bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of healthcare professionals’ communication in trial participation decisions: a qualitative investigation of recruitment consultations and patient interviews across three RCTs
Authors: Farrar Nicola , Elliott Daisy , Jepson Marcus , Young Bridget , Donovan Jenny L. , Conefrey Carmel , Realpe Alba X. , Mills Nicola , Wade Julia , Lim Eric , Stein Robert C. , Caskey Fergus J. , Rooshenas Leila
Published: December 2024

Background

Although the challenges of recruiting to randomised controlled trials (RCTs) are well documented, few studies have focused on the impact that the communication between recruiters and patients has on patients’ participation decisions. Recruiters are thought to influence patient decision-making, but the mechanisms by which this occurs are unclear. The aim of this research was to investigate how patients interpret and use the information conveyed to them by healthcare professionals (HCPs) in trial participation decisions.

Methods

Three pragmatic UK-based multicentre RCTs were purposively sampled to provide contrasting clinical specialities. Data collection was integrated into each RCT, including audio-recordings of patient recruitment consultations and interviews with patients. Where possible, consultation audio-recordings were linked to interviews to explore how information communicated by recruiters was interpreted and used by patients during their decision-making. Data were analysed thematically, using the constant comparison approach.

Results

Twenty audio-recorded recruitment consultations were obtained across the 3 RCTs, combined with 42 interviews with patients who had consented to or declined RCT participation. Consultation and interview data were ‘linked’ for 17 individual patients. Throughout the patient’s clinical pathway, HCPs (both those involved in the RCT and not) influenced patients’ perceptions of treatment need and benefit by indicating that they preferred a particular treatment option for the patient as an individual. Whilst patients valued and were influenced by information conveyed by HCPs, they also drew on support from other sources and ultimately framed RCT participation decisions as their own. Patients’ willingness to be randomised hinged on perceptions of whether they stood to benefit from a particular treatment and the availability of those treatments outside of the trial.

Conclusion

This study supports the need for training and support for healthcare professionals involved throughout the clinical pathway of patients eligible for RCTs, as all healthcare professionals who interact with patients have the potential to influence their perceptions of treatments being compared in the trial.

Trial registration

OPTIMA ISRCTN42400492. Prospectively registered on 26 June 2012.

Prepare for Kidney Care ISRCTN17133653. Prospectively registered on 31 May 2017.

MARS 2 ISRCTN44351742. Retrospectively registered on 5 September 2018.
Reliability of wing morphometrics for species identification of human-biting black flies (Diptera: Simuliidae) in Thailand
Authors: Aupalee Kittipat , Srisuka Wichai , Limsopatham Kwankamol , Sanit Sangob , Takaoka Hiroyuki , Saeung Atiporn
Published: December 2024

Background

Fast and reliable species identification of black flies is essential for research proposes and effective vector control. Besides traditional identification based on morphology, which is usually supplemented with molecular methods, geometric morphometrics (GM) has emerged as a promising tool for identification. Despite its potential, no specific GM techniques have been established for the identification of black fly species.

Methods

Adult female black flies collected using human bait, as well as those reared from pupae, were used in this study. Here, landmark-based GM analysis of wings was assessed for the first time to identify human-biting black fly species in Thailand, comparing this approach with the standard morphological identification method and DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. To explore genetic relationships between species, maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic trees were built. Additionally, three different methods of species delimitation, i.e., assemble species by automatic partitioning (ASAP), generalized mixed yule coalescent (GMYC), and single Poisson tree processes (PTP), were utilized to identify the morphologically defined species. The effectiveness of a COI barcode in identifying black fly species was further examined through the best match (BM) and best close match (BCM) methods.

Results

Seven black fly species, namely Simulium tenebrosum Takaoka, Srisuka & Saeung, 2018 (complex), S. doipuiense Takaoka & Choochote, 2005 (complex), S. nigrogilvum Summers, 1911, S. nodosum Puri, 1933, S. asakoae Takaoka & Davies, 1995, S. chamlongi Takaoka & Suzuki, 1984, and S. umphangense Takaoka, Srisuka & Saeung, 2017 were morphologically identified. Compared with the standard method, the GM analysis based on wing shape showed high success in separating species, achieving an overall accuracy rate of 88.54%. On the other hand, DNA barcoding surpassed wing GM for species identification with a correct identification rate of 98.57%. Species delimitation analyses confirmed the validity of most nominal species, with an exception for S. tenebrosum complex and S. doipuiense complex, being delimited as a single species. Moreover, the analyses unveiled hidden diversity within S. asakoae, indicating the possible existence of up to four putative species.

Conclusions

This study highlights the potential of wing GM as a promising and reliable complementary tool for species identification of human-biting black flies in Thailand.

