bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sexual reproduction contributes to the evolution of resistance‐breaking isolates of the spinach pathogen Peronospora effusa
Authors: Skiadas Petros , Klein Joël , Quiroz‐Monnens Thomas , Elberse Joyce , de Jonge Ronnie , Van den Ackerveken Guido , Seidl Michael F. 
Published: February 2022

SummaryPeronospora effusa causes downy mildew, the economically most important disease of cultivated spinach worldwide. To date, 19 P. effusa races have been denominated based on their capacity to break spinach resistances, but their genetic diversity and the evolutionary processes that contribute to race emergence are unknown. Here, we performed the first systematic analysis of P. effusa races showing that those emerge by both asexual and sexual reproduction. Specifically, we studied the diversity of 26 P. effusa isolates from 16 denominated races based on mitochondrial and nuclear comparative genomics. Mitochondrial genomes based on long‐read sequencing coupled with diversity assessment based on short‐read sequencing uncovered two mitochondrial haplogroups, each with distinct genome organization. Nuclear genome‐wide comparisons of the 26 isolates revealed that 10 isolates from six races could clearly be divided into three asexually evolving groups, in concordance with their mitochondrial phylogeny. The remaining isolates showed signals of reticulated evolution and discordance between nuclear and mitochondrial phylogenies, suggesting that these evolved through sexual reproduction. Increased understanding of this pathogen's reproductive modes will provide the framework for future studies into the molecular mechanisms underlying race emergence and into the P. effusa‐spinach interaction, thus assisting in sustainable production of spinach through knowledge‐driven resistance breeding.
Non‐radiologist perception of the use of artificial intelligence (AI) in diagnostic medical imaging reports
Authors: Lim Sophie Soyeon , Phan Tuan D , Law Meng , Goh Gerard S , Moriarty Heather K , Lukies Matthew W , Joseph Timothy , Clements Warren 
Published: February 2022

AbstractIntroductionIncorporating artificial intelligence (AI) in diagnostic medical imaging reports has the potential to improve efficiency. Although perception of radiologists, radiographers, medical students and patients on AI use in image reporting has been explored, there is limited literature on non‐radiologist clinicians' opinion on this topic.MethodSingle‐centre online survey targeting non‐radiologist medical staff conducted from May to August 2021 at a tertiary referral hospital in Melbourne, Australia. Survey questions revolved around clinicians' level of comfort acting on AI‐generated reports with varying levels of radiologist involvement and scan complexity, opinion on medicolegal responsibility for erroneous AI‐issued reports and perception of data privacy and security.ResultsEighty‐eight responses were collected, including 47.9% of consultants. Non‐radiologist clinicians across all seniorities and specialties felt significantly less comfortable acting on AI‐issued reports compared with radiologist‐issued reports (mean comfort radiologist 6.44/7, mean comfort AI 3.35/7, P < 0.001) but felt equally comfortable with an AI‐hybrid model of care (mean comfort hybrid 6.38/7, P = 0.676). Non‐radiologist clinicians believed that medicolegal responsibility with errors in AI‐issued reports mostly lay with hospitals or health service providers (65.9%) and radiologists (54.5%). Regarding data privacy and security, non‐radiologist clinicians felt significantly less comfortable with AI issuing image reports instead of radiologists (P < 0.001).ConclusionA hybrid AI‐generated radiologist‐confirmed method of image reporting may be the ideal way of integrating AI into clinical practice based on the perception of our referring non‐radiologist medical colleagues. Formal guidelines on medicolegal responsibility and data privacy should be established prior to utilising AI in the clinical setting.
Development of a decellularized hypopharynx with vascular pedicle scaffold for use in reconstructing hypopharynx
Authors: Hou Nan , Lv Die , Xu Xiaoli , Lu Yanqing , Li Jingzhi , Ma Ruina , Tang Ying , Zheng Yun 
Published: February 2022

