Miracle-dz/UniFAR-FTUs huggingface dataset:
eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany

The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity within the Elbe. We sampled three stations in the Elbe, included low and high tide events, as well as two adjoining lakes to compare the recovered faunas. To analyze the data, we employed two different pipelines: the automated mBRAVE pipeline utilizing the BOLD database and one including NCBI BLAST. The number of OTUs with species or higher-level identifications were similar between both approaches with 352 OTUs and 355 OTUs for BLAST and mBRAVE, respectively, however, BLAST searches recovered another 942 unidentified metazoan OTUs. Many taxa were well represented; however, fish species were poorly represented, especially in the Elbe estuary samples. This could be a result of the universal COI primers, which also yielded high read numbers for non-metazoan OTUs, and small-bodies taxa like Rotifera, which might have been sampled together with the eDNA. Our results show a strong tidal influence on the recovered taxa. During low tide, downstream stations resembled sites further upstream, but the former showed a very different OTU composition during high tide and early tide. Such differences might be due to varying impacts of upstream-originating eDNA during tide cycles. Such factors need to be considered when routinely employing eDNA for monitoring programs.
A Type 2 Diabetes Subtype Responsive to ACCORD Intensive Glycemia Treatment

OBJECTIVE Current type 2 diabetes (T2D) management contraindicates intensive glycemia treatment in patients with high cardiovascular disease (CVD) risk and is partially motivated by evidence of harms in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. Heterogeneity in response to intensive glycemia treatment has been observed, suggesting potential benefit for some individuals. RESEARCH DESIGN AND METHODS ACCORD was a randomized controlled trial that investigated whether intensively treating glycemia in individuals with T2D would reduce CVD outcomes. Using a novel approach to cluster HbA1c trajectories, we identified groups in the intensive glycemia arm with modified CVD risk. Genome-wide analysis and polygenic score (PS) were developed to predict group membership. Mendelian randomization was performed to infer causality. RESULTS We identified four clinical groupings in the intensive glycemia arm, and clinical group 4 (C4) displayed fewer CVD (hazard ratio [HR] 0.34; P = 2.01 × 10−3) and microvascular outcomes (HR 0.86; P = 0.015) than those receiving standard treatment. A single-nucleotide polymorphism, rs220721, in MAS1 reached suggestive significance in C4 (P = 4.34 × 10−7). PS predicted C4 with high accuracy (area under the receiver operating characteristic curve 0.98), and this predicted C4 displayed reduced CVD risk with intensive versus standard glycemia treatment (HR 0.53; P = 4.02 × 10−6), but not reduced risk of microvascular outcomes (P < 0.05). Mendelian randomization indicated causality between PS, on-trial HbA1c, and reduction in CVD outcomes (P < 0.05). CONCLUSIONS We found evidence of a T2D clinical group in ACCORD that benefited from intensive glycemia treatment, and membership in this group could be predicted using genetic variants. This study generates new hypotheses with implications for precision medicine in T2D and represents an important development in this landmark clinical trial warranting further investigation.
Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
Efficient solid‐phase synthesis of acetylated lignin and a comparison of the properties of different modified lignins

The chemical modification of lignin can greatly enhance its functionality and exploit its application areas. To avoid the difficulties of separation and environmental pollution in the traditional liquid-phase method, we prepared acetylated lignin by a mechanical-activation-assisted solid-phase synthesis (MASPS) technology with a customized stirring ball mill as a reactor and studied its structure and properties. Ultraviolet–visible analysis showed that the degree of esterification (DE) of the acetylated lignin produced by the MASPS technique was 77.59%, whereas the DEs of those produced by traditional liquid-phase synthesis (LPS) and thermal solid-phase synthesis (TSPS) were only 42.29 and 27.54%, respectively. Fourier transform infrared spectroscopy and NMR analyses indicated that both phenolic hydroxyls and aliphatic hydroxyls participated in the reaction, and the reactivity of the phenolic hydroxyls was higher than that of the aliphatic hydroxyl groups. The acetylation of aliphatic hydroxyl mainly happened at the γ of arylglycerol-β-aryl ether (β-O-4). Scanning electron microscopy analysis showed that the acetylated lignins prepared by MASPS and TSPS were irregular blocks with coarse surfaces and loose structures, whereas the lignin prepared by LPS consisted mostly of regular balls with a smooth surface and a compact structure. Differential scanning calorimetry and thermogravimetric analyses indicated that the glass-transition temperatures and thermal stability of the acetylated lignin increased by orders with the processing techniques of MASPS, TSPS, and LPS. MASPS integrated the activation and reaction in the same equipment without the use of a solvent and showed advantages of a high efficiency, environmental protection, and easy operation. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 44276.
Evaluation of the Mawid mobile healthcare application in delivering services during the COVID-19 pandemic in Saudi Arabia

