bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pinpointing regulatory protein phosphatase 2A subunits involved in beneficial symbiosis between plants and microbes
Authors: Averkina Irina O. , Harris Muhammad , Asare Edward Ohene , Hourdin Berenice , Paponov Ivan A. , Lillo Cathrine 
Published: April 2021

AbstractBackgroundPROTEIN PHOSPHATASE 2A (PP2A) expression is crucial for the symbiotic association between plants and various microbes, and knowledge on these symbiotic processes is important for sustainable agriculture. Here we tested the hypothesis that PP2A regulatory subunits, especiallyB’φandB’θ,are involved in signalling between plants and mycorrhizal fungi or plant-growth promoting bacteria.ResultsTreatment of tomato plants (Solanum lycopersicum)with the plant growth-promoting rhizobacteria (PGPR)Azospirillum brasilenseandPseudomonas simiaeindicated a role for the PP2A B’θ subunit in responses to PGPR. Arbuscular mycorrhizal fungi influencedB’θtranscript levels in soil-grown plants with canonical arbuscular mycorrhizae. In plant roots, transcripts ofB’φwere scarce under all conditions tested and at a lower level than all other PP2A subunit transcripts. In transformed tomato plants with 10-fold enhancedB’φexpression, mycorrhization frequency was decreased in vermiculite-grown plants. Furthermore, the highB’φexpression was related to abscisic acid and gibberellic acid responses known to be involved in plant growth and mycorrhization.B’φoverexpressor plants showed less vigorous growth, and although fruits were normal size, the number of seeds per fruit was reduced by 60% compared to the original cultivar.ConclusionsExpression of theB’θgene in tomato roots is strongly influenced by beneficial microbes. Analysis ofB’φoverexpressor tomato plants and established tomato cultivars substantiated a function ofB’φin growth and development in addition to a role in mycorrhization.
Nationwide cross-sectional study of antimicrobial stewardship and antifungal stewardship programs in inpatient settings in Japan
Authors: Moriyama  Yuki , Ishikane Masahiro , Kusama Yoshiki , Matsunaga Nobuaki , Tajima Taichi , Hayakawa Kayoko , Ohmagari Norio 
Published: April 2021

Abstract
Background
To prevent antimicrobial resistance, both antimicrobial stewardship (AMS) and antifungal stewardship (AFS) in inpatient settings are needed in small/middle-sized hospitals as well as large hospitals.

Methods
We conducted the web-based, self-administered, nationwide cross-sectional study regarding AMS and AFS in inpatient settings in Japan, targeting hospitals that participated in a hospital epidemiology workshop conducted in July 2018. The questionnaire was composed of intervention protocols for use of broad-spectrum antimicrobials and antifungals within 7 or 28 d of beginning usage. These broad-spectrum antimicrobial and antifungal protocols were compared between large (≥501beds) and small/middle-sized (≤500 beds) hospitals.

Results
Of 240 hospitals surveyed, 39 (16%; 18 large and 21 small/middle-sized) responded. The number of hospitals that intervened in the use of broad-spectrum antimicrobials within 7 and 28 d were 17 (44%) and 34 (87%), respectively; those that intervened for antifungals were 3 (8%) and 10 (26%), respectively. Interventions for use of broad-spectrum antimicrobials within 7 d were significantly more frequent in small/middle-sized hospitals compared to large hospitals [13 (61. 9%) vs. 4 (22. 2%), odds ratio = 5.7, 95% confidence interval = 1.4–23.3, p = 0.023].

Conclusions
Small/middle-sized hospitals had more frequent interventions within 7 d of broad-spectrum antimicrobial use than large hospitals. More effort to improve AFS is needed among all hospitals.
Online respondent-driven detection for enhanced contact tracing of close-contact infectious diseases: benefits and barriers for public health practice
Authors: Helms Yannick B. , Hamdiui Nora , Eilers Renske , Hoebe Christian , Dukers-Muijrers Nicole , van den Kerkhof Hans , Timen Aura , Stein Mart L. 
Published: April 2021

Abstract
Background
Online respondent-driven detection (RDD) is a novel method of case finding that can enhance contact tracing (CT). However, the advantages and challenges of RDD for CT have not yet been investigated from the perspective of public health professionals (PHPs). Therefore, it remains unclear if, and under what circumstances, PHPs are willing to apply RDD for CT.

