bluuebunny/crossref_metadata_2025_split huggingface dataset:
A panel of systemic inflammatory response biomarkers for outcome prediction in patients treated with radical cystectomy for urothelial carcinoma
Authors: Schuettfort Victor M. , D'Andrea David , Quhal Fahad , Mostafaei Hadi , Laukhtina Ekaterina , Mori Keiichiro , König Frederik , Rink Michael , Abufaraj Mohammad , Karakiewicz Pierre I. , Luzzago Stefano , Rouprêt Morgan , Enikeev Dmitry , Zimmermann Kristin , Deuker Marina , Moschini Marco , Sari Motlagh Reza , Grossmann Nico C. , Katayama Satoshi , Pradere Benjamin , Shariat Shahrokh F. 
Published: March 2021

ObjectivesTo determine the predictive and prognostic value of a panel of systemic inflammatory response (SIR) biomarkers relative to established clinicopathological variables in order to improve patient selection and facilitate more efficient delivery of peri‐operative systemic therapy.Materials and MethodsThe preoperative serum levels of a panel of SIR biomarkers, including albumin–globulin ratio, neutrophil–lymphocyte ratio, De Ritis ratio, monocyte–lymphocyte ratio and modified Glasgow prognostic score were assessed in 4199 patients treated with radical cystectomy for clinically non‐metastatic urothelial carcinoma of the bladder. Patients were randomly divided into a training and a testing cohort. A machine‐learning‐based variable selection approach (least absolute shrinkage and selection operator regression) was used for the fitting of several multivariable predictive and prognostic models. The outcomes of interest included prediction of upstaging to carcinoma invading bladder muscle (MIBC), lymph node involvement, pT3/4 disease, cancer‐specific survival (CSS) and recurrence‐free survival (RFS). The discriminatory ability of each model was either quantified by area under the receiver‐operating curves or by the C‐index. After validation and calibration of each model, a nomogram was created and decision‐curve analysis was used to evaluate the clinical net benefit.ResultsFor all outcome variables, at least one SIR biomarker was selected by the machine‐learning process to be of high discriminative power during the fitting of the models. In the testing cohort, model performance evaluation for preoperative prediction of lymph node metastasis, ≥pT3 disease and upstaging to MIBC showed a 200‐fold bootstrap‐corrected area under the curve of 67.3%, 73% and 65.8%, respectively. For postoperative prognosis of CSS and RFS, a 200‐fold bootstrap corrected C‐index of 73.3% and 72.2%, respectively, was found. However, even the most predictive combinations of SIR biomarkers only marginally increased the discriminative ability of the respective model in comparison to established clinicopathological variables.ConclusionWhile our machine‐learning approach for fitting of the models with the highest discriminative ability incorporated several previously validated SIR biomarkers, these failed to improve the discriminative ability of the models to a clinically meaningful degree. While the prognostic and predictive value of such cheap and readily available biomarkers warrants further evaluation in the age of immunotherapy, additional novel biomarkers are still needed to improve risk stratification.
Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa
Authors: Odom Karan J. , Araya‐Salas Marcelo , Morano Janelle L. , Ligon Russell A. , Leighton Gavin M. , Taff Conor C. , Dalziell Anastasia H. , Billings Alexis C. , Germain Ryan R. , Pardo Michael , de Andrade Luciana Guimarães , Hedwig Daniela , Keen Sara C. , Shiu Yu , Charif Russell A. , Webster Michael S. , Rice Aaron N. 
Published: March 2021

ABSTRACTAnimals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high‐dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three‐stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross‐taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.
The impact of the COVID‐19 pandemic on hospitalizations for oral and oropharyngeal cancer in Brazil
Authors: da Cunha Amanda Ramos , Antunes José Leopoldo Ferreira , Martins Manoela Domingues , Petti Stefano , Hugo Fernando Neves 
Published: March 2021

