bluuebunny/crossref_metadata_2025_split huggingface dataset:
AMR Escherichia coli and its temporal and spatial variability within the aquatic environment
Authors: Odell Amelia , Eady Paul , Dixon Ronald 
Published: July 2020

Phenotypic and genotypic identification methods have been used to determine the temporal and spatial dynamics of AMR-Escherichia coli in a mainly rural watercourse that receives WWTP-effluent compared to a parallel river which does not. We aimed to investigate the incidence of plasmid-mediated mcr-1and β-lactamase-genes in E. coli recovered from both water and Asellus aquaticus samples throughout two-calendar-years.
Samples of the water and A. aquaticus were recovered from the relevant locations each month. CHROMagar ESBL agar was used throughout to isolate and identify ESBL-E. coli. The presence of AMR-genes was confirmed using the ‘BSAC’ antibiotic-disk-synergy method and PCR analysis to confirm the presence of mcr-1and ESBL-genes. The CHROMagar ESBL agar was found to be 99.7% (n=578) accurate when confirmed with a PCR analysis of the ESBL-genes. Seventy-six-point-six percent (n=449) of the isolated ESBL-E. coli were correctly identified as ESBL-producing organisms using the ‘BSAC’ method. Interestingly 61.9% (n=358) of the ESBL-E. coli were also found to carry the mcr-1 gene.
Our data shows that AMR levels were highest at the WWTP-effluent throughout the two-years for both water and A. aquaticus samples. The incidence of AMR-E. coli 1km downstream of the effluent discharge was equivalent to the parallel river sites, suggesting that the dispersal of AMR from the WWTP-effluent is limited, although AMR-E. coli were found in relatively high numbers at the WWTP-effluent. We argue that the presence of AMR in the freshwater invertebrate A. aquaticus could represent an important route by which AMR can spread from the aquatic environment to the terrestrial environment.
From waste to bioplastics: bio-based conversion of volatile fatty acids to polyhydroxyalkanoates
Authors: Perez-Zabaleta Mariel , Khatami Kasra , Cetecioglu Zeynep 
Published: July 2020

Production of polyhydroxyalkanoates (PHAs) as bio-alternative to petroleum-based plastics is an important field in the biorefinery to move forward in the development of the circular economy. PHAs are bioplastics stored inside microbial cells as carbon reservoirs and can be produced from a broad range of renewable resources such as waste streams. One important waste stream is food waste that can be converted into volatile fatty acids (VFAs) by anaerobic digestion. The produced effluent from food waste is not only rich in VFAs but also, other nutrients such as nitrogen and phosphorus that can be used by the microorganisms to produce PHAs. The aim of this research is to convert VFAs produced from food waste into PHAs, in which two approaches have been studied. The first approach was to use microbial mixed cultures (MMCs) while the second used microbial pure cultures.
The MMCs were enriched in sequencing batch bioreactor cultivations, where nitrogen and carbon starvation were combined to enhance the selection phase. PHA accumulation of the selected cultures was studied in nitrogen-limited fed-batch cultivations. The second approach studied five different PHA producing bacteria: Cupriavidus necator, Burkholderia cepacea, Bacillus megaterium, Bacillus cereus and Bacillus cereus. To select the most promising bacteria, synthetic medium with the same VFAs composition as in MMCs study was used for pre-screening experiments. Both, pure and mixed culture studies, resulted in the production of PHAs containing (R)-3-hydroxybutyrate, (R)-3-hydroxyvalerate and (R)-3-hydroxyhexanoate as monomers and VFAs were consumed with a high rate by the microorganisms.
Elucidation of environment dependent antibiotic resistance mechanisms
Authors: Machado Henrique , Seif Yara , Dillon Nicholas , Tsunemoto Hannah , Pogliano Joseph , Nizet Victor , O. Palsson Berhnard , Lyngby Kgs. 
Published: July 2020

