bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction
Authors: Crawford Jake , Chikina Maria , Greene Casey S.
Published: June 2023

Motivation

Most models can be fit to data using various optimization approaches. While model choice is frequently reported in machine-learning-based research, optimizers are not often noted. We applied two different implementations of LASSO logistic regression implemented in Python’s scikit-learn package, using two different optimization approaches (coordinate descent and stochastic gradient descent), to predict driver mutation presence or absence from gene expression across 84 pan-cancer driver genes. Across varying levels of regularization, we compared performance and model sparsity between optimizers.

Results

After model selection and tuning, we found that coordinate descent (implemented in theliblinearlibrary) and SGD tended to perform comparably.liblinearmodels required more extensive tuning of regularization strength, performing best for high model sparsities (more nonzero coefficients), but did not require selection of a learning rate parameter. SGD models required tuning of the learning rate to perform well, but generally performed more robustly across different model sparsities as regularization strength decreased. Given these tradeoffs, we believe that the choice of optimizers should be clearly reported as a part of the model selection and validation process, to allow readers and reviewers to better understand the context in which results have been generated.

Availability and implementation

The code used to carry out the analyses in this study is available athttps://github.com/greenelab/pancancer-evaluation/tree/master/01_stratified_classification. Performance/regularization strength curves for all genes in the Vogelstein et al. 2013 dataset are available athttps://doi.org/10.6084/m9.figshare.22728644.
Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals
Authors: Jones Benjamin T , Han Jaeil , Zhang He , Hammer Robert E. , Evers Bret M. , Rakheja Dinesh , Acharya Asha , Mendell Joshua T.
Published: June 2023

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion ofZswim8, which encodes an essential TDMD factor. Loss ofZswim8resulted in developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in co-transcribed clusters and examples in which TDMD underlies ‘arm switching’, a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth ofZswim8null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
Gradient organisation of functional connectivity within resting state networks is present from 25 weeks gestation in the human fetal brain
Authors: Moore Jucha Willers , Wilson Siân , Oldehinkel Marianne , Cordero-Grande Lucilio , Uus Alena , Kyriakopoulou Vanessa , Duff Eugene P , O’Muircheartaigh Jonathan , Rutherford Mary A , Andreae Laura C , Hajnal Joseph V , Edwards A David , Beckmann Christian F , Arichi Tomoki , Karolis Vyacheslav R
Published: June 2023

During the third trimester of human gestation, the structure and function of the fetal brain is developing rapidly, laying the foundation for its connectivity framework across the lifespan. During this juncture, resting state functional MRI can be used to identify resting state networks (RSNs) which mature across gestation to resemble canonical RSNs at full term. However, the emergence of finer grain organisation of connectivity within these RSNs in the fetal brain is unknown. Using in-utero resting state fMRI, we performed connectopic mapping analysis to explore the presence of gradients in functional connectivity organisation of 11 cortical RSNs, known as connectopic maps in fetuses aged 25-37 weeks gestation (GW). We hypothesised that, if present, development of connectopic maps would be network specific in the third trimester of gestation, such that this property would be present within the earlier maturing primary sensory and motor networks before those associated with higher association function. In keeping with this, we found smooth connectopic maps in all of the studied RSNs from 25 GW, with the most spatially consistency across gestational age in the primary sensory and motor networks. Voxel-wise permutation testing of the connectopic maps identified local clusters of voxels within networks that significantly covaried with age, specifically in multisensory processing areas, suggesting multisensory processing may be developing during this period. Our analysis shows that functional gradient organisation is already established in the fetal brain and develops throughout gestation, which has strong implications for understanding how cortical organisation subserves the emergence of behaviour in the ensuing period.
Cytoplasmic redox imbalance in the thioredoxin system activates Hsf1 and results in hyperaccumulation of the sequestrase Hsp42 with misfolded proteins
Authors: Gonçalves Davi , Peffer Sara , Morano Kevin A.
Published: June 2023