Methods
Between March and April 2019, we conducted semi-structured interviews with Dutch PHPs responsible for CT in practice. Questions were derived from the ‘diffusion of innovations’ theory. Between May and June 2019, we distributed an online questionnaire among 260 Dutch PHPs to quantify the main qualitative findings. Using different hypothetical scenarios, we assessed anticipated advantages and challenges of RDD, and PHPs’ intention to apply RDD for CT.

Results
Twelve interviews were held, and 70 PHPs completed the online questionnaire. A majority of questionnaire respondents (71%) had a positive intention towards using RDD for CT. Anticipated advantages of RDD were ‘accommodating easy and autonomous participation in CT of index cases and contact persons’, and ‘reaching contact persons more efficiently’. Anticipated challenges were ‘limited opportunities for PHPs to support, motivate, and coordinate the execution of CT’, ‘not being able to adequately convey measures to index cases and contact persons’, and ‘anticipated unrest among index cases and contact persons’. Circumstances under which PHPs anticipated RDD applicable for CT included index cases and contact persons being reluctant to share information directly with PHPs, digitally skilled and literate persons being involved, and large scale CT. Circumstances under which PHPs anticipated RDD less applicable for CT included severe consequences of missing information or contact persons for individual or public health, involvement of complex or impactful measures for index cases and contact persons, and a disease being perceived as severe or sensitive by index cases and their contact persons.

Conclusions
PHPs generally perceived RDD as a potentially beneficial method for public health practice, that may help overcome challenges present in traditional CT, and could be used during outbreaks of infectious diseases that spread via close contact. The circumstances under which CT is performed, appear to strongly influence PHPs’ intention to use RDD for CT.
A hierarchical procedure to select intrauterine and extrauterine factors for methodological validation of preterm birth risk estimation
Authors: Della Rosa Pasquale Anthony , Miglioli Cesare , Caglioni Martina , Tiberio Francesca , Mosser Kelsey H.H. , Vignotto Edoardo , Canini Matteo , Baldoli Cristina , Falini Andrea , Candiani Massimo , Cavoretto Paolo 
Published: April 2021

Abstract
Background
Etiopathogenesis of preterm birth (PTB) is multifactorial, with a universe of risk factors interplaying between the mother and the environment. It is of utmost importance to identify the most informative factors in order to estimate the degree of PTB risk and trace an individualized profile. The aims of the present study were: 1) to identify all acknowledged risk factors for PTB and to select the most informative ones for defining an accurate model of risk prediction; 2) to verify predictive accuracy of the model and 3) to identify group profiles according to the degree of PTB risk based on the most informative factors.

Methods
The Maternal Frailty Inventory (MaFra) was created based on a systematic review of the literature including 174 identified intrauterine (IU) and extrauterine (EU) factors. A sample of 111 pregnant women previously categorized in low or high risk for PTB below 37 weeks, according to ACOG guidelines, underwent the MaFra Inventory. First, univariate logistic regression enabled p-value ordering and the Akaike Information Criterion (AIC) selected the model including the most informative MaFra factors. Second, random forest classifier verified the overall predictive accuracy of the model. Third, fuzzy c-means clustering assigned group membership based on the most informative MaFra factors.

Results
The most informative and parsimonious model selected through AIC included Placenta Previa, Pregnancy Induced Hypertension, Antibiotics, Cervix Length, Physical Exercise, Fetal Growth, Maternal Anxiety, Preeclampsia, Antihypertensives. The random forest classifier including only the most informative IU and EU factors achieved an overall accuracy of 81.08% and an AUC of 0.8122. The cluster analysis identified three groups of typical pregnant women, profiled on the basis of the most informative IU and EU risk factors from a lower to a higher degree of PTB risk, which paralleled time of birth delivery.

Conclusions
This study establishes a generalized methodology for building-up an evidence-based holistic risk assessment for PTB to be used in clinical practice. Relevant and essential factors were selected and were able to provide an accurate estimation of degree of PTB risk based on the most informative constellation of IU and EU factors.
Comparing the characteristics and predicting the survival of patients with head and neck melanoma versus body melanoma: a population-based study
Authors: Ding Yuxin , Jiang Runyi , Chen Yuhong , Jing Jing , Yang Xiaoshuang , Wu Xianjie , Zhang Xiaoyang , Xu Jiali , Xu Piaopiao , LiuHuang Shu Chen , Lu Zhongfa 
Published: April 2021

Abstract
Background
Previous studies reported cutaneous melanoma in head and neck (HNM) differed from those in other regions (body melanoma, BM). Individualized tools to predict the survival of patients with HNM or BM remain insufficient. We aimed at comparing the characteristics of HNM and BM, developing and validating nomograms for predicting the survival of patients with HNM or BM.

