bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbially-mediated pretreatment of aerated oil and gas produced water by addition of phosphorous or activated sludge
Authors: Honeyman Alexander S. , Nicholas Emily R. , Cath Tzahi Y. , Spear John R. 
Published: August 2020

AbstractProduced Water (PW) from oil and gas (O&G) producing wells is a unique source of water in water-stressed regions. Microbiota within O&G formations have been well-studied on site/in-situ, but few applied works have considered their role in the treatment of PW in engineered water treatment systems. Herein, we operated a simple aeration/mixing bench-scale bioreactor fed with produced water under three conditions: 1) PW alone (control; hereafter referred to as ‘baseline’), 2) phosphorous dosed daily as KH2PO4, and 3) activated sludge (AS) dosed daily from a sequence batch membrane bioreactor (SB-MBR). Aerated and mixed PW alone (baseline) was able to attenuate PW chemistry with removal of soluble chemical oxygen demand (sCOD) and ammonia by 27.6% and 17.8%, respectively. Further KH2PO4and AS additions improved water treatment efficiency markedly; in the KH2PO4addition reactor, sCOD and ammonia were reduced by 50.0% and 61.5%, respectively, and in the AS addition reactor by 52.5% and 59.2%, respectively. Microbial consortia determined via 16S rRNA gene amplicons differ in composition between raw PW and all reactors; order Kiloniellales was most common in raw PW while orders Rhodobacterales, Pseudomonadales, and Caulobacterales were most abundant amongst AS, KH2PO4, and baseline conditions, respectively. Several different microbial consortia are capable of treating raw PW which suggests that functional redundancy amongst microbiota in engineered treatment systems may be underappreciated. With simple addition of phosphorous and/or activated sludge to PW as part of a treatment strategy, a higher quality water can then be subjected to conventional treatment and/or local reuse.ImportanceMultiple microbiological communities are capable of treating O&G PW in a simple, applied, engineered setting. The broad possibility of PW treatment by multiple different microbial consortia elucidates the potential for easy, effective, water reuse processes in the hydraulically-stressed arid west as well as any region generating PW from O&G operations.
Quarantine and testing strategies in contact tracing for SARS-CoV-2
Authors: Quilty Billy J , Clifford Samuel , Flasche Stefan , Kucharski Adam J ,   CMMID COVID-19 Working Group, Edmunds W John 
Published: August 2020

SummaryPrevious work has indicated that contact tracing and isolation of index case and quarantine of potential secondary cases can, in concert with physical distancing measures, be an effective strategy for reducing transmission of SARS-CoV-2 (1). Currently, contacts traced manually through the NHS Test and Trace scheme in the UK are asked to self-isolate for 14 days from the day they were exposed to the index case, which represents the upper bound for the incubation period (2). However, following previous work on screening strategies for air travellers (3,4) it may be possible that this quarantine period could be reduced if combined with PCR testing. Adapting the simulation model for contact tracing, we find that quarantine periods of at least 10 days combined with a PCR test on day 9 may largely emulate the results from a 14-day quarantine period in terms of the averted transmission potential from secondary cases (72% (95%UI: 3%, 100%) vs 75% (4%, 100%), respectively). These results assume the delays from testing index cases’ and tracing their contacts are minimised (no longer than 4.5 days on average). If secondary cases are traced and quarantined 1 day earlier on average, shorter quarantine periods of 8 days with a test on day 7 (76% (7%, 100%)) approach parity with the 14 day quarantine period with a 1 day longer delay to the index cases’ test. However, the risk of false-negative PCR tests early in a traced case’s infectious period likely prevents the use of testing to reduce quarantine periods further than this, and testing immediately upon tracing, with release if negative, will avert just 17% of transmission potential on average. In conclusion, the use of PCR testing is an effective strategy for reducing quarantine periods for secondary cases, while still reducing transmission of SARS-CoV-2, especially if delays in the test and trace system can be reduced, and may improve quarantine compliance rates.
Impact of population density on the Covid-19 infected and mortality rates in India
Authors: Bhadra Arunava , Mukherjee Arindam , Sarkar Kabita 
Published: August 2020

