bluuebunny/crossref_metadata_2025_split huggingface dataset:
ModEst: Accurate estimation of genome size from next generation sequencing data
Authors: Pfenninger Markus , Schönnenbeck Philipp , Schell Tilman 
Published: December 2021

AbstractAccurate estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. Here we present a fast, easy‐to‐implement and accurate method to estimate genome size from the number of bases sequenced and the mean sequencing depth. To estimate the latter, we take advantage of the fact that an accurate estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the sequencing depth distribution representing the true underlying distribution. With simulations we show that reasonable genome size estimates can be gained even from low‐coverage (10×), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.
Standardised packs and larger health warnings: visual attention and perceptions among Colombian smokers and non‐smokers
Authors: Sillero‐Rejon Carlos , Mahmoud Osama , Tamayo Ricardo M. , Clavijo‐Alvarez Alvaro Arturo , Adams Sally , Maynard Olivia M. 
Published: December 2021

AbstractAimsTo measure how cigarette packaging (standardised packaging and branded packaging) and health warning size affect visual attention and pack preferences among Colombian smokers and non‐smokers.DesignTo explore visual attention, we used an eye‐tracking experiment where non‐smokers, weekly smokers and daily smokers were shown cigarette packs varying in warning size (30%‐pictorial on top of the text, 30%‐pictorial and text side‐by‐side, 50%, 70%) and packaging (standardised packaging, branded packaging). We used a discrete choice experiment (DCE) to examine the impact of warning size, packaging and brand name on preferences to try, taste perceptions and perceptions of harm.SettingEye‐tracking laboratory, Universidad Nacional de Colombia, Bogotá, Colombia.ParticipantsParticipants (n = 175) were 18 to 40 years old.MeasurementsFor the eye‐tracking experiment, our primary outcome measure was the number of fixations toward the health warning compared with the branding. For the DCE, outcome measures were preferences to try, taste perceptions and harm perceptions.FindingsWe observed greater visual attention to warning labels on standardised versus branded packages (F[3,167] = 22.87, P < 0.001) and when warnings were larger (F[9,161] = 147.17, P < 0.001); as warning size increased, the difference in visual attention to warnings between standardised and branded packaging decreased (F[9,161] = 4.44, P < 0.001). Non‐smokers visually attended toward the warnings more than smokers, but as warning size increased these differences decreased (F[6,334] = 2.92, P = 0.009). For the DCE, conditional trials showed that increasing the warning size from 30% to 70% reduced preferences to try (odds ratio [OR] = 0.48, 95% CI = [0.42,0.54], P < 0.001), taste perceptions (OR = 0.61, 95% CI = [0.54,0.68], P < 0.001); and increased harm perceptions (OR = 0.78, 95% CI = [0.76,0.80], P < 0.001). Compared with branded packaging, standardised packaging reduced our DCE outcome measures with ORs ranging from OR = 0.25 (95% CI = [0.17,0.38], P < 0.001) to OR = 0.79 (95% CI = [0.67,0.93], P < 0.001) across two brands. These effects were more pronounced among non‐smokers, males and younger participants. Unconditional trials showed similar results.ConclusionsStandardised cigarette packaging and larger health warnings appear to decrease positive pack perceptions and have the potential to reduce the demand for cigarette products in Colombia.
Variations in chemical defences and patterns of natural enemy attack between native and introduced populations of fireweed (Senecio madagascariensis): Implications for biological control
Authors: Egli Daniella , Harvey Kerinne J. , Moore Ben D. , Mitchell Christopher , Olckers Terence 
Published: December 2021

