bluuebunny/crossref_metadata_2025 huggingface dataset:
FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets
Authors: Moreno-Mayar J Víctor
Published: October 2021

Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyze their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualization of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.
Suppression of cdc13-2-associated senescence by pif1-m2 requires Ku-mediated telomerase recruitment
Authors: Fekete-Szücs Enikő , Rosas Bringas Fernando R , Stinus Sonia , Chang Michael
Published: October 2021

In Saccharomyces cerevisiae, recruitment of telomerase to telomeres requires an interaction between Cdc13, which binds single-stranded telomeric DNA, and the Est1 subunit of telomerase. A second pathway involving an interaction between the yKu complex and telomerase RNA (TLC1) contributes to telomerase recruitment but cannot sufficiently recruit telomerase on its own to prevent replicative senescence when the primary Cdc13-Est1 pathway is abolished—for example, in the cdc13-2 mutant. In this study, we find that mutation of PIF1, which encodes a helicase that inhibits telomerase, suppresses the replicative senescence of cdc13-2 by increasing reliance on the yKu-TLC1 pathway for telomerase recruitment. Our findings reveal new insight into telomerase-mediated telomere maintenance.
The Association of Prior Intensive Lifestyle Intervention and Diabetes Support and Education With Frailty Prevalence at Long-Term Follow-Up in the Action for Health in Diabetes Extension Study
Authors:   Look AHEAD Research Group, Espinoza Sara E , Hazuda Helen P , Maruthur Nisa M , Bray George A , Johnson Karen C , Synyer Xavier Pi , Newman Anne B , Wing Rena R , Yanovski Susan Z , Gaussoin Sarah A , Houston Denise K , Espinoza Sara E , Hazuda Helen P , Atkinson Karen , Bolin Paula , Bray George A , Clark Jeanne M , Coday Mace , Dutton Gareth , Egan Caitlin , Foreyt John P , Gaussoin Sarah A , Greenway Frank L , Gregg Edward W , Hill James O , Horton Edward S , Houston Denise K , Hubbard Van S , Jakicic John M , Jeffery Robert W , Johnson Karen C , Kahn Steven E , Knowler William C , Lewis Cora E , Maruthur Nisa M , Carey Barbara J Maschak , Middelbeek Roeland J W , Nathan David M , Newman Anne B , Pajewski Nicholas , Patricio Jennifer , Percy Carol , Peters Anne , Sunyer Xavier Pi , Pownall Henry , Redmon Bruce , Steinburg Helmut , Wadden Thomas A , Wing Rena R , Wyatt Holly , Yanovski Susan Z , Zhang Ping
Published: October 2021

Background

Frailty is common in older adults with obesity and diabetes. We compared prevalence of the frailty phenotype between intervention groups in long-term follow-up of Look Action for Health in Diabetes Study (AHEAD), a randomized trial comparing a multidomain intensive lifestyle intervention (ILI) that promoted weight loss and physical activity with a diabetes support and education (DSE) control group in adults with type 2 diabetes and overweight or obesity.

Method

Participants included 2 979 individuals randomized to ILI or DSE in 2001–2004 who completed frailty assessment in Look AHEAD—Extension Wave 1 (2016–2018) at an average age of 72.1 ± 6.2 years. Frailty was assessed using a modified frailty phenotype definition (excluding weight loss) defined as the presence of 3 or more of the following frailty characteristics: weakness, slow gait speed, low physical activity, and exhaustion. Frailty odds by intervention assignment (DSE vs ILI) were estimated using multivariable logistic regression, adjusting for sex, clinic site, and time since randomization.

Results

At median follow-up of 14.0 years (interquartile range: 13.8–14.1), frailty prevalence was 10.9% in ILI compared with 11.6% in DSE (odds ratio for frailty in ILI vs DSE = 0.94, 95% confidence interval: 0.75–1.18, p = .60). Frailty was more prevalent in participants who were older, female, non-White, of lower socioeconomic status, and at baseline had a higher body mass index and waist circumference, longer duration of diabetes, history of cardiovascular disease, and metabolic syndrome.