Graphical Abstract
Sequencing confirms Anopheles stephensi distribution across southern Yemen
Authors: Baheshm Yasser A. , Zayed Alia , Awash Abdullah A. , Follis Madison , Terreri Payton , Samake Jeanne N. , Aljasari Adel , Harwood James F. , Lenhart Audrey , Zohdy Sarah , Al-Eryani Samira M. , Carter Tamar E.
Published: December 2024

The invasion of Anopheles stephensi in Africa warrants investigation of neighboring countries. In this study, genetic analysis was applied to determine the status of An. stephensi in southern Yemen. Cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2) were sequenced in An. stephensi collected in Dar Sa’ad (Aden City), Tuban, Rodoom, Al Mukalla, and Sayhut, and phylogenetic analysis confirmed An. stephensi identity. Our analyses revealed that the ITS2 sequences were identical in all An. stephensi, while COI analysis revealed two haplotypes, one previously reported in northern Horn of Africa and one identified in this study for the first time. Overall, these findings revealed low levels of mitochondrial DNA diversity, which is consistent with a more recent population introduction in parts of southern Yemen relative to the Horn of Africa. Further, whole genomic analysis is needed to elucidate the original connection with invasive populations of An. stephensi in the Horn of Africa.

Graphical Abstract
Glabridin exhibits potent inhibitory effects against Toxoplasma gondii in vitro and in vivo
Authors: Wang Lu , Zhai Bintao , Wang Chen , Elsheikha Hany M. , Guo Haiting , Zheng Xiao-Nan , Zhou Chun‑Xue , Zhu Xing-Quan
Published: December 2024

Background

Toxoplasma gondii is an obligate protozoan parasite capable of infecting a wide range of warm-blooded animals and humans. Current treatment options, primarily pyrimethamine and sulfadiazine, have limitations, such as high recurrence rates, long treatment durations, and limited effectiveness against T. gondii. There is an unmet need for novel, safe, low-toxicity, and highly effective treatments. This study aimed to evaluate the anti-T. gondii effects of glabridin, a natural compound derived from the roots of a widely used medicinal plant.

Methods

The cytotoxicity of glabridin in Vero cells was assessed using a CCK-8 cell viability assay. Quantitative polymerase chain reaction (qPCR) targeting the Tg-529 gene was developed to quantify T. gondii and assess the inhibitory effects of glabridin on parasite proliferation. Ultrastructural changes in T. gondii after treatment were examined using electron microscopy. The levels of reactive oxygen species (ROS) and mitochondrial membrane potential (ΔΨm) were examined to assess the effects of glabridin on ROS levels and ΔΨm in T. gondii tachyzoites. Additionally, metabolomics and transcriptomics analyses were conducted to investigate the mechanisms underlying glabridin’s anti-T. gondii effects.

Results

Glabridin exhibited low toxicity to host cells and effectively inhibited T. gondii invasion and proliferation in vitro in a time-dependent manner. Glabridin-treated tachyzoites exhibited significant structural alterations, along with increased ROS production and a reduction in ΔΨm. Metabolomic analysis indicated that glabridin significantly affected amino acid metabolism pathways in T. gondii. In vivo, glabridin treatment significantly improved survival rates in T. gondii-infected BALB/c mice at a dosage of 100 mg/kg.

Conclusions

This study demonstrates that glabridin has potent anti-T. gondii effects in vitro and in vivo, likely through disruption of amino acid metabolism in the parasite. These findings highlight glabridin’s potential as a promising therapeutic agent for toxoplasmosis.

Graphical abstract
Role of TLR4 activation and signaling in bone remodeling, and afferent sprouting in serum transfer arthritis
Authors: dos Santos Gilson Goncalves , Jiménez-Andrade Juan Miguel , Muñoz-Islas Enriqueta , Candanedo-Quiroz Mariana E. , Cardenas Andrea Gonzalez , Drummond Bronwen , Pham Peter , Stilson Gwendalynn , Hsu Chao-Chin , Delay Lauriane , Navia-Pelaez Juliana M. , Lemes Julia Paes , Miller Yury I. , Yaksh Tony L. , Corr Maripat
Published: December 2024

Background

In the murine K/BxN serum transfer rheumatoid arthritis (RA) model, tactile allodynia persists after resolution of inflammation in male and partially in female wild type (WT) mice, which is absent in Toll-like receptor (TLR)4 deficient animals. We assessed the role of TLR4 on allodynia, bone remodeling and afferent sprouting in this model of arthritis.

Methods

K/BxN sera were injected into male and female mice with conditional or stable TLR4 deletion and controls. Paw swelling was scored and allodynia assessed by von Frey filaments. At day 28, synovial neural fibers were visualized with confocal microscopy and bone density assayed with microCT. Microglial activity and TLR4 dimerization in spinal cords were examined by immunofluorescence and flow cytometry.