Methods
The information of patients with HNM or BM from 2004 to 2015 was obtained from the Surveillance, Epidemiology, and End Results (SEER) database. The HNM group and BM group were randomly divided into training and validation cohorts. We used the Kaplan-Meier method and multivariate Cox models to identify independent prognostic factors. Nomograms were developed via the rms and dynnom packages, and were measured by the concordance index (C-index), the area under the curve (AUC) of the receiver operating characteristic (ROC) curve and calibration plots.

Results
Of 70,605 patients acquired, 21% had HNM and 79% had BM. The HNM group contained more older patients, male sex and lentigo maligna melanoma, and more frequently had thicker tumors and metastases than the BM group. The 5-year cancer-specific survival (CSS) and overall survival (OS) rates were 88.1 ± 0.3% and 74.4 ± 0.4% in the HNM group and 92.5 ± 0.1% and 85.8 ± 0.2% in the BM group, respectively. Eight variables (age, sex, histology, thickness, ulceration, stage, metastases, and surgery) were identified to construct nomograms of CSS and OS for patients with HNM or BM. Additionally, four dynamic nomograms were available on web. The internal and external validation of each nomogram showed high C-index values (0.785–0.896) and AUC values (0.81–0.925), and the calibration plots showed great consistency.

Conclusions
The characteristics of HNM and BM are heterogeneous. We constructed and validated four nomograms for predicting the 3-, 5- and 10-year CSS and OS probabilities of patients with HNM or BM. These nomograms can serve as practical clinical tools for survival prediction and individual health management.
Predicting short stay total hip arthroplasty by use of the timed up and go-test
Authors: Oosting Ellen , Kapitein Paul J. C. , de Vries Suzan V. , Breedveld Ellen 
Published: April 2021

Abstract
Background
One of the most important steps before implementing short stay total hip arthroplasty (THA) is establishing patient criteria. Most existing criteria are mainly based on medical condition, but as physical functioning is associated with outcome after THA, we aim to evaluate the added value of a measure of physical functioning to predict short-stay THA.

Methods
We used retrospective data of 1559 patients who underwent an anterior THA procedure. Logistic regression analyses were performed to study the predictive value of preoperative variables among which preoperative physical functioning by use of the Timed Up and Go test (TUG) for short stay THA (< 36 h). The receiver operating characteristic (ROC) curve and Youden Index were used to define a cutoff point for TUG associated with short stay THA.

Results
TUG was significantly associated with LOS (OR 0.84, 95%CI 0.82–0.87) as analyzed by univariate regression analysis. In multivariate regression, a model with the TUG had a better performance with an AUC of 0.77 (95%CI 0.74–0.79) and a R2 of 0.27 compared to the basic model (AUC 0.75, 95%CI 0.73–0.77, R2 0.24). Patients with a preoperative TUG less than 9.7 s had an OR of 4.01 (95%CI 3.19–5.05) of being discharged within 36 h.

Conclusions
Performance based physical functioning, measured by the TUG, is associated with short stay THA. This knowledge will help in the decision-making process for the planning and expectations in short stay THA protocols with the advantage that the TUG is a simple and fast instrument to be carried out.
Fresher with flavour: young women smokers’ constructions and experiences of menthol capsule cigarettes and regular cigarettes
Authors: Gilbert E. , Ewald A. 
Published: April 2021

