bluuebunny/crossref_metadata_2025 huggingface dataset:
EAT–Lancetdiet score requires minimum intake values to predict higher micronutrient adequacy of diets in rural women of reproductive age from five low- and middle-income countries
Authors: Hanley-Cook Giles T. , Argaw Alemayehu A. , de Kok Brenda P. , Vanslambrouck Katrien W. , Toe Laeticia C. , Kolsteren Patrick W. , Jones Andrew D. , Lachat Carl K.
Published: September 2020

The EAT–LancetCommission promulgated a universal reference diet. Subsequently, researchers constructed an EAT–Lancetdiet score (0–14 points), with minimum intake values for various dietary components set at 0 g/d, and reported inverse associations with risks of major health outcomes in a high-income population. We assessed associations between EAT–Lancetdiet scores, without or with lower bound values, and the mean probability of micronutrient adequacy (MPA) among nutrition-insecure women of reproductive age (WRA) from low- and middle-income countries (LMIC). We analysed single 24-h diet recall data (n1950) from studies in rural DRC, Ecuador, Kenya, Sri Lanka and Vietnam. Associations between EAT–Lancetdiet scores and MPA were assessed by fitting linear mixed-effects models. Mean EAT–Lancetdiet scores were 8·8 (SD1·3) and 1·9 (SD1·1) without or with minimum intake values, respectively. Pooled MPA was 0·58 (SD0·22) and energy intake was 10·5 (SD4·6) MJ/d. A one-point increase in the EAT–Lancetdiet score, without minimum intake values, was associated with a 2·6 (SD0·7) percentage points decrease in MPA (P< 0·001). In contrast, the EAT–Lancetdiet score, with minimum intake values, was associated with a 2·4 (SD1·3) percentage points increase in MPA (P= 0·07). Further analysis indicated positive associations between EAT–Lancetdiet scores and MPA adjusted for energy intake (P< 0·05). Our findings indicate that the EAT–Lancetdiet score requires minimum intake values for nutrient-dense dietary components to avoid positively scoring non-consumption of food groups and subsequently predicting lower MPA of diets, when applied to rural WRA in LMIC.
Economic and stochastic efficiency analysis of alternative cover crop systems in Louisiana
Authors: Wang Hua , Adusumilli Naveen , Gentry Donna , Fultz Lisa
Published: September 2020

Landowners can engage in voluntary conservation with the help of incentive programs. Recommended conservation practices are selected based on management intentions as well as the contribution of those practices to the overall net returns. However, conservation motives are heterogeneous and based on individual risk behavior. Existing cost-share programs might either under-fund or over-fund conservation, which could lead to inefficient management of natural resources. The current analysis evaluates the economic feasibility of variable cover crop strategies, multiple seeding rates, within a soybean production system in silt loam and clay soils. The study utilizes stochastic efficiency with respect to a function, referred to as SERF, for determining the preferred strategies under various risk preferences. The SERF method accounts for the heterogeneity of individual decision-making with regards to conservation adoption. Results indicate that most risk-averse farmers chose tillage radish with medium seeding rate as their preferred strategy. However, as the risk-bearing capacity of an individual increases, the current level of incentives does not motivate to implement conservation. The most preferred plan for risk-neutral farmers is the fallow system in both silt loam and clay soils. The economic and risk assessment framework can improve understanding of the temporal dynamics of different practices and inform policy on conservation structure that promotes agricultural systems that are economically, environmentally, and socially sustainable.
Effective Contact Tracing for COVID-19 Using Mobile Phones: An Ethical Analysis of the Mandatory Use of the Aarogya Setu Application in India
Authors: BASU SAURAV
Published: September 2020

Several digital contact tracing smartphone applications have been developed worldwide in the effort to combat COVID-19 that warn users of potential exposure to infectious patients and generate big data that helps in early identification of hotspots, complementing the manual tracing operations. In most democracies, concerns over a breach in data privacy have resulted in severe opposition toward their mandatory adoption. This paper examines India as a noticeable exception, where the compulsory installation of such a government-backed application, the “Aarogya Setu” has been deemed mandatory in certain situations. We argue that the mandatory app requirement constitutes a legitimate public health intervention during a public health emergency.
Reasons for the low influenza vaccination rate among nurses in Slovenia
Authors: Pavlič Danica Rotar , Maksuti Alem , Podnar Barbara , Kokalj Kokot Mateja
Published: September 2020

Aim:

This study aimed to identify nurses’ views on influenza vaccination and factors that might explain why they do not receive influenza vaccinations, and to examine any ethical issues encountered in the vaccination process.

Background:

All 27 European Union member states and 2 other European countries recommended influenza vaccinations for healthcare workers in 2014–15. Data show that the influenza vaccination rate among nurses in Slovenia is even lower than in other European countries. Slovenian study showed that 41.7% of the respondents had received both the pandemic and the seasonal vaccine. Doctors had the highest level of vaccine coverage, with 44.1%, followed by registered nurses at 23.4%, whereas the lowest level was found among nursing assistants and nursing technicians (17%) at a Ljubljana health clinic.

Methods:

A qualitative study was carried out. Nineteen nurses who did not receive influenza vaccination took part in the study. Thematic interviews were conducted in December 2018. Interview transcripts were read, coded, reviewed and labelled by three independent researchers. The collected material was processed using qualitative content analysis.