Conclusions

Prior randomization to ILI compared with DSE was not associated with a lower prevalence of frailty after a median follow-up of 14.0 years in adults with diabetes and overweight or obesity.
Network approaches for formalizing conceptual models in ecosystem-based management
Authors: Reum Jonathan C P , Kelble Christopher R , Harvey Chris J , Wildermuth Robert P , Trifonova Neda , Lucey Sean M , McDonald P Sean , Townsend Howard
Published: October 2021

Qualitative Network Models (QNMs), Fuzzy Cognitive Maps (FCMs), and Bayesian Belief Networks (BBNs) have been proposed as methods to formalize conceptual models of social–ecological systems and project system responses to management interventions or environmental change. To explore how these different methods might influence conclusions about system dynamics, we assembled conceptual models representing three different coastal systems, adapted them to the network approaches, and evaluated outcomes under scenarios representing increased fishing effort and environmental warming. The sign of projected change was the same across the three network models for 31–60% of system variables on average. Pairwise agreement between network models was higher, ranging from 33 to 92%; average levels of similarity were comparable between network pairs. Agreement measures based on both the sign and strength of change were substantially worse for all model comparisons. These general patterns were similar across systems and scenarios. Different outcomes between models led to different inferences regarding trade-offs under the scenarios. We recommend deployment of all three methods, when feasible, to better characterize structural uncertainty and leverage insights gained under one framework to inform the others. Improvements in precision will require model refinement through data integration and model validation.
Livestock and Risk Group 4 Pathogens: Researching Zoonotic Threats to Public Health and Agriculture in Maximum Containment
Authors: Lewis Charles E , Pickering Bradley
Published: October 2021

Maximum-containment laboratories are a unique and essential component of the bioeconomy of the United States. These facilities play a critical role in the national infrastructure, supporting research on a select set of especially dangerous pathogens, as well as novel, emerging diseases. Understanding the ecology, biology, and pathology at the human-animal interface of zoonotic spillover events is fundamental to efficient control and elimination of disease. The use of animals as human surrogate models or as target-host models in research is an integral part of unraveling the interrelated components involved in these dynamic systems. These models can prove vitally important in determining both viral- and host-factors associated with virus transmission, providing invaluable information that can be developed into better risk mitigation strategies. In this article, we focus on the use of livestock in maximum-containment, biosafety level-4 agriculture (BSL-4Ag) research involving zoonotic, risk group 4 pathogens and we provide an overview of historical associated research and contributions. Livestock are most commonly used as target-host models in high-consequence, maximum-containment research and are routinely used to establish data to assist in risk assessments. This article highlights the importance of animal use, insights gained, and how this type of research is essential for protecting animal health, food security, and the agriculture economy, as well as human public health in the face of emerging zoonotic pathogens. The utilization of animal models in high-consequence pathogen research and continued expansion to include available species of agricultural importance is essential to deciphering the ecology of emerging and re-emerging infectious diseases, as well as for emergency response and mitigation preparedness.
Potential for Machine Learning in Burn Care
Authors: Robb Lydia
Published: October 2021

Burn-related injuries are a leading cause of morbidity across the globe. Accurate assessment and treatment have been demonstrated to reduce the morbidity and mortality. This essay explores the forms of artificial intelligence to be implemented the field of burns management to optimize the care we deliver in the National Health Service (NHS) in the United Kingdom. Machine learning methods that predict or classify are explored. This includes linear and logistic regression, artificial neural networks, deep learning, and decision tree analysis. Utilizing machine learning in burns care holds potential from prevention, burns assessment, predicting mortality, and critical care monitoring to healing time. Establishing a regional or national Machine Learning group would be the first step toward the development of these essential technologies. The implementation of machine learning technologies will require buy-in from the NHS health boards, with significant implications with cost of investment, implementation, employment of machine learning teams, and provision of training to medical professionals.
Disseminated tuberculosis presenting as bilateral neuro-retinitis
Authors: Anton-Vazquez Vanesa , Parthasarathi Padmini , Grimaldi Gabriela , Dhanes Thomas , Rees Angela , Singh Manuraj , Macallan Derek , Arias Mauricio
Published: October 2021

Disseminated tuberculosis (TB) presenting with intraocular involvement is a rare condition, which can lead to profound visual loss if misdiagnosed. We report a case of a 24-year-old Nepalese male with disseminated TB who presented primarily with bilateral vision loss.
ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data
Authors: Inoue Jun
Published: October 2021

Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: 1) Analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and 2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole-genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.
Making Sense of a Complex Notion: Debates on State Religious Neutrality in Canada — A View from Quebec
Authors: Bosset Pierre
Published: October 2021

