bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses
Authors: Simmons Mark P. , Goloboff Pablo A. , Stöver Ben C. , Springer Mark S. , Gatesy John 
Published: April 2023

AbstractGene‐tree‐inference error can cause species‐tree‐inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene‐tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene‐tree branches with 0% approximate‐likelihood‐ratio‐test (SH‐like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson–Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene‐tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent‐tree clades that contradicted concatenation‐tree clades were generally less robust to gene‐tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene‐tree clades (0% SH‐like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony‐based analyses) for improving quantification of gene‐tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene‐tree‐estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.
Artificial neural network prediction of post‐thyroidectomy outcome
Authors: Tsutsumi Kotaro , Goshtasbi Khodayar , Ahmed Khwaja H. , Khosravi Pooya , Tawk Karen , Haidar Yarah M. , Tjoa Tjoson , Armstrong William B. , Abouzari Mehdi 
Published: April 2023

AbstractObjectivesThe goal of this study was to develop a deep neural network (DNN) for predicting surgical/medical complications and unplanned reoperations following thyroidectomy.Design, Setting, and ParticipantsThe 2005–2017 American College of Surgeons National Surgical Quality Improvement Program (ACS‐NSQIP) database was queried to extract patients who underwent thyroidectomy. A DNN consisting of 10 layers was developed with an 80:20 breakdown for training and testing.Main Outcome MeasuresThree primary outcomes of interest, including occurrence of surgical complications, medical complications, and unplanned reoperation were predicted.ResultsOf the 21 550 patients who underwent thyroidectomy, medical complications, surgical complications and reoperation occurred in 1723 (8.0%), 943 (4.38%) and 2448 (11.36%) patients, respectively. The DNN performed with an area under the curve of receiver operating characteristics of .783 (medical complications), .709 (surgical complications) and .703 (reoperations). Accuracy, specificity and negative predictive values of the model for all outcome variables ranged 78.2%–97.2%, while sensitivity and positive predictive values ranged 11.6%–62.5%. Variables with high permutation importance included sex, inpatient versus outpatient and American Society of Anesthesiologists class.ConclusionsWe predicted surgical/medical complications and unplanned reoperation following thyroidectomy via development of a well‐performing ML algorithm. We have also developed a web‐based application available on mobile devices to demonstrate the predictive capacity of our models in real time.
Documenting a Reduction in Signing Space in Nicaraguan Sign Language Using Depth and Motion Capture
Authors: Flaherty Molly , Sato Asha , Kirby Simon 
Published: April 2023

AbstractIn this paper, we use motion tracking technology to document the birth of a brand new language: Nicaraguan Sign Language. Languages are dynamic entities that undergo change and growth through use, transmission, and learning, but the earliest stages of this process are generally difficult to observe as most languages have been used and passed down for many generations. Here, we observe a rare case of language emergence: the earliest stages of the new sign language in Nicaragua. By comparing the signing of the oldest and youngest signers of Nicaraguan Sign Language, we can track how the language itself is changing. Using motion tracking technology, we document a decrease in the size of articulatory space of Nicaraguan Sign Language signers over time. The reduction in articulatory space in Nicaraguan Sign appears to be the joint product of several decades of use and repeated transmission of this new language.
Postural and Gestural Synchronization, Sequential Imitation, and Mirroring Predict Perceived Coupling of Dancing Dyads
Authors: Hartmann Martin , Carlson Emily , Mavrolampados Anastasios , Burger Birgitta , Toiviainen Petri 
Published: April 2023

AbstractBody movement is a primary nonverbal communication channel in humans. Coordinated social behaviors, such as dancing together, encourage multifarious rhythmic and interpersonally coupled movements from which observers can extract socially and contextually relevant information. The investigation of relations between visual social perception and kinematic motor coupling is important for social cognition. Perceived coupling of dyads spontaneously dancing to pop music has been shown to be highly driven by the degree of frontal orientation between dancers. The perceptual salience of other aspects, including postural congruence, movement frequencies, time‐delayed relations, and horizontal mirroring remains, however, uncertain. In a motion capture study, 90 participant dyads moved freely to 16 musical excerpts from eight musical genres, while their movements were recorded using optical motion capture. A total from 128 recordings from 8 dyads maximally facing each other were selected to generate silent 8‐s animations. Three kinematic features describing simultaneous and sequential full body coupling were extracted from the dyads. In an online experiment, the animations were presented to 432 observers, who were asked to rate perceived similarity and interaction between dancers. We found dyadic kinematic coupling estimates to be higher than those obtained from surrogate estimates, providing evidence for a social dimension of entrainment in dance. Further, we observed links between perceived similarity and coupling of both slower simultaneous horizontal gestures and posture bounding volumes. Perceived interaction, on the other hand, was more related to coupling of faster simultaneous gestures and to sequential coupling. Also, dyads who were perceived as more coupled tended to mirror their pair's movements.
The DACRIN data project: A process for harmonising data collection for clinical research in alcohol and other drugs services in New South Wales
Authors: Monds Lauren A. , Topp Libby , Pados Jade , Holmes Jennifer , Lintzeris Nicholas 
Published: April 2023

