bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching: confidence, prediction and tolerance intervals in scientific practice: a tutorial on binary variables
Authors: Hartnack Sonja , Roos Malgorzata 
Published: December 2021

Abstract
Background
One of the emerging themes in epidemiology is the use of interval estimates. Currently, three interval estimates for confidence (CI), prediction (PI), and tolerance (TI) are at a researcher's disposal and are accessible within the open access framework in R. These three types of statistical intervals serve different purposes. Confidence intervals are designed to describe a parameter with some uncertainty due to sampling errors. Prediction intervals aim to predict future observation(s), including some uncertainty present in the actual and future samples. Tolerance intervals are constructed to capture a specified proportion of a population with a defined confidence. It is well known that interval estimates support a greater knowledge gain than point estimates. Thus, a good understanding and the use of CI, PI, and TI underlie good statistical practice. While CIs are taught in introductory statistical classes, PIs and TIs are less familiar.

Results
In this paper, we provide a concise tutorial on two-sided CI, PI and TI for binary variables. This hands-on tutorial is based on our teaching materials. It contains an overview of the meaning and applicability from both a classical and a Bayesian perspective. Based on a worked-out example from veterinary medicine, we provide guidance and code that can be directly applied in R.

Conclusions
This tutorial can be used by others for teaching, either in a class or for self-instruction of students and senior researchers.
Prevalence of HIV and hepatitis B virus among pregnant women in Luanda (Angola): geospatial distribution and its association with socio-demographic and clinical-obstetric determinants
Authors: Vueba Amélia Nkutxi , Almendra Ricardo , Santana Paula , Faria Clarissa , do Céu Sousa Maria 
Published: December 2021

Abstract
Background
HIV and HBV infections remain responsible for high rate of morbidity and mortality in many African Countries, affecting women and newborns. This study aims to analyze the spatial pattern of HIV and HBV infections in pregnant women in Luanda, Angola, and the statistical association between HIV and HBV and socio-economic characteristics, hygiene, and health status.

Methods
Detection of anti-HIV antibodies (total anti-HIV-1, anti-HIV-2 and HIV-1 p24 antigen) and Hepatitis B antigens (HBsAg, HBeAg) and antibodies (anti-HBc Total II, HBc IgM, Anti-HBsT II) was performed by Enzyme Linked Fluorescent Assay (ELFA) in serum samples of 878 pregnant women attended at the Lucrecia Paim Maternity Hospital (LPMH). Data were collected by questionnaire after written consent, and spatial distribution was assessed through a Kernel Density Function. The potential risk factors associated with HIV HBV infection were evaluated using bivariate and multivariate binomial logistic regression analysis.

Results
Anti-HIV antibodies were positive in 118 samples (13.4%) and HBV infection were positive in 226 (25.7%). The seroprevalence of HIV/HBV coinfection was of 6.3%. The results showed that the seroprevalence of HBV was similar in most municipalities: 25.8% in Belas; 26.6% in Viana; 27.6% in Luanda; 19.2% in Cacuaco; and 15.6% Cazenga. For HIV, the seroprevalence was also close ranges among the municipalities: 10.0% in Belas; 14.5% in Viana 14.9% in Luanda and 12.5% in Cazenga. However, the seroprevalence in municipality of in Cacuaco was lower (5.8%) and bivariate and multivariate analysis showed a lower risk for HIV in this area (OR 0.348, CI 0.083–0.986; OR 0.359, CI 0.085–1.021). The multivariate analysis had also showed a significant increased risk for HIV in women with 2 or 3 births (OR 1.860, CI 1.054–3.372).

