bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culturable fungal endophyte communities of primary successional plants on Mount St. Helens, WA, USA
Authors: Wolfe Emily R. , Dove Robyn , Webster Cassandra , Ballhorn Daniel J. 
Published: February 2022

Abstract
Background
While a considerable amount of research has explored plant community composition in primary successional systems, little is known about the microbial communities inhabiting these pioneer plant species. Fungal endophytes are ubiquitous within plants, and may play major roles in early successional ecosystems. Specifically, endophytes have been shown to affect successional processes, as well as alter host stress tolerance and litter decomposition dynamics—both of which are important components in harsh environments where soil organic matter is still scarce.

Results
To determine possible contributions of fungal endophytes to plant colonization patterns, we surveyed six of the most common woody species on the Pumice Plain of Mount St. Helens (WA, USA; Lawetlat'la in the Cowlitz language; created during the 1980 eruption)—a model primary successional ecosystem—and found low colonization rates (< 15%), low species richness, and low diversity. Furthermore, while endophyte community composition did differ among woody species, we found only marginal evidence of temporal changes in community composition over a single field season (July–September).

Conclusions
Our results indicate that even after a post-eruption period of 40 years, foliar endophyte communities still seem to be in the early stages of community development, and that the dominant pioneer riparian species Sitka alder (Alnus viridis ssp. sinuata) and Sitka willow (Salix sitchensis) may be serving as important microbial reservoirs for incoming plant colonizers.
Benchmarking phasing software with a whole-genome sequenced cattle pedigree
Authors: Oget-Ebrad Claire , Kadri Naveen Kumar , Moreira Gabriel Costa Monteiro , Karim Latifa , Coppieters Wouter , Georges Michel , Druet Tom 
Published: February 2022

Abstract
Background
Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium.

Results
After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and the probability that there is no phasing error between a pair of SNPs as a function of their distance. For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb (scenario 2). These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data (scenario 2), FImpute3.0 reconstructed extremely long segments without errors.

Conclusions
We report extremely high phasing accuracies in a typical livestock sample. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments and in the first scenario. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes.
Working in a care home during the COVID-19 pandemic: How has the pandemic changed working practices? A qualitative study
Authors: Hanna Kerry , Giebel Clarissa , Cannon Jacqueline , Shenton Justine , Mason Stephen , Tetlow Hilary , Marlow Paul , Rajagopal Manoj , Gabbay Mark 
Published: February 2022

Abstract
Background
The pandemic has significantly affected care homes’ residents and families through the national visiting restrictions. However, less is known on the impact these changes have had on the care home workforce. The aim of this research was to explore the impact of COVID-19 on the working practices of care home staff, caring for people living with dementia.

Methods
Remote qualitative, semi-structured interviews were conducted with care home staff caring for people living with dementia (PLWD) in the UK.

Results
Participants were recruited to the larger programme of research via convenience sampling. Interviews were conducted via telephone or online platforms. This research employed inductive thematic analysis. Sixteen care home staff were included in this study. Three overarching themes were developed from the analysis that conveyed changes to the everyday working practices of the care home workforce and the impact such changes posed to staff wellbeing: (1) Practical implications of working in a care home during the COVID-19 pandemic; (2); Staff values and changes to the staff roles (3): Impact to the care home staff and concerns for the care sector.

Conclusions
The COVID-19 pandemic has significantly disrupted the daily working practices of care home staff, with staff forced to adopt additional roles on top of increased workloads to compensate for the loss of external agencies and support. Support and guidance must be offered urgently to inform care home staff on how to best adapt to their new working practices, ensuring that they are adequately trained.
Rituximab in combination with gemcitabine plus cisplatin in patients with recurrent and metastatic head and neck squamous cell carcinoma: a phase I trial
Authors: Hsieh Ching-Yun , Lien Ming-Yu , Lin Chen-Yuan , Lo Wen-Jyi , Hua Chung-Hung , Chang Wei-Chao , Chiu Chang-Fang , Lin Ching-Chan 
Published: February 2022

Abstract
Background
The treatment of recurrent or metastatic head and neck squamous-cell carcinoma (R/M HNSCC) remains challenging. Preclinical studies revealed that B cell depletion could modulate the microenvironment and overcome chemoresistance. We conducted a phase I study to evaluate the feasibility and safety of B cell depletion using the anti-CD20 antibody rituximab to treat HNSCC.

