bluuebunny/crossref_metadata_2025 huggingface dataset:
Cerebral microinfarcts affect brain structural network topology in cognitively impaired patients
Authors: Zhang Liwen , Biessels Geert Jan , Hilal Saima , Chong Joanna Su Xian , Liu Siwei , Shim Hee Youn , Xu Xin , Chong Eddie Jun Yi , Wong Zi Xuen , Loke Yng Miin , Venketasubramanian Narayanaswamy , Yeow Tan Boon , Chen Christopher Li-Hsian , Zhou Juan Helen
Published: January 2020

Cerebral microinfarcts (CMIs), a novel cerebrovascular marker, are prevalent in Alzheimer’s disease (AD) and associated with cognitive impairment. Nonetheless, the underlying mechanism of how CMIs influence cognition remains uncertain. We hypothesized that cortical-CMIs disrupted structural connectivity in the higher-order cognitive networks, leading to cognitive impairment. We analyzed diffusion-MRI data of 92 AD (26 with cortical-CMIs) and 110 cognitive impairment no dementia patients (CIND, 28 with cortical-CMIs). We compared structural network topology between groups with and without cortical-CMIs in AD/CIND, and tested whether structural connectivity mediated the association between cortical-CMIs and cognition. Cortical-CMIs correlated with impaired structural network topology (i.e. lower efficiency/degree centrality in the executive control/dorsal attention networks in CIND, and lower clustering coefficient in the default mode/dorsal attention networks in AD), which mediated the association of cortical-CMIs with visuoconstruction dysfunction. Our findings provide the first in vivo human evidence that cortical-CMIs impair cognition in elderly via disrupting structural connectivity.
A Multidimensional Array Representation of State-Transition Model Dynamics
Authors: Krijkamp Eline M. , Alarid-Escudero Fernando , Enns Eva A. , Pechlivanoglou Petros , Hunink M.G. Myriam , Yang Alan , Jalal Hawre J.
Published: January 2020

Cost-effectiveness analyses often rely on cohort state-transition models (cSTMs). The cohort trace is the primary outcome of cSTMs, which captures the proportion of the cohort in each health state over time (state occupancy). However, the cohort trace is an aggregated measure that does not capture information about the specific transitions among health states (transition dynamics). In practice, these transition dynamics are crucial in many applications, such as incorporating transition rewards or computing various epidemiological outcomes that could be used for model calibration and validation (e.g., disease incidence and lifetime risk). In this article, we propose an alternative approach to compute and store cSTMs outcomes that capture both state occupancy and transition dynamics. This approach produces a multidimensional array from which both the state occupancy and the transition dynamics can be recovered. We highlight the advantages of the multidimensional array over the traditional cohort trace and provide potential applications of the proposed approach with an example coded in R to facilitate the implementation of our method.
A Systematic Review of Quality of Life Assessments of Offenders
Authors: Muller Ashley Elizabeth
Published: January 2020

Strength-based theories of rehabilitation emphasize the importance of opportunities for offenders to achieve “good lives” to not re-offend. The extent to which these groups feel enabled to achieve a good life may be measured through subjective, overall quality of life (QoL). The aim is to systematically review the QoL instruments used among detained offenders and synthesize the factors related to their QoL. A systematic literature review was conducted to retrieve articles that assessed the overall QoL of a sample of detained offenders using a validated instrument. The instruments’ specificity, dimensionality, and respondent and administrator burden were assessed, and factors reported as significantly related to QoL were summarized. In total, 41 articles were included in the review: 20 reported on forensic samples and 20 on prisoners, with one study randomly assigning offenders to either forensic treatment or prison. Among the included articles, 12 validated instruments were utilized. Only one instrument, the Forensic Inpatient Quality of Life Questionnaire, was specifically developed for and validated in forensic patients. Detained offending populations reported lower QoL than the general population, and those with untreated mental illness reported the lowest. The most consistent predictors of QoL longitudinally were social factors, while substance use and detention-specific variables were not consistently related. In general, the relationships between poor mental health, loneliness, and poor QoL seen in offenders are also seen among other marginalized populations. To improve the evidence base for QoL assessment in this vulnerable group, current gold standard QoL instruments should be validated in detained populations.
Policing car space and the legal liminality of the automobile
Authors: Bloch Stefano
Published: January 2020

