bluuebunny/crossref_metadata_2025_split huggingface dataset:
Four key challenges in the open‐data revolution
Authors: Salguero‐Gómez Roberto , Jackson John , Gascoigne Samuel J. L. 
Published: September 2021

AbstractIn Focus:Culina, A., Adriaensen, F., Bailey, L. D., et al. (2021) Connecting the data landscape of long‐term ecological studies: The SPI‐Birds data hub.Journal of Animal Ecology,https://doi.org/10.1111/1365‐2656.13388. Long‐term, individual‐based datasets have been at the core of many key discoveries in ecology, and calls for the collection, curation and release of these kinds of ecological data are contributing to a flourishing open‐data revolution in ecology. Birds, in particular, have been the focus of international research for decades, resulting in a number of uniquely long‐term studies, but accessing these datasets has been historically challenging. Culina et al. (2021) introduce an online repository of individual‐level, long‐term bird records with ancillary data (e.g. genetics), which will enable key ecological questions to be answered on a global scale. As well as these opportunities, however, we argue that the ongoing open‐data revolution comes with four key challenges relating to the (1) harmonisation of, (2) biases in, (3) expertise in and (4) communication of, open ecological data. Here, we discuss these challenges and how key efforts such as those by Culina et al. are using FAIR (Findable, Accessible, Interoperable and Reproducible) principles to overcome them. The open‐data revolution will undoubtedly reshape our understanding of ecology, but with it the ecological community has a responsibility to ensure this revolution is ethical and effective.
Planning ahead: Dynamic models forecast blue whale distribution with applications for spatial management
Authors: Barlow Dawn R. , Torres Leigh G. 
Published: September 2021

Abstract

Resources in the ocean are ephemeral, and effective management must therefore account for the dynamic spatial and temporal patterns of ecosystems and species of concern. We focus on the South Taranaki Bight (STB) of New Zealand, where upwelling generates productivity and prey to support an important foraging ground for blue whales that overlaps with anthropogenic pressure from industrial activities.

We incorporate regional ecological knowledge of upwelling dynamics, physical–biological coupling and associated lags in models to forecast sea surface temperature (SST) and net primary productivity (NPP) with up to 3 weeks lead time. Forecasted environmental layers are then implemented in species distribution models to predict suitable blue whale habitat in the STB. Models were calibrated using data from the austral summers of 2009–2019, and ecological forecast skill was evaluated by predicting to withheld data.

Boosted regression tree models skilfully forecasted SST (CV deviance explained = 0.969–0.970) and NPP (CV deviance explained = 0.738–0.824). The subsequent blue whale distribution forecast models had high predictive performance (AUC = 0.889), effectively forecasting suitable habitat on a daily scale with 1–3 weeks lead time.

The spatial location and extent of forecasted blue whale habitat were variable, with the proportion of petroleum and mineral permit areas that overlapped with daily suitable habitat ranging from 0% to 70%. Hence, the STB and these forecast models are well‐suited for dynamic management that could reduce anthropogenic threats to whales while decreasing regulatory burdens to industry users relative to a traditional static protected area.

Synthesis and applications. We develop and test ecological forecast models that predict sea surface temperature, net primary productivity and blue whale suitable habitat up to 3 weeks in the future within New Zealand's South Taranaki Bight region. These forecasts of whale distribution can be effectively applied for dynamic spatial management due to model foundation on quantified links and lags between physical forcing and biological responses. A framework to operationalize these forecasts through a user‐driven application is in development to proactively inform conservation management decisions. This framework is implemented through stakeholder engagement, allows flexibility based on management objectives, and is amenable to improvement as new knowledge and feedback are received.
A Learning Health Systems Approach to Frailty Prediction Using EHR Data
Authors: Bokov Alex , Stevens Kathleen , Tripathy Chandana , Espinoza Sara 
Published: September 2021