AbstractThe Covid-19 is a highly contagious disease which becomes a serious global health concern. The residents living in areas with high population density, such as big or metropolitan cities have a higher probability to come into close contact with others and consequently any contagious disease is expected to spread rapidly in dense areas. However, recently after analyzing Covid-19 cases in the US researchers at the Johns Hopkins Bloomberg School of Public Health, London school of economics and IZA – Institute of Labor Economics conclude that the spread of Covid-19 is not linked with population density. Here we investigate the influence of population density on Covid-19 spread and related mortality in the context of India. After a detailed correlation and regression analysis of infection and mortality rates due to Covid-19 at the district level we find moderate association between Covid-19 spread and population density.
The effect of BMI and physical activity levels on the duration of symptomatic days with Covid-19 infection
Authors: Alataibi Abdulazeem S , Boukelia Boukhemis 
Published: August 2020

AbstractRegular exercise is known to boost immunity, increase immune response to fight infection, as well as speeding up recovery times and healing processes. This study seeks to assess if exercising regularly pre-SARS-CoV-2 (COVID-19) and/or BMI status has an effect on recovery time.A total of 215 people infected with COVD-19 from the Kingdom of Saudi Arabia took part in this study (age 36±16 years, mass 72±15 kg, stature 166±11 cm). Only 10 patients were physically active and fulfil WHO physical activity requirement (Age 30±7 years, Mass 77±9 kg, Stature 176±1 cm).There was a significant difference in recovery time between active and inactive patients (P = 0.00) with active patients’ recovery 2.7 times faster than inactive patients. Active patients showed a lower BMI level (p = 0.043).Anthropometric measurement characteristics and the fitness level could be used in decision making scenarios for the estimation of the risk of complications in patients with COVID-19.Novelty:Covid-19 physical active patients shows faster recovery time.Active patients recorded a BMI of over 25kg/m2, recovered faster than those inactive patients with similar BMI’s.
The Wooden Skull: An Innovation Through The Use Of Local Materials And Technology To Promote The Teaching And Learning Of Human Anatomy
Authors: Mugagga Kintu , Mwarisi Masilili G. , Dare Samuel S. 
Published: August 2020

ABSTRACTSkeleton models are important in facilitating student’s easy retention and recollection of information in the future. These may assist students carry out hands-on practice in order to acquire and practice new skills that are relevant to first aid.The increasing number of medical institutions and medical students attracts the challenge of inadequate facilitation of the teaching and learning processes. This warrants a study and/or an exploration of an alternative solution such as wooden models in order to solve the problem of scarce and ethically restricted human teaching aids.Wooden pieces (50cmlengthx 20cmdiameter) from aJacaranda mimosifoliatree were prepared for the carving process and wooden replicas of human skulls were made. Two experimental groups of randomly selected medical students (60: Active and 60: Control) were separately taught using wooden and natural skull models respectively. The two groups were assessed and evaluated using the natural skull models to compare their understanding of the Anatomy of the skull. Additionally, opinion statements were collected from participants in the active group during the oral examination.Six (6) wooden skull models were produced and used for experimental study. Comparisons of academic scores (mean and median) between Active (students using the wooden skull) and control (students using natural skull) groups showed no statistical significant difference (P ≥ 0.05). Concerning the enhancement of learning skills; the wooden model was constructed in a way that would be able to enhance learning as it would be the natural skull.The wooden skull model, with more improvement in structural formation, can adequately facilitate the teaching and learning of anatomy of the Human skull.This project and the experimental study about utilization of the wooden skull model provides a good potential of using the wooden models to supplement the use of the natural human skull.
In a nutshell, a reciprocal transplant experiment reveals local adaptation and fitness trade-offs in response to urban evolution in an acorn-dwelling ant
Authors: Martin Ryan A. , Chick Lacy D. , Garvin Matthew L. , Diamond Sarah E. 
Published: August 2020

