bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible phonics: a complementary ‘next generation’ approach for teaching early reading
Authors: Boldrini Greta , Fox Amy C. , Savage Robert S. 
Published: October 2022

AbstractWe describe the rationale for‐ and content of‐ a freely available, novel, theoretically driven and evidence‐based approach to improving the teaching of word reading in reception classrooms called ‘Flexible Phonics’. Flexible Phonics (FP) adds measurable value to‐, rather than wholly replacing, existing synthetic phonics programmes. The rationale underpinning the FP approach concerns the need for multi‐componential, maximally efficient, and truly generative approaches to allow early independence in reading for all children that apply to all words in the opaque spelling system of English. Building from these three principles, contemporary reading theory and evidence from cognitive science, linguistics and scaled educational implementation research, FP embodies a 5‐element intervention differentiated to children's current attainment levels. FP augments mandated synthetic phonics through use of quality real books allowing ‘Direct Mapping’ of taught grapheme‐phoneme correspondences, targeted oral vocabulary teaching, strategy‐instruction on ‘Set‐for‐Variability’ and targeted preventative intervention for the most at‐risk readers to then access wider FP content. Implications for policy and enhanced professional practice in English schools are considered.
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton
Authors: Malazarte Jacqueline , Muotka Timo , Jyväsjärvi Jussi , Lehosmaa Kaisa , Nyberg Joel , Huttunen Kaisa‐Leena 
Published: October 2022

AbstractWater‐column bacterial communities are assembled by different mechanisms at different stream network positions, with headwater communities being controlled by mass effects (advection of bacteria from terrestrial soils) while downstream communities are mainly driven by environmental sorting. Conversely, benthic biofilms are colonized largely by the same set of taxa across the entire network. However, direct comparisons of biofilm and bacterioplankton communities along whole stream networks are rare. We used 16S rRNA gene amplicon sequencing to explore the spatiotemporal variability of benthic biofilm (2 weeks old vs. mature biofilm) and water‐column communities at different network positions of a subarctic stream from early summer to late autumn. Amplicon sequence variant (ASV) richness of mature biofilm was about 2.5 times higher than that of early biofilm, yet the pattern of seasonality was the same, with the highest richness in midsummer. Biofilm bacterial richness was unrelated to network position whereas bacterioplankton diversity was negatively related to water residence time and distance from the source. This pattern of decreasing diversity along the network was strongest around midsummer and diminished greatly as water level increased towards autumn. Biofilm communities were phylogenetically clustered at all network positions while bacterioplankton assemblages were phylogenetically clustered only at the most downstream site. Both early and mature biofilm communities already differed significantly between upstream (1st order) and midstream (2nd order) sections. Network position was also related to variation in bacterioplankton communities, with upstream sites harbouring substantially more unique taxa (44% of all upstream taxa) than midstream (20%) or downstream (8%) sites. Some of the taxa that were dominant in downstream sections were already present in the upmost headwaters, and even in riparian soils, where they were very rare (relative abundance <0.01%). These patterns in species diversity and taxonomic and phylogenetic community composition of the riverine bacterial metacommunity were particularly strong for water‐column communities, whereas both early and mature biofilm exhibited weaker spatial patterns. Our study demonstrated the benefits of studying bacterioplankton and biofilm communities simultaneously to allow testing of ecological hypotheses about biodiversity patterns in freshwater bacteria.
Cryptic lineages and standing genetic variation across independent cane toad introductions
Authors: Mittan‐Moreau Cinnamon S. , Kelehear Crystal , Toledo Luís Felipe , Bacon Jamie , Guayasamin Juan M. , Snyder Andrew , Zamudio Kelly R. 
Published: October 2022

