bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature
Authors: Rawlings Anna , O'Connor Eoin , Moody Suzy C. , Dudley Ed , Boddy Lynne , Fowler Mike S. , Fitzpatrick David A. , Doyle Sean , Eastwood Dan C. 
Published: July 2021

Abstract

Decomposition of lignin‐rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress‐selected constituent of the same communities, in response to constant and diurnally cycling temperature.

We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design.

Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under‐enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely, E. glandulosa showed little differential response to the experimental treatments.

Synthesis. By demonstrating temperature‐dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community‐mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well‐annotated genomes.
A comparison of methods for measuring spatial access to health care
Authors: Drake Coleman , Nagy Dylan , Nguyen Thuy , Kraemer Kevin L. , Mair Christina , Wallace David , Donohue Julie 
Published: July 2021

AbstractObjectiveTo compare measures of spatial access to care commonly used by policy makers and researchers with the more comprehensive enhanced two‐step floating catchment area (E2SFCA) method.Study SettingFourteen southwestern Pennsylvania counties.Study DesignWe estimated spatial access to buprenorphine‐waivered prescribers using three commonly used measures—Euclidean travel distance to the closest prescriber, travel time to the closest provider, and provider‐to‐population ratios—and the E2SFCA. Unlike other measures, the E2SFCA captures provider capacity, potential patient volume, and travel time to prescribers.Data Collection/Extraction MethodsWe measured provider capacity as the number of buprenorphine prescribers listed at a given address in the Drug Enforcement Agency's 2020 Controlled Substances Act Registrants Database, and we measured potential patient volume as the number of nonelderly adults in a given census tract as reported by the 2018 American Community Survey. We estimated travel times between potential patients and prescribers with Bing Maps and Mapbox application programming interfaces. We then calculated each spatial access measure using the R programming language. We used each measure of spatial access to identify census tracts in the lowest quintile of spatial access to prescribers.Principal FindingsThe Euclidean distance, travel time, and provider‐to‐population ratio measures identified 48.3%, 47.2%, and 69.9% of the census tracts that the E2SFCA measure identified as being in the lowest quintile of spatial access to care, meaning that these measures misclassify 30%–52% of study area census tracts as having sufficient spatial access to buprenorphine prescribers.ConclusionsMeasures of spatial access commonly used by policy makers do not sufficiently accurately identify geographic areas with relatively low access to prescribers of buprenorphine. Using the E2SFCA in addition to the commonly used measures would allow policy makers to precisely target interventions to increase spatial access to opioid use disorder treatment and other types of health care services.
Relative species abundance estimation in artificial mixtures of insects using mito‐metagenomics and a correction factor for the mitochondrial DNA copy number
Authors: Garrido‐Sanz Lidia , Senar Miquel Àngel , Piñol Josep 
Published: July 2021

AbstractMito‐metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high‐throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single‐species libraries to calibrate the bioinformatic pipeline and mixed‐species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within‐species estimation) but failed to estimate the RSA within a single sample (across‐species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single‐species libraries and the lengths of the whole genomes and mitogenomes.
Lung cancer treatment patterns and factors relating to systemic therapy use in Australia
Authors: Ngo Preston , Goldsbury David E. , Karikios Deme , Yap Sarsha , Yap Mei Ling , Egger Sam , O'Connell Dianne L. , Ball David , Fong Kwun M. , Pavlakis Nick , Rankin Nicole M. , Vinod Shalini , Canfell Karen , Weber Marianne F. 
Published: July 2021