The car is a primary locus for police-civilian interaction as measured by routine legal intrusion into the lives of vulnerable populations – communities of color, undocumented immigrants, and those experiencing homelessness in particular. It is the car’s ability to transport bodies as well as its legal liminality as a hybrid public-private space that facilitates such coercive and carceral contact. I therefore argue for the increased inclusion of the car and contact made with its operators and occupants within studies of policing by geographers. In this article, I provide a review of how car space and the automobile have been discussed by social scientists more broadly, followed by a call for geographers to take the lead in centering the car in research looking at everyday policing and routinized state control of people occupying and moving through public space.
Operational and Safety Impact Analysis of Implementing Emergency Shoulder Use (ESU) for Hurricane Evacuation
Authors: Sharma Rakesh , Faruk Md Omar , El-Urfali Alan
Published: January 2020

The emergency shoulder use (ESU) was implemented in Florida in September 2017 to facilitate mass evacuation before Hurricane Irma made landfall on the shores of Florida. ESU was implemented on the northbound I-75 for about 39 h and eastbound I-4 for about 6 h when the left shoulders were opened for use as travel lanes. This study discusses the operational and safety effects of ESU. The operational effects of ESU were studied and compared with other alternatives including one-way operation (contraflow) and both left and right shoulder use. The findings showed the left shoulder ESU could be an effective alternative to one-way operation. The one-way operation was not a preferred method as it can only be operated during the day time, requires massive resource allocation, and hampers emergency services reaching to different parts of the state. However, ESU on the left shoulder offers minimal disturbance to traffic and is easy to deploy. The safety impact analysis was performed by conducting a descriptive statistical comparison of crash types, severity, and other relevant factors during ESU operations. The crash analysis showed that the observed number of crashes on an urban I-75 segment during ESU operation is commensurate with normal operation with saturated traffic conditions, in contrast a rural segment experienced a higher observed crash rate than the predicted rate with saturated traffic conditions. The predictive analysis of ESU crashes also showed that ESU implementation helped to reduce the expected number of crashes significantly.
Value of Apparent Diffusion Coefficient for Assessing Preoperative T Staging of Low Rectal Cancer and Whether This Is Correlated With Ki-67 Expression
Authors: Ao Weiqun , Bao Xiangdong , Mao Guoqun , Yang Guangzhao , Wang Jian , Hu Jinwen
Published: January 2020

Purpose:

To explore the value of the apparent diffusion coefficient (ADC) in assessing preoperative T staging of low rectal cancer and the correlation between ADC value and Ki-67 expression.

Methods:

Data on 77 patients with a proven pathology of low rectal cancer were retrospectively analyzed. All patients underwent a magnetic resonance imaging scan 1 week prior to operation, and the mean ADC value was measured. All tumors were fully removed, and pathologic staging was determined. The Ki-67 expression was determined using immunohistochemical methods in all patients. The correlation between Ki-67 expression and ADC features was studied.

Results:

A total of 77 patients with low rectal cancer were included in the study. The pathology type was adenocarcinoma. The numbers of patients with pathological stages T1, T2, T3, and T4 were 9, 23, 32, and 13, respectively. The ADC value of all tumors ranged from 0.60 to 1.20 mm2/s. The average Ki-67 proliferation index was 55.3% ± 20.2%. A significant difference was observed between the preoperative ADC value and pathological T staging of low rectal cancer ( P < .01). The more advanced the T stage, the lower the detected ADC values were. A negative correlation was noted between the preoperative ADC value and Ki-67 proliferation index of rectal cancer ( r = −0.71, P < .01). When the Ki-67 proliferation index increased, lower ADC values were detected.

Conclusion:

The ADC values can provide useful information on preoperative tumor staging and may facilitate evaluation of the biological behavior of low rectal cancer. The ADC values should be considered a sensitive image biomarker of rectal cancer.
The Discrepancies Between Individual-Set and Parent-Set Career Goals Scale: Development and Initial Validation
Authors: Sawitri Dian R. , Creed Peter A. , Perdhana Mirwan S.
Published: January 2020

As there was no existing, psychometrically sound scale that directly assessed the discrepancies that young people experience between individual-set career goals and parent-set career goals, we developed and provided initial validation for a 15-item scale for use with young adults. In Study 1, items were developed, reviewed by experts, and administered to a sample of first year, undergraduate Indonesian students ( N = 426, Mage = 18.42 years). We used exploratory factor analysis to reduce the number of items and assess the factor structure and used confirmatory factor analyses on a holdout sample to assess this underlying structure. We then provided evidence for construct validity. Recommendations for use in research and practice are discussed.
What We Owe to Family: The Impact of Special Obligations on Moral Judgment
Authors: McManus Ryan M. , Kleiman-Weiner Max , Young Liane
Published: January 2020

