bluuebunny/crossref_metadata_2025 huggingface dataset:
Are breast biopsy markers underused?
Authors: Frost Rosanna , Vlaskovsky Philip Stephen , Taylor Donna Blanche
Published: October 2020

Introduction

To evaluate current use of breast biopsy markers (BBM) amongst Australian and New Zealand radiologists.

Methods

Radiologists attending a national breast conference were invited to complete an online survey addressing demographics, BBM use following ultrasound, stereotactic, tomosynthesis and MRI‐guided biopsy, frequency of early BBM displacement, preoperative lesion localisation (PLL) and axillary BBM use.

Results

Overall response rate was 52% (60/115). The majority (n = 45) 75% practiced in Australia. 98% had BBMs available in their practice, 40% reported BBM costs weren’t covered by insurance. 27% would use BBMs more often if they were, with some utilising smaller gauge devices for lesion sampling to minimise need for BBM use and patient out‐of‐pocket costs. Ultrasound‐guided procedures were associated with lower rates of clinically significant BBM displacement (P = 0.001). Considering PLL, 44% were able to perform US‐guided PLL in <25% of cases. Poor sonographic visibility was the commonest reason why this wasn’t possible. In the axilla, BBMs were mainly used to mark positive nodes in pre‐neoadjuvant chemotherapy patients.

Conclusion

This survey is the first to provide data on BBM use amongst a sample of predominantly Australian and New Zealand radiologists, and provides compelling evidence of significantly lower incidence of BBM displacement with US‐guided procedures. Our results suggest some radiologists may hesitate to use BBMs due to cost, and this can influence their choice of biopsy technique. Provision of a Medicare item Number for BBMs may lead to increased adoption of best practice guidelines for preoperative diagnosis of breast lesions.
A decade of de novo transcriptome assembly: Are we there yet?
Authors: Hölzer Martin
Published: October 2020

A decade ago, de novo transcriptome assembly evolved as a versatile and powerful approach to make evolutionary assumptions, analyse gene expression, and annotate novel transcripts, in particular, for non‐model organisms lacking an appropriate reference genome. Various tools have been developed to generate a transcriptome assembly, and even more computational methods depend on the results of these tools for further downstream analyses. In this issue of Molecular Ecology Resources, Freedman et al. (Mol Ecol Resourc 2020) present a comprehensive analysis of errors in de novo transcriptome assemblies across public data sets and different assembly methods. They focus on two implicit assumptions that are often violated: First, the assembly presents an unbiased view of the transcriptome. Second, the expression estimates derived from the assembly are reasonable, albeit noisy, approximations of the relative frequency of expressed transcripts. They show that appropriate filtering can reduce this bias but can also lead to the loss of a reasonable number of highly expressed transcripts. Thus, to partly alleviate the noise in expression estimates, they propose a new normalization method called length‐rescaled CPM. Remarkably, the authors found considerable distortions at the nucleotide level, which leads to an underestimation of diversity in transcriptome assemblies. The study by Freedman et al. (Mol Ecol Resourc 2020) clearly shows that we have not yet reached “high‐quality” in the field of transcriptome assembly. Above all, it helps researchers be aware of these problems and filter and interpret their transcriptome assembly data appropriately and with caution.
MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size
Authors: Andrello Marco , Noirot Christelle , Débarre Florence , Manel Stéphanie
Published: October 2020

Multilocus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multilocus genetic processes in arbitrarily complex scenarios. However, the use of forward‐in‐time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, MetaPopGen 2.0, to model multilocus population genetic processes in subdivided populations of arbitrarily large size. It allows for spatial and temporal variation in demographic parameters, age structure, adult and propagule dispersal, variable mutation rates and selection on survival and fecundity. We developed MetaPopGen 2.0 in the R environment to facilitate its use by non‐modeler ecologists and evolutionary biologists. We illustrate the capabilities of MetaPopGen 2.0 for studying adaptation to water salinity in the striped red mullet Mullus surmuletus.
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging
Authors: Lehallier Benoit , Shokhirev Maxim N. , Wyss‐Coray Tony , Johnson Adiv A.
Published: October 2020

We previously identified 529 proteins that had been reported by multiple different studies to change their expression level with age in human plasma. In the present study, we measured the q‐value and age coefficient of these proteins in a plasma proteomic dataset derived from 4263 individuals. A bioinformatics enrichment analysis of proteins that significantly trend toward increased expression with age strongly implicated diverse inflammatory processes. A literature search revealed that at least 64 of these 529 proteins are capable of regulating life span in an animal model. Nine of these proteins (AKT2, GDF11, GDF15, GHR, NAMPT, PAPPA, PLAU, PTEN, and SHC1) significantly extend life span when manipulated in mice or fish. By performing machine‐learning modeling in a plasma proteomic dataset derived from 3301 individuals, we discover an ultra‐predictive aging clock comprised of 491 protein entries. The Pearson correlation for this clock was 0.98 in the learning set and 0.96 in the test set while the median absolute error was 1.84 years in the learning set and 2.44 years in the test set. Using this clock, we demonstrate that aerobic‐exercised trained individuals have a younger predicted age than physically sedentary subjects. By testing clocks associated with 1565 different Reactome pathways, we also show that proteins associated with signal transduction or the immune system are especially capable of predicting human age. We additionally generate a multitude of age predictors that reflect different aspects of aging. For example, a clock comprised of proteins that regulate life span in animal models accurately predicts age.
Critically Endangered marsupial calls residential gardens home
Authors: Van Helden Bronte E. , Close Paul G. , Stewart Barbara A. , Speldewinde Peter C. , Comer Sarah J.
Published: October 2020

