bluuebunny/crossref_metadata_2025 huggingface dataset:
Colletotrichum spp. causing anthracnose on ornamental plants in northern Italy
Authors: Guarnaccia Vladimiro , Martino Ilaria , Gilardi Giovanna , Garibaldi Angelo , Gullino M. Lodovica
Published: October 2020

Species ofColletotrichumare considered among the most important plant pathogens, saprobes and endophytes on a wide range of ornamentals, fruits and vegetables. SeveralColletotrichumspecies have been reported in nurseries and public or private gardens in northern Italy. In this study, the occurrence, diversity and pathogenicity ofColletotrichumspp. associated with several ornamental hosts was explored. Survey were carried out during the 2013–2019 period in Piedmont, Italy. A total of 22Colletotrichumisolates were collected from symptomatic leaves and stems of twoCampanulaspp.,Ceanothus thyrsiflorus,Coreopsis lanceolata,Cyclamen persicum,Hydrangea paniculata,Liquidambar styraciflua,Mahonia aquifoliumandRhyncospermum jasminoides. A multi-locus phylogeny was established based on the basis of three genomic loci (gapdh,actandtub2). The pathogenicity of selected, representative isolates was tested.Colletotrichumisolates were identified as members of four important species complexes: Acutatum,Gloeosporioides,DematiumandDestructivum.Colletotrichum fioriniae,C. nymphaeaeandC. fuscumwere found in association with leaf lesions ofMahonia aquifolium,Campanula rapunculoidesandCoreopsis lanceolata, respectively.Colletotrichum lineola,C. grossumandC. cigarrowere isolated fromCampanula trachelium,Rhyncospermum jasminoidesandLiquidambar styraciflua, respectively.Colletotrichum fructicolawas found to be responsible of anthracnose ofCeanothus thyrsiflorus,Hydrangea paniculata,Cyclamen persicumandLiquidambar styraciflua. All the tested isolates were pathogenic and reproduced identical symptoms to those observed in private gardens and nurseries. The present study improves our understanding ofColletotrichumspp. associated with different ornamental hosts and provides useful information for an effective disease management programme.
The Shepherd, the Volk, and the Middle Class
Authors: Griffiths Elystan
Published: October 2020

Analyzes the transformation of German-language pastoral from a portrayal of the idyllic lives of herdsmen into a vehicle for the concerns and aspirations of the middle class.
Wining and Dining Government Officials: What Drives Political Networking in Chinese Private Ventures?
Authors: Zhang Jianjun , Sun Pei , Qiao Kunyuan
Published: October 2020

Managerial networking with political actors has long been recognized as a crucial co-option strategy to navigate the challenging institutional environment in emerging economies. However, we know much less about what drives thevariationof political networking investment by private ventures. Drawing on resource dependence theory, we unpack the dyadic business-government relations and identify the key organizational and environmental factors that shape the power dependence relationships between private ventures and the government. By examining power imbalance and mutual dependence in this dyadic relationship and considering both the necessity and the capability of political networking, we develop hypotheses regarding the ways in which size-, connection-, and location-based dependencies affect firms’ political networking intensity. These hypotheses are tested through a unique survey of Chinese private ventures. Our study finds that political networking intensity (1) has an inverted U-shaped relationship with firm size, (2) is negatively associated with the presence of embedded political ties while positively associated with that of achieved political connections, and (3) is smaller when the focal firm is located in business development zones. This research bears rich implications for our understanding of corporate political activity in emerging economies from a resource dependence lens.
Oral contraceptive use and risk of suicidal behavior among young women
Authors: Edwards Alexis C. , Lönn Sara Larsson , Crump Casey , Mościcki Eve K. , Sundquist Jan , Kendler Kenneth S. , Sundquist Kristina
Published: October 2020

Background

Oral contraceptive use has been previously associated with an increased risk of suicidal behavior in some, but not all, samples. The use of large, representative, longitudinally-assessed samples may clarify the nature of this potential association.

Methods

We used Swedish national registries to identify women born between 1991 and 1995 (N = 216 702) and determine whether they retrieved prescriptions for oral contraceptives. We used Cox proportional hazards models to test the association between contraceptive use and first observed suicidal event (suicide attempt or death) from age 15 until the end of follow-up in 2014 (maximum age 22.4). We adjusted for covariates, including mental illness and parental history of suicide.

Results

In a crude model, use of combination or progestin-only oral contraceptives was positively associated with suicidal behavior, with hazard ratios (HRs) of 1.73–2.78 after 1 month of use, and 1.25–1.82 after 1 year of use. Accounting for sociodemographic, parental, and psychiatric variables attenuated these associations, and risks declined with increasing duration of use: adjusted HRs ranged from 1.56 to 2.13 1 month beyond the initiation of use, and from 1.19 to 1.48 1 year after initiation of use. HRs were higher among women who ceased use during the observation period.

