bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of spatial demographic maps from polymorphism data using a neural network
Authors: Smith Chris C. R. , Patterson Gilia , Ralph Peter L. , Kern Andrew D. 
Published: August 2024

AbstractA fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo‐referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity‐by‐descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr‐colab/mapNN.
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences
Authors: Romeijn Luuk , Bernatavicius Andrius , Vu Duong 
Published: August 2024

AbstractEfficient and accurate classification of DNA barcode data is crucial for large‐scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi‐head output architecture and multi‐level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI‐BERT and MycoAI‐CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI‐CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning‐based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.
Exonisation of an intronic L1 element in the dystrophin gene associated with X‐linked muscular dystrophy in a Border Collie dog
Authors: Van Poucke Mario , Ledeganck Liesbet , Guo Ling T. , Shelton G. Diane , Bhatti Sofie F. M. , Cornelis Ine , Peelman Luc 
Published: August 2024

AbstractX‐linked recessive dystrophinopathies are the most common muscular dystrophies (MDs) in humans and dogs. To date, 20 breed‐specific MD‐associated variants are described in the canine dystrophin gene (DMD), including one associated with dystrophin‐deficient MD in the Border Collie mixed breed. Here, we report the diagnosis and follow‐up of mild dystrophin‐deficient MD in a 5‐month‐old male Border Collie, associated with a novel DMD variant. Diagnosis was based on neurological examination and laboratory evaluations including creatine kinase activity, electromyography and muscle biopsies with immunofluorescent staining. Inspection of the Sashimi plots of the RNA‐seq data from the affected muscle biopsy led to the discovery of a 162‐bp L1 pseudoexon in DMD intron 63, introducing a frameshift and a premature stop codon (NM_001003343.1: c.9271_9272insN[162] p.(Ala3091fs*21)). Reduced DMD mRNA levels were detected for both the non‐pseudoexon (50× less) and pseudoexon (3× less) containing transcripts in the affected muscle, compared with the level of the non‐pseudoexon containing transcript in a control muscle, resulting in very low dystrophin protein levels and the upregulation of utrophin. Because the variant was only found in the affected dog, not in the healthy mother and grandmother, or in 108 unrelated Border Collies from the Belgian population (46 males and 62 females), it was considered a de novo variant. Although the prognosis for dystrophinopathy is generally regarded as poor, the dog stabilised at the age of 6 months and is still clinically stable at the age of 2 years.
Alcohol use disorder, cannabis use disorder, and eating disorder symptoms among male and female college students
Authors: Pedersen Eric R. , Shute Ireland M. , Buch Keegan D. , Fitzke Reagan E. , Berry Katherine A. , Tran Denise D. , Murray Stuart B. 
Published: August 2024

AbstractBackground and ObjectivesEating disorders (EDs) and substance use disorders are prevalent among college students in the United States, with underlying common mechanisms suggesting co‐occurrence of these in the student population. As treatment prognosis of EDs improves when they are identified and treated with early intervention, it is essential to understand which substance use behaviors associate with EDs in students.MethodsUsing a sample of 471 college students recruited for a study on high risk drinking (i.e., students needed to pregame regularly to be included), we explored the associations between ED symptomatology and two common substances used in this population: alcohol and cannabis. As most research on EDs focuses on female students only or does not separate out males and females, we examined whether sex assigned at birth moderated the association between ED symptomatology and substance use outcomes.ResultsAbout one‐third (32.4%) of the sample screened positive for an ED, with females significantly more likely to screen positive. Males were significantly more likely to screen positive for an alcohol or cannabis use disorder. Screening positive for an ED associated with cannabis use frequency and cannabis use disorder symptoms, but not with alcohol outcomes. Sex moderated the association between ED and cannabis use disorder symptoms, with positive ED screen male students experiencing the highest cannabis use disorder symptoms.Discussion and ConclusionsIt is necessary to further assess how sex differences in substance use and ED symptomatology inform each other.Scientific SignificanceFindings underscore the need to assess and screen for cannabis use disorder among students who screen positive for an ED, and, more specifically, with focused attention on male students with ED symptoms.
Post cardiotomy extracorporeal membrane oxygenation in pediatric patients: Results and neurodevelopmental outcomes
Authors: Varrica Alessandro , Cotza Mauro , Rito Mauro Lo , Satriano Angela , Carboni Giovanni , Saracino Antonio , Reali Matteo , Hafdhullah Mahmood , Ranucci Marco , Giamberti Alessandro 
Published: August 2024