Under Canadian constitutional law, state neutrality acts as an implicit organizing principle for the relations between the state and religions. Neutrality, however, is a polysemic word: conceptions of neutrality vary. Competing versions of neutrality feature in the decisions of Canadian courts. This is starkly evident in decisions that originate from Quebec, where judges have harboured divergent views of neutrality on matters such as the reciting of prayers in town hall meetings or the teaching of religious diversity in schools. This article analyses how the Canadian Supreme Court has manoeuvred through competing conceptions of state religious neutrality. Initially divided, the Court seems to have eventually opted for a type of neutrality that allows the state to recognize the existence of religions in laws and policies, but that also prevents it from indoctrination and from arbitrating between competing viewpoints within religions. This view of neutrality, I argue, is consistent with the principle of multiculturalism and with the Court’s characterization of a ‘free and democratic society’, as this notion is understood in Canada.
Intergovernmental Influence, Managerial Turnover, and City Energy Policy Adoption
Authors: Huang Chien-Shih , Berry Frances
Published: October 2021

Urban sustainability policy provides opportunities for expanding global efforts for climate change mitigation. Yet local governments may not commit to make such policy efforts. It is well recognized that internal and external factors in state and local governments can be potential drivers. Less recognized is that green energy policy adoption can also be impacted by competitive federalism, under which state laws might influence the likelihood of local adoption. Drawing on prior studies on inter-governmental interactions and managerial turnover, we hypothesize the effect of intergovernmental influence, managerial turnover, and their interactions on city adoption of energy efficiency and renewable energy programs. Results of the multilevel regression model indicate that state influence via regulatory or financial tools can encourage city sustainable energy consumption and production, while managerial turnover can inhibit these conditions, but the negative impacts of managerial turnover can be reversed when the successors are recruited externally. Our tests support the existence of both local government free-riding and city mobilization to enact more green policies with externally hired city managers, thereby helping us to distinguish the impact of competitive federalism in local energy policy.
Suicide reporting of LGBTQI+ population in India: An analysis of online media reports of the past decade
Authors: Kar Sujita Kumar , Menon Vikas , Mukherjee Srijeeta , Bascarane Sharmi , Sharma Ginni , Pattnaik Jigyansa Ipsita , Ransing Ramdas , Padhy Susanta Kumar , Agarwal Vivek
Published: October 2021

Background

Imbalanced portrayal of suicide by the media can have adverse public health consequences. We aimed to evaluate the psychosocial context, as well as the quality of media reporting, of suicide among lesbian, gay, bisexual, transgender people, queer and intersex (LGBTQI+) population.

Methods

A cross-sectional study was conducted to evaluate online news reports discussing the suicide of LGBTQI+ persons published between January 2011 and January 2021. Psychosocial factors associated with suicide were extracted from the reports. Quality of suicide reporting was checked against international as well as locally relevant reporting guidelines.

Results

A total of 135 suicide reports from five newspapers were analyzed. Multiple psychosocial stressors were reported in 54.5% of the suicides. Social stigma was the most common factor associated with LGBTQI+ suicide. Several breaches of reporting were noted in relation to mentioning the identity (55.6%) and method of suicide (54.3%) in the title of report and inclusion of the deceased’s photograph (20.4%). Potentially helpful reporting characteristics, such as including educational information (2.2%), mentioning warning signs (12.6%) and suicide support service details (3.7%), were rarely practiced. Local language news articles displayed more frequent and serious violations compared to English news reports.

Conclusion

Indian media reporting of suicide among LGBTQI+ persons is poorly adherent to reporting guidelines.
Placebo response in psoriatic arthritis clinical trials: a systematic review and meta-analysis
Authors: Erre Gian Luca , Mavridis Dimitris , Woodman Richard John , Mangoni Arduino Aleksander
Published: October 2021

Objective

To determine the placebo response rate in PsA randomized clinical trials (RCTs), its contributing factors and impact on the effect size of active treatments.

Methods

We searched multiple databases, from inception to 20 December 2020, for placebo-controlled RCTs in PsA. We used a random-effects meta-analysis to pool the response rates for the ACR20 criteria in the placebo arm, determined the risk difference for treatment vs placebo, and used meta-regression to determine the factors associated with placebo response rates. The risk of bias was assessed in duplicate. The study protocol was registered with PROSPERO: CRD42021226000.

Results

We included 42 RCTs (5050 patients receiving placebo) published between 2000 and 2020. The risk of bias was low in 28 trials, high in four, and with some concerns in 10. The pooled placebo response rate was 20.3% (95% CI: 18.6%, 22.1%; predicted intervals, 11.7–29.0%), with significant between-trial heterogeneity (I2 = 56.8%, P < 0.005). The pooled risk difference for treatment vs placebo was 27% (95% CI: 24%, 31%). In the multivariable meta-regression, there was a 15% (95% CI: 2.9%, 29.8%) increase in the odds of achieving the placebo response for each 5-year increment in publication year (P = 0.016). In addition, the active treatment risk difference decreased for every 5-year increment in publication year (β = −0.053, 95% CI: −0.099, −0.007; P = 0.024) but was not associated with the placebo response.