AbstractUrban-driven evolution is widely evident, but whether these changes confer fitness benefits and thus represent cases of adaptive urban evolution is less clear. We performed a multi-year field reciprocal transplant experiment of acorn-dwelling ants across urban and rural environments. Fitness trade-offs via survival were consistent with local adaptation: we found a survival advantage of the ‘home’ treatments compared to the ‘away’ treatments. Seasonal bias in survival was consistent with evolutionary patterns of gains and losses in thermal tolerance traits across the urbanization gradient, such that rural ants in the urban environment were more vulnerable in the summer, putatively due to low heat tolerance and urban ants in the rural environment were more vulnerable in winter, putatively due to an evolved loss of cold tolerance. The results for fitness via fecundity were more complex. Fecundity differences were present in the rural environment, but not the urban environment, and could reflect mismatched cues for the seasonal production of reproductives. To broadly contextualize our results, we performed a multi-species meta-analysis of urban adaptive evolution studies and found general support for local adaptation. The rural adaptation signal was stronger than for urban adaptation, consistent with the relative differences in time for adaptation to occur.
Microbial activation converts neutrophils into anti-tumor effectors
Authors: Yam Andrew O. , Bailey Jacqueline , Lin Francis , Jakovija Arnolda , Counoupas Claudio , Triccas James A. , Gunzer Matthias , Bald Tobias , Grey Shane T. , Chtanova Tatyana 
Published: August 2020

ABSTRACTNeutrophils infiltrate most solid tumors and their presence is usually correlated with suppression of anti-tumor responses, metastasis and poor prognosis. Here we used microbial bioparticles administered into the tumor microenvironment to transform neutrophils into anti-tumor effectors. Microbially activated neutrophils acquired an effector phenotype associated with pathogen killing and lost vascular endothelial growth factor expression associated with tumor growth and metastasis. They became the dominant immune cell infiltrating the tumor and inhibited tumor growth. Using intravital two-photon microscopy microbially activated neutrophils could be seen forming close contacts with tumor cells resulting in tumor tissue remodeling and tumor cell death. Thus, microbial bioparticle treatment can endow neutrophils with anti-tumor properties, suggesting that neutrophil plasticity in cancer could be exploited for tumor killing. These data highlight a pathway for the rational development of neutrophil-based cancer therapy.
Contributions by N-terminal Domains to NMDA Receptor Currents
Authors: Amico-Ruvio Stacy A. , Paganelli Meaghan A. , Abbott Jamie A. , Myers Jason M. , Kasperek Eileen M , Iacobucci Gary I. , Popescu Gabriela K. 
Published: August 2020

ABSTRACTTo investigate the role of the N-terminal domains (NTDs) in NMDA receptor signaling we used kinetic analyses of one-channel currents and compared the reaction mechanism of recombinant wild-type GluN1/GluN2A and GluN1/GluN2B receptors with those observed for NDT-lacking receptors. We found that truncated receptors maintained the fundamental gating mechanism characteristic of NMDA receptors, which includes a multi-state activation sequence, desensitization steps, and mode transitions. This result establishes that none of the functionally-defined NMDA receptor activation events require the NTD. Notably, receptors that lacked the entire NTD layer retained isoform-specific kinetics. Together with previous reports, these results demonstrate that the entire gating machinery of NMDA receptors resides within a core domain that contains the ligand-binding and the channel-forming transmembrane domains, whereas the NTD and C-terminal layers serve modulatory functions, exclusively.
Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Authors: Suryawanshi Gajendra W. , Arokium Hubert , Kim Sanggu , Khamaikawin Wannisa , Lin Samantha , Shimizu Saki , Chupradit Koollawat , Lee YooJin , Xie Yiming , Guan Xin , Suryawanshi Vasantika , Presson Angela P. , An Dong-Sung , Chen Irvin S. Y. 
Published: August 2020