Results

In the synovium, K/BxN injected WT male and female mice showed robust increases in calcitonin gene related-peptide (CGRP+), tyrosine hydroxylase (TH)+ and GAP43+ nerve fibers. Trabecular bone density by microCT was significantly decreased in K/BxN WT female but not in WT male mice. The number of osteoclasts increased in both sexes of WT mice, but not in Tlr4-/- K/BxN mice. We used conditional strains with Cre drivers for monocytes/osteoclasts (lysozyme M), microglia (Tmem119 and Cx3CR1), astrocytes (GFAP) and sensory neurons (advillin) for Tlr4f/f disruption. All strains developed similar arthritis scores after K/BxN serum injection with the exception being the Tlr4Tmem119 mice which showed a reduction. Both sexes of Tlr4Lyz2, Tlr4Tmem119 and Tlr4Cx3cr1 mice displayed a partial reversal of the chronic pain phenotype but not in Tlr4Avil, and Tlr4Gfap mice. WT K/BxN male mice showed increases in spinal Iba1, but not GFAP, compared to Tlr4-/- male mice. To determine whether spinal TLR4 was indeed activated in the K/BxN mice, flow cytometry of lumbar spinal cords of WT K/BxN male mice was performed and revealed that TLR4 in microglia cells (CD11b+ /TMEM119+) demonstrated dimerization (e.g. activation) and a characteristic increase in lipid rafts.

Conclusion

These results demonstrated a complex chronic allodynia phenotype associated with TLR4 in microglia and monocytic cell lineages, and a parallel spinal TLR4 activation. However, TLR4 is dispensable for the development of peripheral nerve sprouting in this model.
Sex differentially affects pro-inflammatory cell subsets in adipose tissue depots in a diet induced obesity model
Authors: Schuetz Lisa T. , Duran Gayel , Baeten Paulien , Lintsen Daphne , Hermans Doryssa , Chenine Sarah , Verreycken Janne , Vanmierlo Tim , Wouters Kristiaan , Broux Bieke
Published: December 2024

Obesity is a growing pandemic that increases the risk for cardiovascular diseases, type 2 diabetes, and particularly in women also the risk of cancer and neurodegenerative disorders such as dementia and multiple sclerosis. Preclinical studies on obesity focus on male mice as they gain bodyweight faster and show a clear pro-inflammatory phenotype. Here, using male and female mice, we induced obesity by feeding a high fat diet (HFD), and compared adipose tissue (AT) inflammation at the same adiposity stage (% AT/bodyweight) between both sexes. Doing so, we identified that female mice show an increase in the number of pro-inflammatory immune cells in the visceral AT at a lower adiposity stage than male mice, but the effect of HFD is diminished with higher adiposity. Interestingly, only female mice showed an increase in immune cells in the subcutaneous AT after HFD feeding. Nonetheless, we found that pro-inflammatory cytokines in blood plasma mirror the inflammatory stage of the visceral AT in both male and female mice. Uniquely in male mice, myeloid cells in the visceral AT showed a higher inflammasome activation upon HFD. In summary, we showed that adiposity differentially affects immune cells in fat depots based on sex.
Nucleotide-binding oligomerization domain 1 (NOD1) regulates microglial activation in pseudorabies virus infection
Authors: Sun Xiuxiu , Jin Xinxin , Lin Zhengdan , Liu Xi , Yang Junjie , Li Li , Feng Helong , Zhang Wanpo , Gu Changqin , Hu Xueying , Liu Xiaoli , Cheng Guofu
Published: December 2024

The primary cause of viral encephalitis (VE) is invasion of the central nervous system (CNS) by the virus, which leads to neuroinflammation and poses a significant threat to global public health. Microglia, as CNS-resident macrophages, play a crucial role in neuroinflammation and are often identified as the preferred target for the prevention or treatment of VE. In this study, we used pseudorabies virus (PRV)-induced VE in mice and pigs as a model to investigate the regulation of microglial responses during viral encephalitis and explored the mechanism of microglial activation. Cellular experiments revealed that microglial activation was accompanied by cell migration, characteristic morphological changes, phagocytosis, inflammatory cytokine production, and antigen presentation. Transcriptome analysis revealed that genes related to inflammation in PRV-infected BV2 cells were significantly enriched. The expression of the NOD1 gene in BV2 cells was significantly increased during PRV infection, after which NOD1 in BV2 cells was silenced by siRNA and overexpressed via a plasmid. NOD1 was found to be involved in the secretion of cytokines in BV2 cells by regulating the MAPK/NF-κB signalling pathway. Mouse and pig experiments have shown that NOD1 is involved in the secretion of cytokines by microglia by regulating the MAPK/NF-κB signalling pathway during PRV infection.
Developmental patterns of intestinal group 3 innate lymphoid cells in piglets and their response to enterotoxigenic Escherichia coli infection
Authors: Huang Ningning , Ye Ling , Li Hao , Peng Jian , Wei Hongkui
Published: December 2024

Diarrhoea and preweaning mortality in piglets are crucial factors impacting the economic sustainability of the swine industry. Pathogenic infections are among the main causes of diarrhea and mortality. Group 3 innate lymphoid cells (ILC3s) are crucial for safeguarding against pathogenic infections. However, knowledge regarding the development and function of ILC3s in suckling piglets is currently limited. Our findings demonstrate that the development of ILC3s in suckling piglets gradually progresses from day 1 to day 21, with a notable increase observed on day 28. Additionally, the development of NKp46+ILC3s and the production of interleukin (IL)-17A by ILC3s displayed consistent patterns with the changes observed in ILC3s. Notably, interferon (IFN)-γ levels significantly increased on day 14. Moreover, the production of IFN-γ by NKp46+ILC3s was greater than that by NKp46−ILC3s. Importantly, when piglets were subjected to a 4-h challenge with enterotoxigenic Escherichia coli, both the percentages of ILC3s significantly increased, accompanied by increased IL-22 production, highlighting their importance in maintaining intestinal health. The outcomes of this study provide valuable insights for future related research.
FPGA-based dual-layer authentication scheme utilizing AES and ECC for unmanned aerial vehicles
Authors: Roy Kumar Sekhar , Sujith Murikipudi , Bhanu Bandi , Preethi  , Hazarika Ruhul Amin
Published: December 2024