Conclusion

Despite increasing over time, the placebo response for ACR20 in PsA RCTs was not associated with the active treatment effect size.
Fathers’ involvement in early childcare is associated with amygdala resting-state connectivity
Authors: Horstman Lisa I , Riem Madelon M E , Alyousefi-van Dijk Kim , Lotz Anna M , Bakermans-Kranenburg Marian J
Published: October 2021

Becoming a parent requires new skills and frequent task switching during daily childcare. Little is known about the paternal brain during the transition to fatherhood. The present study examined intrinsic neuronal network connectivity in a group of first-time expectant and new fathers (total N = 131) using amygdala seed-based resting-state functional connectivity analysis. Furthermore, we examined the association between paternal involvement (i.e. hours spent in childcare and real-time push notifications on smartphone) and connectivity within the parental brain network in new fathers. There were no significant differences in functional connectivity between expectant and new fathers. However, results show that in new fathers, time spent in childcare was positively related to amygdala connectivity with the supramarginal gyrus, postcentral gyrus and the superior parietal lobule—all regions within the cognition/mentalizing network that have been associated with empathy and social cognition. Our results suggest that fathers’ time investment in childcare is related to connectivity networks in the parental brain.
Impacts for whom? Assessing inequalities in NSF-funded broader impacts using the Inclusion-Immediacy Criterion
Authors: Woodson Thomas , Boutilier Sophia
Published: October 2021

Broader impacts (BI) policies generate debate on the purpose of science, measuring the impact of research, and is an important topic for the science policy community. However, BI policies often fail to determine if R&D funding helps marginalized communities. This paper introduces a new framework, the Inclusion-Immediacy Criterion, that assesses who benefits from research impacts as divided into three groups: (1) advantaged groups; (2) the general population; and (3) marginalized groups. The study analyzes National Science Foundation (NSF) project outcome reports and finds that advantaged groups are the most likely to benefit from NSF-funded research. The study also shows that certain areas of NSF research, such as Social, Behavioral, and Economic Sciences, more efficiently generate impacts for marginalized groups compared to other directorates. This paper further argues that persistent inequalities in BIs limit the potential of R&D to increase prosperity and well-being, two of NSF’s mandated goals.
A new cytometry-based method reveals an accumulation of Nrf2 in dendritic cells exposed to two respiratory sensitizers
Authors: Audry Adrien , Mathiot Julianne , Muller Samuel , Coiscaud Amélie , Langonné Isabelle , Battais Fabrice , Leininger Brigitte , Sponne Isabelle
Published: October 2021

The mechanisms underlying chemical respiratory sensitization are incompletely understood. One of the major cell types involved in this pathology are dendritic cells. In this study, the mechanisms of the NRF2–Keap1 pathway were studied using a bone marrow-derived dendritic cell model exposed to two respiratory sensitizers: ammonium hexachloroplatinate (HCP) and ammonium tetrachloroplatinate (ATCP). Expression levels for two Nrf2-regulated genes, hmox1 and srxn1, were analyzed by real time-quantitative polymerase chain reaction. A flow cytometry-based method was also developed to measure intracellular Nrf2 accumulation in dendritic cells following exposure. Exposure to HCP and ATCP increased both hmox1 and srxn1 gene expression, and was associated with accumulation of Nrf2 protein in cells. Overall, these results show that the respiratory sensitizers, in addition to skin sensitizers, can also induced markers associated with NRF2–Keap1 pathway activation in dendritic cells. This study contributes to a better understanding of the adverse outcome of respiratory sensitization.
Prevention and Detection of Fungicide Resistance Development in Rhizoctonia zeae from Soybean and Corn in Nebraska
Authors: Gambhir Nikita , Kodati Srikanth , Huff Matthew , Silva Flávio , Ajayi-Oyetunde Olutoyosi , Staton Margaret , Bradley Carl , Adesemoye Anthony O. , Everhart Sydney E.
Published: October 2021