Conclusions
Our results underlined the need to improve the screening and clinical follow-up of HIV and HBV in Angola, as well the educational campaigns to prevent not only the morbidity and mortality associated with these diseases, but also their transmission, mainly in women in reproductive age and pregnant, encouraging the pre-natal consultations in order to avoid mother-to-child transmission.
Elevated CSF inflammatory markers in patients with idiopathic normal pressure hydrocephalus do not promote NKCC1 hyperactivity in rat choroid plexus
Authors: Lolansen Sara Diana , Rostgaard Nina , Andreassen Søren Norge , Simonsen Anja Hviid , Juhler Marianne , Hasselbalch Steen Gregers , MacAulay Nanna 
Published: December 2021

Abstract
Background
Idiopathic normal pressure hydrocephalus (iNPH) is a potentially reversible neurological condition of unresolved etiology characterized by a clinical triad of symptoms; gait disturbances, urinary incontinence, and cognitive deterioration. In the present study, we aimed to elucidate the molecular coupling between inflammatory markers and development of iNPH and determine whether inflammation-induced hyperactivity of the choroidal Na+/K+/2Cl− cotransporter (NKCC1) that is involved in cerebrospinal fluid (CSF) secretion could contribute to the iNPH pathogenesis.

Methods
Lumbar CSF samples from 20 iNPH patients (10 with clinical improvement upon CSF shunting, 10 without clinical improvement) and 20 elderly control subjects were analyzed with the novel proximity extension assay technique for presence of 92 different inflammatory markers. RNA-sequencing was employed to delineate choroidal abundance of the receptors for the inflammatory markers found elevated in the CSF from iNPH patients. The ability of the elevated inflammatory markers to modulate choroidal NKCC1 activity was determined by addition of combinations of rat version of these in ex vivo experiments on rat choroid plexus.

Results
11 inflammatory markers were significantly elevated in the CSF from iNPH patients compared to elderly control subjects: CCL28, CCL23, CCL3, OPG, CXCL1, IL-18, IL-8, OSM, 4E-BP1, CXCL6, and Flt3L. One inflammatory marker, CDCP1, was significantly decreased in iNPH patients compared to control subjects. None of the inflammatory markers differed significantly when comparing iNPH patients with and without clinical improvement upon CSF shunting. All receptors for the elevated inflammatory markers were expressed in the rat and human choroid plexus, except CCR4 and CXCR1, which were absent from the rat choroid plexus. None of the elevated inflammatory markers found in the CSF from iNPH patients modulated the choroidal NKCC1 activity in ex vivo experiments on rat choroid plexus.

Conclusion
The CSF from iNPH patients contains elevated levels of a subset of inflammatory markers. Although the corresponding inflammatory receptors are, in general, expressed in the choroid plexus of rats and humans, their activation did not modulate the NKCC1-mediated fraction of choroidal CSF secretion ex vivo. The molecular mechanisms underlying ventriculomegaly in iNPH, and the possible connection to inflammation, therefore remains to be elucidated.
Review of social networks of professionals in healthcare settings—where are we and what else is needed?
Authors: Hu Huajie , Yang Yu , Zhang Chi , Huang Cong , Guan Xiaodong , Shi Luwen 
Published: December 2021

Abstract
Background
Social Network Analysis (SNA) demonstrates great potential in exploring health professional relationships and improving care delivery, but there is no comprehensive overview of its utilization in healthcare settings. This review aims to provide an overview of the current state of knowledge regarding the use of SNA in understanding health professional relationships in different countries.

Methods
We conducted an umbrella review by searching eight academic databases and grey literature up to April 30, 2021, enhanced by citation searches. We completed study selection, data extraction and quality assessment using predetermined criteria. The information abstracted from the reviews was synthesized quantitatively, qualitatively and narratively.

Results
Thirteen reviews were included in this review, yielding 330 empirical studies. The degree of overlaps of empirical studies across included reviews was low (4.3 %), indicating a high diversity of included reviews and the necessity of this umbrella review. Evidence from low- and middle-income countries (LMIC), particularly Asian countries, was limited. The earliest review was published in 2010 and the latest in 2019. Six reviews focused on the construction or description of professional networks and seven reviews reported factors or influences of professional networks. We synthesized existing literature on social networks of health care professionals in the light of (i) theoretical frameworks, (ii) study design and data collection, (iii) network nodes, measures and analysis, and (iv) factors of professional networks and related outcomes. From the perspective of methodology, evidence lies mainly in cross-sectional study design and electronic data, especially administrative data showing “patient-sharing” relationships, which has become the dominant data collection method. The results about the impact of health professional networks on health-related consequences were often contradicting and not truly comparable.