Unmanned aerial vehicles, commonly known as drones, face unique authentication challenges due to their distinct characteristics and operational environments. These challenges include identity management, secure key management, secure communication channels, and limited resources. To address these challenges, we propose a dual-layer authentication scheme utilizing Advanced Encryption Standard and Elliptic Curve Cryptography on Field-Programmable Gate Arrays. This scheme leverages the flexibility and programmability of Field-Programmable Gate Arrays incorporated in drones to enhance security. The integration of Advanced Encryption Standard on Field-Programmable Gate Arrays provides a robust solution to withstand various attacks such as impersonation, tampering, and replay attacks. Simulation results in Xilinx Vivado demonstrate the efficiency and effectiveness of the proposed scheme compared to existing methods.
User velocity estimation in HetNets utilizing vertical and horizontal handover counts via maximum likelihood estimation
Authors: Tiwari Ravi , Paul Sourabh , Singh Manoj Kumar , Rahul Amit Kumar , Akilan K.
Published: December 2024

In this paper, we propose a maximum likelihood estimation (MLE) of user velocity based on Rayleigh distributed handover counts in heterogeneous networks (HetNets). The high density of base stations (BSs) in HetNets leads to mobile users experiencing unnecessary handovers and service outages, emphasizing the importance of mobility management in HetNets. Since user velocity plays an important role in the handover process, its knowledge is necessary for efficient mobility management. Our proposed velocity estimation strategy involves tracking of both vertical and horizontal handovers over a defined period. We utilized mathematical modeling to estimate that the probability mass function (PMF) of the handover counts in the HetNets scenario follows a Rayleigh distribution. We determined the scale parameter by analyzing the close deployment of small cells and macro-cell BSs using stochastic geometry. Our approach assumes a random distribution of BSs based on a homogeneous Poisson point process and investigates the handover-count PMF considering factors such as user velocity, BS density, and the duration of handover-count measurements. Using these statistics, we derived the Cramer–Rao lower bound (CRLB) and applied a MLE technique to estimate user velocity. The MATLAB simulation method is used to validate our approach for the velocity estimation, and the results show the tight closeness of MLE asymptotic variance with CRLB. The numerical analysis indicates that as user velocity increases, the variance of the estimation also increases. Conversely, the simulation results demonstrate that as BS density and the time span for handover-count measurements increase, the velocity estimation error decreases.
Centering autonomy and choice to support oral PrEP utilization among people who inject drugs: qualitative lessons from HPTN 094 INTEGRA
Authors: Perez-Brumer Amaya , Schmidt Rose , Kennedy Rebecca , Lake Jordan E. , Villarreal Yolanda R. , Bornstein Sydney , Kuo Irene , Nieto Omar , Franks Julie , Denis Cecile , El-Bassel Nabila , Shoptaw Steve , Davidson Peter , Smith Laramie R.
Published: December 2024

Background

Oral Pre-exposure prophylaxis (PrEP) is effective in preventing HIV transmission. However, despite high rates of HIV risk behaviors among people who inject drugs (PWID), this population remains underserved by current HIV prevention efforts in the United States. To address this challenge, we conducted an in-depth exploration of perspectives on using oral PrEP among PWID engaged in the HIV Prevention Trials Network (HPTN) 094 INTEGRA Study.

Methods

Guided by the Practical, Robust, Implementation, and Sustainability Model (PRISM), our qualitative study drew on semi-structured interviews conducted as part of the embedded implementation science evaluation of HPTN 094 INTEGRA. Seventy-seven PWID participants from five sites across New York City, Houston, Los Angeles, Philadelphia, and Washington DC were interviewed to assess intervention delivery, care access, and engagement sustainability. Audio files were transcribed verbatim and analyzed via an inductive and deductive thematic approach.

Results

Most participants (n = 46, 59.7%) discussed oral PrEP during their interview, though not directly prompted. Participants discussing PrEP had a mean age of 41.6 years and were predominantly white (54.3%) and cisgender men (60.9%). Among these, 15 participants described using PrEP. All participants had facilitated access to oral PrEP. Yet, the choice to use PrEP was influenced by personal risk perceptions, (mis)information about PrEP, and external factors (i.e. housing, financial security), which, for some, limited the autonomy to use PrEP. Two key themes emerged among participants using PrEP: ease of access and perceptions of high HIV risk. Those not using PrEP described two themes: low risk perception and prioritizing more urgent needs. Among participants not using PrEP a subgroup commonly described ambivalent interest, PrEP knowledge gaps, and PrEP readiness (i.e., contemplation).