Cells employ multiple systems to maintain homeostasis when experiencing environmental stress. For example, the folding of nascent polypeptides is exquisitely sensitive to proteotoxic stressors including heat, pH and oxidative stress, and is safeguarded by a network of protein chaperones that concentrate potentially toxic misfolded proteins into transient assemblies to promote folding or degradation. The redox environment itself is buffered by both cytosolic and organellar thioredoxin and glutathione pathways. How these systems are linked is poorly understood. Here, we determine that specific disruption of the cytosolic thioredoxin system resulted in constitutive activation of the heat shock response inSaccharomyces cerevisiaeand accumulation of the sequestrase Hsp42 into an exaggerated and persistent juxtanuclear quality control (JUNQ) compartment. Terminally misfolded proteins also accumulated in this compartment in thioredoxin reductase (TRR1)-deficient cells, despite apparently normal formation and dissolution of transient cytoplasmic quality control (CytoQ) bodies during heat shock. Notably, cells lackingTRR1andHSP42exhibited severe synthetic slow growth exacerbated by oxidative stress, signifying a critical role for Hsp42 under redox challenged conditions. Finally, we demonstrated that Hsp42 localization patterns intrr1Δcells mimic those observed in chronically aging and glucose-starved cells, linking nutrient depletion and redox imbalance with management of misfolded proteins via a mechanism of long-term sequestration.
Cell type and condition specific functional annotation of schizophrenia associated non-coding genetic variants
Authors: Rummel Christine K. , Gagliardi Miriam , Herholt Alexander , Ahmad Ruhel , Murek Vanessa , Weigert Liesa , Hausruckinger Anna , Maidl Susanne , Jimenez-Barron Laura , Trastulla Lucia , Eder Mathias , Rossner Moritz , Ziller Michael J.
Published: June 2023

Schizophrenia (SCZ) is a highly polygenic disease and genome wide association studies have identified thousands of genetic variants that are statistically associated with this psychiatric disorder. However, our ability to translate these associations into insights on the disease mechanisms has been challenging since the causal genetic variants, their molecular function and their target genes remain largely unknown. In order to address these questions, we established a functional genomics pipeline in combination with induced pluripotent stem cell technology to functionally characterize ~35,000 non-coding genetic variants associated with schizophrenia along with their target genes. This analysis identified a set of 620 (1.7%) single nucleotide polymorphisms as functional on a molecular level in a highly cell type and condition specific fashion. These results provide a high-resolution map of functional variant-gene combinations and offer comprehensive biological insights into the developmental context and stimulation dependent molecular processes modulated by SCZ associated genetic variation.
Extracellular vesicle-mediated trafficking of developmental cues is altered during human brain disease
Authors: Pipicelli Fabrizia , Forero Andrea , Moser Sylvain , Matteo Francesco Di , Baumann Natalia , Grätz Christian , Pisfil Mariano Gonzalez , Bekjarova Zagorka , Pfaffl Michael W. , Canafoglia Laura , Pütz Benno , Kielkowski Pavel , Cernilogar Filippo M. , Maccarrone Giuseppina , Jabaudon Denis , Giaimo Rossella Di , Cappello Silvia
Published: June 2023

Cellular crosstalk is an essential process influenced by numerous factors including secreted vesicles that transfer nucleic acids, lipids, and proteins between cells. Extracellular vesicles (EVs) have been the center of many studies focusing on neuron-to-neuron communication, but the role of EVs in progenitor-to-neuron and -astrocyte communication and whether EVs display cell-type-specific features for cellular crosstalk during neurogenesis is unknown. Here, using human-derived cerebral organoids, neural progenitors, neurons, and astrocytes, we found that many proteins coded by genes associated with neurodevelopmental disorders are transported via EVs. Thus, we characterized the protein content of EVs and showed their cell type-specific dynamics and function during brain development. Changes in the physiological crosstalk between cells can lead to neurodevelopmental disorders. EVs from patients with epilepsy were found altered in composition and function. Alterations in the intracellular and extracellular compartments highlighted a clear dysregulation of protein trafficking. This study sheds new light on the biology of EVs during brain development and neurodevelopmental disorders.

Abstract Figure

Graphical abstract

(left) EV uptake mechanism varies depending on the receiving cell type; NPCs transport neuron EVs (nEVs) and astrocyte EVs (aEVs) to the nucleus, astrocytes localize progenitor EVs (pEVs) to the cytoplasm, and neurons retain pEVs and aEVs along the plasma membrane. (right) Cerebral organoids (COs) from progressive Myoclonus Epilepsy Type I (EPM1) patients release EVs lacking key proteins in neurodevelopment and proteins necessary for EV biogenesis and release. Illustration created using BioRender.
Crystallographic and spectroscopic characterization of two 1-phenyl-1H-imidazoles: 4-(1H-imidazol-1-yl)benzaldehyde and 1-(4-methoxyphenyl)-1H-imidazole
Authors: McClements Isobelle F. , Wiesler Clara R. , Tanski Joseph M.
Published: June 2023

The title compounds, C10H8N2O, (I), and C10H10N2O, (II), are two 1-phenyl-1H-imidazole derivatives, which differ in the substituent para to the imidazole group on the arene ring, i.e. a benzaldehyde, (I), and an anisole, (II). Both molecules pack with different motifs via similar weak C—H...N/O interactions and differ with respect to the angles between the mean planes of the imidazole and arene rings [24.58 (7)° in (I) and 43.67 (4)° in (II)].
A fuzzy synthetic evaluation approach for climate for innovation measurement in construction firms
Authors: Nguyen Minh Van , Nguyen Tu Thanh
Published: June 2023

Purpose

This research aims to identify the climate for innovation variables and to propose an innovative tool to quantitatively assess the degree of climate for innovation of construction firms.

