bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transition metal migration and O2 formation underpin voltage hysteresis in oxygen-redox disordered rocksalt cathodes
Authors: McColl Kit , House Robert A. , Rees Gregory J. , Squires Alexander G. , Coles Samuel W. , Bruce Peter G. , Morgan Benjamin J. , Islam M. Saiful 
Published: September 2022

AbstractLithium-rich disordered rocksalt cathodes display high capacities arising from redox chemistry on both transition-metal ions (TM-redox) and oxygen ions (O-redox), making them promising candidates for next-generation lithium-ion batteries. However, the atomic-scale mechanisms governing O-redox behaviour in disordered structures are not fully understood. Here we show that, at high states of charge in the disordered rocksalt Li2MnO2F, transition metal migration is necessary for the formation of molecular O2 trapped in the bulk. Density functional theory calculations reveal that O2 is thermodynamically favoured over other oxidised O species, which is confirmed by resonant inelastic X-ray scattering data showing only O2 forms. When O-redox involves irreversible Mn migration, this mechanism results in a path-dependent voltage hysteresis between charge and discharge, commensurate with the hysteresis observed electrochemically. The implications are that irreversible transition metal migration should be suppressed to reduce the voltage hysteresis that afflicts O-redox disordered rocksalt cathodes.
Chiral monoterpenes reveal forest emission mechanisms and drought responses
Authors: Byron Joseph , Kreuzwieser Juergen , Purser Gemma , van Haren Joost , Ladd S. Nemiah , Meredith Laura K. , Werner Christiane , Williams Jonathan 
Published: September 2022

AbstractMonoterpenes (C10H16) are emitted in large quantities by vegetation to the atmosphere (>100 TgC year−1), where they readily react with hydroxyl radicals and ozone to form new particles and, hence, clouds, affecting the Earth’s radiative budget and, thereby, climate change1–3. Although most monoterpenes exist in two chiral mirror-image forms termed enantiomers, these (+) and (−) forms are rarely distinguished in measurement or modelling studies4–6. Therefore, the individual formation pathways of monoterpene enantiomers in plants and their ecological functions are poorly understood. Here we present enantiomerically separated atmospheric monoterpene and isoprene data from an enclosed tropical rainforest ecosystem in the absence of ultraviolet light and atmospheric oxidation chemistry, during a four-month controlled drought and rewetting experiment7. Surprisingly, the emitted enantiomers showed distinct diel emission peaks, which responded differently to progressive drying. Isotopic labelling established that vegetation emitted mainly de novo-synthesized (−)-α-pinene, whereas (+)-α-pinene was emitted from storage pools. As drought progressed, the source of (−)-α-pinene emissions shifted to storage pools, favouring cloud formation. Pre-drought mixing ratios of both α-pinene enantiomers correlated better with other monoterpenes than with each other, indicating different enzymatic controls. These results show that enantiomeric distribution is key to understanding the underlying processes driving monoterpene emissions from forest ecosystems and predicting atmospheric feedbacks in response to climate change.
Brainstem ADCYAP1+ neurons control multiple aspects of sickness behaviour
Authors: Ilanges Anoj , Shiao Rani , Shaked Jordan , Luo Ji-Dung , Yu Xiaofei , Friedman Jeffrey M. 
Published: September 2022

