bluuebunny/crossref_metadata_2025 huggingface dataset:
Intelligence and cortical morphometry: caveats in brain-behavior associations
Authors: Lewis John D. , Imani Vandad , Tohka Jussi
Published: May 2024

It is well-established that brain size is associated with intelligence. But the relationship between cortical morphometric measures and intelligence is unclear. Studies have produced conflicting results or no significant relations between intelligence and cortical morphometric measures such as cortical thickness and peri-cortical contrast. This discrepancy may be due to multicollinearity amongst the independent variables in a multivariate regression analysis, or a failure to fully account for the relationship between brain size and intelligence in some other way. Our study shows that neither cortical thickness nor peri-cortical contrast reliably improves IQ prediction accuracy beyond what is achieved with brain volume alone. We show this in multiple datasets, with child data, developmental data, and with adult data; we show this with data acquired either at multiple sites, or at a single site; we show this with data acquired with different MRI scanner manufacturers, or with all data acquired on a single scanner; and we show this with fluid intelligence, full-scale IQ, performance IQ, and verbal IQ. But our point is not really even about IQ; rather we proffer a methodological caveat and potential explanation of the discrepancies in previous results, and which applies broadly.
Fluorescein-guided surgery in high-grade gliomas: focusing on the eloquent and deep-seated areas
Authors: Xiao Yao , Li Mingrui , Wang Xiangyu , Tan Jun , Qin Chaoying , Liu Qing
Published: May 2024

Purpose

The vital function of eloquent and deep brain areas necessitates precise treatment for tumors located in these regions. Fluorescein-guided surgery (FGS) has been widely used for high-grade gliomas (HGGs) resection. Nevertheless, the safety and efficacy of utilizing this technique for resecting brain tumors located in eloquent and deep-seated areas remain uncertain. This study aims to assess the safety and extent of resection of HGGs in these challenging tumors with fluorescein and explore its impact on patient survival.

Methods

A retrospective analysis was conducted on the clinical and radiological data of 67 consecutive patients with eloquent or deep-seated HGGs who underwent surgery between January 2020 and June 2023. Lacroix functional location grade was used to determine the eloquence of the tumors. The comparison between the fluorescence-guided surgery group (FGS, n = 32) and the conventional white-light microscopic surgery group (non-FGS, n = 35) included assessments of extent of resection (EOR), rates of gross total resection (GTR, 100%) and near-total resection (NTR, 99 to 98%), postoperative Neurologic Assessment in Neuro-Oncology (NANO) scores, overall survival (OS), and progression-free survival (PFS), to evaluate the safety and efficacy of fluorescein-guided technology in tumor resection at these specific locations.

Results

Baseline of demographics, lesion location, and pathology showed no significant difference between the two groups. GTR of the FGS group was higher than the non-FGS group (84.4% vs. 60.0%, OR 3.60, 95% CI 1.18–10.28, p < 0.05). The FGS group also showed higher GTR + NTR (EOR ≥ 98%) than the non-FGS group (93.8% vs. 65.7%, OR 7.83, 95% CI 1.86–36.85, p < 0.01). 87.0% of eloquent tumors (Lacroix grade III) in the FGS group achieved GTR + NTR, compared to 52.2% of control group (OR 6.11, 95% CI 1.50–22.78, p < 0.05). For deep-seated tumors, the rate of GTR + NTR in the two groups were 91.7% and 53.3%, respectively (OR 9.62, 95% CI 1.05–116.50, p < 0.05). No significant difference of the preoperative NANO score of the two groups was found. The postoperative NANO score of the FGS group was significantly lower than the non-FGS group (2.56 ± 1.29 vs. 3.43 ± 1.63, p < 0.05). Median OS of the FGS group was 4.2 months longer than the non-FGS group despite no statistical difference (18.2 months vs. 14.0 months, HR 0.63, 95% CI 0.36–1.11, p = 0.112), while PSF was found significantly longer in FGS patients than those of the non-FGS group (11.2 months vs. 7.7 months, HR 0.59, 95% CI 0.35–0.99, p < 0.05).

Conclusion

Sodium fluorescein-guided surgery for high-grade gliomas in eloquent and deep-seated brain regions enables more extensive resection while preserving neurologic function and improve patient survival.
Unravelling epigenetic mechanisms in Cerastoderma edule genome: a comparison of healthy and neoplastic cockles
Authors: Viña-Feás Alejandro , Temes-Rodríguez Javier , Vidal-Capón André , Novas Samuel , Rodríguez-Castro Jorge , Pequeño-Valtierra Ana , Pasantes Juan José , Tubío Jose M. C. , Garcia-Souto Daniel
Published: May 2024

