bluuebunny/crossref_metadata_2025 huggingface dataset:
Does physical ill-health increase the risk of suicide? A census-based follow-up study of over 1 million people
Authors: Onyeka I. N. , Maguire A. , Ross E. , O'Reilly D.
Published: July 2020

Aims

Mental ill-health is a known risk factor for suicide mortality. However, the relationship between physical ill-health and suicide is less clear. This study examined the relationship between different aspects of physical ill-health and the risk of suicide death.

Methods

Data for 1 196 364 adults (aged 18 years and over) were identified from the 2011 Northern Ireland Census and linked to death registrations until the end of 2015. Multivariate logistic regression was used to construct models to test associations with likelihood ratio tests for interactions.

Results

Over one in eight individuals (13.7%) reported multimorbidity (⩾2 physical health conditions) and one in four (25.4%) identified having limitation of daily activities. During follow-up, 51 672 individuals died; 877 due to suicide. The gradient in suicide risk by number of physical conditions disappeared following adjustment for activity limitation. Individuals with a lot of activity limitation were over three times more likely to die by suicide (OR = 3.13, 95% CI 2.50–3.93) compared to those with no limitations though this was reduced to OR = 1.72 (95% CI 1.35–2.20) with adjustment for poor mental health. The relationship between activity limitation and suicide was most pronounced at younger ages (18–34 years).

Conclusions

This study suggests that it is the effect that physical illness has on a person's life, in terms of disruption to daily activity, rather than the number of conditions that predicts suicide risk, especially at younger ages. Improved awareness and better management of mental wellbeing of individuals with physical health conditions may help to reduce suicides, especially in younger people.
A Global Model for Iodine Speciation in the Upper Ocean
Authors: Wadley Martin R. , Stevens David P. , Jickells Tim D. , Hughes Claire , Chance Rosie , Hepach Helmke , Tinel Liselotte , Carpenter Lucy J.
Published: July 2020

An ocean iodine cycling model is presented, which predicts upper ocean iodine speciation. The model comprises a three‐layer advective and diffusive ocean circulation model of the upper ocean and an iodine cycling model embedded within this circulation. The two primary reservoirs of iodine are represented, iodide and iodate. Iodate is reduced to iodide in the mixed layer in association with primary production, linked by an iodine to carbon (I:C) ratio. A satisfactory model fit with observations cannot be obtained with a globally constant I:C ratio, and the best fit is obtained when the I:C ratio is dependent on sea surface temperature, increasing at low temperatures. Comparisons with observed iodide distributions show that the best model fit is obtained when oxidation of iodide back to iodate is associated with mixed layer nitrification. Sensitivity tests, where model parameters and processes are perturbed, reveal that primary productivity, mixed layer depth, oxidation, advection, surface freshwater flux, and the I:C ratio all have a role in determining surface iodide concentrations, and the timescale of iodide in the mixed layer is sufficiently long for nonlocal processes to be important. Comparisons of the modeled iodide surface field with parameterizations by other authors show good agreement in regions where observations exist but significant differences in regions without observations. This raises the question of whether the existing parameterizations are capturing the full range of processes involved in determining surface iodide and shows the urgent need for observations in regions where there are currently none.
Active Thrusting in an Intermontane Basin: The Kumysh Fault, Eastern Tian Shan
Authors: Wang Siyu , Jiao Ruohong , Ren Zhikun , Wu Chuanyong , Ren Guangxue , Zhang Huiping , Lei Qiyun
Published: July 2020

Faulting and folding on the margins of intermontane basins play important roles in accommodating the Cenozoic deformation of the Tian Shan, an intracontinental orogen in central Asia. In the eastern Tian Shan, the southern margin of the elongated Kumysh Basin is bounded by a NE dipping thrust fault, the Kumysh Fault. We report the first investigation of the slip rate of this fault, which is constrained at two sites by profiling the faulted topography and dating the abandoned alluvial fan surfaces. We obtained the topographic data using the satellite stereo imagery and dated geomorphic units using cosmogenic nuclide (10Be) exposure ages and optically stimulated luminescence methods. The results from Monte Carlo simulations of the data suggest an average dip‐slip rate of ~0.35 mm/yr on the Kumysh Fault since 50–60 ka. The “best fit” models indicate an increase after ~5 ka, which may be apparent or caused by the most recent earthquakes. Structural analysis of the displaced strata on a trench wall suggest at least 2.8 m dip offset caused by the late Holocene earthquakes, which is similar to the heights of fault scarps (1.8–2.9 m) on the second youngest alluvial fans (5.6–5.2 ka). Using the dip angle of ~25–40°, we estimate ~0.31 mm/yr shortening rate across the Kumysh Fault during the late Quaternary. By comparing our results with other estimates published in the easternmost Tian Shan, we suggest that deformation within intermontane basins may accommodate up to 50% of the total late Quaternary shortening rate between the Junggar and Tarim blocks, with only the remaining half accommodated by the main, range‐bounding thrusts.
Comparison of Thermal and Microwave Paleointensity Estimates in Specimens Displaying Non‐Ideal Behavior in Thellier‐Style Paleointensity Experiments
Authors: Grappone J. Michael , Biggin Andrew J. , Barrett Thomas J. , Hill Mimi J. , Sprain Courtney J.
Published: July 2020