Abstract Purpose The purpose of this study is to evaluate MAWID mobile application developed by the Ministry of Health, Saudi Arabia, which is used for primary care hospitals appointments management and for tracking and tracing COVID-19. Participants and Methods An online questionnaire-based survey was used for collecting data related to three major factors including Ease of Use, Satisfaction, and Benefits of MAWID application among its users. Out of total 2542 participants, 345 participants completed only a part of the survey, and 204 participants did not use the application. After removing, 549 invalid responses, a final sample of 1993 was included for the data analysis. Results 82.1% of the participants referred MAWID as easy to use application, 79.8% were highly satisfied with the application, and majority of the participants reflected potential benefits of using the application. T-test results have revealed that significant differences existed between males and females, and young and older participants in relation to the Ease of Use and Satisfaction levels associated with MAWID application. Conclusion Mobile applications can be very effective in delivering the healthcare services during pandemics. However, there is a need for regular evaluation and assessment to trach the change in users′ needs and update the app according to the changing requirements.
The use of urban biowaste and excavated soil in the construction sector: A literature review

Soil has been used as building material for thousands of years with a decrease in popularity after the industrial revolution. Nowadays, there is a growing interest in the implementation of unfired soil-based building solutions for their low environmental impact, performances and availability. Traditional soil construction techniques have recurrently included vegetal fibres to enhance soil performance and recent studies highlight a predominant use of agro- and non-agro-waste for unfired soil construction. The article reviews the state-of-the-art of the use of excavated soil and biowaste in the construction industry including a novel focus on urban-only waste and on building technologies using the integration of these two secondary construction material flows. Our literature review highlights a lack of references about the joint use of these secondary resources. Finally, future research orientations are suggested to promote their implementation in the building sector, which could improve urban waste management.
Determination of the refractive index and wavelength‐dependent optical properties of few‐layer CrCl3 within the Fresnel formalism

Based on previous reports on the optical microscopy contrast of mechanically exfoliated few layer CrCl 3 transferred on 285 nm and 270 nm SiO 2 on Si(100), we focus on the experimental determination of an effective mean complex refractive index via a fitting analysis based on the Fresnel equations formalism. Accordingly, the layer and wavelength‐dependent absorbance and reflectance are calculated. Layer and wavelength‐dependent optical contrast curves are then evaluated demonstrating that the contrast is significantly high only around well‐defined wavelength bands. This is validated a posteriori, by experimental UV‐Vis absorbance data. The present study aims to show the way towards the most reliable determination of thickness of the 2D material flakes during exfoliation.
A comparative study on the lipidome of normal knee synovial fluid from humans and horses

The current limitations in evaluating synovial fluid (SF) components in health and disease and between species are due in part to the lack of data on normal SF, because of low availability of SF from healthy articular joints. Our study aimed to quantify species-dependent differences in phospholipid (PL) profiles of normal knee SF obtained from equine and human donors. Knee SF was obtained during autopsy by arthrocentesis from 15 and 13 joint-healthy human and equine donors, respectively. PL species extracted from SF were quantitated by mass spectrometry whereas ELISA determined apolipoprotein (Apo) B-100. Wilcoxon’s rank sum test with adjustment of scores for tied values was applied followed by Holm´s method to account for multiple testing. Six lipid classes with 89 PL species were quantified, namely phosphatidylcholine, lysophosphatidylcholine, sphingomyelin, phosphatidylethanolamine, plasmalogen, and ceramide. Importantly, equine SF contains about half of the PL content determined in human SF with some characteristic changes in PL composition. Nutritional habits, decreased apolipoprotein levels and altered enzymatic activities may have caused the observed different PL profiles. Our study provides comprehensive quantitative data on PL species levels in normal human and equine knee SF so that research in joint diseases and articular lubrication can be facilitated.
Gateway to Global Aging Data: Resources for Cross-National Comparisons of Family, Social Environment, and Healthy Aging.