AbstractAimSystemic therapies for lung cancer are rapidly evolving. This study aimed to describe lung cancer treatment patterns in New South Wales, Australia, prior to the introduction of immunotherapy and latest‐generation targeted therapies.MethodsSystemic therapy utilization and treatment‐related factors were examined for participants in the New South Wales 45 and Up Study with incident lung cancer ascertained by record linkage to the New South Wales Cancer Registry (2006–2013). Systemic therapy receipt to June 2016 was determined using medical and pharmaceutical claims data from Services Australia, and in‐patient hospital records. Factors related to treatment were identified using competing risks regressions.ResultsA total of 1,116 lung cancer cases were identified with a mean age at diagnosis of 72 years and median survival of 10.6 months. Systemic therapy was received by 45% of cases. Among 400 cases with metastatic non–small cell lung cancer, 51% and 28% received first‐ and second‐line systemic therapy, respectively. Among 112 diagnosed with small‐cell lung cancer, 79% and 29% received first‐ and second‐line systemic therapy. The incidence of systemic therapy was lower for participants with indicators of poor performance status, lower educational attainment, and those who lived in areas of socioeconomic disadvantage; and was higher for participants with small‐cell lung cancer histology or higher body mass index.ConclusionThis population‐based Australian study identified patterns of systemic therapy use for lung cancer, particularly small‐cell lung cancer. Despite a universal healthcare system, the analysis revealed socioeconomic disparities in health service utilization and relatively low utilization of systemic therapy overall.
A method for magnetocardiography functional localization based on boundary element method and Nelder–Mead simplex algorithm
Authors: Lu Zhihong , Jiang Dingsong , Yang Jianzhong 
Published: July 2021

AbstractBackgroundThe magnetocardiography (MCG) functional localization can transfer the biomagnetic signal to the electrical activity information inside the heart. The electrical activity is directly related to the physiological function of the heart.MethodsThis study proposes a practical method for MCG functional localization based on the boundary element method (BEM) and the Nelder–Mead (NM) simplex algorithm. Single equivalent moving current dipole (SEMCD) is served as the equivalent cardiac source. The parameters of SEMCD are adapted using the NM simplex algorithm by fitting the measured MCG with the calculated MCG obtained based on BEM. The SEMCD parameters are solved in the sense that the difference between measured and calculated MCG is minimized.ResultsThe factors affecting the localization accuracy of this BEM–NM method were first explored with synthetic signals. Then, the results with real MCG signals show a good agreement between the SEMCD location and the region where ventricle depolarization starts, demonstrating the feasibility of this idea.ConclusionsThis is the first three‐dimensional localization of the onset of ventricular depolarization with the BEM–NM method. The method is promising in the noninvasive localization of lesions for heart diseases.
Protective effect of estradiol copreservation against kidney ischemia‐reperfusion injury
Authors: Zhou Dawei , Leung Junto , Xu Weichen , Ye Shaojun , Dong Caitao , Huang Wanbin , Ye Qifa , Wang Yanfeng 
Published: July 2021

AbstractIschemia‐reperfusion injury (IRI) is the major cause of delayed graft function (DGF) during the posttransplantation period. Estradiol (E2) prevents IRI‐induced kidney dysfunction and tissue injury. However, many side effects limit E2’s in vivo application. Recent evidence uncovers E2’s expanded use in the field of transplantation. We aimed to study if and how E2 exerts protective activity during the period of kidney organ preservation. The autologous kidney transplant model in rats was first established. Rats were divided into 5 groups: normal group (N), sham group (sham), static cold storage (SCS) 4 hours group (control), SCS 4 hours + ethanol (1 µL/mL) group (solvent), and SCS 4 hours + ethanol (1 µL/mL) + E2 (1000 ng/mL) group (E2). ERα expression under hypothermia was measured by western blotting. Moreover, biochemical analyses of plasma levels of creatinine, BUN, estradiol, and testosterone were examined. Among all groups, kidney tissues were collected and processed for further western blot analysis about ERα, eNOS, Bcl‐2, and Bax expression, histological analyses such as H&E staining to evaluate pathological severity. In addition, a TUNEL assay is performed to evaluate apoptosis. E2 copreservation upregulated ERα expression under hypothermia. Moreover, E2 copreservation reduced levels of creatinine and BUN in plasma but without affecting estradiol and testosterone. Further, E2 copreservation increased expression of eNOS and antiapoptotic Bcl‐2 and decreases expression of proapoptotic Bax. E2 copreservation significantly inhibited IRI‐induced apoptosis and evidently improved pathological severity in the kidney of rats. E2 copreservation exerts protective activity against IRI‐induced pro‐inflammatory and proapoptotic effects in kidneys during organ preservation time and improves transplanted kidney function.
PRO‐C3 and ADAPT algorithm accurately identify patients with advanced fibrosis due to alcohol‐related liver disease
Authors: Madsen Bjørn S. , Thiele Maja , Detlefsen Sönke , Kjærgaard Maria , Møller Linda S. , Trebicka Jonel , Nielsen Mette J. , Gudmann Natasja Stæhr , Leeming Diana J. , Karsdal Morten A. , Krag Aleksander ,   the GALAXY consortium
Published: July 2021

