bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints
Authors: Godden Grant T , Kinser Taliesin J , Soltis Pamela S , Soltis Douglas E 
Published: October 2019

Abstract
Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.
A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome
Authors: Varadharajan Srinidhi , Rastas Pasi , Löytynoja Ari , Matschiner Michael , Calboli Federico C F , Guo Baocheng , Nederbragt Alexander J , Jakobsen Kjetill S , Merilä Juha 
Published: October 2019

Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
The Role of Ames Dwarfism and Calorie Restriction on Gut Microbiota
Authors: Wiesenborn Denise S , Gálvez Eric J C , Spinel Lina , Victoria Berta , Allen Brittany , Schneider Augusto , Gesing Adam , Al-Regaiey Khalid A , Strowig Till , Schäfer Karl-Herbert , Masternak Michal M 
Published: October 2019

Abstract
The gut microbiome (GM) represents a large and very complex ecosystem of different microorganisms. There is an extensive interest in the potential role of the GM in different diseases including cancer, diabetes, cardiovascular diseases, and aging. The GM changes over the lifespan and is strongly associated with various age-related diseases. Ames dwarf (df/df) mice are characterized by an extended life- and healthspan, and although these mice are protected from many age-related diseases, their microbiome has not been studied. To determine the role of microbiota on longevity animal models, we investigated the changes in the GM of df/df and normal control (N) mice, by comparing parents before mating and littermate mice at three distinct time points during early life. Furthermore, we studied the effects of a 6-month calorie restriction (CR), the most powerful intervention extending the lifespan. Our data revealed significant changes of the GM composition during early life development, and we detected differences in the abundance of some bacteria between df/df and N mice, already in early life. Overall, the variability of the microbiota by genotype, time-point, and breeding pair showed significant differences. In addition, CR caused significant changes in microbiome according to gastrointestinal (GI) location (distal colon, ileum, and cecum), genotype, and diet. However, the overall impact of the genotype was more prominent than that of the CR. In conclusion, our findings suggest that the gut microbiota plays an important role during postnatal development in long-living df/df mice and CR dietary regimen can significantly modulate the GM.
Uncontrolled Diabetes as an Associated Factor with Dynapenia in Adults Aged 50 Years or Older: Sex Differences
Authors: Nebuloni Clarice Cavalero , Máximo Roberta de Oliveira , de Oliveira Cesar , Alexandre Tiago da Silva 
Published: October 2019

Abstract

Background
Epidemiological studies demonstrate an association between diabetes and low neuromuscular strength (NMS). However, none have grouped participants into nondiabetics (ND), undiagnosed diabetics (UDD), controlled diabetics (CD), and uncontrolled diabetics (UCD) or investigated what glycated hemoglobin levels (HbA1c) are associated with low NMS (dynapenia) by sex.

Methods
We analyzed the association between UDD, CD, and UCD and dynapenia, the extent to which the different groupings of these individuals modifies this association and the association between HbA1c levels and NMS, by sex, in a cross-sectional study involving 5,290 participants ≥50 years from the ELSA study. In the first two analyses, logistic regression models were used with dynapenia (grip strength &lt;26 kg in men and &lt;16 kg in women) as outcome and diabetes (ND, UDD, CD, and UCD) as exposure. Next, linear regression was performed with grip strength as the outcome, and the participants were classified based on HbA1c level as exposure. The models were adjusted by sociodemographic, behavioral, and clinical characteristics.

Results
Compared to ND, only UCD was associated with dynapenia (men OR = 2.37 95% CI 1.36–4.14; women OR = 1.67 95% CI 1.01–2.79). This association was less clear, particularly in women, when CD and UCD groups were merged. HbA1c ≥6.5% in men and ≥8.0% in women were associated with lower NMS.

