bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin
Authors: Ahle Charlotte Marie , Stødkilde-Jørgensen Kristian , Poehlein Anja , Streit Wolfgang R. , Hüpeden Jennifer , Brüggemann Holger 
Published: July 2021

Abstract
Background
Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution.

Results
Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis.

Conclusions
Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.
Research on the correlation between activating transcription factor 3 expression in the human coronary artery and atherosclerotic plaque stability
Authors: Peng J. , Le C. Y. , Xia B. , Wang J. W. , Liu J. J. , Li Z. , Zhang Q. J. , Zhang Q. , Wang J. , Wan C. W. 
Published: July 2021

Abstract
Background
Activating transcription factor 3 (ATF3) is an early response gene that is activated in response to atherosclerotic stimulation and may be an important factor in inhibiting the progression of atherosclerosis. In this study, we directly measured the expression of ATF3 and inflammatory factors in human coronary atherosclerotic plaques to examine the relationship between ATF3 expression, inflammation and structural stability in human coronary atherosclerotic plaques.

Methods
A total of 68 coronary artery specimens were collected from the autopsy group, including 36 cases of sudden death from coronary heart disease (SCD group) and 32 cases of acute death caused by mechanical injury with coronary atherosclerosis (CHD group). Twenty-two patients who had no coronary heart disease were collected as the control group (Con group). The histological structure of the coronary artery was observed under a light microscope after routine HE staining, and the intimal and lesion thicknesses, thickness of the fibrous cap, thickness of necrosis core, degree of lumen stenosis were assessed by image analysis software. Western blotting and immunohistochemistry were used to measure the expression and distribution of ATF3, inflammatory factors (CD45, IL-1β, TNF-α) and matrix metalloproteinase-9 (MMP-9) and vascular cell adhesion molecule 1 (VCAM1) in the coronary artery. The Pearson correlation coefficient was used to analyse the correlation between ATF3 protein expression and inflammatory factors and between ATF3 protein expression and structure-related indexes in the lesion group.

Results
Compared with those in the control group, the intima and necrotic core in the coronary artery were thickened, the fibrous cap became thin and the degree of vascular stenosis was increased in the lesion group, while the intima and necrotic core became thicker and the fibrous cap became thinner in the SCD group than in the CHD group (P < 0.05). There was no or low expression of ATF3, inflammatory factors, VCAM1 and MMP-9 in the control group, and the expression of inflammatory factors, VCAM1 and MMP-9 in the SCD group was higher than that in CHD group, while the expression of ATF3 in the SCD group was significantly lower than that in CHD group (P < 0.05). In the lesion group, the expression of ATF3 was negatively correlated with intimal and necrotic focus thickness, positively correlated with fibrous cap thickness (P < 0.01), and negatively correlated with inflammatory factors, VCAM1 and MMP-9 (P < 0.01).

Conclusions
The expression of ATF3 may be related to the progression and stability of atherosclerotic plaques, and may affect the structural stability of atherosclerotic plaques by regulating the inflammatory response, thus participating in the regulation of atherosclerotic progression.
Overcoming the problems caused by collinearity in mixed-effects logistic model: determining the contribution of various types of violence on depression in pregnant women
Authors: Khalili Sanaz , Faradmal Javad , Mahjub Hossein , Moeini Babak , Ezzati-Rastegar Khadijeh 
Published: July 2021

Abstract
Background
Collinearity is a common and problematic phenomenon in studies on public health. It leads to inflation in variance of estimator and reduces test power. This phenomenon can occur in any model. In this study, a new ridge mixed-effects logistic model (RMELM) is proposed to overcome consequences of collinearity in correlated binary responses.

Methods
Parameters were estimated through penalized log-likelihood with combining expectation maximization (EM) algorithm, gradient ascent, and Fisher-scoring methods. A simulation study was performed to compare new model with mixed-effects logistic model(MELM). Mean square error, relative bias, empirical power, and variance of random effects were used to evaluate RMELM. Also, contribution of various types of violence, and intervention on depression among pregnant women experiencing intimate partner violence(IPV) were analyzed by new and previous models.

Results
Simulation study showed that mean square errors of fixed effects were decreased for RMELM than MELM and empirical power were increased. Inflation in variance of estimators due to collinearity was clearly shown in the MELM in data on IPV and RMELM adjusted the variances.