AbstractNative to South Africa, fireweed (Senecio madagascariensis Poiret; Asteraceae) is an annual or short‐lived perennial herb that is highly invasive in Australia, where it is a target for biological control. Preliminary research indicates that fireweed may be undergoing adaptive changes along its invasion gradient in Australia. Changes, such as a shift in plant chemical defence, may influence fireweed’s interaction with specialist insect herbivores, and hence the efficacy of a biocontrol program. As the testing of biocontrol candidates is a rigorous and lengthy process, confirmation of fireweed’s susceptibility to insect attack may assist in fast tracking candidate suitability, where changes in plant defensive chemistry are found. In a large experimental field study in fireweed’s native range, we compared the susceptibility of Australian and South African populations to insect natural enemy attack (in terms of plant biomass, insect richness and composition). Simultaneously, we assessed the variation in plant pyrrolizidine alkaloid concentrations and composition to rationalise any differences in natural enemy attack between populations. We found no significant differences in plant biomass across fireweed populations, despite significantly higher alkaloid concentrations in Australian populations. The composition of the endophagous (specialist) insect herbivore assemblage was related to alkaloid composition, but there were only minor differences in the assemblage between Australian and South African fireweed populations. Moreover, we found no significant differences in the abundance, richness or Shannon diversity indices of endophagous or ectophagous (generalist) insect herbivores between Australian and South African fireweed populations. Our results suggest that despite variations in chemical defence, Australian fireweed populations displayed neither reduced nor increased susceptibility to specialist insect herbivore attack, supporting the notion that if host‐specific biocontrol agents are released, their impact in Australia is unlikely to be influenced by any changes in plant chemical defence.
High severity fire promotes a more flammable eucalypt forest structure
Authors: Barker James W. , Price Owen F. , Jenkins Meaghan E. 
Published: December 2021

AbstractRecent landscape‐scale wildfires in eastern Australia have made apparent the need for a greater understanding of the flammability dynamics of forested ecosystems. Fire severity is a measure of the impact of a fire on vegetation, but little is known about the landscape‐scale response of the fire‐prone dry sclerophyll forests of eastern Australia to different levels of fire severity. Species in these forests have multiple responses to fire, which can be dependent on the fire severity. In this study, we aimed to determine the effect of fire severity on the vegetation structure, and therefore flammability, of these forests. We addressed two hypotheses that 1) High severity fire would result in a denser understory than low severity fire after 5 years and that 2) High severity fire would reduce the vertical separation between understory and canopy after 5 years. Field surveys of 38 forest sites with differing fire severity but standardised time since fire and forest type, in Sydney region of New South Wales, Australia, were used to test these hypotheses. We found lower canopy cover and greater understory cover (0.5–4 m height) after high severity fire compared with sites which burnt at low severity. Vertical separation was less between the canopy and understory at sites after high severity fire than after low severity fire. The greater quantity of understory fuel and greater vertical continuity in fuel structure observed suggests a potential increase in forest flammability after high severity fire compared with lower severity fires in these forest types.
Morphometrics of nuchal ligament in greyhound in different neck and body positions
Authors: Ismail Sa'ad M.Y. , Murray Christina M. , Olusa Timothy A. O. , Ismail Mustafa M. , Hailat Nabil Q. , Yen Hung‐Hsun , Aldibi'i Ro'ya S. , Fanciullo Milena L. , Davies Helen M.S. 
Published: December 2021