Conclusions
UCD increases the chance of dynapenia in both sexes. The different groupings based on diabetes status modify the association between UCD and dynapenia. The threshold of HbA1c associated with reduced NMS is lower in men compared to women.
Turbidity alters estuarine biodiversity and species composition
Authors: Lunt Jessica , Smee Delbert L 
Published: October 2019

Abstract
Turbidity is widely regarded for modulating primary production and influencing the distribution of submerged aquatic vegetation. Although less well studied, turbidity can also have significant effects on trophic interactions and food webs by modifying light penetration and scattering, influencing foraging ability of visual-hunting predators such as fishes. By interfering with visual foragers, turbidity may shift food webs towards predators that forage with other sensory modalities (e.g. chemoreception and mechanoreception), consequently altering food web structure. We analysed turbidity effects on estuarine community composition and biodiversity in the Gulf of Mexico by analysing an 18-year fisheries-independent data set and assessing communities inhabiting contemporary oyster reefs (Crassostrea virginica). In the long-term data set, elevated turbidity was associated with decreased fish species richness and diversity and higher abundances of benthic species that rely more on chemoreception for foraging and predator avoidance (e.g. crabs). High turbidity may provide a predation refuge for crabs and other benthic organisms that visually oriented fish prey upon. On oyster reefs, crabs readily consume suspension-feeding organisms including newly settled oysters and porcelain crabs (Petrolisthes armatus). Both were significantly less abundant in high turbidity. Human practices that increase turbidity may indirectly influence trophic interactions, species distributions, ecosystem function, and biodiversity.
Trends in the prevalence of cognitive impairment in Chinese older adults: based on the Chinese Longitudinal Healthy Longevity Survey cohorts from 1998 to 2014
Authors: Kuang Weihong , Gao Mingyue , Tian Liantian , Wan Yang , Qiu Peiyuan 
Published: October 2019

Abstract
In the context of a rapidly ageing Chinese population, this study aims to examine trends in the prevalence of cognitive impairment among people ≥65 y of age in China. Our sample is 72 821 adults aged 65–105 y from the seven waves of the Chinese Longitudinal Healthy Longevity Survey, a national mixed longitudinal cohort. The Chinese version of the Mini-Mental State Examination was used to measure CI. Risk factor-adjusted prevalence trend was examined using multilevel regression models. Age-standardized prevalence of cognitive impairment increased from 11.00% in 1998 to 11.84% in 2008 and decreased to 8.88% in 2014. Older age, female gender, less education, rural residence, not married, lack of physical and cognitive activities, suffering from stroke, vision and hearing impairment, and activities of daily living disability were negatively associated with cognitive impairment. Our study suggests a decreasing trend of cognitive impairment prevalence in China. However, whether decreasing prevalence will contribute to a reduced burden of cognitive impairment given the ageing of the population is unknown.
Supplemental effects of dietary nucleotides on intestinal health and growth performance of newly weaned pigs
Authors: Jang Ki Beom , Kim Sung Woo 
Published: October 2019

Abstract
Intestinal challenges upon weaning would increase the needs of nucleotides for enterocyte proliferation, whereas de novo synthesis maybe insufficient. This study aimed to evaluate supplemental effects of dietary nucleotides on intestinal health and growth performance in newly weaned pigs. Fifty newly weaned pigs (19-d-old, 25 barrows and 25 gilts, 4.76 ± 0.42 kg BW) were individually housed and allotted to 5 treatments with increasing nucleotide supplementation (0, 50, 150, 250, and 500 mg/kg) based on a randomized complete block design with the initial BW and sex as blocks. Dietary nucleotides were provided from YT500 (Hinabiotech, Guangzhou, China). Pigs were fed for 21 d based on 2 phases (phase 1: 11 d and phase 2: 10 d) and experimental diets were formulated to meet or exceed nutrient requirements suggested by NRC (2012). Feed intake and BW were recorded. Titanium oxide (0.4%) was added as an indigestible marker from day 17. Plasma collected on day 18 was used to measure tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and malondialdehyde (MDA). Pigs were euthanized on day 21 to collect tissues to evaluate TNF-α, IL-6, MDA, morphology, and crypt cell proliferation rate in the jejunum. Ileal digesta were collected to measure ileal nutrient digestibility. Data were analyzed using contrasts in the MIXED procedure of SAS. Nucleotide supplementation increased (P &lt; 0.05) ADFI in phase 1. Nucleotide supplementation at 50 and 150 mg/kg increased (P &lt; 0.05) ADG in phase 1, whereas increased (P &lt; 0.05) ADFI and tended to increase (P = 0.082) ADG in overall. Increasing nucleotide supplementation changed (quadratic, P &lt; 0.05) villus height-crypt ratio (at 247 mg/kg) and decreased (linear, P &lt; 0.05) crypt cell proliferation rate in the jejunum. Increasing nucleotide supplementation reduced (P &lt; 0.05) jejunal IL-6 (at 50 and 150 mg/kg) and tended to change (quadratic, P = 0.074) plasma MDA (at 231 mg/kg). Nucleotide supplementation at 50 and 150 mg/kg increased (P &lt; 0.05) ileal digestibility of energy and ether extract. In conclusion, nucleotide supplementation at a range of 50 to 250 mg/kg in the diets seems to be beneficial to newly weaned pigs by enhancing growth performance possibly due to reduced intestinal inflammation and oxidative stress as well as improved intestinal villi structure and energy digestibility.
Diarrhea-Predominant Irritable Bowel Syndrome: Medical Management Update
Authors: Andrews Christopher N , Bradette Marc 
Published: October 2019