Conclusions

Young women using oral contraceptives may be at increased risk of suicidal behavior, but risk declines with increased duration of use. Analysis of former users suggests that women susceptible to depression/anxiety are more likely to cease hormonal contraceptive use. Additional studies are necessary to determine whether the observed association is attributable to a causal mechanism.
Nutrigenetics of antioxidant enzymes and micronutrient needs in the context of viral infections
Authors: Birk Ruth
Published: October 2020

Sustaining adequate nutritional needs of a population is a challenging task in normal times and a priority in times of crisis. There is no ‘one-size-fits-all’ solution that addresses nutrition. In relevance to the COVID-19 (coronavirus disease 2019) pandemic crisis, viral infections in general and RNA viruses in particular are known to induce and promote oxidative stress, consequently increasing the body’s demand for micronutrients, especially those related to antioxidant enzymic systems, thus draining the body of micronutrients, and so hindering the human body’s ability to cope optimally with oxidative stress. Common polymorphisms in major antioxidant enzymes, with world population minor allele frequencies ranging from 0·5 to 50 %, are related to altered enzymic function, with substantial potential effects on the body’s ability to cope with viral infection-induced oxidative stress. In this review we highlight common SNP of the major antioxidant enzymes relevant to nutritional components in the context of viral infections, namely: superoxide dismutases, glutathione peroxidases and catalase. We delineate functional polymorphisms in several human antioxidant enzymes that require, especially during a viral crisis, adequate and potentially additional nutritional support to cope with the pathological consequences of disease. Thus, in face of the COVID-19 pandemic, nutrition should be tightly monitored and possibly supplemented, with special attention to those carrying common polymorphisms in antioxidant enzymes.
Mismatch between self-estimated and objectively assessed exercise capacity in patients with congenital heart disease varies in regard to complexity of cardiac defects
Authors: Woile Julius M. , Dirks Stefan , Danne Friederike , Berger Felix , Ovroutski Stanislav
Published: October 2020

Aim:

Regular evaluation of physical capacity takes a crucial part in long-term follow-up in patients with congenital heart disease (CHD). This study aims to examine the accuracy of self-estimated exercise capacity compared to objective assessments by cardiopulmonary exercise testing in patients with CHD of various complexity.

Methods:

We conducted a single centre, cross-sectional study with retrospective analysis on 382 patients aged 8–68 years with various CHD who completed cardiopulmonary exercise tests. Peak oxygen uptake was measured. Additionally, questionnaires covering self-estimation of exercise capacity were completed. Peak oxygen uptake was compared to patient’s self-estimated exercise capacity with focus on differences between complex and non-complex defects.

Results:

Peak oxygen uptake was 25.5 ± 7.9 ml/minute/kg, corresponding to 75.1 ± 18.8% of age- and sex-specific reference values. Higher values of peak oxygen uptake were seen in patients with higher subjective rating of exercise capacity. However, oxygen uptake in patients rating their exercise capacity as good (mean oxygen uptake 78.5 ± 1.6%) or very good (mean oxygen uptake 84.8 ± 4.8%) was on average still reduced compared to normal. In patients with non-complex cardiac defects, we saw a significant correlation between peak oxygen uptake and self-estimated exercise capacity (spearman-rho −0.30, p < 0.001), whereas in patients with complex cardiac defects, no correlation was found (spearman-rho −0.11, p < 0.255).

Conclusion:

The mismatch between self-estimated and objectively assessed exercise capacity is most prominent in patients with complex CHD.

Registration number at Charité Universitätsmedizin Berlin Ethics Committee: EA2/106/14.
Use of In Situ Simulation to Improve Emergency Department Readiness for the COVID-19 Pandemic
Authors: Aljahany Muna , Alassaf Wajdan , Alibrahim Ahmed A. , Kentab Osama , Alotaibi Abdullah , Alresseeni Abdulaziz , Algarni Abdulaziz , Algaeed Hamad A. , Aljaber Mohammed I. , Alruwaili Badriyah , Aljohani Khalid
Published: October 2020

Introduction:

During the world-wide coronavirus disease 2019 (COVID-19) outbreak, there is an urgent need to rapidly increase the readiness of hospitals. Emergency departments (EDs) are at high risk of facing unusual situations and need to prepare extensively in order to minimize risks to health care providers (HCPs) and patients. In situ simulation is a well-known method used in training to detect system gaps that could threaten safety.

Study Objectives:

One objective is to identify gaps, test hospital systems, and inform necessary modifications to the standard processes required by patients with COVID-19 presenting at the hospital. The other objective is to improve ED staff confidence in managing such patients, and to increase their skills in basic and advanced airway management and proper personal protective equipment (PPE) techniques.