Cancer is a multifaceted genetic disease characterized by the acquisition of several essential hallmarks. Notably, certain cancers exhibit horizontal transmissibility, observed across mammalian species and diverse bivalves, the latter referred to as hemic neoplasia. Within this complex landscape, epigenetic mechanisms such as histone modifications and cytosine methylation emerge as fundamental contributors to the pathogenesis of these transmissible cancers. Our study delves into the epigenetic landscape of Cerastoderma edule, focusing on whole-genome methylation and hydroxymethylation profiles in heathy specimens and transmissible neoplasias by means of Nanopore long-read sequencing. Our results unveiled a global hypomethylation in the neoplastic specimens compared to their healthy counterparts, emphasizing the role of DNA methylation in these tumorigenic processes. Furthermore, we verified that intragenic CpG methylation positively correlated with gene expression, emphasizing its role in modulating transcription in healthy and neoplastic cockles, as also highlighted by some up-methylated oncogenic genes. Hydroxymethylation levels were significantly more elevated in the neoplastic samples, particularly within satellites and complex repeats, likely related to structural functions. Additionally, our analysis also revealed distinct methylation and activity patterns in retrotransposons, providing additional insights into bivalve neoplastic processes. Altogether, these findings contribute to understanding the epigenetic dynamics of bivalve neoplasias and shed light on the roles of DNA methylation and hydroxymethylation in tumorigenesis. Understanding these epigenetic alterations holds promise for advancing our broader understanding of cancer epigenetics.
Socioeconomic equality in initiation of biologic treatment in Danish patients with inflammatory bowel disease
Authors: Petersen Sofie Ronja , Fogh Rasmussen Nathalie , Overgaard Donskov Agnete , Thygesen Lau Caspar , Olsen Kim Rose , Juel Ahrenfeldt Linda , Andersen Vibeke
Published: May 2024

Background

Low socioeconomic status is associated with disadvantages in health outcomes and delivery of medical care in patients with Inflammatory Bowel Disease (IBD). Inequality in the utilisation of biologic treatment is largely unexplored.

Aim

To explore the potential association of socioeconomic status and time to first biologic treatment in a population-based IBD cohort.

Methods

All 37,380 IBD incidences between 2000 and 2017 from the Danish National Patient Register were identified and linked to socioeconomic information including educational level, income and occupational status at diagnosis. Hazard ratios for receiving biologic treatment among socioeconomic groups were estimated using Cox proportional hazard regression.

Results

No difference in time between diagnosis and biologic treatment initiation was found comparing patients with upper secondary, vocational, or academic education to those with lower secondary education in patients with IBD. Patients with Crohn’s disease in the two highest income quartiles received biologic treatment earlier (HR 1.16; 95% CI: 1.04; 1.30 & HR 1.15; 95% CI: 1.03; 1.30). An elevated treatment rate was found for persons with “other” occupational status (unspecified source of income) compared to employed persons in patients with ulcerative colitis (HR 1.36; 95% CI: 1.11; 1.66), but not in patients with Crohn’s disease.

Conclusion

This study revealed equal initiation of biologic treatment among patients with IBD across different educational background, income and occupational status. However, results are limited to a setting with free universal healthcare coverage and treatment needs should be considered and addressed in future research.
Observing S-Matrix Pole Flow in Resonance Interplay
Authors: Chilcott Matthew , Gayen Samyajit , Croft James , Thomas Ryan , Kjærgaard Niels
Published: May 2024

We provide an overview of experiments exploring resonances in the collision of ultracold clouds of atoms. Using a laser-based accelerator that capitalises on the energy resolution provided by the ultracold atomic setting, we unveil resonance phenomena such as Feshbach and shape resonances in their quintessential form by literally photographing the halo of outgoing scattered atoms. We exploit the tunability of magnetic Feshbach resonances to instigate an interplay between scattering resonances. By experimentally recording the scattering in a parameter space spanned by collision energy and magnetic field, we capture the imprint of the S-matrix pole flow in the complex energy plane. After revisiting experiments that place a Feshbach resonance in the proximity of a shape resonance and an anti-bound state, respectively, we discuss the possibility of using S-matrix pole interplay between two Feshbach resonances to create a bound-state-in-the-continuum.
Decomposition of the mechanical stress tensor: from the compressible Navier–Stokes equation to a turbulent potential flow model
Authors: Di Nucci Carmine , Michele Simone , Di Risio Marcello
Published: May 2024

We frame the mechanical stress tensor decomposition in a general procedure which involves the Helmholtz–Hodge decomposition. We highlight the impact of the mechanical stress tensor decomposition on the Navier–Stokes equation, with emphasis on the dissipation function. For fluids with low compressibility, we draw some insights on the Reynolds Averaged Navier–Stokes equations, and on the Reynolds stress tensor decomposition. We derive a turbulent potential flow model, and investigate the transition from viscous potential flow to turbulent potential flow. Under low Mach number approximation, we apply the turbulent potential flow model to one-dimensional propagation of large amplitude pressure waves in liquid-filled pipe.
Review: Application of hydrogeological models coupled with agent-based models to address sustainable groundwater management in Latin America
Authors: Rojas Scheffer Verónica
Published: May 2024