Research ObjectiveTo predict occurrence of preventable patient safety events using only data elements that are almost universally supported in EHR systems.Study DesignWe drew a random sample was drawn from the EHR records of adult patients not restricted to any particular age range or diagnosis and therefore representative of a real‐world health system population. This sample was subdivided into a developmental and a test subset. We used the Rockwood Deficit Accumulation method to construct a frailty index from ICD10 codes, lab value‐flags, and vital signs on a per‐visit basis with a rolling two‐year time‐window (EFI, electronic frailty index). The Cox proportional hazard model was used to model days elapsed from a randomly selected visit to the first occurrence of the selected outcomes (which are also based on routinely available EHR data elements). In contrast to previous studies, we treated EFI as a time‐varying predictor with multiple follow‐ups per patient, which is more realistic than relying on one static time‐point. We used a representative sample of the adult patient population rather than limiting it to older individuals and found EFI to be a useful metric even at relatively young ages.Population StudiedWe accessed EHR data for 14,844 patients randomly sampled from our academic health center's data warehouse which supports our ACT/SHRINE node and is regularly updated from our institution's EHR system.Principal FindingsWe found that this electronic frailty index was robustly predictive of ED utilization, hospitalization, discharge from hospital to SNF/ICF, hospital readmission, all‐cause mortality, and complications including in‐hospital trauma and infections.ConclusionsThough currently frailty indexes are most used in geriatrics and gerontology, we find evidence that age‐related declines follow a lifelong trajectory that is observable in patient charts even in younger patients (18–45).Implications for Policy or PracticeFrailty predicts poor patient outcomes and healthcare services utilization. Accurate assessment of frailty can inform clinical management decisions and assist with anticipating healthcare resource utilization. Deficit accumulation indexes have a much simpler algorithm than most other frailty scores (e.g. HCC‐RAF). Because they capture a large number of conditions, they are robust against missing data and variations between disparate data sources. To further reduce barriers to implementation and accelerate the evolution of this tool, we are making the source code freely available under and open source license. Our next goal will be a side‐by‐side comparison of HCC‐RAF and EFI for predicting the outcomes presented here as well as cost of care. If EFI can be shown to out‐perform CMS risk scores, the implications for value‐based care will be significant.Primary Funding SourceNational Institutes of Health.
Anaerobic oxidation of methane mediated by microbial extracellular respiration
Authors: Zhang Xueqin , Yuan Zhiguo , Hu Shihu 
Published: September 2021

SummaryAnaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane‐oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET‐mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET‐mediated AOM is discussed with both methane‐oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET‐mediated AOM, raising open research questions for future research.
Sex‐specific effect of prenatal alcohol exposure on N‐methyl‐D‐aspartate receptor function in orbitofrontal cortex pyramidal neurons of mice
Authors: Licheri Valentina , Chandrasekaran Jayapriya , Bird Clark W. , Valenzuela C. Fernando , Brigman Jonathan L. 
Published: September 2021

AbstractBackgroundAlcohol consumption during pregnancy can produce behavioral and cognitive deficits that persist into adulthood. These include impairments in executive functions, learning, planning, and cognitive flexibility. We have previously shown that moderate prenatal alcohol exposure (PAE) significantly impairs reversal learning, a measure of flexibility mediated across species by different brain areas that include the orbital frontal cortex (OFC). Reversal learning is likewise impaired by genetic or pharmacological inactivation of GluN2B subunit‐containing N‐methyl‐D‐aspartate receptors (NMDARs). In the current study, we tested the hypothesis that moderate PAE persistently alters the number and function of GluN2B subunit‐containing NMDARs in OFC pyramidal neurons of adult mice.MethodsWe used a rodent model of fetal alcohol spectrum disorders and left offspring undisturbed until adulthood. Using whole‐cell, patch‐clamp recordings, we assessed NMDAR function in slices from 90‐ to 100‐day‐old male and female PAE and control mice. Pharmacologically isolated NMDA receptor‐mediated evoked excitatory postsynaptic currents (NMDA‐eEPSCs) were recorded in the absence and presence of the GluN2B antagonist, Ro25‐6981(1 µM). In a subset of littermates, we evaluated the level of GluN2B protein expression in the synaptic fraction using Western blotting technique.ResultsOur results indicate that PAE females show significantly larger (~23%) NMDA‐eEPSC amplitudes than controls, while PAE induced a significant decrease (~17%) in NMDA‐eEPSC current density of pyramidal neurons recorded in slices from male mice. NMDA‐eEPSC decay time was not affected in PAE‐exposed mice from either sex. The contribution of GluN2B subunit‐containing NMDARs to the eEPSCs was not significantly altered by PAE. Moreover, there were no significant changes in protein expression in the synaptic fraction of either PAE males or females.ConclusionsThese findings suggest that low‐to‐moderate PAE modulates NMDAR function in pyramidal neurons in a sex‐specific manner, although we did not find evidence that the effect is mediated by dysfunction of synaptic GluN2B subunit‐containing NMDARs.
A Western diet with alcohol in drinking water recapitulates features of alcohol‐associated liver disease in mice
Authors: Schonfeld Michael , O’Neil Maura , Villar Maria T. , Artigues Antonio , Averilla Janice , Gunewardena Sumedha , Weinman Steven A. , Tikhanovich Irina 
Published: September 2021