Although people often recognize the moral value of impartial behavior (i.e., not favoring specific individuals), it is unclear when, if ever, people recognize the moral value of partiality. The current studies investigated whether information about special obligations to specific individuals, particularly kin, is integrated into moral judgments. In Studies 1 and 2, agents who helped a stranger were judged as more morally good and trustworthy than those who helped kin, but agents who helped a stranger, instead of kin were judged as less morally good and trustworthy than those who did the opposite. In Studies 3 and 4, agents who simply neglected a stranger were judged as less morally bad and untrustworthy than those who neglected kin. Study 4 also demonstrated that the violation (vs. fulfillment) of perceived obligations underlaid all judgment patterns. Study 5 demonstrated boundary conditions: When occupying roles requiring impartiality, agents who helped a stranger instead of kin were judged as more morally good and trustworthy than agents who did the opposite. These findings illuminate the importance of obligations in structuring moral judgment.
Study on the effect of leading and trailing-edge serrations on flat-plate broadband noise
Authors: Shah Dilip A , Hamid Husain A , Kumar M Praveen , Atul Bhise Tanmay , Kumar GC Vishnu
Published: January 2020

The results of a comparative study on the reduction of broadband noise for several combinations of a flat plate with serrations encountering a low-turbulence fluid flow are computed and documented. The four combinations under study are triangular serrations on leading-edge only, triangular serrations on trailing-edge only, triangular serrations on the leading and trailing edges, and ogival serrations on the leading and trailing edges. Serrations based on the trailing edge are normalized in terms of its chord length. A computational study was carried out using computational fluid dynamics models to simulate the variety of serrated flat plates. Commercial computational fluid dynamics software ANSYS Fluent 16.0 was used. A quantifiable reduction in the broadband noise was found in most of the variations in the serrated geometries. The particular case of the serrations considered in the present study having triangular serrations on both leading and trailing edges of the flat plate proved to be the most effective in terms of broadband noise reduction.
The feasibility analysis of calculating proptosis by simple Pythagorean theorem
Authors: Zhang Weili , Zeng Junlin , Huang Qinying , Liu Zhichang , Li Jinying
Published: January 2020

Purpose:

We propose a new method to analyze the feasibility of calculating proptosis on the basis of simple Pythagorean theorem.

Method:

This is a non-inferiority trial, and the registration number is ChiCTR1900026490. The absolute value of proptosis of two eyes of patients without eye injury or diseases visiting our clinic from December 2017 to June 2019 was measured by computed tomography, Hertel exophthalmometer, and by simple Pythagorean theorem. With the application of MedCalc software version 19.0.4, the differences between these methods in two eyes were showed by Bland and Altman plot.

Results:

A 95% limit of agreement between computed tomography and Hertel exophthalmometer is −0.7 to 0.62 mm in right eye proptosis. A total of 4.44% (4/90) points were outside 95% limit of agreement. Similarly, the same method was used to compare the proptosis between computed tomography and other ways. We also compared the proptosis measured by homolateral and heterolateral simple Pythagorean theorem method in order to find out the consistence between them. The points in all Bland and Altman plots were lower than 5%, which means that the results of comparison between any two methods had a good consistency in the measurement of proptosis of both eyes.

Conclusion:

Pythagorean theorem can be applied to evaluate proptosis and has a good consistency comparing with computed tomography and the Hertel exophthalmometer. The method can be used for measuring proptosis of unilateral orbital, maxillofacial trauma, and dysplasia accurately. It is practical in clinical use of proptosis assessment because of its accuracy, reliability, and simplicity.
Cross-cultural Encounters in Urban Festivals: Between Liberation and Domination
Authors: Koefoed Lasse , de Neergaard Maja , Simonsen Kirsten
Published: January 2020