Determining the strength of the ancient geomagnetic field is vital to our understanding of the core and geodynamo, but obtaining reliable measurements of the paleointensity is fraught with difficulties. Over a quarter of magnetic field strength estimates within the global paleointensity database from 0 to 5 Ma come from Hawaii. Two previous studies on the SOH1 drill core gave inconsistent, apparently method‐dependent paleointensity estimates, with an average difference of 30%. The paleointensity methods employed in the two studies differed both in demagnetization mechanism (thermal or microwave radiation) and Thellier‐style protocol (perpendicular and original Thellier protocols)—both variables that could cause the strong differences in the estimates obtained. Paleointensity experiments have therefore been conducted on 79 specimens using the previously untested combinations of thermal‐perpendicular and microwave‐original Thellier methods to analyze the effects of demagnetization mechanism and protocol in isolation. We find that, individually, neither demagnetization mechanism nor protocol entirely explains the differences in paleointensity estimates. Specifically, we found that non‐ideal multidomain‐like effects are enhanced using the original Thellier protocol (independent of demagnetization mechanism), often resulting in paleointensity overestimation. However, we also find evidence, supporting recent findings from the 1960 Kilauea lava flow, that microwave‐perpendicular experiments performed without partial thermal remanent magnetization checks can produce underestimates of the paleointensity due to unaccounted‐for sample alteration at higher microwave powers. Together, these findings support that the true paleointensities fall between the estimates previously published and emphasize the need for future studies (thermal or microwave) to use protocols with both partial thermal remanent magnetization checks and a means of detecting non‐ideal grain effects.
Drought Onset and Termination in India
Authors: Shah Deep , Mishra Vimal
Published: July 2020

Despite the implications of meteorological drought propagation to agricultural, hydrological, and groundwater droughts, the focus of previous studies has been primarily on meteorological droughts in India. We use the well‐calibrated and evaluated Variable Infiltration Capacity‐ Simple Groundwater Model (VIC‐SIMGM) to simulate soil moisture, runoff, and groundwater storage variability in India for the 1951–2016 period. The Integrated Drought Index (IDI) that combines meteorological, agricultural, hydrological, and groundwater droughts was developed for the 1951–2016 period for India. Using a spatial clustering algorithm based on the traditional interpoint distance metric, eight homogeneous clusters based on IDI were identified. The majority of clusters in India experience the onset and termination of droughts during the summer monsoon season (June–September). The analysis of moisture back trajectories using the Hybrid Single‐Particle Lagrangian Integrated Trajectory (HYSPLIT) model showed that the Arabian Sea and Bay of Bengal are the two major moisture sources for the identified clusters in India. We performed the Empirical Orthogonal Function (EOF) and Maximum Covariance Analysis (MCA) using monthly IDI and Sea Surface Temperature (SST) to evaluate the influence of long‐term climate variability on droughts in India. Droughts based on 1‐month IDI that affect a majority of drought clusters are associated with the positive phase of El Nino Southern Oscillations (ENSO) and Indian Ocean Dipole (IOD). On the other hand, drought clusters in the Gangetic Plain and peninsular India are affected by the SST warming over the Indian Ocean. Overall, drought clusters based on IDI, their moisture source, and large‐scale teleconnection can assist in drought management and assessment in India.
Efficient full-path optical calculation of scalar and vector diffraction using the Bluestein method
Authors: Hu Yanlei , Wang Zhongyu , Wang Xuewen , Ji Shengyun , Zhang Chenchu , Li Jiawen , Zhu Wulin , Wu Dong , Chu Jiaru
Published: July 2020

Efficient calculation of the light diffraction in free space is of great significance for tracing electromagnetic field propagation and predicting the performance of optical systems such as microscopy, photolithography, and manipulation. However, existing calculation methods suffer from low computational efficiency and poor flexibility. Here, we present a fast and flexible calculation method for computing scalar and vector diffraction in the corresponding optical regimes using the Bluestein method. The computation time can be substantially reduced to the sub-second level, which is 105 faster than that achieved by the direct integration approach (~hours level) and 102 faster than that achieved by the fast Fourier transform method (~minutes level). The high efficiency facilitates the ultrafast evaluation of light propagation in diverse optical systems. Furthermore, the region of interest and the sampling numbers can be arbitrarily chosen, endowing the proposed method with superior flexibility. Based on these results, full-path calculation of a complex optical system is readily demonstrated and verified by experimental results, laying a foundation for real-time light field analysis for realistic optical implementation such as imaging, laser processing, and optical manipulation.
Suppressing DRP1-mediated mitochondrial fission and mitophagy increases mitochondrial apoptosis of hepatocellular carcinoma cells in the setting of hypoxia
Authors: Lin Xia-Hui , Qiu Bai-Quan , Ma Min , Zhang Rui , Hsu Shu-Jung , Liu Hua-Hua , Chen Jun , Gao Dong-Mei , Cui Jie-Feng , Ren Zheng-Gang , Chen Rong-Xin
Published: July 2020