AbstractBackgroundCurrent understanding of hematopoiesis is largely derived from mouse models that are physiologically distant from humans. Humanized mice provide the most physiologically relevant small animal model to study human diseases, most notably preclinical gene-therapy studies. However, the clonal repopulation dynamics of human hematopoietic stem and progenitor cells (HSPC) in these animal models is only partially understood. Using a new clonal tracking methodology designed for small sample volumes, we aim to reveal the underlying clonal dynamics of human cell repopulation in a mouse environment.MethodsHumanized BLT (bone marrow-liver-thymus) mice were generated by transplanting lentiviral vector transduced human fetal liver HSPC (FL-HSPC) in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice implanted with a piece of human fetal thymus. We developed a methodology to track vector integration sites (VIS) in a mere 25µl of mouse blood for longitudinal and quantitative clonal analysis of human HSPC repopulation in mouse environment. We explored transcriptional and epigenetic features of human HSPC for possible VIS bias.Results897 HSPC clones were longitudinally tracked in BLT mice—providing a first-ever demonstration of clonal dynamics and competitive expansion of therapeutic and control vector-modified human cell populations simultaneously repopulating in the same humanized mice. The polyclonal repopulation stabilized at 19 weeks post-transplant and the contribution of the largest clone doubled within 4 weeks. Moreover, 550 (∼60%) clones persisted over 6 weeks and were highly shared between different organs. The normal clonal profiles confirmed the safety of our gene therapy vectors. Multi-omics analysis of human FL-HSPC revealed that 54% of vector integrations in repopulating clones occurred within ±1kb of H3K36me3-enriched regions.ConclusionsHuman repopulation in mice is polyclonal and stabilizes more rapidly than that previously observed in humans. VIS preference for H3K36me3 has no apparent negative effects on HSPC repopulation. Our study provides a methodology to longitudinally track clonal repopulation in small animal models extensively used for stem cell and gene-therapy research and with lentiviral vectors designed for clinical applications. Results of this study provide a framework for understanding the clonal behavior of human HPSC repopulating in a mouse environment, critical for translating results from humanized mice models to the human settings.
Deep Feature Extraction for Resting-State Functional MRI by Self-Supervised Learning and Application to Schizophrenia Diagnosis
Authors: Hashimoto Yuki , Ogata Yosuke , Honda Manabu , Yamashita Yuichi 
Published: August 2020

AbstractIn this study, we propose a novel deep-learning technique for functional MRI analysis. We introduced an “identity feature” by a self-supervised learning schema, in which a neural network is trained solely based on the MRI-scans; furthermore, training does not require any explicit labels. The proposed method demonstrated that each temporal slice of resting state functional MRI contains enough information to identify the subject. The network learned a feature space in which the features were clustered per subject for the test data as well as for the training data; this is unlike the features extracted by conventional methods including region of interests pooling signals and principle component analysis. In addition, using a simple linear classifier for the identity features, we demonstrated that the extracted features could contribute to schizophrenia diagnosis. The classification accuracy of our identity features was higher than that of the conventional functional connectivity. Our results suggested that our proposed training scheme of the neural network captured brain functioning related to the diagnosis of psychiatric disorders as well as the identity of the subject. Our results together highlight the validity of our proposed technique as a design for self-supervised learning.
Sub-Millimetre Resolution Laminar Fmri Using Arterial Spin Labelling in Humans at 7 T
Authors: Kashyap Sriranga , Ivanov Dimo , Havlicek Martin , Huber Laurentius , Poser Benedikt A. , Uludağ Kâmil 
Published: August 2020