AbstractTimely diagnosis and treatment of oral and oropharyngeal cancers are central for the patient's survival. Our objective was to document the impact of the COVID‐19 pandemic on the rate of hospitalizations due to these cancers in Brazil's National Health System (SUS). The number of hospitalizations by these cancers during the first periods of the pandemic—and between the same period of 2016 to 2019—was retrieved from the SUS Hospital Information System. We compared hospitalization rates between pre‐ and pandemic periods, by State. The hospitalization rate for oral and oropharyngeal cancer during the pandemic was lower than that of the same period of previous years. The decline between 2019 and 2020 was of 49.3%, reaching 60% in the North. The reduction in hospitalization during an extended period suggests that oral and oropharyngeal cancer care will be postponed, with potentially detrimental impact on survival.
Family treatment court participation and permanency in a rural setting: Outcomes from a rigorous quasi‐experiment
Authors: Lloyd Sieger Margaret H. , Becker Jessica , Brook Jody 
Published: March 2021

AbstractSubstance‐affected families are frequently cited as the most challenging families to serve within the child welfare context, particularly in rural settings where treatment services may be few and far between. Growing evidence suggests that family treatment courts (FTCs) may be more effective than their traditional counterpart at achieving key child welfare goals; however, prior studies have been limited in their methodological rigour. This study used treatment and matched comparison data to test foster care exit patterns of families with children in foster care due to parental substance use. Treatment group data were collected on a sample of 91 children with open dependency cases in an integrated FTC in a rural Midwestern town. Propensity score nearest neighbour one‐to‐two matching was used to identify a comparison group of 146 children. Findings suggest that FTC participation significantly influenced foster care exits. Survival analyses revealed that FTC children were 170% more likely to reunify, and 58% more likely to achieve permanency, than comparison cases. The effect of FTC participation on likelihood of reunification and likelihood of permanency was stronger when models estimated outcomes from FTC start date, rather than child removal date. Implications for social work practice, research, and education are discussed.
A Phase I, Randomized, Double‐Blind, Placebo‐Controlled, Single‐Dose and Multiple‐Rising‐Dose Study of the BTK Inhibitor TAK‐020 in Healthy Subjects
Authors: Esfandiari Ehsanollah , Chen Mary , Smithson Glennda , Blair Derek , Faessel Helene , Wagner John , Mclean Lachy , Fedyk Eric R. 
Published: March 2021

Bruton’s tyrosine kinase (BTK) is a target for treatment of hematologic malignancies and autoimmune diseases. TAK‐020 is a highly selective covalent BTK inhibitor that inhibits both B cell receptor and fragment crystallizable receptor signaling. We assessed the safety/tolerability and pharmacokinetics/pharmacodynamics (PDs) of TAK‐020 in healthy subjects. Each cohort of the single‐rising dose (n = 72; 9 cohorts) and the multiple‐rising dose (n = 48; 6 cohorts) portions of the study comprised six TAK‐020‐treated and two placebo‐treated, subjects aged 18–55 years (inclusive). The PD effects were assessed by measuring BTK occupancy and the inhibition of fragment crystallizable epsilon receptor 1 (FcεRI)‐mediated activation of basophils. Overall, treatment‐emergent adverse events (TEAEs) were similar to placebo; there were no serious TEAEs or no TEAEs leading to discontinuation. TAK‐020 was rapidly absorbed (median time to maximum plasma concentration (Tmax) 45–60 minutes) with a half‐life of ~ 3–9 hours at doses ≥ 2.5 mg. TAK‐020 exposure was generally dose proportional for single doses ≤ 70 mg and after multiple doses of ≤ 60 mg once daily. Target occupancy was dose dependent, with doses ≥ 2.5 mg yielding maximum and sustained occupancy > 70% for > 96 hours. Single doses ≥ 4.4 mg reduced FcεRI‐mediated activation of basophils by > 80% and comparable inhibition was observed with daily dosing ≥3.75 mg for 9 days. Inhibition persisted for 24–72 hours postdose and the duration generally increased with dose. TAK‐020 was generally well‐tolerated in healthy subjects after single and multiple doses and demonstrated target engagement and pathway modulation. The PD effects outlasted drug exposures, as expected for covalent inhibition of BTK.
Drugs used for the treatment of cerebral and disseminated infections caused by free‐living amoebae
Authors: Taravaud Alexandre , Fechtali‐Moute Zineb , Loiseau Philippe M. , Pomel Sébastien 
Published: March 2021