This paper is part of a wider research project on Paradoxical Spaces: Encountering the Other in Public Space that explores how cultural difference is practiced and negotiated in different public spaces in Copenhagen. The present case focus on encounters at two urban festivals: Kulturhavn (Cultural Harbur) and Smag Verden (Taste the World)—both multicultural and both initiated by the Municipality of Copenhagen. The festivals are seen as sites for ongoing dialogue and negotiation of identity and belonging. The celebration, performances, and pleasure of festivals can empower the body, break down social and cultural distance, and for a moment suspend everyday life. They are related to laughter and freedom, but can also be exclusive, alienating, and a vehicle of the inserting of the hegemonic order. The aim of the paper is to discover how the festivals work as social and material mediators of cross-cultural encounters—how they give rise to different modes of encounters and how they balance between liberation and similarities. They are both organized by the municipality of Copenhagen, who invite voluntary organizations and cultural associations every year to participate in organizing the two festivals. They both cover a broad range of cultural activities such as dance, music, food, sport, and theatre, and they share the vision of celebrating the cultural diversity of the city. We chose these two festivals in order to explore variations in the way the festivals are experienced and encountered; the focus of the analysis is on how festivals with many similarities in location and formal conditions can give rise to rather different modes of encounters. The aim of the paper is to explore how the festivals work as social and material mediators of cross-cultural encounters. How do the two festivals give rise to different modes of encounters? How do they balance between liberation and domination in a differential way? Drawing on empirical material obtained through participant observation and framed by theoretical conceptualization of cross-cultural encounters, multicultural festivals, and aesthetic politics, the paper explores embodied encounters at the two festivals. It focuses on the role of the festivals as social and material mediators of encounters and negotiation of identities. The paper concludes on the paradoxical character of the festivals, involving antagonistic embodiments of performance, pleasure, and politics.
Transnational interdependency and healthcare system change: The role of humanitarian and development aid in shaping health policy in Jordan
Authors: Lupieri Sigrid , Frisina Doetter Lorraine
Published: January 2020

This article examines the role of external financing as a form of transnational economic interdependency in shaping healthcare system change in Jordan. More specifically, this exploratory study traces the trajectory of Jordan’s healthcare policy such as regards public financing, investment in infrastructure, and policy priorities – especially, efforts at universalism and health as a human right – over the years 2008–2018. During this period of observation, the Jordanian healthcare system was subject to various exogenous shocks in the form of recurrent and large influxes of refugees from Iraq and Syria. Regarded as a crisis, the growing presence of the refugee population introduced a significant increase in humanitarian and development aid that brought with it resources for both the displaced and host populations. This study examines whether increased external financing in the form of overseas development aid necessarily translates into healthcare system expansion for both citizens and refugees. This article will contribute to filling the gap in knowledge and understanding of the complex interdependencies which influence the evolution of healthcare policies in a country not only affected by an ongoing refugee crisis, but also at the geopolitical crossroads of international interests in the Middle East region.
Boundaries of Authority: An introduction
Authors: Simmons A. J.
Published: January 2020

This is the Introduction to the symposium on A. John Simmons, Boundaries of Authority (Oxford: Oxford University Press, 2016). The Symposium contains articles by David Miller, Cara Nine, and Anna Stilz, and a response by the author.
A model-based calibration approach for structural fault diagnosis using piezoelectric impedance measurements and a finite element model
Authors: Ezzat Ahmed Aziz , Tang Jiong , Ding Yu
Published: January 2020

The electromechanical coupling property of piezoelectric transducers gives rise to a promising class of structural fault diagnosis methods often referred to collectively as impedance-based approaches. One active line of research in the related literature is the development of data-driven methods that can leverage the available experimental impedance measurements to accurately pinpoint the location and severity of structural faults. In this article, we offer a new perspective to the problem by casting the impedance-based fault diagnosis into a statistical calibration formulation, which has gained a wide popularity in the industrial statistics community in the past two decades. Specifically, we decide to estimate the values of the fault attributes (e.g. location and severity) that achieve the closest match between the outputs from a finite element model and those experimentally solicited from the host structure. We further propose to couple this statistical formulation with a pre-screening procedure to reduce the calibration search space and mitigate parameter identifiability issues. In addition to the merit of capably diagnosing structural faults, the proposed approach extends various useful concepts from the statistical calibration literature to the structural health monitoring applications, such as the construction of surrogate models for modeling and predicting impedance changes, the explicit use of a bias function to correct for inherent inadequacies in finite element models, as well as the ability to produce continuous probability distributions for quantifying a fault’s severity. These additional benefits substantially enhance both the fault diagnosis capability and computational efficiency. We demonstrate the effectiveness of the proposed approach using two simulated and two experimental case studies from the literature.
Mechanical properties and water absorption characteristics of composites reinforced with cotton fibres recovered from textile waste
Authors: Kamble Zunjarrao , Behera Bijoya Kumar
Published: January 2020