Transarterial embolization/transarterial chemoembolization (TAE/TACE) is the acceptable palliative treatment for hepatocellular carcinoma (HCC), mainly through ischemic necrosis induced by arterial embolization. However, how HCC cells survive under such ischemic hypoxic condition remains unclear, which can be exploited to potentiate TAE/TACE treatment. We hypothesized that targeting mitophagy can increase HCC cell apoptosis during hypoxia. HCC cells were subjected to hypoxia and then mitophagy was quantified. The role of dynamin-related protein 1 (DRP1) in hypoxia-induced HCC mitophagy was determined. Moreover, the synergistic effect of hypoxia and DRP1 inhibitor on HCC apoptosis was assessed in vitro and in vivo. Clinical association between DRP1 expression and outcome for HCC patients was validated. HCC cells that survived hypoxia showed significantly increased DRP1-mediated mitochondrial fission and mitophagy compared with cells in normoxia. Hypoxia induced mitophagy in surviving HCC cells by enhancing DRP1 expression and its translocation into the mitochondria and excessive mitochondrial fission into fragments. Blocking the DRP1 heightened the possibility of hypoxic cytotoxicity to HCC cells due to impaired mitophagy and increased the mitochondrial apoptosis, which involved decreased in mitochondrial membrane potential and mitochondrial release of apoptosis-inducing factor and cytochrome c. Additionally, DRP1 inhibitor Mdivi-1 suppressed the in vivo growth of hypoxia-exposed HCC cells. High expression of DRP1 was significantly associated with shorter survival in HCC patients. In conclusion, our results demonstrate that blocking DRP1-mediated mitochondrial fission and mitophagy increases the incidence of mitochondrial apoptosis of HCC cells during hypoxia, suggesting the new approach of targeting mitophagy to potentiate TAE/TACE.
Mutations in sphingolipid metabolism genes are associated with ADHD
Authors: Henriquez-Henriquez Marcela , Acosta Maria T. , Martinez Ariel F. , Vélez Jorge I. , Lopera Francisco , Pineda David , Palacio Juan D. , Quiroga Teresa , Worgall Tilla S. , Deckelbaum Richard J. , Mastronardi Claudio , Molina Brooke S. G. ,   the MTA Cooperative Group, Vitiello Benedetto , Severe Joanne B. , Jensen Peter S. , Arnold L. Eugene , Hoagwood Kimberly , Richters John , Vereen Donald R. , Hinshaw Stephen P. , Elliott Glen R. , Wells Karen C. , Epstein Jeffery N. , Murray Desiree W. , Conners C. Keith , March John , Swanson James , Wigal Timothy , Cantwell Dennis P. , Abikoff Howard B. , Hechtman Lily , Greenhill Laurence L. , Newcorn Jeffrey H. , Molina Brooke S. G. , Hoza Betsy , Pelham William E. , Gibbons Robert D. , Marcus Sue , Hur Kwan , Kraemer Helena C. , Hanley Thomas , Stern Karen , Arcos-Burgos Mauricio , Muenke Maximilian
Published: July 2020

Attention deficit hyperactivity disorder (ADHD) is the most prevalent neurodevelopmental disorder in children, with genetic factors accounting for 75–80% of the phenotypic variance. Recent studies have suggested that ADHD patients might present with atypical central myelination that can persist into adulthood. Given the essential role of sphingolipids in myelin formation and maintenance, we explored genetic variation in sphingolipid metabolism genes for association with ADHD risk. Whole-exome genotyping was performed in three independent cohorts from disparate regions of the world, for a total of 1520 genotyped subjects. Cohort 1 (MTA (Multimodal Treatment study of children with ADHD) sample, 371 subjects) was analyzed as the discovery cohort, while cohorts 2 (Paisa sample, 298 subjects) and 3 (US sample, 851 subjects) were used for replication. A set of 58 genes was manually curated based on their roles in sphingolipid metabolism. A targeted exploration for association between ADHD and 137 markers encoding for common and rare potentially functional allelic variants in this set of genes was performed in the screening cohort. Single- and multi-locus additive, dominant and recessive linear mixed-effect models were used. During discovery, we found statistically significant associations between ADHD and variants in eight genes (GALC,CERS6,SMPD1,SMPDL3B,CERS2,FADS3,ELOVL5, andCERK). Successful local replication for associations with variants inGALC,SMPD1, andCERS6was demonstrated in both replication cohorts. Variants rs35785620, rs143078230, rs398607, and rs1805078, associated with ADHD in the discovery or replication cohorts, correspond to missense mutations with predicted deleterious effects. Expression quantitative trait loci analysis revealed an association between rs398607 and increasedGALCexpression in the cerebellum.
Tauopathy in the young autistic brain: novel biomarker and therapeutic target
Authors: Grigg Iris , Ivashko-Pachima Yanina , Hait Tom Aharon , Korenková Vlasta , Touloumi Olga , Lagoudaki Roza , Van Dijck Anke , Marusic Zlatko , Anicic Mirna , Vukovic Jurica , Kooy R. Frank , Grigoriadis Nikolaos , Gozes Illana
Published: July 2020