Urbanization is one of the biggest global threats to biodiversity. However, urban areas can offer opportunities for biodiversity conservation because of the assortment of resources and numerous taxa that occur in these habitats. While the use of gardens by animals is well documented, the ability of native fauna to exclusively use (i.e. reside in) them is largely uninvestigated and therefore constrains our current understanding of their conservation ‘value’. We aimed to determine whether individuals of a threatened species can exclusively reside in gardens for several months of their life, and the frequency that novel resources (i.e. non‐natural) are used compared to natural ones. We predicted that individuals captured in gardens would use both bushland and residential habitat, and use natural resources more frequently than novel resources because of the assumption that remnant habitat is more suitable than modified gardens. Using the Critically Endangered western ringtail possum (Pseudocheirus occidentalis) as a case study, we captured 20 individuals in gardens and radio‐tracked them for a period of 95 ± 3.3 days to determine their habitat use. Contrary to our predictions, for the duration of our study individuals exclusively resided within gardens, irrespective of proximity to bushland, and used novel resources more frequently than natural resources for all behaviours. We also found that over half (53%) of all the captured female possums had pouch young, and at the conclusion of the study, male possums were on average 43 g heavier. Our results exemplify that gardens can be of sufficient quality to support individuals, and that these modified habitats should be incorporated into conservation policy in urban landscapes. Given the extensive number of threatened species located within cities globally, our finding that a threatened species can reside exclusively within gardens further highlights the conservation opportunity that residential landscapes and cities offer wildlife.
Endodontic management of mandibular second molar fused to odontome with 12‐month follow‐up using cone beam computed tomography: A case report
Authors: Nangia Divya , Dinkar Sumit , Nawal Ruchika Roongta , Talwar Sangeeta
Published: October 2020

Fusion is a developmental anomaly characterised by the union of two adjacent teeth or tooth‐like substance. Odontomes are malformation of the dental tissue which arise during normal tooth development. They are usually asymptomatic but often associated with tooth eruption disturbance. In this paper, we report a rare case of fusion involving permanent mandibular second molar with an odontome, which led to a partial eruption of the molar as well as its devitalisation. Successful endodontic management was carried out in this case with a supplementary disinfection procedure using XP Endo finisher (FKG Dentaire, La Chaux‐de‐Fonds, Switzerland). The use of high‐end diagnostic imaging modalities such as cone beam computed tomography (CBCT) helped in making a confirmatory diagnosis; determining the treatment plan before undertaking the actual treatment; for better understanding of the fused tooth's complicated root morphology; and for its effective management and to follow up this unusual case for 12 months.
An international multidisciplinary consensus statement on the prevention of opioid‐related harm in adult surgical patients
Authors: Levy N. , Quinlan J. , El‐Boghdadly K. , Fawcett W. J. , Agarwal V. , Bastable R. B. , Cox F. J. , de Boer H. D. , Dowdy S. C. , Hattingh K. , Knaggs R. D. , Mariano E. R. , Pelosi P. , Scott M. J. , Lobo D. N. , Macintyre P. E.
Published: October 2020

This international multidisciplinary consensus statement was developed to provide balanced guidance on the safe peri‐operative use of opioids in adults. An international panel of healthcare professionals evaluated the literature relating to postoperative opioid‐related harm, including persistent postoperative opioid use; opioid‐induced ventilatory impairment; non‐medical opioid use; opioid diversion and dependence; and driving under the influence of prescription opioids. Recommended strategies to reduce harm include pre‐operative assessment of the risk of persistent postoperative opioid use; use of an assessment of patient function rather than unidimensional pain scores alone to guide adequacy of analgesia; avoidance of long‐acting (modified‐release and transdermal patches) opioid formulations and combination analgesics; limiting the number of tablets prescribed at discharge; providing deprescribing advice; avoidance of automatic prescription refills; safe disposal of unused medicines; reducing the risk of opioid diversion; and better education of healthcare professionals, patients and carers. This consensus statement provides a framework for better prescribing practices that could help reduce the risk of postoperative opioid‐related harm in adults.
Letter: population mortality from COVID‐19 and latitude—data from China
Authors: Liu Nanyang , Li Hao
Published: October 2020

LINKED CONTENT

This article is linked to Rhodes et al papers. To view these articles, visit https://doi.org/10.1111/apt.15777 and https://doi.org/10.1111/apt.16058
High‐resolution stratigraphy of Quaternary fluvial deposits in the Makó Trough and the Danube‐Tisza Interfluve, Hungary, based on magnetic susceptibility data
Authors: Püspöki Zoltán , Fogarassy‐Pummer Tímea , Thamó‐Bozsó Edit , Falus György , Cserkész‐Nagy Ágnes , Szappanos Bálint , Márton Emő , Lantos Zoltán , Szabó Szilárd , Stercel Ferenc , Tóth‐Makk Ágnes , Mcintosh Richard W. , Szőcs Teodóra , Pálóczy Péter , Fancsik Tamás
Published: October 2020