AbstractBackgroundFlavour capsule cigarettes are one of the fastest growing segments of the tobacco market, and there is evidence that Australian young people are increasingly using menthol flavoured capsule cigarettes. This qualitative research examines how young women construct and experience menthol flavour capsule cigarettes as part of their smoking practices, and explores the perceived differences between menthol capsule cigarettes and regular cigarettes. Semi-structured face-to-face in-depth interviews were conducted with 41 Australian young women smokers, using a constructivist grounded theory approach.ResultsFindings reveal that the perceived fresh and improved taste of menthol and the ability to customise the smoking process positively contributed to young women’s experiences of smoking menthol capsule cigarettes. In particular, menthol capsule flavour cigarettes were constructed by the young women as “fresh”, “light” and “minty”, and “popping” the menthol capsule allowed the young women to personalise their smoking experience.ConclusionThese results indicate that specific public health campaigns and legislation should be developed to counter the powerfully alluring effects and the innovative appeal of menthol capsule cigarettes.
Transcriptomic biomarker pathways associated with death in HIV-infected patients with cryptococcal meningitis
Authors: Vlasova-St Louis Irina , Musubire Abdu K. , Meya David B. , Nabeta Henry W. , Mohei Hesham , Boulware David R. , Bohjanen Paul R. 
Published: April 2021

AbstractBackgroundCryptococcal meningitis (CM) is a major cause of death in HIV-infected patients in sub-Saharan Africa. Many CM patients experience cryptococcosis-associated immune reconstitution inflammatory syndrome (C-IRIS), which is often fatal. We sought to identify transcriptomic biomarker pathways in peripheral blood that are associated with or predict the development of death or fatal C-IRIS among patients with CM who were enrolled in the Cryptococcal Optimal ART Timing Trial.MethodsWe assessed peripheral blood gene expression using next-generation RNA sequencing in 4 groups of patients with CM: (1) no C-IRIS or Death; (2) C-IRIS survivors; (3) fatal C-IRIS; (4) Death without C-IRIS. Gene expression was assessed at the time of ART initiation, at 1, 4, and 8 weeks on ART, and at the time of C-IRIS events.ResultsWe identified 12 inflammatory and stress response pathways, including interferon type 1 signaling, that were upregulated at the time of ART initiation in patients with future fatal C-IRIS, as compared with survivors. The upregulation of transcripts involved in innate immunity (inflammasome, Toll-like receptor signaling), was observed at the time of fatal or nonfatal C-IRIS events. At the time of fatal C-IRIS events, numerous transcripts within fMLP, Rho family GTPases, HMGB1, and other acute phase response signaling pathways were upregulated, which reflects the severity of inflammation and systemic oxidative stress. Patients who died without recognized C-IRIS also had increased expression of pathways associated with oxidative stress and tissue damage.ConclusionsOur results showed that overactivated innate immunity, involving Toll-like receptor/inflammasome pathways, and inflammation-induced oxidative stress, are associated with fatal outcomes. The results of this study provide insight into the molecular drivers of death and fatal C-IRIS to inform future diagnostic test development or guide targeted treatments.
Analysis of equity and social inclusiveness of national urban development policies and strategies through the lenses of health and nutrition
Authors: Onwujekwe Obinna , Mbachu Chinyere Ojiugo , Ajaero Chukwuedozie , Uzochukwu Benjamin , Agwu Prince , Onuh Juliana , Orjiakor Charles Tochukwu , Odii Aloysius , Mirzoev Tolib 
Published: April 2021

Abstract
Introduction
Rapid urbanization increases competition for scarce urban resources and underlines the need for policies that promote equitable access to resources. This study examined equity and social inclusion of urban development policies in Nigeria through the lenses of access to health and food/nutrition resources.

Method
Desk review of 22 policy documents, strategies, and plans within the ambit of urban development was done. Documents were sourced from organizational websites and offices. Data were extracted by six independent reviewers using a uniform template designed to capture considerations of access to healthcare and food/nutrition resources within urban development policies/plans/strategies in Nigeria. Emerging themes on equity and social inclusion in access to health and food/nutirition resources were identified and analysed.

Results
Access to health and food/nutrition resources were explicit in eight (8) and twelve (12) policies/plans, respectively. Themes that reflect potential policy contributions to social inclusion and equitable access to health resources were: Provision of functional and improved health infrastructure; Primary Health Care strengthening for quality health service delivery; Provision of safety nets and social health insurance; Community participation and integration; and Public education and enlightenment. With respect to nutrition resources, emergent themes were: Provision of accessible and affordable land to farmers; Upscaling local food production, diversification and processing; Provision of safety nets; Private-sector participation; and Special considerations for vulnerable groups.