The propensity of pathogens to evolve resistance to antibiotics used in clinical infectious disease therapeutics has been an increasing concern in recent decades. Acquisition of resistance often translates into treatment failure and puts patients at risk of serious adverse outcomes. Current laboratory testing of antibiotic susceptibility does not account for the different microenvironments that bacteria encounter within the human body, providing results that often do not translate into the clinic. Our goal is to better understand evolutionary strategies employed by Staphylococcus aureus in development of resistance in distinct environments.
We used adaptive laboratory evolution (ALE) to generate isogenic strains resistant to several antibiotics. Different media were used to mimic distinct environments and multi-omics approaches applied in the understanding of resistance mechanisms.
Evolved strains presented phenotypes similar to those observed in clinical resistant isolates. Mutational analysis indicated that resistance was specific and condition-dependent. Distinct mutations led to resistance phenotypes under a particular environmental condition, but these mutations did not necessarily translate into resistance under a different environmental condition. Furthermore, resistant strains possessed distinct transcriptional landscapes, even when the same systems were mutated, suggesting that similar evolutionary paths translate into distinct resistance mechanisms.
We identified several resistance mechanisms employed by S. aureus that were not only environment-dependent, but also environment specific. Additionally, we showed that ALE can be applied in pathogens of interest to study antibiotic resistance evolution and prediction of clinical resistance mechanisms, as supported by the significant overlap of mutations identified via ALE and those reported in clinical isolates.
Can m6A-modified RNA be used as an Anti-Viral Target?
Authors: Barker Amy M. , RÖder Konstantin , Pasquali Samuela , Foster Richard , Whitehouse Adrian 
Published: July 2020

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a DNA virus associated with several HIV-associated malignancies.
Like all herpesviruses, KSHV has a biphasic life cycle encompassing a latent state and lytic replication. The KSHV replication and transcription activator viral protein, encoded from open reading frame 50 (ORF50), is the key viral protein which drives the switch between the latent and lytic phases (Guito and Lukac, 2012). We have recently demonstrated that KSHV manipulates the host cell N6-methyl adenosine (m6A) RNA modification pathway to enhance viral gene expression. Specifically, we have shown that the KSHV ORF50 transcript is m6A methylated, allowing the recruitment of the m6A reader protein, Staphylococcal nuclease domain-containing protein 1 (SND-1), resulting in the stabilisation of the ORF50 transcript and efficient KSHV lytic replication (Baquero-Perez et al. 2019).
Further analysis of the m6A modified site with the ORF50 transcript has identified an RNA stem-loop, termed ORF50-1, which is a m6A-modified 43-mer, essential for SND-1 binding, thought to occur in a secondary structure/ sequence-dependent manner. Taking this into consideration, novel ligands have been assessed as effective anti-viral reagents. The importance of A versus m6A within the lytic phase of KSHV’s lifecycle will be investigated by combining in silicoscreening with biophysical techniques and cell based assays.
Effectiveness of COCOA, a COVID-19 contact notification application, in Japan
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi 
Published: July 2020

AbstractBackgroundCOCOA, a contact reporting application in Japan, was launched at the end of June 2020.ObjectWe assessed effectiveness of COCOA.MethodAfter developing a simple susceptible–infected–recovery model with COCOA and voluntary restrictions against going out (VRG), we assumed that COCOA can reduce infectiousness by 10–50% points through self-quarantine at home after receiving notification from COCOA.ResultsCOCOA alone is insufficient to halt an outbreak. Even if the entire population were to use COCOA, the reproduction number would be 1.31. However, if VRG were 15%, about half of the maximum VRG effectiveness under the emergency state declaration, then 10% COCOA use by a population can reduce the reproduction number to less than one.ConclusionSignificant effects of COCOA for reducing the reproduction number were found. However, without VRG, COCOA alone is insufficient to control an outbreak.
Covid-19 and dysregulated cerebral perfusion: observations with multimodal MRI
Authors: Henry-Feugeas Marie-Cécile , Gaudemer Augustin , Lescure Xavier , Dossier Antoine , Sonneville Romain , Ehmer Carsten , Choquet Christophe , Israel Theresa , Simon Agathe Raynaud , Borie Raphael , Amarenco Pierre , Khalil Antoine 
Published: July 2020