Conclusions

Qualitative findings highlight that facilitated PrEP access was insufficient to motivate use for many participants. Rather, PrEP decision-making process (i.e., choice) was linked to risk perception and individuals’ capability to leverage PrEP as a resource based on their circumstances (i.e., autonomy). Participants’ descriptions of the centrality of choice and autonomy for PrEP use underscore that ease of access is a necessary pre-condition, but person-centered interventions should also address housing, financial stability, and urgent medical conditions to promote PrEP utilization among PWID.

Clinical trial registration

NCT04804027.
Mapping young farmers’ choice to pursue Geographical Indication in a rural context: application of fuzzy cognitive map
Authors: Consentino Federica , Peri Iuri , Litrico Mattia , Spina Daniela , Vindigni Gabriella
Published: December 2024

The shortage of young people in agriculture and the decline of rural areas are increasingly pressing issues that capture the attention of European policymakers and researchers. Despite the low rate of youth involved in agricultural production, recent data reveal a significant proportion of young farmers in Italy that are engaged in geographical indication (GI) production. Statistics provide trend analysis, but they alone are not sufficient in clarifying the motivations behind young people’s decision-making. We conducted a qualitative study of Sicilian youth involved in GI to understand their motivations to pursue GI certification and the implications for youth embeddedness in rural areas. Using a fuzzy cognitive map (FCM), qualitative data have been translated in quantitative, giving evidence on key variables and their inter-relationships that influence young people's decision-making in a GI complex system. A total of twenty-two categorized variables have been identified. Results show how the young entrepreneurs' thinking in GI is structured, based on the cause-effect relationships between the variables. This study finds evidence that the GI system facilitates young generations of farmers in developing a personal approach to modern agribusiness starting from traditions and origins. At the same time, it gives evidence of a new perspective for involving young people in agricultural careers. In this sense, the present research contributes to the literature on factors that add attractiveness to the agricultural sector, to lead researchers and policymakers in dealing with alternative strategies for incentivizing youth involvement in farming.
Can criminology sway the public? How empirical findings about deterrence affect public punishment preferences
Authors: Rose Brendan , Kuiper Malouke Esra , Reinders Folmer Chris , van Rooij Benjamin
Published: December 2024

Background setting

Punitive approaches to deter offending remain popular despite limited evidence of their effectiveness. This study investigated what effect presenting empirical criminological findings about the effectiveness of deterrence to a general public has on their punishment preferences. It builds on earlier research showing that such presentation reduces the public’s inclination towards strict punishment. The present study extended this research by exploring whether the impact of scientific evidence on public punishment preferences is affected by crime severity and by exploring cognitive and psychological factors that may underpin this relationship.

Methods

Using a vignette study paradigm, a general public sample of 330 participants were asked to make hypothetical punishment decisions to reduce crime (whether or not to double sentences) for one of three crime types that varied in severity. For each crime type, half of participants were additionally provided with a summary of research on the deterrent effect of punitive policy measures.

Results

Presenting scientific evidence reduced participants' preferences for stronger punishment and that this effect remained consistent regardless of crime severity—ranging from burglary to homicide. In addition, we did not find evidence that difference in individuals’ cognitive style, negative emotional reactions, perceptions about seriousness, or beliefs about redeemability moderated or mediated this relationship.

Conclusions

This study provides compelling findings that further clarify the circumstances required for scientific evidence to be successfully disseminated to a general public to bring their punishment preferences more in line with the state of empirical science.
Identification of a novel subtype of SPP1 + macrophages expressing SIRPα: implications for tumor immune evasion and treatment response prediction
Authors: Chen Kun , Li Yida , Ni Jianjiao , Yang Xi , Zhou Yue , Pang Yechun , Ye Ruiting , Chen Hongru , Yu Silai , Wang Peng , Zhu Zhengfei
Published: December 2024

Background

SPP1 + macrophages are among the major phagocytic cells, yet promoting tumor immune evasion and predicting unfavorable prognosis, in various cancer types. Meanwhile, the predictive value of the abundance of SPP1 + macrophages in patients receiving immunotherapy remains debatable, indicating the potential existence of subtypes of SPP1 + macrophages with diverse biological functions.

Methods

The single cell RNA sequencing data of myeloid cells integrated from several cancers including esophageal squamous cell carcinoma was analyzed for characterizing the function and cellular interactions of SPP1 + macrophages expressing SIRPα. Multiplexed immunohistochemistry was used to quantify the quantity and spatial distribution of SPP1 + macrophages expressing SIRPα. Kaplan–Meier method was used for survival analysis. In vitro and in vivo studies investigating the function of SPP1 + macrophages were performed.

Results

SPP1 + macrophages possessed a high phagocytic signature and could engulf more tumor cells in vitro and in vivo. SIRPα expression could represent the phagocytic activity of SPP1 + macrophages and delineated subsets of SPP1 + macrophages with different functions. SPP1 + SIRPα + macrophages showed close spatial distance to tumor cells and positively correlated with PD1 + CD8 + T cells. A high abundance of SPP1 + SIRPα + macrophages at baseline corresponded to patients’ response to PD-1/PD-L1 inhibitors.