AbstractInfections induce a set of pleiotropic responses in animals, including anorexia, adipsia, lethargy and changes in temperature, collectively termed sickness behaviours1. Although these responses have been shown to be adaptive, the underlying neural mechanisms have not been elucidated2–4. Here we use of a set of unbiased methodologies to show that a specific subpopulation of neurons in the brainstem can control the diverse responses to a bacterial endotoxin (lipopolysaccharide (LPS)) that potently induces sickness behaviour. Whole-brain activity mapping revealed that subsets of neurons in the nucleus of the solitary tract (NTS) and the area postrema (AP) acutely express FOS after LPS treatment, and we found that subsequent reactivation of these specific neurons in FOS2A-iCreERT2 (also known as TRAP2) mice replicates the behavioural and thermal component of sickness. In addition, inhibition of LPS-activated neurons diminished all of the behavioural responses to LPS. Single-nucleus RNA sequencing of the NTS–AP was used to identify LPS-activated neural populations, and we found that activation of ADCYAP1+ neurons in the NTS–AP fully recapitulates the responses elicited by LPS. Furthermore, inhibition of these neurons significantly diminished the anorexia, adipsia and locomotor cessation seen after LPS injection. Together these studies map the pleiotropic effects of LPS to a neural population that is both necessary and sufficient for canonical elements of the sickness response, thus establishing a critical link between the brain and the response to infection.
Geographical characterisation of British urban form and function using the spatial signatures framework
Authors: Fleischmann Martin , Arribas-Bel Daniel 
Published: September 2022

AbstractThe spatial arrangement of the building blocks that make up cities matters to understand the rules directing their dynamics. Our study outlines the development of the national open-source classification of space according to its form and function into a single typology. We create a bespoke granular spatial unit, the enclosed tessellation, and measure characters capturing its form and function within a relevant spatial context. Using K-Means clustering of individual enclosed tessellation cells, we generate a classification of space for the whole of Great Britain. Contiguous enclosed tessellation cells belonging to the same class are merged forming spatial signature geometries and their typology. We identify 16 distinct types of spatial signatures stretching from wild countryside, through various kinds of suburbia to types denoting urban centres according to their regional importance. The open data product presented here has the potential to serve as boundary delineation for other researchers interested in urban environments and policymakers looking for a unique perspective on cities and their structure.
A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns
Authors: Butt Ahmad Hassan , Alkhalifah Tamim , Alturise Fahad , Khan Yaser Daanial 
Published: September 2022

AbstractEnhancers regulate gene expression, by playing a crucial role in the synthesis of RNAs and proteins. They do not directly encode proteins or RNA molecules. In order to control gene expression, it is important to predict enhancers and their potency. Given their distance from the target gene, lack of common motifs, and tissue/cell specificity, enhancer regions are thought to be difficult to predict in DNA sequences. Recently, a number of bioinformatics tools were created to distinguish enhancers from other regulatory components and to pinpoint their advantages. However, because the quality of its prediction method needs to be improved, its practical application value must also be improved. Based on nucleotide composition and statistical moment-based features, the current study suggests a novel method for identifying enhancers and non-enhancers and evaluating their strength. The proposed study outperformed state-of-the-art techniques using fivefold and tenfold cross-validation in terms of accuracy. The accuracy from the current study results in 86.5% and 72.3% in enhancer site and its strength prediction respectively. The results of the suggested methodology point to the potential for more efficient and successful outcomes when statistical moment-based features are used. The current study's source code is available to the research community at https://github.com/csbioinfopk/enpred.
Spatio-temporal predictions of COVID-19 test positivity in Uppsala County, Sweden: a comparative approach
Authors: van Zoest Vera , Varotsis Georgios , Menzel Uwe , Wigren Anders , Kennedy Beatrice , Martinell Mats , Fall Tove 
Published: September 2022

AbstractPrevious spatio-temporal COVID-19 prediction models have focused on the prediction of subsequent number of cases, and have shown varying accuracy and lack of high geographical resolution. We aimed to predict trends in COVID-19 test positivity, an important marker for planning local testing capacity and accessibility. We included a full year of information (June 29, 2020–July 4, 2021) with both direct and indirect indicators of transmission, e.g. mobility data, number of calls to the national healthcare advice line and vaccination coverage from Uppsala County, Sweden, as potential predictors. We developed four models for a 1-week-window, based on gradient boosting (GB), random forest (RF), autoregressive integrated moving average (ARIMA) and integrated nested laplace approximations (INLA). Three of the models (GB, RF and INLA) outperformed the naïve baseline model after data from a full pandemic wave became available and demonstrated moderate accuracy. An ensemble model of these three models slightly improved the average root mean square error to 0.039 compared to 0.040 for GB, RF and INLA, 0.055 for ARIMA and 0.046 for the naïve model. Our findings indicate that the collection of a wide variety of data can contribute to spatio-temporal predictions of COVID-19 test positivity.
Synaptic inputs to displaced intrinsically-photosensitive ganglion cells in macaque retina
Authors: Bordt Andrea S. , Patterson Sara S. , Kuchenbecker James A. , Mazzaferri Marcus A. , Yearick Joel N. , Yang Emma R. , Ogilvie Judith Mosinger , Neitz Jay , Marshak David W. 
Published: September 2022