Findings:

Thirteen categories and four themes were identified and coded, which enabled an understanding of the nurses’ views regarding influenza vaccination. Most of their experiences were positive in one way: they recognised the importance of vaccination and people’s awareness of it. However, they did not obtain the influenza vaccine themselves. The main barriers to vaccination were doubt regarding the vaccine’s effectiveness, the potential for side effects, the belief that young healthcare professionals are well protected and not at high risk, an overrated trust in their own immune systems, and the belief that pharmaceutical industry marketing was targeting them. The nurses suggested several ways that vaccination could be promoted and improved vaccination coverage achieved. These findings call attention to the importance of recognising both the need for targeted information for the nurses and the need for different approaches to healthcare provision.
Ernährung bei Diabetes mellitus
Authors: Fäh David
Published: September 2020

Zusammenfassung. Was für die Allgemeinbevölkerung als ausgewogene Ernährung angeschaut wird, gilt im Grundsatz auch für Personen mit Diabetes. Die dürftige wissenschaftliche Evidenzlage rechtfertigt keine dogmatische Haltung mit strikten Ge- und Verboten von Nährstoffen oder Lebensmitteln. Vielmehr sind in einer ausgewogenen Ernährung alle Makronährstoffgruppen vertreten, wobei eine Reduktion der Kalorienzufuhr gleichermassen erfolgreich über Kohlenhydrate oder Fette passieren kann. Ideal sind Produkte hoher Qualität sowie mit geringer und schonender Verarbeitung wie faserreiche Stärkeprodukte und kaltgepresste pflanzliche Öle. Der Nutzen einer erhöhten Proteinzufuhr bezüglich Diabetesmanagement und Gewichtskontrolle kristallisiert sich zunehmend. Als Quellen sollten jedoch eher pflanzliche oder Milchprodukte herangezogen werden als rotes oder verarbeitetes Fleisch. Die mediterrane Ernährungsweise und Konzepte mit vergleichbarem wissenschaftlichem Fundament erfüllen am ehesten die Kriterien einer «geeigneten» Ernährung für Diabetespatienten. Obwohl Alkohol dicht ist an leeren Kalorien, spricht nichts dagegen, den Genuss darin eingebettet zu tolerieren. Angesichts der individuell unterschiedlichen Stoffwechselreaktion auf gleiche Lebensmittel und unter Berücksichtigung der dürftigen Beweislage ist eine personalisierte Herangehensweise angebrachter denn je.
Computer vision in autism spectrum disorder research: a systematic review of published studies from 2009 to 2019
Authors: de Belen Ryan Anthony J. , Bednarz Tomasz , Sowmya Arcot , Del Favero Dennis
Published: September 2020

The current state of computer vision methods applied to autism spectrum disorder (ASD) research has not been well established. Increasing evidence suggests that computer vision techniques have a strong impact on autism research. The primary objective of this systematic review is to examine how computer vision analysis has been useful in ASD diagnosis, therapy and autism research in general. A systematic review of publications indexed on PubMed, IEEE Xplore and ACM Digital Library was conducted from 2009 to 2019. Search terms included [‘autis*’ AND (‘computer vision’ OR ‘behavio* imaging’ OR ‘behavio* analysis’ OR ‘affective computing’)]. Results are reported according to PRISMA statement. A total of 94 studies are included in the analysis. Eligible papers are categorised based on the potential biological/behavioural markers quantified in each study. Then, different computer vision approaches that were employed in the included papers are described. Different publicly available datasets are also reviewed in order to rapidly familiarise researchers with datasets applicable to their field and to accelerate both new behavioural and technological work on autism research. Finally, future research directions are outlined. The findings in this review suggest that computer vision analysis is useful for the quantification of behavioural/biological markers which can further lead to a more objective analysis in autism research.
Toward diagnostic relevance of the αVβ5, αVβ3, and αVβ6 integrins in OA: expression within human cartilage and spinal osteophytes
Authors: Charlier Edith , Deroyer Céline , Neuville Sophie , Plener Zelda , Malaise Olivier , Ciregia Federica , Gillet Philippe , Reuter Gilles , Salvé Mallory , Withofs Nadia , Hustinx Roland , de Seny Dominique , Malaise Michel G.
Published: September 2020

We previously reported 18FPRGD2 uptake by the coxofemoral lining, intervertebral discs and facet joint osteophytes in OA using PET/SCAN imaging. However, the molecular mechanism by which the PRGD2 tracer interacts with joint tissues and osteophytes in OA remains unclear. As PRGD2 ligands are expected to belong to the RGD-specific integrin family, the purpose of this study was (i) to determine which integrin complexes display the highest affinity for PRGD2-based ligands, (ii) to analyze integrin expression in relevant tissues, and (iii) to test integrin regulation in chondrocytes using OA-related stimuli to increase the levels of fibrosis and ossification markers. To this end, the affinity of PRGD2-based ligands for five heterodimeric integrins was measured by competition with 125I-echistatin. In situ analyses were performed in human normal vs. OA cartilage and spinal osteophytes. Osteophytes were characterized by (immuno-)histological staining. Integrin subunit expression was tested in chondrocytes undergoing dedifferentiation, osteogenic differentiation, and inflammatory stimulation. The integrins αVβ5, αVβ3, and αVβ6 presented the highest affinity for PRGD2-based ligands. In situ, the expression of these integrins was significantly increased in OA compared to normal cartilage. Within osteophytes, the mean integrin expression score was significantly higher in blood vessels, fibrous areas, and cells from the bone lining than in osteocytes and cartilaginous zones. In vitro, the levels of integrin subunits were significantly increased during chondrocyte dedifferentiation (except for β6), fibrosis, and osteogenic differentiation as well as under inflammatory stimuli. In conclusion, anatomical zones (such as OA cartilage, intervertebral discs, and facet joint osteophytes) previously reported to show PRGD2 ligand uptake in vivo expressed increased levels of αVβ5, αVβ3, and β6 integrins, whose subunits are modulated in vitro by OA-associated conditions that increase fibrosis, inflammation, and osteogenic differentiation. These results suggest that the increased levels of integrins in OA compared to normal tissues favor PRGD2 uptake and might explain the molecular mechanism of OA imaging using the PRGD2-based ligand PET/CT.
Controllable gelation of artificial extracellular matrix for altering mass transport and improving cancer therapies
Authors: Zheng Di-Wei , Hong Sheng , Zhang Qiu-Ling , Dong Xue , Pan Pei , Song Wen-Fang , Song Wen , Cheng Si-Xue , Zhang Xian-Zheng
Published: September 2020