Methods:

This is a quasi-experimental study in which 20 unannounced mock codes were carried out in ED resuscitation and isolation rooms. A checklist was designed, validated, and used to evaluate team performances in three areas: donning, basic and advanced airway skills, and doffing. A pre- and post-intervention survey was used to evaluate staff members’ perceived knowledge of ED procedures related to COVID-19 and their airway management skills.

Results:

A total of 20 mock codes were conducted in the ED. Overall, 16 issues that posed potential harm to staff or patients were identified and prioritized for immediate resolution. Approximately 57.4% of HCPs felt comfortable dealing with suspected/confirmed, unstable COVID-19 cases after mock codes, compared with 33.3% beforehand (P = .033). Of ED HCPs, 44.4% felt comfortable performing airway procedures for suspected/confirmed COVID-19 cases after mock codes compared with 29.6% beforehand. Performance of different skills was observed to be variable following the 20 mock codes. Skills with improved performance included: request of chest x-ray after intubation (88.0%), intubation done by the most experienced ED physician (84.5%), and correct sequence and procedure of PPE (79.0%).

Conclusion:

Mock codes identified significant defects, most of which were easily fixed. They included critical equipment availability, transporting beds that were too large to fit through doors, and location of biohazard bins. Repeated mock codes improved ED staff confidence in dealing with patients, in addition to performance of certain skills. In situ simulation proves to be an effective method for increasing the readiness of the ED to address the COVID-19 pandemic and other infection outbreaks.
KOLMOGOROV CONDITIONALIZERS CAN BE DUTCH BOOKED (IF AND ONLY IF THEY ARE EVIDENTIALLY UNCERTAIN)
Authors: MEEHAN ALEXANDER , ZHANG SNOW
Published: October 2020

A vexing question in Bayesian epistemology is how an agent should update on evidence which she assigned zero prior credence. Some theorists have suggested that, in such cases, the agent should update by Kolmogorov conditionalization, a norm based on Kolmogorov’s theory of regular conditional distributions. However, it turns out that in some situations, a Kolmogorov conditionalizer will plan to always assign a posterior credence of zero to the evidence she learns. Intuitively, such a plan is irrational and easily Dutch bookable. In this paper, we propose a revised norm, Kolmogorov–Blackwell conditionalization, which avoids this problem. We prove a Dutch book theorem and converse Dutch book theorem for this revised norm, and relate our results to those of Rescorla (2018).
RIGOUR AND PROOF
Authors: TATTON-BROWN OLIVER
Published: October 2020

This paper puts forward a new account of rigorous mathematical proof and its epistemology. One novel feature is a focus on how the skill of reading and writing valid proofs is learnt, as a way of understanding what validity itself amounts to. The account is used to address two current questions in the literature: that of how mathematicians are so good at resolving disputes about validity, and that of whether rigorous proofs are necessarily formalizable.
A Cultural Framework of Care and Social Protection for Older People in India
Authors: Burholt Vanessa , Maruthakutti Rangasamy , Maddock Carol A.
Published: October 2020

Abstract. This article applies a cultural political economy lens within a sustainable livelihood framework and examines how cultural norms and values as well as social protection amplify or attenuate livelihood shocks leading to care-home entry. We used framework analysis and higher-level interpretive analysis of data from interviews with 30 older care-home residents from three districts in Tamil Nadu, India, to understand the practices that allow the social welfare system to function alongside the beliefs and values legitimizing these practices. Results reveal a divergence between the value orientation of social-protection policy and cultural practices which constrains the choices available for care in later life and reinforces culturally constructed inequalities rather than protecting or remediating livelihood shocks and loss of assets.
Finding Value in the Margins to Build a Bioeconomy
Authors: Sidder Aaron
Published: October 2020

Monetizing environmental services of biofuel feedstocks could incentivize farmers to take advantage of marginal agricultural lands while also benefiting the landscape.
Reactive Flow and Homogenization in Anisotropic Media
Authors: Roded R. , Aharonov E. , Holtzman R. , Szymczak P.
Published: October 2020

The evolution of heterogeneous and anisotropic media in the uniform dissolution regime (low Damköhler number) is studied here using a numerical network model. The uniform dissolution extensively homogenizes the medium and therefore the flow field. The homogenization is further enhanced when the surface reaction is transport controlled—when slow diffusion of dissolved ions away from the mineral surface leads to the reduction of the global dissolution rate. Under those conditions, diffusive transport is more effective in narrow channels, which selectively enlarge, leading to an initial steep rise of the permeability. However, as dissolution proceeds, the void space widens and the overall dissolution rate drops, and permeability enhancement slows down. Finally, we review the relevance of these results to various processes in geological systems ranging from diagenesis and karst evolution, to carbon geosequestration. These findings provide fundamental insights into reactive transport processes in fractured and porous media and evolution of permeability, tortuosity, anisotropy, and bulk reaction rates in geological systems.
Pathogenesis and multidisciplinary management of medication-related osteonecrosis of the jaw
Authors: He Lina , Sun Xiangyu , Liu Zhijie , Qiu Yanfen , Niu Yumei
Published: October 2020