AbstractThis study was conducted to describe the morphometrics of nuchal ligament and investigate the effects of different neck and body positions on the nuchal ligament in greyhounds. Nine adult greyhounds cadavers without any locomotion abnormalities were dissected through the neck musculature on the left side to expose the nuchal ligament. Three pins were placed to mark regions of interest on the nuchal ligament: at one cm cranial to the site of origin (the most dorsal point of the spinous process of the first thoracic vertebra), at the midpoint of the nuchal ligament and one cm caudal to the nuchal ligament site of insertion (close to the caudal aspect of the spinous process of the axis). Each cadaver was positioned on a masonite board and placed on a table on the floor in their lateral recumbency and seven different standardized body positions; P1–P7 were mimicked using goniometers and metal wires. Photographs were taken by positioning and fixing the camera above the nuchal ligament region. The length and widths (W1, W2 and W3) of nuchal ligament were measured using Image Pro software (Image‐Pro Express version 5.0) on standardized photographs of each of seven different body and neck positions. The length of nuchal ligament in relation to the neutral position (P1) was less (− 7%, p > 0·05) in P6 (neck elevated) and increased in all other positions (+1%, p > 0·05 for P2, +19%, p < 0·05 for P3, +37%, p < 0·05 for P4, +1%, p > 0·05 for P5, +40%, p < 0·05 for P7). Nuchal ligament width at the middle (W2) decreased significantly with P4 (− 26%, p < 0·05), and P7 (− 32%, p < 0·05). Also, nuchal ligament width at the site of origin (W3) decreased significantly with P4 (− 24%, p < 0·05) and P7 (−35%, p < 0·05). These findings reflect the need for clinical and biomechanical studies to describe in‐depth the gross anatomy of the nuchal ligament in greyhounds. They suggest that different neck and body positions change the shape, and hence, the function of the nuchal ligament during movement.
Risk factors for late recurrence in patients with nonvalvular atrial fibrillation after radiofrequency catheter ablation
Authors: Peng Zhang , Wen‐Heng Liu , Qing Zhao , Pin Sun , Shang‐Lang Cai , Mao‐Jing Wang , Ya‐Qi Pan 
Published: December 2021

AbstractObjectiveTo identify the risk factors for postoperative atrial fibrillation (AF) recurrence in nonvalvular AF patients undergoing radiofrequency catheter ablation (CA).MethodsWe retrospectively reviewed the data from 426 of 450 AF patients who underwent CA. Patients were divided into two groups according to recurrence after the operation; the risk factors for AF recurrence were analyzed. A stratification system for lesions was created based on the cutoff of the risk factors; the associations among the subgroups and the AF recurrence rate were analyzed.ResultsAF recurrence occurred in 98 (23.0%) patients. Univariate analysis demonstrated that AF type, hypertrophic cardiomyopathy, left atrial diameter (LAD), left ventricular ejection fraction (LVEF), serum albumin, and D‐dimer concentrations were associated with AF recurrence. AF type (OR =2.907, p < .001), serum albumin concentration (OR =1.112, p < .05), and LAD (OR =1.115, p < .001) were independent risk factors for AF recurrence. The area under the ROC curve of LAD for the prediction of AF recurrence was 0.722 (95% CI: 0.664~0.779) and that of serum albumin for the prediction of AF recurrence was 0.608 (95% CI: 0.545~0.672). Further stratification revealed that patients with persistent or paroxysmal AF with LAD ≥43.5 mm and serum albumin concentration ≥42.2 g/L had a higher rate of AF recurrence than the reference group.ConclusionAtrial fibrillation type, LAD, and serum albumin concentration are risk factors for AF recurrence after CA in patients with nonvalvular AF. Patients with persistent AF with LAD ≥43.5 mm and serum albumin concentration ≥42.2 g/L have a higher risk of late AF recurrence after surgery.
Trends in the use of biologicals and their treatment outcomes among patients with inflammatory bowel diseases – a Danish nationwide cohort study
Authors: Zhao Mirabella , Sall Jensen Morten , Knudsen Torben , Kelsen Jens , Coskun Mehmet , Kjellberg Jakob , Burisch Johan 
Published: December 2021