Global alterations in the metabolic network provide substances and energy to support tumor progression. To fuel these metabolic processes, extracellular matrix (ECM) plays a dominant role in supporting the mass transport and providing essential nutrients. Here, we report a fibrinogen and thrombin based coagulation system to construct an artificial ECM (aECM) for selectively cutting-off the tumor metabolic flux. Once a micro-wound is induced, a cascaded gelation of aECM can be triggered to besiege the tumor. Studies on cell behaviors and metabolomics reveal that aECM cuts off the mass transport and leads to a tumor specific starvation to inhibit tumor growth. In orthotopic and spontaneous murine tumor models, this physical barrier also hinders cancer cells from distant metastasis. The in vivo gelation provides an efficient approach to selectively alter the tumor mass transport. This strategy results in a 77% suppression of tumor growth. Most importantly, the gelation of aECM can be induced by clinical operations such as ultrasonic treatment, surgery or radiotherapy, implying this strategy is potential to be translated into a clinical combination regimen.
Author Correction: Constraining the rise of oxygen with oxygen isotopes
Authors: Killingsworth B. A. , Sansjofre P. , Philippot P. , Cartigny P. , Thomazo C. , Lalonde S. V.
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Urine metabolomics based prediction model approach for radiation exposure
Authors: Tyagi Ritu , Maan Kiran , Khushu Subash , Rana Poonam
Published: September 2020

The radiological incidents and terrorism have demanded the need for the development of rapid, precise, and non-invasive technique for detection and quantification of exposed dose of radiation. Though radiation induced metabolic markers have been thoroughly investigated, but reproducibility still needs to be elucidated. The present study aims at assessing the reliability and reproducibility of markers using nuclear magnetic resonance (NMR) spectroscopy and further deriving a logistic regression model based on these markers. C57BL/6 male mice (8–10 weeks) whole body γ-irradiated and sham irradiated controls were used. Urine samples collected at 24 h post dose were investigated using high resolution NMR spectroscopy and the datasets were analyzed using multivariate analysis. Fifteen distinguishable metabolites and 3 metabolic pathways (TCA cycle, taurine and hypotaurine metabolism, primary bile acid biosynthesis) were found to be amended. ROC curve and logistic regression was used to establish a diagnostic model as Logit (p) = log (p/1 − p) = −0.498 + 13.771 (tau) − 3.412 (citrate) − 34.461 (α-KG) + 515.183 (fumarate) with a sensitivity and specificity of 1.00 and 0.964 respectively. The findings demonstrate the proof of concept and the potential of NMR based metabolomics to establish a prediction model that can be implemented as a promising mass screening tool during triage.
Accuracy and precision of small saccades
Authors: Poletti Martina , Intoy Janis , Rucci Michele
Published: September 2020

Despite recent advances on the mechanisms and purposes of fine oculomotor behavior, a rigorous assessment of the precision and accuracy of the smallest saccades is still lacking. Yet knowledge of how effectively these movements shift gaze is necessary for understanding their functions and is helpful in further elucidating their motor underpinnings. Using a combination of high-resolution eye-tracking and gaze-contingent control, here we examined the accuracy and precision of saccades aimed toward targets ranging from $$7^\prime$$

7
′

to $$80^\prime$$

80
′

eccentricity. We show that even small saccades of just 14–$$20^\prime$$

20
′

are very effective in centering the stimulus on the retina. Furthermore, we show that for a target at any given eccentricity, the probability of eliciting a saccade depends on its efficacy in reducing the foveal offset. The pattern of results reported here is consistent with current knowledge on the motor mechanisms of microsaccade production.
Rhizodegradation of PAHs differentially altered by C3 and C4 plants
Authors: Sivaram Anithadevi Kenday , Subashchandrabose Suresh Ramraj , Logeshwaran Panneerselvan , Lockington Robin , Naidu Ravi , Megharaj Mallavarapu
Published: September 2020