AbstractBackgroundMouse models of alcohol‐associated liver disease vary greatly in their ease of implementation and the pathology they produce. Effects range from steatosis and mild inflammation with the Lieber–DeCarli liquid diet to severe inflammation, fibrosis, and pyroptosis seen with the Tsukamoto–French intragastric feeding model. Implementation of all of these models is limited by the labor‐intensive nature of the protocols and the specialized skills necessary for successful intragastric feeding. We thus sought to develop a new model to reproduce features of alcohol‐induced inflammation and fibrosis with minimal operational requirements.MethodsOver a 16‐week period, mice were fed ad libitum with a pelleted high‐fat Western diet (WD; 40% calories from fat) and alcohol added to the drinking water. We found the optimal alcohol consumption to be that at which the alcohol concentration was 20% for 4 days and 10% for 3 days per week. Control mice received WD pellets with water alone.ResultsAlcohol consumption was 18 to 20 g/kg/day in males and 20 to 22 g/kg/day in females. Mice in the alcohol groups developed elevated serum transaminase levels after 12 weeks in males and 10 weeks in females. At 16 weeks, both males and females developed liver inflammation, steatosis, and pericellular fibrosis. Control mice on WD without alcohol had mild steatosis only. Alcohol‐fed mice showed reduced HNF4α mRNA and protein expression. HNF4α is a master regulator of hepatocyte differentiation, down‐regulation of which is a known driver of hepatocellular failure in alcoholic hepatitis.ConclusionA simple‐to‐administer, 16‐week WD alcohol model recapitulates the inflammatory, fibrotic, and gene expression aspects of human alcohol‐associated steatohepatitis.
Integrative data analysis of self‐efficacy in 4 clinical trials for alcohol use disorder
Authors: Kruger Eric S. , Serier Kelsey N. , Pfund Rory A. , McKay James R. , Witkiewitz Katie 
Published: September 2021

AbstractBackgroundSelf‐efficacy has been proposed as a key predictor of alcohol treatment outcomes and a potential mechanism of success in achieving abstinence or drinking reductions following alcohol treatment. Integrative data analysis, where data from multiple studies are combined for analyses, can be used to synthesize analyses across multiple alcohol treatment trials by creating a commensurate measure and controlling for differential item functioning (DIF) to determine whether alcohol treatments improve self‐efficacy.MethodThe current study used moderated nonlinear factor analysis (MNLFA) to examine the effect of treatment on self‐efficacy across four different treatment studies (N = 3720; 72.5% male, 68.4% non‐Hispanic white). Self‐efficacy was measured using the Alcohol Abstinence Self‐Efficacy Scale (AASE) in the COMBINE Study (n = 1383) and Project MATCH (n = 1726), and the Drug Taking Confidence Questionnaire (DTCQ) in two studies of Telephone Continuing Care (TEL Study 1: n = 303; TEL Study 2: n = 212). DIF was examined across time, study, treatment condition, marital status, age, and sex.ResultsWe identified 12 items from the AASE and DTCQ to create a commensurate measure of self‐efficacy using MNLFA. All active treatments, including cognitive–behavioral treatment, a combined behavioral intervention, medication management, motivation enhancement treatment, telephone continuing care, twelve‐step facilitation, and relapse prevention, were associated with significant increases in self‐efficacy from baseline to posttreatment that were maintained for up to a year. Importantly, treatment as usual in community settings, which consisted of weekly group therapy that included addiction counseling and twelve‐step recovery support, was not associated with significant increases in self‐efficacy.ConclusionsAlcohol self‐efficacy increases following treatment and numerous evidence‐based treatments are associated with significant increases in self‐efficacy, which are maintained over time. Community treatment that focuses solely on addiction counseling and twelve‐step support may not promote increases in self‐efficacy.
Psychiatric Admissions, Referrals, and Suicidal Behavior Before and During the COVID‐19 Pandemic in Denmark: A Time‐Trend Study
Authors: Rømer Troels Boldt , Christensen Rune Haubo Bojesen , Blomberg Stig Nikolaj , Folke Fredrik , Christensen Helle Collatz , Benros Michael Eriksen 
Published: September 2021