Agent-based models (ABMs) have long been applied in economics and social science research. The combination or coupling of these models with those of natural systems is a more recent application, and their use in conjunction with groundwater flow and transport models can be considered an innovative way to take advantage of their potential. In the Latin American region, sustainable management of groundwater resources can still be considered understudied. Among other characteristics, the existence of large transboundary aquifers in the region adds a further complication for addressing the sustainability of groundwater resource use. In this type of system, the impacts of joint regulations for utilization by different countries, the diversity of socioeconomic drivers and the conservation interests of each group of users might be consistently represented and explored through flow models coupled with ABMs. This review of the scientific literature aims to compile up-to-date information regarding the application of hydrogeological models coupled with agent-based models, focusing on their contributions to the sustainable management of groundwater resources and analyzing their potential for the Latin American region.
Enhancing music rhythmic perception and performance with a VR game
Authors: Pesek Matevž , Hirci Nejc , Žnideršič Klara , Marolt Matija
Published: May 2024

This study analyzes the effect of using a virtual reality (VR) game as a complementary tool to improve users’ rhythmic performance and perception in a remote and self-learning environment. In recent years, remote learning has gained importance due to various everyday situations; however, the effects of using VR in such situations for individual and self-learning have yet to be evaluated. In music education, learning processes are usually heavily dependent on face-to-face communication with a teacher and are based on a formal or informal curriculum. The aim of this study is to investigate the potential of gamified VR learning and its influence on users’ rhythmic sensory and perceptual abilities. We developed a drum-playing game based on a tower defense scenario designed to improve four aspects of rhythmic perceptual skills in elementary school children with various levels of music learning experience. In this study, 14 elementary school children received Meta Quest 2 headsets for individual use in a 14-day individual training session. The results showed a significant increase in their rhythmical skills through an analysis of their rhythmic performance before and after the training sessions. In addition, the experience of playing the VR game and using the HMD setup was also assessed, highlighting some of the challenges of currently available affordable headsets for gamified learning scenarios.
The assessment of the impact of antiepileptic drugs on cognitive functions via N-200/P-300 potentials and neuropsychological measures
Authors: Shafiyev Javid , Karadaş Ömer
Published: May 2024

Objective

The effects of antiseizure medications (ASMs) on cognitive functions have not been fully elucidated. The primary aim of this study was to demonstrate potential changes in cognitive functions in patients diagnosed with epilepsy from both neuropsychological and electrophysiological perspectives. Our secondary objective was to assess the effects of administered ASM on cognitive functions by categorizing patients into different monotherapy and polytherapy groups.

Materials and methods

A single-center, prospective patient registry study was conducted between May 2022 and June 2023. The inclusion criteria included epilepsy patients aged 18 to 50 years who were receiving ASM) treatment, either as inpatients or outpatients, and who did not have any syndromic diagnosis that may lead to cognitive disfunciton (such as primary progressive myoclonic epilepsies, Down syndrome and so on), and did not diagnosed previously or during examination that could affect dementia or cognitive functions. Patients who were scheduled to initiate new ASM treatment were evaluated using the Montreal Cognitive Assessment (MoCA) scale and Event-Related Potentials (ERP) assessment both before commencing treatment and three months thereafter.

Results

A total of 320 participants were included in the study; 20 healthy controls and 300 epilepsy patients were included. Statistically significant differences were observed between the healthy control group and the epilepsy group in terms of average Montreal Cognitive Assessment (MoCA) scores and event-related potentials (ERPs) (n200, p300 latencies, n2p3 amplitudes) (p<0.05). Similarly, statistically significant differences were observed between the monotherapy and polytherapy groups in terms of average MoCA and ERP scores (p<0.05).

Conclusion

This study demonstrated the detrimental effects of certain ASMs, particularly topiramate and carbamazepine, on cognitive functions. Furthermore, the negative impact on cognitive performance became more pronounced with an increasing number of concurrently used ASMs (polytherapy), with topiramate showing notable effects.
Barriers and drivers to the development of an effective water reuse chain: insights from an Italian water utility
Authors: Neri Alessandra , Rizzuni Andrea , Garrone Paola , Cagno Enrico
Published: May 2024

Widespread adoption of water reuse technologies is critical to the development of a circular economy and to reduce the pressure on increasingly scarce freshwater resources. However, the adoption of water reuse technologies involves a complex and multi-level decision-making process, influenced by different factors that hinder or support such adoption, namely barriers and drivers. The present research provides a first identification of such factors from a value chain perspective. To do so, the paper first conceptualises the water reuse value chain, including the actors and stages required to bring collected wastewater to the reuse destination. It then conducts an exploratory case study in the context of an Italian water utility facing increasing water stress. External barriers such as societal perceptions and lack of demand for recycled water emerge as particularly influential in hindering the adoption of water reuse technologies. Drivers emerge from both the external and internal environment, with the level of water scarcity and the effectiveness of collaboration and coordination between different institutional and policy actors being particularly strong. Barriers and drivers are found to be of varying relevance depending on the characteristics of the facilities and the reuse value chain analysed, including the operational status of the reclamation facility, the type of final reuse, and the roles in the value chains. The paper provides relevant implications for academics, policymakers, and adopters of water reuse technologies for a more circular and environmentally sustainable water sector, offering useful insights for decision-makers in related sectors.