The primary aim of this research is to develop thermoset composites reinforced with cotton fibres extracted from textile waste. These composites are mainly targeted to replace timber in its application for furniture items and in some visible and non-visible automotive components. The pre-consumer cotton textile wastes such as cutting waste, in garment manufacturing, and defective fabrics were converted into the fibrous form called ‘shoddy’, using rag-tearing technique. The fibrous web of shoddy was produced using the carding machine. This web was used for developing thermoset composites as a reinforcement material. The thermoset composites with four different fibre volume fraction values, namely 0.1, 0.2, 0.3 and 0.4 were developed using compression moulding technique. The developed composites were characterised by mechanical properties, dynamic mechanical properties, thermal degradation behaviour and water absorption behaviour. The mechanical properties of the composites were found comparable with that of commercial wood. These composites can be used to develop a dashboard panel. The composites developed in this research have shown low water diffusion coefficient values as compared with pine, oak and linden wood.
Using consensus methods to develop a Social Prescribing Learning Needs Framework for practitioners in Wales
Authors: Wallace C , Elliott M , Thomas S , Davies-McIntosh E , Beese S , Roberts G , Ruddle N , Groves K , Rees S , Pontin D
Published: January 2020

Aims:

Social prescribing is being widely implemented in Wales, but there is no consensus on the necessary learning, training and education needs for people delivering social prescribing. The purpose of the study was to develop an education and training needs conceptual framework for social prescribers in Wales, which could be used by commissioners and providers for the development of social prescribing curricula.

Methods:

This study used two consensus methods. First, Group Concept Mapping using Concept Systems Global MaxTM software which identified the important and available learning needs of 18 ( n = 18) geographically spread social prescribing practitioners. Second, a world café style workshop asked 85 ( n = 85) social prescribers to identify when training and support would be most appropriate and valuable in developing their role and skills.

Results:

A Social Prescribing Learning Needs Framework was developed identifying important learning needs and their availability across a timeline from induction onwards. This was conceptualised from a group concept mapping cluster map and go-zone report. The map comprises five clusters of statements (compassion, interpersonal relationships, socioeconomic disadvantage, networking and monitoring data) from the original 120 statements of learning needs identified by participants. The Go-Zone report displayed how each learning need was rated by participants on scales of importance and availability. A large number of training needs (45%) that were identified as important, are not currently available to social prescribers. All training needs were placed within the first year of the social prescriber working timeline, with 39% placed in an induction period.

Conclusion:

The use of two different consensus methods enabled social prescribers geographically spread across Wales to engage with the study. The Social Prescribing Learning Needs Framework will be used to inform the commissioning and decommissioning of training for people delivering social prescribing in Wales.
QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
Authors: Anyansi Christine , Keo Arlin , Walker Bruce J. , Straub Timothy J. , Manson Abigail L. , Earl Ashlee M. , Abeel Thomas
Published: January 2020

Background

Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M. tuberculosis within a sample. Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such as M. tuberculosis.

Here we present QuantTB, a method to identify and quantify individual M. tuberculosis strains in whole genome sequencing data. QuantTB uses SNP markers to determine the combination of strains that best explain the allelic variation observed in a sample. QuantTB outputs a list of identified strains, their corresponding relative abundances, and a list of drugs for which resistance-conferring mutations (or heteroresistance) have been predicted within the sample.

Results

We show that QuantTB has a high degree of resolution and is capable of differentiating communities differing by less than 25 SNPs and identifying strains down to 1× coverage. Using simulated data, we found QuantTB outperformed other metagenomic strain identification tools at detecting strains and quantifying strain multiplicity. In a real-world scenario, using a dataset of 50 paired clinical isolates from a study of patients with either reinfections or relapses, we found that QuantTB could detect mixed infections and reinfections at rates concordant with a manually curated approach.

Conclusion

QuantTB can determine infection multiplicity, identify hetero-resistance patterns, enable differentiation between relapse and re-infection, and clarify transmission events across seemingly unrelated patients – even in low-coverage (1×) samples. QuantTB outperforms existing tools and promises to serve as a valuable resource for both clinicians and researchers working with clinical TB samples.
The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation
Authors: Zhang Yating , An Dong , Li Changsheng , Zhao Zhixuan , Wang Wenqin
Published: January 2020

Background

Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles.

Results

Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli.

Conclusions

The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Authors: Li Xiaohong , Cooper Nigel G. F. , O’Toole Timothy E. , Rouchka Eric C.
Published: January 2020

Background

High-throughput RNA sequencing (RNA-seq) has evolved as an important analytical tool in molecular biology. Although the utility and importance of this technique have grown, uncertainties regarding the proper analysis of RNA-seq data remain. Of primary concern, there is no consensus regarding which normalization and statistical methods are the most appropriate for analyzing this data. The lack of standardized analytical methods leads to uncertainties in data interpretation and study reproducibility, especially with studies reporting high false discovery rates. In this study, we compared a recently developed normalization method, UQ-pgQ2, with three of the most frequently used alternatives including RLE (relative log estimate), TMM (Trimmed-mean M values) and UQ (upper quartile normalization) in the analysis of RNA-seq data. We evaluated the performance of these methods for gene-level differential expression analysis by considering the factors, including: 1) normalization combined with the choice of a Wald test fromDESeq2and an exact test/QL (Quasi-likelihood) F-Test fromedgeR; 2) sample sizes in two balanced two-group comparisons; and 3) sequencing read depths.