SummaryBackgroundTherapeutic management of inflammatory bowel diseases (IBD) is rapidly evolving, with an expanding armoury of biological drugs at our disposal. However, real‐world findings about treatment persistence and the impact of biologicals on surgery remain inconsistent.AimsThis study aimed to investigate trends in biological use and surgery rates in a nationwide cohort of biological‐naïve IBD patients.MethodsPatients with IBD who initiated biological treatment between 2011 and 2018 were identified in the Danish National Patient Registry. Data on use of biologicals, surgeries and healthcare costs were retrieved and analysed for time trends.ResultsBetween 2011 and 2018, a total of 6,036 IBD (51% ulcerative colitis (UC), 49% Crohn's disease (CD)) patients received biological treatment for the first time. Cumulative use of biologicals increased from 5.0% to 10.8% among UC and 8.9%‐14.5% among CD patients. Infliximab remained the most‐prescribed first‐line biological for UC and CD. Treatment persistence was 44.3% and 16.9% after 1 and 3 years in UC, compared to 59.9% and 33.6% in CD patients. Overall, 32.8% of patients switched to a second biological. Surgery rates decreased in both UC (P = 0.015) and CD (P = 0.008) patients and remained significant for UC in the Cox regression model (P = 0.002). Outpatient and surgical costs also fell among both UC and CD patients.ConclusionsPersistence rates for first‐line biologicals among IBD patients were low and one‐third switched treatment. Surgery rates and direct costs decreased over time, but whether this is related to the use of biologicals has yet to be determined.
Archaeological and archaeometric investigation of the Roman marble cargos of Porto Cervo (Arzachena, Sassari, Italy) and Secche della Meloria (Livorno, Italy)
Authors: Beltrame Carlo , Antonelli Fabrizio 
Published: December 2021

AbstractMinero‐petrographic and geochemical analyses carried out on 35 samples of marble blocks belonging to shipwrecked cargos at Porto Cervo (Arzachena, Sassari, Italy) (23 samples) and Secche della Meloria (Livorno, Italy) (12 samples) indicated that the marble originated from the Apuan Alps (Italy), which implies that the ships presumably came from the Roman city of Luna. Ceramic finds enabled the dating of one shipwreck to the end of the second/beginning of the third centuries ce and the other one to the first–second centuries ce. After an archaeological discussion, authors propose that the destination of the important Porto Cervo cargo (around 222 tonnes) could have been Africa or Sicily, while a site on the way to Portus (Rome) is suggested as a possible destination for the smaller (84 tonnes) Secche della Meloria shipment.
Compositional modification of nonmetallic inclusions in bloomery iron during post‐smelting treatments and its implication
Authors: Park Jang Sik 
Published: December 2021

AbstractThe chemical composition of nonmetallic inclusions in finished iron artifacts often holds key information on the smelting and post‐smelting processes applied during their production. This possibility was tested with special iron objects deemed product intermediaries from a royal tomb constructed at Gyongju, the former capital of the Silla state during the Korean Three Kingdoms period (c. 300–668 ce). Metallographic examination identified two distinct groups of inclusions with features unique to slags derived from smelting in (a) bloomery furnaces and (b) blast furnaces. Clear evidence was also noted that type ‘a’ inclusions, when subjected to an environment of high carbon activity as in a carburization process, underwent a significant change in chemical composition and microstructure to emulate the other type. This observation is expected to remove significant ambiguities encountered in connecting slag compositions to pertinent engineering processes.
Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture
Authors: Sasazaki Shinji 
Published: December 2021

AbstractThe polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality‐related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.
Perinatal outcomes in women with sickle cell disease: a matched cohort study from London, UK
Authors: Oakley Laura L. , Mitchell Sian , von Rege Inez , Hadebe Ruth , Howard Jo , Robinson Susan E. , Oteng‐Ntim Eugene 
Published: December 2021

SummaryThere are limited data on contemporary outcomes for women with sickle cell disease (SCD) in pregnancy. We conducted a single‐site matched cohort study, comparing 131 pregnancies to women with SCD between 2007 and 2017 to a comparison group of 1310 pregnancies unaffected by SCD. Restricting our analysis to singleton pregnancies that reached 24 weeks of gestation, we used conditional Poisson regression to estimate adjusted risk ratios (aRRs) for perinatal outcomes. Infants born to mothers with SCD were more likely to be small for gestational age [aRR 1·69, 95% confidence interval (CI) 1·13–2·48], preterm (aRR 2·62, 95% CI 1·82–3·78) and require Neonatal Unit (NNU) admission (aRR 3·59, 95% CI 2·18–5·90). Pregnant women with SCD were at higher risk of pre‐eclampsia/eclampsia (aRR 3·53, 95% CI 2·00–6·24), more likely to receive induction of labour (aRR 2·50, 95% CI 1·82–1·76) and caesarean birth (aRR 1·44, 95% CI 1·18–1·76). In analysis stratified by genotype, the risk of adverse outcomes was highest in haemoglobin SS (HbSS) pregnancies (n = 80). There was no strong evidence that haemoglobin SC (HbSC) pregnancies (n = 46) were at higher risk of preterm birth, caesarean delivery, or NNU admission. Pre‐eclampsia/eclampsia was more frequently observed in HbSC pregnancies. Despite improvements in the care of pregnant women with SCD, the increased risk of adverse perinatal outcomes remains.
Can the Mind Command the Body?
Authors: Berent Iris 
Published: December 2021