Given our recent discovery of somatic mutations in autism spectrum disorder (ASD)/intellectual disability (ID) genes in postmortem aged Alzheimer’s disease brains correlating with increasing tauopathy, it is important to decipher if tauopathy is underlying brain imaging results of atrophy in ASD/ID children. We concentrated on activity-dependent neuroprotective protein (ADNP), a prevalent autism gene. The unique availability of multiple postmortem brain sections of a 7-year-old male, heterozygous for ADNP de novo mutation c.2244Adup/p.His559Glnfs*3 allowed exploration of tauopathy, reflecting on a general unexplored mechanism. The tested subject exhibited autism, fine motor delays, severe intellectual disability and seizures. The patient died after multiple organ failure following liver transplantation. To compare to other ADNP syndrome mutations, immortalized lymphoblastoid cell lines from three different patients (including ADNP p.Arg216*, p.Lys408Valfs*31, and p.Tyr719* heterozygous dominant mutations) and a control were subjected to RNA-seq. Immunohistochemistry, high-throughput gene expression profiles in numerous postmortem tissues followed. Comparisons to a control brain and to extensive datasets were used. Live cell imaging investigated Tau-microtubule interaction, protecting against tauopathy. Extensive child brain tauopathy paralleled by multiple gene expression changes was discovered. Tauopathy was explained by direct mutation effects on Tau-microtubule interaction and correction by the ADNP active snippet NAP. Significant pathway changes (empirical P value < 0.05) included over 100 genes encompassing neuroactive ligand–receptor and cytokine–cytokine receptor interaction, MAPK and calcium signaling, axon guidance and Wnt signaling pathways. Changes were also seen in steroid biosynthesis genes, suggesting sex differences. Selecting the most affected genes by the ADNP mutations for gene expression analysis, in multiple postmortem tissues, identified Tau (MAPT)-gene-related expression changes compared with extensive normal gene expression (RNA-seq) databases. ADNP showed relatively reduced expression in the ADNP syndrome cerebellum, which was also observed for 25 additional genes (representing >50% of the tested genes), including NLGN1, NLGN2, PAX6, SMARCA4, and SNAP25, converging on nervous system development and tauopathy. NAP provided protection against mutated ADNP disrupted Tau-microtubule association. In conclusion, tauopathy may explain brain-imaging findings in ADNP syndrome children and may provide a new direction for the development of tauopathy protecting drug candidates like NAP in ASD/ID.
In vivo human brain expression of histone deacetylases in bipolar disorder
Authors: Tseng Chieh-En J. , Gilbert Tonya M. , Catanese Mary C. , Hightower Baileigh G. , Peters Amy T. , Parmar Anjali J. , Kim Minhae , Wang Changning , Roffman Joshua L. , Brown Hannah E. , Perlis Roy H. , Zürcher Nicole R. , Hooker Jacob M.
Published: July 2020

The etiology of bipolar disorder (BD) is unknown and the neurobiological underpinnings are not fully understood. Both genetic and environmental factors contribute to the risk of BD, which may be linked through epigenetic mechanisms, including those regulated by histone deacetylase (HDAC) enzymes. This study measures in vivo HDAC expression in individuals with BD for the first time using the HDAC-specific radiotracer [11C]Martinostat. Eleven participants with BD and 11 age- and sex-matched control participants (CON) completed a simultaneous magnetic resonance – positron emission tomography (MR-PET) scan with [11C]Martinostat. Lower [11C]Martinostat uptake was found in the right amygdala of BD compared to CON. We assessed uptake in the dorsolateral prefrontal cortex (DLPFC) to compare previous findings of lower uptake in the DLPFC in schizophrenia and found no group differences in BD. Exploratory whole-brain voxelwise analysis showed lower [11C]Martinostat uptake in the bilateral thalamus, orbitofrontal cortex, right hippocampus, and right amygdala in BD compared to CON. Furthermore, regional [11C]Martinostat uptake was associated with emotion regulation in BD in fronto-limbic areas, which aligns with findings from previous structural, functional, and molecular neuroimaging studies in BD. Regional [11C]Martinostat uptake was associated with attention in BD in fronto-parietal and temporal regions. These findings indicate a potential role of HDACs in BD pathophysiology. In particular, HDAC expression levels may modulate attention and emotion regulation, which represent two core clinical features of BD.
Capsaicin consumption reduces brain amyloid-beta generation and attenuates Alzheimer’s disease-type pathology and cognitive deficits in APP/PS1 mice
Authors: Wang Jun , Sun Bin-Lu , Xiang Yang , Tian Ding-Yuan , Zhu Chi , Li Wei-Wei , Liu Yu-Hui , Bu Xian-Le , Shen Lin-Lin , Jin Wang-Sheng , Wang Zhen , Zeng Gui-Hua , Xu Wei , Chen Li-Yong , Chen Xiao-Wei , Hu Zhian , Zhu Zhi-Ming , Song Weihong , Zhou Hua-Dong , Yu Jin-Tai , Wang Yan-Jiang
Published: July 2020