Results

Using the MAQC RNA-seq datasets with small sample replicates, we found that UQ-pgQ2 normalization combined with an exact test can achieve better performance in term of power and specificity in differential gene expression analysis. However, using an intra-group analysis of false positives from real and simulated data, we found that a Wald test performs better than an exact test when the number of sample replicates is large and that a QL F-test performs the best given sample sizes of 5, 10 and 15 for any normalization. The RLE, TMM and UQ methods performed similarly given a desired sample size.

Conclusion

We found the UQ-pgQ2 method combined with an exact test/QL F-test is the best choice in order to control false positives when the sample size is small. When the sample size is large, UQ-pgQ2 with a QL F-test is a better choice for the type I error control in an intra-group analysis. We observed read depths have a minimal impact for differential gene expression analysis based on the simulated data.
Discussing overweight in children during a regular consultation in general practice: a qualitative study
Authors: van der Maas Joline C. , Corbee Ronald J. , Kroese Floor M. , de Ridder Denise T. D. , Vos Rimke C. , Nielen Mirjam , Monninkhof Evelyn
Published: January 2020

Background

Overweight in children is a rising problem leading to serious consequences later in life. The Dutch guideline ‘Obesity’ for general practitioners recommends discussing obesity in children regardless of the reason of consultation and provides diagnostic and therapeutic tools. However, limited literature indicates that general practitioners experience barriers to discuss this topic. The aim of this study was to determine current perceived barriers of general practitioners in discussing overweight during a regular consultation in children aged 4 to 12 years and to what extent they discuss the topic. Furthermore, we attempt to get more insight in the specific needs and ideas for improvement among GPs.

Methods

A semi-structured in-depth interview study was conducted. Dutch general practitioners with a broad range of demographic characteristics were invited to participate. The transcripts were analysed using a modified version of the constant comparative method. Using this method, we identified perceived barriers of general practitioners.

Results

Ten general practitioners were included in the study. Four major themes were identified in the interviews: absence of physical or mental complaints related to overweight, internal barriers of the general practitioners, the child’s family background and logistics. Major barriers appeared to be a low consultation rate of these children, the sensitivity of the topic (e.g. fear for children’s or parents’ reactions and/or disturbance of the relation, influence on the self-esteem of the child, resistance in the parents), the absence of a long-standing relation between general practitioner and child or parent, the background of the child and lack of time or prioritizing.

Conclusion

Dutch general practitioners indicate to experience barriers and need tools for how to discuss children’s overweight during regular consultations within the limited time available. The low consultation rate among children aged 4 to 12 years due to lack of physical complaints is mentioned as a new and important barrier. Therefore, the prior focus might be raising awareness among parents concerning overweight in children aged 4 to 12 years and, thereby, stressing the potential supporting role of primary care professionals in tackling the overweight of their child.
Intensive psychotherapy and case management for Karen refugees with major depression in primary care: a pragmatic randomized control trial
Authors: Northwood Andrea K. , Vukovich Maria M. , Beckman Alison , Walter Jeffrey P. , Josiah Novia , Hudak Leora , O’Donnell Burrows Kathleen , Letts James P. , Danner Christine C.
Published: January 2020

Background

Despite an unparalleled global refugee crisis, there are almost no studies in primary care addressing real-world conditions and longer courses of treatment that are typical when resettled refugees present to their physician with critical psychosocial needs and complex symptoms. We studied the effects of a year of psychotherapy and case management in a primary care setting on common symptoms and functioning for Karen refugees (a newly arrived population in St Paul, Minnesota) with depression.

Methods

A pragmatic parallel-group randomized control trial was conducted at two primary care clinics with large resettled Karen refugee patient populations, with simple random allocation to 1 year of either: (1) intensive psychotherapy and case management (IPCM), or (2) care-as-usual (CAU). Eligibility criteria included Major Depression diagnosis determined by structured diagnostic clinical interview, Karen refugee, ages 18–65. IPCM (n = 112) received a year of psychotherapy and case management coordinated onsite between the case manager, psychotherapist, and primary care providers; CAU (n = 102) received care-as-usual from their primary care clinic, including behavioral health referrals and/or brief onsite interventions. Blinded assessors collected outcomes of mean changes in depression and anxiety symptoms (measured by Hopkins Symptom Checklist-25), PTSD symptoms (Posttraumatic Diagnostic Scale), pain (internally developed 5-item Pain Scale), and social functioning (internally developed 37-item instrument standardized on refugees) at baseline, 3, 6 and 12 months. After propensity score matching, data were analyzed with the intention-to-treat principle using repeated measures ANOVA with partial eta-squared estimates of effect size.