AbstractPeople naturally intuit that an agent's ethereal thoughts can cause its body to move. Per intuitive physics; however, one body can only interact with another. Are people, then, covertly puzzled by the capacity of thoughts to command the body? Experiment 1 first confirms that thoughts (e.g., thinking about a cup) are indeed perceived as ethereal—as less detectible in the body (brain), and more likely to exist in the afterlife relative to matched percepts (e.g., seeing a cup). Experiments 2–5 show that thoughts are considered less likely to cause behavior than percepts (e.g., thinking of a cup vs. seeing one). Furthermore, mind–body causation is more remarkable when its bodily consequences are salient (e.g., moving an arm vs. brain activation). Finally, epistemic causes are remarkable only when they are ascribed to mental‐ (e.g., “thinking”) but not to physical states (“activation”). Together, these results suggest that mind–body interactions elicit a latent dualist dissonance.
Anthropogenic pressures coincide with Neotropical biodiversity hotspots in a flagship butterfly group
Authors: Doré Maël , Willmott Keith , Leroy Boris , Chazot Nicolas , Mallet James , Freitas André V. L. , Hall Jason P. W. , Lamas Gerardo , Dasmahapatra Kanchon K. , Fontaine Colin , Elias Marianne 
Published: December 2021

AbstractAimThe biodiversity crisis has highlighted the need to assess and map biodiversity in order to prioritize conservation efforts. Clearwing butterflies (tribe Ithomiini) have been proposed as biological indicators for habitat quality in Neotropical forests, which contain the world's richest biological communities. Here, we provide maps of different facets of Ithomiini diversity across the Neotropics to identify areas of evolutionary and ecological importance for conservation and evaluate their overlap with current anthropogenic threats.LocationNeotropics.MethodsWe ran species distribution models on a data set based on 28,986 georeferenced occurrences representing 388 ithomiine species to generate maps of geographic rarity, taxonomic, phylogenetic and Müllerian mimetic wing pattern diversity. We quantified and mapped the overlap of diversity hotspots with areas threatened by or providing refuge from current anthropogenic pressures.ResultsThe eastern slopes of the Andes formed the primary hotspot of taxonomic, phylogenetic and mimetic diversity, with secondary hotspots in Central America and the Atlantic Forest. Most diversity indices were strongly spatially correlated. Nevertheless, species‐poor communities on the Pacific slopes of the Andes also sheltered some of the geographically rarest species. Overall, tropical montane forests that host high species and mimetic diversity as well as rare species and mimicry rings appeared particularly under threat.Main conclusionsRemote parts of the Upper Amazon may act as refuges against current anthropogenic pressures for a limited portion of Ithomiini diversity. Furthermore, it is likely that the current threat status may worsen with ongoing climate change and deforestation. In this context, the tropical Andes occupy a crucial position as the primary hotspot for multiple facets of biodiversity for ithomiine butterflies, as they do for angiosperms, tetrapods and other insect taxa. Our results support the role of ithomiine butterflies as a suitable flagship indicator group for Neotropical butterfly diversity and reinforce the position of the tropical Andes as a flagship region for biodiversity conservation in general, and insect and butterfly conservation in particular.