bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and predictors of vaccine hesitancy in an urbanized agglomeration of New Delhi, India
Authors: Cherian Vinu , Saini Narinder Kumar , Sharma Arun Kumar , Philip Joel 
Published: January 2021

Abstract

Background
The immunization program has been an important part of Indian public health policy for three decades; yet only 62% of children are being fully immunized. Vaccine hesitancy is a major contributor to the immunization gap that needs to be addressed.

Methods
A cross-sectional descriptive study of prevalence and predictors of vaccine hesitancy was conducted in 350 households having at least one child in the age group of 13–24 months. Statistical analysis was done using chi-square test and logistic regression.

Results
The prevalence of vaccine hesitancy was 28.9%. Fear of needles, concern about pain during vaccination, lack of family support, and apprehension regarding side effects were ascertained as reasons for vaccine hesitancy. The type of family, time taken to reach the health facility and antenatal care received by the mother were significant predictors of vaccine hesitancy.

Conclusion
The prevalence of vaccine hesitancy was found to be high. In 2019, the World Health Organization earmarked vaccine hesitancy as one of the major roadblocks to better global health. A better understanding of the subject can help public health agencies enhance vaccination coverage, not just in children but also as a tool to protect entire populations in this age of re-emerging epidemics.
A case–control study of occupational risk factors for pancreatic cancer in poultry plant workers: a random forest approach
Authors: Faramawi Mohammed F , Abouelenein Saly , Johnson Eric 
Published: January 2021

Abstract

Background
Poultry plant workers are exposed to chemical carcinogens and oncogenic viruses in their work environment. Our objective was to identify jobs and workplaces related to poultries that could increase the pancreatic cancer risk.

Methods
We conducted a case–control study within a defined cohort of poultry workers. We used a random forest algorithm to identify features that could increase pancreatic cancer in the poultry plant workers.

Results
The mean age of participants was 59.49 years. The majority of the study participants were females (51.30%) and Whites (71.0%). The following workplaces and job tasks had an association with increased pancreatic cancer mortality: working in chicken and turkey plants, working in plants where food products were processed and canned, working in a place where poultry and animals where present, working as a hunter for game animals, working as a veterinarian in places had animals and different poultry birds, working in pet houses and working in places where birds were handled and killed. The accuracy and the area under the curve of the model were 72.3 and 71.50%.

Conclusion
Chicken and turkey plant workers could be at risk for pancreatic cancer mortality. We need to confirm the results in future studies.
Remission in SLE—do DORIS criteria match the treating physician’s judgment? A cross-sectional study to assess reasons for discordance
Authors: Mucke Johanna , Düsing Christina , Klose Nora , Schneider Matthias , Chehab Gamal 
Published: January 2021

Abstract

Objectives
The definition of an accurate target for a treat-to-target approach in SLE has been challenging over past years, and recently the DORIS definitions of remission were presented by the international DORIS task force. It was our aim to assess the frequency of DORIS remission and LLDAS in our SLE cohort and their agreement with the treating physician’s (DORIS-) independent remission judgement. Patient characteristics leading to lack of agreement and incoherence ought to be identified.

Methods
In this monocentric cross-sectional study, patients with SLE were enrolled and assessed between September 2016 and December 2017. DORIS remission definitions were applied and after the clinical consultation, the treating physicians gave his/her opinion on whether the patient was in remission. Regression analyses were performed to identify parameters influencing physician remission.

Results
A total of 233 patients were included (87.6% female); 99 (42.5%) patients fulfilled any of the four DORIS remission definitions, while 126 patients were in remission according to their physician’s judgement. We observed discordance in the assessment of remission in 53 patients (22.7%). Physician remission was influenced by disease activity [odds ratio (OR) 0.76, 95% CI: 0.63, 0.90], disease and/or treatment-related damage (OR 0.78, 95% CI: 0.62, 0.98) and the presence of ds-DNA antibodies (OR 2.47, 95% CI: 1.06, 6.04).

Conclusions
DORIS remission proved an achievable target in our outpatient clinic. Still we found discordance regarding DORIS remission and the treating physician’s judgement with a greater number of patients considered in remission by their physicians.
Meta-analysis of latent tuberculosis in healthcare workers in Iran: a retrospective review
Authors: Sepehri NazaninZahra , Saghanezhad Seyed Mohammad , Khoddami Farshad , Arasteh Amin , Delirakbariazar Marziyeh , Khaledi Azad 
Published: January 2021

