynamic vibration absorber (PABH-DVA), consisting of a symmetric ABH-DVA with partitions in the radial direction of the disc, is proposed. By using a plate as host structure, both simulation and experiment were carried out and the results show the new PABH-DVA yields better damping performing than the original symmetric ABH-DVA. To further reveal the mechanism which enables damping enhancement, the coupling coefficients of the two ABH-DVAs were calculated and compared. The simulation results show that the PABH-DVA has more coupled modes, with sometimes lower coupling coefficients than the symmetric ABH-DVA. The influence of the frequency ratio and modal mass were further analyzed and used to explain the reasons why the PABH-DVA delivers higher damping performance. The influence of the number of slits and their orientation were also discussed.
The legacy of one hundred years of climate change for organic carbon stocks in global agricultural topsoils
Authors: Poeplau Christopher , Dechow Rene
Published: February 2023

Soil organic carbon (SOC) of agricultural soils is observed to decline in many parts of the world. For deconfounding management and climate change effects, the latter needs to be estimated comprehensively. In this study, an established FAO framework was used to model global agricultural topsoil SOC stock dynamics from 1919 to 2018 as attributable to climate change. On average, global agricultural topsoils lost 2.5 ± 2.3 Mg C ha− 1 with constant net primary production (NPP) or 1.6 ± 3.4 Mg C ha− 1 when NPP was modified by temperature and precipitation. Regional variability could be explained by the complex patterns of changes in temperature and moisture, as well as initial SOC stocks. However, average SOC losses have been an intrinsic and persistent feature of climate change in all climatic zones. This needs to be taken into consideration in reporting or accounting frameworks and halted in order to mitigate climate change and secure soil health.
Hypofractionated Radiotherapy with Helical Tomotherapy Improved the Efficacy of Multiple Brain MetastasesLong-term Follow-up Results of a Phase II Trial
Authors: Ma Yuchao , Liu Qingfeng , Zhang Hongmei , Tian Yuan , Xu Yingjie , Bi Nan , Chen Xuesong , Wang Wenqing , Wang Kai , Huang Xiaodong , Zhao Ruizhi , Yang Siran , Yi Junlin , Li Ye-xiong , Xiao Jianping , Zhang Ye
Published: February 2023

Purpose: Multiple brain metastases (BMs) remain a therapeutic challenge. Helical tomotherapy (HT) is a novel equipment which has shown favorable dosimetric properties in previous studies. The aim of this single institutional phase II trial was to investigate the feasibility and toxicity of hypofractionated radiotherapy (HFRT) with or without simultaneous whole brain radiotherapy (WBRT) by HT in treating patients with multiple BMs.
Methods:Patients with at least 3 BMs were enrolled. All the patients were treated with HT. The prescribed dose was 40 Gy in 20 fractions for WBRT and 60 Gy in 20 fractions for BMs simultaneously. For patients who had prior WBRT or refusing WBRT, focal HFRT for the lesions with optimized doses based on tumor volumes and locations were given. The primary endpoint was 1y-intracranial progression free survival (IPFS).
Results: Between September 2014 and June 2017, 69 patients were enrolled and finally been analyzed. The median follow-up time was 40.1 months. The 1-year IPFS rate was 80.5%. The median survival time was 18.1 months (95% CI, 15.5- 20.7). The 1-year local control, overall survival and brain metastasis-specific survival rates were 96.4%, 71.0% and 94.6%, respectively. The 2-year rates were 87.6%, 51.1% and 39.1%, respectively. Only 1 patient (1.4%) had Grade 3 hematological toxicity and the radiation necrosis rate was 2.9%.
Conclusion: Helical tomotherapy was well tolerated and could significantly extend IPFS compared with historical controls in multiple BMs.
Frequency of Abo/rh Blood Groups Among Patients With Diabetes Mellitus in Luanda, Angola
Authors: Sacomboio Euclides Nenga Manuel , Pululo Sandra Alberto , Sebastião Cruz S. , Tchivango Adelino Tchilanda , Silveira Silvana da Rocha , Costa Mauricio da , Sousa Carlos Alberto Pinto , Ekundi-Valentim Eduardo , Cassinela Edson Kuatelela
Published: February 2023