Medication-related osteonecrosis of the jaw (MRONJ) is a serious side effect of bone-modifying agents and inhibits angiogenesis agents. Although the pathogenesis of MRONJ is not entirely clear, multiple factors may be involved in specific microenvironments. The TGF-β1 signalling pathway may have a key role in the development of MRONJ. According to the clinical stage, multiple variables should be considered when selecting the most appropriate treatment. Therefore, the prevention and management of treatment of MRONJ should be conducted in patient-centred multidisciplinary team collaborative networks with oncologists, dentists and dental specialists. This would comprise a closed responsibility treatment loop with all benefits directed to the patient. Thus, in the present review, we aimed to summarise the pathogenesis, risk factors, imaging features, clinical staging, therapeutic methods, prevention and treatment strategies associated with MRONJ, which may provide a reference that can inform preventive strategies and improve the quality of life for patients in the future.
ADHD-like behaviors caused by inactivation of a transcription factor controlling the balance of inhibitory and excitatory neuron development in the mouse anterior brainstem
Authors: Morello Francesca , Voikar Vootele , Parkkinen Pihla , Panhelainen Anne , Rosenholm Marko , Makkonen Aki , Rantamäki Tomi , Piepponen Petteri , Aitta-aho Teemu , Partanen Juha
Published: October 2020

The neural circuits regulating motivation and movement include midbrain dopaminergic neurons and associated inhibitory GABAergic and excitatory glutamatergic neurons in the anterior brainstem. Differentiation of specific subtypes of GABAergic and glutamatergic neurons in the mouse embryonic brainstem is controlled by a transcription factor Tal1. This study characterizes the behavioral and neurochemical changes caused by the absence of Tal1 function. The Tal1cko mutant mice are hyperactive, impulsive, hypersensitive to reward, have learning deficits and a habituation defect in a novel environment. Only minor changes in their dopaminergic system were detected. Amphetamine induced striatal dopamine release and amphetamine induced place preference were normal in Tal1cko mice. Increased dopamine signaling failed to stimulate the locomotor activity of the Tal1cko mice, but instead alleviated their hyperactivity. Altogether, the Tal1cko mice recapitulate many features of the attention and hyperactivity disorders, suggesting a role for Tal1 regulated developmental pathways and neural structures in the control of motivation and movement.
Microplastic regulation should be more precise to incentivize both innovation and environmental safety
Authors: Mitrano Denise M. , Wohlleben Wendel
Published: October 2020

The presence of plastic in the environment has sparked discussion amongst scientists, regulators and the general public as to how industrialization and consumerism is shaping our world. Here we discuss restrictions on the intentional use of primary microplastics: small solid polymer particles in applications ranging from agriculture to cosmetics. Microplastic hazards are uncertain, and actions are not similarly prioritized by all actors. In some instances, replacement is technically simple and easily justified, but in others substitutions may come with more uncertainty, performance questions and costs. Scientific impact assessment of primary microplastics compared to their alternatives relies on a number of factors, such as microplastic harm, existence of replacement materials and the quality, cost and hazards of alternative materials. Regulations need a precise focus and must be enforceable by these measurements. Policymakers must carefully evaluate under which contexts incentives to replace certain microplastics can stimulate innovation of new, more competitive and environmentally conscious materials.
Identification of key sequence features required for microRNA biogenesis in plants
Authors: Rojas Arantxa M. L. , Drusin Salvador I. , Chorostecki Uciel , Mateos Julieta L. , Moro Belén , Bologna Nicolas G. , Bresso Edgardo G. , Schapire Arnaldo , Rasia Rodolfo M. , Moreno Diego M. , Palatnik Javier F.
Published: October 2020

MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis.
Electropolymerization of robust conjugated microporous polymer membranes for rapid solvent transport and narrow molecular sieving
Authors: Zhou Zongyao , Li Xiang , Guo Dong , Shinde Digambar B. , Lu Dongwei , Chen Long , Liu Xiaowei , Cao Li , Aboalsaud Ammar M. , Hu Yunxia , Lai Zhiping
Published: October 2020