Pyrosequencing of 16S ribosomal RNA (rRNA) was employed to characterize bacterial communities colonizing the rhizosphere of plants with C3 and C4 photosynthetic pathways grown in soil contaminated with polycyclic aromatic hydrocarbons (PAHs) after 60 and 120 days. The results of this study exhibited a clear difference in bacterial diversity between the rhizosphere and non-rhizosphere samples and between the rhizospheres of the C3 and C4 plants after 120 days. In both C3 and C4 rhizospheres, an incremental change in PAHs degrading bacterial genera was observed in the 120th day samples compared to the 60th day ones. Among the PAHs degrading bacterial genera,Pseudomonasshowed good resistance to PAHs in the 120th day rhizosphere of both C3 and C4 plants. Conversely, the genusSphingomonasshowed sensitivity to PAHs in the 120th day rhizosphere soils of C3 plants only. Also, a significant increase in the PAHs degrading genera was observed at 120th day in the C4 rhizosphere in comparison to the C3 rhizosphere, which was reflected in a reduced PAHs concentration measured in the soil remediated with C4 plants rather than C3 plants. These results suggest that the rhizoremediation of PAHs was primarily governed by the plant photosystems, which led to differences in root secretions that caused the variation in bacterial diversity seen in the rhizospheres. This study is the first report to demonstrate the greater effectiveness of C4 plants in enhancing the PAHs degrading bacterial community than C3 plants.
Metabolomic biomarkers in midtrimester maternal plasma can accurately predict the development of preeclampsia
Authors: Lee Seung Mi , Kang Yujin , Lee Eun Mi , Jung Young Mi , Hong Subeen , Park Soo Jin , Park Chan-Wook , Norwitz Errol R. , Lee Do Yup , Park Joong Shin
Published: September 2020

Early identification of patients at risk of developing preeclampsia (PE) would allow providers to tailor their prenatal management and adopt preventive strategies, such as low-dose aspirin. Nevertheless, no mid-trimester biomarkers have as yet been proven useful for prediction of PE. This study investigates the ability of metabolomic biomarkers in mid-trimester maternal plasma to predict PE. A case–control study was conducted including 33 pregnant women with mid-trimester maternal plasma (gestational age [GA], 16–24 weeks) who subsequently developed PE and 66 GA-matched controls with normal outcomes (mid-trimester cohort). Plasma samples were comprehensively profiled for primary metabolic and lipidomic signatures based on gas chromatography time-of-flight mass spectrometry (GC-TOF MS) and liquid chromatography Orbitrap mass spectrometry (LC-Orbitrap MS). A potential biomarker panel was computed based on binary logistic regression and evaluated using receiver operating characteristic (ROC) analysis. To evaluate whether this panel can be also used in late pregnancy, a retrospective cohort study was conducted using plasma collected from women who delivered in the late preterm period because of PE (n = 13) or other causes (n = 21) (at-delivery cohort). Metabolomic biomarkers were compared according to the indication for delivery. Performance of the metabolomic panel to identify patients with PE was compared also to a commonly used standard, the plasma soluble fms-like tyrosine kinase-1/placental growth factor (sFlt-1/PlGF) ratio. In the mid-trimester cohort, a total of 329 metabolites were identified and semi-quantified in maternal plasma using GC-TOF MS and LC-Orbitrap-MS. Binary logistic regression analysis proposed a mid-trimester biomarker panel for the prediction of PE with five metabolites (SM C28:1, SM C30:1, LysoPC C19:0, LysoPE C20:0, propane-1,3-diol). This metabolomic model predicted PE better than PlGF (AUC [95% CI]: 0.868 [0.844–0.891] vs 0.604 [0.485–0.723]) and sFlt-1/PlGF ratio. Analysis of plasma from the at-delivery cohort confirmed the ability of this biomarker panel to distinguish PE from non-PE, with comparable discrimination power to that of the sFlt-1/PlGF ratio. In conclusion, an integrative metabolomic biomarker panel in mid-trimester maternal plasma can accurately predict the development of PE and showed good discriminatory power in patients with PE at delivery.
Thermal melanism explains macroevolutionary variation of dorsal pigmentation in Eurasian vipers
Authors: Martínez-Freiría Fernando , Toyama Ken S. , Freitas Inês , Kaliontzopoulou Antigoni
Published: September 2020

Colouration may endorse thermoregulatory and antipredatory functions in snakes. Thethermal melanism hypothesispredicts that dark-coloured individuals are ecologically favoured in cool climates. However, the loss of aposematic and cryptic colourations may imply high predation for melanistic snakes. Here, we used the monophyletic group of Eurasian vipers (subfamily Viperinae) to test whether an increase in the extent of dark area inside the characteristic zigzag dorsal pattern is associated to colder environments. We measured two colouration traits in zigzag-patterned individuals (number of dorsal marks and weighted pigmentation index) and used a phylogenetic comparative approach to explore macroevolutionary patterns of dorsal pigmentation and test whether its extent is associated to ecogeographic characteristics of lineages’ ranges. Phylogenetically-naïve and phylogenetically-informed analyses yielded a significant association between the degree of pigmentation of the zigzag pattern and environmental variables such as solar radiation, elevation and latitude. The degree of pigmentation of the zigzag pattern is highlighted as an adaptive trait that matches range attributes mirroring cold environments irrespective of the phylogeny. These results constitute the first large-scale evidence supporting the thermal melanism hypothesis in snakes, opening new avenues of inquiry for the mechanisms that shape the evolution of colour phenotypes.
CO oxidation and organic dyes degradation over graphene–Cu and graphene–CuNi catalysts obtained by solution combustion synthesis
Authors: Khort Alexander , Romanovski Valentin , Leybo Denis , Moskovskikh Dmitry
Published: September 2020