AbstractIntroductionStandardised data collection processes allow for harmonisation and comparison of data across different studies and services. This project aimed to develop a ‘core dataset’ to serve as the default collection when designing future studies and evaluations, building upon data routinely collected in clinical alcohol and other drugs (AOD) settings in NSW, Australia.MethodsA working group was established, comprising clinicians, researchers, data managers and consumers from public sector and non‐government organisation AOD services in the NSW Drug and Alcohol Clinical Research and Improvement Network. A series of Delphi meetings occurred to reach consensus on the data items to be included in the core dataset for three domains: demographics, treatment activity and substance use variables.ResultsThere were 20–40 attendees at each meeting. An initial consensus criterion of having received >70% of the vote was established. Given the difficulty in reaching consensus for most items, subsequently, this was changed to eliminate items that received <5 votes, after which the item receiving the most votes would be selected.Discussions and ConclusionsThis important process received considerable interest and buy‐in across the NSW AOD sector. Ample opportunity for discussion and voting was provided for the three domains of interest, allowing participants to contribute their expertise and experience to inform decisions. As such, we believe the core dataset includes the best options currently available to collect data for these domains in the NSW AOD context, and potentially more broadly. This foundational study may inform other attempts to harmonise data across AOD services.
Formalization and its Discontents: Conceptual Fallacies and Ways Forward
Authors: Gallien Max , Boogaard Vanessa van den 
Published: April 2023

ABSTRACTThe concept of formalization has long underpinned policy interventions and measures intended to connect informal entities with state institutions or formal economic structures. However, despite the policy enthusiasm, the outcomes of formalization policies have frequently been disappointing. This article argues that this disconnect lies in the concept of formalization itself and that common approaches to formalization are often rooted in three conceptual fallacies: a binary distinction between formal and informal economic actors, a lack of appreciation for the diversity of informal economic actors and the idea that ‘becoming’ formal necessarily spurs positive externalities. These conceptual confusions pay insufficient attention to contextual complexity and the political and social dynamics that shape informality in a given context and they are frequently rooted in the practicalities and power structures that shape knowledge creation in this area. This article demonstrates this through case studies of tax registration and property titling. Thus, it argues for a new research agenda on formalization that challenges both its conventional conceptual foundations and the practices of research that engage with it.
Fast and high‐quality decision‐making: The role of behavioral integration
Authors: Shepherd Neil , Mooi Erik , Elbanna Said , Lou Bowen 
Published: April 2023

AbstractDecision speed and quality are both vital for organizational survival and prosperity. However, they are assumed to be in tension, and there has been limited theory development concerning whether, and if so how, both are attainable. To address this gap, we turn to behavioral integration which captures the intensity of intrateam interactions. While behavioral integration is considered an antecedent of decision quality, it is presumed to slow decision‐making, and overall, there remains a “black box” surrounding the mechanisms, behaviors, and processes which transmit behavioral integration to decision outcomes. Our theoretical account challenges the notion of behavioral integration being an impediment to decision speed, and we present new theory and evidence—comprising a mixed‐method field study—explaining how behavioral integration acts as a key driver of both decision speed and quality while theorizing decision uncertainty as a new and important boundary condition.
Assessment of women's contribution in small‐scale fisheries in Indian Sundarbans: Issues, strategies, and way forward for sustainability
Authors: Roy Aparna , Manna Ranjan K. , Ghosh Souvik , Sahu Sanjeev K. , Das Basanta K. 
Published: April 2023