Alzheimer’s disease (AD) is the most common cause of age-related dementia and is currently incurable. The failures of current clinical trials and the establishment of modifiable risk factors have shifted the AD intervention from treatment to prevention in the at-risk population. Previous studies suggest that there is a geographic overlap between AD incidence and spicy food consumption. We previously reported that capsaicin-rich diet consumption was associated with better cognition and lower serum Amyloid-beta (Aβ) levels in people aged 40 years and over. In the present study, we found that intake of capsaicin, the pungent ingredient in chili peppers, reduced brain Aβ burden and rescued cognitive decline in APP/PS1 mice. Our in vivo and in vitro studies revealed that capsaicin shifted Amyloid precursor protein (APP) processing towards α-cleavage and precluded Aβ generation by promoting the maturation of a disintegrin and metalloproteinase 10 (ADAM10). We also found that capsaicin alleviated other AD-type pathologies, such as tau hyperphosphorylation, neuroinflammation and neurodegeneration. The present study suggests that capsaicin is a potential therapeutic candidate for AD and warrants clinical trials on chili peppers or capsaicin as dietary supplementation for the prevention and treatment of AD.
Considerations for the treatment of pancreatic cancer during the COVID-19 pandemic: the UK consensus position
Authors: Jones Christopher M. , Radhakrishna Ganesh , Aitken Katharine , Bridgewater John , Corrie Pippa , Eatock Martin , Goody Rebecca , Ghaneh Paula , Good James , Grose Derek , Holyoake Daniel , Hunt Arabella , Jamieson Nigel B. , Palmer Daniel H. , Soonawalla Zahir , Valle Juan W. , Hawkins Maria A. , Mukherjee Somnath
Published: July 2020

The coronavirus disease 2019 (COVID-19) pandemic epicentre has moved to the USA and Europe, where it is placing unprecedented demands on healthcare resources and staff availability. These service constraints, coupled with concerns relating to an increased incidence and severity of COVID-19 among patients with cancer, should lead to re-consideration of the risk–benefit balance for standard treatment pathways. This is of particular importance to pancreatic cancer, given that standard diagnostic modalities such as endoscopy may be restricted, and that disease biology precludes significant delays in treatment. In light of this, we sought consensus from UK clinicians with an interest in pancreatic cancer for management approaches that would minimise patient risk and accommodate for healthcare service restrictions. The outcomes are described here and include recommendations for treatment prioritisation, strategies to bridge to later surgical resection in resectable disease and factors that modify the risk–benefit balance for treatment in the resectable through to the metastatic settings. Priority is given to strategies that limit hospital visits, including through the use of hypofractionated precision radiotherapy and chemoradiotherapy treatment approaches.
Expanding the phenotype associated to KMT2A variants: overlapping clinical signs between Wiedemann–Steiner and Rubinstein–Taybi syndromes
Authors: Di Fede Elisabetta , Massa Valentina , Augello Bartolomeo , Squeo Gabriella , Scarano Emanuela , Perri Anna Maria , Fischetto Rita , Causio Francesco Andrea , Zampino Giuseppe , Piccione Maria , Curridori Elena , Mazza Tommaso , Castellana Stefano , Larizza Lidia , Ghelma Filippo , Colombo Elisa Adele , Gandini Maria Chiara , Castori Marco , Merla Giuseppe , Milani Donatella , Gervasini Cristina
Published: July 2020

Lysine-specific methyltransferase 2A (KMT2A) is responsible for methylation of histone H3 (K4H3me) and contributes to chromatin remodeling, acting as “writer” of the epigenetic machinery. Mutations in KMT2A were first reported in Wiedemann–Steiner syndrome (WDSTS). More recently, KMT2A variants have been described in probands with a specific clinical diagnosis comprised in the so-called chromatinopathies. Such conditions, including WDSTS, are a group of overlapping disorders caused by mutations in genes coding for the epigenetic machinery. Among them, Rubinstein–Taybi syndrome (RSTS) is mainly caused by heterozygous pathogenic variants in CREBBP or EP300. In this work, we used next generation sequencing (either by custom-made panel or by whole exome) to identify alternative causative genes in individuals with a RSTS-like phenotype negative to CREBBP and EP300 mutational screening. In six patients we identified different novel unreported variants in KMT2A gene. The identified variants are de novo in at least four out of six tested individuals and all of them display some typical RSTS phenotypic features but also WDSTS specific signs. This study reinforces the concept that germline variants affecting the epigenetic machinery lead to a shared molecular effect (alteration of the chromatin state) determining superimposable clinical conditions.
A global dataset of surface water and groundwater salinity measurements from 1980–2019
Authors: Thorslund Josefin , van Vliet Michelle T. H.
Published: July 2020

