bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pushing the boundaries of lithium battery research with atomistic modelling on different scales
Authors: Morgan Lucy M , Mercer Michael P , Bhandari Arihant , Peng Chao , Islam Mazharul M , Yang Hui , Holland Julian , Coles Samuel W , Sharpe Ryan , Walsh Aron , Morgan Benjamin J , Kramer Denis , Islam M Saiful , Hoster Harry E , Edge Jacqueline Sophie , Skylaris Chris-Kriton 
Published: November 2021

Abstract
Computational modelling is a vital tool in the research of batteries and their component materials. Atomistic models are key to building truly physics-based models of batteries and form the foundation of the multiscale modelling chain, leading to more robust and predictive models. These models can be applied to fundamental research questions with high predictive accuracy. For example, they can be used to predict new behaviour not currently accessible by experiment, for reasons of cost, safety, or throughput. Atomistic models are useful for quantifying and evaluating trends in experimental data, explaining structure-property relationships, and informing materials design strategies and libraries. In this review, we showcase the most prominent atomistic modelling methods and their application to electrode materials, liquid and solid electrolyte materials, and their interfaces, highlighting the diverse range of battery properties that can be investigated. Furthermore, we link atomistic modelling to experimental data and higher scale models such as continuum and control models. We also provide a critical discussion on the outlook of these materials and the main challenges for future battery research.
Child Maltreatment and Mental Health in Middle Childhood: A Longitudinal Study in Japan
Authors: Isumi Aya , Doi Satomi , Ochi Manami , Kato Tsuguhiko , Fujiwara Takeo 
Published: November 2021

Abstract
Toxic stress caused by child maltreatment can lead to adverse mental health outcomes in later life, yet unmeasured confounding has been a major issue in many previous studies. To examine the association between child maltreatment and resilience and behavior problems among early elementary school-age children, we used data from a population-based longitudinal survey targeting all first-grade children in 2015 in Adachi City, a ward in Tokyo, Japan. Children whose caregivers provided valid responses during the 2015 (first grade; ages 6–7 years), 2016 (second grade; ages 7–8 years), and 2018 (fourth grade; ages 9–10 years) waves of the study were included in the analysis (n = 2,920). Fixed-effects regression models revealed that child maltreatment was inversely associated with resilience (β = −0.89, 95% confidence interval (CI): −1.05, −0.72) and prosocial behavior (β = −0.03, 95% CI: −0.05, −0.003) and positively associated with behavior problems (β = 0.32, 95% CI: 0.27, 0.37) over 4 years of follow-up (2015–2018), after controlling for all time-invariant confounders and measured time-varying confounders and survey year. These associations were consistent across sex. Child maltreatment may hamper the development of resilience and prosocial behavior and induce behavior problems in early elementary school children over time. Future researchers should identify modifiable protective factors for better mental health among maltreated children.
Advancing the Social Epidemiology Mission of theAmerican Journal of Epidemiology
Authors: Gilman Stephen E , Aiello Allison , Galea Sandro , Howe Chanelle J , Kawachi Ichiro , Lovasi Gina S , Dean Lorraine T , Oakes J Michael , Siddiqi Arjumand , Glymour M Maria 
Published: November 2021

AbstractSocial epidemiology is concerned with how social forces influence population health. Rather than focusing on a single disease (as in cancer or cardiovascular epidemiology) or a single type of exposure (e.g., nutritional epidemiology), social epidemiology encompasses all the social and economic determinants of health, both historical and contemporary. These include features of social and physical environments, the network of relationships in a society, and the institutions, politics, policies, norms and cultures that shape all of these forces. This commentary presents the perspective of several editors at the Journal with expertise in social epidemiology. We articulate our thinking to encourage submissions to the Journal that: 1) expand knowledge of emerging and underresearched social determinants of population health; 2) advance new empirical evidence on the determinants of health inequities and solutions to advance health equity; 3) generate evidence to inform the translation of research on social determinants of health into public health impact; 4) contribute to innovation in methods to improve the rigor and relevance of social epidemiology; and 5) encourage critical self-reflection on the direction, challenges, successes, and failures of the field.
Tenuazonic acid production is dispensable for virulence, but its biosynthetic gene expression pattern is associated with the infection of Pyricularia oryzae
Authors: Kashiwa Takeshi , Motoyama Takayuki , Yoshida Kazuko , Yun Choong-Soo , Osada Hiroyuki 
Published: November 2021