Design/methodology/approach

14 climate-for-innovation variables were identified from a literature review and discussion with experienced practitioners. After that, a questionnaire survey was developed to collect data. Factor analysis was used to analyze data gathered from 157 completed responses. Then, fuzzy synthetic evaluation (FSE) was employed to assess the degree of climate for innovation in Vietnamese construction firms.

Findings

Climate-for-innovation variables were categorized into four factors by factor analysis. The FSE analysis shows leadership is the most critical category of four factors, followed by working culture, organization and employee commitment. The calculation also illustrates that the climate for innovation in Vietnamese construction firms is at a moderate level.

Originality/value

This research is one of the first integrated climate for innovation of construction firms in a comprehensive formulation. The formulation provides the decision-makers with a reliable tool to evaluate the degree of climate for innovation, thus having appropriate strategies to develop sustainable innovation performance within their organizations.
A domain model for geometric modeling in support of the automated BIM modeling
Authors: Yang Lin , Li Qiming , Pan Wei
Published: June 2023

Purpose

This research aims to argue that manual geometric modeling is blocking the building information modeling (BIM) promotion to small-size companies. Therefore, it is necessary to study a manner of automated modeling to reduce the dependence of BIM implementation on manpower. This paper aims to make a study into such a system to propose both its theory and prototype.

Design/methodology/approach

This research took a prototyping as the methodology, which consists of three steps: (1) proposing a theoretical framework supporting automated geometric modeling process; (2) developing a prototype system based on the framework; (3) conducting a testing for the prototype system on its performance.

Findings

Previous researches into automated geometric modeling only respectively focused on a specific procedure for a particular engineering domain. No general model was abstracted to support generic geometric modeling. This paper, taking higher level of abstraction, proposed such a model that can describe general geometric modeling process to serve generic automated geometric modeling systems.

Research limitations/implications

This paper focused on only geometric modeling, skipping non-geometric information of BIM. A complete BIM model consists of geometric and non-geometric data. Therefore, the method of combination of them is on the research agenda.

Originality/value

The model proposed by this paper provide a mechanism to translate engineering geometric objects into textual representations, being able to act as the kernel of generic automated geometric modeling systems, which are expected to boost BIM promotion in industry.
Trust recovery tactics in financial services: the moderating role of service failure severity
Authors: Raza Ali , Tsiotsou Rodoula , Sarfraz Muhammad , Ishaq Muhammad Ishtiaq
Published: June 2023

Purpose

Given the fierce competition in financial services, service failure management and trust restoration tactics are becoming strategic priorities. Studies investigating trust restoration have increased over the years due to the significance of trust in services and the frequency of trust violations. Drawing on the sense-making and defensive approaches of attribution theory, this study aims to explore the effectiveness of various trust recovery tactics (e.g. apology, explanation, and investigation) in financial services considering the prevalence of service failure severity.

Design/methodology/approach

Based on a scenario-based survey, this study gathered data from 402 consumers of different banks in Pakistan. The study analyzed the data using ordinary least square regressions and structural equation modeling.

Findings

The study indicated that explanation is more effective in repairing character-competence and commitment-based trust, while investigation remained highly effective for inducing congruence-based trust. Interestingly, an apology was more effective for communication-based trust repairing, while context-based trust recovery was unaffected against all recovery tactics. Despite the prevalence of severe service failure, recovery actions proved fully effective for character-competence and commitment-based trust while partially effective for congruence-based trust recovery. This study also found that severe service failure undermines the effectiveness of recovery actions in repairing communication and context-based trust.

Originality/value

The study extends the literature on trust recovery by integrating sense-making and defensive attribution theory. The sense-making approach contributes to the existing knowledge on trust recovery by elucidating how consumers and service providers develop a shared understanding to facilitate the recovery mechanism of multidimensional trust in financial services.
Natural resource abundance and income inequality: a case study of Algeria
Authors: Chekouri Sidi Mohammed
Published: June 2023

Purpose

This study aims to present an empirical investigation on the effect of natural resource rent on income inequality in Algeria over the period 1980–2020.

Design/methodology/approach

The analysis is carried out by using the novel developed method dynamic autoregressive distributed lag (ARDL) simulation technique alongside the Kernel-based regularized least squares.

Findings

The bounds test revealed a long-run relationship between natural resource rent and income inequality. Our estimation results suggest that natural resource rent, GDP per capita and government expenditures are all associated with lower income inequality in the short and long term. Moreover, the author found that better institutional quality is more likely to reduce income inequality in Algeria. This empirical finding is further validated by the counterfactual shocks from the dynamic ARDL simulation, which reveal a significant decrease in predicted income inequality following a positive change in resource rents and a gradual, significant increase in inequality after a negative change in resource rents.