AbstractWidespread introduced species can be leveraged to investigate the genetic, ecological and adaptive processes underlying rapid evolution and range expansion, particularly the contributions of genetic diversity to adaptation. Rhinella marina, the cane toad, has been a focus of invasion biology for decades in Australia. However, their introduction history in North America is less clear. Here, we investigated the roles of introduction history and genetic diversity in establishment success of cane toads across their introduced range. We used reduced representation sequencing (ddRAD) to obtain 34,000 SNPs from 247 toads in native (French Guiana, Guyana, Ecuador, Panama, Texas) and introduced (Bermuda, southern Florida, northern Florida, Hawaiʻi, Puerto Rico) populations. Unlike all other cane toad introductions, we found that Florida populations were more closely related to native Central American lineages (R. horribilis), than to native Southern American lineages (R. marina). Furthermore, we found high levels of diversity and population structure in the native range, corroborating suggestions that R. marina is a species complex. We also found that introduced populations exhibit only slightly lower genetic diversity than native populations. Together with demographic analyses, this indicates founding populations of toads in Florida were larger than previously reported. Lastly, within R. marina, only one of 245 putatively adaptive SNPs showed fixed differences between native and introduced ranges, suggesting that putative selection in these introduced populations is based upon existing genetic variation. Our findings highlight the importance of genetic sequencing in understanding biological introductions and hint at the role of standing genetic variation in range expansion.
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest
Authors: Arjona Yurena , Arribas Paula , Salces‐Castellano Antonia , López Heriberto , Emerson Brent C. , Andújar Carmelo 
Published: October 2022

AbstractSoils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly “denoise” and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.
The bacterial virulence factor NleA undergoes host‐mediated O‐linked glycosylation
Authors: Burns Lindsay , Giannakopoulou Natalia , Zhu Lei , Xu Yong Zhong , Khan Rufaida H. , Bekal Sadjia , Schurr Erwin , Schmeing T. Martin , Gruenheid Samantha 
Published: October 2022

AbstractEnterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) are gastrointestinal pathogens responsible for severe diarrheal illness. EHEC and EPEC form “attaching and effacing” lesions during colonization and, upon adherence, inject proteins directly into host intestinal cells via the type III secretion system (T3SS). Injected bacterial proteins have a variety of functions but generally alter host cell biology to favor survival and/or replication of the pathogen. Non‐LEE‐encoded effector A (NleA) is a T3SS‐injected effector of EHEC, EPEC, and the related mouse pathogen Citrobacter rodentium. Studies in mouse models indicate that NleA has an important role in bacterial virulence. However, the mechanism by which NleA contributes to disease remains unknown. We have determined that the following translocation into host cells, a serine and threonine‐rich region of NleA is modified by host‐mediated mucin‐type O‐linked glycosylation. Surprisingly, this region was not present in several clinical EHEC isolates. When expressed in C. rodentium, a non‐modifiable variant of NleA was indistinguishable from wildtype NleA in an acute mortality model but conferred a modest increase in persistence over the course of infection in mixed infections in C57BL/6J mice. This is the first known example of a bacterial effector being modified by host‐mediated O‐linked glycosylation. Our data also suggests that this modification may confer a selective disadvantage to the bacteria during in vivo infection.
Exposure and behavioral responses of tagged beluga whales (Delphinapterus leucas) to ships in the Pacific Arctic
Authors: Martin Morgan J. , Halliday William D. , Storrie Luke , Citta John J. , Dawson Jackie , Hussey Nigel E. , Juanes Francis , Loseto Lisa L. , MacPhee Shannon A. , Moore Lisa , Nicoll Adrian , O'Corry‐Crowe Gregory , Insley Stephen J. 
Published: October 2022