ABSTRACT
Tenuazonic acid (TeA) is a toxin produced by the rice blast fungus Pyricularia oryzae. Although knockout of the TeA biosynthetic gene TAS1 did not affect the virulence of P. oryzae, constitutive TAS1 expression suppressed its infection. TAS1 expression was induced alongside transition of P. oryzae infection behavior. The results suggested that controlling TeA biosynthesis is important for P. oryzae infection.
Validation of predicted anonymous proteins simply using Fisher’s exact test
Authors: Claverie Jean-Michel , Santini Sébastien 
Published: November 2021

Abstract

Motivation
Genomes sequencing has become the primary (and often the sole) experimental method to characterize newly discovered organisms, in particular from the microbial world (bacteria, archaea, viruses). This generates an ever increasing number of predicted proteins the existence of which is unwarranted, in particular among those without homolog in model organisms. As a last resort, the computation of the selection pressure from pairwise alignments of the corresponding ‘Open Reading Frames’ (ORFs) can be used to validate their existences. However, this approach is error-prone, as not usually associated with a significance test.

Results
We introduce the use of the straightforward Fisher’s exact test as a postprocessing of the results provided by the popular CODEML sequence comparison software. The respective rates of nucleotide changes at the nonsynonymous versus synonymous position (as determined by CODEML) are turned into entries into a 2 × 2 contingency table, the probability of which is computed under the Null hypothesis that they should not behave differently if the ORFs do not encode actual proteins. Using the genome sequences of two recently isolated giant viruses, we show that strong negative selection pressures do not always provide a solid argument in favor of the existence of proteins.
COBREXA.jl: constraint-based reconstruction and exascale analysis
Authors: Kratochvíl Miroslav , Heirendt Laurent , Wilken St Elmo , Pusa Taneli , Arreckx Sylvain , Noronha Alberto , van Aalst Marvin , Satagopam Venkata P , Ebenhöh Oliver , Schneider Reinhard , Trefois Christophe , Gu Wei 
Published: November 2021

AbstractSummaryCOBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism community models.Availability and implementationhttps://doi.org/10.17881/ZKCR-BT30.Supplementary informationSupplementary data are available at Bioinformatics online.
Chromosome numbers and heterochromatin variation in introgressed and non-introgressed populations ofEpidendrum(Orchidaceae: Epidendroideae): interspecific transfers of heterochromatin lead to divergent variable karyotypes in the parental populations
Authors: Nollet Felipe , Medeiros Neto Enoque , Cordeiro Joel M P , Buril Maria Teresa , Chase Mark W , Felix Leonardo P 
Published: November 2021

AbstractSome groups in Epidendrum have stable chromosome numbers, whereas the species of Epidendrum subgenus Amphiglottium exhibit high levels of chromosome number variability and other genomic alterations. Polyploidy and dysploidy have both been invoked to explain chromosome number variation in the subgenus, but little is known about what is driving the high frequency of chromosome modification within some species in this group. To test whether hybridization and introgression are involved, we use fluorochrome staining to evaluate the chromosome numbers and heterochromatin bands in E. subgenus Amphiglottium, including individual parental genotypes from introgressed and non-introgressed populations. Two main types of heterochromatin were observed forming CMA and DAPI bands in Epidendrum spp. B chromosomes were identified in some individuals. In non-introgressed populations, E. secundum has three cytotypes, 2n = 28, 56 and 84, found in different parts of its geographical range and a small number of DAPI bands. In introgressed populations of E. secundum, there was dysploid variation among individuals that were morphologically typical parental plants, and in one introgressed population a high number of DAPI bands was observed in what appeared on morphological grounds to be pure parental individuals. Our data corroborate the hypothesis that hybridization and introgression play a role in generating chromosome variation (number and form) and heterochromatin diversification in E. subgenus Amphiglottium.
High dream recall frequency is associated with an increase of both bottom-up and top-down attentional processes
Authors: Ruby Perrine , Masson Rémy , Chatard Benoit , Hoyer Roxane , Bottemanne Laure , Vallat Raphael , Bidet-Caulet Aurélie 
Published: November 2021