Background
Diabetes is a chronic disease characterized by alterations in glucose, lipid, and protein metabolism, which can be identified by detecting high blood glucose levels. In this study we evaluated the frequency of ABO/Rh blood groups in patients with diabetes treated in Luanda, during the second half of 2020.
Methods
This was an observational, analytical, prospective study with a quantitative approach conducted with 100 patients with diabetes.
Results
The mean age of patients was 48,4±14 years old. Patients males (63%) with a mean age of 47.9±14.5 years old, secondary educational level (33%), and living in urbanized areas from Luanda (33%), which were the most prevalent in this studied population. About 57% did not exercise before the disease and did not have the disease in the family (51%). About 71% of the patients used insulin to treat diabetes. ORh+ and ARh+ blood groups were the most frequent. The majority of the patients were less than 4 years with diabetes.
Conclusion
We concluded that the patients most affected by diabetes were the elderly, males, from urbanized areas, and with blood groups ORh+ or ARh+. Further studies assessing the relationship between ABO/Rh blood groups and diabetes among the Angolan population are needed.
Once a week consumption of Western diet over twelve weeks promotes sustained insulin resistance and non-alcoholic fat liver disease in C57BL/6J mice
Authors: Demaria Thainá Magalhães , Crepaldi Leticia Diniz , Costa-Bartuli Emylle , Branco Jessica Ristow , Zancan Patricia , Sola-Penna Mauro
Published: February 2023

The Western diet (high in fat and sucrose) consumption is a highly prevalent feature in the whole world, mainly due to the increasing consumption of ultra-processed foods (UPF), which are cheaper and easier-to-eat, as compared to fresh and highly nutritive meals. Epidemiological studies have associated UPF consumption with development of obesity, non-alcoholic fat liver disease (NAFLD) and insulin resistance. For molecular studies, mice fed with Western diets have been used to characterize signaling pathways involved in these diet-induced pathologies. However, these studies fed mice continuously with the diets, which is not compatible with what occurs in real life, when consumption is occasional. Here, we fed mice once-a-week with a high fat, high sucrose (HFHS) diet and compared these animals with those fed continuously with HFHS diet or with a standard diet. Our results show that after a single day of consuming HFHS, animals presented impaired oral glucose tolerance test (oGTT) as compared to control group. Although this impairment was reversed after 24 hours consuming regular diet, repetition of HFHS consumption once-a-week aggravated the picture such as after 12-weeks, oGTT impairment was not reversed after 6 days under control diet. Liver steatosis, inflammation, impaired insulin signaling pathway and endoplasmic reticulum stress are similar comparing animals that consumed HFHS once-a-week with those that continuously consumed HFHS, though weekly-fed animals did not gain as much weight. Therefore, we conclude that regimen of one day HFHS plus 6 days normal diet over 12 weeks is sufficient to induce insulin resistance and NAFLD in mice.
Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa
Authors: Ramphal Upasana , Tshiabuila Derek , Ramphal Yajna , Giandhari Jennifer , Heerden Carel van , Baxter Cheryl , wyk Stephanie van , Maharaj Arisha , Pillay Sureshnee , Laguda-Akingba Oluwakemi , San James Emmanuel , Wilkinson Eduan , Lessells Richard , de Oliveira Tulio
Published: February 2023