Conclusion
There is sub-optimal consideration of access to health and nutrition resources in urban development policies in Nigeria. Equity and social inclusivity in access to health and nutrition resources should be underscored in future policies.
Habitat influences skeletal morphology and density in the snailfishes (family Liparidae)
Authors: Gerringer M. E. , Dias A. S. , von Hagel A. A. , Orr J. W. , Summers A. P. , Farina S. 
Published: April 2021

AbstractWe tested the hypothesis that deep-sea fishes have poorly mineralized bone relative to shallower-dwelling species using data from a single family that spans a large depth range. The family Liparidae (snailfishes, Cottiformes) has representatives across the entire habitable depth range for bony fishes (0 m–> 8000 m), making them an ideal model for studying depth-related trends in a confined phylogeny. We used micro-computed tomography (micro-CT) scanning to test three aspects of skeletal reduction in snailfishes (50 species) across a full range of habitat depths: 1) reduction of structural dimensions, 2) loss of skeletal elements, and 3) reduction in bone density. Using depth data from the literature, we found that with increasing depth, the length of the dentary, neurocranium, and suborbital bones decreases. The ventral suction disk decreases width with increasing maximum habitat depth and is lost entirely in some deeper-living taxa, though not all. Although visual declines in bone density in deeper-living taxa were evident across full skeletons, individual densities of the lower jaw, vertebra, suction disk, hypural plate, and otoliths did not significantly decline with any depth metric. However, pelagic and polar taxa tended to show lower density bones compared to other species in the family. We propose that skeletal reductions allow snailfishes to maintain neutral buoyancy at great depths in the water column, while supporting efficient feeding and locomotion strategies. These findings suggest that changes in skeletal structure are non-linear and are driven not only by hydrostatic pressure, but by other environmental factors and by evolutionary ancestry, calling the existing paradigm into question.
Radiomics for prediction of radiation-induced lung injury and oncologic outcome after robotic stereotactic body radiotherapy of lung cancer: results from two independent institutions
Authors: Bousabarah Khaled , Blanck Oliver , Temming Susanne , Wilhelm Maria-Lisa , Hoevels Mauritius , Baus Wolfgang W. , Ruess Daniel , Visser-Vandewalle Veerle , Ruge Maximilian I. , Treuer Harald , Kocher Martin 
Published: April 2021

Abstract
Objectives
To generate and validate state-of-the-art radiomics models for prediction of radiation-induced lung injury and oncologic outcome in non-small cell lung cancer (NSCLC) patients treated with robotic stereotactic body radiation therapy (SBRT).

Methods
Radiomics models were generated from the planning CT images of 110 patients with primary, inoperable stage I/IIa NSCLC who were treated with robotic SBRT using a risk-adapted fractionation scheme at the University Hospital Cologne (training cohort). In total, 199 uncorrelated radiomic features fulfilling the standards of the Image Biomarker Standardization Initiative (IBSI) were extracted from the outlined gross tumor volume (GTV). Regularized models (Coxnet and Gradient Boost) for the development of local lung fibrosis (LF), local tumor control (LC), disease-free survival (DFS) and overall survival (OS) were built from either clinical/ dosimetric variables, radiomics features or a combination thereof and validated in a comparable cohort of 71 patients treated by robotic SBRT at the Radiosurgery Center in Northern Germany (test cohort).

Results
Oncologic outcome did not differ significantly between the two cohorts (OS at 36 months 56% vs. 43%, p = 0.065; median DFS 25 months vs. 23 months, p = 0.43; LC at 36 months 90% vs. 93%, p = 0.197). Local lung fibrosis developed in 33% vs. 35% of the patients (p = 0.75), all events were observed within 36 months. In the training cohort, radiomics models were able to predict OS, DFS and LC (concordance index 0.77–0.99, p < 0.005), but failed to generalize to the test cohort. In opposite, models for the development of lung fibrosis could be generated from both clinical/dosimetric factors and radiomic features or combinations thereof, which were both predictive in the training set (concordance index 0.71– 0.79, p < 0.005) and in the test set (concordance index 0.59–0.66, p < 0.05). The best performing model included 4 clinical/dosimetric variables (GTV-Dmean, PTV-D95%, Lung-D1ml, age) and 7 radiomic features (concordance index 0.66, p < 0.03).

Conclusion
Despite the obvious difficulties in generalizing predictive models for oncologic outcome and toxicity, this analysis shows that carefully designed radiomics models for prediction of local lung fibrosis after SBRT of early stage lung cancer perform well across different institutions.