SummaryThe pathogenesis of encephalopathy-associated Covid-19 is still unclear. Multimodal brain MRI in 25 Covid-19 patients with neurological symptoms revealed angiographic and brain perfusion changes suggesting an under-recognized dysregulated brain perfusion not identified by morphological neuroimaging alone. Endothelial dysfunction, a key pathomechanism of dysregulated brain perfusion, may contribute to central-nervous-system disturbances in Covid-19.
COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme
Authors: Kendall Michelle , Milsom Luke , Abeler-Dörner Lucie , Wymant Chris , Ferretti Luca , Briers Mark , Holmes Chris , Bonsall David , Abeler Johannes , Fraser Christophe 
Published: July 2020

AbstractIn May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.
Optogenetic control of small GTPases reveals RhoA-mediated intracellular calcium signaling
Authors: Inaba Hironori , Miao Qianqian , Nakata Takao 
Published: July 2020

AbstractRho/Ras family small GTPases are known to regulate numerous cellular processes, including cytoskeletal reorganization, cell proliferation, and cell differentiation. These processes are also controlled by Ca2+, and consequently, crosstalk between these signals is considered likely. However, systematic quantitative evaluation is not yet reported. Thus, we constructed optogenetic tools to control the activity of small GTPases (RhoA, Rac1, Cdc42, Ras, Rap, and Ral) using an improved light-inducible dimer system (iLID). Using these optogenetic tools, we investigated calcium mobilization immediately after small GTPase activation. Unexpectedly, we found that a transient intracellular calcium elevation was specifically induced by RhoA activation in RPE1 and HeLa cells. These findings were confirmed in all the cell lines tested in this study. Of note, molecular mechanisms were identified to be different among cell types. In RPE1 and HeLa cells, RhoA activated phospholipase C epsilon (PLCε) at the plasma membrane, which in turn induced Ca2+release from the endoplasmic reticulum (ER). The RhoA-PLCε axis induced calcium-dependent NFAT nuclear translocation, suggesting it does activate intracellular calcium signaling.
Analyzing cannabinoid-induced abnormal behavior in a zebrafish model
Authors: Hasumi Akihiro , Maeda Hideyuki , Yoshida Ken-ichi 
Published: July 2020

AbstractThis study investigated the locomotor activity and responses under stressful conditions to assess marijuana-induced abnormal behavior in zebrafish larvae (Danio rerio), as an alternative to the standard rodent model. To induce the desired symptoms, cannabidiol and WIN55,212-2, two chemical components derived from marijuana plants, were used. A repeated light and dark test was used to assess how drug exposure influenced locomotive responses. Subjects were examined after moderate cannabidiol and WIN55,212-2 exposure and 24 h after relocation into untreated water. Cannabidiol did not produce a dose-dependent inhibitory effect on locomotor activity; 0.5 and 10 μg/mL cannabidiol decreased total distance and velocity, and 10 μg/mL cannabidiol attenuated responses in the darkness. No differences between the control and cannabidiol-treated groups were apparent after 24 h in fresh water. WIN55,212-2 at 0.5 and 1 μg/mL almost completely stopped fish activity even in darkness and at 10 μg/mL induced mortality. Spending 24 h in fresh water almost reversed drug-induced immobilization, even in WIN55,212-2-treated groups. Subjects were evaluated for responses to additional cannabidiol after WIN55,212-2 exposure. Cannabidiol attenuated WIN55,212-2-induced abnormal immobilization, whereas commensurate doses of cannabidiol and WIN55,212-2 produced a mixed response. In conclusion, the behavioral effects of marijuana depend on the ratio of the two different cannabinoid properties. The repeated light and dark test might be a suitable method for drug-induced behavioral assay.
A Deep Semi-Supervised Framework for Accurate Modelling of Orphan Sequences
Authors: Moffat Lewis , Jones David T. 
Published: July 2020