AbstractIn five islands of Indian Sundarbans, issues were identified related to women fishers associated with small‐scale fisheries (SSF) and strategies were formulated to address them in the context of “Voluntary Guidelines for Securing Sustainable Small‐Scale Fisheries” formulated by FAO being followed by signatory nations. Women were actively involved in different fisheries‐related sectors for earning their livelihoods. Despite the significant contribution of women in livelihood and nutritional security, their roles are often unrecognized leading to unfair distribution of benefits between men and women. The strategic and practical gender constraints were identified; “lack of awareness and low social participation” was the major factor as perceived by women fishers with the highest score (86.06). It was identified that gender‐sensitive extension approaches, training methodologies, and region‐specific appropriate technologies are to be applied to uplift the women members of the fishers' community associated with SSF. The aforesaid findings may be considered as precursors for formulating location‐specific strategies to address the gender gap and to create gender equality in SSF that will lead to increased productivity and sustainability of SSF across the world.
Change in monarch winter abundance over the past decade: A Red List perspective
Authors: Meehan Timothy D. , Crossley Michael S. 
Published: April 2023

Abstract
Assessing invertebrate species for the IUCN Red List under Criterion A frequently involves fitting an appropriate statistical model to available abundance data and calculating a 10‐year change (TYC) estimate from predicted abundances. When the rate of change has not been constant across the entire time series, models that accommodate variable change rates are recommended.
The monarch butterfly (Danaus plexippus) was recently added to the IUCN Red List (A2ab Endangered) based on analysis of data on winter abundances in Mexico and the western USA between 1993 and 2020. TYC estimates in the monarch assessment came from models that assumed constant change rates. We conducted a Bayesian analysis of the same data using models that accommodated variable change rates and used those models to compute TYC estimates.
Our results suggested that monarch population change rates have not been constant over the study period. The analysis yielded a model‐averaged TYC estimate of +5.23%, which was not statistically distinguishable from 0% and was considerably different from values of −46% and −72% in the assessment. The Bayesian posterior probability of a TYC value below −30% (A2ab Vulnerable) was 0.15 and that of a TYC value below −50% (A2ab Endangered) was 0.03.
We recommend that researchers evaluating monarch conservation status consider using abundance models with variable change rates, as models with constant change rates may not accurately predict the trajectory of monarch abundances into the future.
Physical therapy in diabetic foot ulcer: Research progress and clinical application
Authors: Huang Hao , Xin Rujuan , Li Xiaolong , Zhang Xinyue , Chen Zhongjian , Zhu Quangang , Tai Zongguang , Bao Leilei 
Published: April 2023

AbstractDiabetes foot ulcer (DFU) is one of the most intractable complications of diabetes and is related to a number of risk factors. DFU therapy is difficult and involves long‐term interdisciplinary collaboration, causing patients physical and emotional pain and increasing medical costs. With a rising number of diabetes patients, it is vital to figure out the causes and treatment techniques of DFU in a precise and complete manner, which will assist alleviate patients' suffering and decrease excessive medical expenditure. Here, we summarised the characteristics and progress of the physical therapy methods for the DFU, emphasised the important role of appropriate exercise and nutritional supplementation in the treatment of DFU, and discussed the application prospects of non‐traditional physical therapy such as electrical stimulation (ES), and photobiomodulation therapy (PBMT) in the treatment of DFU based on clinical experimental records in ClinicalTrials.gov.
To wear or not to wear? The influence of regulatory focus and individual cultural orientation on face mask wearing
Authors: Wen Yuan , Gupta Shipra , Coskun Merve 
Published: April 2023

AbstractDuring the COVID‐19 pandemic, much focus has been placed on the healthcare benefits of wearing face masks, yet some people resist wearing them. Though mask mandates may enhance face mask adoption in the short run, the effectiveness of such mandates, in the long run, remains questionable. Thus, understanding of psychological and sociological mechanisms behind wearing face masks becomes pertinent. This study by examining these underlying mechanisms, tends to answer two research questions: (1) How does regulatory focus impact one's behavior to wear face masks? (2) How does the impact of regulatory focus on this behavior vary under different cultural orientations? Drawing on the theory of regulatory fit, we found that people with a prevention focus will have fewer concerns about wearing face masks than people with a promotion focus. In addition, we also found that prevention‐focused people who exhibited a cultural orientation with higher levels of collectivism, masculinity, power distance, and uncertainty avoidance had fewer concerns about face mask wearing perception and were more likely to wear face masks than did promotion‐focused people with the same cultural orientation. The implications of these findings on the relevant literature and practice are also discussed.
Vulnerable consumer experiences of (dis)empowerment with consumer protection regulations
Authors: Hazzouri Mohammed El , El‐Bialy Rowan , Veresiu Ela , Main Kelley J. 
Published: April 2023