AbstractBackgroundThe increasing complexity of congenital cardiac surgery has led to greater utilization of extracorporeal membrane oxygenation (ECMO) support for children post‐surgery. This study aims to identify risk factors for mortality and brain injury in pediatric patients requiring post‐cardiotomy ECMO and to evaluate their neurological outcomes.MethodsThis retrospective study includes pediatric patients with congenital heart diseases who required ECMO after surgery. Risk factors for in‐hospital mortality and brain injury were assessed. Neurodevelopmental status was determined using the Pediatric Cerebral Performance Category (PCPC) Scale at discharge and during follow‐up.ResultsBetween October 2014 and May 2021, 2651 pediatric patients underwent cardiac surgery, with 90 (3.4%) requiring ECMO. The mean age was 0.6 years, ranging from 1 day to 13 years and 7 months. ECMO was implemented for 45 patients due to CPB weaning failure (NW‐CPB), 24 due to postoperative low‐cardiac output syndrome (LCOS), and 21 for extracorporeal cardiopulmonary resuscitation (E‐CPR). ECMO weaning was achieved in 73 patients (81%), with an overall mortality rate of 36%. Pre‐implant lactate levels (OR: 1.13, 95% CI: 1.03–1.25; p = 0.009) and peak bilirubin levels (OR: 1.04, 95% CI: 0.87–1.24; p = 0.69) were risk factors for in‐hospital mortality. Survival rates were 79% for LCOS, 60% for NW‐CPB, and 48% for E‐CPR. Brain injury incidence was 33%, with E‐CPR being a significant risk factor (p = 0.006) and NW‐CPB being protective (p = 0.001). Follow‐up in November 2023 showed significant improvement in neurodevelopmental status (p < 0.001).ConclusionElevated pre‐implant lactate and elevated bilirubin levels during ECMO are major risk factors for mortality. E‐CPR is the primary risk factor for brain injury. Follow‐up revealed significant improvements in neurodevelopmental outcomes.
Meta‐analysis of an integrated archaeobiological and environmental dataset: Revealing hidden trends in Chalcolithic and Bronze Age socio‐economies in southern Central Asia
Authors: Rouse Lynne M. , Haruda Ashleigh , Hunter Sydney A. , Kroll Sonja 
Published: August 2024

AbstractWe present the results of multivariate and exploratory statistical analyses of a large dataset that includes zooarchaeological, archaeobotanical, chrono‐cultural and proxy environmental data. Data are drawn from published specialist reports from 39 archaeological sites and include 49 distinct chronological contexts dated from the Chalcolithic to Bronze Age (c.5300–1500 BCE) in southern Central Asia. Results support broad observations on the stability of agro‐pastoral subsistence, while indicating that the environment had a minor influence in comparison with the economic and cultural use of species, as revealed through subtle variations across sites and as packages of co‐occurring taxa that link sites within integrated socio‐economies.
Factors affecting peripheral neuropathy induced by nanoparticle albumin‐bound paclitaxel in patients with pancreatic cancer
Authors: Kang Minseo , Yoo Seunghyun , Jung Yeolmae , Lim Hayun , Lee Myeong Hwan , Ryu Ji Kon , Lee Jangik I. 
Published: August 2024