Abstract
Event-related potentials (ERPs) associated with the involuntary orientation of (bottom-up) attention toward an unexpected sound are of larger amplitude in high dream recallers (HR) than in low dream recallers (LR) during passive listening, suggesting different attentional functioning. We measured bottom-up and top-down attentional performance and their cerebral correlates in 18 HR (11 women, age = 22.7 years, dream recall frequency = 5.3 days with a dream recall per week) and 19 LR (10 women, age = 22.3, DRF = 0.2) using EEG and the Competitive Attention Task. Between-group differences were found in ERPs but not in behavior. The results show that HR present larger ERPs to distracting sounds than LR even during active listening, arguing for enhanced bottom-up processing of irrelevant sounds. HR also presented larger contingent negative variation during target expectancy and P3b to target sounds than LR, speaking for an enhanced recruitment of top-down attention. The attentional balance seems preserved in HR since their performances are not altered, but possibly at a higher resource cost. In HR, increased bottom-up processes would favor dream recall through awakening facilitation during sleep and enhanced top-down processes may foster dream recall through increased awareness and/or short-term memory stability of dream content.
The 30-day readmission rate of same-day discharge protocol following catheter ablation for atrial fibrillation: a propensity score-matched analysis from National Readmission Database
Authors: Sahashi Yuki , Kuno Toshiki , Tanaka Yoshihiro , Passman Rod , Briasoulis Alexandros , Malik Aaqib H 
Published: November 2021

Abstract

Aims
The effectiveness and safety of same-day discharge (SDD) for catheter ablation (CA) for atrial fibrillation (AF) has not been fully elucidated using a large nationwide database. This study aimed to evaluate the all-cause readmission rates within 30-days among patients receiving CA for AF with an SDD protocol compared with a conventional overnight stay (ONS).

Methods and results
We performed a retrospective cohort study using the US Nationwide Readmission Database. The primary outcome was all-cause 30-day readmission following discharge in patients receiving CA and a secondary outcome was requiring total healthcare cost. A 1 : 3 propensity score matching was conducted to compare the safety and efficacy within both SDD and ONS group. Among 30 776 patients [mean 67.2 ± 11.4 years, 12 590 female (41.5%)] who received CA from 2016 through 2018, 440 (1.42%) patients were discharged on the same-day following CA (SDD group), and the remaining 30 336 patients stayed at least one night in the hospital (ONS group). A propensity score analysis generated 1751 matched pairs (440 in the SDD group; 1311 in the ONS group). The 30-day readmission following discharge was not significantly higher in the SDD group than the ONS group (SDD vs. ONS: 12.7% vs. 9.7%; hazard ratio: 1.17, 95% confidence interval: 0.76–1.81, P = 0.47). Healthcare cost was significantly higher in the ONS group ($25 237 ± 14 036 vs. $30 749 ± 16 383; P &lt; 0.01).

Conclusion
In this nationwide database study, there was no significant difference in the all-cause 30-day readmission following SDD for CA compared with ONS.
Recognizing sinonasal cancer in primary care: a matched case–control study using electronic records
Authors: Khan Tuba , El-Sockary Yusera , Hamilton William T , Shephard Elizabeth A 
Published: November 2021

Abstract

Background
Cancers of the nasopharynx, nasal cavity, and accessory sinuses (“sinonasal”) are rare in England, with around 750 patients diagnosed annually. There are no specific National Institute for Health and Care Excellence (NICE) referral guidelines for these cancers and no primary care research published.