Graphene and its analogs in combination with metal nanopowders are among the most promising catalysts for various industry valuable processes. The newly obtained solution combustion synthesized graphene–Cu and graphene–CuNi nanocomposites were examined in heterogeneous catalysis of thermal activated CO oxidation and photoactivated degradation of acid telon blue and direct blue dyes. The nanocomposites are characterized by a closely connected solution combustion synthesized graphene-metal structure with a number of graphene layers from 1 to 3 and fine metal grains sizes of 31 nm (Cu) and 14 nm (CuNi). The experimental data showed the obtained graphene-metal nanocomposites are among the most effective catalysts for CO oxidation with a temperature of 100% conversion of 150 °C and 200 °C for Cu and CuNi containing catalysts, respectively. At the same time, both nanopowders were found inactive for dyes degradation.
Identification of PIEZO1 as a potential prognostic marker in gliomas
Authors: Zhou Wenjianlong , Liu Xiangxiang , van Wijnbergen Jan Willem Maurits , Yuan Linhao , Liu Yuan , Zhang Chuanbao , Jia Wang
Published: September 2020

In multiple solid tumours, including gliomas, the mechanical properties change as the disease progresses. If and how mechanical cues regulate tumour cell proliferation is currently not fully studied. PIEZO1 has recently been identified as a crucial mechanosensitive cation channel in multiple solid tumours. However, we didn’t find any clinical data describing the association between PIEZO1 expression and glioma. To investigate the role of PIEZO1 in gliomas, we analysed PIEZO1 gene expression at the transcriptome level, genomic profiles and the association of PIEZO1 with clinical practice. In total, 1633 glioma samples with transcriptome data, including data from the Chinese Glioma Genome Atlas RNAseq, the Cancer Genome Atlas RNAseq and GSE16011 databases, were included in this study. Clinical information and genomic profiles including somatic mutations were also obtained. We found that PIEZO1 expression was highly correlated with malignant clinical and molecular subtypes of glioma. Gene ontology analysis showed that expression of PIEZO1 was correlated with tumour microenvironment-related genes that encode proteins involved in extracellular matrix (ECM) organization, angiogenesis and cell migration. Additionally, PIEZO1 was shown to be involved in tumour progression by serving as the central checkpoint of multiple ECM remodelling-related signalling pathways to modulate tumour cell proliferation and the tumour microenvironment in turn. Finally, high PIEZO1 expression was correlated with reduced survival time and acted as a robust biomarker for poor prognosis in gliomas. Taken together, the results indicated that high PIEZO1 expression is closely associated with highly malignant gliomas. Importantly, PIEZO1 serves as a key factor involved in sensing mechanical properties in the tumour and can regulate both tumour cells and their microenvironment to promote glioma progression, and it is also a potential therapeutic target for the treatment of gliomas.
DJ-1 (Park7) affects the gut microbiome, metabolites and the development of innate lymphoid cells (ILCs)
Authors: Singh Yogesh , Trautwein Christoph , Dhariwal Achal , Salker Madhuri S. , Alauddin Md , Zizmare Laimdota , Pelzl Lisann , Feger Martina , Admard Jakob , Casadei Nicolas , Föller Michael , Pachauri Vivek , Park David S. , Mak Tak W. , Frick Julia-Stefanie , Wallwiener Diethelm , Brucker Sara Y. , Lang Florian , Riess Olaf
Published: September 2020

The proper communication between gut and brain is pivotal for the maintenance of health and, dysregulation of the gut-brain axis can lead to several clinical disorders. In Parkinson’s disease (PD) 85% of all patients experienced constipation many years before showing any signs of motor phenotypes. For differential diagnosis and preventive treatment, there is an urgent need for the identification of biomarkers indicating early disease stages long before the disease phenotype manifests. DJ-1 is a chaperone protein involved in the protection against PD and genetic mutations in this protein have been shown to cause familial PD. However, how the deficiency of DJ-1 influences the risk of PD remains incompletely understood. In the present study, we provide evidence that DJ-1 is implicated in shaping the gut microbiome including; their metabolite production, inflammation and innate immune cells (ILCs) development. We revealed that deficiency of DJ-1 leads to a significant increase in two specific genera/species, namelyAlistipesandRikenella. In DJ-1 knock-out (DJ-1-/-) mice the production of fecal calprotectin and MCP-1 inflammatory proteins were elevated. Fecal and serum metabolic profile showed that malonate which influences the immune system was significantly more abundant in DJ-1−/−mice. DJ-1 appeared also to be involved in ILCs development. Further, inflammatory genes related to PD were augmented in the midbrain of DJ-1−/−mice. Our data suggest that metabolites and inflammation produced in the gut could be used as biomarkers for PD detection. Perhaps, these metabolites and inflammatory mediators could be involved in triggering inflammation resulting in PD pathology.
Compound specific isotope analysis of lipid residues provides the earliest direct evidence of dairy product processing in South Asia
Authors: Chakraborty Kalyan Sekhar , Slater Greg F. , Miller Heather M.-L. , Shirvalkar Prabodh , Rawat Yadubirsingh
Published: September 2020