AbstractAccurate modelling of a single orphan protein sequence in the absence of homology information has remained a challenge for several decades. Although not as performant as their homology-based counterparts, single-sequence bioinformatic methods are not constrained by the requirement of evolutionary information and so have a swathe of applications and uses. By taking a bioinformatics approach to semi-supervised machine learning we develop Profile Augmentation of Single Sequences (PASS), a simple but powerful framework for developing accurate single-sequence methods. To demonstrate the effectiveness of PASS we apply it to the mature field of secondary structure prediction. In doing so we develop S4PRED, the successor to the open-source PSIPRED-Single method, which achieves an unprecedentedQ3score of 75.3% on the standard CB513 test. PASS provides a blueprint for the development of a new generation of predictive methods, advancing our ability to model individual protein sequences.
The prevalence of antibodies to SARS-CoV-2 among blood donors in China
Authors: Chang Le , Hou Wangheng , Zhao Lei , Zhang Yali , Wang Yanbin , Wu Linfeng , Xu Tingting , Wang Lilin , Wang Juan , Ma Jian , Wang Lan , Zhao Junpeng , Xu Jing , Dong Juan , Yan Ying , Yang Ru , Li Yu , Guo Fei , Cheng Wenjuan , Su Yingying , Zeng Jinfeng , Han Wei , Cheng Tong , Zhang Jun , Yuan Quan , Xia Ningshao , Wang Lunan 
Published: July 2020

AbstractObjectivesThe prevalence of antibodies to SARS-CoV-2 among blood donors in China remains unknown. To reveal the missing information, we investigated the seroprevalence of SARS-CoV-2 antibodies among blood donors in the cities of Wuhan, Shenzhen, and Shijiazhuang of China.
DesignCross-sectional studySettingThree blood centers, located in the central, south and north China, respectively, recruiting from January to April 2020.Participants38,144 healthy blood donors donated in Wuhan, Shenzhen and Shijiazhuang were enrolled, who were all met the criteria for blood donation during the COVID-19 pandemic in China.Main outcome measuresSpecific antibodies against SARS-CoV-2 including total antibody (TAb), IgG antibody against receptor-binding domain of spike protein (IgG-RBD) and nucleoprotein (IgG-N), and IgM. Pseudotype lentivirus-based neutralization test was performed on all TAb-positive samples. In addition, anonymous personal demographic information, including gender, age, ethnicity, occupation and educational level, and blood type were collected.ResultsA total of 519 samples from 410 donors were confirmed by neutralization tests. The SARS-CoV-2 seroprevalence among blood donors was 2.29% (407/17,794, 95%CI: 2.08% to 2.52%) in Wuhan, 0.029% (2/6,810, 95%CI: 0.0081% to 0.11%) in Shenzhen, and 0.0074% (1/13,540, 95%CI: 0.0013% to 0.042%) in Shijiazhuang, respectively. The earliest emergence of SARS-CoV-2 seropositivity in blood donors was identified on January 20, 2020 in Wuhan. The weekly prevalence of SARS-CoV-2 antibodies in Wuhan’s blood donors changed dynamically and were 0.08% (95%CI: 0.02% to 0.28%) during January 15 to 22 (before city lockdown), 3.08% (95%CI: 2.67% to 3.55%) during January 23 to April 7 (city quarantine period) and 2.33% (95%CI: 2.06% to 2.63%) during April 8 to 30 (after lockdown easing). Female and older-age were identified to be independent risk factors for SARS-CoV-2 seropositivity among donors in Wuhan.ConclusionsThe prevalence of antibodies to SARS-CoV-2 among blood donors in China was low, even in Wuhan city. According to our data, the earliest emergence of SARS-CoV-2 in Wuhan’s donors should not earlier than January, 2020. As most of the population of China remained uninfected during the early wave of COVID-19 pandemic, effective public health measures are still certainly required to block viral spread before a vaccine is widely available.
Predicting primer and panel off-target rate in QIAseq targeted DNA panels using convolutional neural networks
Authors: Xu Chang , Padmanabhan Raghavendra , Reinecke Frank , DiCarlo John , Wang Yexun 
Published: July 2020