AbstractThe payday lending industry has been characterized as predatory, which has led to tougher government interventions. However, research on how stricter consumer protection regulations affect actual vulnerable consumers' lived experiences remains seriously underdeveloped. Following in‐depth interviews with financially excluded and therefore vulnerable payday loan consumers, this study finds that increased payday loan industry regulations are perceived by consumers as either empowering, disempowering, or simultaneously (dis)empowering. Accordingly, practical implications are developed to help public policy makers navigate vulnerable consumers' ambivalent relationship with consumer protection regulations.
Early‐stage detection of root freezing injuries of Scots pine (Pinus sylvestris L.) seedlings by impedance loss factor and hydraulic conductance
Authors: Repo Tapani , Ballandras Julien , Kilpeläinen Jouni , Wu Dongxia , Domisch Timo 
Published: April 2023

AbstractThe condition of the root system affects the quality of seedlings in forestry and horticulture. Previously, the electrical impedance loss factor (δ) and the reverse‐flow hydraulic conductance (Kr) of the roots of Scots pine seedlings were found to increase when assessed a few days after frost damage. How these variables change with time after the root damage is unknown. We arranged an experiment with 1.5‐year‐old Scots pine seedlings exposed to −5°C or − 30°C, with the control seedlings kept at 3°C. Then, δ and Kr of roots were monitored for 5 weeks in favorable growing conditions. The properties of the roots were observed to be in a dynamic state after the damage. A significant difference in δ was found between the test temperatures −30°C versus −5°C and 3°C (p = 0.004 and p < 0.001, respectively). The clearest effect of freezing injuries on δ of roots was observed in the first measurement 1 week after the freezing test. The temperature significantly affected Kr, too, with a significant difference between the low‐temperature treated plants −30°C versus −5°C and control (p < 0.001, respectively). The difference in Kr between −30°C and the other two temperatures increased with time and was the largest in the last samples, taken after 5 weeks. We conclude that the impedance loss factor may detect root damage if the measurements occur early enough after the damage, but a longer time difference (3–5 weeks) is needed according to the reverse‐flow hydraulic conductance.
Purple Rehmannia: Investigation of the activation of R2R3‐MYB transcription factors involved in anthocyanin biosynthesis
Authors: Zuo Xin , Miao Chunyan , Li Mingming , Gu Li , Yang Xu , Song Ci , Li Mingjie , Du Jiafang , Xie Caixia , Liu Xiangyang , Sun Hongzheng , Li Lianzhen , Zhang Zhongyi , Wang Fengqing 
Published: April 2023

AbstractEngineering anthocyanin biosynthesis in herbs could provide health‐promoting foods for improving human health. Rehmannia glutinosa is a popular medicinal herb in Asia, and was a health food for the emperors of the Han Dynasty (59 B.C.). In this study, we revealed the differences in anthocyanin composition and content between three Rehmannia species. On the 250, 235 and 206 identified MYBs in the respective species, six could regulate anthocyanin biosynthesis by activating the ANTHOCYANIDIN SYNTHASE (ANS) gene expression. Permanent overexpression of the Rehmannia MYB genes in tobacco strongly promoted anthocyanin content and expression levels of NtANS and other genes. A red appearance of leaves and tuberous/roots was observed, and the total anthocyanin content and the cyanidin‐3‐O‐glucoside content were significantly higher in the lines overexpressing RgMYB41, RgMYB42, and RgMYB43 from R. glutinosa, as well as RcMYB1 and RcMYB3 in R. chingii and RhMYB1 from R. henryi plants. Knocking out of RcMYB3 by CRISPR/Cas9 gene editing resulted in the discoloration of the R. chingii corolla lobes, and decreased the content of anthocyanin. R. glutinosa overexpressing RcMYB3 displayed a distinct purple color in the whole plants, and the antioxidant activity of the transgenic plants was significantly enhanced compared to WT. These results indicate that Rehmannia MYBs can be used to engineer anthocyanin biosynthesis in herbs to improve their additional value, such as increased antioxidant contents.