bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonhomogeneous Markov chain for estimating the cumulative risk of multiple false positive screening tests
Authors: Golmakani Marzieh K , Hubbard Rebecca A , Miglioretti Diana L 
Published: May 2021

AbstractScreening tests are widely recommended for the early detection of disease among asymptomatic individuals. While detecting disease at an earlier stage has the potential to improve outcomes, screening also has negative consequences, including false positive results which may lead to anxiety, unnecessary diagnostic procedures, and increased healthcare costs. In addition, multiple false positive results could discourage participating in subsequent screening rounds. Screening guidelines typically recommend repeated screening over a period of many years, but little prior research has investigated how often individuals receive multiple false positive test results. Estimating the cumulative risk of multiple false positive results over the course of multiple rounds of screening is challenging due to the presence of censoring and competing risks, which may depend on the false positive risk, screening round, and number of prior false positive results. To address the general challenge of estimating the cumulative risk of multiple false positive test results, we propose a nonhomogeneous multistate model to describe the screening process including competing events. We developed alternative approaches for estimating the cumulative risk of multiple false positive results using this multistate model based on existing estimators for the cumulative risk of a single false positive. We compared the performance of the newly proposed models through simulation studies and illustrate model performance using data on screening mammography from the Breast Cancer Surveillance Consortium. Across most simulation scenarios, the multistate extension of a censoring bias model demonstrated lower bias compared to other approaches. In the context of screening mammography, we found that the cumulative risk of multiple false positive results is high. For instance, based on the censoring bias model, for a high‐risk individual, the cumulative probability of at least two false positive mammography results after 10 rounds of annual screening is 40.4.
Identifying the active ingredients of cardiac rehabilitation: A behaviour change technique and qualitative analysis
Authors: McAuliffe Hannah , Mc Sharry Jenny , Dunne Denise , Byrne Molly , Meade Oonagh 
Published: May 2021

ObjectivesDespite evidence that cardiac rehabilitation (CR) can be effective, the active ingredients or behaviour change techniques (BCTs) constituting effective CR remain unclear. There is also a lack of research surrounding patient and facilitator perceptions of active ingredients. This study sought to identify the active ingredients of a community‐based CR programme and explore patient and facilitator perceptions of the active ingredients.DesignA multimethod design conducted in two stages, a BCT coding stage and a qualitative stage.MethodsThe BCT coding stage involved the observation and audio recording of ten sessions from a community‐based CR programme and the collection of programme materials. Data were coded using the BCT Taxonomy version 1 (Ann Behav Med, 46, 2013, 81). During the qualitative stage, six focus groups were carried out separately with patients (n = 16) and facilitators (n = 4). Qualitative data were analysed using an inductive thematic analysis.ResultsThe BCT coding phase identified 34 BCTs, many of which were highlighted by patients and facilitators. Patients and facilitators felt the group effort, motivation provided by facilitators, individualized care, knowledge gained, acceptance, and fear reduction enabled change. The majority of BCTs identified in the qualitative stage were also identified in the BCT coding stage, excluding a component related to self‐acceptance. Facilitators felt the programme was limited by duration and inadequate psychological support.ConclusionsThe study provides a comprehensive overview of objectively coded BCTs and perceived active ingredients of CR. The findings can be used to inform future refinement and improvement of CR.
Chemotherapy for non‐Hodgkin lymphoma in the hemodialysis patient: A comprehensive review
Authors: Yasuda Hajime , Yasuda Mutsuko , Komatsu Norio 
Published: May 2021