Graphical abstract
The importance of diversity in local food systems: a network analysis of food-related interactions in the Indigenous food system on St. Paul Island, Alaska
Authors: Zimmermann Silja , Dermody Brian J. , Davis Natalie , Divine Lauren M. , Padula Veronica M. , Lestenkof-Zacharof Kadyn , Wassen Martin J. , Dorresteijn Ine
Published: May 2024

Arctic Indigenous food systems are typified by diverse social interactions that maintain food security. Given the numerous challenges Arctic Indigenous communities face, it is important to understand diversity in these systems and how they are impacted by change. This study adopts a mixed methods approach that combines participatory methods with network analysis to assess the diversity of food-related interactions between different actor types in the mixed food system on St. Paul Island, Alaska. We conducted 36 interviews with local food system actors to identify current food security challenges and food-related interactions in the local food system. We used network analysis to investigate the diversity of interactions in the food system quantitatively. We simulated the effects of two key food security challenges (out-migration and knowledge loss) on food system diversity and explored interventions to increase diversity. Qualitative data from the same interviews were used to embed our results in the lived realities of the St. Paul Island community. Our approach reveals diverse interactions in the local food system, reflecting both subsistence and market-based elements of the St. Paul Island mixed economy. While both challenges threaten the system's diversity, out-migration presents a more immediate risk to food system diversity than knowledge loss. We advocate for targeting a combination of food system interventions at the community level to enhance food system diversity effectively. Our research contributes to understanding the importance of diversity for Arctic Indigenous food security and emphasizes the need to recognize the complex interactions between food system interventions and their implications for Arctic Indigenous communities.
CTNND1 is involved in germline predisposition to early-onset gastric cancer by affecting cell-to-cell interactions
Authors: Herrera-Pariente Cristina , Bonjoch Laia , Muñoz Jenifer , Fernàndez Guerau , Soares de Lima Yasmin , Mahmood Romesa , Cuatrecasas Miriam , Ocaña Teresa , Lopez-Prades Sandra , Llargués-Sistac Gemma , Domínguez-Rovira Xavier , Llach Joan , Luzko Irina , Díaz-Gay Marcos , Lazaro Conxi , Brunet Joan , Castillo-Manzano Carmen , García-González María Asunción , Lanas Angel , Carrillo Marta , Hernández San Gil Raquel , Quintero Enrique , Sala Nuria , Llort Gemma , Aguilera Lara , Carot Laura , Diez-Redondo Pilar , Jover Rodrigo , Ramon y Cajal Teresa , Cubiella Joaquín , Castells Antoni , Balaguer Francesc , Bujanda Luis , Castellví-Bel Sergi , Moreira Leticia
Published: May 2024

Background

CDH1 and CTNNA1 remain as the main genes for hereditary gastric cancer. However, they only explain a small fraction of gastric cancer cases with suspected inherited basis. In this study, we aimed to identify new hereditary genes for early-onset gastric cancer patients (EOGC; < 50 years old).

Methods

After germline exome sequencing in 20 EOGC patients and replication of relevant findings by gene-panel sequencing in an independent cohort of 152 patients, CTNND1 stood out as an interesting candidate gene, since its protein product (p120ctn) directly interacts with E-cadherin. We proceeded with functional characterization by generating two knockout CTNND1 cellular models by gene editing and introducing the detected genetic variants using a lentiviral delivery system. We assessed β-catenin and E-cadherin levels, cell detachment, as well as E-cadherin localization and cell-to-cell interaction by spheroid modeling.

Results

Three CTNND1 germline variants [c.28_29delinsCT, p.(Ala10Leu); c.1105C > T, p.(Pro369Ser); c.1537A > G, p.(Asn513Asp)] were identified in our EOGC cohorts. Cells encoding CTNND1 variants displayed altered E-cadherin levels and intercellular interactions. In addition, the p.(Pro369Ser) variant, located in a key region in the E-cadherin/p120ctn binding domain, showed E-cadherin mislocalization.

Conclusions

Defects in CTNND1 could be involved in germline predisposition to gastric cancer by altering E-cadherin and, consequently, cell-to-cell interactions. In the present study, CTNND1 germline variants explained 2% (3/172) of the cases, although further studies in larger external cohorts are needed.
A machine learning model for predicting the lymph node metastasis of early gastric cancer not meeting the endoscopic curability criteria
Authors: Kato Minoru , Hayashi Yoshito , Uema Ryotaro , Kanesaka Takashi , Yamaguchi Shinjiro , Maekawa Akira , Yamada Takuya , Yamamoto Masashi , Kitamura Shinji , Inoue Takuya , Yamamoto Shunsuke , Kizu Takashi , Takeda Risato , Ogiyama Hideharu , Yamamoto Katsumi , Aoi Kenji , Nagaike Koji , Sasai Yasutaka , Egawa Satoshi , Akamatsu Haruki , Ogawa Hiroyuki , Komori Masato , Akihiro Nishihara , Yoshihara Takeo , Tsujii Yoshiki , Takehara Tetsuo
Published: May 2024

Background

We developed a machine learning (ML) model to predict the risk of lymph node metastasis (LNM) in patients with early gastric cancer (EGC) who did not meet the existing Japanese endoscopic curability criteria and compared its performance with that of the most common clinical risk scoring system, the eCura system.