Objective
To identify and quantify clinical features of sinonasal cancer in UK primary care patients.

Methods
This matched case–control study used UK Clinical Practice Research Datalink (CPRD) data. Patients were aged ≥40 years with a diagnosis of sinonasal cancer between January 1, 2000 and December 31, 2009 and had consulted their GP in the year before diagnosis. Clinical features of sinonasal cancer were analysed using conditional logistic regression. Positive predictive values (PPVs) for single and combined features were calculated.

Results
In total, 155 cases and 697 controls were studied. Nine symptoms and one abnormal investigation were significantly associated with the cancer: nasal mass; odds ratio, 95 (95% confidence interval 7.0, 1315, P = 0.001); head and neck lumps, 68 (12, 387, P &lt; 0.001); epistaxis, 17 (3.9, 70, P &lt; 0.001); rhinorrhoea, 14 (4.6, 44, P &lt; 0.001); visual disturbance, 12 (2.2, 67, P = 0.004); sinusitis, 7.3 (2.2, 25, P = 0.001); sore throat, 6.0 (2.0, 18, P = 0.001); otalgia, 5.4 (1.6, 18, P = 0.007); headache, 3.6 (1.4, 9.5, P = 0.01); raised white cell count, 8.5 (2.8, 27, P &lt; 0.001). Combined PPVs for epistaxis/rhinorrhoea, epistaxis/sinusitis, and rhinorrhoea/sinusitis were 0.62%.

Conclusion
This is the first primary care study identifying epistaxis, sinusitis, and rhinorrhoea as part of the clinical prodrome of sinonasal cancer. Although no PPVs meet the 3% NICE referral threshold, these results may help clinicians identify who warrants safety-netting and possible specialist referral, potentially reducing the number of advanced-stage diagnoses of sinonasal cancer.
Biosurfactant production by halophilic yeasts isolated from extreme environments in Botswana
Authors: Loeto Daniel , Jongman Mosimanegape , Lekote Lerato , Muzila Mbaki , Mokomane Margaret , Motlhanka Koketso , Ndlovu Thando , Zhou Nerve 
Published: November 2021

ABSTRACTNine morphologically distinct halophilic yeasts were isolated from Makgadikgadi and Sua pans, as pristine and extreme environments in Botswana. Screening for biosurfactant production showed that Rhodotorula mucilaginosa SP6 and Debaryomyces hansenii MK9 exhibited the highest biosurfactant activity using Xanthocercis zambesiaca seed powder as a novel and alternative inexpensive carbon substrate. Chemical characterization of the purified biosurfactants by Fourier Transform Infra-Red spectroscopy suggested that the biosurfactant from R. mucilaginosa SP6 was a rhamnolipid-type whereas the biosurfactant from D. hansenii MK9 was a sophorolipid-type. The two biosurfactants exhibited antimicrobial activities against eight pathogenic bacteria and fungal strains (Proteus vulgaris, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Micrococcus luteus, Cryptococcus neoformans, Candida albicans and Aspergilus niger). The sophorolopid-type biosurfactant was found to be the most potent among the antimicrobial drug resistant strains tested. The findings open up prospects for the development of environmentally friendly antimicrobial drugs that use an inexpensive source of carbon to reduce the costs associated with the production of biosurfactants.
Detection and modelling of strong topography of mid-mantle structures beneath the North Atlantic
Authors: Saki Morvarid , Thomas Christine , Abreu Rafael 
Published: November 2021