AbstractBackgroundHypopharynx reconstruction after hypopharyngectomy is still a great challenge. Perfusion decellularization is for extracellular matrix (ECM) scaffolding and had been used in organ reconstruction. Our study aimed to prepare an acellular, natural, three‐dimensional biological hypopharynx with vascular pedicle scaffold as the substitute materials to reconstruct hypopharynx.ResultScanning electron microscope and histology staining showed that the decellularized hypopharynx with vascular pedicle scaffold retained intact native anatomical ECM structure. Myoblasts were observed on the recellularized scaffolds with bone marrow mesenchymal stem cells induced by 5‐azacytidine implanted in the rabbit greater omentum by immunohistochemical analysis.ConclusionThe decellularized hypopharynx with vascular pedicle scaffold prepared by detergent perfusion in our study has a potential to be an alternative material to pharynx reconstruction.
Bayesian Nonparametric Analysis for the Detection of Spikes in Noisy Calcium Imaging Data
Authors: D'Angelo Laura , Canale Antonio , Yu Zhaoxia , Guindani Michele 
Published: February 2022

Abstract
Recent advancements in miniaturized fluorescence microscopy have made it possible to investigate neuronal responses to external stimuli in awake behaving animals through the analysis of intracellular calcium signals. An ongoing challenge is deconvolving the temporal signals to extract the spike trains from the noisy calcium signals' time series. In this article, we propose a nested Bayesian finite mixture specification that allows the estimation of spiking activity and, simultaneously, reconstructing the distributions of the calcium transient spikes' amplitudes under different experimental conditions. The proposed model leverages two nested layers of random discrete mixture priors to borrow information between experiments and discover similarities in the distributional patterns of neuronal responses to different stimuli. Furthermore, the spikes' intensity values are also clustered within and between experimental conditions to determine the existence of common (recurring) response amplitudes. Simulation studies and the analysis of a dataset from the Allen Brain Observatory show the effectiveness of the method in clustering and detecting neuronal activities.
A Hierarchical Model for Analyzing Multisite Individual-Level Disease Surveillance Data from Multiple Systems
Authors: Zhang Yuzi , Chang Howard H. , Cheng Qu , Collender Philip A. , Li Ting , He Jinge , Remais Justin V. 
Published: February 2022

Abstract
Passive surveillance systems are widely used to monitor diseases occurrence over wide spatial areas due to their cost-effectiveness and integration into broadly distributed healthcare systems. However, such systems are generally associated with imperfect ascertainment of disease cases and with heterogeneous capture probabilities arising from factors such as differential access to care. Augmenting passive surveillance systems with other surveillance efforts provides a way to estimate the true number of incident cases. We develop a hierarchical modeling framework for analyzing data from multiple surveillance systems that allows for individual-level covariate-dependent heterogeneous capture probabilities, and borrows information across surveillance sites to improve estimation of the true number of incident cases. Inference is carried out via a two-stage Bayesian procedure. Simulation studies illustrated superior performance of the proposed approach with respect to bias, root mean square error, and coverage compared to a model that does not borrow information across sites. We applied the proposed model to data from three surveillance systems reporting pulmonary tuberculosis (PTB) cases in a major center of ongoing transmission in China. The analysis yielded bias-corrected estimates of PTB cases from the passive system and led to the identification of risk factors associated with PTB rates, as well as factors influencing the operating characteristics of the implemented surveillance systems.
Influx of kynurenine into the brain is involved in the reduction of ethanol consumption induced by Ro 61‐8048 after chronic intermittent ethanol in mice
Authors: Gil de Biedma‐Elduayen Leticia , Giménez‐Gómez Pablo , Morales‐Puerto Nuria , Vidal Rebeca , Núñez‐de la Calle Carlos , Gutiérrez‐López María Dolores , O'Shea Esther , Colado María Isabel 
Published: February 2022