SummaryBackgroundAlcohol is a main cause of preventable deaths and frequently leads to the development of alcohol‐related liver disease. Due to the lack of diagnostics, patients are commonly diagnosed after developing clinical manifestations. Recently, the biomarker PRO‐C3 was shown to accurately identify fibrosis due to non‐alcoholic fatty liver disease.AimTo assess the diagnostic accuracy of PRO‐C3, the ADAPT score and best‐performing non‐patented serological test to detect advanced alcohol‐related liver fibrosis.MethodsWe enrolled 426 patients with alcohol overuse in a prospective biopsy‐controlled study. We evaluated the accuracy of PRO‐C3 and the PRO‐C3‐based algorithm ADAPT to detect advanced liver fibrosis.ResultsThe accuracy of PRO‐C3 was good with an AUROC of 0.85 (95% CI 0.79‐0.90). The best‐performing non‐patented test was the Forns index with an AUROC of 0.83 (95% CI 0.78‐0.89). The ADAPT algorithm performed better as compared to both the Forns index and PRO‐C3 alone with an AUROC = 0.88 (95% CI 0.83‐0.93).ConclusionPRO‐C3 is a new marker with high accuracy to detect advanced alcohol‐related liver fibrosis. The diagnostic accuracy of PRO‐C3 can be further improved by using the ADAPT algorithm in which the test outperforms currently available non‐patented serological fibrosis markers. The study is registered in the Odense Patient Data Exploratory Network (OPEN) under study identification numbers OP_040 (https://open.rsyd.dk/OpenProjects/da/openProject.jsp?openNo=40) and OP_239 (https://open.rsyd.dk/OpenProjects/openProject.jsp?openNo=239&lang=da).
A qualitative study of dental professionals' and patients' knowledge and perceptions of the impact of periodontal disease on systemic health and quality of life
Authors: Wong Li Beng , Kunnasegaran Sree Gaithiri , Yap Adrian Ujin , Allen Patrick Finbarr 
Published: July 2021

AbstractObjectivesThis qualitative study of dental professionals and patients with periodontal disease: (1) explored their knowledge and perceptions on the impact of periodontal disease on systemic health and quality of life (QoL); (2) assessed their familiarity with QoL instruments used to measure the impact of periodontal disease.MethodsIn‐depth semi‐structured face‐to‐face interviews were conducted with 10 dental professionals and 10 patients selected using purposive sampling. Audio recordings of the interviews were transcribed verbatim, coded and analysed using NVivo software (version 11, QSR International), followed by an inductive thematic analysis of the data.ResultsThree themes were identified for the dental professionals: (1) knowledge of periodontal disease, systemic health and QoL; (2) experience in managing patients with periodontal disease to improve their QoL; (3) perceived value of having a disease‐specific QoL instrument for periodontal disease. Three themes were identified for patients with periodontal disease: (1) knowledge of periodontal disease, systemic health and QoL; (2) experience and perception of how periodontal treatment can improve QoL; (3) perceived value of having a disease‐specific QoL instrument for periodontal disease. Both groups were knowledgeable about the relationship between periodontal disease, systemic health and QoL and had experienced how periodontal treatment could improve QoL. Both groups also agreed that a disease‐specific QoL instrument for periodontal disease would be beneficial.ConclusionsBoth the dental professionals and patients with periodontal disease were aware of the relationship between periodontal disease, systemic health and QoL, including the benefits of periodontal treatment in improving QoL. The value of developing a disease‐specific QoL instrument for periodontal disease was recognized by both groups.
SOX2 plays a crucial role in cell proliferation and lineage segregation during porcine pre‐implantation embryo development
Authors: Lee Mingyun , Choi Kwang‐Hwan , Oh Jong‐Nam , Kim Seung‐Hun , Lee Dong‐Kyung , Choe Gyung Cheol , Jeong Jinsol , Lee Chang‐Kyu 
Published: July 2021