AbstractChemotherapy for non‐Hodgkin lymphoma (NHL) in the hemodialysis (HD) patient is a challenging situation. Because many drugs are predominantly eliminated by the kidneys, chemotherapy in the HD patient requires special considerations concerning dose adjustments to avoid overdose and toxicities. Conversely, some drugs are removed by HD and may expose the patient to undertreatment, therefore the timing of drug administration in relation to HD sessions must be carefully planned. Also, the metabolites of some drugs show different toxicities and dialysability as compared with the parent drug, therefore this must also be catered for. However, the pharmacokinetics of many chemotherapeutics and their metabolites in HD patients are unknown, and the fact that NHL patients are often treated with distinct multiagent chemotherapy regimens makes the situation more complicated. In a realm where uncertainty prevails, case reports and case series reporting on actual treatment and outcomes are extremely valuable and can aid physicians in decision making from drug selection to dosing. We carried out an exhaustive review of the literature and adopted 48 manuscripts consisting of 66 HD patients undergoing 71 chemotherapy regimens for NHL, summarized the data, and provide recommendations concerning dose adjustments and timing of administration for individual chemotherapeutics where possible. The chemotherapy regimens studied in this review include, but are not limited to, rituximab, cyclophosphamide + vincristine + prednisolone (CVP) and cyclophosphamide + doxorubicin + vincristine + prednisolone (CHOP)‐like regimens, chlorambucil, ibrutinib, bendamustine, methotrexate, platinum compounds, cytarabine, gemcitabine, etoposide, ifosfamide, melphalan, busulfan, fludarabine, mogamulizumab, brentuximab vedotin, and 90Y‐ibritumomab tiuxetan.
Adverse childhood experiences and developmental disabilities: risks, resiliency, and policy
Authors: Morgart Kiley , Harrison Joyce Nolan , Hoon Alexander H , Wilms Floet Anna Maria 
Published: May 2021

Thanks to the seminal work of Robert Anda and Vincent Felitti, it is now widely accepted that adverse childhood experiences (ACEs) can have lifelong effects on physical, behavioral, and mental health and that many adult diseases can be considered developmental disorders that began early in life. Genomics has advanced the neurobiological understanding that underpins ACEs, wellness, and disease, which are modulated through stress pathways and epigenetic modifications. While data are currently limited, children with developmental disabilities have an increased ACE risk compared to typically developing peers. This recognition has important ramifications for health and policy interventions that address the root causes of ACEs, especially in this vulnerable population. With increased societal recognition, advances in policy will lead to medical, financial, and public benefits in years to come, hopefully changing healthcare models from ‘sick care’ to ‘well care’.
What this paper adds

Adverse childhood experience (ACE) research has refocused medicine from the question ‘What is wrong with you?’ to ‘What happened to you?’.

Adopting ACE research into public policy can redirect healthcare models from providing ‘sick care’ to promoting ‘well care’.

Not exploring the role of ACEs in children with developmental disabilities leads to further vulnerability and morbidity.

ACEs can be mitigated by early identification and implementation of evidence‐based interventions.
Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain
Authors: Yu Yanyan , Cui Min , Xiao Yutong , Chang Mengyu , Wang Cong , Zhao Lu , Cao Yanhong , Miao Yuan , Chen Zhijie , Han Shijie , Zheng Junqiang 
Published: May 2021

AbstractThe floodplain ecosystem plays an important role in the mediation or regulation of regional ecological functions, and is the heart of ecosystem functions based on soil microbial communities. In the present study, we investigate the patterns and assembly processes of soil microbial communities along nine profile depths (up to 280 cm in depth) of three stages of floodplain community succession (channel bar, newly deposited river beach and tender floodplain) and farmland in the floodplain of the lower Yellow River. Generally, the bacterial community in agricultural soil had the highest diversity, whereas the archaeal community in the tender floodplain had the highest diversity. Compared to bacteria, the co‐occurrence network of archaea was more complex and stable and had high connectivity. Our data suggest that the resistance of bacteria and archaea to environmental changes in deep soil was higher when compared to that in surface soil. Furthermore, stochastic and deterministic processes acted concurrently to regulate the assembly of the soil microbial community in the floodplain ecosystems. However, the relative contributions of the stochastic process and deterministic process are different between the bacterial community and the archaeal community. The lowest contribution of the stochastic process in the bacterial community was in the subsoil, whereas in the archaeal community, it was the opposite. For ecological selection, bacterial communities in different soil profiles, in the succession stages and in the farmland, were mainly selected through homogeneous selection, whereas archaeal communities were selected through heterogeneous selection. Compared with the three floodplain succession stages, the microbial communities of agricultural lands were more assembled by deterministic processes.Highlights
Stochastic and deterministic processes act concurrently to regulate the assembly of soil microbial community in the floodplain ecosystems.
The assembly of the bacterial community was mainly affected by the homogeneous selection.
The archaeal community was mainly affected by the heterogeneous selection.
The microbial communities of agricultural lands were more assembled by deterministic processes.
Chemical composition of soil organic carbon from mixed aspen‐conifer forests characterized with Fourier transform infrared spectroscopy
Authors: Román Dobarco Mercedes , Jacobson Astrid R. , Van Miegroet Helga 
Published: May 2021