Background: Genomic surveillance, with the aid of next-generation sequencing (NGS) technologies, revolutionized the SARS-CoV-2 pandemic. Coupled with high-performance analysis software, methodologies such as the Ion Torrent S5 and Illumina MiSeq dramatically improved the genomic surveillance capacity within South Africa during the height of the pandemic. Using de-identified remnant samples collected from Eastern Cape and analysis software, Genome Detective and NextClade, we compared the sequencing process, genomic coverage, quantification of mutations, and clade classification from sequence data generated by these two common “benchtop” NGS platforms.
Results: Sequence data analysis revealed success rates of 175/183 (96%) and 172/183 (94%) on the Ion Torrent S5 and Illumina MiSeq, respectively. Internal quality metrics were assessed in terms of genomic coverage (>80%) and the number of mutations identified (<100). A greater number of higher-genomic coverage sequences were generated on the Ion Torrent S5 (99%) than on the Illumina MiSeq (80%) and <100 mutations was obtained by both platforms. Ion Torrent S5 generated high coverage sequences from samples having a broader range of viral loads (VL) compared to the Illumina MiSeq, which was less successful in sequencing samples with lower viral loads. Clade assignments were comparable across platforms which accurately differentiated between Beta (<45%) and Delta (≤30%) VOCs. A disparity in clade assignment was observed in <10% of sequences due to poor coverage obtained on the Illumina MiSeq, followed by a failure rate of ≤6% across the two platforms. Manual library preparation found both methods similar in terms of sample processing, handling of larger sample quantities, and clade assignment for SARS-CoV-2. Variability between the Ion Torrent S5 and Illumina MiSeq was observed in sequencing run duration (3,5 hrs vs 36 hrs), sequencing process (semi-automation vs manual), genomic coverage (99% vs 80%), and viral load requirements (broad range vs high VL).
Conclusion: The Illumina MiSeq and Ion Torrent S5 are both reliable platforms capable of performing WGS with the use of amplicons and providing specific, accurate, and high throughput analysis of the SARS-CoV-2 whole viral genomes. Both sequencing platforms are feasible platforms for the genomic surveillance of SARS-CoV-2, each with its specific advantages and trade-offs.
Association between dietary hardness and cognitive dysfunction among Japanese men in their 60s: a cross-sectional study
Authors: Fujiwara Aya , Fukunaga Ami , Murakami Kentaro , Inoue Yosuke , Nakagawa Tohru , Yamamoto Shuichiro , Konishi Maki , Mizoue Tetsuya
Published: February 2023

Background: Although the association between dietary components (e.g. nutrients, foods, and dietary patterns) and cognitive dysfunction has been extensively investigated, a limited number of studies have been conducted on dietary hardness, despite its possible role in increasing masticatory activity and improving cognitive function. We aimed to examine the cross-sectional association between the hardness of habitual diet and cognitive dysfunction among Japanese men in their 60s.
Methods: Data were obtained from 1,494 men aged 60– 69 years who participated in the baseline survey of Hitachi Health Study II (2017–2020). Dietary hardness was assessed using the information on the habitual intake of solid foods, which was assessed using a brief-type, self-administered diet history questionnaire, and the magnitude of masticatory muscle activity required for consuming each food item, which was available in a published database. The sum of masticatory muscle activity involved in consuming food items was used as an estimate of dietary hardness. Cognitive dysfunction was defined as a score ≤ 13 points on the test battery for screening for Alzheimer’s disease (MSP-1100). Logistic regression models were used to examine the association between dietary hardness and cognitive dysfunction.
Results: The mean (standard deviation) age of participants was 63.5 (3.5) years. The prevalence of cognitive dysfunction was 7.5%. The odds ratios (95% confidence intervals) for cognitive dysfunction in the second and third tertiles were: 0.76 (0.46, 1.25) and 0.86 (0.53, 1.39), respectively, after adjustment for socio-demographic factors (P for trend = 0.70). After further adjustment for protective nutrient intake against cognitive dysfunction, the corresponding figures were 0.72 (0.43, 1.21) and 0.79 (0.43, 1.45), respectively (P for trend = 0.60).
Conclusions: Hardness of the habitual diet was not associated with the prevalence of cognitive dysfunction among Japanese men in their 60s. Future prospective studies are necessary to investigate the association between dietary hardness estimated a validated questionnaire and cognitive dysfunctions.
CD47 antisense oligonucleotide treatment attenuates obesity and its-associated metabolic dysfunction
Authors: Gwag Taesik , Li Dong , Ma Eric , Guo Zhenheng , Liang Ying , Wang Shuxia
Published: February 2023