AbstractArctic marine mammals face a multitude of challenges linked to climate change, including increasing anthropogenic noise from ship traffic. The beluga whale (Delphinapterus leucas), a predominately Arctic endemic cetacean, relies heavily on acoustic communication, with documented overlap between their vocalizations and hearing range and ship noise. Some belugas migrate through areas with the highest levels of ship traffic in the Pacific Arctic and exposure to ship noise is highly probable. Here, we document the responses of nine satellite‐tagged Eastern Beaufort Sea belugas to encounters with ships in the Beaufort, Chukchi, and Bering Seas during July–December 2018. We report 177 occasions when ships were within 125 km of tagged belugas and quantified changes in lateral and vertical movements to investigate individual behavioral responses to ship approaches within 50 km (n = 23). Belugas' swim speed was negatively correlated with ship distance, showing possible changes in swim speed up to 79 km away. Changes in lateral and vertical movements, indicating disruption of behavior, were observed when some ships passed within 50 km. These findings corroborate previous studies that have shown behavioral responses of belugas to ships at distances far beyond visual range, implying belugas react to low‐amplitude ship noise near ambient levels.
Five‐year surveillance study of clinical and environmental Triazole‐ResistantAspergillus fumigatus isolates in Iran
Authors: Khojasteh Shaghayegh , Abastabar Mahdi , Haghani Iman , Valadan Reza , Ghazanfari Sahar , Abbasi Kiana , Ahangarkani Fatemeh , Zarrinfar Hossein , Khodavaisy Sadegh , Badali Hamid 
Published: October 2022

AbstractBackgroundInvasive aspergillosis is one of the most common fungal infections and azole resistance in Aspergillus fumigatus (ARAf) is a growing medical concern in high‐risk patients. To our knowledge, there is no comprehensive epidemiological surveillance study on the prevalence and incidence of ARAf isolates available in Iran.ObjectivesThe study aimed to report a five‐year survey of triazole phenotypes and genotype patterns concerning the resistance in clinical and environmental A. fumigatus in Iran.MethodsDuring the study time frame (2016–2021), a total of 1208 clinical and environmental Aspergillus species were collected. Isolates were examined and characterised by in vitro antifungal susceptibility testing (CLSI M38 broth microdilution) and cyp51A sequencing.ResultsIn total, 485 Aspergillus section Fumigati strains were recovered (clinical, n = 23; 4.74% and environment, n = 462; 95.26%). Of which A. fumigatus isolates were the most prevalent species (n = 483; 99.59%). Amphotericin B and the echinocandins demonstrated good in vitro activity against the majority of isolates in comparison to triazole. Overall, 16.15% (n = 78) of isolates were phenotypically resistant to at least one of the azoles. However, 9.73% of A. fumigatus isolates for voriconazole were classified as resistant, 89.03% were susceptible, and 1.24% were intermediate. While, for itraconazole and posaconazole, using the epidemiological cut‐off value 16.15% and 6.83% of isolates were non‐wild types, respectively. Remarkably, in 21.79% (n = 17) phenotypically resistant isolates, no mutations were detected within the cyp51A gene.ConclusionAlthough the incidence of ARAf varies from country to country, in Iran the rate has ranged from 3.3% to 18%, significantly increasing from 2013 to 2021. Strikingly, a quarter of the phenotypically resistant isolates harboured no mutations in the cyp51A gene. It seems that other mechanisms of resistance are importantly increasing. To fill a gap in our understanding of the mechanism for azole resistance in the non‐cyp51A strains, we highly recommend further and more extensive monitoring of the soil with or without exposure to fungicides in agricultural and hospital areas.
AMPHORAE FROM BAETICA. NEW DATA RELEVANT TO RURAL PRODUCTION IN THE GUADALQUIVIR VALLEY (FIRST CENTURY BC–FIFTH/SIXTH CENTURIES AD)
Authors: González Tobar Iván 
Published: October 2022

SummaryOne of the most prolific areas of agrarian production of the Roman Empire was the Guadalquivir valley of Hispania Baetica. The current study was carried out in the region downstream from Corduba (Córdoba), the capital of Baetica. Knowledge of amphorae from this zone, often underrepresented at consumption sites, has in recent times undergone a complete renewal. This study thus offers an overview of the main archaeological results concerning amphora production based on fieldwork carried out between 2016 and 2020. It sheds light on a heretofore unknown early activity dating to the Augustan period followed by variable dynamics during the first three centuries of the first millennium. The findings also allow a delving deeper into the mechanisms of the sector during Late Antiquity, widening the repertoire of amphorae originating from the area.
WEIGHTS, CURRENCY BARS AND METROLOGY AT DANEBURY HILLFORT. FROM WEIGHING TO VALUE ASSESSMENT?
Authors: Poigt Thibaud 
Published: October 2022