Methods
Ten patients were enrolled in two protocols. The first four patients treated using protocol 1 received rituximab 1000 mg on days −14 and −7, followed by gemcitabine/cisplatin every 3 weeks, and rituximab was administered every 6 months thereafter. Because of disease hyperprogression, protocol 1 was amended to protocol 2, which consisted of the concomitant administration of rituximab 375 mg/m2 and gemcitabine/cisplatin every 3 weeks. Another six patients were enrolled and treated using protocol 2.

Results
Three patients treated using protocol 1 exhibited rapid disease progression, and the remaining patient could not undergo evaluation after rituximab treatment. Conversely, no unpredicted harm was observed in the six patients treated using protocol 2. Among these patients, one achieved complete response, and two had partial responses. The disease-free durations in these patients were 7.0, 6.2, and 7.1 months, respectively. Immune cell analysis revealed a higher ratio of cytotoxic T cells to regulatory T cells in responders than in non-responders.

Conclusions
B cell depletion using rituximab alone in patients with HNSCC can cause hyperprogressive disease. Contrarily, the co-administration of rituximab and cisplatin/gemcitabine was feasible and safe.

Trial registration
ClinicalTrials.gov Identifier: NCT04361409, 24 April 2020, retrospectively registered
The progression of the tobacco epidemic in India on the national and regional level, 1998-2016
Authors: Shaikh Rufi , Janssen Fanny , Vogt Tobias 
Published: February 2022

Abstract
Background
Evidence regarding the progression of the tobacco epidemic remains fragmented in low- and middle-income countries. In India, most of the studies that examined tobacco consumption focused on one time point, on the country as a whole, and on men. Despite important gender differences in tobacco consumption, vast economic and cultural differences exist within India. We, therefore, assessed the progression of the tobacco epidemic in India on both the national and the regional level, by gender.

Methods
We use information on current tobacco use among Indians aged 15–49 from three rounds of the National Family Health Survey (NFHS) (1998-99, 2005-06, 2015-16) to estimate the age-standardized sex specific smoking and smokeless tobacco prevalence across India and its states.

Results
Age-standardized tobacco use prevalence in India increased between 1998-1999 and 2005-2006, and declined from 2005-2006 to 2015–2016, simultaneously for men and women. There are substantial spatial differences in the progression of the tobacco epidemic in India. While tobacco use declined in the majority of states, we observe high and increasing use for men in the north-eastern states of Manipur, Mizoram and Nagaland, and for women in the western state of Gujarat and north-eastern state of Manipur. We observed even more states with a recent increasing prevalence in either tobacco smoking or smokeless tobacco. Throughout, prevalence of tobacco use has been higher among men than women for all Indian regions, and remained higher than the national average in the north-eastern states.

Conclusions
Our results suggest that India and the majority of its states experienced a ‘compressed tobacco epidemic’ in which the prevalence of tobacco consumption increased and decreased simultaneously for women and men over a comparatively short period of time. Despite the overall progress India made in reducing tobacco use, further lowering tobacco consumption remains a public health priority, as the prevalence of smoking and/or smokeless tobacco use remains high in a number of states. We therefore conclude that tobacco regulations should be expanded with the aim of reducing the overall health burden associated with tobacco consumption across India.
Determining intention, fast food consumption and their related factors among university students by using a behavior change theory
Authors: Didarloo Alireza , Khalili Surur , Aghapour Ahmad Ali , Moghaddam-Tabrizi Fatemeh , Mousavi Seyed Mortaza 
Published: February 2022

Abstract
Background
Today, with the advancement of science, technology and industry, people’s lifestyles such as the pattern of people’s food, have changed from traditional foods to fast foods. The aim of this survey was to examine and identify factors influencing intent to use fast foods and behavior of fast food intake among students based on the theory of planned behavior (TPB).

Methods
A cross-sectional study was conducted among 229 university students. The study sample was selected and entered to the study using stratified random sampling method. Data were collected using a four-part questionnaire including Participants’ characteristics, knowledge, the TPB variables, and fast food consumption behavior. The study data were analyzed in SPSS software (version 16.0) using descriptive statistics (frequencies, Means, and Standard Deviation) and inferential statistics (t-test, Chi-square, correlation coefficient and multiple regressions).