The early evidence of domesticated animals and human–animal interaction in South Asia can be traced back to the seventh millennium BCE; however, our understanding of their use is incomplete and limited to the analysis of animal bones from archaeological sites. By the third millennium BCE with the emergence of the Indus Civilization, cattle and water-buffalo became the primary domesticates and outnumbered any other animals at the majority of the Indus settlements. Based on the analysis of skeletal remains and ethnographic data, a number of studies have suggested that cattle and water-buffalo were utilized for their meat, dairy, hides, and other labor-oriented jobs. While some of these claims are backed by empirical data, others are primarily discussed as hypotheses, for example, the exploitation of dairy. In this paper, by analyzing the absorbed lipid residues from fifty-nine ceramic sherds recovered from an agro-pastoral settlement that was occupied during the peak of the Indus period around mid- to late third millennium BCE, we provide the earliest direct evidence of dairy product processing, particularly from cattle and possibly from some water-buffalo. By providing direct evidence of animal product processing, we identify the use of primary domesticated animals and other resources in the diet during the Indus Civilization.
Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application
Authors: Bär Julian , Boumasmoud Mathilde , Kouyos Roger D. , Zinkernagel Annelies S. , Vulin Clément
Published: September 2020

Populations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through antibiotic challenges and secure population survival. This heterogeneity can be studied in complex environmental or clinical samples by spreading the bacteria on agar plates and monitoring time to growth resumption in order to infer their metabolic state distribution. We present ColTapp, the Colony Time-lapse application for bacterial colony growth quantification. Its intuitive graphical user interface allows users to analyze time-lapse images of agar plates to monitor size, color and morphology of colonies. Additionally, images at isolated timepoints can be used to estimate lag time. Using ColTapp, we analyze a dataset of Staphylococcus aureus time-lapse images including populations with heterogeneous lag time. Colonies on dense plates reach saturation early, leading to overestimation of lag time from isolated images. We show that this bias can be corrected by taking into account the area available to each colony on the plate. We envision that in clinical settings, improved analysis of colony growth dynamics may help treatment decisions oriented towards personalized antibiotic therapies.
Influence of the surface viscous stress on the pinch-off of free surfaces loaded with nearly-inviscid surfactants
Authors: Ponce-Torres A. , Rubio M. , Herrada M. A. , Eggers J. , Montanero J. M.
Published: September 2020

We analyze the breakup of a pendant water droplet loaded with SDS. The free surface minimum radius measured in the experiments is compared with that obtained from a numerical solution of the Navier–Stokes equations for different values of the shear and dilatational surface viscosities. This comparison shows the small but measurable effect of the surface viscous stresses for sufficiently small spatiotemporal distances from the breakup point, and allows to establish upper bounds for the values of the shear and dilatational viscosities. We study numerically the distribution of Marangoni and viscous stresses over the free surface as a function of the time to the pinching, and describe how surface viscous stresses grow in the pinching region as the free surface approaches its breakup. When Marangoni and surface viscous stresses are taken into account, the surfactant is not swept away from the thread neck in the time interval analyzed. Surface viscous stresses eventually balance the driving capillary pressure in in the pinching region for small enough values of the time to pinching. Based on this result, we propose a scaling law to account for the effect of the surface viscosities on the last stage of temporal evolution of the neck radius.
Author Correction: Genome-wide human brain eQTLs: In-depth analysis and insights using the UKBEC dataset
Authors: Sng Letitia M. F. , Thomson Peter C. , Trabzuni Daniah
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed
Authors: Fernández-Coll Llorenç , Potrykus Katarzyna , Cashel Michael , Balsalobre Carlos
Published: September 2020

There is a growing appreciation for the diverse regulatory consequences of the family of proteins that bind to the secondary channel of E. coli RNA polymerase (RNAP), such as GreA, GreB or DksA. Similar binding sites could suggest a competition between them. GreA is characterised to rescue stalled RNAP complexes due to its antipause activity, but also it is involved in transcription fidelity and proofreading. Here, overexpression of GreA is noted to be lethal independent of its antipause activity. A library of random GreA variants has been used to isolate lethality suppressors to assess important residues for GreA functionality and its interaction with the RNA polymerase. Some mutant defects are inferred to be associated with altered binding competition with DksA, while other variants seem to have antipause activity defects that cannot reverse a GreA-sensitive pause site in a fliC::lacZ reporter system. Surprisingly, apparent binding and cleavage defects are found scattered throughout both the coiled-coil and globular domains. Thus, the coiled-coil of GreA is not just a measuring stick ensuring placement of acidic residues precisely at the catalytic centre but also seems to have binding functions. These lethality suppressor mutants may provide valuable tools for future structural and functional studies.
Turning date palm waste into carbon nanodots and nano zerovalent iron composites for excellent removal of methylthioninium chloride from water
Authors: Ahmad Munir , Akanji Mutair A. , Usman Adel R. A. , Al-Farraj Abdullah S. F. , Tsang Yiu Fai , Al-Wabel Mohammad I.
Published: September 2020