AbstractGanglion cells are the projection neurons of the retina. Intrinsically photosensitive retinal ganglion cells (ipRGCs) express the photopigment melanopsin and also receive input from rods and cones via bipolar cells and amacrine cells. In primates, multiple types of ipRGCs have been identified. The ipRGCs with somas in the ganglion cell layer have been studied extensively, but less is known about those with somas in the inner nuclear layer, the “displaced” cells. To investigate their synaptic inputs, three sets of horizontal, ultrathin sections through central macaque retina were collected using serial block-face scanning electron microscopy. One displaced ipRGC received nearly all of its excitatory inputs from ON bipolar cells and would therefore be expected to have ON responses to light. In each of the three volumes, there was also at least one cell that had a large soma in the inner nuclear layer, varicose axons and dendrites with a large diameter that formed large, extremely sparse arbor in the outermost stratum of the inner plexiform layer. They were identified as the displaced M1 type of ipRGCs based on this morphology and on the high density of granules in their somas. They received extensive input from amacrine cells, including the dopaminergic type. The vast majority of their excitatory inputs were from OFF bipolar cells, including two subtypes with extensive input from the primary rod pathway. They would be expected to have OFF responses to light stimuli below the threshold for melanopsin or soon after the offset of a light stimulus.
Assessment of the uncertainty and interpretability of deep learning models for mapping soil salinity using DeepQuantreg and game theory
Authors: Mohammadifar Aliakbar , Gholami Hamid , Golzari Shahram 
Published: September 2022

AbstractThis research introduces a new combined modelling approach for mapping soil salinity in the Minab plain in southern Iran. This study assessed the uncertainty (with 95% confidence limits) and interpretability of two deep learning (DL) models (deep boltzmann machine—DBM) and a one dimensional convolutional neural networks (1DCNN)—long short-term memory (LSTM) hybrid model (1DCNN-LSTM) for mapping soil salinity by applying DeepQuantreg and game theory (Shapely Additive exPlanations (SHAP) and permutation feature importance measure (PFIM)), respectively. Based on stepwise forward regression (SFR)—a technique for controlling factor selection, 18 of 47 potential controls were selected as effective factors. Inventory maps of soil salinity were generated based on 476 surface soil samples collected for measuring electrical conductivity (ECe). Based on Taylor diagrams, both DL models performed well (RMSE < 20%), but the 1DCNN-LSTM hybrid model performed slightly better than the DBM model. The uncertainty range associated with the ECe values predicted by both models estimated using DeepQuantilreg were similar (0–25 dS/m for the 1DCNN-LSTM hybrid model and 2–27 dS/m for DBM model). Based on the SFR and PFIM (permutation feature importance measure)—a measure in game theory, four controls (evaporation, sand content, precipitation and vertical distance to channel) were selected as the most important factors for soil salinity in the study area. The results of SHAP (Shapely Additive exPlanations)—the second measure used in game theory—suggested that five factors (evaporation, vertical distance to channel, sand content, cation exchange capacity (CEC) and digital elevation model (DEM)) have the strongest impact on model outputs. Overall, the methodology used in this study is recommend for applications in other regions for mapping environmental problems.
Research on construction deformation prediction and disaster warning of karst slope based on mutation theory
Authors: Qi Yanli , Tian Gang , Bai Mingzhou , Song Linlin 
Published: September 2022