Results
The monthly frequency of fast food consumption among students was reported 2.7 times. The TPB explained 35, 23% variance of intent to use fast food and behavior of fast food intake, respectively. Among the TPB variables, knowledge (r = .340, p < 0.001) and subjective norm (r = .318, p < 0.001) were known as important predictors of intention to consume fast foods - In addition, based on regression analyses, intention (r = .215, p < 0.05), perceived behavioral control (r = .205, p < 0.05), and knowledge (r = .127, p < 0.05) were related to fast food consumption, and these relationships were statistically significant.

Conclusions
The current study showed that the TPB is a good theory in predicting intent to use fast food and the actual behavior. It is supposed that health educators use from the present study results in designing appropriate interventions to improve nutritional status of students.
Age, period, and cohort effects on trends in outpatient addiction care utilization in the general Berlin population from 2008 to 2016
Authors: Specht Sara , Schwarzkopf Larissa , Braun-Michl Barbara , Seitz Nicki-Nils , Wildner Manfred , Kraus Ludwig 
Published: February 2022

Abstract
Background
The aim of this study was to decompose independent effects of age, period, and cohort on trends in outpatient addiction care utilization resulting from alcohol (AUD) and illicit substances use disorders (ISUD). Decomposing trends in addiction care utilization into their independent effects by age, period, and cohort may lead to a better understanding of utilization patterns.

Methods
Individuals seeking help in Berlin outpatient addiction care facilities between 2008 and 2016 with an age range of 18–81 years for AUD (n = 46,706) and 18–70 years for ISUD (n = 51,113) were standardized to the general Berlin population using data from the German Federal Statistical Office. Classification of utilization as AUD- (F10) or ISUD-related (F11, F12, F14, F15, F16, F18, F19) help-seeking was based on primary diagnoses according to the International Statistical Classification of Diseases and Related Health Problems. Age was measured in years and period as year of data collection. Cohort was defined as the mathematical difference between period and age. Age, period, and cohort analyses were conducted using the intrinsic estimator model on AUD- and ISUD-related outpatient addiction care utilization.

Results
Age effects on AUD-related utilization were highest in 18- to 19-year-old and in 39- to 59-year-old individuals. ISUD-related utilization declined almost continuously with increasing age. Period effects on AUD- and ISUD-related utilization were small. AUD-related utilization was highest in cohorts born from 1951 to 1986. ISUD-related utilization increased in cohorts born between 1954 and 1973 where utilization peaked, followed by a decline of the same order.

Conclusions
Age and cohort effects were the strongest drivers of trends in AUD- and ISUD-related outpatient addiction care utilization. Onset of help-seeking in earlier phases of AUD development should be enhanced as well as help-seeking for AUD and ISUD in general. The highest cohort-related rates in the baby boomer and following cohorts for AUD and ISUD underline an increased demand for addiction care.
Expressions of actor power in implementation: a qualitative case study of a health service intervention in South Africa
Authors: Schneider Helen , Mukinda Fidele , Tabana Hanani , George Asha 
Published: February 2022

AbstractBackgroundImplementation frameworks and theories acknowledge the role of power as a factor in the adoption (or not) of interventions in health services. Despite this recognition, there is a paucity of evidence on how interventions at the front line of health systems confront or shape existing power relations. This paper reports on a study of actor power in the implementation of an intervention to improve maternal, neonatal and child health care quality and outcomes in a rural district of South Africa.MethodsA retrospective qualitative case study based on interviews with 34 actors in three ‘implementation units’ – a district hospital and surrounding primary health care services – of the district, selected as purposefully representing full, moderate and low implementation of the intervention, some three years after it was first introduced. Data are analysed using Veneklasen and Miller’s typology of the forms of power – namely ‘power over’, ‘power to’, ‘power within’ and ‘power with’.ResultsMultiple expressions of actor power were evident during implementation and played a plausible role in shaping variable implementation, while the intervention itself acted to change power relations. As expected, a degree of buy-in of managers (with power over) in implementation units was necessary for the intervention to proceed. Beyond this, the ability to mobilise collective action (power with), combined with support from champions with agency (power within) were key to successful implementation. However, local empowerment may pose a threat to hierarchical power (power over) at higher levels (district and provincial) of the system, potentially affecting sustainability.ConclusionsA systematic approach to the analysis of power in implementation research may provide insights into the fate of interventions. Intervention designs need to consider how they shape power relations, especially where interventions seek to widen participation and responsiveness in local health systems.
Meta-analysis of economic evaluation studies: data harmonisation and methodological issues
Authors: Bagepally Bhavani Shankara , Chaikledkaew Usa , Chaiyakunapruk Nathorn , Attia John , Thakkinstian Ammarin 
Published: February 2022