Novel carbon nanodots (nCD-DBC) and nano zero-valent iron composites (nZVI-DBC) were synthesized using date palm waste-derived biochar (DBC). The synthesized materials were analyzed for chemical and structural composition by using FTIR, SEM, XRD, and TGA, and evaluated for their methylthioninium chloride dye (MB) removal efficiency from contaminated aqueous solutions. pH 7.0 was found optimum for the highest MB removal in sorption batch studies. Kinetics sorption of MB onto the sorbents was best described by pseudo-second-order (R2 = 0.93–0.99) and Elovich models (R2 = 0.86–0.97) implying that sorption was being controlled by chemisorption. Langmuir model predicted maximum sorption capacities for nCD-DBC, nZVI-DBC, and DBC were 1558.66, 1182.90, and 851.67 mg g−1, respectively, which correlated with the results of kinetics sorption. Likewise, nCD-DBC yielded the highest partition coefficient (7067 mL g−1), followed by nZVI-DBC (1460 mL g−1), and DBC (930 mL g−1). Post-sorption XRD, FTIR, and SEM analyses depicted the binding of MB onto the sorbents. It was suggested that electrostatic interactions, π–π electron donor-accepter interactions, degradation, and diffusion were responsible for MB removal by the synthesized materials. Therefore, the nCD-DBC, nZVI-DBC, and DBC can potentially be used for scavenging MB dye from contaminated aqueous solutions.
Comparative clinical outcomes of dronedarone and sotalol in Asian patients with atrial fibrillation: a nationwide cohort study
Authors: Lee So-Ryoung , Choi Eue-Keun , Kim Ji-Hyun , Kim Jung-Ae , Kwon Tae-Yeon , Lee Young Eun , Oh Seil
Published: September 2020

We aimed to evaluate the effectiveness and safety of dronedarone versus sotalol in real-world practice in Asian patients with atrial fibrillation (AF). Using the Korean nationwide claims database from August 2013 to December 2016, we identified patients with AF recently prescribed dronedarone or sotalol and analyzed the hospitalization risk and all-cause death until December 2017. Overall, 3119 and 1575 patients treated with dronedarone and sotalol, respectively, were included. After propensity score weighting, no significant differences were observed between the treatment groups. Dronedarone use was associated with a lower risk of all-cause hospitalization than sotalol use (hazard ratio [HR], 0.79; 95% confidence interval [CI], 0.70–0.88). The dronedarone group demonstrated a significantly lower risk of cardiovascular (CV) hospitalization than the sotalol group (HR 0.62, 95% CI 0.53–0.72); however, no significant difference was observed in non-CV hospitalization. No difference in the risk of all-cause death was observed between groups. The dronedarone group was significantly less likely to receive nonpharmacological treatment for AF than the sotalol group (HR 0.63, 95% CI 0.51–0.77). In a large-scale population of Asian patients with AF, dronedarone was associated with a lower risk of CV hospitalization and a lower need for nonpharmacological treatment for AF than sotalol.
Base-resolution methylomes of gliomas bearing histone H3.3 mutations reveal a G34 mutant-specific signature shared with bone tumors
Authors: Sangatsuda Yuhei , Miura Fumihito , Araki Hiromitsu , Mizoguchi Masahiro , Hata Nobuhiro , Kuga Daisuke , Hatae Ryusuke , Akagi Yojiro , Amemiya Takeo , Fujioka Yutaka , Arai Yasuhito , Yoshida Akihiko , Shibata Tatsuhiro , Yoshimoto Koji , Iihara Koji , Ito Takashi
Published: September 2020

Two recurrent mutations, K27M and G34R/V, in H3F3A, encoding non-canonical histone H3.3, are reported in pediatric and young adult gliomas, whereas G34W mutation is prevalent in bone tumors. In contrast to K27M mutation, it remains elusive how G34 mutations affect the epigenome. Here we performed whole-genome bisulfite sequencing of four G34R-mutated gliomas and the G34V-mutated glioma cell line KNS-42 for comparison with gliomas harboring K27M and no mutations in H3F3A and with G34W-mutated bone tumors. G34R-mutated gliomas exhibited lower global methylation levels, similar CpG island (CGI) methylation levels, and compromised hypermethylation of telomere-proximal CGIs, compared to the other two glioma subgroups. Hypermethylated regions specific to G34R-mutated gliomas were enriched for CGIs, including those of OLIG1, OLIG2, and canonical histone genes in the HIST1 cluster. They were notably hypermethylated in osteosarcomas with, but not without, G34W mutation. Independent component analysis revealed that G34 mutation-specific components shared a significant similarity between glioma and osteosarcoma, suggesting that G34 mutations exert characteristic methylomic effects regardless of the tumor tissue-of-origin. CRISPR/Cas9-mediated disruption of G34V-allele in KNS-42 cells led to demethylation of a subset of CGIs hypermethylated in G34R-mutated gliomas. These findings will provide a basis for elucidating epigenomic roles of G34 oncohistone in tumorigenesis.
Evaluation of the expression stability of reference genes in Apis mellifera under pyrethroid treatment
Authors: Wieczorek Przemysław , Frąckowiak Patryk , Obrępalska-Stęplowska Aleksandra
Published: September 2020

Honeybees (Apis mellifera L.), which unquestionably play an economically important role in pollination and agricultural production, are at risk of decline. To study changes in gene expression in insects upon exposure to pesticides or other external stimuli, appropriate reference genes are required for data normalization. Since there is no such gene that is absolutely invariable under all experimental conditions, the aim of this study was to identify the most stable targets suitable for subsequent normalization in quantitative experiments based on real-time polymerase chain reaction in honeybee research. Here, we evaluated the expression of fifteen candidate housekeeping genes from three breeding lines of honeybees treated with pyrethroids to identify the most stable genes. The tested insects were exposed to deltamethrin or lambda-cyhalothrin, and then, changes in the accumulation of selected transcripts were assessed, followed by statistical analyses. We concluded that AmRPL32, AmACT and AmRPL13a were the commonly recorded most stable genes in honeybees treated with the selected pyrethroids.
Improvement of glymphatic–lymphatic drainage of beta-amyloid by focused ultrasound in Alzheimer’s disease model
Authors: Lee Youngsun , Choi Yoori , Park Eun-Joo , Kwon Seokjun , Kim Hyun , Lee Jae Young , Lee Dong Soo
Published: September 2020