AbstractObjectivesGene regulation in early embryos has been widely studied for a long time because lineage segregation gives rise to the formation of a pluripotent cell population, known as the inner cell mass (ICM), during pre‐implantation embryo development. The extraordinarily longer pre‐implantation embryo development in pigs leads to the distinct features of the pluripotency network compared with mice and humans. For these reasons, a comparative study using pre‐implantation pig embryos would provide new insights into the mammalian pluripotency network and help to understand differences in the roles and networks of genes in pre‐implantation embryos between species.Materials and methodsTo analyse the functions of SOX2 in lineage segregation and cell proliferation, loss‐ and gain‐of‐function studies were conducted in pig embryos using an overexpression vector and the CRISPR/Cas9 system. Then, we analysed the morphological features and examined the effect on the expression of downstream genes through immunocytochemistry and quantitative real‐time PCR.ResultsOur results showed that among the core pluripotent factors, only SOX2 was specifically expressed in the ICM. In SOX2‐disrupted blastocysts, the expression of the ICM‐related genes, but not OCT4, was suppressed, and the total cell number was also decreased. Likewise, according to real‐time PCR analysis, pluripotency‐related genes, excluding OCT4, and proliferation‐related genes were decreased in SOX2‐targeted blastocysts. In SOX2‐overexpressing embryos, the total blastocyst cell number was greatly increased but the ICM/TE ratio decreased.ConclusionsTaken together, our results demonstrated that SOX2 is essential for ICM formation and cell proliferation in porcine early‐stage embryogenesis.
How has access to legal cannabis changed over time? An analysis of the cannabis retail market in Canada 2 years following the legalisation of recreational cannabis
Authors: Myran Daniel T. , Staykov Emiliyan , Cantor Nathan , Taljaard Monica , Quach Bradley I. , Hawken Steven , Tanuseputro Peter 
Published: July 2021

AbstractIntroductionThis study describes the legal recreational cannabis market across Canada over the 2 years following legalisation. We compared changes in access to the legal cannabis retail market for all provinces and territories (jurisdictions) in Canada and explored differences between jurisdictions.MethodsWe collected data for all legal cannabis stores in Canada over five time periods following legalisation in October 2018. We examined the following measures by jurisdiction and retail model (public vs. private operation): absolute and per capita store numbers, hours of operation and store access across neighbourhoods.ResultsTwo years following legalisation, there were a total of 1183 legal cannabis stores open across Canada (3.7 stores per 100 000 individuals aged 15+). There was wide variation between jurisdictions in access to retail stores, with the lowest stores per capita in Quebec and Ontario (0.6 and 1.6 per 100 000), and the highest in Alberta and Yukon (14.3 per 100 000 in both). Jurisdictions with private retail models had more stores (4.8 vs. 1.0 per 100 000), held greater median weekly hours (80 vs. 69) and experienced greater store growth over time compared to public models. After adjusting for confounders, there were 1.96 times (95% confidence intervals: 1.84, 2.09) more cannabis stores within 1000 m of the lowest‐ compared to the highest‐income quintile neighbourhoods.Discussion and ConclusionsWhile access to the recreational cannabis retail market has increased following legalisation, there is substantial variation in access between jurisdictions and evidence of concentration in lower‐income neighbourhoods. These differences may contribute to disparities in cannabis use and harms.
Falling through the Cracks: Digital Infrastructures of Social Protection in Ecuador
Authors: Palacio Ludeña María Gabriela 
Published: July 2021