AbstractIn the study of deformation prediction and disaster warning during karst slope construction, the influencing factors and deformation law should be comprehensively considered. The layout of the deformation monitoring points of karst slope is affected by the thickness of karst overburden soil, dissolution and fragmentation degree, karst development degree, slope cracking degree, fault or weak interlayer and other factors. In this paper, the author aimed at the problem of construction deformation prediction and disaster warning of karst slope, proposed an improved model of cusp mutation by applying and optimizing the cusp mutation model, analysed the deformation trend and sudden change type of the slope, and obtained the critical control early warning value of slope deformation. Therefore, it is feasible to analyse the deformation and mutation characteristics of karstified slope by using a virtual reality-mutation model. In addition, based on the empirical formula of the slope sliding limit deformation rate and grey prediction model, the critical control warning value of slope deformation is obtained, which provides a basis to quantify the deformation index of risk evaluation. This method provides a new idea to predict karst slope construction deformation and catastrophic deformation warning and has a reference value for similar engineering examples.
Construction of a culture protocol for functional bile canaliculi formation to apply human iPS cell-derived hepatocytes for cholestasis evaluation
Authors: Horiuchi Shinichiro , Kuroda Yukie , Oyafuso Ryota , Komizu Yuji , Takaki Takashi , Maeda Kazuya , Ishida Seiichi 
Published: September 2022

AbstractCholestatic toxicity causes the failure of pharmaceutical agents during drug development and, thus, should be identified at an early stage of drug discovery and development. The formation of functional bile canaliculi in human hepatocytes is required for in vitro cholestasis toxicity tests conducted during the early stage of drug development. In this study, we investigated the culture conditions required for the formation of bile canaliculi using human-induced pluripotent stem cell-derived hepatocytes (hiPSC-Heps). When hiPSC-Heps were sandwich-cultured under the condition we established, extended bile canaliculi were formed on the whole well surfaces. Biliary efflux transporters were localized in the formed bile canaliculi structures which had junctional complexes. After the model substrates of the biliary efflux transporters were taken up into cells, their subsequent excretion into the bile canaliculi was observed and was found to be impeded by each inhibitor of the biliary efflux transporter. These findings suggest that bile canaliculi have transporter-specific bile excretion abilities. We will continue to study the application of this culture protocol to cell-based cholestasis assay system. As a result, the culture protocol could lead to a highly predictable, robust cell-based cholestasis assay system because it forms functional bile canaliculi reproducibly and efficiently.
An innovative model for conductivity of graphene-based system by networked nano-sheets, interphase and tunneling zone
Authors: Zare Yasser , Rhee Kyong Yop 
Published: September 2022

AbstractThis study presents a simple equation for the conductivity of graphene-filled nanocomposites by considering graphene size, amount of filler in the net, interphase deepness, tunneling size, and properties of the net. The amount of nanoparticles in the net is related to the percolation threshold and effective filler content. The novel model is analyzed using the measured conductivity of numerous examples and the factors’ impacts on the conductivity. Both experienced data and parametric examinations verify the correctness of the novel model. Among the studied factors, filler amount and interphase deepness implicitly manage the conductivity from 0 to 7 S/m. It is explained that the interphase amount affects the operative quantity of nanofiller, percolation threshold, and amount of nets.
An intelligent methodology for the use of multi-criteria decision analysis in impact assessment: the case of real-world offshore construction
Authors: Tsakalerou Mariza , Efthymiadis Damianos , Abilez Almat 
Published: September 2022