AbstractBackgroundIn the context of ever-growing health expenditure and limited resources, economic evaluations aid in making evidence-informed policy decisions. Cost-utility analysis (CUA) is often used, and CUA data synthesis is also desirable, but methodological issues are challenged. Hence, we aim to provide a step-by-step process to prepare the CUA data for meta-analysis.MethodsData harmonisation methods were constructed specifically considering CUA methodology, including inconsistent reports, economic parameters, heterogeneity (i.e., country’s income, time horizon, perspective, modelling approaches, currency, willingness to pay). An incremental net benefit (INB) and its variance were estimated and pooled across studies using a basic meta-analysis by COMER.ResultsFive scenarios show how to obtain INB and variance with various reported data: Study reports the mean and variance (Scenario 1) or 95% confidence interval (Scenario 2) of ΔC, ΔE, and ICER for INB/variance calculations. Scenario 3: ΔC, ΔE, and variances are available, but not for the ICER; a Monte Carlo was used to simulate ΔC and ΔE data, variance and covariance can be then estimated leading INB calculation. Scenario-4: Only the CE plane was available, ΔC and ΔE data can be extracted; means of ΔC, ΔE, and variance/covariance can be estimated accordingly, leading to INB/variance estimates. Scenario-5: Only mean cost/outcomes and ICER are available but not for variance and the CE-plane. A variance INB can be borrowed from other studies which are similar characteristics, including country income, ICERs, intervention-comparator, time period, country region, and model type and inputs (i.e., discounting, time horizon).ConclusionOut data harmonisation and meta-analytic methods should be useful for researchers for the synthesis of economic evidence to aid policymakers in decision making.
Modelling spatiotemporal trends in the frequency of genetic mutations conferring insecticide target-site resistance in African mosquito malaria vector species
Authors: Hancock Penelope A. , Lynd Amy , Wiebe Antoinette , Devine Maria , Essandoh John , Wat’senga Francis , Manzambi Emile Z. , Agossa Fiacre , Donnelly Martin J. , Weetman David , Moyes Catherine L. 
Published: February 2022

Abstract
Background
Resistance in malaria vectors to pyrethroids, the most widely used class of insecticides for malaria vector control, threatens the continued efficacy of vector control tools. Target-site resistance is an important genetic resistance mechanism caused by mutations in the voltage-gated sodium channel (Vgsc) gene that encodes the pyrethroid target-site. Understanding the geographic distribution of target-site resistance, and temporal trends across different vector species, can inform strategic deployment of vector control tools.

Results
We develop a Bayesian statistical spatiotemporal model to interpret species-specific trends in the frequency of the most common resistance mutations, Vgsc-995S and Vgsc-995F, in three major malaria vector species Anopheles gambiae, An. coluzzii, and An. arabiensis over the period 2005–2017. The models are informed by 2418 observations of the frequency of each mutation in field sampled mosquitoes collected from 27 countries spanning western and eastern regions of Africa. For nine selected countries, we develop annual predictive maps which reveal geographically structured patterns of spread of each mutation at regional and continental scales. The results show associations, as well as stark differences, in spread dynamics of the two mutations across the three vector species. The coverage of ITNs was an influential predictor of Vgsc allele frequencies, with modelled relationships between ITN coverage and allele frequencies varying across species and geographic regions. We found that our mapped Vgsc allele frequencies are a significant partial predictor of phenotypic resistance to the pyrethroid deltamethrin in An. gambiae complex populations.

Conclusions
Our predictive maps show how spatiotemporal trends in insecticide target-site resistance mechanisms in African An. gambiae vary across individual vector species and geographic regions. Molecular surveillance of resistance mechanisms will help to predict resistance phenotypes and track their spread.