Background and PurposeThe kynurenine pathway has been proposed as a target for modulating drug abuse. We previously demonstrated that inhibition of kynurenine 3‐monooxygenase (KMO), using Ro 61‐8048, reduces ethanol consumption in a binge drinking model. Here, we investigate the effect of the kynurenine pathway modulation in ethanol‐dependent mice.Experimental ApproachAdult male and female mice were subjected to a Chronic Intermittent Ethanol (CIE) paradigm. On the last day of CIE, mice were treated with Ro 61‐8048, Ro 61‐8048 + PNU‐120596, a positive allosteric modulator of α7nAChR, and Ro 61‐8048 + L‐leucine or probenecid, which blocks the influx or efflux of kynurenine from the brain, respectively. Ethanol, water consumption and preference were measured and kynurenine levels in plasma and limbic forebrain were determined.Key ResultsRo 61‐8048 decreases consumption and preference for ethanol in both sexes exposed to the CIE model, an effect that was prevented by PNU‐120596. The Ro 61‐8048‐induced decrease in ethanol consumption depends on the influx of kynurenine into the brain.Conclusion and ImplicationsInhibition of KMO reduces ethanol consumption and preference in both male and female mice subjected to CIE model by a mechanism involving α7nAChR. Moreover, this centrally‐mediated effect depends on the influx of peripheral kynurenine to the brain and can be prolonged by blocking the efflux of kynurenine from the brain. Here, for the first time, we demonstrate that the modulation of the kynurenine pathway is an effective strategy for the treatment of ethanol dependence in both sexes.
Changes in help‐seeking intentions among young people living in families impacted by mental illness attending Australian Kookaburra Kids Foundation camps
Authors: Davies Grace , Deane Frank P. , Williams Virginia , Giles Chris 
Published: February 2022

AbstractYoung people living in families impacted by familial mental illness are at increased risk of various negative mental and physical health outcomes. Prevention and early intervention programmes are useful in mitigating the risk of transgenerational transmission of mental illness. Therapeutic recreation camps constitute a novel approach to mental health early intervention and prevention for these young people, incorporating educational experiences within a peer‐based environment. This study assessed the outcomes of attending the Australian Kookaburra Kids Foundation camps for young people living in families impacted by familial mental illness. A pre‐post design was used with 237 young people between 8 and 18 years old. Mixed analyses of variance (ANOVAs) found significant improvements in young people's mental health knowledge and intentions to seek help using an anonymous telephone helpline after attending the programme. Results also revealed that males became more likely to seek help from regular contacts within their established networks after attending the programme. These findings contribute towards an increased understanding of the extant help‐seeking processes involved among an at‐risk population, with focused attention on subgroups who are less likely to seek help for their issues.
Negotiating master narratives: The practice of ‘counterstorying’ in children's personal narratives about family‐related adversities
Authors: Michelson Stina 
Published: February 2022

AbstractOnly limited attention has been drawn to children's narrative practice of negotiating cultural ideas about who they are and what they can do. This paper focuses on children living in families where adults have psychosocial problems and analyses how they negotiate different family‐related and/or societal master narratives about their identity and agency. Twenty‐two children, 6–17 years old, have been interviewed about themselves and their lives. The findings suggest three master narratives as central in children's telling: the story of the child as problem bearer, the story of the child as inheritor of psychosocial problems and the story of the child as an unknowledgeable object. The analysis shows that children negotiate these master narratives by positioning and repositioning themselves and others in, and through, their telling. The core contribution of the study is the notion that children's problem descriptions contain important information about both material and discursive aspects of the problematic situation. Through listening to children's stories, social work practitioners and researchers can deepen their understanding of how the individual child relates to, and negotiates, wider cultural ideas about identity and agency. This knowledge is relevant in the pursuit of matching support with the child's needs and perspective.
“Splitting the bill” for conservation: Perceptions and uptake of financial incentives by landholders managing privately protected areas
Authors: Selinske Matthew J. , Howard Natasha , Fitzsimons James A. , Hardy Mathew J. , Knight Andrew T. 
Published: February 2022