Pore size uniformity is one of the most critical parameters in determining membrane separation performance. Recently, a novel type of conjugated microporous polymers (CMPs) has shown uniform pore size and high porosity. However, their brittle nature has prevented them from preparing robust membranes. Inspired by the skin-core architecture of spider silk that offers both high strength and high ductility, herein we report an electropolymerization process to prepare a CMP membrane from a rigid carbazole monomer, 2,2’,7,7’-tetra(carbazol-9-yl)-9,9’-spirobifluorene, inside a robust carbon nanotube scaffold. The obtained membranes showed superior mechanical strength and ductility, high surface area, and uniform pore size of approximately 1 nm. The superfast solvent transport and excellent molecular sieving well surpass the performance of most reported polymer membranes. Our method makes it possible to use rigid CMPs membranes in pressure-driven membrane processes, providing potential applications for this important category of polymer materials.
Forest production efficiency increases with growth temperature
Authors: Collalti A. , Ibrom A. , Stockmarr A. , Cescatti A. , Alkama R. , Fernández-Martínez M. , Matteucci G. , Sitch S. , Friedlingstein P. , Ciais P. , Goll D. S. , Nabel J. E. M. S. , Pongratz J. , Arneth A. , Haverd V. , Prentice I. C.
Published: October 2020

Forest production efficiency (FPE) metric describes how efficiently the assimilated carbon is partitioned into plants organs (biomass production, BP) or—more generally—for the production of organic matter (net primary production, NPP). We present a global analysis of the relationship of FPE to stand-age and climate, based on a large compilation of data on gross primary production and either BP or NPP. FPE is important for both forest production and atmospheric carbon dioxide uptake. We find that FPE increases with absolute latitude, precipitation and (all else equal) with temperature. Earlier findings—FPE declining with age—are also supported by this analysis. However, the temperature effect is opposite to what would be expected based on the short-term physiological response of respiration rates to temperature, implying a top-down regulation of carbon loss, perhaps reflecting the higher carbon costs of nutrient acquisition in colder climates. Current ecosystem models do not reproduce this phenomenon. They consistently predict lower FPE in warmer climates, and are therefore likely to overestimate carbon losses in a warming climate.
A universal method for depositing patterned materials in situ
Authors: Chen Yifan , Hung Siu Fai , Lo Wing Ki , Chen Yang , Shen Yang , Kafenda Kim , Su Jia , Xia Kangwei , Yang Sen
Published: October 2020

Current techniques of patterned material deposition require separate steps for patterning and material deposition. The complexity and harsh working conditions post serious limitations for fabrication. Here, we introduce a single-step and easy-to-adapt method that can deposit materials in-situ. Its methodology is based on the semiconductor nanoparticle assisted photon-induced chemical reduction and optical trapping. This universal mechanism can be used for depositing a large selection of materials including metals, insulators and magnets, with quality on par with current technologies. Patterning with several materials together with optical-diffraction-limited resolution and accuracy can be achieved from macroscopic to microscopic scale. Furthermore, the setup is naturally compatible with optical microscopy based measurements, thus sample characterisation and material deposition can be realised in-situ. Various devices fabricated with this method in 2D or 3D show it is ready for deployment in practical applications. This method will provide a distinct tool in material technology.
Author Correction: SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate
Authors: Olagnier David , Farahani Ensieh , Thyrsted Jacob , Blay-Cadanet Julia , Herengt Angela , Idorn Manja , Hait Alon , Hernaez Bruno , Knudsen Alice , Iversen Marie Beck , Schilling Mirjam , Jørgensen Sofie E. , Thomsen Michelle , Reinert Line S. , Lappe Michael , Hoang Huy-Dung , Gilchrist Victoria H. , Hansen Anne Louise , Ottosen Rasmus , Nielsen Camilla G. , Møller Charlotte , van der Horst Demi , Peri Suraj , Balachandran Siddharth , Huang Jinrong , Jakobsen Martin , Svenningsen Esben B. , Poulsen Thomas B. , Bartsch Lydia , Thielke Anne L. , Luo Yonglun , Alain Tommy , Rehwinkel Jan , Alcamí Antonio , Hiscott John , Mogensen Trine H. , Paludan Søren R. , Holm Christian K.
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Biofilm dynamics: linking in situ biofilm biomass and metabolic activity measurements in real-time under continuous flow conditions
Authors: Klopper Kyle B. , de Witt Riaan N. , Bester Elanna , Dicks Leon M. T. , Wolfaardt Gideon M.
Published: October 2020