Conclusions
Methodological limitations, inconsistent findings, and lack of evidence from LMIC imply an urgent need for further investigations. The potential for broader utilization of SNA among providers remains largely untapped and the findings of this review may contain important value for building optimal healthcare delivery networks.

PROSPERO registration number
The protocol was published and registered with PROSPERO, the International Prospective Register of Systematic Reviews (CRD42020205996).
4D Structural root architecture modeling from digital twins by X-Ray Computed Tomography
Authors: Herrero-Huerta Monica , Meline Valerian , Iyer-Pascuzzi Anjali S. , Souza Augusto M. , Tuinstra Mitchell R. , Yang Yang 
Published: December 2021

Abstract
Background
Breakthrough imaging technologies may challenge the plant phenotyping bottleneck regarding marker-assisted breeding and genetic mapping. In this context, X-Ray CT (computed tomography) technology can accurately obtain the digital twin of root system architecture (RSA) but computational methods to quantify RSA traits and analyze their changes over time are limited. RSA traits extremely affect agricultural productivity. We develop a spatial–temporal root architectural modeling method based on 4D data from X-ray CT. This novel approach is optimized for high-throughput phenotyping considering the cost-effective time to process the data and the accuracy and robustness of the results. Significant root architectural traits, including root elongation rate, number, length, growth angle, height, diameter, branching map, and volume of axial and lateral roots are extracted from the model based on the digital twin. Our pipeline is divided into two major steps: (i) first, we compute the curve-skeleton based on a constrained Laplacian smoothing algorithm. This skeletal structure determines the registration of the roots over time; (ii) subsequently, the RSA is robustly modeled by a cylindrical fitting to spatially quantify several traits. The experiment was carried out at the Ag Alumni Seed Phenotyping Facility (AAPF) from Purdue University in West Lafayette (IN, USA).

Results
Roots from three samples of tomato plants at two different times and three samples of corn plants at three different times were scanned. Regarding the first step, the PCA analysis of the skeleton is able to accurately and robustly register temporal roots. From the second step, several traits were computed. Two of them were accurately validated using the root digital twin as a ground truth against the cylindrical model: number of branches (RRMSE better than 9%) and volume, reaching a coefficient of determination (R2) of 0.84 and a P < 0.001.

Conclusions
The experimental results support the viability of the developed methodology, being able to provide scalability to a comprehensive analysis in order to perform high throughput root phenotyping.
Use and effects of implementation strategies for practice guidelines in nursing: a systematic review
Authors: Cassidy Christine E. , Harrison Margaret B. , Godfrey Christina , Nincic Vera , Khan Paul A. , Oakley Patricia , Ross-White Amanda , Grantmyre Hilary , Graham Ian D. 
Published: December 2021

AbstractBackgroundPractice guidelines can reduce variations in nursing practice and improve patient care. However, implementation of guidelines is complex and inconsistent in practice. It is unclear which strategies are effective at implementing guidelines in nursing. This review aimed to describe the use and effects of implementation strategies to facilitate the uptake of guidelines focused on nursing care.MethodsWe conducted a systematic review of five electronic databases in addition to the Cochrane Effective Practice and Organization of Care (EPOC) Group specialized registry. Studies were included if implementation of a practice guideline in nursing and process or outcome of care provided by nurses were reported. Two reviewers independently screened studies, assessed study quality, extracted data, and coded data using the EPOC taxonomy of implementation strategies. For those strategies not included in the EPOC taxonomy, we inductively categorized these strategies and generated additional categories. We conducted a narrative synthesis to analyze results.ResultsThe search identified 46 papers reporting on 41 studies. Thirty-six studies used a combination of educational materials and educational meetings. Review findings show that multicomponent implementation strategies that include educational meetings, in combination with other educational strategies, report positive effects on professional practice outcomes, professional knowledge outcomes, patient health status outcomes, and resource use/expenditures. Twenty-three of the 41 studies employed implementation strategies not listed within the EPOC taxonomy, including adaptation of practice guidelines to local context (n = 9), external facilitation (n = 14), and changes to organizational policy (n = 3). These implementation strategies also corresponded with positive trends in patient, provider, and health system outcomes.ConclusionsNursing guideline implementation may benefit from using the identified implementation strategies described in this review, including participatory approaches such as facilitation, adaptation of guidelines, and organizational policy changes. Further research is needed to understand how different implementation strategy components work in a nursing context and to what effect. As the field is still emerging, future reviews should also explore guideline implementation strategies in nursing in quasi or non-experimental research designs and qualitative research studies.
Implementation Science and Implementation Science Communications: a refreshed description of the journals’ scope and expectations
Authors: Wensing Michel , Sales Anne , Wilson Paul , Armstrong Rebecca , Kislov Roman , Rankin Nicole M. , Ramaswamy Rohit , Xu Dong 
Published: December 2021