SummaryThis paper studies the metrological characteristics of a series of balance weights recovered at Danebury hillfort (Stockbridge, Hampshire). It is based on the use of 3D‐digitalization to virtually reconstruct broken weights and statistical analysis to approach their metrology. The results of this investigation suggests the use of two weighing units during the Late Iron Age at Danebury, one of 309 g and another of 257.7 g. The comparison of the weighing metrology inferred with currency bars found on the settlement and elsewhere suggests that a complex practice of weighing and counting linked the use of weights and iron bars.
Voltage mapping and pulmonary vein isolation in master athletes with atrial fibrillation
Authors: Liu Brian , Pagan Eric , Beccarino Nicholas , Chang David , Dulmovits Eric , Beldner Stuart 
Published: October 2022

AbstractBackgroundMaster athletes encompass a wide range of exercise enthusiasts. At the extreme, there is an increased risk of atrial fibrillation (AF). Therapies aimed at rate or rhythm control are often limited given unfavorable side effects. Although studies suggest an increase in left atrial (LA) fibrosis in this population, minimal electrophysiologic data exist regarding the LA voltage mapping and the efficacy of AF ablation with pulmonary vein isolation (PVI).MethodsIn a retrospective single‐center study, we reviewed AF ablations (pulmonary vein isolation and assessment/ablation of non‐pulmonary vein triggers) performed in extreme master athletes with AF. We define “extreme” as those who have repeatedly competed in long distance endurance events for a > 10‐year period. Bipolar voltage mappings obtained through PENTARAY Catheter (Biosense Webster) were reviewed using CARTO. LA scarring was defined as an area of less than 0.1 mV. All patients were monitored as outpatients for AF recurrence.ResultsBetween January 2018 and February 2022, 16 patients (11 marathon runners, four long distance cyclers, and one marathon swimmer) underwent AF ablations. All patients in the cohort were male with an average CHA2DS2‐VASc score of 1.2 ± 0.8 and left atrial volume of 34.4 cc/m2 ± 9.9. A total of eight patients (50%) had persistent AF. One patient (6.3%) had LA scar on bipolar voltage mapping, whom also had a non‐pulmonary vein trigger of AF. Bidirectional blocks of the four pulmonary veins were achieved by radiofrequency (RF) ablation in all patients. Freedom from documented recurrence of AF up to 24 months was 93.8%. One patient (6.3%) had recurrence of AF at 14 months and underwent successful cardioversion.ConclusionIn our series of extreme master athletes with AF, the incidence of LA scarring on bipolar voltage mapping was low and the recurrence of AF following PVI by RF ablation was minimal.
The role of short‐term grass pollen exposure in food skin‐prick test reactivity, food allergy, and eczema flares in children
Authors: Idrose Nur Sabrina , Lodge Caroline J. , Peters Rachel L. , Douglass Jo A. , Koplin Jennifer J. , Lowe Adrian J. , Perrett Kirsten P. , Tang Mimi L. K. , Newbigin Ed J. , Abramson Michael J. , Erbas Bircan , Vicendese Don , Dharmage Shyamali C. 
Published: October 2022