Originality/value

The present study is the first to use the dynamic ARDL model to investigate the impact of positive and negative changes in natural resource rent on income inequality in Algeria.
Dreaming digital or chasing new real pathways? Unveiling the determinants shaping Saudi youth's digital entrepreneurial intention
Authors: Aloulou Wassim , Ayadi Faouzi , Ramadani Veland , Dana Léo-Paul
Published: June 2023

Purpose

The purpose of this study, based on the theory of planned behaviour (TPB) and digital entrepreneurship literature, is to unveil the role of digital entrepreneurial knowledge and entrepreneurial role models in shaping digital entrepreneurial intentions (DEIs) among Saudi Youth through a moderated mediation perspective. This study aims to propose that the relationship between digital entrepreneurial knowledge and intention is mediated by main TPB antecedents under the moderating role of entrepreneurial role models.

Design/methodology/approach

Data were collected from a sample of 487 Saudi students from three main Saudi public universities located in Riyadh using an online survey questionnaire. By applying SEM, this study builds and tests the measurement and structural models to examine the hypothesised relationships among main variables.

Findings

Results revealed that the main antecedents of TPB (namely, attitudes towards digital entrepreneurship and perceived control behaviour) are significantly related to DEI. In addition, digital entrepreneurial knowledge indicates indirect effects on intentions via these two antecedents. However, entrepreneurial role models exert only a negative and significant moderating effect on the relationship between perceived behaviour control and DEI.

Research limitations/implications

This study contributes to the literature by showing how most of the TPB antecedents can play a mediating role between digital entrepreneurial knowledge and the intentions of Saud Youth. The main limitation of this study is that it was not possible to generalise the findings. Future research directions are proposed to add new insights.

Practical implications

The results of this study have clear implications for both theory (entrepreneurship scholars) by investigating DEI and its determinants and for practice (entrepreneurship educators and policymakers) by promoting digital entrepreneurship among youth through university-based awareness and building capability programs and curricula.

Originality/value

The study helps to understand the role of digital entrepreneurial knowledge in shaping DEI through the development of an extended TPB intention-based model. The findings also indicate that digital entrepreneurial knowledge has indirect effects on Youth's intentions. The findings show insights related to the influence of entrepreneurial role models on TPB antecedents in the transitional context of Saudi Arabia.
Sustainable innovations in Malaysia’s public procurement: strategic policy initiatives and coherences
Authors: Ishak Nur Faiza , Thiruchelvam Vinesh
Published: June 2023

Purpose

The purpose of this study is to discuss policy review in the interest of sustainable innovations in Malaysia’s public procurement. This study also offers the overall relationship between existing policies related to sustainable innovations in public procurement and the coherences towards the four dimensions of sustainable innovations.

Design/methodology/approach

This study outlines the current policies in Malaysia which are related to sustainable innovation initiatives and explores the cohesiveness that appears disconnected and understood separately. Policy content analysis is conducted on the current policies related to sustainable innovations in the context of Malaysia’s public procurement.

Findings

This study observed that the current policies related to sustainable innovations in public procurement are actually interconnected with each other through a hierarchical framework. This study also demonstrates that the 12th Malaysia Plan has comprehensively encompassed every aspect of the environment, social, economic and innovation to contribute to one primary goal – green economic growth.

Research limitations/implications

The proposed policy framework is expected to be beneficial for the administrator executive among the civil servant to connect the independent policies and, at the same time, contribute to the overall goal of green economic growth. Through a broad policy structure too, this study helps the industry player to recognize their potential in any area related to sustainable innovation.

Originality/value

The policy framework illustrated is new to the literature, especially in Malaysia’s context. The compilation of current policy grounded by the 12th Malaysia Plan has not been presented in any publications.
Does green innovation mediate corporate social responsibility and environmental performance? Empirical evidence from emerging markets
Authors: Bonsu Mandella Osei-Assibey , Guo Yongsheng , Zhu Xiaoxian
Published: June 2023

Purpose

This paper examines the mediation role of green innovation in the relationship between corporate social responsibility and environmental performance of manufacturing firms in Ghana.

Design/methodology/approach

The paper chose African emerging markets and surveyed managers from manufacturing firms. With 301 questionnaires qualified for this study’s final analyses, the authors adopt the multiple regression with mediation models to estimates the nexus among study variables.

Findings

Results evidence that both corporate social responsibility and green innovation has a positive and significant impact on environmental performance. Interestingly, the authors find that corporate social responsibility significantly improves environmental performance through green innovation indicating that firms could essentially build their dynamic resource and innovation capabilities in sustainability leading to enhanced environmental performance.

Research limitations/implications

This paper develops a dynamic resource-based view of firm environmental performance illustrating how firms use resources to build strategic capabilities for competitive advantage, which leads to improved environmental performance. The paper highlights the mediation role of green innovation on corporate social responsibility and environmental performance relationships.