OBJECTIVES The Gateway to Global Aging Data (Gateway; g2aging.org) is a data and information platform developed to facilitate cross-country analyses on aging, especially those using the international family of Health and Retirement studies. We provide a brief introduction to the Gateway to Global Aging Data, discussing its potential for cross-national comparisons of family, social environment, and healthy aging. METHODS We summarize the survey metadata, study characteristics, and harmonized data available from the Gateway, describing the population represented in each study. We portray cohort characteristics and key measures of health and social environment from 37 countries in North America, Europe, and Asia using harmonized data. RESULTS Significant cross-country heterogeneity was observed in many measures of family, social environment, and healthy aging indicators. For example, there was a three-fold difference in co-residence with children, ranging from 14% in Sweden to over 46% in Spain and Korea in 2014. From 2002-2014, the difference between informal care receipt in individuals of low and high wealth decreased by 6% in the US and remained unchanged in England. The percentage of individuals aged 50-59 living alone in 2012 varied fifteen-fold, from a low of 2% in China to a high of 30% in Mexico. DISCUSSION By partnering with nationally representative studies around the globe, the Gateway to Global Aging Data facilitates comparative research on aging through the provision of easy-to-use harmonized data files and other valuable tools.
Physicians’ attitude towards webinars and online education amid COVID-19 pandemic: When less is more

Background Since the declaration of COVID-19 as a pandemic, all scientific medical activities were shifted to an online format, in the form of webinars, to maintain continuing medical education (CME). We aimed to assess physicians’ attitude among different medical specialties towards this sudden and unexpected shift of traditional face-to-face meetings into webinars, and to suggest future recommendations. Methods We conducted a cross-sectional, internet-based survey study using a 25-item questionnaire, from November 1 and November 15, 2020. The survey was created and distributed to physicians from different medical and surgical specialties and from different countries via several social media platforms, using a snowball technique. Results A total of 326 physicians responded; 165 (50.6%) were females, mean age of responders was 38.7 ± 7.5 years. The majority of responses (93.2%) came from Arab countries. Of them, 195 (59.8%) reported attending more webinars compared to the same period last year, with average of 3 per month. As regard to the general impression; 244 (74.8%) were “strongly satisfied” or “satisfied”, with the most satisfaction for “training courses: by 268 (82.2%), and “International conferences” by 218 (66.9%). However, 246 respondents (75.5%) felt overwhelmed with the number and frequency of webinars during the pandemic, 171 (52.5%) reported attending less than 25% of webinars they are invited to, 205 (62.8%) disagreed that webinars can replace in-person meetings after the pandemic, and 239 (73.3%) agreed that online meetings need proper regulations. Conclusions Webinars comprised a major avenue for education during COVID-19 pandemic, with initial general satisfaction among physicians. However, this paradigm shift was sudden and lacked proper regulations. Despite initial satisfaction, the majority of physicians felt overwhelmed with the number and frequency of webinars. Physicians’ satisfaction is crucial in planning future educational activities, and considering that this current crisis will most likely have long lasting effects, webinars should be viewed as complementing traditional in-person methods, rather than replacement. In this study, we are suggesting recommendations to help future regulation of this change.
Rapid serum‐free/suspension adaptation: Medium development using a definitive screening design for Chinese hamster ovary cells

The biopharmaceutical industry prefers to culture the mammalian cells in suspension with a serum‐free media (SFM) due to improved productivity and process consistency. However, mammalian cells preferentially grow as adherent cells in a complete medium (CM) containing serum. Therefore, cells require adaptation from adherence in CM to suspension culture in SFM. This work proposes an adaptation method that includes media supplementation during the adaption of Chinese hamster ovary cells. As a result, the adaptation was accelerated compared to the traditional repetitive subculturing. Ca2+/Mg2+ supplementation significantly reduced the doubling time compared to the adaptation without supplementation during the adaptation of adherent cells from 100% CM to 75% CM (p < 0.05). Furthermore, a definitive screening design (DSD) was applied to select essential nutrients during the adaptation from 10% CM to 0% CM. The main effects of Ca2+ and Dulbecco's modified essential medium (DMEM) were found significant to both viable cell density and viability at harvest. Additionally, the interaction term between Ca2+ and DMEM was found significant, which highlights the ability of DSD to capture interaction terms. Eventually, the media supplementation method resulted in adaptation SFM in 27 days, compared to the previously reported 66 days. Additionally, the membrane surface integrin expression was found significantly decreased when adherent cells were adapted to suspension. Moreover, the Ca2+/Mg2+ supplementation correlated with faster integrin recovery after trypsinization. However, faster integrin recovery did not contribute to the accelerated cell growth when subculturing from 100% CM to 75% CM.
Developing and validating a school-based screening tool of Fundamental Movement Skills (FUNMOVES) using Rasch analysis