High‐resolution stratigraphical architecture of a Quaternary fluvial succession in the Makó Trough and the Danube‐Tisza Interfluve (Pannonian Basin, Hungary) was investigated based on low field magnetic susceptibility (MS) measurements of seven fully cored boreholes, interpreted on the basis of the early postglacial magnetic susceptibility episodes previously described in the Körös and Jászság Basins. To confirm the reliability of the Dévaványa and Vésztő MS records (Körös Basin), the published magnetostratigraphical data were re‐investigated revealing the consequent arrangement of the MS peaks correlated with the Jingbian section and the short‐lived polarity reversals correlated with the Geomagnetic Instability Time Scale. The Quaternary climatic regime in the Körös Basin begins in the late Pliocene at 2.7 Ma. The correlation between the Körös Basin (Dévaványa) and Makó Trough (Mindszent) was confirmed by the multi‐proxy spectral investigation of the Mindszent section, revealing ~100‐ and ~41‐ka cycles in the MS, colour, logged spontaneous potential and resistivity records. Based on MS records of the seven boreholes, the base of the Quaternary can be identified irrespective of the facies, age and climatic phase of the lowermost Quaternary strata. By performing MS and log correlation of 131 boreholes, extended unconformities were detected in the Quaternary profiles in the Danube‐Tisza Interfluve (~1070±10, ~1920±10 and ~2300±10 ka) interpreted as sequence boundaries. Sedimentological and mineralogical data reveal a significant change at ~725–606 ka likely as a response to the ‘mid‐Pleistocene transition’, leading to the multiple branching of the Danube. SEM data revealed that ilmenite is also responsible for the development of the early postglacial magnetic susceptibility episodes. This increases the stratigraphical potential of fluvial successions with catchment area that contain metamorphic rocks. A gradual retreat of permafrost zone determines long‐term temporal trends of the climatically controlled fluvial magnetic susceptibility episodes, causing upward decreasing trends in the time series.
Convergence and divergence in lizard colour polymorphisms
Authors: Stuart‐Fox Devi , Aulsebrook Anne , Rankin Katrina J. , Dong Caroline M. , McLean Claire A.
Published: October 2020

Colour polymorphic species are model systems for examining the evolutionary processes that generate and maintain discrete phenotypic variation in natural populations. Lizards have repeatedly evolved strikingly similar polymorphic sexual signals in distantly related lineages, providing an opportunity to examine convergence and divergence in colour polymorphism, correlated traits and associated evolutionary processes. Herein, we synthesise the extensive literature on lizard colour polymorphisms in both sexes, including recent advances in understanding of the underlying biochemical, cellular and genetic mechanisms, and correlated behavioural, physiological and life‐history traits. Male throat, head or ventral colour morphs generally consist of red/orange, yellow and white/blue morphs, and sometimes mixed morphs with combinations of two colours. Despite these convergent phenotypes, there is marked divergence in correlated behavioural, physiological and life‐history traits. We discuss the need for coherence in morph classification, particularly in relation to ‘mixed’ morphs. We highlight future research directions such as the genetic basis of convergent phenotypes and the role of environmental variation in the maintenance of polymorphism. Research in this very active field promises to continue to provide novel insights with broad significance to evolutionary biologists.
Bird diversity and endemism along a land‐use gradient in Madagascar: The conservation value of vanilla agroforests
Authors: Martin Dominic Andreas , Andriafanomezantsoa Rouvah , Dröge Saskia , Osen Kristina , Rakotomalala Eric , Wurz Annemarie , Andrianarimisa Aristide , Kreft Holger
Published: October 2020

Land‐use change is the most important driver of biodiversity loss worldwide and particularly so in the tropics, where natural habitats are transformed into large‐scale monocultures or heterogeneous landscape mosaics of largely unknown conservation value. Using birds as an indicator taxon, we evaluated the conservation value of a landscape mosaic in northeastern Madagascar, a biodiversity hotspot and the center of global vanilla production. We assessed bird species richness and composition by conducting point counts across seven prevalent land‐use types (forest‐ and fallow‐derived vanilla agroforests, woody and herbaceous fallow that are part of a shifting cultivation system, rice paddy, forest fragment and contiguous old‐growth forest). We find that old‐growth forest had the highest species richness, driven by a high share of endemics. Species richness and community composition in forest‐derived vanilla agroforest were similar to forest fragment, whereas fallow‐derived vanilla agroforest was most comparable to woody fallow. The open land‐use types herbaceous fallow and rice paddy had fewest species. Across forest fragments, vanilla agroforests, and woody fallows, endemic bird species richness was positively correlated to landscape‐scale forest cover. We conclude that both fallow‐ and forest‐derived vanilla agroforests play an important but contrasting role for bird conservation: Fallow‐derived agroforests are less valuable but take fallow land out of the shifting cultivation cycle, possibly preventing further degradation. Conversely, forest‐derived agroforests contribute to forest degradation but may avoid total loss of tree cover from forest fragments. Considering the land‐use history of agroforests may thus be a promising avenue for future research beyond the case of vanilla.

