bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference
Authors: Beaulieu Jeremy M , O’Meara Brian C , Gilchrist Michael A 
Published: December 2020

Abstract
Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright–Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position-dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical data set of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE-specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.
Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence
Authors: Murray Gemma G R , Charlesworth Jane , Miller Eric L , Casey Michael J , Lloyd Catrin T , Gottschalk Marcelo , Tucker Alexander W (Dan) , Welch John J , Weinert Lucy A 
Published: December 2020

Abstract
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations
Authors: Lee HoJoon , Shuaibi Ahmed , Bell John M , Pavlichin Dmitri S , Ji Hanlee P 
Published: December 2020

Abstract
Cancer genome sequencing has led to important discoveries such as the identification of cancer genes. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software package, KmerVC, to validate the given somatic mutations from sequencing data. Our program validates the occurrence of a mutation based on statistically significant difference in frequency of k-mers with and without a mutation from matched normal and tumor sequences. Third, we tested our method on both simulated and cancer genome sequencing data. Counting k-mer involving mutations effectively validated true positive mutations including insertions and deletions across different individual samples in a reproducible manner. Thus, we demonstrated a straightforward approach for rapidly validating mutations from cancer genome sequencing data.
Quality of Literature Searches Published in Leading Neurosurgical Journals: A Review of Reviews
Authors: O’Donohoe Tom J , Bridson Tahnee L , Shafik Christopher G , Wynne David , Dhillon Rana S , Tee Jin W 
Published: December 2020

AbstractBACKGROUNDThere is mounting evidence that the search strategies upon which systematic reviews (SRs) are based frequently contain errors are incompletely reported or insensitive.OBJECTIVETo appraise the quality of search strategies in the 10 leading specialty neurosurgical journals and identify factors associated with superior searches.METHODSThis research-on-research study systematically surveyed SRs published in the 10 leading neurosurgical journals between 01/10/2017 and 31/10/2019. All SRs were eligible for assessment using a predefined coding manual that was adapted from the preferred reporting items for systematic reviews and meta-analyses (PRISMA), a measurement tool to assess systematic reviews (AMSTAR), and Cochrane Collaboration guidelines. The PubMed interface was used to search the MEDLINE database, which was supplemented by individual journal searches. Descriptive statistics were utilized to identify factors associated with improved search strategies.RESULTSA total of 633 articles were included and contained a median of 19.00 (2.00-1654.00) studies. Less than half (45.97%) of included search strategies were considered to be reproducible. Aggregated reporting score was positively associated with in-text reference to reporting guideline adherence (τb = 0.156,P < .01). The number of articles retrieved by a search (τb = 0.11,P < .01) was also associated with the reporting of a reproducible search strategy.CONCLUSIONThis study demonstrates that the search strategies used in neurosurgical SRs require improvement. In addition to increasing awareness of reporting standards, we propose that this be achieved by the incorporation of PRISMA and other guidelines into article submission and peer-review processes. This may lead to the conduct of more informative SRs, which may result in improved clinician decision-making and patient outcomes.
Spatial decoupling of light absorption and reaction sites in n-Si photocathodes for solar water splitting
Authors: Wang Shujie , Wang Tuo , Liu Bin , Li Huimin , Feng Shijia , Gong Jinlong 
Published: December 2020

Abstract
Metal-insulator-semiconductor (MIS) photocathodes offer a simple alternative to p-n junction photocathodes in photoelectrochemical water splitting. However, the parasitic light absorption of catalysts and metal layers in the MIS junction, as well as the lack of low work function metals to form a large band offset with p-Si, severely limit their performance. This paper describes an MIS photocathode fabricated from n-Si, rather than the commonly used p-Si, to spatially decouple light absorption from reaction sites, which enables the majority carriers, instead of the commonly used minority carriers, to drive the surface reaction, making it possible to place the reaction sites far away from the light absorption region. Thus, the catalysts could be moved to the backside of the MIS junction to avoid light shielding. Moreover, the adoption of n-Si unlocks a variety of high work function materials for photovoltage generation. The obtained n-Si MIS photocathode exhibits an applied bias photon-to-current efficiency of 10.26% with a stability up to 300 h.
Affordability of nutritious foods for complementary feeding in South Asia
Authors: Ryckman Theresa , Beal Ty , Nordhagen Stella , Murira Zivai , Torlesse Harriet 
Published: December 2020