Conclusions
According to simulation results and analyzing IPV data, this new estimator is appropriate to deal with collinearity problems in the modelling of correlated binary responses.
A generic outcome assessment of mobility capacity in neurorehabilitation: measurement properties of the de Morton Mobility Index
Authors: Braun Tobias , Marks Detlef , Thiel Christian , Grüneberg Christian 
Published: July 2021

Abstract
Background
Mobility capacity is a key outcome domain in neurorehabilitation. The de Morton Mobility Index (DEMMI), an established and generic outcome assessment of mobility capacity in older patients, is promising for use in neurorehabilitation. The aim of this study was to examine the measurement properties of the DEMMI in rehabilitation inpatients with neurological conditions.

Methods
Cross-sectional study including a mixed sample of adult inpatients in a neurorehabilitation hospital. Structural validity, unidimensionality and measurement invariance (Rasch analysis), construct validity, internal consistency reliability, and inter-rater reliability of the DEMMI (scale range: 0–100 points) were established. The minimal detectable change, the 95% limits of agreement, and possible floor and ceiling effects were calculated to indicate interpretability.

Results
We analyzed validity (n = 348) and reliability (n = 133) in two samples. In both samples, the majority of participants had a sub-acute stroke or Parkinson’s disease.
Rasch analysis indicated unidimensionality with an overall fit to the model (chi-square = 59.4, P = 0.074). There was no relevant measurement invariance by disease group. Hypotheses-based correlation analyses (DEMMI and other functional outcome assessments) showed sufficient construct validity. Internal consistency reliability (Cronbach’s alpha = 0.94) and inter-rater reliability (intraclass correlation coefficient = 0.94; 95% confidence interval: 0.91–0.95) were sufficient. The minimal detectable change with 90% confidence was 15.0 points and the limits of agreement were 39%. No floor or ceiling effects were observed.

Conclusions
Results indicate sufficient measurement properties of the DEMMI in rehabilitation inpatients with neurological conditions. The DEMMI can be used as a generic outcome assessment of mobility capacity in neurorehabilitation.

Trial registration
German Clinical Trials Register (DRKS00004681). Registered May 6, 2013.
The effects of bright light treatment on affective symptoms in people with dementia: a 24-week cluster randomized controlled trial
Authors: Kolberg Eirin , Hjetland Gunnhild Johnsen , Thun Eirunn , Pallesen Ståle , Nordhus Inger Hilde , Husebo Bettina S. , Flo-Groeneboom Elisabeth 
Published: July 2021

AbstractBackgroundThe majority of people with dementia have behavioral and psychological symptoms of dementia (BPSD), including depression, anxiety and agitation. These may be elicited or aggravated by disrupted circadian rhythms. Bright light treatment (BLT) is a promising non-pharmacological approach to the management of BPSD, but previous research has yielded mixed results.MethodsEight nursing home dementia units (1 unit = 1 cluster) with 78 patients were invited to participate in a cluster randomized controlled trial from September 2017 to April 2018 investigating the effects of BLT on sleep and circadian rhythms (primary outcome) and BPSD (secondary outcome). Ceiling mounted LED-panels were installed in the intervention group (four units), providing light at 1000 lx and 6000 K (vertically at 1.2 m) between 10 a.m. and 3 p.m., with lower values in the mornings and evenings. Standard indoor light was used in the control group (four units). BPSD were assessed with The Cornell Scale for Depression in Dementia (CSDD) and the Neuropsychiatric Inventory Nursing Home Version (NPI-NH). Data collection took place at baseline and after 8, 16 and 24 weeks. Multilevel regression models with and without false discovery rate correction were used for the analysis, with baseline values and dementia stage entered as covariates.ResultsSixty-nine patients were included in the study at baseline. Compared to the control group, the intervention group had a larger reduction on the composite scores of both the CSDD (95% CI = − 6.0 – − 0.3) and the NPI-NH (95% CI = − 2.2 – − 0.1), as well as on the NPI-NH Affect sub-syndrome, and the CSDD Mood related signs sub-scale at follow-up after 16 weeks. With FDR correction, the group difference was significant on the CSDD Mood related signs sub-scale (95% CI = − 2.7 – − 0.8) and the NPI-NH Affect sub-syndrome (95% CI = − 1.6 – − 0.2). No differences were found between conditions at weeks 8 or 24.ConclusionCompared to the control condition, affective symptoms were reduced after 16 weeks in the group receiving BLT, suggesting BLT may be beneficial for nursing home patients with dementia.Trial registrationClinicalTrials.govIdentifier:NCT03357328. Retrospectively registered on November 29, 2017.
Factor structure and sex invariance of the temporal experience of pleasure scale (TEPS) in Chinese university students and clinical population
Authors: Fang Shulin , Huang Xiaodan , Zhang Panwen , He Jiayue , Luo Xingwei , Zhang Jianghua , Xiong Yan , Luo Fusheng , Wang Xiaosheng , Yao Shuqiao , Wang Xiang 
Published: July 2021

Abstract
Background
A motivation dimension of the core psychiatric symptom anhedonia additional has been suggested. The Temporal Experience of Pleasure Scale (TEPS) has been reported to assess anticipatory and consummatory pleasure separately in multiple factor-structure models. This study explored the factor structure of a Chinese version of the 18-item TEPS and further explored the measurement invariance of the TEPS across sex and clinical status (non-clinical, psychiatric).