Results

Of 214 participants, 193 completed a baseline and follow up assessment (90.2%). IPCM patients showed significant improvements in depression, PTSD, anxiety, and pain symptoms and in social functioning at all time points, with magnitude of improvement increasing over time. CAU patients did not show significant improvements. The largest mean differences observed between groups were in depression (difference, 5.5, 95% CI, 3.9 to 7.1,P < .001) and basic needs/safety (difference, 5.4, 95% CI, 3.8 to 7.0,P < .001).

Conclusions

Adult Karen refugees with depression benefited from intensive psychotherapy and case management coordinated and delivered under usual conditions in primary care. Intervention effects strengthened at each interval, suggesting robust recovery is possible.

Trial registration

clinicaltrials.gov Identifier:NCT03788408. Registered 20 Dec 2018. Retrospectively registered.
Effects of a smartphone-based videoconferencing program for older nursing home residents on depression, loneliness, and quality of life: a quasi-experimental study
Authors: Tsai Hsiu-Hsin , Cheng Ching-Yu , Shieh Wann-Yun , Chang Yue-Cune
Published: January 2020

Background

Smartphones can optimize the opportunities for interactions between nursing home residents and their families. However, the effectiveness of smartphone-based videoconferencing programs in enhancing emotional status and quality of life has not been explored. The purpose of this study was to evaluate of the effect of a smartphone-based videoconferencing program on nursing home residents’ feelings of loneliness, depressive symptoms and quality of life.

Methods

This study used a quasi-experimental research design. Older residents from seven nursing homes in Taiwan participated in this study. Nursing homes (NH) were randomly selected as sites for either the intervention group (5 NH) or the control group (2 NH); NH residents who met the inclusion criteria were invited to participate. The intervention group was comprised of 32 participants; the control group was comprised of 30 participants. The intervention group interacted with their family members once a week for 6 months using a smartphone and a “LINE” application (app). Data were collected with self-report instruments: subjective feelings of loneliness, using the University of California Los Angeles Loneliness Scale; depressive symptoms, using the Geriatric Depression Scale; and quality of life using the SF-36. Data were collected at four time points (baseline, and at 1-month, 3-months and 6-months from baseline). Data were analysed using the generalized estimating equation approach.

Results

After the intervention, as compared to those in the control group, participants in interventional group had significant decreases in baseline loneliness scores at 1 months (β = − 3.41, p < 0.001), 3 months (β = − 5.96, p < 0.001), and 6 months (β = − 7.50, p < 0.001), and improvements in physical role (β = 36.49, p = 0.01), vitality (β = 13.11, p < 0.001) and pain scores (β = 16.71, p = 0.01) at 6 months. However, changes in mean depression scores did not significantly differ between groups.

Conclusions

Smartphone-based videoconferencing effectively improved residents’ feelings of loneliness, and physiological health, vitality and pain, but not depressive symptoms. Future investigations might evaluate the effectiveness of other media-based technologies in nursing homes as well as their effectiveness within and between different age cohorts.
Estimating nationwide cases of sexually transmitted diseases in 2015 from sentinel surveillance data in Japan
Authors: Kawado Miyuki , Hashimoto Shuji , Ohta Akiko , Oba Mari S. , Uehara Ritei , Taniguchi Kiyosu , Sunagawa Tomimasa , Nagai Masaki , Murakami Yoshitaka
Published: January 2020

Background

The rates of newly diagnosed cases of sexually transmitted diseases, including genital chlamydial infection and gonorrhea, are important for prevention and control of these diseases. However, nationwide rates are not reported in Japan.

Methods

We used the number of cases of sexually transmitted diseases reported by nationwide sentinel surveillance in 2015, together with the number of all disease outpatients in September 2014 at all medical institutions, drawn from the Survey of Medical Institutions of Japan. The number of cases of sexually transmitted diseases in the total population was estimated using the ratio estimation method with the number of all disease outpatients as auxiliary information. This method is currently used for estimating influenza cases from sentinel surveillance data in Japan.

Results

The estimated number of newly diagnosed cases per 100,000 population in 2015 in Japan was 244 (95% confidence interval 211–277) for genital chlamydial infection, 87 (95% confidence interval 74–100) for genital herpes, 61 (95% confidence interval 29–93) for condyloma acuminatum, and 89 (95% confidence interval 64–113) for gonorrhea.