AbstractThis editorial provides a comprehensive consolidated overview of the scope and expectations of Implementation Science and Implementation Science Communications. We remain most interested in rigorous empirical studies of the implementation of evidence-based healthcare practices (including interventions, technologies, and policies) and the de-implementation of practices that are demonstrated to be of low or no benefit. Implementation strategies (e.g., continuing professional education, organizational changes, and financial incentives to enhance the uptake of evidence-based practices) are of central interest to the journals. We see the field as large and complex, with a wide literature that is published in many venues. We urge people for whom it is new to spend some time reading the existing literature, and learning the scope of the work that has already been done, and published, in our journals and in an increasing number of other journals in the field.
Radiation pneumonitis in patients with non-small-cell lung cancer receiving chemoradiotherapy and an immune checkpoint inhibitor: a retrospective study
Authors: Jang Jeong Yun , Kim Su Ssan , Song Si Yeol , Kim Yeon Joo , Kim Sung-woo , Choi Eun Kyung 
Published: December 2021

Abstract
Background
Immunotherapy has been administered to many patients with non-small-cell lung cancer (NSCLC). However, only few studies have examined toxicity in patients receiving an immune checkpoint inhibitor (ICI) after concurrent chemoradiotherapy (CCRT). Therefore, we performed a retrospective study to determine factors that predict radiation pneumonitis (RP) in these patients.

Methods
We evaluated the size of the planning target volume, mean lung dose (MLD), and the lung volume receiving more than a threshold radiation dose (VD) in 106 patients. The primary endpoint was RP ≥ grade 2, and toxicity was evaluated.

Results
After CCRT, 51/106 patients were treated with ICI. The median follow-up period was 11.5 months (range, 3.0–28.2), and RP ≥ grade 2 occurred in 47 (44.3%) patients: 27 and 20 in the ICI and non-ICI groups, respectively. Among the clinical factors, only the use of ICI was associated with RP (p = 0.043). Four dosimetric variables (MLD, V20, V30, and V40) had prognostic significance in univariate analysis for occurrence of pneumonitis (hazard ratio, p-value; MLD: 2.3, 0.009; V20: 2.9, 0.007; V30: 2.3, 0.004; V40: 2.5, 0.001). Only V20 was a significant risk factor in the non-ICI group, and MLD, V30, and V40 were significant risk factors in the ICI group. The survival and local control rates were superior in the ICI group than in the non-ICI group, but no significance was observed.

Conclusions
Patients receiving ICI after definitive CCRT were more likely to develop RP, which may be related to the lung volume receiving high-dose radiation. Therefore, several factors should be carefully considered for patients with NSCLC.
A method for in vivo treatment verification of IMRT and VMAT based on electronic portal imaging device
Authors: Zhang Jun , Li Xiuqing , Lu Miaomiao , Zhang Qilin , Zhang Xile , Yang Ruijie , Chan Maria F. , Wen Junhai 
Published: December 2021

Abstract
Background
Intensity-modulated radiation therapy (IMRT) and volume-modulated arc therapy (VMAT) are rather complex treatment techniques and require patient-specific quality assurance procedures. Electronic portal imaging devices (EPID) are increasingly used in the verification of radiation therapy (RT). This work aims to develop a novel model to predict the EPID transmission image (TI) with fluence maps from the RT plan. The predicted TI is compared with the measured TI for in vivo treatment verification.