Methods

We used data from 4,042 consecutive patients with EGC from 21 institutions who underwent endoscopic submucosal dissection (ESD) and/or surgery between 2010 and 2021. All resected EGCs were histologically confirmed not to satisfy the current Japanese endoscopic curability criteria. Of all patients, 3,506 constituted the training cohort to develop the neural network-based ML model, and 536 constituted the validation cohort. The performance of our ML model, as measured by the area under the receiver operating characteristic curve (AUC), was compared with that of the eCura system in the validation cohort.

Results

LNM rates were 14% (503/3,506) and 7% (39/536) in the training and validation cohorts, respectively. The ML model identified patients with LNM with an AUC of 0.83 (95% confidence interval, 0.76–0.89) in the validation cohort, while the eCura system identified patients with LNM with an AUC of 0.77 (95% confidence interval, 0.70–0.85) (P = 0.006, DeLong’s test).

Conclusions

Our ML model performed better than the eCura system for predicting LNM risk in patients with EGC who did not meet the existing Japanese endoscopic curability criteria.

Mini-abstract

We developed a neural network-based machine learning model that predicts the risk of lymph node metastasis in patients with early gastric cancer who did not meet the endoscopic curability criteria.
The implementation of an inflammatory bowel disease-specific enhanced recovery after surgery protocol: an observational cohort study
Authors: Lin V. , Poulsen J. K. , Juvik A. F. , Roikjær O. , Gögenur I. , Fransgaard T.
Published: May 2024

Background

The implementation of Enhanced Recovery After Surgery (ERAS) protocols has resulted in improved postoperative outcomes in colorectal cancer surgery. The evidence regarding feasibility and impact on outcomes in surgery for inflammatory bowel disease (IBD) is limited.

Methods

We performed a retrospective observational cohort study, comparing patient trajectories before and after implementing an IBD-specific ERAS protocol at Zealand University Hospital. We assessed the occurrence of serious postoperative complications of Clavien-Dindo grade 3 or higher as our primary outcome, with postoperative length of stay in days and rate of readmissions as secondary outcomes, using χ2, Mann–Whitney test, and odds ratios adjusted for sex and age.

Results

From 2017 to 2023, 394 patients were operated on for IBD and included in our study. In the ERAS cohort, 39/250 patients experienced a postoperative complication of Clavien-Dindo grade 3 or higher compared to 27/144 patients in the non-ERAS cohort (15.6% vs. 18.8%, p = 0.420) with an adjusted odds ratio of 0.73 (95% CI 0.42–1.28). There was a significantly shorter postoperative length of stay (median 4 vs. 6 days, p < 0.001) in the ERAS cohort compared to the non-ERAS cohort. Readmission rates remained similar (22.4% vs. 16.0%, p = 0.125).

Conclusions

ERAS in IBD surgery was associated with faster patient recovery, but without an impact on the occurrence of serious postoperative complications and rate of readmissions.
Personal values and social behavior in early childhood: Understanding the contribution of social information processing and attitudes
Authors: Elizarov Einat , Ziv Yair , Benish-Weisman Maya
Published: May 2024

Values, defined by Schwartz (1994) as basic motivational cognitive structures, guide life goals, transcend contexts, and affect individuals’ courses of action differently depending on their preferred values. With young children, an important question that emerges is what factors underlie the linkages between their preferred motivations (i.e., preferred values) and their behavior tendencies in key social contexts. This study proposed one potential socio-cognitive mechanism that may explain how children’s values are linked to their prosocial and antisocial behaviors in kindergarten via their values-oriented social information processing patterns (SIP) and their attitudes toward their kindergarten. The sample included 121 children (59 girls; Mage = 67.45 months). Children’s values, values-oriented SIP patterns, and attitudes toward kindergarten class were examined in one-on-one interviews. Teachers reported on the children’s social behaviors. Results showed children’s preferences for self-transcendence values were linked to their more prosocial behaviors and less antisocial behaviors in class via their self-transcendence values-oriented SIP patterns and their positive attitudes toward kindergarten. The findings offer important insights into the socio-cognitive elements that drive values-behavior relationships, as well as the links between various facets of young children’s social cognition and their social behavior in kindergarten.
Indel variation in the mitochondrial ND5 region supports monophyly of the tribe Hippoglossoidini (sensu Vinnikov et al. 2018) within the family Pleuronectidae
Authors: Kurihara Hiroaki , Shirai Shigeru M. , Fujiwara Kunihiro , Ikeda Minoru
Published: May 2024

Indel (insertion–deletion) events observed in the genome represent irreversible mutational processes, making indel regions crucial characteristics for discussing phylogenetic relationships. The tribe Hippoglossoidini is a recently proposed taxonomic group based on the molecular phylogenetic analyses of both mitochondrial (mt) and nuclear DNA sequences. However, no synapomorphic characteristics have been identified within this tribe, either morphologically or molecularly. In the present study, we sequenced the ND5 region of mtDNA in the righteye flounder species and conducted interspecific comparisons. We found a 12 bp indel immediately upstream of the stop codon in the ND5 region. A comparative analysis of this region with outgroup species from the Paralichthyidae revealed that the indel was a unique insertion shared by the common ancestor of the Hippoglossoidini species, providing irreversible evidence to support the monophyly of this taxonomic group (synapomorphic characters).
The prognostic genes model of breast cancer drug resistance based on single-cell sequencing analysis and transcriptome analysis
Authors: Liu Yao , Dong Lun , Ma Jing , Chen Linghui , Fang Liaoqiong , Wang Zhibiao
Published: May 2024