AimChemotherapy‐induced peripheral neuropathy (CIPN) is a major toxicity limiting the use of nab‐paclitaxel (Nab‐P) in treating patients with pancreatic cancer. The aim of this study was to identify the factors affecting CIPN using patient‐reported outcome measures and the minimally invasive volumetric absorptive microsampling (VAMS) technique.MethodsThe maximum concentrations of paclitaxel (Cmax) were measured from 81 VAMS samples collected from 44 participants with pancreatic cancer. The association between CIPN development and demographic, clinical and pharmacokinetic factors was determined using univariable and multivariable logistic regression. The association between CIPN severity and the factors was evaluated using Spearman's rank correlation. The impact of Cmax and the number of treatment cycles on the severity was assessed using multivariable linear regression.ResultsThe development of CIPN was significantly associated with cumulative dose (odds ratio 1.005, 95% confidence interval [CI] 1.003‐1.007), treatment cycles (3.47, 2.25‐5.85), alkaline phosphate (0.992, 0.985‐0.998) and age (1.092, 1.020‐1.179), with an area under the receiver operating characteristic curve of 0.89 (95% CI 0.83‐0.95). The severity of CIPN significantly worsened with increasing cumulative dose (coefficient 0.58, 95% CI 0.44‐0.69), treatment cycles (0.57, 0.44‐0.68) and age (0.18, 0.00‐0.35). The severity of CIPN was predictable from treatment cycles (P = .0002) and Cmax (P = .01).ConclusionThe higher the cumulative dose of Nab‐P, treatment cycles and age, the more frequently and severely do the patients experience CIPN. In predicting the severity of CIPN using Cmax, minimally invasive VAMS is a feasible alternative to venous blood sampling.
Balancing exploration and exploitation? The impact of cost and inhibitory control on information gathering in early childhood
Authors: Iwasaki Shoko , Moriguchi Yusuke , Sekiyama Kaoru 
Published: August 2024

AbstractThe information‐seeking behaviour of adults focuses on optimizing the gathering and utilizing information to minimize search costs. In contrast, children tend to engage in information search during decision‐making with less consideration for costs. This difference in behaviour is believed to be linked to the development of executive functions. Therefore, the present study aimed to investigate the relationship between executive function and cost‐related information‐gathering behaviour. We assessed 56 children aged 4–6 years, involving three tasks: an information‐gathering task, an inhibitory control and a working memory task. In the information‐gathering task, children participated in both non‐cost and cost conditions, where they were given the opportunity to freely gather information or incur a cost to acquire information. The findings revealed that children with higher inhibitory control tended to gather less information when a cost was involved. This highlights the important role of inhibitory control in shaping information‐seeking behaviour in early childhood.
Baicalein Enhances Radiosensitivity in Colorectal Cancer via JAK2/STAT3 Pathway Inhibition
Authors: Yu Qingqing , Tang Rongjun , Mo Weixing , Zhao Linfang , Li Lingdi 
Published: August 2024

ABSTRACTRadiation resistance is a crucial factor influencing therapeutic outcomes in colorectal cancer (CRC). Baicalein (BE), primarily derived from Scutellaria baicalensis, has demonstrated anti‐CRC properties. However, the impact of BE on the radiosensitivity of CRC remains unclear. This study aimed to evaluate the radiosensitization effects of BE and elucidate its mechanism in CRC radiotherapy. We established an in vitro radioresistant cell model (CT26‐R) using parental CRC cells (CT26) subjected to ionizing radiation (IR). CT26‐R cells were pretreated with or without BE, followed by transfection with pcDNA‐NC and pcDNA‐JAK2. The proliferation of CT26‐R cells treated with BE and IR was assessed using a colony formation assay. A CRC animal model was developed in BALB/c mice via CT26‐R cell transplantation. The radiosensitizing effect of BE on CRC was evaluated in vivo. TUNEL assay was conducted to detect apoptosis in tumor tissue. The expression levels of p‐STAT3, JAK2, PD‐L1, and SOCS3 in vitro and in vivo were measured by western blotting. Our results demonstrated that BE significantly increased radiosensitivity in vitro and in vivo and enhanced apoptosis in tumor tissues. Additionally, BE significantly downregulated the expression of p‐STAT3, JAK2, and PD‐L1, and significantly upregulated SOCS3 expression. These in vivo effects were reversed by pcDNA‐JAK2. In summary, our data suggest that BE enhances CRC radiosensitivity by inhibiting the JAK2/STAT3 pathway.
First‐in‐human study evaluating safety, pharmacokinetics, and pharmacodynamics of lorundrostat, a novel and highly selective aldosterone synthase inhibitor
Authors: Shimizu Hidetoshi , Tortorici Michael A. , Ohta Yoshiyasu , Ogawa Kei , Rahman Sheikh Mohammed Ashfaq , Fujii Aya , Hiraga Yuki , Kawai Mizue , Sugimoto‐Kawabata Kanami , van Iersel Mattheus (Thijs) , van Lier Jan Jaap , Djedjos Stephen , Slingsby B. T. , Rodman David M. 
Published: August 2024