AbstractObjectiveTo assess the patterns in psychiatric admissions, referrals, and suicidal behavior before and during the COVID‐19 pandemic.MethodsThis study utilized health records from hospitals and Emergency Medical Services (EMS) covering 46% of the Danish population (n = 2,693,924). In a time‐trend study, we compared the number of psychiatric in‐patients, referrals to mental health services and suicidal behavior in years prior to the COVID‐19 pandemic to levels during the first lockdown (March 11 – May 17, 2020), inter‐lockdown period (May 18 – December 15, 2020), and second lockdown (December 16, 2020 – February 28, 2021).ResultsDuring the pandemic, the rate of psychiatric in‐patients declined compared to pre‐pandemic levels (RR = 0.95, 95% CI = 0.94 – 0.96, p < 0.01), with the largest decrease of 19% observed three weeks into the first lockdown. Referrals to mental health services were not significantly different (RR = 1.01, 95% CI = 0.92 – 1.10, p = 0.91) during the pandemic; neither was suicidal behavior among hospital contacts (RR = 1.04, 95% CI = 0.94 – 1.14, p = 0.48) nor EMS contacts (RR = 1.08, 95% CI = 1.00 – 1.18, p = 0.06). Similar trends were observed across nearly all age groups, sexes, and types of mental disorders examined. In the age group <18, an increase in the rate of psychiatric in‐patients (RR = 1.11, 95% CI = 1.07 – 1.15, p < 0.01) was observed during the pandemic; however, this did not exceed the pre‐pandemic, upwards trend in psychiatric hospitalizations in the age group <18 (p = 0.78).ConclusionThe COVID‐19 pandemic has been associated with a decrease in psychiatric hospitalizations, while no significant change was observed in referrals to mental health services and suicidal behavior. Psychiatric hospitalizations among children and adolescents increased during the pandemic; however, this appears to be a continuation of a pre‐pandemic trend.
Nutritional content and bioconversion efficiency of Hermetia illucens (Diptera: Stratiomyidae): harvest as larvae or prepupae?
Authors: Parry Nina J , Weldon Christopher W 
Published: September 2021

AbstractMost research on nutritional composition that relates to use of fly larvae as an alternative ingredient in animal feed has focused on the prepupal stage of Hermetia illucens. However, crude protein and lipid content of H. illucens larvae vary dramatically during larval development, and little evidence has been presented to support use of prepupae for animal feed. The aim of this study was to establish the nutritional value of larvae and prepupae of H. illucens reared on organic waste streams for use in animal feed. The effect of harvesting of either larvae or prepupae on waste reduction was also measured. Freshly hatched neonates (90 mg) were placed on 12 kg of mixed pre‐consumer waste and held at 28°C. Moisture content, crude protein, crude lipid, ash, fibre, survival, total biomass, individual larval biomass, waste reduction and bioconversion on a dry matter basis were determined and compared between larvae harvested on Day 15 and prepupae harvested on Day 20. Prepupae had higher fibre content than larvae, while moisture content, crude protein, crude lipid and ash did not differ between the two groups. Total biomass was higher in larvae than in prepupae due to mortality between the two stages. Size of individual larvae was very similar between the two groups. In terms of nutritional content or biomass production, it is not detrimental to harvest larvae early or to harvest a mixture of larvae and prepupae or prepupae only. However, harvesting later, when larvae have become prepupae, would lead to a reduction in potential harvest and total biomass output, especially as survival declines over time. Bioconversion and waste reduction did not differ between Day 15 and Day 20, indicating that nutrient recovery from waste was not improved by harvesting at the prepupal stage.
Comparison of major histocompatibility complex‐B variability in Sri Lankan indigenous chickens with five global chicken populations using MHC‐B SNP panel
Authors: Manjula P. , Fulton J. E. , Seo D. , Lee J. H. 
Published: September 2021