AbstractThe high prevalence of stunting and micronutrient deficiencies among children in South Asia has lifelong health, educational, and economic consequences. For children aged 6–23 months, undernutrition is influenced by inadequate intake of complementary foods containing nutrients critical for growth and development. The affordability of nutrients lacking in young children’s diets in Bangladesh, India, and Pakistan was assessed in this study. Using data from nutrient gap assessments and household surveys, household food expenditures were compared with the cost of purchasing foods that could fill nutrient gaps. In all 3 countries, there are multiple affordable sources of vitamin A (orange-fleshed vegetables, dark leafy greens, liver), vitamin B12 (liver, fish, milk), and folate (dark leafy greens, liver, legumes, okra); few affordable sources of iron and calcium (dark leafy greens); and no affordable sources of zinc. Affordability of animal-source protein varies, with several options in Pakistan (fish, chicken, eggs, beef) and India (fish, eggs, milk) but few in Bangladesh (eggs). Approaches to reduce prices, enhance household production, or increase incomes are needed to improve affordability.
Observations of the [C i] (3P1–3P0) emission toward the massive star-forming region RCW 38: Further evidence for highly-clumped density distribution of the molecular gas
Authors: Izumi Natsuko , Fukui Yasuo , Tachihara Kengo , Fujita Shinji , Torii Kazufumi , Kamazaki Takeshi , Kaneko Hiroyuki , Silva Andrea , Iono Daisuke , Momose Munetake , Sugimoto Kanako , Nakazato Takeshi , Kosugi George , Maekawa Jun , Takahashi Shigeru , Yoshino Akira , Asayama Shin’ichiro 
Published: December 2020

Abstract
We present observations of the 3P1–3P0 fine-structure line of atomic carbon using the ASTE 10m sub-mm telescope towards RCW 38, the youngest super star cluster in the Milky Way. The detected [C i] emission is compared with the CO J = 1–0 image cube presented in Fukui et al. (2016, ApJ, 820, 26) which has an angular resolution of 40″ (∼0.33 pc). The overall distribution of the [C i] emission in this cluster is similar to that of the 13CO emission. The optical depth of the [C i] emission was found to be τ = 0.1–0.6, suggesting mostly optically thin emission. An empirical conversion factor from the [C i] integrated intensity to the H2 column density was estimated as X[C i]$= 6.3 \times 10 ^{20}\:$cm−2 K−1 km−1 s (for visual extinction: AV ≤ 10 mag) and 1.4 × 1021 cm−2 K−1 km−1 s (for AV of 10–100 mag). The column density ratio of the [C i] to CO (N[C i]$/N_{\rm CO}$) was derived as ∼0.1 for AV of 10–100 mag, which is consistent with that of the Orion cloud presented in Ikeda et al. (2002, ApJ, 571, 560). However, our results cover an AV regime of up to 100 mag, which is wider than the coverage found in Orion, which reaches up to ∼60 mag. Such a high [C i]$/$CO ratio in a high-AV region is difficult to explain via the plane-parallel photodissociation region model, which predicts that this ratio is close to 0 due to the heavy shielding of the ultraviolet (UV) radiation. Our results suggest that the molecular gas in this cluster is highly clumpy, allowing deep penetration of UV radiation even at averaged AV values of 100 mag. Recent theoretical works have presented models consistent with such clumped gas distribution with a sub-pc clump size (e.g., Tachihara et al. 2018, arXiv:1811.02224).
A Healing Journey with Chronic Pain: A Meta-Ethnography Synthesizing 195 Qualitative Studies
Authors: Toye Francine , Belton Joletta , Hannink Erin , Seers Kate , Barker Karen 
Published: December 2020

Abstract

Objective
There is a large body of research exploring what it means for a person to live with chronic pain. However, existing research does not help us understand what it means to recover. We aimed to identify qualitative research that explored the experience of living with chronic pain published since 2012 and to understand the process of recovery.

Design
A synthesis of qualitative research using meta-ethnography.

Methods
We used the seven stages of meta-ethnography. We systematically searched for qualitative research, published since 2012, that explored adults’ experiences of living with, and being treated for, chronic pain. We used constant comparison to distill the essence of ideas into themes and developed a conceptual model.

Results
We screened 1,328 titles and included 195 studies. Our conceptual model indicates that validation and reconnection can empower a person with chronic pain to embark on a journey of healing. To embark on this journey requires commitment, energy, and support.