Conclusion

A novel subtype of SPP1 + macrophages expressing SIRPα was identified and their abundance predicted patients’ response to PD-1/PD-L1 inhibitors.
Does dose matter? Parental attendance in a preventive intervention for anxious and sad children
Authors: Bania Elisabeth Valmyr , Ytreland Kristin , Sund Anne Mari , Lydersen Stian , Neumer Simon Peter , Adolfsen Frode , Martinsen Kristin , Rasmussen Lene-Mari Potulski , Ingul Jo Magne
Published: December 2024

Background

International studies show increasing prevalence of anxiety and depression among children. Parents are vital for children in all aspects of life, also in supporting their offspring in promoting better mental health, life skills and reducing emotional difficulties. Therefore, involving parents in interventions aimed at preventing development of anxiety and depression is natural. In treatment studies, targeted parental involvement has been difficult to prove effective. However, few existing studies investigate the effect of parental involvement in preventive interventions.

Objective

We aimed to explore whether attendance influenced the change in child’s emotional symptoms post intervention and one-year later reported by parents.

Method

Parents of children attending an indicated preventive intervention named EMOTION, who took part in a high parental involvement condition were included in this study (n = 385). High involvement entailed 5 parent group sessions. Using linear mixed models, we investigated whether attendance in the parent groups influenced the parent-reported levels of children’s emotional symptoms post-intervention and at one-year follow-up.

Results

Parents who did not attend parent sessions reported significantly larger reductions in child anxiety symptoms over time than attending parents. There was no such effect on child depression. However, parents who attended sessions reported significantly higher depression symptoms than non-attendees at baseline. Further, attending more parent sessions did not significantly impact either symptom measure.

Discussion

Given the non-significant differences of parental attendance in this study, future studies could examine less resource demanding interventions for children with emotional difficulties. When the child is struggling with anxiety and depression, the parent’s role in child’s life could be vital for symptom amelioration. The challenge is finding effective, evidence-based methods to involve parents, to reduce child emotional difficulties and improve their quality of life.

Conclusions

In this preventive study, attendance in parent sessions has limited effect on parent-reported symptoms of child emotional difficulties.
Do executive functions and processing speed mediate the relationship between socioeconomic status and educational achievement? Analysis of an observational birth cohort study
Authors: Mooney Kate E. , Cheung Rachael W. , Blower Sarah L. , Allen Richard J. , Waterman Amanda
Published: December 2024

Background

There are large and persistent social inequalities in children’s educational attainment, with children from more socioeconomically disadvantaged families consistently having lower attainment. Despite this being widely reported, the mechanisms underlying the association between socioeconomic disadvantage and educational attainment are not well understood. It is important to understand the potential mechanisms by which socioeconomic disadvantage may impede on educational outcomes, as this knowledge could then be used to help target possible interventions to improve educational outcomes for socioeconomically disadvantaged children. Children’s executive functions (including working memory and inhibition) and processing speed abilities may underlie these inequalities, however, the previous literature regarding this is limited. This study examined longitudinal mediating mechanisms between socioeconomic status (SES) and educational achievement, using a socioeconomically deprived and ethnically diverse cohort.

Methods

Data from the Born in Bradford longitudinal cohort study was analysed using Structural Equation Modelling (n = 4201; 28% White British, 56% Pakistani heritage, 16% Other; 54% Female). SES was measured before birth, executive functions and processing speed were measured in middle childhood (Mage=8.45 years), and educational achievement was obtained through educational records (Mage=10.85 years). All models adjusted for child gender, age, language ability, ethnicity, and mother immigration status.

Results

Executive functions significantly mediated the association between SES and educational achievement (B = 0.109), whilst processing speed did not. Examination of executive function components revealed that working memory significantly mediated the associated between SES and educational achievement (B = 0.100), whilst inhibition did not. Working memory appeared to account for a large proportion (39%) of the total effect of SES on educational achievement.

Conclusions

These results, and the theoretical mechanisms linking working memory to educational achievement, both indicate the importance of finding ways to support children with working memory difficulties in the classroom. This is an important avenue for future research and may be useful for closing the socioeconomic gap in educational achievement.
A benchmark for computational analysis of animal behavior, using animal-borne tags
Authors: Hoffman Benjamin , Cusimano Maddie , Baglione Vittorio , Canestrari Daniela , Chevallier Damien , DeSantis Dominic L. , Jeantet Lorène , Ladds Monique A. , Maekawa Takuya , Mata-Silva Vicente , Moreno-González Víctor , Pagano Anthony M. , Trapote Eva , Vainio Outi , Vehkaoja Antti , Yoda Ken , Zacarian Katherine , Friedlaender Ari
Published: December 2024

Background

Animal-borne sensors (‘bio-loggers’) can record a suite of kinematic and environmental data, which are used to elucidate animal ecophysiology and improve conservation efforts. Machine learning techniques are used for interpreting the large amounts of data recorded by bio-loggers, but there exists no common framework for comparing the different machine learning techniques in this domain. This makes it difficult to, for example, identify patterns in what works well for machine learning-based analysis of bio-logger data. It also makes it difficult to evaluate the effectiveness of novel methods developed by the machine learning community.