AbstractForest species control the quantity and chemistry of organic matter input, which in interaction with the soil physicochemical properties, environmental conditions and microbial community associated with a given ecosystem may result in specific patterns of soil organic carbon (SOC) stabilization and chemistry. The objectives of this study were: (a) to characterize the chemistry of soil organic matter and SOC fractions across the gradient from pure aspen (Populus tremuloidesMichx.) to pure conifer (Abies lasiocarpa(Hook.) Nutt. andPseudotsuga menziesii(Mirbel) Franco) stands in semi‐arid montane forests, and (b) to determine whether the effect of overstory composition on SOC chemistry was patent beyond the influence of site conditions and microbial decomposer community. We used Fourier transform infrared spectroscopy to analyse the chemistry of bulk soil (BS), light fraction (LF) and mineral‐associated SOC (MoM) from mineral soils (0–15 cm) sampled across the natural gradient of aspen and mixed conifer stands from northern and southern Utah. Vegetation overstory had a subtle effect on the MoM fraction, indicating higher proportion of aliphatic C with aspen dominance, whereas there were no differences in LF chemistry between vegetation types. Independently of the vegetation cover type, the MoM fraction was enriched in aliphatic C compared to the LF, although the proportion of polysaccharides and C‐O groups increased in the MoM fraction for plot samples. Differentiation between spectra from soils developed on sedimentary rock and soils developed on basalt, quartzite and limestone, highlighted the influence of parent material and mineralogy on MoM chemistry. The patterns in SOC fractions' chemistry do not allow an affirmation that greater SOC storage under aspen is due to the accumulation of recalcitrant compounds (i.e., aliphatic C) and controlled by litter chemistry. Rather, they suggest that the ensemble of litter chemistry, microbial community and soil properties in aspen stands enhances SOC storage.HighlightsVegetation overstory and site characteristics (e.g., parent material) influence SOC chemistry and stabilization patterns.Light fraction SOC spectra did not differ between forest species in the aspen‐conifer ecotone.The proportion of aliphatic C in mineral‐associated organic carbon (MoM) increased with aspen dominance.The effect of overstory composition on MoM chemistry was patent beyond the influence of site conditions and microbial decomposer community.
Deciphering choreographies of elaborate courtship displays of golden‐collared manakins using markerless motion capture
Authors: Janisch Judith , Perinot Elisa , Fusani Leonida , Quigley Cliodhna 
Published: May 2021

AbstractCourtship displays are complex behaviours that evolve mainly through sexual selection. Males of golden‐collared manakins (Manacus vitellinus) gather in leks and perform very elaborate courtship displays in forest courts to attract females. The rapid movements of the display, that involve acrobatic jumps between saplings, are challenging to record and investigate. Here we describe the use of a combination of tools to quantify the choreographies of manakin displays and reveal previously unknown aspects of the courtship. To test the prediction that aspects of male jump trajectories vary among males and may be subject to female choice, we evaluated whether parameters including take‐off angle and velocity vary between individual males and displays. We used a custom‐built synchronized camera system to record courtship displays in the field, under highly variable lighting conditions. We then used automatic image pattern recognition software to track the movements of the birds and extract three‐dimensional (3D) coordinates of the birds' movements. After post‐processing and cleaning of the raw 3D data, we compared automated and manually produced annotations to test the reliability of the 3D tracking methods. A subsequent analysis of tracked movements revealed that individual males performed their displays consistently across different recordings. We found that males express extreme values of force when they jump off saplings and the jump trajectory has a ballistic shape, confirming that no additional propulsion is provided by the wings. We also applied the analysis approach to non‐jumping birds and found that they move at greater heights than jumping males. The acquired knowledge and the developed methods will allow us to compare different males in relation to courtship success in order to understand the role of choreographies in mate choice.
Quantitative assessment of the potential for soil improvement by planting Miscanthus on saline‐alkaline soil and the underlying microbial mechanism
Authors: Xu Yi , Zheng Cheng , Liang Le , Yi Zili , Xue Shuai 
Published: May 2021