Previous study from our lab has revealed a new role of CD47 in regulating adipose tissue function, energy homeostasis and the development of obesity and metabolic disease in CD47 deficient mice. In this study, the therapeutic potential of an antisense oligonucleotide (ASO) targeting to CD47 in obesity and its-associated complications was determined in two obese mouse models (diet induced and genetic models). In diet induced obesity, male C57BL6 mice were fed with high fat (HF) diet to induce obesity and then treated with CD47ASO or control ASO for 8 weeks. In genetic obese mouse model, male six-week old ob/ob mice were treated with ASOs for 9 weeks. We found that CD47ASO treatment reduced HF diet-induced weight gain, decreased fat mass, prevented dyslipidemia, and improved glucose tolerance. These changes were accompanied by reduced inflammation in white adipose tissue and decreased hepatic steatosis. This protection was also seen in CD47ASO treated ob/ob mice. Mechanistically, CD47ASO treatment increased mice physical activity and energy expenditure, contributing to weight loss and improved metabolic outcomes in obese mice. Collectively, these findings suggest that CD47ASO might serve as a new treatment option for obesity and its-associated metabolic complications.
The Systematic Development of Guidance for Parents on Talking to their Children about Weight
Authors: Gillison Fiona , Grey Elisabeth , Baber Fran , Chater Angel , Atkinson Lou , Gahagan Alison
Published: February 2023

Background: The prevalence of overweight and obesity in children is increasing, alongside increases in rates of children’s anxiety and worry about their weight. In many countries children’s weight is measured, and parents are made aware if a child has overweight or obesity. However, many parents are concerned that raising their child’s awareness of their weight, and talking to children about their weight could harm their wellbeing. The aim of this project was to develop guidance for parents on constructive ways to talk to children about weight when they need to, while prioritising their child’s wellbeing.
Methods: The project followed a mixed-methods design: Phase 1 involved the collection and collation of evidence including (a) two systematic literature reviews to identify the associations between parent-child weight talk, and broader health discussions, and children’s wellbeing, (b) interviews with children, and (c) development and refinement of narrative messaging. Phase 2 involved the development of a conceptual model and mapping primary findings to techniques and content within a draft document, aimed at providing guidance for parents on talking to children about weight. Phase 3 involved a modified Delphi process with 29 stakeholders to refine and agree a final version of the guidance.
Results: An acceptable draft guidance was agreed following two stages of feedback from Delphi participants. Key areas for debate and adaptation included: encouraging discussion about health and growth with lesser focus on weight; finding ways to reduce stigma and perceptions of blame; emphasising a whole-family approach; inclusive representation of diversity among children and families.
Conclusions: Consensus on the content of guidance for parents on talking to children about weight was achieved through a process of evidence review, expert input, and collaborative engagement. The next steps are to measure the impact of the resource on improving the experience of parents and children in communicating about weight.
In situ programming acid-base pair proton-conductive channels of perfluorosulfonic acid membrane for fuel cells
Authors: Zhang Wenxing , Zhao Shengqiu , Wang Rui , Zhang Aojie , Huang Yi , Tang Haolin
Published: February 2023