Conclusions
The innovation of our study is to conceptualize healing as an ongoing and iterating journey rather than a destination. Health interventions for chronic pain would usefully focus on validating pain through meaningful and acceptable explanations; validating patients by listening to and valuing their stories; encouraging patients to connect with a meaningful sense of self, to be kind to themselves, and to explore new possibilities for the future; and facilitating safe reconnection with the social world. This could make a real difference to people living with chronic pain who are on their own healing journeys.
Sensitivity to change and clinical correlations of the novel DACtylitis glObal Sonographic (DACTOS) score in psoriatic arthritis
Authors: Girolimetto Nicolò , Zabotti Alen , Tinazzi Ilaria , Possemato Niccolò , Costa Luisa , Batticciotto Alberto , Canzoni Marco , Citriniti Giorgia , Lucia Orazio De , Figus Fabiana , Idolazzi Luca , McConnel Rebecca , Peluso Rosario , Sakellariou Garifallia , Tullio Annarita , Salvarani Carlo , Scarpa Raffaele , Iagnocco Annamaria , Caso Francesco , Macchioni Pierluigi 
Published: December 2020

Abstract

Objective
The aim of the study is to assess the performance of the DACTOS (DACtylitis glObal Sonographic) score in a PsA dactylitis clinical setting. In particular, we evaluated the ability of DACTOS to identify the affected fingers, its sensitivity to change after treatment, the correlations between DACTOS and clinical parameters, and the capacity of the score to identify the treatment responders.

Methods
Forty-six consecutive patients with symptomatic PsA hand dactylitis were enrolled. A total of seventy-three dactylitic digits were evaluated clinically and sonographically before and after treatment in this observational and prospective study. Clinical assessment included the Leeds Dactylitis Index-basic (LDI-b) score and visual analogue scales for pain (VAS-p) and functional impairment (VAS-FI). Sonographic lesions were investigated using high-frequency ultrasound with grey scale and power Doppler features according to the DACTOS score. Correlations between the DACTOS score and the clinical parameters were assessed at baseline, 1 month (T1) and 3 months (T3).

Results
We observed significant improvements in all of the assessed clinical parameters and the DACTOS scores after dactylitis treatment. There was a statistically significant correlation between the variation of all clinical parameters (VAS-p, VAS-FI and LDI-b) and the DACTOS score at T1 and T3 evaluations. We found statistically significant differences in the DACTOS score between clinical responder and non-responder groups (P &lt; 0.001) and between clinical remission and non-remission groups (P &lt; 0.001).

Conclusion
The DACTOS score performs well in real-life clinical settings in terms of sensitivity to change and correlations with clinical features in PsA dactylitis.
APPLICATIONS OF OPTICALLY STIMULATED LUMINESCENCE IN MEDICAL DOSIMETRY
Authors: Yukihara Eduardo G , Kron Tomas 
Published: December 2020

AbstractIf the first decade of the new millennium saw the establishment of a more solid foundation for the use of the Optically Stimulated Luminescence (OSL) in medical dosimetry, the second decade saw the technique take root and become more widely used in clinical studies. Recent publications report not only characterization and feasibility studies of the OSL technique for various applications in radiotherapy and radiology, but also the practical use of OSL for postal audits, estimation of staff dose, in vivo dosimetry, dose verification and dose mapping studies. This review complements previous review papers and reports on the topic, providing a panorama of the new advances and applications in the last decade. Attention is also dedicated to potential future applications, such as LET dosimetry, 2D/3D dosimetry using OSL, dosimetry in magnetic resonance imaging-guided radiotherapy (MRIgRT) and dosimetry of extremely high dose rates (FLASH therapy).
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees
Authors: Bossert Silas , Murray Elizabeth A , Pauly Alain , Chernyshov Kyrylo , Brady Seán G , Danforth Bryan N 
Published: December 2020

AbstractSummarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree, and RAxML. We study their performance in the phylogenomic framework of $&gt;$800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus Pseudapis, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (ModelFinder program). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for Pseudapis s. l. and map the distribution of distinct morphological features of the group. [ASTRAL; Bees; concordance; gene tree estimation error; IQ-Tree; MrBayes, Nomiinae; PhyloBayes; RAxML; phylogenomics; stemminess]
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
Authors: Lopes Fernando , Oliveira Larissa R , Kessler Amanda , Beux Yago , Crespo Enrique , Cárdenas-Alayza Susana , Majluf Patricia , Sepúlveda Maritza , Brownell Robert L , Franco-Trecu Valentina , Páez-Rosas Diego , Chaves Jaime , Loch Carolina , Robertson Bruce C , Acevedo-Whitehouse Karina , Elorriaga-Verplancken Fernando R , Kirkman Stephen P , Peart Claire R , Wolf Jochen B W , Bonatto Sandro L 
Published: December 2020

AbstractThe phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.]