ABSTRACTLaminar fMRI at ultra-high magnetic field strength is typically carried out using the Blood Oxygenation Level-Dependent (BOLD) contrast. Despite its unrivalled sensitivity to detecting activation, the BOLD contrast is limited in its spatial specificity due to signals stemming from intra-cortical ascending and pial veins. Alternatively, regional changes in perfusion (i.e., cerebral blood flow through tissue) are colocalised to neuronal activation, which can be non-invasively measured using arterial spin labelling (ASL) MRI. In addition, ASL provides a quantitative marker of neuronal activation in terms of perfusion signal, which is simultaneously acquired along with the BOLD signal. However, ASL for laminar imaging is challenging due to the lower SNR of the perfusion signal and higher RF power deposition i.e., specific absorption rate (SAR) of ASL sequences. In the present study, we present for the first time in humans, isotropic sub-millimetre spatial resolution functional perfusion images using Flow-sensitive Alternating Inversion Recovery (FAIR) ASL with a 3D-EPI readout at 7T. We show that robust statistical activation maps can be obtained with perfusion-weighting in a single session. We observed the characteristic BOLD amplitude increase towards the superficial laminae, and, in apparent discrepancy, the relative perfusion profile shows a decrease of the amplitude and the absolute perfusion profile a much smaller increase towards the cortical surface. Considering the draining vein effect on the BOLD signal using model-based spatial ‘convolution’, we show that the empirically measured perfusion and BOLD profiles are, in fact, consistent with each other. This study demonstrates that laminar perfusion fMRI in humans is feasible at 7T and that caution must be exercised when interpreting BOLD signal laminar profiles as direct representation of the cortical distribution of neuronal activity.
e-MutPath: Computational modelling reveals the functional landscape of genetic mutations rewiring interactome networks
Authors: Li Yongsheng , McGrail Daniel J. , Burgman Brandon , Yi S. Stephen , Sahni Nidhi 
Published: August 2020

ABSTRACTUnderstanding the functional impact of cancer somatic mutations represents a critical knowledge gap for implementing precision oncology. It has been increasingly appreciated that the ‘edgotype’ of a genomic mutation provides a fundamental link between genotype and phenotype. However, specific effects on biological signaling networks for the majority of mutations are largely unknown by experimental approaches. To resolve this challenge, we developed e-MutPath, a network-based computational method to identify candidate ‘edgetic’ mutations that perturb functional pathways. e-MutPath identifies informative paths that could be used to distinguish disease risk factors from neutral elements and to stratify disease subtypes with clinical relevance. The predicted targets are enriched in cancer vulnerability genes, known drug targets but depleted for proteins associated with side effects, demonstrating the power of network-based strategies to investigate the functional impact and perturbation profiles of genomic mutations. Together, e-MutPath represents a robust computational tool to systematically assign functions to genetic mutations, especially in the context of their specific pathway perturbation effect. The code for e-MutPath is available as a user-friendly R package at the GitHub website (https://github.com/lyshaerbin/eMutPath).
Audio-visual interactions in egocentric distance perception: Ventriloquism effect and aftereffect
Authors: Hládek Ľuboš , Seitz Aaron R , Kopčo Norbert 
Published: August 2020

AbstractThe processes of audio-visual integration and of visually-guided re-calibration of auditory distance perception are not well understood. Here, the ventriloquism effect (VE) and aftereffect (VAE) were used to study these processes in a real reverberant environment. Auditory and audio-visual (AV) stimuli were presented, in interleaved trials, over a range of distances from 0.7 to 2.04 m in front of the listener, whose task was to judge the distance of auditory stimuli or of the auditory components of AV stimuli. The relative location of the visual and auditory components of AV stimuli was fixed within a session such that the visual component was presented from distance 30% closer (V-closer) than the auditory component, 30% farther (V-farther), or aligned (V-aligned). The study examined the strength of VE and VAE as a function of the reference distance and of the direction of the visual component displacement, and the temporal profile of the build-up/break-down of these effects. All observed effects were approximately independent of target distance when expressed in logarithmic units. The VE strength, measured in the AV trials, was roughly constant for both directions of visual-component displacement such that, on average, the responses shifted in the direction of the visual component by 72% of the audio-visual disparity. The VAE strength, measured on the interleaved auditory-only trials, was stronger in the V-farther than the V-closer condition (44% vs. 31% of the audio-visual disparity, respectively). The VAE persisted to post-adaptation auditory-only blocks of trials, however it was weaker and the V-farther/V-closer asymmetry was reduced. The rates of build-up/break-down of the VAE were also asymmetrical, with slower adaptation in the V-closer condition. These results suggest that, on a logarithmic scale, the AV distance integration is symmetrical, independent of the direction of induced shift, while the visually-induced auditory distance re-callibration is asymmetrical, stronger and faster when evoked by more distant visual stimuli.