Practical implications

This study's results provide significant insights to owners and managers of manufacturing companies to integrate corporate social responsibility and green innovation to ensure environmental performance and sustainability. Furthermore, policy makers should encourage green innovation when design sustainable development systems in the manufacturing industry.

Originality/value

The paper provides a valuable model showing how green innovation mediates corporate social responsibility to improve environmental performance and build competitive advantages considering both small, medium, and large manufacturing enterprises in emerging countries.
Cyberspace as a fifth dimension of national security: trade measure exceptions
Authors: Garibaldi Stephanie , Deane Felicity
Published: June 2023

Purpose

The purpose of this paper is to demonstrate that the national security exception will not allow governments to respond to cyberspace threats within the confines of the world trade organization (WTO) rules.

Design/methodology/approach

This paper is a desktop study of international trade laws with a specific focus on the convergence of cybersecurity measures and the national security exception provisions of the WTO.

Findings

The trends towards cybersecurity measures may mean there will inevitably be an evolution of trade norms. The question is, will the collective of the WTO be a part of the evolution, or merely an observer? In the authors’ view, it is crucial that it is the former.

Originality/value

This study makes three contributions. It provides a literature review and discussion on cybersecurity and the impact on trade. It demonstrates that the national security exception provision will not excuse these measures, and it aims to underscore the importance of the WTO as a community of nations where negotiation on important global issues is possible.
Toward Black abolition theory within radical abolition studies: upending practices, structures, and epistemes of domination
Authors: Turner Kia , Wallace Darion , Miles-Langaigne Danielle , Deras Essence
Published: June 2023

Purpose

This study aims to present radical abolition studies, which encourages us to (re)member that the abolition of institutions and systems is incomplete without the abolition of their attendant epistemes of domination. The authors draw on the etymology of the word radical to encourage abolitionist praxis to grab systemic harm at its epistemological roots. Within radical abolition studies, this study presents Black abolition theory, which aims to make explicit a theorization of Blackness and works to abolish the episteme of anti-Blackness.

Design/methodology/approach

This paper offers Black abolition theory within radical abolition studies to reground abolition in its Black theoretical roots and to interrogate the concept of anti-Blackness and other epistemes of domination in abolitionist study and practice. Using a close reading of W.E.B. Du Bois’ Black Reconstruction, and subsequent books and articles in abolition studies and educational studies that reference it, the authors highlight Du Bois’ original conceptualization of abolitionism as an ultimate refutation of a racial-social order and anti-Blackness. The authors then put Michael Dumas and kihana ross’ theory of BlackCrit into conversation with abolitionist and educational theory to push forward Black abolition theory.

Findings

Radical abolition studies and its attendant strand of Black abolition theory presented in this paper encourages scholars and practitioners to go beyond the dismantling of current instantiations of systemic harm for Black and other minoritized people – such as the school as it currently operates – and encourages the questioning and dismantling of the epistemes of domination sitting at the foundation of these systems of harm.

Originality/value

Black abolition theory contextualizes abolition in education by rooting abolitionist educational praxis in Black lineages. More generally, radical abolition studies encourages further research, study and collaboration in partnership with others who have historically participated in the fight against being labeled as subhuman to upend all epistemes of domination.
Developing student's skills and work readiness: an experiential learning framework
Authors: Shore Adam , Dinning Track
Published: June 2023

Purpose

This paper outlines a contemporary conceptual framework for the embedding of experiential learning into a business consultancy module. Experiential learning is a fundamental teaching approach that allows students to apply theory into a working business context.

Design/methodology/approach

As a conceptual and not an empirical paper, the methodological approach was to draw upon the literature reviewed and to build a framework to support student learning through a business consultancy module.

Findings

Exploration of the literature suggests that there are four elements critical to student learning in experiential learning environments: action, reflection, social and context. A framework has been developed utilising these elements with the interaction between the factors being key to developing learning.

Research limitations/implications

So far, the framework is conceptual, and further research is needed to explore its use when staff members are developing these types of modules and to understand the interaction of the factors over the course of the student learning experience.