AbstractPhytoremediation using Miscanthus is a valuable technique for the restoration of saline‐alkaline soil, but the potential is not quantified. To assess this potential, a 5 years field experiment was conducted on saline‐alkaline soils with three genotypes of Miscanthus and an unplanted control. The bulk soil (0–20‐cm depth) physicochemical properties were measured annually from 2015 to 2018, while the bacterial and fungal community structures of the rhizosphere soil were investigated by high‐throughput sequencing after 5 years under Miscanthus (2018). The results showed that Miscanthus cultivation on saline‐alkaline soil reduced soil salinization and improved soil fertility on this site. Specifically, compared with the blank control, the five‐years Miscanthus cultivation (mean of three different genotypes pooled) decreased the soil pH by 0.33 units (8.78–8.45) and electrical conductivity by 23.4 μS/cm (226.7–203.3 μS/cm), as well as increasing soil organic matter content from 18.9 to 34.9 g/kg and total potassium content from 15.2 to 18.0 g/kg. In addition, the soil improvement was more pronounced with a longer duration of growth. Miscanthus remediates saline‐alkaline soils by altering the microbial community compositional abundance rather than its diversity. The improvement is due to enrichment of beneficial bacteria leading to soil desalinization (e.g., by Gemmatimonadaceae), litter decomposition (e.g., by Chitinophagaceae), plant growth promotion (e.g., by Micrococcaceae), and the reduction of harmful fungi (e.g., Pleosporales and Chitinophagaceae). Soil pH, electrical conductivity, organic matter, and total potassium were the main physicochemical properties affecting bacterial and fungal communities. Our results quantify the soil improvement potential of Miscanthus and clarify the underlying microbial mechanisms, laying a solid foundation for further implementation of saline‐alkaline soil phytoremediation using Miscanthus. In the future, more extensive multi‐location trials are required to assess if these improvements are seen across a wide diversity of environments.
Geographic variation in the robustness of pollination networks is mediated by modularity
Authors: Liu Hanlun , Liu Zheyi , Zhang Minhua , Bascompte Jordi , He Fangliang , Chu Chengjin 
Published: May 2021

AbstractAimExtinctions and coextinctions seriously threaten global plant–pollinator assemblies, and thus a better understanding of the geographic variability in their robustness is urgently required. Although the geographic patterns of species extinction rates are frequently explored, it remains largely unknown how the subsequent coextinction risk of species varies across environments. We hypothesize that the geographic variation of network robustness to extinctions is mediated by modularity – the tendency of a network to be organized in modules of strongly interacting species – because modularity buffers perturbations and varies across environments.LocationGlobal.Time periodCurrent.Major taxa studiedFlowering plants and their animal pollinators.MethodsUsing 79 pollination networks, we first explored the variation of network robustness across geographic and climatic gradients and, second, analysed the role of modularity in explaining the association between robustness and those environmental gradients. We quantified the robustness of taxonomic, functional and phylogenetic diversity of pollinators under simulated coextinctions triggered by specialist‐first, generalist‐first, and random plant removals.ResultsOnly the robustness of phylogenetic diversity under specialist‐first removals showed a global latitudinal trend by which robustness increased towards the tropics on mainlands but increased towards the poles on islands. Generally, robustness was strongly promoted by modularity, and also directly dampened by insularity and precipitation seasonality (PS). Through the mediation of modularity, robustness was indirectly increased by actual evapotranspiration and PS, and decreased by the interaction between PS and insularity. Besides, network size and sampling area affected robustness but did not influence modularity.Main conclusionsThe indirect environmental effect on robustness via modularity was prevalent, which supports our hypothesis and reveals the importance of network structure in mediating the geographic variation of network robustness. The global pattern of robustness indicates the phylogenetic diversity of pollinators is relatively vulnerable to the loss of specialist plants in tropical islands and high‐latitude mainland compared to other regions.
Real‐world outcomes with recombinant factor IX Fc fusion protein (rFIXFc) prophylaxis: Longitudinal follow‐up in a national adult cohort
Authors: O'Donovan Mairead , Bergin Catherine , Quinn Eimear , Singleton Evelyn , Roche Sheila , Benson Julie , Bird Rachel , Byrne Mary , Duggan Cleona , Gilmore Ruth , Ryan Kevin , O'Donnell James S. , O’Connell Niamh M. 
Published: May 2021