The goal of this research was to advance the foundational knowledge required to quantify and mitigate fungicide resistance in Rhizoctonia zeae, the seedling disease pathogen of soybean and corn. In vitro sensitivity to azoxystrobin, fludioxonil, sedaxane, and/or prothioconazole was determined for 91 R. zeae isolates obtained mostly from soybean and corn fields in Nebraska. Isolates were sensitive to fludioxonil, sedaxane, and prothioconazole (EC50 < 3 µg/ml) and had a positively skewed EC50 distribution. Isolates were not sensitive to azoxystrobin in vitro (EC50 > 100 µg/ml) or in planta. Application of azoxystrobin did not significantly decrease disease severity or improve total dry weight of the soybean plants (P > 0.05). The risk of resistance development in R. zeae was estimated by characterizing its population structure. Eighty-one R. zeae isolates were genotyped using six microsatellite markers. Results showed that the population has a mixed mode of reproduction and is structured according to geographic region, suggesting limited dispersal. These population characteristics suggest that R. zeae has an intermediate risk of resistance development. Overall, this research established the current status of fungicide sensitivity in R. zeae in Nebraska and estimated its risk of resistance development, which can inform fungicide resistance management for R. zeae.
Diversity Matters: A 21-Year Review of Trends in Resident Recruitment into Surgical Specialties
Authors: Mohan Anita T. , Banuelos Joseph , Cespedes-Gomez Omar , Kapoor Trishul , Moran Steven L. , Heller Stephanie F. , Dozois Eric J. , Nelson Heidi , Stulak John M. , Martinez-Jorge Jorys
Published: October 2021

Background:

Diversity within the healthcare workforce is essential to improve quality of care, although evaluation of diversity within surgical training remains limited. This study analyzed diversity in recruitment of residents into surgical subspecialties at a large academic medical institution and national trends.

Methods:

A 21-year cross-sectional study of medical school graduates accepted into all surgical subspecialty training programs was performed. The institutional cohort was divided into two groups (1997–2006, 2007–2017). Subspecialty acceptance rates were determined between 2011 and 2018. Data on candidate demographics including gender, race, ethnicity, citizenship, and origin of medical education at a single institution and nationally were extracted.

Results:

Two thousand found hundred seventy-two residents were included in this study. From 1997 to 2018, female acceptances increased from 21.1% to 29.7% (p < 0.01), non-White increased from 27.9% to 31.8% (p = 0.01), and international medical graduates decreased from 28.8% to 25.5% (p = 0.02). There was no significant change in accepted Hispanic and Non-US candidates. Female subspecialty rates for subspecialties increased nationally and was comparable to our cohort, except in general surgery. Hispanic subspecialty acceptance rates were less than 10% and Black/African American acceptance rates remained less than 5% across subspecialties nationally and at our institution.

Conclusion:

Diversity in surgical training has modestly progressed over the last two decades, but the degree of positive change has not been universal and highlights the critical need for improvement and action. Continued institution driven and collaborative strategies are essential to promote diversity in recruitment across all surgical specialties that has implications on our future workforce and surgical leadership.
Elimination of hepatitis B virus infection in children: experience and challenge in China
Authors: Tang Jie , Luo Yu-Qian , Zhou Yi-Hua
Published: October 2021

Chronic hepatitis B virus (HBV) infection is a serious health issue because of its severe sequelae. Prevention of mother-to-child transmission (MTCT) of HBV is critical to eliminate chronic HBV infection. Here, we reviewed the progress toward the elimination of HBV infection in children in China in the recent decade. A universal hepatitis B vaccination program started from 2002 has been intensified, with the coverage of timely birth dose >95% of all newborn infants from 2012. Since 2011, China has taken a nationwide program to administer hepatitis B immunoglobulin (HBIG) with free of charge in all neonates of HBV-infected mothers, leading to a significant increment of timely use of HBIG. The prevalence of hepatitis B surface antigen (HBsAg) was declined from around 10% among children in 1980s to <0.5% among children born after 2011. Administration of oral antiviral agents in HBV-infected pregnant women with HBV DNA >2 × 105 U/mL during the third trimester is increasing, which will further reduce MTCT of HBV. However, there are some challenges in the elimination of HBV infection in children, which need to overcome by the concerted efforts. Nevertheless, it is anticipated that China will achieve the goal set by the World Health Organization that the prevalence of HBsAg in children aged <5 years is ≤0.1% by 2030.
Risk factors of sudden cardiac death in hypertrophic cardiomyopathy
Authors: Hong Ying , Su Wilber W. , Li Xiaoping
Published: October 2021

Purpose of review

Hypertrophic cardiomyopathy (HCM) is one of the leading causes of sudden cardiac death (SCD) in younger people and athletes. It is crucial to identify the risk factors for SCD in individuals with HCM. This review, based on recent systematic literature studies, will focus on the risk factors for SCD in patients with HCM.

Recent findings

An increasing number of studies have further explored the risk factors for SCD in patients with HCM, and new risk markers have emerged accordingly. In addition, more accurate SCD risk estimation and stratification methods have been proposed and continuously improved.