Methods
Best-fit factor structure of the TEPS was examined in a non-clinical cohort of 7410 undergraduates, randomized into sample 1 (N = 3755) for exploratory factor analysis (EFA) and sample 2 (N = 3663) for confirmatory factor analysis (CFA). Additionally, serial CFA was conducted to evaluate measurement invariance across sex and between clinical (N = 313) and non-clinical (N = 341) samples.

Results
EFA supported a new four-factor structure with a motivation component, based on the original two-factor model (consummatory pleasure with/without motivation drive, anticipatory pleasure with/without motivation drive). CFA confirmed the four-factor model as the best-fit structure and revealed a second-order hierarchy in non-clinical and clinical samples. Full scalar invariance was observed across clinical and non-clinical samples and across sex in the clinical sample; only partial scalar invariance was observed across sex in the non-clinical sample.

Conclusions
A four-factor structured TEPS can assess motivation-driving dimensions of anticipatory and consummatory pleasure, consistent with the recently advanced multidimensional structure of anhedonia. CFA and measurement invariance results support application of the TEPS for assessing motivation aspects of anhedonia.
The impact of out-of pocket payments of households for dental healthcare services on catastrophic healthcare expenditure in Iran
Authors: Woldemichael Abraha , Rezaei Satar , Kazemi Karyani Ali , Ebrahimi Mohammad , Soltani Shahin , Aghaei Abbas 
Published: July 2021

Abstract
Background
Dental healthcare is the costliest and single most source of the financial barrier to seeking and use of needed healthcare. Hence, this study aims to analyses impact of out-of-pocket (OOP) payments for dental services on prevalence catastrophic healthcare expenditure (CHE) among Iranian households during 2018.

Methods
We performed a cross-sectional analysis to determine the prevalence rate of CHE due to use of dental healthcare services among 38,858 Iranian households using the 2018 Household Income and Expenditure Survey (HIES) survey data of Iran. The WHO approach was used to determine the CHE due to use of dental care services at the 40% of household capacity to pay (CTP). Multiple logistic regression models were used to obtain the odds of facing with CHE among households that paid for any dental healthcare services over the last month while adjusting for covariates included in the model. These findings were reported for urban, rural areas and also for low, middle and high human development index HDI across provinces.

Results
The study indicated that the prevalence of CHE among households that used and did not used dental services over the last month was 16.5% (95% CI: 14.9 to 18.3) and 4.3% (95% CI: 4.1 to 4.6), respectively. The adjusted odds ratio (AOR) for the covariates revealed that the prevalence of CHE for the overall households that used dental healthcare service was 6.2 times (95% CI: 5.4 to 7.1) than those that did not use dental healthcare services. The urban households that used dental healthcare had 7.8 times (95%CI: 6.4–9.4) while the rural ones had 4.7 times (95% CI: 3.7–5.7) higher odds of facing CHE than the corresponding households that did not use dental healthcare services.

Conclusions
The study indicates that out-of-pocket costs for dental care services impose a substantial financial burden on household’s budgets at the national and subnational levels. Alternative health care financing strategies and policies targeted to the reduction in CHE in general and CHE due to dental services in particular are urgently required in low and middle income countries such as Iran.
Health workers’ perceptions on where and how to integrate tobacco use cessation services into tuberculosis treatment; a qualitative exploratory study in Uganda
Authors: Rutebemberwa Elizeus , Nyamurungi Kellen , Joshi Surabhi , Olando Yvonne , Mamudu Hadii M. , Pack Robert P. 
Published: July 2021