AbstractGlobally, privately protected area (PPA) programs are increasing in size and number. Participating in a PPA program can be fiscally challenging for landholders (e.g., enrollment costs; potential reduction in land value; opportunity costs; costs of ongoing management). Government and nongovernmental organizations often offer financial incentives to landholders, in addition to nonfinancial incentives, to encourage program enrollment and ongoing biodiversity management. In Australia, where conservation covenanting programs have been ongoing for several decades, a diversity of financial incentives is available to landholders. We surveyed 527 conservation covenantors from three states in southeast Australia to investigate the uptake, use, experience and preference for financial incentives. Less than half of covenantors received a financial incentive to enroll, but most applied for some form of incentive after enrollment, predominantly to help with management costs. Covenantors identified challenges in accessing incentives, such as being unaware of funding opportunities or experiencing confusing application processes. We found land rates rebates to be the preferred financial incentive among covenantors, in part due to the perception that covenantors should not have to pay full rates on covenanted land. Our results suggest that while covenantors do not participate in PPA programs for financial incentives, effectively and efficiently deploying financial incentives can reduce the financial burdens of PPA management, potentially increasing the effectiveness of conservation efforts.
Application of a patient‐centered reverse translational systems‐based approach to understand mechanisms of an adverse drug reaction of immune checkpoint inhibitors
Authors: Kim Sarah , Lahu Gezim , Vakilynejad Majid , Soldatos Theodoros G. , Jackson David B. , Lesko Lawrence J. , Trame Mirjam N. 
Published: February 2022

AbstractImmunotherapy became a key pillar of cancer therapeutics with the approvals of ipilimumab, nivolumab, and pembrolizumab, which inhibit either cytotoxic T‐lymphocyte antigen‐4 (CTLA‐4) or programmed death‐1 (PD‐1) that are negative regulators of T‐cell activation. However, boosting T‐cell activation is often accompanied by autoimmunity, leading to adverse drug reactions (ADRs), including high grade 3–4 colitis and its severe complications whose prevalence may reach 14% for combination checkpoint inhibitors. In this research, we investigated how mechanistic differences between anti‐CTLA‐4 (ipilimumab) and anti‐PD‐1 (nivolumab and pembrolizumab) affect colitis, a general class toxicity. The data analytical platform Molecular Health Effect was utilized to map population ADR data from the US Food and Drug Administration (FDA) Adverse Event Reporting System to chemical and biological databases for hypothesis generation regarding the underlying molecular mechanisms causing colitis. Disproportionality analysis was used to assess the statistical relevance between adverse events of interest and molecular causation. We verified that the anti‐CTLA‐4 drug is associated with an approximately three‐fold higher proportional reporting ratio associated with colitis than those of the anti‐PD‐1 drugs. The signal of the molecular mechanisms, including signaling pathways of inflammatory cytokines, was statistically insignificant to test the hypothesis that the severer rate of colitis associated with ipilimumab would be due to a greater magnitude of T‐cell activation as a result of earlier response of the anti‐CTLA‐4 drug in the immune response. This patient‐centered systems‐based approach provides an exploratory process to better understand drug pair adverse events at pathway and target levels through reverse translation from postmarket surveillance safety reports.
Clinical, pathologic, and molecular analyses of superficial low‐grade fibromyxoid sarcoma in two young patients: A rare and deceptive mimic of benignancy
Authors: Modi Mitul B. , Pei Susan , Hedberg Matthew L. , Fischer Andrew S. , Guerrero Jessenia , Carreon Chrystalle Katte , Cooper Kumarasen , Seykora John T. 
Published: February 2022

AbstractLow‐grade fibromyxoid sarcoma (LGFMS) is a histopathologically deceptive soft tissue neoplasm with bland cytology, which is typically encountered in deep soft tissue of adults. We report two cases of superficial LGFMS in young patients (16 and 21 years old, respectively), which were difficult to diagnose on histopathologic and clinical findings alone. LGFMS commonly mimics benign neoplasms such as cellular neurothekeoma, fibromatosis, neurofibroma, and perineurioma. Malignancies included in the differential diagnosis are soft tissue neoplasms such as dermatofibrosarcoma protuberans and myxofibrosarcoma. A high degree of reported variation in pattern and cellularity among LGFMS further complicates the diagnosis. Careful examination and appropriate immunohistochemistry panels including MUC4 are essential for narrowing the differential diagnosis. Molecular studies for possible FUS translocation can confirm the diagnosis of LGFMS. Sufficient sampling and workup of these lesions are critical, especially in younger patients. Young age and superficial presentation can easily sway dermatopathologists/dermatologists toward an incorrect diagnosis of benignancy.
Development of a Bayesian estimation tool to determine the optimal duration of apixaban discontinuation before a high‐bleeding risk procedure
Authors: Gibert Audrick , Lanoiselée Julien , Janisset Luc , Pernod Gilles , Ollier Edouard , Delavenne Xavier 
Published: February 2022