The identification of independent risk factors for HCM-related SCD would likely contribute to risk stratification. However, it is difficult to predict SCD with absolute certainty, as the annual incidence of SCD in adult patients with HCM is approximately 1%. The review discusses the established risk factors, such as a family history of SCD, unexplained syncope and some new risk factors. Taken together, the findings of this review demonstrate that there is a need for further research on individual risk factors and that SCD risk stratification in HCM patients remains a clinical challenge.
Total Intravenous Anesthesia in a Malignant Hyperthermia-Susceptible Patient with Klinefelter Syndrome Undergoing Orthognathic Surgery
Authors: Lee Ju-Young , Choi Min Ho , Park Je-Uk
Published: October 2021

A patient with Klinefelter syndrome and skeletal Class III malocclusion experienced a malignant hyperthermia-like reaction while undergoing orthognathic surgery. The patient fully recovered after prompt diagnosis and management, and surgery was reattempted under total intravenous anesthesia. The patient was discharged without any anesthetic complications and was satisfied with the surgical results. This is the first described case of a malignant hyperthermia-like event in a patient with Klinefelter syndrome. Total intravenous anesthesia may be safely administered in malignant hyperthermia-susceptible patients who require orthognathic surgery.
Preregistration in diverse contexts: a preregistration template for the application of cognitive models
Authors: Crüwell Sophia , Evans Nathan J.
Published: October 2021

In recent years, open science practices have become increasingly popular in psychology and related sciences. These practices aim to increase rigour and transparency in science as a potential response to the challenges posed by the replication crisis. Many of these reforms—including the increasingly usedpreregistration—have been designed for purely experimental work that tests straightforward hypotheses with standard inferential statistical analyses, such as assessing whether an experimental manipulation has an effect on a variable of interest. But psychology is a diverse field of research. The somewhat narrow focus of the prevalent discussions surrounding and templates for preregistration has led to debates on how appropriate these reforms are for areas of research with more diverse hypotheses and more intricate methods of analysis, such as cognitive modelling research within mathematical psychology. Our article attempts to bridge the gap between open science and mathematical psychology, focusing on the type of cognitive modelling that Crüwellet al.(Crüwell S, Stefan AM, Evans NJ. 2019 Robust standards in cognitive science.Comput. Brain Behav.2, 255–265) labelledmodel application, where researchers apply a cognitive model as ameasurement toolto test hypotheses about parameters of the cognitive model. Specifically, we (i) discuss several potential researcher degrees of freedom within model application, (ii) provide the first preregistration template for model application and (iii) provide an example of a preregistered model application using our preregistration template. More broadly, we hope that our discussions and concrete proposals constructively advance the mostly abstract current debate surrounding preregistration in cognitive modelling, and provide a guide for how preregistration templates may be developed in other diverse or intricate research contexts.
Tourism and urban development as drivers for invertebrate diversity loss on tropical islands
Authors: Steibl Sebastian , Franke Jonas , Laforsch Christian
Published: October 2021

Oceanic islands harbour a disproportionately high number of endemic and threatened species. Rapidly growing human populations and tourism are posing an increasing threat to island biota, yet the ecological consequences of these human land uses on small oceanic island systems have not been quantified. Here, we investigated and compared the impact of tourism and urban island development on ground-associated invertebrate biodiversity and habitat composition on oceanic islands. To disentangle tourism and urban land uses, we investigated Indo-Pacific atoll islands, which either exhibit only tourism or urban development, or remain uninhabited. Within the investigated system, we show that species richness, abundance and Shannon diversity of the investigated invertebrate community are significantly decreased under tourism and urban land use, relative to uninhabited islands. Remote-sensing-based spatial data suggest that habitat fragmentation and a reduction in vegetation density are having significant effects on biodiversity on urban islands, whereas land use/cover changes could not be linked to the documented biodiversity loss on tourist islands. This offers the first direct evidence for a major terrestrial invertebrate loss on remote oceanic atoll islands due to different human land uses with yet unforeseeable long-term consequences for the stability and resilience of oceanic island ecosystems.
Muscular adaptations in swimming scale worms (Polynoidae, Annelida)
Authors: Allentoft-Larsen Marc C. , Gonzalez Brett C. , Daniels Joost , Katija Kakani , Osborn Karen , Worsaae Katrine
Published: October 2021

Annelids are predominantly found along with the seafloor, but over time have colonized a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuous swimming behaviour required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea or caves and which exhibit crawling, occasional swimming or continuous swimming, respectively. Their parapodial musculature was reconstructed using microCT and computational three-dimensional analyses, and the muscular functions were interpreted from video recordings of their locomotion. Since most benthic scale worms are able to swim for short distances using body and parapodial muscle movements, suitable musculature for swimming is already present. Our results indicate that rather than rearrangements or addition of muscles, a shift to a pelagic lifestyle is mainly accompanied by structural loss of muscle bundles and density, as well as elongation of extrinsic dorsal and ventral parapodial muscles. Our study documents clear differences in locomotion and musculature among closely related annelids with different lifestyles as well as points to myoanatomical adaptations for accessing the water column.
Social context affects camouflage in a cryptic fish species
Authors: Encel Stella A. , Ward Ashley J. W.
Published: October 2021