Methods

To address this, we present the Bio-logger Ethogram Benchmark (BEBE), a collection of datasets with behavioral annotations, as well as a modeling task and evaluation metrics. BEBE is to date the largest, most taxonomically diverse, publicly available benchmark of this type, and includes 1654 h of data collected from 149 individuals across nine taxa. Using BEBE, we compare the performance of deep and classical machine learning methods for identifying animal behaviors based on bio-logger data. As an example usage of BEBE, we test an approach based on self-supervised learning. To apply this approach to animal behavior classification, we adapt a deep neural network pre-trained with 700,000 h of data collected from human wrist-worn accelerometers.

Results

We find that deep neural networks out-perform the classical machine learning methods we tested across all nine datasets in BEBE. We additionally find that the approach based on self-supervised learning out-performs the alternatives we tested, especially in settings when there is a low amount of training data available.

Conclusions

In light of these results, we are able to make concrete suggestions for designing studies that rely on machine learning to infer behavior from bio-logger data. Therefore, we expect that BEBE will be useful for making similar suggestions in the future, as additional hypotheses about machine learning techniques are tested. Datasets, models, and evaluation code are made publicly available at https://github.com/earthspecies/BEBE, to enable community use of BEBE.
Navigating motherhood: biological and landscape factors affecting postpartum movement in white-tailed deer
Authors: Holland Angela M. , Haus Jacob M. , Dion Justin R. , Rogerson Joseph E. , Bowman Jacob L.
Published: December 2024

Background

Population growth and management in cervid species is dependent on reproductive ecology and factors influencing juvenile survival. Aspects of the female’s movement behavior likely affect juvenile survival and movement patterns of pregnant and lactating females differ from non-pregnant or non-lactating females. Explanations for these differing movement patterns include change in nutritional demands for the female, isolation during parturition, and predator avoidance. White-tailed deer (Odocoileus virginianus) are an important managed cervid and a better understanding of their reproductive ecology, including the relationships between resources, movement, and juvenile survival, can better inform management.

Methods

Our objective was to determine if biological factors, such as female age, fawn age, number of fawns, as well as characteristics of prepartum range affected the female’s postpartum daily movement or overlap of space used pre- and postpartum in Sussex County, Delaware, USA (2,420 km2). We collected GPS locations 2 weeks pre- and postpartum on 22 individual females from 2016 to 2017. In total, we recorded data from 263 days of postpartum movement for an average of 12 days/individual. We used a hierarchical modeling process to test biological factors and prepartum home range characteristics on two aspects of postpartum movement behavior, mean hourly displacements and daily use of prepartum home range.

Results

Mean hourly displacement decreased with increased female age and increased with number of known fawns alive and the female’s home range size prior to parturition. We found that as fawns aged the doe increased use of the prepartum home range.

Conclusions

Our results indicate that younger females are moving more than older females during lactation potentially to access higher quality habitat. This increased movement increases nutritional demand and may play a role in fawn survival. Females are more likely to use more of their prepartum home range as fawns age, a finding congruent with previous research. This differentiation in metric response (movement rate vs. space use) emphasizes the complexities of movement ecology and the importance of considering multiple dependent variables for complex behavior.
PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84
Authors: Wang Sheng-Shan , Chang Wei-Bin , Hsieh Ming-Chien , Chen Szu-Yu , Liao Dah-Jing , Liao Ching-Ying , Shen Wei-Chiang , Chen Hong-Hua , Chen Chieh-Yi , Chen Yi-Chia , Lin Yueh-Lin , Tung Chih-Wei , Chen Ruey-Shyang , Chung Chia-Lin
Published: December 2024

Background

Rice blast caused by Pyricularia oryzae is a major threat to rice production worldwide. Tainung 84 (TNG84) is an elite japonica rice cultivar developed through the traditional pedigree method. It has maintained superior blast resistance since its release in 2010. This study aimed to investigate the genetic factors underlying the durable resistance of TNG84 in Taiwan.