Originality/value

The originality comes from the intersection and interaction between the core factors in experiential learning, which enables this framework to move thinking beyond more static models and hence work in a more fluid student learning environment.
Bone dysplasia in Hutchinson‐Gilford progeria syndrome is associated with dysregulated differentiation and function of bone cell populations
Authors: Cabral Wayne A. , Stephan Chris , Terajima Masahiko , Thaivalappil Abhirami A. , Blanchard Owen , Tavarez Urraca L. , Narisu Narisu , Yan Tingfen , Wincovitch Stephen M. , Taga Yuki , Yamauchi Mitsuo , Kozloff Kenneth M. , Erdos Michael R. , Collins Francis S.
Published: June 2023

Hutchinson‐Gilford progeria syndrome (HGPS) is a premature aging disorder affecting tissues of mesenchymal origin. Most individuals with HGPS harbor a de novo c.1824C > T (p.G608G) mutation in the gene encoding lamin A (LMNA), which activates a cryptic splice donor site resulting in production of the toxic “progerin” protein. Clinical manifestations include growth deficiency, lipodystrophy, sclerotic dermis, cardiovascular defects, and bone dysplasia. Here we utilized the LmnaG609G knock‐in (KI) mouse model of HGPS to further define mechanisms of bone loss associated with normal and premature aging disorders. Newborn skeletal staining of KI mice revealed altered rib cage shape and spinal curvature, and delayed calvarial mineralization with increased craniofacial and mandibular cartilage content. MicroCT analysis and mechanical testing of adult femurs indicated increased fragility associated with reduced bone mass, recapitulating the progressive bone deterioration that occurs in HGPS patients. We investigated mechanisms of bone loss in KI mice at the cellular level in bone cell populations. Formation of wild‐type and KI osteoclasts from marrow‐derived precursors was inhibited by KI osteoblast‐conditioned media in vitro, suggesting a secreted factor(s) responsible for decreased osteoclasts on KI trabecular surfaces in vivo. Cultured KI osteoblasts exhibited abnormal differentiation characterized by reduced deposition and mineralization of extracellular matrix with increased lipid accumulation compared to wild‐type, providing a mechanism for altered bone formation. Furthermore, quantitative analyses of KI transcripts confirmed upregulation of adipogenic genes both in vitro and in vivo. Thus, osteoblast phenotypic plasticity, inflammation and altered cellular cross‐talk contribute to abnormal bone formation in HGPS mice.
Position statement from the Editors of Anaesthesia and Anaesthesia Reports on best practice in academic medical publishing
Authors: Wiles M. D. , Klein A. A. , Shelton C. L. ,   the Editors
Published: June 2023

It is essential that academic publishing complies with the highest standards in terms of ethics, research conduct and manuscript preparation. This protects the rights and welfare of research participants, ensures the integrity of study results and aids the communication and dissemination of novel findings into clinical practice. This position statement outlines the current policies and practices of the Editors of Anaesthesia and Anaesthesia Reports in relation to academic medical publishing.
Long‐term oncological outcome of reduced‐port laparoscopic surgery (single‐incision plus one port) as a technical option for rectal cancer
Authors: Ishii Yoshiyuki , Ochiai Hiroki , Sako Hiroyuki , Watanabe Masahiko
Published: June 2023

Background

The purpose of this study was to clarify the oncological safety of reduced‐port laparoscopic surgery (single‐incision plus one port) (RPS) for patients with rectal cancer.

Methods

The clinicopathological data of 63 selected patients with clinical Stage I‐III (T1‐3 and N0‐2) rectal cancer who underwent RPS of radical anterior resection between 2012 and 2017 were retrospectively analyzed. The median distance of tumor from anal verge was 11 cm. Ordinarily, a multiport platform with three channels was placed in the 3‐cm umbilical incision, and another 5‐ or 12‐mm port was placed in the right lower abdomen.

Results

The median operative time, amount of intraoperative bleeding, number of harvested lymph nodes, and length of distal margin were 272 min, 10 mL, 22 nodes, and 4.0 cm, respectively, and there was one (2%) patient with involvement of the radial margin. There were eight patients (13%) who required additional ports, and one patient (2%) who converted to open surgery. Intra‐ and postoperative complications occurred in one (2%) and 12 patients (19%), respectively. The median length of postoperative hospital stay was 8 days. The median follow‐up period was 79 months, and incisional hernia was observed in 3 (5%) patients at the platform site not the port site, and cancer recurrence occurred in four patients (6%). The 5‐year relapse‐free and overall survival rates were 100% and 100% in the patients with pathological Stage I disease, 94% and 100% in the patients with pathological Stage II disease, and 83% and 89% in the patients with pathological Stage III disease, respectively.

Conclusion

RPS in the selected patients with rectal cancer, performed by an expert laparoscopic surgeon, may be technically safe and oncologically acceptable as well as multiport laparoscopic surgery.
Bayesian Model Selection for Generalized Linear Mixed Models
Authors: Xu Shuangshuang , Ferreira Marco A. R. , Porter Erica M. , Franck Christopher T.
Published: June 2023