Crypsis, or the ability to avoid detection and/or recognition, is an important and widespread anti-predator strategy across the animal kingdom. Many animals are able to camouflage themselves by adapting their body colour to the local environment. In particular, rapid changes in body colour are often critical to the survival of cryptic prey which rely on evading detection by predators. This is especially pertinent for animals subject to spatio-temporal variability in their environment, as they must adapt to acute changes in their visual surroundings. However, which features of the local environment are most relevant is not well understood. In particular, little is known about how social context interacts with other environmental stimuli to influence crypsis. Here, we use a common cryptic prey animal, the goby (
Pseudogobius
species 2) to examine how the presence and body colour of conspecifics influence the rate and extent to which gobies change colour. We find that solitary gobies change colour to match their background faster and to a greater extent than gobies in pairs. Further, we find that this relationship holds irrespective of the colour of nearby conspecifics. This study demonstrates the importance of social context in mediating colour change in cryptic animals.
Post-bifurcation behaviour of elasto-capillary necking and bulging in soft tubes
Authors: Emery Dominic , Fu Yibin
Published: October 2021

Previous linear bifurcation analyses have evidenced that an axially stretched soft cylindrical tube may develop an infinite-wavelength (localized) instability when one or both of its lateral surfaces are under sufficient surface tension. Phase transition interpretations have also highlighted that the tube admits a final evolved ‘two-phase’ state. How the localized instability initiates and evolves into the final ‘two-phase’ state is still a matter of contention, and this is the focus of the current study. Through a weakly nonlinear analysis conducted for a general material model, the initial
sub-critical
bifurcation solution is found to be localized bulging or necking depending on whether the axial stretch is greater or less than a certain threshold value. At this threshold value, an exceptionally
super-critical
kink-wave solution arises in place of localization. A thorough interpretation of the anticipated post-bifurcation behaviour based on our theoretical results is also given, and this is supported by finite-element method simulations.
Shallow water theory for structured bathymetry
Authors: Marangos C. , Porter R.
Published: October 2021

A shallow water theory is developed which applies to surface wave propagation over structured bathymetry comprising rapid abrupt fluctuations in depth between two smoothly varying levels. Using a homogenization approach coupled to the depth-averaging process which underpins shallow water modelling, governing equations for the wave elevation are derived which explicitly relate local spatially varying anisotropy of wave speeds to properties of the microstructured bed. The model is applied to two water wave scattering problems both to demonstrate the complex wave propagation characteristics exhibited by structured beds and to provide examples of how to use structured beds to engineer bespoke wave propagation. This includes propagating waves with practically zero reflection and loss of form through circular bends in channels.
Vassiliev measures of complexity of open and closed curves in 3-space
Authors: Panagiotou Eleni , Kauffman Louis H.
Published: October 2021

In this article, we define Vassiliev measures of complexity for open curves in 3-space. These are related to the coefficients of the enhanced Jones polynomial of open curves in 3-space. These Vassiliev measures are continuous functions of the curve coordinates; as the ends of the curve tend to coincide, they converge to the corresponding Vassiliev invariants of the resulting knot. We focus on the second Vassiliev measure from the enhanced Jones polynomial for closed and open curves in 3-space. For closed curves, this second Vassiliev measure can be computed by a Gauss code diagram and it has an integral formulation, the double alternating self-linking integral. The double alternating self-linking integral is a topological invariant of closed curves and a continuous function of the curve coordinates for open curves in 3-space. For polygonal curves, the double alternating self-linking integral obtains a simpler expression in terms of geometric probabilities.
Influence of the growth gradient on surface wrinkling and pattern transition in growing tubular tissues
Authors: Liu Rui-Cheng , Liu Yang , Cai Zongxi
Published: October 2021