The tools used to study biofilms generally involve either destructive, end-point analyses or periodic measurements. The advent of the internet of things (IoT) era allows circumvention of these limitations. Here we introduce and detail the development of the BioSpec; a modular, nondestructive, real-time monitoring system, which accurately and reliably track changes in biofilm biomass over time. The performance of the system was validated using a commercial spectrophotometer and produced comparable results for variations in planktonic and sessile biomass. BioSpec was combined with the previously developed carbon dioxide evolution measurement system (CEMS) to allow simultaneous measurement of biofilm biomass and metabolic activity and revealed a differential response of these interrelated parameters to changing environmental conditions. The application of this system can facilitate a greater understanding of biofilm mass–function relationships and aid in the development of biofilm control strategies.
High-throughput computational screening for two-dimensional magnetic materials based on experimental databases of three-dimensional compounds
Authors: Torelli Daniele , Moustafa Hadeel , Jacobsen Karsten W. , Olsen Thomas
Published: October 2020

We perform a computational screening for two-dimensional (2D) magnetic materials based on experimental bulk compounds present in the Inorganic Crystal Structure Database and Crystallography Open Database. A recently proposed geometric descriptor is used to extract materials that are exfoliable into 2D derivatives and we find 85 ferromagnetic and 61 antiferromagnetic materials for which we obtain magnetic exchange and anisotropy parameters using density functional theory. For the easy-axis ferromagnetic insulators we calculate the Curie temperature based on a fit to classical Monte Carlo simulations of anisotropic Heisenberg models. We find good agreement with the experimentally reported Curie temperatures of known 2D ferromagnets and identify 10 potentially exfoliable 2D ferromagnets that have not been reported previously. In addition, we find 18 easy-axis antiferromagnetic insulators with several compounds exhibiting very strong exchange coupling and magnetic anisotropy.
Density functional theory-based electric field gradient database
Authors: Choudhary Kamal , Ansari Jaafar N. , Mazin Igor I. , Sauer Karen L.
Published: October 2020

The deviation of the electron density around the nuclei from spherical symmetry determines the electric field gradient (EFG), which can be measured by various types of spectroscopy. Nuclear Quadrupole Resonance (NQR) is particularly sensitive to the EFG. The EFGs, and by implication NQR frequencies, vary dramatically across materials. Consequently, searching for NQR spectral lines in previously uninvestigated materials represents a major challenge. Calculated EFGs can significantly aid at the search’s inception. To facilitate this task, we have applied high-throughput density functional theory calculations to predict EFGs for 15187 materials in the JARVIS-DFT database. This database, which will include EFG as a standard entry, is continuously increasing. Given the large scope of the database, it is impractical to verify each calculation. However, we assess accuracy by singling out cases for which reliable experimental information is readily available and compare them to the calculations. We further present a statistical analysis of the results. The database and tools associated with our work are made publicly available by JARVIS-DFT (https://www.ctcms.nist.gov/~knc6/JVASP.html) and NIST-JARVIS API (http://jarvis.nist.gov/).
Brain activity and transcriptional profiling in mice under chronic jet lag
Authors: Gao Qian , Khan Suliman , Zhang Luoying
Published: October 2020

Shift work is known to be associated with an increased risk of neurological and psychiatric diseases, but how it contributes to the development of these diseases remains unclear. Chronic jet lag (CJL) induced by shifting light-dark cycles repeatedly is a commonly used protocol to mimic the environmental light/dark changes encountered by shift workers. Here we subjected wildtype mice to CJL and performed positron emission tomography imaging of glucose metabolism to monitor brain activities. We also conducted RNA sequencing using prefrontal cortex and nucleus accumbens tissues from these animals, which are brain regions strongly implicated in the pathology of various neurological and psychiatric conditions. Our results reveal the alterations of brain activities and systematic reprogramming of gene expression in brain tissues under CJL, building hypothesis for how CJL increases the susceptibility to neurological and psychiatric diseases.
The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis
Authors: Hotta Kohji , Dauga Delphine , Manni Lucia
Published: October 2020

Ciona robusta(Ciona intestinalistype A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives of vertebrates. InCiona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing the developmental ontology, we acquired different time-lapse movies, confocal microscope images and histological serial section images for each developmental event from the hatching larva stage (17.5 h post fertilization) to the juvenile stage (7 days post fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource "TunicAnatO", which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.
Manipulation of the gut microbiota by the use of prebiotic fibre does not override a genetic predisposition to heart failure
Authors: Jama Hamdi A. , Fiedler April , Tsyganov Kirill , Nelson Erin , Horlock Duncan , Nakai Michael E. , Kiriazis Helen , Johnson Chad , Du Xiao-Jun , Mackay Charles R. , Marques Francine Z. , Kaye David M.
Published: October 2020