Abstract in Malagasay is available with online material
Neurobiological Sensitivity to Social Rewards and Punishments Moderates Link Between Peer Norms and Adolescent Risk Taking
Authors: Telzer Eva H. , Jorgensen Nathan A. , Prinstein Mitchell J. , Lindquist Kristen A.
Published: October 2020

Although peer influence is a strong predictor of adolescents’ risk‐taking behaviors, not all adolescents are susceptible to their peer group. One hundred and thirty‐six adolescents (Mage = 12.79 years) completed an fMRI scan, measures of perceived peer group norms, and engagement in risky behavior. Ventral striatum (VS) sensitivity when anticipating social rewards and avoiding social punishments significantly moderated the association between perceived peer norms and adolescents’ own risk behaviors. Perceptions of more deviant peer norms were associated with increased risky behavior, but only for adolescents with high VS sensitivity; adolescents with low VS sensitivity were resilient to deviant peer norms, showing low risk taking regardless of peer context. Findings provide a novel contribution to the study of peer influence susceptibility.
Gender differences in response to an opportunistic brief intervention for obesity in primary care: Data from the BWeL trial
Authors: Tudor Kate , Tearne Sarah , Jebb Susan A. , Lewis Amanda , Adab Peymane , Begh Rachna , Jolly Kate , Daley Amanda , Farley Amanda , Lycett Deborah , Nickless Alecia , Aveyard Paul
Published: October 2020

Weight loss programmes appeal mainly to women, prompting calls for gender‐specific programmes. In the United Kingdom, general practitioners (GPs) refer nine times as many women as men to community weight loss programmes. GPs endorsement and offering programmes systematically could reduce this imbalance. In this trial, consecutively attending patients in primary care with obesity were invited and 1882 were enrolled and randomized to one of two opportunistic 30‐second interventions to support weight loss given by GPs in consultations unrelated to weight. In the support arm, clinicians endorsed and offered referral to a weight loss programme and, in the advice arm, advised that weight loss would improve health. Generalized linear mixed effects models examined whether gender moderated the intervention. Men took effective weight loss action less often in both arms (support: 41.6% vs 60.7%; advice: 12.1% vs 18.3%; odds ratio (OR) = 0.38, 95% confidence interval (CI), 0.27, 0.52, P < .001) but there was no evidence that the relative effect differed by gender (interaction P = .32). In the support arm, men accepted referral and attended referral less often, 69.3% vs 82.4%; OR = 0.48, 95% CI, 0.35, 0.66, P < .001 and 30.4% vs 47.6%; OR = 0.48, 95% CI, 0.36, 0.63, P < .001, respectively. Nevertheless, the gender balance in attending weight loss programmes closed to 1.6:1. Men and women attended the same number of sessions (9.7 vs 9.1 sessions, P = .16) and there was no evidence weight loss differed by gender (6.05 kg men vs 4.37 kg women, P = .39). Clinician‐delivered opportunistic 30‐second interventions benefits men and women equally and reduce most of the gender imbalance in attending weight loss programmes.
Re‐Examining the Effect of Top‐Down Linguistic Information on Speaker‐Voice Discrimination
Authors: Quinto Ashley , Abu El Adas Sandy , Levi Susannah V.
Published: October 2020

The current study replicated and extended the results from a study conducted by Narayan, Mak, and Bialystok (2017) that found effects of top‐down linguistic information on a speaker discrimination task by examining four conditions: rhymes (day‐bay), compounds (day‐dream), reverse compounds (dream‐day), and unrelated words (day‐bee). The original study found that participants were more likely to judge two words to be spoken by the same speaker if the words cohered lexically (created lexical compounds such as day‐dream) or were phonologically related (rhymes, such as day‐bay), but their study contained two limitations: (a) Same‐ and different‐speaker trials were analyzed separately, which obscures effects of response bias, and (b) cross‐gender pairs were used in the different‐speaker trials, potentially inflating performance. The current study addresses these limitations by including only within‐gender trials and by examining sensitivity and bias using signal detection theory. Our results not only provide support of the original study but also provide clear evidence that listeners are biased to judge two words as being produced by the same person when they share either phonological information (rhymes) or lexical‐semantic coherence (compounds). Thus, the current study provides an important modified replication of previous research.
PRKAR2B‐HIF‐1α loop promotes aerobic glycolysis and tumour growth in prostate cancer
Authors: Xia Lei , Sun Jian , Xie Shaowei , Chi Chenfei , Zhu Yinjie , Pan Jiahua , Dong Baijun , Huang Yiran , Xia Weiliang , Sha Jianjun , Xue Wei
Published: October 2020

Objectives

Reprogramming of cellular metabolism is profoundly implicated in tumorigenesis and can be exploited to cancer treatment. Cancer cells are known for their propensity to use glucose‐dependent glycolytic pathway instead of mitochondrial oxidative phosphorylation for energy generation even in the presence of oxygen, a phenomenon known as Warburg effect. The type II beta regulatory subunit of protein kinase A (PKA), PRKAR2B, is highly expressed in castration‐resistant prostate cancer (CRPC) and contributes to tumour growth and metastasis. However, whether PRKAR2B regulates glucose metabolism in prostate cancer remains largely unknown.