SummaryIn the present study, we investigated the major histocompatibility complex (MHC)‐B haplotypes diversity of Sri Lankan indigenous chickens from three different geographical sites consisting of highly mixed populations using 90 SNPs in the MHC‐B region. A total of 48 haplotypes were identified. Those included 37 novel haplotypes and 11 previously identified ‘standard’ haplotypes. The MHC‐linked marker, LEI0258, had 23 alleles showing less diversity than defined by MHC‐B SNP haplotypes. Among those identified haplotypes, five standard haplotypes—BSNP‐O02, BSNP‐M01, BSNP‐A04, BSNP‐K03, BSNP‐T04—were most commonly observed, suggesting past introgression of imported breeds. Comparison of the MHC‐B haplotypes of Sri Lankan and four other global populations with previously defined haplotypes indicated the sharing of 23 standard haplotypes with common origins. Novel haplotypes are population‐specific and not shared among the geographical boundaries. Backyard indigenous chickens are unselected, highly crossbred, and generally thrive under dynamic environmental conditions. Hence free‐range production systems may be responsible for maintaining high diversity in the MHC‐B region with novel haplotypes.
Baby wipes and nappy rash – what is the relationship? A review
Authors: Mactaggart Emma , Orchard David , Mui Tam Mei 
Published: September 2021

AbstractBaby wipes are a commonly used cleansing method for infants. A literature review has been performed to assess if using baby wipes is beneficial or harmful compared to water and cloth in terms of nappy rash. This includes a detailed analysis of baby wipe ingredients, as many skin irritants as well as allergens are identified. MedLine, Embase and PubMed were searched and after 420 titles and abstracts were screened, 21 studies remained for inclusion. Baby wipes are deemed as superior to water and cloth in the majority of the literature. However, no definitive conclusion can be drawn as many studies are also industry funded. The most notable allergens identified are fragrances, such as linalool, cocamidopropyl betaine (surfactant), formaldehyde‐releasing preservatives and other preservatives, including methylisothiazolinone and methylchloroisothiazolinone. As not all allergens are listed on the label accurately, this can be misleading for the consumer.
Association study of transition of laboratory marker levels and transition of disease activity of atopic dermatitis patients treated with dupilumab
Authors: Mizuno Maki , Horiguchi Go , Teramukai Satoshi , Ichiyama Susumu , Ito Michiko , Hoashi Toshihiko , Kanda Naoko , Saeki Hidehisa 
Published: September 2021

AbstractBackgroundDupilumab, a fully human monoclonal antibody that blocks signalling pathways of interleukin (IL)‐4 and IL‐13, is effective in treating patients with atopic dermatitis (AD). We previously showed that transitions of serum thymus and activation‐regulated chemokine (TARC) levels and eosinophil numbers were strongly associated with that of AD activity and that the transitions of serum lactate dehydrogenase (LDH) and immunoglobulin E (IgE) levels were weakly and not associated with that of AD activity, respectively, in patients treated without dupilumab.ObjectivesThe purpose of this study was to elucidate whether the association of the transition of laboratory marker levels and transition of disease activity in dupilumab‐treated AD patients (present study) was different from that in patients who are not treated with dupilumab (previous study).MethodsSixty AD outpatients treated with dupilumab were included in this study. Associations between the transition of the eczema area and severity index (EASI) score and those of above‐mentioned laboratory marker levels were evaluated using a mixed effects model of EASI as the response variable, laboratory markers as fixed effects and patients as random effects.ResultsThe transitions of serum TARC and LDH levels were associated strongly with that of AD activity, but the transitions of serum IgE level and eosinophil numbers were associated with that of AD activity intermediately and weakly, respectively.ConclusionsLaboratory markers are useful for evaluating the effects of treatments for AD, but the meaning of each laboratory marker depends on the drugs used for treatment.