We propose a Bayesian model selection approach for generalized linear mixed models (GLMMs). We consider covariance structures for the random effects that are widely used in areas such as longitudinal studies, genome-wide association studies, and spatial statistics. Since the random effects cannot be integrated out of GLMMs analytically, we approximate the integrated likelihood function using a pseudo-likelihood approach. Our Bayesian approach assumes a flat prior for the fixed effects and includes both approximate reference prior and half-Cauchy prior choices for the variances of random effects. Since the flat prior on the fixed effects is improper, we develop a fractional Bayes factor approach to obtain posterior probabilities of the several competing models. Simulation studies with Poisson GLMMs with spatial random effects and overdispersion random effects show that our approach performs favorably when compared to widely used competing Bayesian methods including deviance information criterion and Watanabe–Akaike information criterion. We illustrate the usefulness and flexibility of our approach with three case studies including a Poisson longitudinal model, a Poisson spatial model, and a logistic mixed model. Our proposed approach is implemented in the R package GLMMselect that is available on CRAN.
A Fully Integrated Pipeline for Visual Carotid Morphology Analysis
Authors: Eulzer P. , von Deylen F. , Hsu W.‐C. , Wickenhöfer R. , Klingner C. M. , Lawonn K.
Published: June 2023

Analyzing stenoses of the internal carotids – local constrictions of the artery – is a critical clinical task in cardiovascular disease treatment and prevention. For this purpose, we propose a self‐contained pipeline for the visual analysis of carotid artery geometries. The only inputs are computed tomography angiography (CTA) scans, which are already recorded in clinical routine. We show how integrated model extraction and visualization can help to efficiently detect stenoses and we provide means for automatic, highly accurate stenosis degree computation. We directly connect multiple sophisticated processing stages, including a neural prediction network for lumen and plaque segmentation and automatic global diameter computation. We enable interactive and retrospective user control over the processing stages. Our aims are to increase user trust by making the underlying data validatable on the fly, to decrease adoption costs by minimizing external dependencies, and to optimize scalability by streamlining the data processing. We use interactive visualizations for data inspection and adaption to guide the user through the processing stages. The framework was developed and evaluated in close collaboration with radiologists and neurologists. It has been used to extract and analyze over 100 carotid bifurcation geometries and is built with a modular architecture, available as an extendable open‐source platform.
Memory‐Efficient GPU Volume Path Tracing of AMR Data Using the Dual Mesh
Authors: Zellmann Stefan , Wu Qi , Ma Kwan‐Liu , Wald Ingo
Published: June 2023

A common way to render cell‐centric adaptive mesh refinement (AMR) data is to compute the dual mesh and visualize that with a standard unstructured element renderer. While the dual mesh provides a high‐quality interpolator, the memory requirements of the dual meshdata structureare significantly higher than those of the original grid, which prevents rendering very large data sets. We introduce a GPU‐friendly data structure and a clustering algorithm that allow for efficient AMR dual mesh rendering with a competitive memory footprint. Fundamentally, any off‐the‐shelf unstructured element renderer running on GPUs could be extended to support our data structure just by adding agridletelement type in addition to the standard tetrahedra, pyramids, wedges, and hexahedra supported by default. We integrated the data structure into a volumetric path tracer to compare it to various state‐of‐the‐art unstructured element sampling methods. We show that our data structure easily competes with these methods in terms of rendering performance, but is much more memory‐efficient.
Don't Peek at My Chart: Privacy‐preserving Visualization for Mobile Devices
Authors: Zhang Songheng , Ma Dong , Wang Yong
Published: June 2023

Data visualizations have been widely used on mobile devices like smartphones for various tasks (e.g., visualizing personal health and financial data), making it convenient for people to view such data anytime and anywhere. However, others nearby can also easily peek at the visualizations, resulting in personal data disclosure. In this paper, we propose a perception‐driven approach to transform mobile data visualizations into privacy‐preserving ones. Specifically, based on human visual perception, we develop a masking scheme to adjust the spatial frequency and luminance contrast of colored visualizations. The resulting visualization retains its original information in close proximity but reduces visibility when viewed from a certain distance or farther away. We conducted two user studies to inform the design of our approach (N=16) and systematically evaluate its performance (N=18), respectively. The results demonstrate the effectiveness of our approach in terms of privacy preservation for mobile data visualizations.
Illustrative Motion Smoothing for Attention Guidance in Dynamic Visualizations
Authors: Eschner Johannes , Mindek Peter , Waldner Manuela
Published: June 2023

3D animations are an effective method to learn about complex dynamic phenomena, such as mesoscale biological processes. The animators' goals are to convey a sense of the scene's overall complexity while, at the same time, visually guiding the user through a story of subsequent events embedded in the chaotic environment. Animators use a variety of visual emphasis techniques to guide the observers' attention through the story, such as highlighting, halos – or by manipulating motion parameters of the scene. In this paper, we investigate the effect of smoothing the motion of contextual scene elements to attract attention to focus elements of the story exhibiting high‐frequency motion. We conducted a crowdsourced study with 108 participants observing short animations with two illustrative motion smoothing strategies: geometric smoothing through noise reduction of contextual motion trajectories and visual smoothing through motion blur of context items. We investigated the observers' ability to follow the story as well as the effect of the techniques on speed perception in a molecular scene. Our results show that moderate motion blur significantly improves users' ability to follow the story. Geometric motion smoothing is less effective but increases the visual appeal of the animation. However, both techniques also slow down the perceived speed of the animation. We discuss the implications of these results and derive design guidelines for animators of complex dynamic visualizations.
The State of the Art in Creating Visualization Corpora for Automated Chart Analysis
Authors: Chen Chen , Liu Zhicheng
Published: June 2023