Materials and methods

Loss‐of‐function and gain‐of‐function studies were used to investigate the regulatory role of PRKAR2B in aerobic glycolysis. Real‐time qPCR, Western blotting, luciferase reporter assay and chromatin immunoprecipitation were employed to determine the underlying mechanisms.

Results

PRKAR2B was sufficient to enhance the Warburg effect as demonstrated by glucose consumption, lactate production and extracellular acidification rate. Mechanistically, loss‐of‐function and gain‐of‐function studies showed that PRKAR2B was critically involved in the tumour growth of prostate cancer. PRKAR2B was able to increase the expression level of hypoxia‐inducible factor 1α (HIF‐1α), which is a key mediator of the Warburg effect. Moreover, we uncovered that HIF‐1α is a key transcription factor responsible for inducing PRKAR2B expression in prostate cancer. Importantly, inhibition of glycolysis by the glycolytic inhibitor 2‐deoxy‐d‐glucose (2‐DG) or replacement of glucose in the culture medium with galactose (which has a much lower rate than glucose entry into glycolysis) largely compromised PRKAR2B‐mediated tumour‐promoting effect. Similar phenomenon was noticed by genetic silencing of HIF‐1α.

Conclusions

Our study identified that PRKAR2B‐HIF‐1α loop enhances the Warburg effect to enable growth advantage in prostate cancer.
Histone H3K79 demethylation by KDM2B facilitates proper DNA replication through PCNA dissociation from chromatin
Authors: Kang Joo‐Young , Park Jin Woo , Hahm Ja Young , Jung Hyeonsoo , Seo Sang‐Beom
Published: October 2020

Objectives

The level of histone H3 lysine 79 methylation is regulated by the cell cycle and involved in cell proliferation. KDM2B is an H3K79 demethylase. Proliferating cell nuclear antigen (PCNA) is a component of the DNA replication machinery. This study aimed at elucidating a molecular link between H3K79me recognition of PCNA and cell cycle control.

Materials and methods

We generated KDM2B‐depleted 293T cells and histone H3‐K79R mutant‐expressing 293T cells. Western blots were primarily utilized to examine the H3K79me level and its effect on subsequent PCNA dissociation from chromatin. We applied IP, peptide pull‐down, isothermal titration calorimetry (ITC) and ChIP experiments to show the PCNA binding towards methylated H3K79 and DNA replication origins. Flow cytometry, MTT, iPOND and DNA fibre assays were used to assess the necessity of KDM2B for DNA replication and cell proliferation.

Results

We revealed that KDM2B‐mediated H3K79 demethylation regulated cell cycle progression. We found that PCNA bound chromatin in an H3K79me‐dependent manner during S phase. KDM2B was responsible for the timely dissociation of PCNA from chromatin, allowing to efficient DNA replication. Depletion of KDM2B aberrantly enriched chromatin with PCNA and caused slow dissociation of residual PCNA, leading to a negative effect on cell proliferation.

Conclusions

We suggested a novel interaction between PCNA and H3K79me. Thus, our findings provide a new mechanism of KDM2B in regulation of DNA replication and cell proliferation.
Impact of censusing and research on wildlife populations
Authors: Kilpatrick A. Marm , Hoyt Joseph R. , King R. Andrew , Kaarakka Heather M. , Redell Jennifer A. , White J. Paul , Langwig Kate E.
Published: October 2020

Population monitoring and research are essential for conserving wildlife, but these activities may directly impact the populations under study. These activities are often restricted to minimize disturbance, and impacts must be weighed against knowledge gained. However, few studies have quantified the effects of research or census‐related visitation frequency on populations, and low visitation rates have been hypothesized to have little effect. Hibernating bats have been hypothesized to be especially sensitive to visitation because they have limited energetic stores to survive winter, and disturbance may partly deplete these stores. We examined the effect of site visitation frequency on population growth rates of three species of hibernating bats, little brown bats (Myotis lucifugus), Indiana bats (Myotis sodalis) and tri‐colored bats (Perimyotis subflavus), both before and after detection of the disease white‐nose syndrome. We found no evidence that more frequent visits decreased population growth rates for any of these species. Estimated coefficients were either the opposite sign as hypothesized (population growth rates increased with visitation frequency) or were very small (difference in population growth rates 0.067% [SE 2.5%]–1.8% [SE 9.8%]) relative to spatial and temporal variation (5.9–32%). In contrast, white‐nose syndrome impacts on population growth rates were easily detected and well‐characterized statistically (effect sizes 4.4–8.0; severe population declines occurred in the second and third years after pathogen detection) indicating that we had sufficient power to detect effects. These results indicate that visitation frequency (for M. sodalis: annual vs. semi‐annual counts; for M. lucifugus and P. subflavus: 1–3 three research visits per year) had undetectable impacts on bat population growth rates both with and without the additional stress of an emerging infectious disease. Knowledge gained from censuses and research may outweigh disturbance due to human visitation if it can be used to understand and conserve the species.
Co‐designing behavior change interventions to conserve biodiversity
Authors: Bowie Matthew J. , Dietrich Timo , Cassey Phillip , Veríssimo Diogo
Published: October 2020