SUMMARYThere is mounting evidence for the presence of seismic reflectors in the mantle at a depth of around 1000 km, however, the cause for these reflectors is not yet well established and published observations show a range of depth estimates for these structures. Discussion is also still ongoing whether it is one global or several different reflectors. Here, we investigate the presence of seismic reflectors beneath the North Atlantic using a large number of PP and SS underside reflections. We analyse over 2600 earthquakes with Mw ≥ 5.7 and use array seismic methods to improve the visibility of the small-amplitude reflected signals. The measured time lag between PP/SS arrivals and their corresponding precursors on robust stacks are used to estimate the depth of the reflector. Our results reveal the presence of mid-mantle structure beneath the North Atlantic in a depth range of ∼700–1300 km, consistent for both P- and S-wave observations. The reflector depth is shallower than 1000 km beneath the southern part of the investigation area and deepens seemingly abruptly towards the northern part of the North Atlantic. We find polarity variations in a region of strong depth change which we assume to be due to wave interference. Using 3-D waveform modelling, we implement models with strong topography as well as models with two overlapping reflectors and two separated reflectors and show that a large step in reflector depth over a short lateral distance, as imaged with our data set, can be resolved, while the discrimination between strong topography and two overlapping and separated reflectors, respectively, is also possible. The variations in precursor polarity can also be observed in our synthetic data in the region of strong topography confirming our assumption of wave interference for generating apparent precursor polarity and waveform changes. While the opposite polarity can be produced by the two overlapping reflectors as well, the strong topography model is preferred in this region, since we do detect only one reflected signal in our observations.
Evaluating use of web-based interventions: an example of a Dutch sexual health intervention
Authors: Metz Gido , Roosjen Hanneke , Zweers Wessel , Crutzen Rik 
Published: November 2021

Summary
With the current increase in web-based interventions, the question of how to measure, and consequently improve engagement in such interventions is gaining more importance. Modern day web analytics tools make it easy to monitor use of web-based interventions. However, in this article, we propose that it would be more meaningful to first examine how the developers envisioned the use of the intervention to establish behavior change (i.e. intended use), before looking into how the intervention is ultimately used with web analytics (i.e. actual use). Such an approach responds to the regularly expressed concern that behavioral interventions are often poorly described, leading to less meaningful evaluations as it is not clear what exactly is being evaluated. Using a page on chlamydia prevention (104 557 pageviews in 2020) from a Dutch sexual health intervention (Sense), we demonstrate the value of acyclic behavior change diagrams (ABCDs) as a method to visualize intended use of an intervention. ABCDs show at a glance how behavior change principles are applied in an intervention and target determinants of behavior. Based on this ABCD, we investigate actual use of the intervention, using web analytics tool Matomo. Despite being intended to stimulate STI-testing, only 14% of the 35 347 transfers from this page led to the STI-testing page and a high bounce rate (79%) and relatively high exit rate were reported (69%). Recommendations to further interpret the data are given. This real-life example demonstrates the potential of combining ABCDs and Matomo as methods to gain insight into use of web-based interventions.
Projecting climate-driven shifts in demersal fish thermal habitat in Iceland's waters
Authors: Mason Julia G , Woods Pamela J , Thorlacius Magnús , Guðnason Kristinn , Saba Vincent S , Sullivan Patrick J , Kleisner Kristin M 
Published: November 2021

AbstractAs climate change shifts marine species distribution and abundance worldwide, projecting local changes over decadal scales may be an adaptive strategy for managers and industry. In Iceland, one of the top fish-producing nations globally, long-term monitoring enables model simulations of groundfish species habitat distribution. We used generalized additive models to characterize suitable thermal habitat for 51 fish species in Iceland's waters. We projected changes in suitable thermal habitat by midcentury with an ensemble of five general circulation models from the Coupled Model Intercomparison Program 6 (CMIP6) and NOAA (CM2.6) and two scenarios (SSP 5-8.5 and SSP 2-4.5). We found a general northward shift in suitable thermal habitat distribution, with variable regional dynamics among species. Species thermal bias index was a weak predictor of projected thermal habitat change, with warmer-water species more likely to see increases in thermal habitat and southern warm-edge range expansions. While these results isolate the effects of future changes in temperature, providing an indication of suitable thermal habitat, low model explanatory power suggests that additional variables may improve distribution projections. Such projections might serve as guideposts to inform long-term management decisions about regional and species-specific suitability for Iceland's fisheries, infrastructure investment, and risk evaluation under climate change.