Salinization of freshwater resources is a growing water quality challenge, which may negatively impact both sectoral water-use and food security, as well as biodiversity and ecosystem services. Although monitoring of salinity is relatively common compared to many other water quality parameters, no compilation and harmonisation of available datasets for both surface and groundwater components have been made yet at the global scale. Here, we present a new global salinity database, compiled from electrical conductivity (EC) monitoring data of both surface water (rivers, lakes/reservoirs) and groundwater locations over the period 1980–2019. The data were assembled from a range of sources, including local to global salinity databases, governmental organizations, river basin management commissions and water development boards. Our resulting database comprises more than 16.3 million measurements from 45,103 surface water locations and 208,550 groundwater locations around the world. This database could provide new opportunities for meta-analyses of salinity levels of water resources, as well as for addressing data and model-driven questions related to historic and future salinization patterns and impacts.
GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies
Authors: Větrovský Tomáš , Morais Daniel , Kohout Petr , Lepinay Clémentine , Algora Camelia , Awokunle Hollá Sandra , Bahnmann Barbara Doreen , Bílohnědá Květa , Brabcová Vendula , D’Alò Federica , Human Zander Rainier , Jomura Mayuko , Kolařík Miroslav , Kvasničková Jana , Lladó Salvador , López-Mondéjar Rubén , Martinović Tijana , Mašínová Tereza , Meszárošová Lenka , Michalčíková Lenka , Michalová Tereza , Mundra Sunil , Navrátilová Diana , Odriozola Iñaki , Piché-Choquette Sarah , Štursová Martina , Švec Karel , Tláskal Vojtěch , Urbanová Michaela , Vlk Lukáš , Voříšková Jana , Žifčáková Lucia , Baldrian Petr
Published: July 2020

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface athttps://globalfungi.com. The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
Japan prefectural emission accounts and socioeconomic data 2007 to 2015
Authors: Long Yin , Yoshida Yoshikuni , Zhang Haoran , Zheng Heran , Shan Yuli , Guan Dabo
Published: July 2020

In the wake of the Fukushima nuclear disaster, Japan largely moved away from nuclear power generation and turned back towards an energy sector dominated by fossil fuels. As a result, the pace towards reaching emission reduction targets has largely slowed down. This situation indicates that higher emissions will continue to be generated if there is no appropriate and efficient measurement implemented to bridge the energy demand gap. To contribute adequate mitigation policies, a detailed inventory of both CO2 emissions and socioeconomic factors, both at the national and regional level, should be issued. Thereby, this work contributes to a time-series emission with a record of 47 prefectures in Japan as well as their associated socioeconomic features. The compiled emission inventory is based on three major fossil fuels and 26 sectors with careful emission allocations for regional electricity generation. This dataset is uniformly formatted and can be expected to provide vital information to set regional reduction allowances and sectoral reduction priorities.
Author Correction: Employing fingerprinting of medicinal plants by means of LC-MS and machine learning for species identification task
Authors: Kharyuk Pavel , Nazarenko Dmitry , Oseledets Ivan , Rodin Igor , Shpigun Oleg , Tsitsilin Andrey , Lavrentyev Mikhail
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Evaluation of various commodities for the development of the yellow mealworm, Tenebrio molitor
Authors: Rumbos Christos I. , Karapanagiotidis Ioannis T. , Mente Eleni , Psofakis Pier , Athanassiou Christos G.
Published: July 2020

We evaluated the suitability of forty-four commodities (i.e., cereal flours and meals, non-flour, cereal commodities, legumes and various commodities of vegetative and animal origin) as oviposition and feeding substrates for the yellow mealworm,Tenebrio molitor. ΤenT. molitoradults were introduced in plastic vials containing 30 g of each commodity. At the end of the 1 week period, all adults were removed, and mortality was determined; then the vials were further incubated for additional 9 weeks. After this time, the vials were opened, and the larvae of each vial were separated from the feeding substrate, counted and weighed as a group. The efficiency of ingested food conversion was calculated for each substrate. Finally, proximate composition was calculated to determine the nutrient components of the feeding substrates tested and theT. molitorlarvae that fed on various selected substrates. In general, adult reproduction was clearly favoured by most amylaceous substrates tested, which was in contrast to the tested legumes on which fewer offspring were produced. Similar effects were observed for larval development. Feeding on selected substrates exerted an impact on the nutrient composition ofT. molitorlarvae, with a high protein content of the substrate usually resulting in a high protein content of the larvae.
Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing
Authors: Paris Mathilde , Boyer Roxane , Jaenichen Rita , Wolf Jochen , Karageorgi Marianthi , Green Jack , Cagnon Mathilde , Parinello Hugues , Estoup Arnaud , Gautier Mathieu , Gompel Nicolas , Prud’homme Benjamin
Published: July 2020

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of theD. suzukiigenome and to annotate it in a way that facilitates comparisons withD. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-qualityD. suzukiigenome assembly. It is one of the largestDrosophilagenomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings theD. suzukiistrain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to studyD. suzukii.
A machine learning framework for computationally expensive transient models
Authors: Kumar Prashant , Sinha Kushal , Nere Nandkishor K. , Shin Yujin , Ho Raimundo , Mlinar Laurie B. , Sheikh Ahmad Y.
Published: July 2020

Transient simulations of dynamic systems, using physics-based scientific computing tools, are practically limited by availability of computational resources and power. While the promise of machine learning has been explored in a variety of scientific disciplines, its application in creation of a framework for computationally expensive transient models has not been fully explored. Here, we present an ensemble approach where one such computationally expensive tool, discrete element method, is combined with time-series forecasting via auto regressive integrated moving average and machine learning methods to simulate a complex pharmaceutical problem: development of an agitation protocol in an agitated filter dryer to ensure uniform solid bed mixing. This ensemble approach leads to a significant reduction in the computational burden, while retaining model accuracy and performance, practically rendering simulations possible. The developed machine-learning model shows good predictability and agreement with the literature, demonstrating its tremendous potential in scientific computing.
Quantum teleportation mediated by surface plasmon polariton
Authors: Jiang Xin-He , Chen Peng , Qian Kai-Yi , Chen Zhao-Zhong , Xu Shu-Qi , Xie Yu-Bo , Zhu Shi-Ning , Ma Xiao-Song
Published: July 2020