Methods
The fluence map was extracted from the RT plan and corrections of penumbra, response, global field output, attenuation, and scatter were applied before the TI was calculated. The parameters used in the model were calculated separately for central axis and off-axis points using a series of EPID measurement data. Our model was evaluated using a CIRS thorax phantom and 20 clinical plans (10 IMRT and 10 VMAT) optimized for head and neck, breast, and rectum treatments.

Results
Comparisons of the predicted and measured images were carried out using a global gamma analysis of 3%/2 mm (10% threshold) to validate the accuracy of the model. The gamma pass rates for IMRT and VMAT were greater than 97.2% and 94.5% at 3%/2 mm, respectively.

Conclusion
We have developed an accurate and straightforward EPID-based quality assurance model that can potentially be used for in vivo treatment verification of the IMRT and VMAT delivery.
Is the femoral component flexion affected by the sagittal femoral shaft bowing in conventional intramedullary guided TKA?
Authors: Zhang Xiaofeng , Wang Qianjin , Xu Xingquan , Chen Dongyang , Bao Zhengyuan , Yao Yao , Wu Dengxian , Wang Bin , Xu Zhihong , Jiang Qing 
Published: December 2021

Abstract
Background
The aim of the present study was to investigate the influence of sagittal femoral bowing on sagittal femoral component alignment, and whether there was correlation between sagittal femoral component alignment and coronal femoral component alignment.

Methods
We retrospectively reviewed 77 knees in 71 patients who had undergone primary TKA for advanced osteoarthritis. All surgeries were performed by using a standard medial parapatellar approach. The osteotomy was performed with a conventional technique using an intramedullary rod for the femur and a mechanical extramedullary guiding system for the tibia. All patients enrolled in the study were evaluated with full-length lower extremity load-bearing standing scanograms, and the patients had preoperative and postoperative radiographs of the knees. Coronal femoral bowing angle (cFBA), sagittal femoral bowing angle (sFBA), and postoperatively, mechanical tibiofemoral angle of the knee (mTFA), β angle (femoral component flexion angle) were measured. The radiographic results of both groups were compared using Student's t test. A two-sided Pearson correlation coefficient was obtained to identify the correlations between FBA in the coronal and sagittal planes, as well as FBA and age or BMI, sFBA and β angle, cFBA and mTFA. Comparison of FSB incidence between different genders was made using Chi-square test. The p value < 0.05 indicates a statistically significant difference.

Results
The mean sFBA, cFBA, β angle, mTFA were 9.34° ± 3.56°(range 1°–16°), 3.25° ± 3.79°(range − 7° to −17°), 3.91° ± 3.15°(range − 1° to −13°), 0.60° ± 1.95°(range − 3° to −6°), respectively. There was no correlation between age and sFBA (CC = 0.192, p = 0.194) or cFBA (CC = 0.192, p = 0.194); similarly, there was no correlation between age and sFBA (CC = 0.067, p = 0.565) or cFBA (CC = 0.069, p = 0.549). The sFBA was correlated with cFBA and β angle (CC = 0.540, p < 0.01; CC = 0.543, p < 0.01, respectively), and the cFBA was correlated with mTFA (CC = 0.430, p < 0.01). There was no significant difference (p = 0.247) of cFBA between the patients with sFSB and the patients without sFSB.

Conclusions
The current study showed that the sFBA was correlated with cFBA in the patients undergoing TKA and the patients with sFSB usually presented non-cFSB. We also found that sFSB could affect the femoral component alignment in the sagittal plane and cFSB could affect the femoral component alignment in the coronal plane. The sFBA or cFBA was not correlated with age, BMI, or gender.