Many threats to biodiversity are the result of human actions, which means that changing human behavior can positively alter the trajectory of our current biodiversity crisis. While there is an increasing number of behavior change interventions being implemented in biodiversity conservation, their design is rarely informed by the people they try to influence, thereby lowering the probability of success. Building successful interventions requires substantial audience research, but this can be challenging for conservation projects with perennially limited time and resources. Here, we critically discuss co‐design as a useful and effective approach for gathering audience insights relatively quickly, allowing conservation practitioners to integrate end‐user voices when they would otherwise be excluded from intervention design. Specifically, we present a seven‐step co‐design process, providing an outline and guidance for how to generate more user‐centric intervention ideas and transform them into feasible prototype interventions. Further, we show how we applied this seven‐step process with coffee consumers in a sustainable conservation context. This study outlines contributions that showcase the value of user‐centered design approaches to behavior change interventions for biodiversity conservation.
Functional connectivity in the developing language network in 4‐year‐old children predicts future reading ability
Authors: Jasińska Kaja K. , Shuai Lan , Lau Airey N. L. , Frost Stephen , Landi Nicole , Pugh Kenneth R.
Published: October 2020

Understanding how pre‐literate children's language abilities and neural function relate to future reading ability is important for identifying children who may be at‐risk for reading problems. Pre‐literate children are already proficient users of spoken language and their developing brain networks for language become highly overlapping with brain networks that emerge during literacy acquisition. In the present longitudinal study, we examined language abilities, and neural activation and connectivity within the language network in pre‐literate children (mean age = 4.2 years). We tested how language abilities, brain activation, and connectivity predict children's reading abilities 1 year later (mean age = 5.2 years). At Time 1, children (n = 37) participated in a functional near infrared spectroscopy (fNIRS) experiment of speech processing (listening to words and pseudowords) and completed a standardized battery of language and cognitive assessments. At Time 2, children (n = 28) completed standardized reading assessments. Using psychophysiological interaction (PPI) analyses, we observed significant connectivity between the left IFG and right STG in pre‐literate children, which was modulated by task (i.e., listening to words). Neural activation in left IFG and STG and increased task‐modulated connectivity between the left IFG and right STG was predictive of multiple reading outcomes. Increased connectivity was associated later with increased reading ability.
Action prediction during real‐time parent‐infant interactions
Authors: Monroy Claire , Chen Chi‐Hsin , Houston Derek , Yu Chen
Published: October 2020

Social interactions provide a crucial context for early learning and cognitive development during infancy. Action prediction—the ability to anticipate an observed action—facilitates successful, coordinated interaction and is an important social‐cognitive skill in early development. However, current knowledge about infant action prediction comes largely from screen‐based laboratory tasks. We know little about what infants’ action prediction skills look like during real‐time, free‐flowing interactions with a social partner. In the current study, we used head‐mounted eyetracking to quantify 9‐month‐old infants’ visual anticipations of their parents’ actions during free‐flowing parent–child play. Our findings reveal that infants do anticipate their parents’ actions during dynamic interactions at rates significantly higher than would be expected by chance. In addition, the frequency with which they do so is associated with child‐led joint attention and hand‐eye coordination. These findings are the first to reveal infants’ action prediction behaviors in a more naturalistic context than prior screen‐based studies, and they support the idea that action prediction is inherently linked to motor development and plays an important role in infants’ social‐cognitive development. A video abstract of this article can be viewed at https://www.youtube.com/watch?v=9HrmcicfiqE
Aortic valve area calculation using 3D transesophageal echocardiography: Implications for aortic stenosis severity grading
Authors: Beneduce Alessandro , Capogrosso Cristina , Moroni Francesco , Ancona Francesco , Falasconi Giulio , Pannone Luigi , Stella Stefano , Ingallina Giacomo , Melillo Francesco , Ancona Marco Bruno , Romano RT Vittorio , Palmisano Anna , Latib Azeem , Colombo Antonio , Montorfano Matteo , Esposito Antonio , Agricola Eustachio
Published: October 2020

Aims

Aortic stenosis (AS) grading by 2D‐transthoracic echocardiography (2D‐TTE) aortic valve area (AVA) calculation is limited by left ventricular outflow tract (LVOT) area underestimation. The combination of Doppler parameters with 3D LVOT area obtained by multidetector computed tomography (MDCT) can improve AS grading, reconciling discordant 2D‐TTE findings. This study aimed to systematically evaluate the role of 3D‐transesophageal echocardiography (3D‐TEE) in AS grading using MDCT as reference standard.

Methods and results

288 patients (81 ± 6.3 years, 52.4% female) with symptomatic AS underwent 2D‐TTE, 3D‐TEE, and MDCT for transcatheter aortic valve implantation. Doppler parameters were combined with 3D LVOT areas measured by manual and semi‐automated software 3D‐TEE and by MDCT to calculate AVA, reassessing AS severity. Both 3D‐TEE modalities demonstrated good correlation with MDCT, with excellent intra‐observer and inter‐observer variability. Compared to MDCT, 3D‐TEE measurements significantly underestimated AVA (PANOVA < .0001), although the difference was clinically acceptable. Compared to 2D‐TTE, 3D‐TEE manual and semi‐automated software reclassified severe AS in 21.9% and 25.2% of cases, respectively (P < .0001), overcame grading parameters discordance in more than 40% of cases in patients with low‐gradient AS (P < .0001) and reduced the proportion of low‐flow states in nearly 75% of cases when combined to stroke volume index assessment (P < .0001). 3D‐TEE imaging modalities showed a reduction in the proportion of patients with low‐gradient and pathological AVA as defined by 2D‐TTE, and improved AVA and mean pressure gradient agreement with current guidelines cutoff values.