AbstractApixaban is a direct oral anticoagulant (DOAC). Many studies have shown that it shows high pharmacokinetic interindividual and intraindividual variability (IIV). The risk of hemorrhage is a major concern for patients treated with apixaban to undergo an operation or an invasive procedure. Due to this large pharmacokinetic variability, the current recommendations concerning the optimal duration of apixaban discontinuation before a high‐bleeding risk procedure concern the general population and not a specific patient. The aim of this study was (1) to investigate by simulation the distribution of decay time of apixaban concentration and (2) to develop and validate an easy‐to‐use web tool to estimate the individual decay time of apixaban in a “real‐life” situation. A systematic review of the literature was conducted to select the relevant pharmacokinetic models for the creation of the web tool. For each model, pharmacokinetic profiles were simulated and the time to reach concentrations below the threshold of 30 ng/ml (T30) was calculated. One of the selected models was chosen to perform a Bayesian estimation and predict the optimal duration of apixaban discontinuation before a high‐bleeding risk procedure. All these results were concatenated into the PrevBleed application developed with the R Shiny package.
Corporeal generosity: Breastfeeding bodies and female‐dominated workplaces
Authors: Burns Elaine , Gannon Susanne , Pierce Heather , Hugman Sky 
Published: February 2022

AbstractWhile gender equality at work and the gendered parameters of workplace conditions are of interest to feminist researchers, this paper brings together sociological and public health perspectives to interrogate factors impacting women who return to work (RTW) while maintaining breastfeeding. Our inquiry is focused on female‐dominated professions, teaching, nursing, and midwifery, and our findings suggest that breastfeeding obstacles exist even when gender‐inclusive policies appear to support women. Workplaces generate both overt and subtle barriers to breastfeeding, which force many women to stop earlier than they intended or create ongoing worry about maintaining breastmilk supply. Interviews with participants who maintained breastfeeding after RTW generated three overarching themes: women's determination to get back into the workforce, not wanting to “rock the boat”, and the difficulty in keeping their “head above water”. Despite workplace policies that appeared to support breastfeeding, the workplace catered to a supposedly gender‐neutral worker and policies did not translate into practice. Given the many sacrifices that women make to maintain breastfeeding, the level of workplace apathy was surprising, especially in female dominated professions. Our research foregrounds breastfeeding corporeality, not as excess but as an inevitable and essential feature of workplaces, which needs to be acknowledged and accommodated.
Land, property relations, and urban planning: New histories from colonial India
Authors: Sengupta Kaustubh Mani 
Published: February 2022

AbstractThis article looks at the recent scholarship on urban property in colonial India. Histories of cities of British India have been dominated by issues of racial segregation, discourse of planning, ways of social control as well as negotiation and resistance of the indigenous population in fashioning the urban space. The new scholarship brings in economic considerations of the state and the private actors squarely to the foreground to argue that land and property was at the heart of urban governance. Putting forward a materialist interpretation of the production of colonial urban space, these histories provide a lens to view the complex and complicated processes through which land turned into commodity. The article discusses three major issues relating to urban property regime as have been argued variously in these writings: first, it looks at the very constitution of the meaning of property and rights to property; second, it studies the various meanings of ‘value’ of a land; and lastly, it considers the question of workings of the property market in relation to housing and rent. The readings suggest that specific political, socio‐economic, and ecological context of each city shaped much of the deliberations and responses to the emergence and consolidation of a property regime.