The development of rapid and dependable proton transport channels is crucial for proton exchange membrane fuel cells (PEMFCs) operating in low humidity conditions. Herein, an NH-Zr framework rich in basic sites was in situ constructed in a perfluorosulfonic acid (PFSA) solution, and PFSA-NH-Zr hybrid proton exchange membranes were prepared. The introduced NH-Zr framework successfully induced proton conducting groups (-SO3H) reorganization along the NH-Zr framework, resulting in the formation of fast ion transport channels. Meanwhile, under low humidity, the acid-base pairs between N-H (NH-Zr framework) and -SO3H (PFSA) promoted the protonation/deprotonation and the subsequent proton leap via the Grotthuss processes. Especially, the hybrid membrane PFSA-NH-Zr-1 with suitable NH-Zr content had a promising proton conductivity of 0.031 S/cm at 80°C, 40% RH, and 0.292 S/cm at 80°C, 100% RH, which were approximately 33% and 40% higher than the pristine PFSA membrane (0.023 S/cm and 0.209 S/cm), respectively. In addition, the maximum power density of the hybrid proton exchange membrane was 0.726 W/cm2, which was nearly 20% higher than the pristine PFSA membrane (0.604 W/cm2) under 80°C, 40% RH. This work established a referable strategy for developing high-performance proton exchange membranes under low RH conditions.
A Brain Connectome Biomarker for Sleep Health
Authors: Wang Yulin , Genon Sarah , Dong Debo , Zhou Feng , Li Chengyu , He Qinghua , Qiu Jiang , Feng Tingyong , Chen Hong , Lei Xu
Published: February 2023

Sleep health is both conceptually and operationally a composite concept containing multiple domains of sleep. In line with this, high dependence and interaction across different domains of sleep health encourage a transition in sleep health research from categorical to dimensional approaches that integrate neuroscience and sleep health. Here, we seek to identify the covariance patterns between multiple-sleep health domains and distributed intrinsic functional connectivity by applying a multivariate approach (partial least squares). This multivariate analysis revealed a composite sleep health dimension co-varying with connectivity patterns involving the attentional and thalamic networks and which appear relevant at the neuromolecular level. These findings were further replicated and generalized to several unseen independent datasets. Critically, the identified sleep-health related connectome showed diagnostic potential for insomnia disorder. These results together delineate a brain connectome biomarker for sleep health with high potential for clinical translation.
Estimating plastic pollution levels in rivers through harmonized monitoring strategies
Authors: Emmerik Tim van , Kirschke Sabrina , Schreyers Louise , Nath Shuvojit , Schmidt Christian , Wendt-Potthoff Katrin
Published: February 2023

Plastic pollution in freshwater environments is an emerging threat to ecosystem health and human livelihood. Plastics that accumulate in rivers and lakes over long time periods have direct local impact, and may eventually also reach the world’s oceans. Monitoring river plastic pollution is therefore key to quantify, understand and reduce plastics in all aquatic ecosystems. Unfortunately, global river plastic monitoring is still in its early stage. The lack of harmonization between ongoing monitoring efforts compromises the direct comparison and combination of available data. Recently, the United Nations Environment Programme (UNEP) launched guidelines on plastic monitoring in rivers and lakes, to provide a starting point for practitioners and scientists towards harmonized data collection, analysis, and reporting. Here, we demonstrate the application of those guidelines through a practical workflow to support to design effective plastic monitoring strategies. The workflow is a five-step iterative approach that aims to match the defined research goal or question to the available resources and river basin characteristics. To test the relevance of the workflow in different settings, we applied the workflow to three rivers across relevant gradients, including geography, hydrology, and plastic pollution levels. In the Rhine basin (Switzerland, France, Germany, the Netherlands) we showed that urban areas and tributaries may act as entry points of plastic pollution. For the Odaw basin (Ghana) we compared floating, terrestrial and riverbank plastics, identifying source and accumulation zones. Finally, in the Mekong river (Cambodia) we quantified the contribution of the city of Phnom Penh to plastic pollution through quantifying the plastic mass balance in the Mekong-Tonle Sap-Bassac region. We show that despite the simplicity of the selected methods and the limited duration of the data collection, a harmonized approach can provide crucial insights in the state of plastic pollution in very different river basins. Although each case study focused on one specific goal, each one is directly transferable to any river globally. Data collection is key in reaching local, regional and global goals on reducing plastic pollution. With our paper we aim to provide a simple workflow to support the design of effective and comparable river plastic monitoring strategies.
Dietary protein intake and mortality among survivors of liver cirrhosis: a prospective cohort study
Authors: Daftari Ghazal , Tehrani Asal Neshatbini , Pashayee-khamene Fereshteh , Karimi Sara , Ahmadzadeh Saleheh , Hekmatdoost Azita , Salehpour Amin , Yari Zahra
Published: February 2023