ABSTRACTWhile cash transfers gain prominence as a response to the COVID‐19 pandemic, there is a strong impulse to regard them as a stepping‐stone towards the formalization of employment and universalization of social protection. This contribution problematizes how populations in informality are included in narrowly targeted social assistance interventions, which are heavily reliant on targeted schemes and fail to make informality legible to programme administrators. The focus of the article lies in the politics of exclusion and inclusion that permeate digital infrastructures, particularly data infrastructures such as social registries, that are used to target Ecuador's most prominent social assistance programme, Bono de Desarrollo Humano, and the COVID‐related programme Bono de Protección Familiar. The article is based on ethnographic work, interviews and narrative analysis. It finds that social registries compiled for proxy means testing weaken the link between eligibility and informal employment and obscure the processes that perpetuate precarity. More recent data innovations, such as machine learning, are also insufficient to locate vulnerable workers as they learn from historical social registries data and replicate their biases, for example by overlooking non‐poor areas where informal employment also occurs. Data infrastructures have shifted attention to the technicalities of the selection of beneficiaries and away from power imbalances in the design of social assistance, despite their selectivity and politics.
Effect of donor‐specific blood transfusions on allotransplanted teeth in a monkey model: Histoquantification of periodontal healing
Authors: Schwartz Ole , Thomsen Mogens , Dickmeiss Ebbe , Andreasen Jens Ove 
Published: July 2021

AbstractBackground/AimsPre‐transplant blood transfusions have previously shown a positive effect on organ allograft survival in humans and various animal species. The aims of this study were, first, to evaluate the effect of pre‐transplant donor‐specific blood transfusions on periodontal healing of fully developed allotransplanted teeth in monkeys; and second, to investigate the immune response against donor antigens and to determine a possible correlation between alloimmune reactions and histopathological signs of rejection.Material and MethodsTwenty monkeys (Cercopithecus aethiops) were divided into ten pairs with similar sizes of incisors. One monkey in each pair gave three transfusions to the other monkey with 1‐week intervals. One week after the last transfusion, each pair exchanged simultaneously a central maxillary incisor and a lateral mandibular incisor. The corresponding central maxillary and mandibular lateral incisors were autotransplanted to the contralateral sockets. All teeth were treated endodontically per‐operatively. Histocompatibility was evaluated by mixed lymphocyte culture before the first transfusion, while alloantibodies and cell‐mediated alloresponses were measured before transfusions and at 2 and 8 weeks after transplantation. All animals were sacrificed 8 weeks after tooth transplantation. Serial sections of the transplanted teeth were quantified histologically.ResultsMixed lymphocyte cultures showed positive reactions in 19 of 20 cases, indicating incompatibility. The majority of the monkeys developed antibodies towards the tooth donor. Cell‐mediated cytotoxicity was negative in all monkeys. Histoquantification revealed a mean score of 70% normal periodontal ligament (PDL) in autotransplanted teeth, with 5% ankylosis. The allografts had a mean score of 17% normal PDL and 63% ankylosis, with no significant influence of transfusion. However, in the mandibular grafts, a tendency towards a positive transfusion effect was seen.ConclusionsDonor‐specific blood transfusion did not reduce ankylosis in tooth allografts. The healing of mandibular incisor tooth allografts was improved, but not that of maxillary incisors. Donor‐specific antibodies showed no effect on the survival of allograft PDL.