AbstractIntroductionIn 2017, all people with severe haemophilia B (PWSHB) in Ireland switched from standard half‐life (SHL) recombinant FIX (rFIX) to rFIX Fc fusion protein (rFIXFc) prophylaxis.AimsTo evaluate prophylaxis regimens, bleeding rates and factor usage for two years of rFIXFc prophylaxis in a real‐world setting.MethodsData collected retrospectively from electronic diaries and medical records of PWSHB for a two‐year period on rFIXFc prophylaxis were compared with paired baseline data on SHL rFIX treatment.Results28 PWSHB (≥18 years) were enrolled, and at switchover 79% were receiving prophylaxis and 21% episodic treatment with SHL rFIX. At 24 months following switchover, all remained on rFIXFc prophylaxis with reduced infusion frequency; median dose per infusion once weekly (55 IU/kg, 20/28), every 10 days (63 IU/kg, 2/28) or every 14 days (98 IU/kg, 6/28). Median annualised bleed rate improved significantly on rFIXFc prophylaxis (2.0 versus 3.3 on SHL FIX) (p = 0.01). Median FIX trough level with once‐weekly infusions was 0.09 IU/ml (0.06–0.14 IU/ml). Management of bleeding episodes was similar with rFIXFc and SHL rFIX; one infusion was sufficient to treat 74% and 77% of bleeds, respectively, with similar total median treatment per bleeding episode. Factor consumption reduced by 28% with rFIXFc prophylaxis (57 IU/kg/week, range 40–86 IU/kg/week) compared with SHL rFIX (79 IU/kg/week, range 44–210 IU/kg/week) (p = 0.002).ConclusionThis study provides important insights into real‐world experience of switching to rFIXFc prophylaxis in an adult population, demonstrating high rates of prophylaxis, with reduced infusion frequency, bleeding and FIX consumption.
Helicobacter pylori induces gastric cancer via down‐regulating miR‐375 to inhibit dendritic cell maturation
Authors: Zhang Zhenxing , Chen Simiao , Fan Menghui , Ruan Guojing , Xi Tao , Zheng Lufeng , Guo Le , Ye Feng , Xing Yingying 
Published: May 2021

AbstractBackgroundRecent studies and clinical samples have demonstrated that Helicobacter pylori could induce the downregulation of miR‐375 in the stomach and promote gastric carcinogenesis. However, whether the immune cells are affected by Helicobacter pylori due to the downregulation of miR‐375 is unclear.Materials and methodsIn this study, we constructed an overexpression and knockdown of miR‐375 and Helicobacter pylori infection cell models in vitro. In addition, the maturity of dendritic cells (DCs) and the expression of IL‐6, IL‐10, and VEGF at the transcriptional and translational levels were analyzed. Changes in the JAK2‐STAT3 signaling pathway were detected. In vivo, the number changes in CD4+ T and CD8+ T cells and the size changes of tumors via models of transplantable subcutaneous tumors were also analyzed.ResultsA cell model of Helicobacter pylori and gastric cancer was used to identify the expression of miR‐375 and the maturity of dendritic cells. This study found that Helicobacter pylori could downregulate miR‐375, which regulates the expression of cytokines IL‐6, IL‐10, and VEGF in the stomach. MiR‐375 regulated the expression of cytokines IL‐6, IL‐10, and VEGF through the JAK2‐STAT3 signaling pathway in vitro. In addition, we found that Helicobacter pylori regulates the maturation of dendritic cells through miR‐375. These results were further verified in vivo, and miR‐375 diminishes tumor size was also demonstrated. This study showed that immature DCs caused a decrease in the number of CD4+ and CD8+ T cells.ConclusionsThis study demonstrated that Helicobacter pylori can inhibit miRNA‐375 expression in the stomach. Downregulated miR‐375 activates the JAK2‐STAT3 pathway. Activating the JAK2‐STAT3 signaling pathway promotes the secretion of IL‐6, IL‐10, and VEGF, leading to immature differentiation of DCs and induction of gastric cancer.