AbstractDysregulation of the mineralocorticoid hormone aldosterone is an increasingly prevalent cause of hypertension. Aldosterone synthase (CYP11B2) shares 93% homology to 11β‐hydroxylase (CYP11B1), which produces cortisol. Lorundrostat, a highly selective inhibitor of CYP11B2, is a potential safe and effective treatment for aldosterone‐dependent, uncontrolled hypertension, including treatment‐resistant hypertension. Lorundrostat showed highly selective inhibition of CYP11B2 in vitro, with 374‐fold selectivity for CYP11B2 vs. CYP11B1. A first‐in‐human study of single ascending doses ranging from 5 to 800 mg and multiple ascending doses ranging from 40 to 360 mg once daily was conducted in healthy participants. After single‐ and multiple‐dose administration, lorundrostat plasma levels peaked 1–3 h after administration with a t1/2 of 10–12 h. Plasma aldosterone decreased up to 40% with single 100‐mg to 200‐mg doses and up to 70% with single 400 to 800‐mg doses. Plasma aldosterone returned to baseline within 16 h after single 100‐mg doses and multiple once‐daily 120‐mg doses. Lorundrostat demonstrated a favorable safety profile in healthy participants. Dose‐ and exposure‐dependent inhibition of renal tubular sodium reabsorption was observed across a clinically relevant dose range with no suppression of basal or cosyntropin‐stimulated cortisol production and only a modest increase in mean serum potassium.
Evaluation of PRAME immunohistochemistry in cutaneous vascular neoplasms reveals frequent expression in primary and post‐irradiation cutaneous angiosarcomas
Authors: Krajisnik Andrea , Rezaee Neda , Duncan Eleanor R. , Balzer Bonnie L. , Shon Wonwoo 
Published: August 2024

AbstractBackgroundPreferentially expressed antigen in melanoma (PRAME) has been extensively studied in cutaneous melanocytic tumors and has proven valuable as a diagnostic adjunct in routine dermatopathology practice. However, its expression in cutaneous vascular neoplasms, particularly angiosarcomas (AS), remains largely unexplored.MethodsTo further explore PRAME expression in cutaneous AS, 18 cases of post‐irradiation and 13 cases of primary cutaneous AS were evaluated for PRAME. For comparison, sections from 11 deep soft tissue/visceral AS, 10 Kaposi sarcomas, 8 microvenular hemangiomas, 7 infantile hemangiomas, 8 atypical vascular lesions, 6 epithelioid hemangioendotheliomas, 6 pyogenic granulomas, 6 papillary endothelial hyperplasias, 6 epithelioid hemangiomas, 3 capillovenous malformations, 3 hobnail hemangiomas, 2 spindle cell hemangiomas, 2 pseudomyogenic hemangioendotheliomas, and 2 composite hemangioendotheliomas were also retrieved.ResultsOverall, 22 of 31 (70.9%; 12 post‐irradiation and 10 primary) cutaneous AS were positive for PRAME. In contrast, only 1 of 11 (9.1%) deep soft tissue/visceral AS showed diffuse and strong PRAME nuclear staining. All other tumor types were negative for PRAME, except for 5 of 7 (71.4%) infantile hemangiomas, which demonstrated rare (<5%; four cases) and 1+ (5–25%; one case) nuclear staining.ConclusionsIn this study, we have demonstrated frequent nuclear PRAME expression in cutaneous AS. PRAME immunohistochemistry may serve as a valuable additional marker in selected clinical settings.
Barriers and system improvements for physical activity promotion after gestational diabetes: A qualitative exploration of the views of healthcare professionals
Authors: Ioannou Elysa , Humphreys Helen , Homer Catherine , Purvis Alison 
Published: August 2024