Conclusion

3D‐TEE AVA calculation is a reliable tool for AS grading with excellent reproducibility and good correlation with MDCT measurements.
sampbias, a method for quantifying geographic sampling biases in species distribution data
Authors: Zizka Alexander , Antonelli Alexandre , Silvestro Daniele
Published: October 2020

Geo‐referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility are ubiquitous but may differ in strength among taxonomic groups and data sets. Although several factors have been described to influence human access (such as presence of roads, rivers, airports and cities), quantifying their specific and combined effects on recorded occurrence data remains challenging. Here we present sampbias, an algorithm and software for quantifying the effect of accessibility biases in species occurrence data sets. sampbias uses a Bayesian approach to estimate how sampling rates vary as a function of proximity to one or multiple bias factors. The results are comparable among bias factors and data sets. We demonstrate the use of sampbias on a data set of mammal occurrences from the island of Borneo, showing a high biasing effect of cities and a moderate effect of roads and airports. sampbias is implemented as a well‐documented, open‐access and user‐friendly R package that we hope will become a standard tool for anyone working with species occurrences in ecology, evolution, conservation and related fields.
Preparing the hair follicle canal for hair shaft emergence
Authors: Mesler Arlee L. , Benedeck Rachel E. , Wong Sunny Y.
Published: October 2020

The emergence of hair is a defining event during mammalian skin development, but the cellular mechanisms leading to the opening of the hair follicle canal remain poorly characterized. Our previous studies have shown that early hair buds possess a central column of differentiated keratinocytes expressing Keratin 79 (K79), which marks the future hair follicle opening. Here, we report that during late embryogenesis and early postnatal development, K79+ cells at the distal tips of these columns downregulate E‐cadherin, change shape, recede and undergo cell death. These changes likely occur independently of sebaceous glands and the growing hair shaft, and serve to create an orifice for hair to subsequently emerge. Defects in this process may underlie phenomena such as ingrown hair or may potentially contribute to upper hair follicle pathologies including acne, hidradenitis suppurativa and infundibular cysts.
In silico assessment of the potential of basalt amendments to reduce N2O emissions from bioenergy crops
Authors: Blanc‐Betes Elena , Kantola Ilsa B. , Gomez‐Casanovas Nuria , Hartman Melennie D. , Parton William J. , Lewis Amy L. , Beerling David J. , DeLucia Evan H.
Published: October 2020

The potential of large‐scale deployment of basalt to reduce N2O emissions from cultivated soils may contribute to climate stabilization beyond the CO2‐removal effect from enhanced weathering. We used 3 years of field observations from maize (Zea mays) and miscanthus (Miscanthus × giganteus) to improve the nitrogen (N) module of the DayCent model and evaluate the potential of basalt amendments to reduce N losses and increase yields from two bioenergy crops. We found 20%–60% improvement in our N2O flux estimates over previous model descriptions. Model results predict that the application of basalt would reduce N2O emissions by 16% in maize and 9% in miscanthus. Lower N2O emissions responded to increases in the N2:N2O ratio of denitrification with basalt‐induced increases in soil pH, with minor contributions from the impact of P additions (a minor component of some basalts) on N immobilization. The larger reduction of N2O emissions in maize than in miscanthus was likely explained by a synergistic effect between soil pH and N content, leading to a higher sensitivity of the N2:N2O ratio to changes in pH in heavily fertilized maize. Basalt amendments led to modest increases in modeled yields and the nitrogen use efficiency (i.e., fertilizer‐N recover in crop production) of maize but did not affect the productivity of miscanthus. However, enhanced soil P availability maintained the long‐term productivity of crops with high nutrient requirements. The alleviation of plant P limitation led to enhanced plant N uptake, thereby contributing to lower microbial N availability and N2O emissions from crops with high nutrient requirements. Our results from the improved model suggest that the large‐scale deployment of basalt, by reducing N2O fluxes of cropping systems, could contribute to the sustainable intensification of agriculture and enhance the climate mitigation potential of bioenergy with carbon capture and storage strategies.
Root canal treatment of compromised teeth as alternative treatment for patients receiving bisphosphonates: 60‐month results of a prospective clinical study
Authors: Zamparini F. , Pelliccioni G. A. , Spinelli A. , Gissi D. B. , Gandolfi M. G. , Prati C.
Published: October 2020

Aim

This 60‐month prospective study aimed to evaluate tooth survival and healing rates after root canal treatment in patients taking bisphosphonates (BPs). Secondary outcomes were complications and clinical variables observed during and after treatment.

Methods

Root canal treatment was performed using manual K‐file canal instrumentation and a carrier‐based filling technique with an epoxy resin‐based sealer. Teeth without adequate root/crown integrity were restored by trained operators at the tissue level (TL group) to prevent occlusal/mechanical stress and to enable periapical lesion healing without the risk of root fracture. Other teeth were restored with normal occlusal contacts (OC group). Healthy patients who had undergone one or more root canal treatments of the same type constituted the control group. The relationships of the following variables to survival and health status were examined (chi‐squared test and multivariate analysis, P = 0.05): age, gender, smoking habit, tooth location, treatment type, BPs treatment, BPs exposure, initial periapical index (PAI) and occlusal restoration. Survival curves were constructed using Kaplan–Meier analysis, with extraction serving as the end‐point.