AbstractFree‐living amoebae (FLAs) are protozoa developing autonomously in diverse natural or artificial environments. The FLAs Acanthamoeba spp., Balamuthia mandrillaris, and Naegleria fowleri represent a risk for human health as they can become pathogenic and cause severe cerebral infections, named granulomatous amoebic encephalitis (GAE), Balamuthia amoebic encephalitis (BAE), and primary amoebic meningoencephalitis (PAM), respectively. Additionally, Acanthamoeba sp. can also rarely disseminate to diverse organs, such as the skin, sinuses, or bones, and cause extracerebral disseminated acanthamebiasis (EDA). No consensus treatment has been established for cerebral FLA infections or EDA. The therapy of cerebral and disseminated FLA infections often empirically associates a large diversity of drugs, all exhibiting a high toxicity. Nevertheless, these pathologies lead to a high mortality, above 90% of the cases, even in the presence of a treatment. In the present work, a total of 474 clinical cases of FLA infections gathered from the literature allowed to determine the frequency of usage, as well as the efficacy of the main drugs and drug combinations used in the treatment of these pathologies. The efficacy of drug usage was determined based on the survival rate after drug administration. The most efficient drugs, drug combinations, and their mechanism of action were discussed in regard to the present recommendations for the treatment of GAE, EDA, BAE, and PAM. At the end, this review aims to provide a useful tool for physicians in their choice to optimize the treatment of FLA infections.
MRI measures of hypothalamic injury are associated with glucagon‐like peptide‐1 receptor agonist treatment response in people with hypothalamic obesity
Authors: Perez Francisco A. , Elfers Clinton , Yanovski Jack A. , Shoemaker Ashley H. , Abuzzahab M. Jennifer , Roth Christian L. 
Published: March 2021

AbstractAimTo evaluate whether neuroimaging‐delineated regions of hypothalamic injury are associated with a differential treatment response to a glucagon‐like peptide‐1 receptor agonist (GLP‐1RA) in patients with hypothalamic obesity (HO).Materials and MethodsWe performed a prespecified secondary analysis of a randomized, multicentre, double‐blind, placebo‐controlled trial of people aged 10–25 years with hypothalamic injury and HO randomized to the GLP‐1RA exenatide once‐weekly (ExQW) or placebo for 36 weeks. Subjects underwent MRI prior to enrolment and the degree of hypothalamic damage was assessed using an integrative hypothalamic lesion score (HLS). Mammillary body (MB) damage was specifically determined. The main clinical endpoints were % change in body mass index (BMI) and change in % body fat. Nested ANCOVA models including a treatment × imaging measure interaction were compared using partial F‐tests to assess whether the effect of ExQW treatment differed by severity of hypothalamic damage.ResultsComplete data were available in 35/42 randomized participants (placebo, n = 15; ExQW, n = 20). ExQW‐treated patients with worse HLS or bilateral MB damage had greater reductions in % body fat at 36 weeks (interaction coefficient estimates for HLS: −0.9%, 95% CI –1.6% to −0.2%, p = .02; for MB damage: −7.4%, 95% CI –10.1% to −4.7%, p < .001, respectively) but not for BMI % change. Similarly, patients with more damaged and smaller MB cross‐sectional areas had greater reductions in % body fat following ExQW (interaction coefficient estimate 0.3%, 95% CI 0.2%–0.4%, p < .001).ConclusionsIn people with HO, greater hypothalamic damage as determined by MRI, in particular MB injury, is associated with greater reductions in adiposity following GLP‐1RA treatment.
A new, highly aggressive race of Austropuccinia psidii infects a widely planted, myrtle rust‐resistant, eucalypt genotype in Brazil
Authors: Almeida Rosiane F. , Machado Patrícia S. , Damacena Michelle B. , Santos Samuel A. , Guimarães Lúcio M.S. , Klopfenstein Ned B. , Alfenas Acelino C. 
Published: March 2021