BackgroundHere we review the status of latent tuberculosis (LTB) in Iranian healthcare workers (HCWs).MethodsA literature search was conducted using keywords according to the Preferred Reporting Items for Systematic Review and Meta-Analyses instructions. Cross-sectional studies published from 1 January 2000 through 1 January 2019 were retrieved. Meta-analysis was performed using Comprehensive Meta-Analysis software using the random effects model, Cochran's Q and I2 tests. Publication bias was estimated by funnel plot and Egger's linear regression test.ResultsAmong 774 articles retrieved in the primary literature search, 21 studies met the eligibility criteria. No publication bias was observed among the included studies (p=0.07). The prevalence of LTB ranged from 7% to 63% in Iranian HCWs from different geographical areas. The overall combined prevalence of LTB among Iranian HCWs was 30.9% (95% confidence interval 24.2 to 38.5). Also, 52.4% of the included studies showed a significant correlation between occupation and LTB incidence (p&lt;0.05).ConclusionsThe prevalence of LTB was high among Iranian HCWs. This requires developing comprehensive information databases and surveillance systems for detecting LTB among HCWs. It is also essential to periodically screen for LTB in HCWs to provide a timely diagnosis of the infection. It is recommended to perform a tuberculin skin test, a useful tool for screening and treatment of LTB, on an annual basis in HCWs.
A review of models applied to the geographic spread of Zika virus
Authors: Li Sabrina L , Messina Jane P , Pybus Oliver G , Kraemer Moritz U G , Gardner Lauren 
Published: January 2021

Abstract
In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.
Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices
Authors: Chiumenti Michela , Navarro Beatriz , Candresse Thierry , Flores Ricardo , Di Serio Francesco 
Published: January 2021

Abstract
With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.
Prioritization of putatively detrimental variants in euploid miscarriages
Authors: Buonaiuto Silvia , Di Biase Immacolata , Aleotti Valentina , Ravaei Amin , Marino Adriano De , Damaggio Gianluca , Chierici Marco , Pulijala Madhuri , D’Ambrosio Palmira , Esposito Gabriella , Ayub Qasim , Furlanello Cesare , Greco Pantaleo , Capalbo Antonio , Rubini Michele , Biase Sebastiano Di , Colonna Vincenza 
Published: January 2021

ABSTRACTMiscarriage is the spontaneous termination of a pregnancy before 24 weeks of gestation. We studied the genome of euploid miscarried embryos from mothers in the range of healthy adult individuals to understand genetic susceptibility to miscarriage not caused by chromosomal aneuploidies. We developed GP, a pipeline that we used to prioritize 439 unique variants in 399 genes, including genes known to be associated with miscarriages. Among the prioritized genes we found STAG2 coding for the cohesin complex subunit, for which inactivation in mouse is lethal, and TLE4 a target of Notch and Wnt, physically interacting with a region on chromosome 9 associated to miscarriages.
Zorro versus Covid-19: fighting the pandemic with face masks
Authors: Damette Olivier 
Published: January 2021

AbstractTo confront the global Covid-19 pandemic and reduce the spread of the virus, we need to better understand if face mask use is effective to contain the outbreak and investigate the potential drivers in favor of mask adoption. It is highly questionable since there is no consensus among the general public despite official recommendations. For the first time, we conduct a panel econometric exercise to assess the dynamic impact of face mask use on both infected cases and fatalities at a global scale. We reveal a negative impact of mask wearing on fatality rates and on the Covid-19 number of infected cases. The delay of action varies from around 7 days to 28 days concerning infected cases but is more longer concerning fatalities. We also document the increasing adoption of mask use over time. We find that population density and pollution levels are significant determinants of heterogeneity regarding mask adoption across countries, while altruism, trust in government and demographics are not. Surprisingly, government effectiveness and income level (GDP) have an unexpected influence. However, strict government policies against Covid-19 have the most significant effect on mask use. Therefore, the most effective way of increasing the level of mask wearing is to enforce strict laws on the wearing of masks.
Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease
Authors: Chamorro Nayaret , Montero David A. , Gallardo Pablo , Farfán Mauricio , Contreras Mauricio , De la Fuente Marjorie , Dubois Karen , Hermoso Marcela A. , Quera Rodrigo , Pizarro-Guajardo Marjorie , Paredes-Sabja Daniel , Ginard Daniel , Rosselló-Móra Ramon , Vidal Roberto 
Published: January 2021

ABSTRACTInflammatory bowel diseases (IBD), which include ulcerative colitis (UC) and Crohn’s disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBD have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of the IBD and the dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identify a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward toward understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBD.
Quality Control Metrics for Whole Blood Transcriptome Analysis in the Parkinson’s Progression Markers Initiative (PPMI)
Authors: Hutchins Elizabeth , Craig David , Violich Ivo , Alsop Eric , Casey Bradford , Hutten Samantha , Reimer Alyssa , Whitsett Timothy G. , Crawford Karen L. , Toga Arthur W , Levy Shawn , Robinson Madison , Prasad Nripesh , Gibbs J. Raphael , Cookson Mark R. , Van Keuren-Jensen Kendall ,   Parkinson Progression Marker Initiative
Published: January 2021