Surface plasmon polaritons (SPPs) are collective excitations of free electrons propagating along a metal-dielectric interface. Although some basic quantum properties of SPPs, such as the preservation of entanglement, the wave-particle duality of a single plasmon, the quantum interference of two plasmons, and the verification of entanglement generation, have been shown, more advanced quantum information protocols have yet to be demonstrated with SPPs. Here, we experimentally realize quantum state teleportation between single photons and SPPs. To achieve this, we use polarization-entangled photon pairs, coherent photon–plasmon–photon conversion on a metallic subwavelength hole array, complete Bell-state measurements and an active feed-forward technique. The results of both quantum state and quantum process tomography confirm the quantum nature of the SPP mediated teleportation. An average state fidelity of $$0.889\pm 0.004$$

0.889
±
0.004

and a process fidelity of $$0.820\pm 0.005$$

0.820
±
0.005

, which are well above the classical limit, are achieved. Our work shows that SPPs may be useful for realizing complex quantum protocols in a photonic-plasmonic hybrid quantum network.
Fabrication of 3D binder-free graphene NiO electrode for highly stable supercapattery
Authors: Agudosi Elochukwu Stephen , Abdullah Ezzat Chan , Numan Arshid , Mubarak Nabisab Mujawar , Aid Siti Rahmah , Benages-Vilau Raúl , Gómez-Romero Pedro , Khalid Mohammad , Omar Nurizan
Published: July 2020

Electrochemical stability of energy storage devices is one of their major concerns. Polymeric binders are generally used to enhance the stability of the electrode, but the electrochemical performance of the device is compromised due to the poor conductivity of the binders. Herein, 3D binder-free electrode based on nickel oxide deposited on graphene (G-NiO) was fabricated by a simple two-step method. First, graphene was deposited on nickel foam via atmospheric pressure chemical vapour deposition followed by electrodeposition of NiO. The structural and morphological analyses of the fabricated G-NiO electrode were conducted through Raman spectroscopy, X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), and energy dispersive X-ray spectroscopy (EDS). XRD and Raman results confirmed the successful growth of high-quality graphene on nickel foam. FESEM images revealed the sheet and urchin-like morphology of the graphene and NiO, respectively. The electrochemical performance of the fabricated electrode was evaluated through cyclic voltammetry (CV), galvanostatic charge–discharge (GCD), and electrochemical impedance spectroscopy (EIS) in aqueous solution at room temperature. The G-NiO binder-free electrode exhibited a specific capacity of ≈ 243 C g−1 at 3 mV s−1 in a three-electrode cell. A two-electrode configuration of G-NiO//activated charcoal was fabricated to form a hybrid device (supercapattery) that operated in a stable potential window of 1.4 V. The energy density and power density of the asymmetric device measured at a current density of 0.2 A g−1 were estimated to be 47.3 W h kg−1 and 140 W kg−1, respectively. Additionally, the fabricated supercapattery showed high cyclic stability with 98.7% retention of specific capacity after 5,000 cycles. Thus, the proposed fabrication technique is highly suitable for large scale production of highly stable and binder-free electrodes for electrochemical energy storage devices.
Genome wide association analysis of a stemborer egg induced “call-for-help” defence trait in maize
Authors: Tamiru Amanuel , Paliwal Rajneesh , Manthi Samuel J. , Odeny Damaris A. , Midega Charles A. O. , Khan Zeyaur R. , Pickett John A. , Bruce Toby J. A.
Published: July 2020

Tritrophic interactions allow plants to recruit natural enemies for protection against herbivory. Here we investigated genetic variability in induced responses to stemborer egg-laying in maize Zea mays (L.) (Poaceae). We conducted a genome wide association study (GWAS) of 146 maize genotypes comprising of landraces, inbred lines and commercial hybrids. Plants were phenotyped in bioassays measuring parasitic wasp Cotesia sesamiae (Cameron) (Hymenoptera: Braconidae) attraction to volatiles collected from plants exposed to stemborer Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) eggs. Genotyping-by-sequencing was used to generate maize germplasm SNP data for GWAS. The egg-induced parasitoid attraction trait was more common in landraces than in improved inbred lines and hybrids. GWAS identified 101 marker-trait associations (MTAs), some of which were adjacent to genes involved in the JA-defence pathway (opr7, aos1, 2, 3), terpene biosynthesis (fps3, tps2, 3, 4, 5, 7, 9, 10), benzoxazinone synthesis (bx7, 9) and known resistance genes (e.g. maize insect resistance 1, mir1). Intriguingly, there was also association with a transmembrane protein kinase that may function as a receptor for the egg elicitor and other genes implicated in early plant defence signalling. We report maize genomic regions associated with indirect defence and provide a valuable resource for future studies of tritrophic interactions in maize. The markers identified may facilitate selection of indirect defence by maize breeders.
Using diffusion tensor imaging to detect cortical changes in fronto-temporal dementia subtypes
Authors: Torso M. , Bozzali M. , Cercignani M. , Jenkinson M. , Chance S. A.
Published: July 2020