Drainage of parenchymal waste through the lymphatic system maintains brain homeostasis. Age-related changes of glymphatic–lymphatic clearance lead to the accumulation beta-amyloid (Aβ) in dementia models. In this study, focused ultrasound treatment in combination with microbubbles (FUS-MB) improved Aβ drainage in early dementia model mice, 5XFAD. FUS-MB enhanced solute Aβ clearance from brain, but not plaques, to cerebrospinal fluid (CSF) space and then deep cervical lymph node (dCLN). dCLN ligation exaggerated memory impairment and progress of plaque formation and also the beneficial effects of FUS-MB upon Aβ removal through CSF-lymphatic routes. In this ligation model, FUS-MB improved memory despite accumulation of Aβ in CSF. In conclusion, FUS-MB enhances glymphatic–lymphatic clearance of Aβ mainly by increasing brain-to-CSF Aβ drainage. We suggest that FUS-MB can delay dementia progress in early period and benefits of FUS-MB depend on the effect of Aβ disposal through CSF-lymphatics.
Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy
Authors: Caldas Lucio Ayres , Carneiro Fabiana Avila , Higa Luiza Mendonça , Monteiro Fábio Luiz , da Silva Gustavo Peixoto , da Costa Luciana Jesus , Durigon Edison Luiz , Tanuri Amilcar , de Souza Wanderley
Published: September 2020

SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Here, we investigated the interaction of this new coronavirus with Vero cells using high resolution scanning electron microscopy. Surface morphology, the interior of infected cells and the distribution of viral particles in both environments were observed 2 and 48 h after infection. We showed areas of viral processing, details of vacuole contents, and viral interactions with the cell surface. Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2.
The electrophysiological effect of cannabidiol on hERG current and in guinea-pig and rabbit cardiac preparations
Authors: Orvos Péter , Pászti Bence , Topal Leila , Gazdag Péter , Prorok János , Polyák Alexandra , Kiss Tivadar , Tóth-Molnár Edit , Csupor-Löffler Boglárka , Bajtel Ákos , Varró András , Hohmann Judit , Virág László , Csupor Dezső
Published: September 2020

Cannabis use is associated with cardiovascular adverse effects ranging from arrhythmias to sudden cardiac death. The exact mechanism of action behind these activities is unknown. The aim of our work was to study the effect of cannabidiol (CBD), tetrahydrocannabinol and 11-nor-9-carboxy-tetrahydrocannabinol on cellular cardiac electrophysiological properties including ECG parameters, action potentials, hERG and IKr ion channels in HEK cell line and in rabbit and guinea pig cardiac preparations. CBD increased action potential duration in rabbit and guinea pig right ventricular papillary muscle at lower concentrations (1 µM, 2.5 µM and 5 µM) but did not significantly change it at 10 µM. CBD at high concentration (10 µM) decreased inward late sodium and L-type calcium currents as well. CBD inhibited hERG potassium channels with an IC50 value of 2.07 µM at room temperature and delayed rectifier potassium current with 6.5 µM at 37 °C, respectively. The frequency corrected QT interval (QTc) was significantly lengthened in anaesthetized guinea pig without significantly changing other ECG parameters. Although the IC50 value of CBD was higher than literary Cmax values after CBD smoking and oral intake, our results raise the possibility that hERG and potassium channel inhibition might have a role in the possible proarrhythmic adverse effects of cannabinoids in situations where metabolism of CBD impaired and/or the repolarization reserve is weakened.
Influence of number of membership functions on prediction of membrane systems using adaptive network based fuzzy inference system (ANFIS)
Authors: Babanezhad Meisam , Masoumian Armin , Nakhjiri Ali Taghvaie , Marjani Azam , Shirazian Saeed
Published: September 2020

In membrane separation technologies, membrane modules are used to separate chemical components. In membrane technology, understanding the behavior of fluids inside membrane module is challenging, and numerical methods are possible by using computational fluid dynamics (CFD). On the other hand, the optimization of membrane technology via CFD needs time and computational costs. Artificial Intelligence (AI) and CFD together can model a chemical process, including membrane technology and phase separation. This process can learn the process by learning the neural networks, and point by point learning of CFD mesh elements (computing nodes), and the fuzzy logic system can predict this process. In the current study, the adaptive neuro-fuzzy inference system (ANFIS) model and different parameters of ANFIS for learning a process based on membrane technology was used. The purpose behind using this model is to see how different tuning parameters of the ANFIS model can be used for increasing the exactness of the AI model and prediction of the membrane technology. These parameters were changed in this study, and the accuracy of the prediction was investigated. The results indicated that with low number of inputs, poor regression was obtained, less than 0.32 (R-value), but by increasing the number of inputs, the AI algorithm led to an increase in the prediction capability of the model. When the number of inputs increased to 4, the R-value was increased to 0.99, showing the high accuracy of model as well as its high capability in prediction of membrane process. The AI results were in good agreement with the CFD results. AI results were achieved in a limited time and with low computational costs. In terms of the categorization of CFD data-set, the AI framework plays a critical role in storing data in short memory, and the recovery mechanism can be very easy for users. Furthermore, the results were compared with Particle Swarm Optimization (PSOFIS), and Genetic Algorithm (GAFIS). The time for prediction and learning were compared to study the capability of the methods in prediction and their accuracy.