Results

Quantitative trait locus (QTL) mapping was conducted using 122 F2 individuals and F2:3 families derived from the cross of TNG84 and a susceptible japonica cultivar Tainan 11 (TN11). Using 733 single nucleotide polymorphisms (SNPs) obtained through genotyping-by-sequencing and three P. oryzae isolates (D41-2, 12CY-MS1-2, and 12YL-TT4-1) belonging to different physiological races and Pot2 lineages, a major QTL was identified in the region of 52–54 cM (9.54–15.16 Mb) on chromosome 12. Fine-mapping using 21 F5:6 recombinants delimited the QTL to a 140.4-kb region (10.78 to 10.93 Mb) containing the known resistance gene Ptr. Sequencing analysis indicated that TNG84 carries the resistant PtrA allele and TN11 carries the susceptible PtrD allele. Investigation of the Ptr haplotypes in 41 local japonica rice cultivars revealed that eight PtrA-containing cultivars (19.5%) consistently exhibited good field resistance in Taiwan from 2008 to 2024. Subsequently, a few F5:6 lines (P026, P044, P092, and P167) lacking the resistant Ptr allele were observed to exhibit a resistant phenotype against P. oryzae 12YL-TT4-1-lab. Trait-marker association analyses using eight F6:7 homozygous recombinants, 378 BC1F2 from P044 backcrossed to TN11, and 180 BC1F2 from P092 backcrossed to TN11, identified Piz-t on chromosome 6 and a new QTL located between 3.3 Mb and 4.4 Mb on chromosome 12 (designated as qBR12_3.3–4.4). Analysis of 12 selected BC1F2:3 lines derived from P044 demonstrated that in the absence of Ptr and Piz-t, qBR12_3.3–4.4 alone reduced the disease severity index from approximately 6.3 to 3.9.

Conclusions

PtrA is likely the primary gene responsible for the broad-spectrum and durable resistance of TNG84. Piz-t confers narrow-spectrum resistance, while qBR12_3.3–4.4 contributes partial resistance. The discovery of qBR12_3.3–4.4 has provided a new source of blast resistance, and the markers developed in this study can be utilized in future breeding programs.
A systematic review of deep learning applications in database query execution
Authors: Milicevic Bogdan , Babovic Zoran
Published: December 2024

Modern database management systems (DBMS), primarily designed as general-purpose systems, face the challenging task of efficiently handling data from diverse sources for both analytical services and online transactional processing (OLTP). The volume of data has grown significantly, with distributions ranging from linear to highly skewed, sometimes involving very slow changes or rapid, intensive updates. Recent research in this field has been significantly influenced by advances in machine learning (ML), particularly deep learning (DL), and these developments have led to the application of various ML algorithms to enhance the efficiency of different parts of the query execution engine. While previous research studies were mostly focused on identifying drawbacks to individual components, such as the query optimizer, there is a notable lack of studies examining the applicability and effectiveness of various machine learning approaches across multiple aspects of the query execution engine. This article aims to provide a systematic review of approaches that apply deep learning models at various levels within the query execution engine. We categorize these approaches into three groups based on how such models are applied: improving performance of index structures and consequently data manipulation algorithms, query optimization tasks, and externally controlling query optimizers through parameter tuning. Furthermore, we discuss the key challenges associated with implementing deep learning algorithms in DBMS.
Respiratory physiotherapy for critically ill children: concern regarding a recommendation
Authors: Shime Nobuaki
Published: December 2024

The guideline entitled “Japanese Clinical Practice Guidelines for Rehabilitation in Critically Ill Patients 2023” was published by the Japanese Society of Intensive Care Medicine in 2023. However, there is an issue with the clinical question and recommendation for respiratory physiotherapy in mechanically ventilated children. Although the evidence was based on two randomized controlled trials regarding prone positioning, the recommendation may have risk of misunderstanding as a recommendation for all respiratory physiotherapy. There are abundant evidence-based recommendations against chest physiotherapy for infants with bronchiolitis with no benefit and possible adverse events. Revising the recommendation for respiratory physiotherapy in critically ill, mechanically ventilated children should be considered.
Do personal recommendations need to be personalized? Investigating the relationships between student differences and educational recommendations
Authors: Dai Yiling , Hoppe Heinz Ulrich , Flanagan Brendan , Takami Kyosuke , Ogata Hiroaki
Published: December 2024

Educational recommender systems have been supporting personalized learning in various ways. However, less discussion is conducted about whether and how to personalize the strategies to generate recommendations based on student differences. In this study, we aim at investigating how students judge recommendations based on different strategies, and how these judgments relate to student characteristics. We conducted a large-scale questionnaire survey to measure students’ Big-Five personality traits, confidence in the subjects, and their judgments on six types of recommendations. The answers collected from 735 high school students in Japan indicate that students had different judgments across different recommendation strategies, but similarly for English and mathematics. Furthermore, the correlations between student characteristics and their judgments on recommendations were stronger if the subject to learn was inconsistent with the subject they preferred. The results provide insights on how to design educational recommendations that not only cater to students’ traits, but also help foster and enhance their traits for better learning.
Spatial and temporal variations of the 3-year earthquake swarm activities leading up to the M7.6 Noto Peninsula earthquake and interpretations of their activities
Authors: Kumazawa Takao , Ogata Yosihiko
Published: December 2024

The seismic swarm activity that began and expanded in four separate regions in the northern Noto Peninsula at the end of 2020 was followed by the M6.5 earthquake in May 2023, which cascaded into the M7.6 earthquake on New Year’s Day 2024. To this series of earthquake events, we estimate temporal changes in the background intensity of the nonstationary ETAS model by inversion for each region. We then interpret how this series of earthquakes was driven by subsurface fluid motion and slow slip at each stage, based on the correspondence between the background seismicity changes and the temporal changes in oblique distance and elevation differences between nearby GNSS stations, as well as the spatiotemporal earthquake patterns.

Graphical Abstract