Breast cancer (BC) represents a multifaceted malignancy, with escalating incidence and mortality rates annually. Chemotherapy stands as an indispensable approach for treating breast cancer, yet drug resistance poses a formidable challenge. Through transcriptome data analysis, we have identified two sets of genes exhibiting differential expression in this context. Furthermore, we have confirmed the overlap between these genes and those associated with exosomes, which were subsequently validated in cell lines. The investigation screened the identified genes to determine prognostic markers for BC and utilized them to formulate a prognostic model. The disparities in prognosis and immunity between the high- and low-risk groups were validated using the test dataset. We have discerned different BC subtypes based on the expression levels of prognostic genes in BC samples. Variations in prognosis, immunity, and drug sensitivity among distinct subtypes were examined. Leveraging data from single-cell sequencing and prognostic gene expression, the AUCell algorithm was employed to score individual cell clusters and analyze the pathways implicated in high-scoring groups. Prognostic genes (CCT4, CXCL13, MTDH, PSMD2, and RAB27A) were subsewoquently validated using RT-qPCR. Consequently, we have established a model for predicting prognosis in breast cancer that hinges on drug resistance and ERGs. Furthermore, we have evaluated the prognostic value of this model. The genes identified as prognostic markers can now serve as a reference for precise treatment of this condition.
Toxic tasting: how capuchin monkeys avoid grasshoppers’ chemical defenses
Authors: Rufo Henrique P. , Ferreira Luiza G. , Ottoni Eduardo B. , Falótico Tiago
Published: May 2024

Platyrrhines consume many species of arthropods in the order Orthoptera. Some species of orthopterans can produce chemical defenses that render them toxic or unpalatable and thus act as predator deterrents. These species include the stick grasshoppers (family Proscopiidae), which are widely distributed in the Caatinga biome in northeastern Brazil, which comprises part of the distribution of capuchin monkeys. Capuchin monkeys are omnivores and consume a wide variety of foods, including unpleasant-tasting, potentially toxic items, which they need to learn how to process. We describe the processing of stick grasshoppers (Stiphra sp.) by wild capuchin monkeys (Sapajus libidinosus) that live in Serra da Capivara National Park, Brazil, and compare how individuals of different age classes handle these potentially toxic food items. S. libidinosus predominantly avoided consuming the digestive tract, which contains toxic compounds, when feeding on stick grasshoppers. Immatures took longer than adults to process the stick grasshoppers, indicating that capuchins need to learn how to process the toxic digestive tract of these prey to avoid consuming it.
Prevalence of nasopharyngeal myiasis in roe deer (Capreolus capreolus) from an area with high sympatry between wild and domestic ungulates in Central Spain
Authors: Martínez-Calabuig Néstor , Panadero Rosario , Varas Gonzalo , Remesar Susana , López Ceferino M. , Saldaña Ana , Díaz Pablo , Díez-Baños Pablo , Morrondo Patrocinio , García-Dios David
Published: May 2024

Infestation by the sheep bot fly Oestrus ovis was firstly reported in a single roe deer from Central Spain in 2022. For assessing the current situation of nasal myiases in this ungulate in this area, the nasopharyngeal cavities of 184 roe deer hunted in Central Spain between January-June 2023 were examined. All larvae were recovered and morphologically identified; in addition, species identification was molecularly confirmed in a subset of specimens. Forty-four roe deer (23.9%; CI 95 17.95–30.74) were positive for different Oestrinae larval stages. Twenty-six animals (14.1%; CI 95 9.44–20.02%) were infested by the roe deer nasal bot fly (Cephenemyia stimulator) with a mean intensity of 35.2 (SD 49.71) larvae/infested animal, and eighteen (9.8%; CI 95 5.90-15.02%) roe deer harboured the sheep bot fly (O. ovis), with a mean intensity of 2.0 (SD 1.33) larvae/infested animal. No mixed infestations by both Oestrinae were found in a single animal. All larval instars (L1, L2 and L3) of both species were identified. Most C. stimulator specimens were located at the nasal turbinates, and a small percentage (3.2%) at the pharynx; all O. ovis larvae were found at the nasal turbinates. Since O. ovis is highly prevalent in sheep and goat flocks from Central Spain, the high sympatry between roe deer and small ruminant populations in the studied area may have increased the risk of cross-infection. Moreover, the finding of mature L3 of O. ovis suggests that this species can complete its life cycle in roe deer. Therefore, monitoring bot flies in sheep and goat flocks as well as in sympatric wild ruminants is strongly recommended for achieving an optimum control of nasal myiases.
Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis
Authors: Liu Ziqing , Tanke Natalie T. , Neal Alexandra , Yu Tianji , Branch Tershona , Sharma Arya , Cook Jean G. , Bautch Victoria L.
Published: May 2024

Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of S-phase proliferative tip cells relative to stalk cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip and stalk cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest and dynamics at the front. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.
Gender and endogenous knowledge inclusion for agroforestry systems improvement in Benin, West Africa
Authors: Houndjo Kpoviwanou Marie Reine Jésugnon , Wédjangnon Adigla Appolinaire , Houètchégnon Towanou , Sourou Bienvenue Nawan Kuiga , Ouinsavi Christine A. I. Nougbodé
Published: May 2024

In West Africa, and Benin particularly, local forest resources can potentially contribute to both increasing and stabilizing soil productivity. However, these resources continue to be neglected with efforts instead concentrated on promoting exotic species. This study aimed to prioritize local agroforestry species on agricultural landscape by investigating the gendered, socio-demographic and agro-pedological factors of local knowledge and use of agroforestry species amongst small-holder farmers in Benin. An agroforestry inventory combined with an ethno-agroforestry survey was conducted on 364 farms with 364 farmers. A cluster analysis based on farmers' socio-demographic and agroecological factors was used to cluster farmers into two homogeneous agroforestry systems. Median score, species diversity and ecological networks were established for these two systems. Results illustrate that gendered difference exist between the priority that farmers give to multi-purpose species and this prioritization depends on priority ecosystem services for farmers and gender. Therefore, it would be useful first to consider gender and specific needs of each category of farmer to optimize the choice of agroforestry species to be promoted in such systems. The successful introduction of identified species through extension programs requires more advanced research related to the real contribution of these species to farmland fertilization, as well as the nutrient transmission pathways to associated crops in an agroforestry system to address simultaneously specific ecological, economic and socio-cultural sustainability criteria, as well as improved crop production.
A Pilot Randomized Controlled Trial of the Family Assessment and Feedback Intervention (FAFI): Effects on Mental Health Literacy and Attitudinal Engagement with Health Supports and Services
Authors: Ivanova Masha Y. , Hall Allison , Weinberger Stanley , Buckingham Sara L. , Copeland William E. , Crockett Phoenix , Dainer-Best Justin , D’Alberto Casey , Dewey Lauren , Foret DeShan , Galano Maria , Goodrich Lisa , Holly Lindsay , Lane Nalini Emily , Leahy Maureen , Lerner Mathew , Marsh Jasmine , McGinnis Ellen W. , Paiva-Salisbury Melissa , Shaw Judith S. , Swift Pamela , Tinker Rebekah , Hudziak James J.
Published: May 2024

This randomized controlled trial tested the Family Assessment and Feedback Intervention (FAFI), a new intervention to enhance family engagement with emotional and behavioral health services. The FAFI is a guided conversation with families about results of their multidimensional assessment that is set in the context of motivational enhancement. It differs from other assessment-with-feedback interventions by extending the focus of assessment beyond the target child to parents and the family environment, addressing parental emotional and behavioral problems and competencies, spanning a broad range of children’s and parents’ strengths and difficulties, and being generalizable to many settings and practitioners. Participants were 81 families in primary care pediatrics. The FAFI was associated with a significant increase in parental mental health literacy and with an increase in parental attitudinal engagement with health supports and services that closely approached statistical significance (p = .052), while controlling for children’s age and gender and family socioeconomic status.
Non-linear Mendelian randomization: detection of biases using negative controls with a focus on BMI, Vitamin D and LDL cholesterol
Authors: Hamilton Fergus W. , Hughes David A. , Spiller Wes , Tilling Kate , Davey Smith George
Published: May 2024

Mendelian randomisation (MR) is an established technique in epidemiological investigation, using the principle of random allocation of genetic variants at conception to estimate the causal linear effect of an exposure on an outcome. Extensions to this technique include non-linear approaches that allow for differential effects of the exposure on the outcome depending on the level of the exposure. A widely used non-linear method is the residual approach, which estimates the causal effect within different strata of the non-genetically predicted exposure (i.e. the “residual” exposure). These “local” causal estimates are then used to make inferences about non-linear effects. Recent work has identified that this method can lead to estimates that are seriously biased, and a new method—the doubly-ranked method—has been introduced as a possibly more robust approach. In this paper, we perform negative control outcome analyses in the MR context. These are analyses with outcomes onto which the exposure should have no predicted causal effect. Using both methods we find clearly biased estimates in certain situations. We additionally examined a situation for which there are robust randomised controlled trial estimates of effects—that of low-density lipoprotein cholesterol (LDL-C) reduction onto myocardial infarction, where randomised trials have provided strong evidence of the shape of the relationship. The doubly-ranked method did not identify the same shape as the trial data, and for LDL-C and other lipids they generated some highly implausible findings. Therefore, we suggest there should be extensive simulation and empirical methodological examination of performance of both methods for NLMR under different conditions before further use of these methods. In the interim, use of NLMR methods needs justification, and a number of sanity checks (such as analysis of negative and positive control outcomes, sensitivity analyses excluding removal of strata at the extremes of the distribution, examination of biological plausibility and triangulation of results) should be performed.
Sampling efficiency and nucleic acid stability during long-term sampling with different bioaerosol samplers
Authors: Bøifot Kari Oline , Skogan Gunnar , Dybwad Marius
Published: May 2024