Results

In total, 65 patients with 109 root canal‐treated teeth who were taking BPs were included. At 60 months, data from 57 patients (52F, 5M; median age 65.7 ± 8.6 years) who had undergone 96 root canal treatments were analysed (drop‐out rate = 16.9%). The survival rate was 85%, and the success rate was 76%. The control group consisted of 46 patients (21F, 25M; median age 60.3 ± 7.2 years) who had undergone 102 root canal treatments. The survival rate was 88%, with 12 teeth lost during follow‐up. The success rate was 73%. In the BP group, 55 teeth were restored normally (OC group) and 41 teeth were restored at the tissue level (TL group). No difference in the success or survival rate was observed between the BP and control groups (P > 0.05). Univariate Kaplan–Meier analysis revealed that only tooth type significantly affected survival status in the BP group. The analysis revealed the clinical relevance of smoking, tooth location and initial PAI on patients’ health status (P < 0.05).

Conclusion

Root canal treatments and post‐endodontic restoration with tissue‐level filling procedures represent a safe approach for severely damaged teeth in patients receiving BPs having comparable results to root filled teeth restored with occlusal contacts and to the control group.
Fracture resistance of human roots filled with mineral trioxide aggregate mixed with phosphate‐buffered saline, with and without calcium hydroxide pre‐medication
Authors: Żuk‐Grajewska E. , Saunders W. P. , Chadwick R. G.
Published: October 2020

Aim

To compare the fracture strength of extracted human roots with apical plugs of mineral trioxide aggregate (MTA) mixed with either Ca‐ and Mg‐free phosphate‐buffered saline (PBS) or water, with and without calcium hydroxide (CH) canal pre‐medication.

Methodology

A total of 180 single‐rooted human teeth were prepared to resemble immature roots and divided into groups (n = 20). The negative control received canal irrigation only, and the positive control received intracanal treatment with CH for either two or twelve weeks. MTA mixed with water was used in Group 1: (i) without CH pre‐medication – MTA(W); (ii) after 2 weeks CH pre‐medication – 2/52CH + MTA(W); and (iii) after 12‐week CH pre‐medication – 12/52 CH + MTA(W). MTA mixed with PBS was used in Group 2: (i) without CH pre‐medication – MTA(PBS); (ii) after 2‐week CH pre‐medication – 2/52CH + MTA(PBS); and (iii) after 12‐week CH pre‐medication – 12/52 CH + MTA(PBS). A compressive force was applied to each root until the point of fracture. The results were analysed by the Kruskal–Wallis and Dunn’s multiple comparisons tests (P < 0.05).

Results

There was no significant difference between groups MTA(W), MTA(PBS) and 2/52CH + MTA(PBS), and all three groups were significantly (P < 0.01, P < 0.05 and P < 0.05, respectively) more resistant to fracture than the negative control. Within Group 1, the samples that received two‐ (P < 0.01) and twelve‐week (P < 0.001) CH pre‐treatment were more prone to fracture than those which did not. No difference was found amongst the control groups. The roots of the MTA(PBS) group had a higher dependability (P < 0.05) than the MTA(W) group when compared by the Weibull modulus. The difference was also present when a 2‐week CH pre‐medication was used.

Conclusions

Mineral trioxide aggregate mixed with Ca‐ and Mg‐free phosphate‐buffered saline had a significant strengthening effect on the fracture resistance of structurally weak roots, even when short‐term calcium hydroxide pre‐medication had been used. MTA mixed with water lost its strengthening effect on human roots when 2‐ or 12‐week CH pre‐treatment had been used. Use of CH dressing for up to 12 weeks had no negative effect on fracture resistance of human roots.
Pretreatment eliminates throat irritation by water yam and facilitates the development of functional cookies
Authors: Najeeb Fyroos , Theagarajan Radhika , Dutta Sayantani , Moses Jeyan A. , Anandharamakrishnan Chinnaswamy
Published: October 2020

Water yam (Dioscoreaalata) provides sufficient nutrients in terms of protein (10.075 ± 0.02%), fibre (3.40 ± 0.03%) and minerals (potassium and phosphorous). However, due to the presence of anti‐nutritional factors such as saponins, water yam causes throat irritation. Consequently, it is less preferred among consumers, and thus, the commercial importance of yam tubers has been limited. The current investigation aims to reduce the saponin content of water yam by pretreatment of yam tubers at the optimised conditions (blanching with 0.2% potassium metabisulphite, 0.5% tartaric acid and 0.5% citric acid) that rendered a 50% reduction in the saponin content (1.65% to 0.86%). The said nutritious yam flour was utilised as a replacement of refined wheat flour (13%) in the development of functional cookies. The yam cookies showed higher mineral content (phosphorous: 116.20 ± 0.80 mg/100 g; potassium: 221.11 ± 0.98 mg/100 g). Reduced water activity and incorporation of antioxidants in yam cookies decreased the peroxide value of the same during storage attesting its higher shelf‐life.