AbstractIn QIAseq targeted DNA panels, synthetic primers (short single-strand DNA sequences) are used for target enrichment via complementary DNA binding. Off-target priming could occur in this process when a primer binds to some loci where the DNA sequences are identical or very similar to the target template. These off-target DNA segments go through the rest of the workflow, wasting sequencing resources in unwanted regions. Off-target cannot be avoided if some segments of the target region are repetitive throughout the genome, nor can it be quantified until after sequencing. But if off-target rates can be prospectively predicted, scientists can make informed decisions about investment on high off-target panels.We developedpordle(predictingoff-target rate withdeep learning andepcr07), a convolutional neural network (CNN) model to predict off-target binding events of a given primer. The neural network was trained using 10 QIAseq DNA panels with 29,274 unique primers and then tested on an independent QIAseq panel with 7,576 primers. The model predicted a 10.5% off-target rate for the test panel, a -0.1% bias from the true value of 10.6%. The model successfully selected the better primer (in terms of off-target rate) for 89.2% of 3,835 pairs of close-by primers in the test panel whose off-target rates differ by at least 10%. The order-preserving property may help panel developers select the optimal primer from a group of candidates, which is a common task in panel design.
Development and application of a cultivation platform for mammalian suspension cell lines with single-cell resolution (MaSC)
Authors: Schmitz Julian , Täuber Sarah , Westerwalbesloh Christoph , von Lieres Eric , Noll Thomas , Grünberger Alexander 
Published: July 2020

AbstractIn bioproduction processes cellular heterogeneity can cause unpredictable process outcomes or even provoke process failure. Still, cellular heterogeneity is not examined systematically in bioprocess research and development. One reason for this shortcoming are the applied average bulk analyses, which are not able to detect cell-to-cell differences. In this work we present a microfluidic tool for single-cell cultivation of mammalian suspension cells (MaSC). The design of our platform allows long-term cultivation at highly controllable environments. As model system CHO K1 cells were cultivated over 150 h. Growth behavior was analyzed on single-cell level and resulted in growth rates between 0.85 – 1.16 d-1, which are comparable to classical cultivation approaches such as shake flask and labscale bioreactor. At the same time, heterogeneous growth and division behavior, e.g., unequal division time, as well as rare cellular events like polynucleation or reversed mitosis were observed, which would have remained undetected in a standard population analysis based on average measurements. Therefore, MaSC will open the door for systematic single-cell analysis of mammalian suspension cells. Possible fields of application represent basic research topics like cell-to-cell heterogeneity studies, clonal stability, pharmaceutical drug screening and stem cell research, as well as bioprocess related topics such as media development and novel scale-down approaches.
Key attributes of designers' competency for prevention through design (PtD) practices in construction: a review
Authors: Che Ibrahim Che Khairil Izam , Belayutham Sheila , Manu Patrick , Mahamadu Abdul-Majeed 
Published: July 2020

PurposeDesigners have a key role to play in the Prevention through Design (PtD) practices in construction projects. Nonetheless, previous studies indicated that the issue of competencies to perform and sustain such practices over time is of a significant concern. This study aims to explore the key attributes of designers' competencies for PtD practices in construction.Design/methodology/approachBy using the Scopus database, a total of 86 papers related to PtD in construction published in peer-reviewed journals were reviewed and analysed using the well-established systematic literature review (SLR) methodology.FindingsThe review indicates that in order to be competent in PtD implementation, designers need to be equipped with tacit and explicit knowledge, technical and soft skills and experience related to PtD. Furthermore, the review identifies attributes of these competencies. Additionally, a framework that links key PtD elements/principles with the PtD competencies is presented.Practical implicationsThe findings would enable contribution to the industry by providing the necessary references for design organisations to improve their designers' PtD competencies and hence, be able to meet their responsibility under relevant occupational safety and health (OSH) legislative framework.Originality/valueThis study extends the PtD literature in the construction context by providing deeper insights into the conceptualisation of relationship between competent designers and PtD elements. The novelty also lies in the consolidation of PtD competency attributes for designers in construction that could act as a reference for any future developments related to PtD competency assessment for designers.