AbstractThe Michael J. Fox Foundation’s Parkinson’s Progression Markers Initiative (PPMI) is an observational study to comprehensively evaluate Parkinson’s disease (PD) patients using imaging, biologic sampling, clinical and behavioural assessments to identify biomarkers of PD progression. As part of this study, we obtained 4,756 whole blood samples from 1,570 subjects at baseline, 0.5, 1, 2, and 3 years from enrollment in the study. We isolated RNA and performed whole transcriptome sequencing in this longitudinal cohort. Here, we describe and quantify technical variability associated with this dataset through the use of pooled reference samples, including plate distribution, RNA quality, and outliers. This large, uniformly processed dataset is available to researchers at https://www.ppmi-info.org.
A New Sensory Skill Shows Automaticity and Integration Features in Multisensory Interactions
Authors: Negen James , Bird Laura-Ashleigh , Slater Heather , Thaler Lore , Nardini Marko 
Published: January 2021

ABSTRACTPeople can learn new sensory skills that augment their perception, such as human echolocation. However, it is not clear to what extent these can become an integral part of the perceptual repertoire. Can they show automatic use, integrated with the other senses, or do they remain cognitively-demanding, cumbersome, and separate? Here, participants learned to judge distance using an echo-like auditory cue. We show that use of this new skill met three key criteria for automaticity and sensory integration: (1) enhancing the speed of perceptual decisions; (2) processing through a non-verbal route and (3) integration with vision in an efficient, Bayes-like manner. We also show some limits following short training: integration was less-than-optimal, and there was no mandatory fusion of signals. These results demonstrate key ways in which new sensory skills can become automatic and integrated, and suggest that sensory augmentation systems may have benefits beyond current applications for sensory loss.
Heat shock protein gene expression is higher and more variable with thermal stress and mutation accumulation inDaphnia
Authors: Scheffer Henry , Coate Jeremy , Ho Eddie K. H. , Schaack Sarah 
Published: January 2021

AbstractUnderstanding the genetic architecture of the stress response and its ability to evolve in response to different stressors requires an integrative approach. Here we quantify gene expression changes in response to two stressors associated with global climate change and habitat loss—heat shock and mutation accumulation. We measure expression levels for two Heat Shock Proteins (HSP90 and HSP60)—members of an important family of conserved molecular chaperones that have been shown to play numerous roles in the cell. While HSP90 assists with protein folding, stabilization, and degradation throughout the cell, HSP60 primarily localizes to the mitochondria and mediatesde novofolding and stress-induced refolding of proteins. We perform these assays inDaphnia magnaoriginally collected from multiple genotypes and populations along a latitudinal gradient, which differ in their annual mean, maximum, and range of temperatures. We find significant differences in overall expression between loci (10-fold), in response to thermal stress (~6x increase) and with mutation accumulation (~4x increase). Importantly, stressors interact synergistically to increase gene expression levels when more than one is applied (increasing, on average, >20x). While there is no evidence for differences among the three populations assayed, individual genotypes vary considerably in HSP90 expression. Overall, our results support previous proposals that HSP90 may act as an important buffer against not only heat, but also mutation, and expands this hypothesis to include another member of the gene family acting in a different domain of the cell.
Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices
Authors: Wolfe Marnin D. , Chan Ariel W. , Kulakow Peter , Rabbi Ismail , Jannink Jean--Luc 
Published: January 2021

AbstractDiverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomicmateselection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. We were able to predict all genetic variances and most covariances with non-zero accuracy. We also tested a directional dominance model and found significant inbreeding depression for most traits and a boost in total merit accuracy for root yield. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with excellent breeding values) and varieties (progeny with top performance).Author SummaryBreeders typically use truncation selection and invest significant resources evaluating progeny to find exceptional genotypes. We extended genetic variance and trait covariance prediction to include dominance and predicting the multivariate selection index variance. We enable mate selection based on potential to produce future parents (progeny with excellent breeding values) and/or varieties (progeny with top performance). Using cross-validation, we demonstrate that genetic variances and covariances can be predicted with non-zero accuracy in cassava, a staple tropical root crop.
Rhizoliths identified as prehistoric filing tools for fishhook production on San Nicolas Island, California
Authors: Wärmländer Sebastian K.T.S. , Smith Kevin N. , Vellanoweth René L. , Moritz Ryan , Jansson Kjell , Gooding Tim , Kendig William E. , Sholts Sabrina B. 
Published: January 2021

AbstractChemical analysis of archeological objects can provide important clues about their purpose and function. In this study, we used scanning electron microscopy (SEM) and chemical spectroscopy (SEM-EDS and XRD) to identify a white residue present on cylindrical rhizoliths from a component at an archaeological site (CA-SNI-25) on San Nicolas Island, California, dated ca. AD 1300 to 1700. The residue was found to consist of biogenic calcite and aragonite particles, different in composition and morphology from the CaCO3 particles in the rhizoliths, but identical to marine shell material. These results, together with observations of surface micro-wear patterning on fishhooks and rhizoliths, replicative experiments,insitu spatial analysis, and other archaeological evidence, show that rhizoliths were used as files in a larger tool kit for crafting shell fishhooks. Our findings shed new light on the technological innovations devised by Native Americans to exploit the rich marine resources surrounding the Channel Islands, and provide the first analytical evidence for the use of rhizoliths as a production tool.