Growth-induced pattern formations in curved film-substrate structures have attracted extensive attention recently. In most existing literature, the growth tensor is assumed to be homogeneous or piecewise homogeneous. In this paper, we aim at clarifying the influence of a growth gradient on pattern formation and pattern evolution in bilayered tubular tissues under plane-strain deformation. In the framework of finite elasticity, a bifurcation condition is derived for a general material model and a generic growth function. Then we suppose that both layers are composed of neo-Hookean materials. In particular, the growth function is assumed to decay linearly either from the inner surface or from the outer surface. It is found that a gradient in the growth has a weak effect on the critical state, compared with the homogeneous growth type where both layers share the same growth factor. Furthermore, a finite-element model is built to validate the theoretical model and to investigate the post-buckling behaviours. It is found that the associated pattern transition is not controlled by the growth gradient but by the ratio of the shear modulus between two layers. Different morphologies can occur when the modulus ratio is varied. The current analysis could provide useful insight into the influence of a growth gradient on surface instabilities and suggests that a homogeneous growth field may provide a good approximation on interpreting complicated morphological formations in multiple systems.
A Bose–Einstein condensate is a Bose condensate in the laboratory ground state
Authors: McPhail A. V. H. , Hoogerland M. D.
Published: October 2021

Bose–Einstein condensates of weakly interacting, ultra-cold atoms have become a workhorse for exploring quantum effects on atomic motion, but does this condensate need to be in the ground state of the system? Researchers often perform transformations so that their Hamiltonians are easier to analyse. However, changing Hamiltonians can require an energy shift. We show that transforming into a rotating or oscillating frame of reference of a Bose condensate does not then satisfy Einstein’s requirement that a condensate exists in the zero kinetic energy state. We show that Bose condensation can occur above the ground state and at room temperature, referring to recent literature.
PT-symmetry and supersymmetry: interconnection of broken and unbroken phases
Authors: Pal Adipta , Modak Subhrajit , Shukla Aradhya , Panigrahi Prasanta K.
Published: October 2021

The broken and unbroken phases ofPTand supersymmetry in optical systems are explored for a complex refractive index profile in the form of a Scarf potential, under the framework of supersymmetric quantum mechanics. The transition from unbroken to the broken phases ofPT-symmetry, with the merger of eigenfunctions near the exceptional point is found to arise from two distinct realizations of the potential, originating from the underlying supersymmetry. Interestingly, inPT-symmetric phase, spontaneous breaking of supersymmetry occurs in a parametric domain, possessing non-trivial shape invariances, under reparametrization to yield the corresponding energy spectra. One also observes a parametric bifurcation behaviour in this domain. Unlike the real Scraf potential, inPT-symmetric phase, a connection between complex isospecrtal superpotentials and modified Korteweg-de Vries equation occurs, only with certain restrictive parametric conditions. In the brokenPT-symmetry phase, supersymmetry is found to be intact in the entire parameter domain yielding the complex energy spectra, with zero-width resonance occurring at integral values of a potential parameter.
Genomic analysis of distinct bleaching tolerances among cryptic coral species
Authors: Rose Noah H. , Bay Rachael A. , Morikawa Megan K. , Thomas Luke , Sheets Elizabeth A. , Palumbi Stephen R.
Published: October 2021

Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the
Acropora hyacinthus
species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener,
Acropora millepora
. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.
Grand challenges in biodiversity–ecosystem functioning research in the era of science–policy platforms require explicit consideration of feedbacks
Authors: O'Connor Mary I. , Mori Akira S. , Gonzalez Andrew , Dee Laura E. , Loreau Michel , Avolio Meghan , Byrnes Jarrett E. K. , Cheung William , Cowles Jane , Clark Adam T. , Hautier Yann , Hector Andrew , Komatsu Kimberly , Newbold Tim , Outhwaite Charlotte L. , Reich Peter B. , Seabloom Eric , Williams Laura , Wright Alexandra , Isbell Forest
Published: October 2021

Feedbacks are an essential feature of resilient socio-economic systems, yet the feedbacks between biodiversity, ecosystem services and human wellbeing are not fully accounted for in global policy efforts that consider future scenarios for human activities and their consequences for nature. Failure to integrate feedbacks in our knowledge frameworks exacerbates uncertainty in future projections and potentially prevents us from realizing the full benefits of actions we can take to enhance sustainability. We identify six scientific research challenges that, if addressed, could allow future policy, conservation and monitoring efforts to quantitatively account for ecosystem and societal consequences of biodiversity change. Placing feedbacks prominently in our frameworks would lead to (i) coordinated observation of biodiversity change, ecosystem functions and human actions, (ii) joint experiment and observation programmes, (iii) more effective use of emerging technologies in biodiversity science and policy, and (iv) a more inclusive and integrated global community of biodiversity observers. To meet these challenges, we outline a five-point action plan for collaboration and connection among scientists and policymakers that emphasizes diversity, inclusion and open access. Efforts to protect biodiversity require the best possible scientific understanding of human activities, biodiversity trends, ecosystem functions and—critically—the feedbacks among them.