We present a state‐of‐the‐art report on visualization corpora in automated chart analysis research. We survey 56 papers that created or used a visualization corpus as the input of their research techniques or systems. Based on a multi‐level task taxonomy that identifies the goal, method, and outputs of automated chart analysis, we examine the property space of existing chart corpora along five dimensions: format, scope, collection method, annotations, and diversity. Through the survey, we summarize common patterns and practices of creating chart corpora, identify research gaps and opportunities, and discuss the desired properties of future benchmark corpora and the required tools to create them.
The survival outcomes of prophylactic lateral neck dissection for medullary thyroid carcinoma, a retrospective cohort study
Authors: Hao Weijing , Zhao Jingzhu , Guo Fengli , Zhang Jinming , Gu Pengfei , Ruan Xianhui , Zhang Wei , Zheng Xiangqian , Gao Ming
Published: June 2023

Objectives

The purpose of this study was to evaluate the benefits of prophylactic lymph node dissection in medullary thyroid carcinoma (MTC) patients without radiographically lateral neck metastases.

Design

Retrospective cohort study.

Setting

Tianjin Medical University Cancer Institute and Hospital.

Participants

Patients who underwent primary surgery for MTC between 2011 and 2019 and without structural disease of the lateral neck preoperatively.

Main outcome measures

Locoregional recurrence, disease‐free survival (DFS), and overall survival (OS) were examined.

Results

The patients were divided into two groups: the central lymph node dissection (CLND) only group and the prophylactic lateral lymph node dissection (PLND) group, which included CLND and ipsilateral lateral lymph node dissection (LLND). A total of 89 patients were included: 71 patients in the CLND group and 18 patients in the PLND group. Although there were no significant differences in age, gender, multifocality, capsule invasion or TNM stage between the two groups, the tumour size and preoperative median calcitonin levels were different. The recurrence rate was 4.2% for the CLND group and 5.6% for the PLND group (p > 0.05). DFS among the CLND and PLND groups was 95.4% and 94.4%, and OS among the groups was 100% and 94.1% (p > 0.05) at 5 years. The biochemical cure rates were similar.

Conclusions

PLND in the absence of structural disease of the lateral neck preoperatively is not associated with improved survival in patients with sporadic MTC.
SVM‐ABC based cancer microarray (gene expression) hybrid method for data classification
Authors: Gulande Punam , Awale R N
Published: June 2023

Microarray technology presents a challenge due to the large dimensionality of the data, which can be difficult to interpret. To address this challenge, the article proposes a feature extraction‐based cancer classification technique coupled with artificial bee colony optimization (ABC) algorithm. The ABC‐support vector machine (SVM) method is used to classify the lung cancer datasets and compared them with existing techniques in terms of precision, recall, F‐measure, and accuracy. The proposed ABC‐SVM has the advantage of dealing with complex nonlinear data, providing good flexibility. Simulation analysis was conducted with 30% of the data reserved for testing the proposed method. The results indicate that the proposed attribute classification technique, which uses fewer genes, performs better than other modalities. The classifiers, such as naïve Bayes, multi‐class SVM, and linear discriminant analysis, were also compared and the proposed method outperformed these classifiers and state‐of‐the‐art techniques. Overall, this study demonstrates the potential of using intelligent algorithms and feature extraction techniques to improve the accuracy of cancer diagnosis using microarray gene expression data.
Evolution of butterfly seasonal plasticity driven by climate change varies across life stages
Authors: Nielsen Matthew E. , Nylin Sören , Wiklund Christer , Gotthard Karl
Published: June 2023

Photoperiod is a common cue for seasonal plasticity and phenology, but climate change can create cue–environment mismatches for organisms that rely on it. Evolution could potentially correct these mismatches, but phenology often depends on multiple plastic decisions made during different life stages and seasons that may evolve separately. For example, Pararge aegeria (Speckled wood butterfly) has photoperiod‐cued seasonal life history plasticity in two different life stages: larval development time and pupal diapause. We tested for climate change‐associated evolution of this plasticity by replicating common garden experiments conducted on two Swedish populations 30 years ago. We found evidence for evolutionary change in the contemporary larval reaction norm—although these changes differed between populations—but no evidence for evolution of the pupal reaction norm. This variation in evolution across life stages demonstrates the need to consider how climate change affects the whole life cycle to understand its impacts on phenology.