Background
Liver cirrhosis is a worldwide burden and is associated with poor clinical outcomes, including increased mortality. The beneficial effects of dietary modifications in reducing morbidity and mortality are inevitable.
Aim
The current study aimed to evaluate the potential association of dietary protein intake with the cirrhosis-related mortality.
Methods
In this cohort study, 121 ambulatory cirrhotic patients with at least 6 months of cirrhosis diagnosis were followed-up for 48 months. A 168-item validated food frequency questionnaire was used for dietary intake assessment. Total dietary protein was classified as dairy, vegetable and animal protein. We estimated crude and multivariable-adjusted hazard ratios (HRs) with 95% confidence intervals (CIs), applying Cox proportional hazard analyses.
Results
After full adjustment for confounders, analyses showed that total (HR = 0.38, 95% CI = 0.2–1.1, p trend = 0.045) and dairy (HR = 0.38, 95% CI = 0.13–1.1, p trend = 0.046) protein intake was associated with a 62% lower risk of cirrhosis-related mortality. While a higher intake of animal protein was associated with a 3.8-fold increase in the risk of mortality in patients (HR = 3.8, 95% CI = 1.7–8.2, p trend = 0.035). Higher intake of vegetable protein was inversely but not significantly associated with mortality risk.
Conclusion
Comprehensive evaluation of the associations of dietary protein intake with cirrhosis-related mortality indicated that a higher intake of total and dairy protein and a lower intake of animal protein are associated with a reduced risk of mortality in cirrhotic patients
A novel nomogram predicting overt hepatic encephalopathy after transjugular intrahepatic portosystemic shunt in portal hypertension patients
Authors: Liao Yong , Zhang Lin , Yue Zhen-dong , Fan Zhen-hua , Wu Yi-fan , Zhang Yu , Dong Cheng-bin , Wang Xiu-qi , Cui Ting , Meng Ming-ming , Bao Li , Liu Fu-quan , Wang Lei
Published: February 2023

Rationale and Objectives: We aim to develop a nomogram to predict overt hepatic encephalopathy (OHE) after transjugular intrahepatic portosystemic shunt (TIPS) in patients with portal hypertension, according to demographic/clinical indicators such as age, creatinine, blood ammonia, indocyanine green retention rate at 15 minutes (ICG-R15) and percentage of Portal pressure gradient (PPG) decline.
Materials and Methods: In this retrospective study, 296 patients with portal hypertension who received elective TIPS in Beijing Shijitan Hospital from June 2018 to June 2020 were included. These patients were randomly divided into a training cohort (n=207) and a validation cohort (n=89). According to the occurrence of OHE, patients were assigned to OHE group and non-OHE group. Both univariate and multivariate analyses were performed to determine independent variables for predicting OHE after TIPS. Accordingly, receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA) were used to compare the accuracy and superiority of a novel model with conventional Child-Pugh and MELD scoring model.
Results: Age (OR=1.036, 95% CI:1.002-1.070, p=0.037), Creatinine (OR=1.011, 95% CI:1.003-1.019, p=0.009), Blood ammonia (OR=1.025, 95% CI:1.006-1.044, p=0.011), ICG-R15 (OR=1.030, 95% CI:1.009-1.052, p=0.004) and Percentage decline in PPG (OR=1.068, 95% CI:1.029-1.109, p=0.001) were independent risk factors for OHE after TIPS using multifactorial analysis. A nomogram was constructed using a well-fit calibration curve for each of these five covariates. When compared to Child-Pugh and MELD score, this new nomogram has a better predictive value (C-index=0.828, 95% CI:0.761-0.896). Consistently, this finding was reproduceable in validation cohort and confirmed with DCA.
Conclusion: A unique nomogram was developed to predict OHE after TIPS in patients with PHT, with a high prediction sensitivity and specificity performance than commonly applied scoring systems.