Background A large proportion of children are not able to perform age-appropriate fundamental movement skills (FMS). Thus, it is important to assess FMS so that children needing additional support can be identified in a timely fashion. There is great potential for universal screening of FMS in schools, but research has established that current assessment tools are not fit for purpose. Objective To develop and validate the psychometric properties of a FMS assessment tool designed specifically to meet the demands of universal screening in schools. Methods A working group consisting of academics from developmental psychology, public health and behavioural epidemiology developed an assessment tool (FUNMOVES) based on theory and prior evidence. Over three studies, 814 children aged 4 to 11 years were assessed in school using FUNMOVES. Rasch analysis was used to evaluate structural validity and modifications were then made to FUNMOVES activities after each study based on Rasch results and implementation fidelity. Results The initial Rasch analysis found numerous psychometric problems including multidimensionality, disordered thresholds, local dependency, and misfitting items. Study 2 showed a unidimensional measure, with acceptable internal consistency and no local dependency, but that did not fit the Rasch model. Performance on a jumping task was misfitting, and there were issues with disordered thresholds (for jumping, hopping and balance tasks). Study 3 revealed a unidimensional assessment tool with good fit to the Rasch model, and no further issues, once jumping and hopping scoring were modified. Implications The finalised version of FUNMOVES (after three iterations) meets standards for accurate measurement, is free and able to assess a whole class in under an hour using resources available in schools. Thus FUNMOVES has the potential to allow schools to efficiently screen FMS to ensure that targeted support can be provided and disability barriers removed.
An application of Bayesian Belief Networks to assess management scenarios for aquaculture in a complex tropical lake system in Indonesia

A Bayesian Belief Network, validated using past observational data, is applied to conceptualize the ecological response of Lake Maninjau, a tropical lake ecosystem in Indonesia, to tilapia cage farms operating on the lake and to quantify its impacts to assist decision making. The model captures ecosystem services trade-offs between cage farming and native fish loss. It is used to appraise options for lake management related to the minimization of the impacts of the cage farms. The constructed model overcomes difficulties with limited data availability to illustrate the complex physical and biogeochemical interactions contributing to triggering mass fish kills due to upwelling and the loss in the production of native fish related to the operation of cage farming. The model highlights existing information gaps in the research related to the management of the farms in the study area, which is applicable to other tropical lakes in general. Model results suggest that internal phosphorous loading (IPL) should be recognized as one of the primary targets of the deep eutrophic tropical lake restoration efforts. Theoretical and practical contributions of the model and model expansions are discussed. Short- and longer-term actions to contribute to a more sustainable management are recommended and include epilimnion aeration and sediment capping.
CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks

Fire blight is a destructive plant disease caused by Erwinia amylovora affecting pome fruit trees, and responsible for large yield declines, long phytosanitary confinements, and high economic losses. In Portugal, the first major fire blight outbreaks occurred in 2010 and 2011, and although later considered eradicated, the emergence of other outbreaks in recent years stressed the need to characterize the E. amylovora populations associated with these outbreaks. In this regard, CRISPR genotyping, assessment of three virulence markers, and semi-quantitative virulence bioassays, were carried out to determine the genotype, and assess the virulence of thirty-six E. amylovora isolates associated with outbreaks occurring between 2010 and 2017 and affecting apple and pear orchards located in the country central-west, known as the main producing region of pome fruits in Portugal. The data gathered reveal that 35 E. amylovora isolates belong to one of the widely-distributed CRISPR genotypes (5-24-38 / D-a-α) regardless the host species, year and region. Ea 680 was the single isolate revealing a new CRISPR genotype due to a novel CR2 spacer located closer to the leader sequence and therefore thought to be recently acquired. Regarding pathogenicity, although dot-blot hybridization assays showed the presence of key virulence factors, namely hrpL (T3SS), hrpN (T3E) and amsG from the amylovoran biosynthesis operon in all E. amylovora isolates studied, pathogenicity bioassays on immature pear slices allowed to distinguish four virulence levels, with most of the isolates revealing an intermediate to severe virulence phenotype. Regardless the clonal population structure of the E. amylovora associated to the outbreaks occurring in Portugal between 2010 and 2017, the different virulence phenotypes, suggests that E. amylovora may have been introduced at different instances into the country. This is the first study regarding E. amylovora in Portugal, and it discloses a novel CRISPR genotype for this bacterium.