Abstract
Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, which impacts the quality of life, work productivity and social activities of patients. Diarrhea-predominant IBS (IBS-D) is one of several subtypes, and accounts for approximately one third of all cases. Currently available treatments are typically unable to alleviate the cardinal symptoms of IBS-D, including abdominal pain and diarrhea, and a clinical unmet need remains for an effective treatment which simultaneously relieves multiple symptoms. Patients may benefit from a multipronged, individualized approach, including dietary modifications, and psychological and pharmacological therapies. The aim of this review is to provide an update on the available and upcoming treatment options for IBS-D in Canada, with reference to the recently updated Canadian IBS consensus guidelines. Initial treatment approaches include lifestyle modifications, dietary modifications, and non-prescription therapies such as peppermint oil. While some medications such as tricyclic antidepressants are also used to treat IBS-D symptoms, eluxadoline and rifaximin are the only two pharmacological therapies approved for the treatment of IBS-D in Canada. Key clinical trial data for the currently available pharmacological options are presented to provide an overview of the efficacy and safety of these agents
Evaluating Soybean Aphid-Resistant Varieties in Different Environments to Estimate Financial Outcomes
Authors: Dean Ashley N , Pritchard Shelby , Tyndall John C , Hodgson Erin W , O’Neal Matthew E 
Published: October 2019

Abstract
Farmers face many choices when selecting seed for soybean (Glycine max (L.) Merr.) production, including highly desired herbicide tolerance traits. Despite the convenience of herbicide tolerance, resistant weeds and technology fees may reduce utility and profitability of these varieties, especially when commodity prices are low. Sporadic outbreaks of soybean aphid (Aphis glycines Matsumura, Hemiptera: Aphididae) that require insecticide use for optimal yield can be a further complication for farmers in Iowa. Soybean aphid-resistant varieties are commercially available, but in limited genetic backgrounds without herbicide tolerance. We hypothesized yield and value of resistance traits will vary based on the environment. We established plots at two locations with different risks of soybean aphid outbreaks and used two planting dates at each location to mimic different yield environments. In 2016 and 2017, we planted four varieties that varied in their susceptibility to soybean aphids and glyphosate, and applied insecticides if aphid populations reached an economic threshold. Regardless of genetic background, aphid-resistant varieties prevented populations from reaching the economic threshold at all environments. We observed no significant difference in yield between resistant and susceptible varieties, revealing this trait is as effective at protecting yield as an insecticide application on susceptible varieties at the high-risk location. We also explored the value of each variety in different environments. Resistant varieties produced greater potential net revenue than susceptible varieties at the high-risk location, while the opposite occurred at the low-risk location. Resistant varieties with herbicide tolerance, if made available, would be the most valuable across all environments.
Integrating Probability and Nonprobability Samples for Survey Inference
Authors: Wiśniowski Arkadiusz , Sakshaug Joseph W , Perez Ruiz Diego Andres , Blom Annelies G 
Published: October 2019