Increasing evidence supports a role for the gut microbiota in the development of cardiovascular diseases such as hypertension and its progression to heart failure (HF). Dietary fibre has emerged as a modulator of the gut microbiota, resulting in the release of gut metabolites called short-chain fatty acids (SCFAs), such as acetate. We have shown previously that fibre or acetate can protect against hypertension and heart disease in certain models. HF is also commonly caused by genetic disorders. In this study we investigated whether the intake of fibre or direct supplementation with acetate could attenuate the development of HF in a genetic model of dilated cardiomyopathy (DCM) due to overexpression of the cardiac specific mammalian sterile 20-like kinase (Mst1). Seven-week-old male mice DCM mice and littermate controls (wild-type, C57BL/6) were fed a control diet (with or without supplementation with 200 mM magnesium acetate in drinking water), or a high fibre diet for 7 weeks. We obtained hemodynamic, morphological, flow cytometric and gene expression data. The gut microbiome was characterised by 16S rRNA amplicon sequencing. Fibre intake was associated with a significant shift in the gut microbiome irrespective of mouse genotype. However, neither fibre or supplementation with acetate were able to attenuate cardiac remodelling or cardiomyocyte apoptosis in Mst1 mice. Furthermore, fibre and acetate did not improve echocardiographic or hemodynamic parameters in DCM mice. These data suggest that although fibre modulates the gut microbiome, neither fibre nor acetate can override a strong genetic contribution to the development of heart failure in the Mst1 model.
Generation of human induced pluripotent stem cell-derived liver buds with chemically defined and animal origin-free media
Authors: Sekine Keisuke , Ogawa Shimpei , Tsuzuki Syusaku , Kobayashi Tatsuya , Ikeda Kazuki , Nakanishi Noriko , Takeuchi Kenta , Kanai Eriko , Otake Yugo , Okamoto Satoshi , Kobayashi Tsuyoshi , Takebe Takanori , Taniguchi Hideki
Published: October 2020

Advances in organoid technology have broadened the number of target diseases and conditions in which human induced pluripotent stem cell (iPSC)-based regenerative medicine can be applied; however, mass production of organoids and the development of chemically defined, animal origin-free (CD-AOF) media and supplements are unresolved issues that hamper the clinical applicability of these approaches. CD-AOF media and supplements ensure the quality and reproducibility of culture systems by lowering lot-to-lot variations and the risk of contamination with viruses or toxins. We previously generated liver organoids from iPSCs, namely iPSC-liver buds (iPSC-LBs), by mimicking the organogenic interactions among hepatocytes, endothelial cells (ECs), and mesenchymal cells (MCs) and recently reported the mass production of iPSC-LBs derived entirely from iPSCs (all iPSC-LBs), which should facilitate their large-scale production for the treatment of liver failure. However, in previous studies we used media originating from animals for differentiation except for the maintenance of undifferentiated iPSCs. Therefore, we developed a CD-AOF medium to generate all iPSC-LBs. We first developed a CD-AOF medium for hepatocytes, ECs, and stage-matched MCs, i.e., septum transversum mesenchyme (STM), in 2D cultures. We next generated all iPSC-LBs by incubating individual cell types in ultra-low attachment micro-dimple plates. The hepatic functions of all iPSC-LBs generated using the CD-AOF medium were equivalent to those of all iPSC-LBs generated using the conventional medium both in vitro and in vivo. Furthermore, we found that this CD-AOF medium could be used in several cell culture settings. Taken together, these results demonstrate the successful development of a CD-AOF medium suitable for all iPSC-LBs. The protocol developed in this study will facilitate the clinical applicability of all iPSC-LBs in the treatment of liver diseases.
SeMSA: a compact super absorber optimised for broadband, low-frequency noise attenuation
Authors: McKay Andrew , Davis Ian , Killeen Jack , Bennett Gareth J.
Published: October 2020

The attenuation of low-frequency broadband noise in a light, small form-factor is an intractable challenge. In this paper, a new technology is presented which employs the highly efficient visco-thermal loss mechanism of a micro-perforated plate (MPP) and successfully lowers its frequency response by combining it with decorated membrane resonators (DMR). Absorption comes from the membranes but primarily from the MPP, as the motion of the two membranes causes a pressure differential across the MPP creating airflow through the perforations. This combination of DMR and MPP has led to the Segmented Membrane Sound Absorber (SeMSA) design, which is extremely effective at low-frequency broadband sound absorption and which can achieve this at deep sub-wavelength thicknesses. The technology is compared to other absorbers to be found in the literature and the SeMSA outperforms them all in either the 20–1000 Hz or 20–1200 Hz range for depths of up to 120 mm. This was verified through analytical, finite element and experimental analyses.
Late first trimester circulating microparticle proteins predict the risk of preeclampsia < 35 weeks and suggest phenotypic differences among affected cases
Authors: McElrath Thomas F. , Cantonwine David E. , Gray Kathryn J. , Mirzakhani Hooman , Doss Robert C. , Khaja Najmuddin , Khalid Malik , Page Gail , Brohman Brian , Zhang Zhen , Sarracino David , Rosenblatt Kevin P.
Published: October 2020