Fronto-temporal dementia (FTD) is a common type of presenile dementia, characterized by a heterogeneous clinical presentation that includes three main subtypes: behavioural-variant FTD, non-fluent/agrammatic variant primary progressive aphasia and semantic variant PPA. To better understand the FTD subtypes and develop more specific treatments, correct diagnosis is essential. This study aimed to test the discrimination power of a novel set of cortical Diffusion Tensor Imaging measures (DTI), on FTD subtypes. A total of 96 subjects with FTD and 84 healthy subjects (HS) were included in the study. A “selection cohort” was used to determine the set of features (measurements) and to use them to select the “best” machine learning classifier from a range of seven main models. The selected classifier was trained on a “training cohort” and tested on a third cohort (“test cohort”). The classifier was used to assess the classification power for binary (HS vs. FTD), and multiclass (HS and FTD subtypes) classification problems. In the binary classification, one of the new DTI features obtained the highest accuracy (85%) as a single feature, and when it was combined with other DTI features and two other common clinical measures (grey matter fraction and MMSE), obtained an accuracy of 88%. The new DTI features can distinguish between HS and FTD subgroups with an accuracy of 76%. These results suggest that DTI measures could support differential diagnosis in a clinical setting, potentially improve efficacy of new innovative drug treatments through effective patient selection, stratification and measurement of outcomes.
Prevalence of susceptibility patterns of opportunistic bacteria in line with CLSI or EUCAST among Haemophilus parainfluenzae isolated from respiratory microbiota
Authors: Kosikowska Urszula , Andrzejczuk Sylwia , Grywalska Ewelina , Chwiejczak Edyta , Winiarczyk Stanisław , Pietras-Ożga Dorota , Stępień-Pyśniak Dagmara
Published: July 2020

The application of CLSI and EUCAST guidelines led to many discrepancies. Various doubts have already appeared in preliminary stages of microbiological diagnostics of Haemophilus spp. A total of 87 H. parainfluenzae isolates were obtained from throat or nasopharyngeal swabs from adults 18 to 70 years old, both healthy volunteers and patients with chronic diseases between 2013 to 2015 in eastern Poland. Haemophilus spp. were identified by colony morphology, Gram-staining, API NH and MALDI-TOF MS technique. Both susceptibility to various antimicrobials and phenotypes of Haemophilus spp. resistance to beta-lactams were determined. Statistically significant association between applied guidelines and drug resistance patterns were observed to as follows: ampicillin, cefuroxime, cefotaxime, amoxicillin-clavulanate, azithromycin, tetracycline and trimethoprim-sulfamethoxazole. Resistance phenotypes according to CLSI vs. EUCAST were as follows: 3.4% vs. 8.0% for BLNAR and 6.9% vs. 19.5% for BLPACR isolates. In conclusion, this is the first study that reports comparative analysis of drug susceptibility interpretation using CLSI and EUCAST of haemophili rods from human respiratory microbiota in Poland. In case of susceptible, increased exposure (formerly intermediate) category of susceptibility within H. parainfluenzae isolates we have observed EUCAST as more restrictive than CLSI. Moreover, BLNAI and BLPAI phenotype isolates have been observed, as well as BLPBR using only CLSI or EUCAST guidelines, respectively.
Contamination of wounds with fecal bacteria in immuno-suppressed mice
Authors: Karner Lisa , Drechsler Susanne , Metzger Magdalena , Slezak Paul , Zipperle Johannes , Pinar Guadalupe , Sterflinger Katja , Leisch Friedrich , Grillari Johannes , Osuchowski Marcin , Dungel Peter
Published: July 2020

Immunocompromised patients are predisposed to chronically infected wounds. Especially ulcers in the dorsal region often experience secondary polymicrobial infections. However, current wound infection models mostly use single-strain bacteria. To mimic clinically occurring infections caused by fecal contamination in immunocompromised/immobile patients, which differ significantly from single-strain infections, the present study aimed at the establishment of a new mouse model using infection by fecal bacteria. Dorsal circular excision wounds in immunosuppressed mice were infected with fecal slurry solution in several dilutions up to 1:8,000. Impact of immunosuppressor, bacterial load and timing on development of wound infections was investigated. Wounds were analyzed by scoring, 3D imaging and swab analyses. Autofluorescence imaging was not successful. Dose-finding of cyclophosphamide-induced immunosuppression was necessary for establishment of bacterial wound infections. Infection with fecal slurry diluted 1:166 to 1:400 induced significantly delayed wound healing (p < 0.05) without systemic reactions. Swab analyses post-infection matched the initial polymicrobial suspension. The customized wound score confirmed significant differences between the groups (p < 0.05). Here we report the establishment of a simple, new mouse model for clinically occurring wound infections by fecal bacteria and the evaluation of appropriate wound analysis methods. In the future, this model will provide a suitable tool for the investigation of complex microbiological interactions and evaluation of new therapeutic approaches.