AbstractMyrtle rust (MR) caused by Austropuccinia psidii is one of the most important diseases affecting eucalypt (Eucalyptus) plantations in Brazil. Over the years, selection and planting of MR‐resistant clones has been the primary strategy for MR management. In May 2013, young trees of the GG100 hybrid (E. grandis × E. urophylla) clone—widely planted in Brazil and previously classified as resistant to MR—were infected by A. psidii in Minas Gerais, Brazil. In this study, artificial inoculations of a eucalypt clone set with differential reactions to A. psidii races were used to discover a new race of A. psidii (race 5) that was highly aggressive on the majority of eucalypt clones tested. In addition, only this new race successfully infected eucalypt G26 and 847 genotypes, which were formerly classified as resistant to the four previously known races of A. psidii. Since G26 genotype is homozygous for Ppr1 (a major resistance gene against A. psidii), this is the first report of MR resistance breakdown in a eucalypt genotype homozygous for Ppr1. Our findings demonstrate that this new A. psidii race is highly aggressive and capable of infecting a larger number of eucalypt genotypes compared with the previously known A. psidii races 1, 2, 3, and 4.
Plant functional type indirectly affects peatland carbon fluxes and their sensitivity to environmental change
Authors: Whitaker Jeanette , Richardson Harriett R. , Ostle Nicholas J. , Armstrong Alona , Waldron Susan 
Published: March 2021

AbstractThe sensitivity of peatland carbon (C) fluxes to changes in climate and hydrology are uncertain due to the complex interactions between plants and peat properties. In this study we examine how peat cores taken from under three plant functional types (PFT) (bryophyte, graminoid and ericoid) differ in their biotic and abiotic properties and how this indirectly modulates the response of C fluxes to environmental change. Peat cores taken from under three PFTs had their aboveground vegetation removed to exclude direct plant‐mediated effects, and were incubated in a temperature × water table factorial experiment at 12, 14 and 16°C (air temperature) with the water table level −25, −15 or −5 cm below the peat surface. Carbon dioxide (CO2) and methane (CH4) fluxes were measured over 11 months. Emissions of CO2and CH4increased with temperature, with strong positive (CH4) and negative (CO2) interactions with increasing water table level. There were significant effects of removed PFT on the environmental sensitivity of CH4, but not CO2fluxes. CH4emissions were greatest in peat with graminoid PFT removed at the warmest temperature but these indirect effects were not explained by peat abiotic or biotic properties, which did not differ between PFTs. These results show that climate change‐induced expansion of graminoids in northern peatlands will have direct and indirect effects on C fluxes and the stability of peatland C stores. These responses will be determined by the interactive effects of vegetation composition, hydrology and warming on methane‐cycling microbial communities.HighlightsPeatland carbon flux strength under a changing climate is influenced by PFT.Peat from under graminoid PFT emits more methane than peat from under bryophyte or ericoid PFT.Prior PFT cover influenced methane emissions, but did not affect peat abiotic or biotic properties.Increases in graminoid cover with climate change could indirectly increase peatland methane fluxes.
How pore structure non‐stationarity compromises flow properties representativity (REV) for soil samples: Pore‐scale modelling and stationarity analysis
Authors: Gerke Kirill M. , Karsanina Marina V. 
Published: March 2021