AbstractBackgroundTobacco use is associated with exacerbation of tuberculosis (TB) and poor TB treatment outcomes. Integrating tobacco use cessation within TB treatment could improve healing among TB patients. The aim was to explore perceptions of health workers on where and how to integrate tobacco use cessation services into TB treatment programs in Uganda.MethodsBetween March and April 2019, nine focus group discussions (FGDs) and eight key informant interviews were conducted among health workers attending to patients with tuberculosis on a routine basis in nine facilities from the central, eastern, northern and western parts of Uganda. These facilities were high volume health centres, general hospitals and referral hospitals. The FGD sessions and interviews were tape recorded, transcribed verbatim and analysed using content analysis and the Chronic Care Model as a framework.ResultsRespondents highlighted that just like TB prevention starts in the community and TB treatment goes beyond health facility stay, integration of tobacco cessation should be started when people are still healthy and extended to those who have been healed as they go back to communities. There was need to coordinate with different organizations like peers, the media and TB treatment supporters. TB patients needed regular follow up and self-management support for both TB and tobacco cessation. Patients needed to be empowered to know their condition and their caretakers needed to be involved. Effective referral between primary health facilities and specialist facilities was needed. Clinical information systems should identify relevant people for proactive care and follow up. In order to achieve effective integration, the health system needed to be strengthened especially health worker training and provision of more space in some of the facilities.ConclusionsTobacco cessation activities should be provided in a continuum starting in the community before the TB patients get to hospital, during the patients’ interface with hospital treatment and be given in the community after TB patients have been discharged. This requires collaboration between those who carry out health education in communities, the TB treatment supporters and the health workers who treat patients in health facilities.
Onset of effects of non-pharmaceutical interventions on COVID-19 infection rates in 176 countries
Authors: Nader Ingo W. , Zeilinger Elisabeth L. , Jomar Dana , Zauchner Clemens 
Published: July 2021

Abstract
Background
During the initial phase of the global COVID-19 outbreak, most countries responded with non-pharmaceutical interventions (NPIs). In this study we investigate the general effectiveness of these NPIs, how long different NPIs need to be in place to take effect, and how long they should be in place for their maximum effect to unfold.

Methods
We used global data and a non-parametric machine learning model to estimate the effects of NPIs in relation to how long they have been in place. We applied a random forest model and used accumulated local effect (ALE) plots to derive estimates of the effectiveness of single NPIs in relation to their implementation date. In addition, we used bootstrap samples to investigate the variability in these ALE plots.

Results
Our results show that closure and regulation of schools was the most important NPI, associated with a pronounced effect about 10 days after implementation. Restrictions of mass gatherings and restrictions and regulations of businesses were found to have a more gradual effect, and social distancing was associated with a delayed effect starting about 18 days after implementation.

Conclusions
Our results can inform political decisions regarding the choice of NPIs and how long they need to be in place to take effect.
Gaps and opportunities for cervical cancer prevention, diagnosis, treatment and care: evidence from midterm review of the Zimbabwe cervical Cancer prevention and control strategy (2016–2020)
Authors: Tapera Oscar , Nyakabau Anna M. , Simango Ndabaningi , Guzha Bothwell T. , Jombo-Nyakuwa Shamiso , Takawira Eunice , Mapanga Angeline , Makosa Davidzoyashe , Madzima Bernard 
Published: July 2021

Abstract
Background
Cervical cancer is the fourth most common cancer amongst women globally and it accounts for the majority of cancer deaths among females in Zimbabwe. The objective of this midterm review analysis was to identify the gaps and opportunities for cervical cancer prevention, diagnosis, treatment, and care to inform the next cervical cancer strategy in Zimbabwe.

Methods
A mixed methods approach was used for the midterm review. Secondary data was collected from programme documents, published and grey literature. Primary data was collected in six provinces through key informant interviews with officials and focus group discussions with beneficiaries. After data analysis, a draft report was presented to a technical working group to validate the findings and to fill in any gaps.

Results
This midterm review revealed a myriad of gaps of the strategy particularly in diagnosis, treatment and care of cervical cancer and the primary focus was on secondary prevention. There was no data to quantify the level of awareness and advocacy for cervical cancer prevention. Our results revealed that there was no data on the proportion of women who ever tested for cervical cancer which existed nationally. Our findings suggest that some health facilities were screening women above 50 years old using VIAC, which is an inappropriate approach for those women. Quality control of VIAC and treatment of precancers were not part of the strategy. Pathological services were not efficient and effective due to lack of resources and additionally data on investigations were not routinely collected and available at the national level. Other gaps identified were limited funding, human resources, equipment, and commodities as well as lack of leadership at the national level to coordinate the various components of the cervical cancer programme. There are also numerous opportunities identified to build upon some successes realized to date.

Conclusions
Our findings emphasized the importance of effective and holistic planning in cervical cancer screening programmes in low-resource settings. In addition, huge investments are required in cervical cancer programmes and governments need to take centre role in mobilizing the requisite resources.