AbstractImpact assessment of large-scale projects involves a plethora of technical, economic, social, and environmental factors that must be assessed along with the expectations of the stakeholders of each project. While impact assessment is required for a development project to receive regulatory approval to proceed, it is also an invaluable tool during the design phase of complex projects, providing for informed decision-making. Molding multiple perspectives of diverse stakeholders into a single collective choice is a key challenge in the process. Multi-Criteria Decision Analysis (MCDA) is the methodology used to rank a finite number of decision options based on a finite set of evaluation criteria. Different MCDA techniques, however, may lead to different decisions when applied to the same problem while different sets of criteria and weights may rank choices differently even when the same method is applied. This is a cause of concern, and even acrimony, amongst the stakeholders, often leading to protracted periods of negotiation and delaying project launching. The objective of this paper is to present an intelligent system to ameliorate the effects of the inherent subjectivity in MCDA techniques and to develop a consensus amongst the stakeholders in a data-driven setting. A case study from the field of offshore construction is used as a running example. This case study, informed by real-world experience in the field, demonstrates succinctly the issues involved and illustrates clearly the proposed intelligent methodology and its merits.
A population-level data linkage study to explore the association between health facility level factors and unintended pregnancy in Bangladesh
Authors: Khan Md. Nuruzzaman , Harris Melissa L. , Huda Md. Nazmul , Loxton Deborah 
Published: September 2022

AbstractThe objective of this study was to investigate the effects of health facility-level factors, including the availability of long-acting modern contraceptives (LAMC) at the nearest health facility and its distance from women’s homes, on the occurrence of unintended pregnancy that resulted in a live birth. We analysed the 2017/18 Bangladesh Demographic and Health Survey data linked with the 2017 Bangladesh Health Facility Survey. The weighted sample comprised 5051 women of reproductive age, who had at least one live birth within 3 years of the survey. The outcome variable was women’s intention to conceive at their most recent pregnancy that ended with a live birth. The major explanatory variables were the health facility level factors. A multi-level multinomial logistic regression model was used to assess the association of the outcome variable with explanatory variables adjusting for individual, household, and community-level factors. Nearly 21% of the total respondents reported that their most recent live birth was unintended at conception. Better health facility management systems and health facility infrastructure were found to be 14–30% protective of unintended pregnancy that resulted in a live birth. LAMC availability at the nearest health facility was associated with a 31% reduction (95% CI 0.50–0.92) in the likelihood of an unwanted pregnancy that resulted in a live birth. Health facility readiness to provide LAMC was also associated with a 14–16% reduction in unintended pregnancies that ended with a birth. The likelihood of unintended pregnancy that resulted in a live birth increased around 20–22% with the increased distance of the nearest health facility providing LAMC from the women’s homes.The availability of health facilities near women’s homes and access to LAMC can significantly reduce unintended pregnancy. Policies and programs to ensure access and affordability of LAMC across current health facilities and to increase the number of health facilities are recommended.
Repetitive nociceptive stimulation increases spontaneous neural activation similar to nociception-induced activity in mouse insular cortex
Authors: Kobayashi Shutaro , O’Hashi Kazunori , Kobayashi Masayuki 
Published: September 2022

AbstractRecent noninvasive neuroimaging technology has revealed that spatiotemporal patterns of cortical spontaneous activity observed in chronic pain patients are different from those in healthy subjects, suggesting that the spontaneous cortical activity plays a key role in the induction and/or maintenance of chronic pain. However, the mechanisms of the spontaneously emerging activities supposed to be induced by nociceptive inputs remain to be established. In the present study, we investigated spontaneous cortical activities in sessions before and after electrical stimulation of the periodontal ligament (PDL) by applying wide-field and two-photon calcium imaging to anesthetized GCaMP6s transgenic mice. First, we identified the sequential cortical activation patterns from the primary somatosensory and secondary somatosensory cortices to the insular cortex (IC) by PDL stimulation. We, then found that spontaneous IC activities that exhibited a similar spatiotemporal cortical pattern to evoked activities by PDL stimulation increased in the session after repetitive PDL stimulation. At the single-cell level, repetitive PDL stimulation augmented the synchronous neuronal activity. These results suggest that cortical plasticity induced by the repetitive stimulation leads to the frequent PDL stimulation-evoked-like spontaneous IC activation. This nociception-induced spontaneous activity in IC may be a part of mechanisms that induces chronic pain.