Abstract
Survey data collection costs have risen to a point where many survey researchers and polling companies are abandoning large, expensive probability-based samples in favor of less expensive nonprobability samples. The empirical literature suggests this strategy may be suboptimal for multiple reasons, among them that probability samples tend to outperform nonprobability samples on accuracy when assessed against population benchmarks. However, nonprobability samples are often preferred due to convenience and costs. Instead of forgoing probability sampling entirely, we propose a method of combining both probability and nonprobability samples in a way that exploits their strengths to overcome their weaknesses within a Bayesian inferential framework. By using simulated data, we evaluate supplementing inferences based on small probability samples with prior distributions derived from nonprobability data. We demonstrate that informative priors based on nonprobability data can lead to reductions in variances and mean squared errors for linear model coefficients. The method is also illustrated with actual probability and nonprobability survey data. A discussion of these findings, their implications for survey practice, and possible research extensions are provided in conclusion.
Bringing the city to the country: relationships between streetscape vegetation type and bird assemblages in a major regional centre
Authors: Champness Brendan S , Palmer Grant C , Fitzsimons James A 
Published: October 2019

Abstract
Urbanisation is a leading cause of biodiversity loss and habitat fragmentation internationally, and the conservation of representative native assemblages is a challenge confronting environmental managers in expanding urban landscapes. This study investigates the bird assemblages occurring in a rapidly growing regional centre, Ballarat, southeastern Australia. It aims to examine the relationships between urbanisation and bird communities in a regional city by investigating the differences in bird assemblage composition related to the type of vegetation (native or exotic) in urban streetscapes. Bird surveys were completed across four broad habitat types: remnant vegetation, exotic streetscapes, native streetscapes and newly developed streetscapes. Each habitat type had three 1 ha replicate sites. Results show that remnant vegetation fringing residential areas and native streetscapes supported around 60% more native bird species than exotic and newly developed streetscapes. Avian species composition was significantly different between broad habitat types, with remnant vegetation and native streetscapes maintaining representative native bird assemblages, but exotic streetscapes and newly developed streetscapes were dominated by introduced birds. Our results show that, for representative native bird assemblages to be maintained in urban areas, the maintenance of remnant and native vegetation is essential.
Management of Melanoma Patients by Non-Dermatologists in the Military Health System: A Retrospective Observational Study
Authors: Helmandollar Kenneth J , Lorei Nathan C , Clement Barak C , Hoverson Kara R , Logemann Nicholas F 
Published: October 2019

Abstract

Introduction
Compared to their civilian counterparts, military personnel can have more exposure to sunlight and, as recent studies have shown, do have an increased incidence of melanoma. Given the inherent challenges service members may face in getting appropriate care whether because of operational tempo, deployments, and/or austere locations, many are initially diagnosed by specialties other than dermatology. In this study, we sought to determine if patients within the military health system were receiving appropriate follow-up management after biopsies by non-dermatologists led to the diagnosis of melanoma by pathology.

Materials and Methods
Using the Co-Path system, 1,000 patients were identified who had first time biopsies positive for melanoma. Of these, 73 were originally biopsied by non-dermatologists. Retrospective medical record review was performed to determine specialties of the non-dermatologists, staging of melanoma at diagnosis, referrals to specialists and dermatologists, and adherence to National Comprehensive Cancer Network guidelines. The study protocol was approved by the Walter Reed National Military Medical Center Institutional Review Board, protocol number WRNMMC-EDO-2017-0030, in compliance with all applicable federal regulations governing the protection of human subject research.

Results
Family medicine physicians made up the majority of non-dermatologists involved in performing biopsies that led to the diagnosis of melanoma in this study. Most patients were Stage I (pT1a), and the average time from initial biopsy to further wide excision biopsy was 18 days. Sixty-seven of the 73 patients biopsied by non-dermatologists received referrals to dermatologists, and 55 of the 67 patients followed through with being seen. Follow-up full body skin exams were performed on 55 of the 73 patients, with dermatologists conducting the majority of them. National Comprehensive Cancer Network guidelines were followed in 45 of the 73 patients, with an additional 24 patients having insufficient evidence to determine if guidelines were adhered to.

Conclusion
Our study demonstrated that a number of different specialties outside of dermatology are involved in performing biopsies on patients in which melanoma is a concern. Although the results show that the majority of patients biopsied by non-dermatologists received appropriate follow-up care, there is still room to improve to ensure that all melanoma patients receive referrals to and are seen by dermatologists after a diagnosis of melanoma.