We hypothesize that first trimester circulating micro particle (CMP) proteins will define preeclampsia risk while identifying clusters of disease subtypes among cases. We performed a nested case–control analysis among women with and without preeclampsia. Cases diagnosed < 34 weeks’ gestation were matched to controls. Plasma CMPs were isolated via size exclusion chromatography and analyzed using global proteome profiling based on HRAM mass spectrometry. Logistic models then determined feature selection with best performing models determined by cross-validation. K-means clustering examined cases for phenotypic subtypes and biological pathway enrichment was examined. Our results indicated that the proteins distinguishing cases from controls were enriched in biological pathways involved in blood coagulation, hemostasis and tissue repair. A panel consisting of C1RL, GP1BA, VTNC, and ZA2G demonstrated the best distinguishing performance (AUC of 0.79). Among the cases of preeclampsia, two phenotypic sub clusters distinguished cases; one enriched for platelet degranulation and blood coagulation pathways and the other for complement and immune response-associated pathways (corrected p < 0.001). Significantly, the second of the two clusters demonstrated lower gestational age at delivery (p = 0.049), increased protein excretion (p = 0.01), more extreme laboratory derangement (p < 0.0001) and marginally increased diastolic pressure (p = 0.09). We conclude that CMP-associated proteins at 12 weeks’ gestation predict the overall risk of developing early preeclampsia and indicate distinct subtypes of pathophysiology and clinical morbidity.
Analysis of vasovagal syncope in the blood collection room in patients undergoing phlebotomy
Authors: Yoshimoto Akira , Yasumoto Atsushi , Kamiichi Yuko , Shibayama Haruna , Sato Masaya , Misawa Yoshiki , Morita Kazuharu , Ono Yoshikazu , Sone Shinji , Satoh Tomoaki , Yatomi Yutaka
Published: October 2020

Vasovagal syncope (VVS) is well-known to occur in patients undergoing phlebotomy, however, there have been no large-scale studies of the incidence of VVS in the blood collection room. The aim of our present retrospective study was to investigate the conditions of phlebotomy and determine the incidence/factors predisposing to the development of VVS. We investigated 677,956 phlebotomies performed in outpatients in the blood collection room, to explore factors predisposing to the development of VVS. Our analysis revealed an overall incidence of VVS of 0.004% and suggested that use of more than 5 blood collection tubes and a waiting time of more than 15 min were associated with a higher risk of VVS. The odds ratios of these factors were 8.10 (95% CI 3.76–17.50) and 3.69 (95% CI 0.87–15.60), respectively. This is the large-scale study to analyze factors of the development of VVS in the blood collection room, and according to our results, use of a large number of blood collection tubes and a prolonged waiting time for phlebotomy may be risk factors for the development of VVS.
Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Authors: Tong Li , Wu Po-Yen , Phan John H. , Hassazadeh Hamid R. ,   SEQC Consortium, Jones Wendell D. , Shi Leming , Fischer Matthias , Mason Christopher E. , Li Sheng , Xu Joshua , Shi Wei , Wang Jian , Thierry-Mieg Jean , Thierry-Mieg Danielle , Hertwig Falk , Berthold Frank , Hero Barbara , Liao Yang , Smyth Gordon K. , Kreil David , Łabaj Paweł P. , Megherbi Dalila , Schroth Gary , Fang Hong , Tong Weida , Wang May D.
Published: October 2020

To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline’s performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.
Microbial community dynamics in phyto-thermotherapy baths viewed through next generation sequencing and metabolomics approach
Authors: Franciosi Elena , Narduzzi Luca , Paradiso Antonella , Carlin Silvia , Tuohy Kieran , Beretta Alberto , Mattivi Fulvio
Published: October 2020

Phyto-thermotherapy is a treatment consisting in immersing oneself in baths of self-heating alpine grass, to benefit of the heat and rich aromatic components released by the process. The aim of this study was to characterize the bacterial and fungal diversity of three phyto-thermal baths (PTB) performed in three different months, and to compare the data with the profile of the volatile organic compounds (VOCs) of the process. All the data collected showed that PTBs were structured in two stages: the first three days were characterised by an exponential rise of the temperature, a fast bacterial development, higher microbial diversity and higher concentrations of plant aliphatic hydrocarbons. The second stage was characterised by a stable high temperature, shrinkage of the microbial diversity with a predominance of few bacterial and fungi species and higher concentrations of volatiles of microbial origin. Erwinia was the dominant microbial species during the first stage and probably responsible of the self-heating process. In conclusion, PTBs has shown both similarities with common self-heating processes and important peculiarities such as the absence of pathogenic bacteria and the dominance of plant terpenoids with health characteristics among the VOCs confirming the evidence of beneficial effects in particular in the first three days.