AbstractBackgroundWhile the relationship between pollen and respiratory allergies is well‐documented, the role of short‐term pollen exposure in food allergy and eczema flares has not previously been explored. We aimed to investigate these associations in a population‐based sample of children.MethodsWe investigated 1‐ (n = 1108) and 6‐year‐old (n = 675) children in the grass pollen season from the HealthNuts cohort. Grass pollen concentrations were considered on the day of testing (lag 0), up to three days before (lag 1‐lag 3) and cumulatively (lag 0–3). Associations between grass pollen and food skin‐prick test reactivity (SPT ≥ 2 mm at age 1 year and ≥ 3 mm at age 6 years), eczema flares, challenge‐confirmed food allergy, reaction threshold to oral food challenges (OFC), and serum food‐specific IgE levels were analyzed using either logistic or quantile regression models. Atopy and family history of allergic disease were considered as potent effect modifiers.ResultsGrass pollen at lag 0–3 (every 20 grains/m3 increase) was associated with an up to 1.2‐fold increased odds of food SPT reactivity and eczema flares in 6‐year‐olds. In 1‐year‐olds, the associations were only observed for peanut in those with a family history of food allergy. Increasing grass pollen concentrations were associated with a lower reaction threshold to OFC and higher serum IgE levels in peanut‐allergic 1‐year‐olds only.ConclusionIncreasing grass pollen concentration was associated with increased risk of food SPT reactivity and eczema flares in children. The associations in peanut‐allergic infants may be related to immune activation and/or peanut and grass pollen cross‐reactivity leading to a lower reaction threshold.
Small for gestational age is associated with reduced lung function in middle age: A prospective study from first to fifth decade of life
Authors: Tandra Melvin , Walters E. Haydn , Perret Jennifer , Lowe Adrian J. , Lodge Caroline J. , Johns David P. , Thomas Paul S. , Bowatte Gayan , Davis Peter G. , Abramson Michael J. , Dharmage Shyamali C. , Bui Dinh S. 
Published: October 2022

AbstractBackground and ObjectiveThe association between birth weight, particularly relative to gestational age, and adult lung function is uncertain. We investigated the associations between birth weight relative to gestational age and measures of lung function in middle age, and mediation of these associations by adult height.MethodsParticipants in the Tasmanian Longitudinal Health Study who had both known birth weight and lung function assessment at age 45 years were included (n = 849). Linear regression models were fitted to investigate the association between small for gestational age and birth weight with post‐bronchodilator lung function measures (forced expiratory volume in 1 second [FEV1], forced vital capacity [FVC], FEV1/FVC, diffusing capacity for carbon monoxide [DLco], residual volume [RV] and total lung capacity [TLC]), adjusting for potential confounders. The contribution of adult height as a mediator of these associations was investigated.ResultsCompared with infants born with normal weight for gestational age, those born small for gestational age had reduced FEV1 (coefficient: −191 ml [95%CI: −296, −87]), FVC (−205 ml [−330, −81]), TLC (−292 ml [−492, −92]), RV (−126 ml [−253, 0]) and DLco (−0.42 mmol/min/kPa [−0.79, −0.041]) at age 45 years. However, they had comparable FEV1/FVC. For every 1 kg increase in birth weight, lung function indices increased by an average of 117 ml (95%CI: 40, 196) for FEV1, 124 ml (30, 218) for FVC, 215 ml (66, 365) for TLC and 0.36 mmol/min/kPa (0.11, 0.62) for DLco, independent of gestational age, but again not for FEV1/FVC. These associations were significantly mediated by adult height (56%–90%).ConclusionSmall for gestational age was associated with reduced lung function that is likely due to smaller lungs with little evidence of any specific parenchymal impairment.
Functioning strategies of the research groups' leaders in the context of funding and policy instabilities☆
Authors: Jaime Astrid , Pérez‐Martelo Constanza , Herrera Bernardo , Ordóñez‐Matamoros Gonzalo , Vinck Dominique 
Published: October 2022

AbstractWe explore the strategies implemented by Research Groups' Leaders while coping with unstable contexts, characterized by incoherence and lack of coordination among different policy discourses and instruments, and scarce resources. We focus on a country where these conditions are present: Colombia. In doing so, we study two cases, one in nanotechnology and another one in biomedical engineering. Interviews, focus groups and workshops allowed us to identify and validate strategies grouped in four popular sayings, proper to local idiosyncrasy, highlighting the role of home institutions and principal investigators in facing such situations with resilience and resourcefulness, and even taking advantage of them. We find that Research Groups' Leaders use strategies such as: adapting, balancing agendas and funding sources, networking, and taking advantage of the support programs available at their home institution to continue functioning. These are setting the ground for a further survey which could pretend some generalization. However, policymakers could consider these findings when defining policy instruments or for assessing their effectiveness or impacts.