Conclusion

We estimated the nationwide number of newly diagnosed cases of sexually transmitted diseases in Japan from sentinel surveillance data. This provides useful information for public health policy-making.
Prevalence of chronic kidney disease in the Lazio region, Italy: a classification algorithm based on health information systems
Authors: Marino Claudia , Ferraro Pietro Manuel , Bargagli Matteo , Cascini Silvia , Agabiti Nera , Gambaro Giovanni , Davoli Marina
Published: January 2020

Background

Estimating CKD prevalence is difficult. Information on CKD prevalence is rather scanty in Italy and available figures come from surveys in selected geographical areas. Administrative data have been already demonstrated to be an effective tool in estimating the epidemiological burden of diseases, however there is limited experience in literature as far as CKD is concerned.

Methods

The aim of this study is to develop an algorithm based on regional Health Administrative Databases to identify individuals with CKD and provide estimates of disease prevalence in Lazio Region (Italy); about 5.500.000 inhabitants in 2017. A population-level analysis based on a record-linkage strategy using data from Health Administrative Databases has been applied in Lazio Region. CKD cases were identified between January 1, 2012 and December 31, 2017 using Outpatient Specialist Service Information System, Hospital Discharge Registry, Ticket Exemption Registry and Drug Dispensing Registry. Age-specific and standardized prevalence rates were calculated by gender. CKD cases were classified as higher and lower severity.

Results

The algorithm identified 99,457 individuals with CKD (mean age 71 years, 55.8% males). The exclusive contributions of each regional source used were: 35,047 (35.2%) from Outpatient Specialist Service Information System, 27,778 (27.9%) from Hospital Discharge Registry, 4143 (4.2%) from Ticket Exemption Registry and 463 (0.5%) from Drug Dispensing Registry; 5.1% of cases were found in all databases. The standardized prevalence rate at December 31, 2017 was 1.76, 2.06% for males and 1.50% for females. The prevalence increased with age, rising from 0.33% (age 0–18) up to 14.18% (age 85+) among males and from 0.25% up to 8.18% among females. The proportion of CKD individuals with lower severity disease was 78.7% in both genders.

Conclusions

The proposed algorithm represents a novel tool to monitor the burden of CKD disease, that can be used by the regional government to guide the development and implementation of evidence-based pathways of care for CKD patients. The high prevalence of people with CKD of lower severity should be carefully considered in order to promote diagnosis and optimal management at early stages.
Comorbidity prevalence among cancer patients: a population-based cohort study of four cancers
Authors: Fowler Helen , Belot Aurelien , Ellis Libby , Maringe Camille , Luque-Fernandez Miguel Angel , Njagi Edmund Njeru , Navani Neal , Sarfati Diana , Rachet Bernard
Published: January 2020

Background

The presence of comorbidity affects the care of cancer patients, many of whom are living with multiple comorbidities. The prevalence of cancer comorbidity, beyond summary metrics, is not well known. This study aims to estimate the prevalence of comorbid conditions among cancer patients in England, and describe the association between cancer comorbidity and socio-economic position, using population-based electronic health records.

Methods

We linked England cancer registry records of patients diagnosed with cancer of the colon, rectum, lung or Hodgkin lymphoma between 2009 and 2013, with hospital admissions records. A comorbidity was any one of fourteen specific conditions, diagnosed during hospital admission up to 6 years prior to cancer diagnosis. We calculated the crude and age-sex adjusted prevalence of each condition, the frequency of multiple comorbidity combinations, and used logistic regression and multinomial logistic regression to estimate the adjusted odds of having each condition and the probability of having each condition as a single or one of multiple comorbidities, respectively, by cancer type.

Results

Comorbidity was most prevalent in patients with lung cancer and least prevalent in Hodgkin lymphoma patients. Up to two-thirds of patients within each of the four cancer patient cohorts we studied had at least one comorbidity, and around half of the comorbid patients had multiple comorbidities. Our study highlighted common comorbid conditions among the cancer patient cohorts. In all four cohorts, the odds of having a comorbidity and the probability of multiple comorbidity were consistently highest in the most deprived cancer patients.

Conclusions

Cancer healthcare guidelines may need to consider prominent comorbid conditions, particularly to benefit the prognosis of the most deprived patients who carry the greater burden of comorbidity. Insight into patterns of cancer comorbidity may inform further research into the influence of specific comorbidities on socio-economic inequalities in receipt of cancer treatment and in short-term mortality.