AbstractAimPhysical activity is an important behaviour for managing the ten times increased risk of type 2 diabetes after gestational diabetes. Previous studies exploring physical activity promotion in healthcare focus on general practitioners but have not explored the gestational diabetes pathway. Therefore, this paper explores the barriers to and suggestions for, activity promotion along the gestational diabetes healthcare pathway.MethodsThe paper was written in accordance with the Standards for Reporting Qualitative Research. Patient and Public Involvement with women who had lived experiences of gestational diabetes informed purposeful sampling by identifying which healthcare professional roles should be targeted in participant recruitment. Participants were recruited through word‐of‐mouth, that is, email and connections with local healthcare service leads. Twelve participants took part in semi‐structured one‐to‐one interviews, analysed using reflexive thematic analysis.ResultsParticipants included a Public Health Midwife (n = 1), Diabetes Midwifes (n = 3), Diabetes Dietitian (n = 1), Diabetes Consultants (n = 2), Diabetes Specialist Nurse (n = 1), general practitioners (n = 2), Practice nurse (n = 1) and a Dietitian from the UK National Diabetes Prevention Program (n = 1). Six themes were generated: ‘management of gestational diabetes takes precedent’, ‘poor continuity of care’, ‘lack of capacity to promote PA’, ‘beliefs about the acceptability of PA promotion’, ‘resources to support conversations about PA’ and ‘adapting healthcare services for women post‐gestational diabetes’.ConclusionsDuring pregnancy messaging around physical activity is consistent, yet this is specific for managing gestational diabetes and is not followed through postnatally. Improvements in continuity of care are necessary, in addition to ensuring the availability and links with wider exercise and activity schemes.
Prohydrojasmon treatment of Brassica juncea alters the performance and behavioural responses of the cabbage aphid, Brevicoryne brassicae
Authors: Ali Jamin , Xiao Feng , Alam Aleena , Li Liu Jia , Ji YunLiang , Chao Wu Hai , Weibo Qin , Xie Aocong , Zengyi Bi , M. Abdel Hafez Mogeda , Ghramh Hamed A. , Khan Khalid Ali , Tonğa Adil , Chen Rizhao 
Published: August 2024

AbstractPlants encounter a myriad of biotic and abiotic stresses throughout their life cycle, among which aphids pose a significant challenge as herbivorous insect pests. Aphids cause both direct damage through feeding and indirect damage by transmitting viruses. Given the growing concerns about insecticide resistance and the non‐target effects of synthetic insecticides, there is an urgent need to develop novel pest control strategies that are dependent on plant defence strategies. In this study, we assessed the effects of exogenous prohydrojasmon (PDJ), a derivative of jasmonic acid, at 24 h (PDJ24) and 48 h (PDJ48) post‐treatment on the cabbage aphid, Brevicoryne brassicae L. (Hemiptera: Aphididae), feeding on Brassica juncea L. (Brassicaceae). The impact of PDJ treatments was assessed by conducting performance bioassays (survival and fecundity) and behavioural bioassays (settlement and attraction to volatiles in an olfactometer). Our findings reveal that the exogenous application of PDJ did not significantly affect on the performance and behaviour of B. brassicae at 24‐h post‐treatment. However, PDJ treatment significantly reduced the performance of B. brassicae at 48‐h post‐treatment, and affected the behaviour in terms of reduced settlement on and attraction to volatiles of PDJ‐treated plants. These results suggest that PDJ has the potential to effectively induce defences in Brassica against sucking pests. This study provides valuable insights into possibility of employing PDJ as an alternative approach for sustainable pest management in agriculture.