AbstractClassic soil physics relies heavily on the concept of representative elementary volume (REV), which is necessary to perform upscaling from the studied soil samples and parameterize continuum scale hydrological models (e.g., based on Richards or Darcy equations). In this paper, we explore the boundaries of the classic REV concept and conventional representativity studies that claim REV for any given physical property, and that its values converge to a steady value with increasing sample volume. We chose two undisturbed soil samples of standard size from Ah and B horizons, subcropped two subvolumes within each of them and performed pore‐scale flow simulations using binarized X‐ray microtomography scans as input data. The volume of the simulation domains was 9003 voxels, with a physical volume within two orders of magnitude of the whole soil core. Based on the 3D pore geometry images and the resulting flow velocity and pressure fields, we performed REV analysis for the saturated hydraulic conductivity and porosity. Although in general subvolumes showed classical REV behaviour (convergence of porosity and saturated hydraulic conductance (Ksat)to plateau‐like behaviour), their flow properties converged to different REV values. We also evaluated the stationarity of pore structures by computing the directional correlation functions to explain the observed non‐unique behaviour. We concluded that neither of the studied samples can be considered to be representative due to their structural non‐stationarity. We extensively discussed the implications of these results for the upscaling and parameterization of continuum‐scale flow models. We argued that the plateau in Ksat (or any other physical property) is a necessary, but insufficient, condition for the REV, which requires (at least) pore structure stationarity as an additional criterion. REV as a concept is much broader than previously anticipated and the possibility of establishing REVs in structured soils will require an analysis of tensorial flow properties with correct boundary conditions, multiscale soil structure imaging with stationarity analysis, and pore‐scale simulations on fused multiscale images.Highlights
Ksat analysis within subvolumes showed classical REV behaviour but resulted in non‐unique REVs for the soil samples studied
Based on the stationarity analysis we argued that the conventional soil core samples studied were not REVs
Plateau‐like behaviour in physical properties is a necessary but insufficient condition for REV
Soil structure information is necessary to properly establish REV or upscale flow properties
Carbon sequestration in artificial silicate soils facilitated by arbuscular mycorrhizal fungi and glomalin‐related soil protein
Authors: Son Yejin , Stott Kevin , Manning David A. C. , Cooper Julia M. 
Published: March 2021

AbstractIn urban areas, pre‐existing concrete‐based demolition wastes and purposely introduced crushed dolerite have been used to create artificial soils, which capture carbon (C) as carbonate minerals and offset greenhouse gas (GHG) emissions. Arbuscular mycorrhizal fungi (AMF) can enhance capture of C in artificial soils through production of glomalin‐related soil protein (GRSP), which facilitates soil organic carbon (SOC) storage and aggregation, and may also enhance precipitation of soil inorganic carbon (SIC). In this paper, we show how different mixtures of dolerite and concrete affect AMF community structure and function, GRSP fractions, and soil organic and inorganic carbon contents. We used nine demonstration plots, 1 m deep, to simulate a constructed urban soil, consisting of different proportions (0, 30, 50, 70 and 100%) of either crushed concrete demolition waste or dolerite quarry fines and sown to a species‐rich meadow mixture, to investigate AMF colonization and community structure (using DNA terminal restriction fragment length polymorphism), contents of easily‐extractable and difficultly‐extractable GRSP, and both organic and inorganic carbon contents. All artificial soils supported functioning AMF communities with different levels of GRSP, SIC and SOC. The 100% dolerite and 100% concrete soils had higher values of difficultly‐to‐extract GRSP andSOC than pure sand, whereas 100% concrete had higher AMF colonization and SOC than sand. AMF community analysis indicated that high GRSP producing species were abundant in 100% dolerite and 100% concrete. These findings demonstrate that there is potential to incorporate demolition waste or dolerite products into the land to support environmental sustainability and enhance soil C sequestration.Highlights
In constructed soils, crushed concrete and dolerite more effectively enhance GRSP and soil organic and inorganic carbon contents than sand.
Use of crushed concrete and dolerite in plant‐growing substrates is a novel way to combat climate change.