Aerosol microbiome studies have received increased attention as technological advancements have made it possible to dive deeper into the microbial diversity. To enhance biomass collection for metagenomic sequencing, long-term sampling is a common strategy. While the impact of prolonged sampling times on microorganisms’ culturability and viability is well-established, its effect on nucleic acid stability remains less understood but is essential to ensure representative sample collection. This study evaluated four air samplers (SKC BioSampler, SASS3100, Coriolis μ, BioSpot-VIVAS 300-P) against a reference sampler (isopore membrane filters) to identify nucleic acid stability during long-term sampling. Physical sampling efficiencies determined with a fluorescent tracer for three particle sizes (0.8, 1, and 3 μm), revealed high efficiencies (> 80% relative to reference) for BioSampler, SASS3100, and BioSpot-VIVAS for all particle sizes, and for Coriolis with 3 μm particles. Coriolis exhibited lower efficiency for 0.8 μm (7%) and 1 μm (50%) particles. During 2-h sampling with MS2 and Pantoea agglomerans, liquid-based collection with Coriolis and BioSampler showed a decrease in nucleic acid yields for all test conditions. BioSpot-VIVAS displayed reduced sampling efficiency for P. agglomerans compared to MS2 and the other air samplers, while filter-based collection with SASS3100 and isopore membrane filters, showed indications of DNA degradation for 1 μm particles of P. agglomerans after long-term sampling. These findings show that long-term air sampling affects nucleic acid stability in both liquid- and filter-based collection methods. These results highlight bias produced by bioaerosol collection and should be considered when selecting an air sampler and interpreting aerosol microbiome data.
Quantum Reference Frames on Finite Homogeneous Spaces
Authors: Głowacki Jan , Loveridge Leon , Waldron James
Published: May 2024

We present an operationally motivated treatment of quantum reference frames in the setting that the frame is a covariant positive operator valued measure (POVM) on a finite homogeneous space, generalising the principal homogeneous spaces studied in previous work. We focus on the case that the reference observable is the canonical covariant projection valued measure on the given space, and show that this gives rise to a rank-one covariant POVM on the group, which can be seen as a system of coherent states.
Farming non-typical sentient species: ethical framework requires passing a high bar
Authors: Mullan Siobhan , Nogueira Selene S. C. , Nogueira-Filho Sérgio , Zanella Adroaldo , Rooney Nicola , Held Suzanne D. E. , Mendl Michael
Published: May 2024

More widespread farming of species not typically used as livestock may be part of a sustainable approach for promoting human health and economic prosperity in a world with an increasing population; a current example is peccary farming in the Neotropics. Others have argued that species that are local to a region and which are usually not farmed should be considered for use as livestock. They may have a more desirable nutrient profile than species that are presently used as livestock. It may also reduce the pressure from hunting on other wild species, and cause less environmental damage than exotic species. We propose a sentiocentric utilitarian framework that could be used to decide whether species that are local, but generally not used as livestock, should be farmed. To illustrate the use of our decision-making framework, we employ two contrasting neotropical case studies: the Spotted Paca (Cuniculus paca) and the Capybara (Hydrochoerus hydrochaeris). We argue that it may be acceptable to use non-sentient species that are typically not farmed as livestock. However, research should determine whether farming them offers human, environmental or sustainability benefits. In addition, we recommend that if invertebrate species are considered for farming, research should be conducted to determine the likelihood that they are sentient. Finally, given the ethical failings of current livestock farming practices, we argue that a high bar must be met if ‘new’ species that are sentient are to be farmed.
Psychometric Evaluation of the Metacognitions Questionnaire – Short Form (MCQ-30) in Generalized Anxiety Disorder: Reliability, Validity and Utility in a Clinical Sample
Authors: White Julia A. , Rapee Ronald M. , Stapinski Lexine A. , Abbott Maree J.
Published: May 2024

The Metacognitions Questionnaire – Short Form (MCQ-30) was designed as a parsimonious measure of the metacognitive beliefs and processes implicated in the maintenance of Generalized Anxiety Disorder (GAD). The present study sought to examine the psychometric properties and clinical utility of the MCQ-30 among people with GAD. One hundred and thirty-nine adults diagnosed with GAD and 76 non-clinical controls completed the MCQ-30 and self-report measures of worry, fear of anxiety, attempted thought suppression, distress, GAD symptoms, and interference. A five-factor structure was evaluated using confirmatory factor analysis (CFA). Among the clinical sample, CFA supported the construct validity of the scale, although the relationship between the factors differed from community samples. Evidence was found for the internal consistency, test-retest reliability, and concurrent, convergent and criterion validity of the MCQ-30 in people with GAD. The treatment sensitivity and clinical responsiveness of the scale were also demonstrated, with the Uncontrollability and Danger Beliefs subscale identified as the most accurate predictor of clinical status. This subscale also exhibited the strongest correlations with most symptom measures, highlighting the cardinal role played by negative beliefs about worry in maintaining clinical levels of GAD. This study provides the first evidence of the reliability, validity and clinical utility of the MCQ-30 with people diagnosed with GAD.