bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex interplay between the microfluidic and optical properties of Hoplia sp. beetles
Authors: Pavlović Danica , Salatić Branislav , Ćurčić Srećko , Milovanović Petar , Pantelić Dejan V. 
Published: November 2024

Abstract
Background
All living organisms exist in a world affected by many external influences, especially water and light. Photonic nanostructures present in certain insects, have evolved over time in response to diverse environmental conditions, facilitating communication within and between species, camouflage, thermoregulation, hydration, and more. Up to now, only a few insect species have been discovered whose elytron changes its color due to permeation of water (or its vapor) through cuticle.

Results
Here we report on a scarabaeid beetle Hoplia argentea remarkable in its ability to shift from green to brownish-red when exposed to water, demonstrating reversible changes. Here we show that elytron and scales form a complex and efficient micro/nano-optofluidic system. Water is channeled into the elytral lacunae, then transported internally to the petals of the scales, where it is wicked inside each scale, pushing the entrapped air out. Wicking is a very fast process, occurring during a few seconds. The advantage of this principle is in extremely high pressure (approximately 15 bar) produced by capillary forces, which expediates permeation of air. We present optical models that explain the physical mechanisms behind the coloration, detailing how superhydrophilic properties influence optical behavior.

Conclusion
Species within the genus Hoplia exhibit diverse coloration strategies, likely linked to their specific ecological niches. These organisms have evolved intricate optical and microfluidic systems that facilitate rapid alterations in body coloration, potentially serving purposes such as environmental camouflage and thermoregulation. Studying microfluidic and optical properties of the elytra will not only enhance our understanding of the biological purposes behind color change but also inspires design of artificial biomimetic devices. Dynamic fluid flow patterns, described in this paper, are fairly constant and unique and can be used in security applications as a, so called, physically unclonable functions (PUF). More broadly, this kind of microfluidic system can be used for controlled drug release, sensing, hydraulic and pneumatic pumping.
BerryPortraits: Phenotyping Of Ripening Traits in cranberry (Vaccinium macrocarpon Ait.) with YOLOv8
Authors: Loarca Jenyne , Wiesner-Hanks Tyr , Lopez-Moreno Hector , Maule Andrew F. , Liou Michael , Torres-Meraz Maria Alejandra , Diaz-Garcia Luis , Johnson-Cicalese Jennifer , Neyhart Jeffrey , Polashock James , Sideli Gina M. , Strock Christopher F. , Beil Craig T. , Sheehan Moira J. , Iorizzo Massimo , Atucha Amaya , Zalapa Juan 
Published: November 2024

Abstract
BerryPortraits (Phenotyping of Ripening Traits) is open source Python-based image-analysis software that rapidly detects and segments berries and extracts morphometric data on fruit quality traits such as berry color, size, shape, and uniformity. Utilizing the YOLOv8 framework and community-developed, actively-maintained Python libraries such as OpenCV, BerryPortraits software was trained on 512 postharvest images (taken under controlled lighting conditions) of phenotypically diverse cranberry populations (Vaccinium macrocarpon Ait.) from the two largest public cranberry breeding programs in the U.S. The implementation of CIELAB, an intuitive and perceptually uniform color space, enables differentiation between berry color and berry brightness, which are confounded in classic RGB color channel measurements. Furthermore, computer vision enables precise and quantifiable color phenotyping, thus facilitating inclusion of researchers and data analysts with color vision deficiency. BerryPortraits is a phenotyping tool for researchers in plant breeding, plant genetics, horticulture, food science, plant physiology, plant pathology, and related fields. BerryPortraits has strong potential applications for other specialty crops such as blueberry, lingonberry, caneberry, grape, and more. As an open source phenotyping tool based on widely-used python libraries, BerryPortraits allows anyone to use, fork, modify, optimize, and embed this software into other tools or pipelines.
Study of rotavirus genotypes G and P in one Egyptian center-cross-sectional study
Authors: Mahmoud AbelRahman Eid , Zaki Maysaa El Sayed , Mohamed Eman Hamdy , Fahmy Ehab M. , Hamam Sanaa Samir Mohamed , Alsayed Mona Abdellatif 
Published: November 2024

Abstract
Background
Rotavirus-associated gastroenteritis is a common health problem in children, different variations of rotavirus genotypes differ according to geographic locations and the practice of wide-scale vaccination. Therefore, the present study aimed to detect both the G and P genotypes of rotavirus in children ≤ 5 years old in one center in Egypt as a cross-sectional study, to correlate the genotypes with various demographic and clinical data in infected children and to evaluate the common mixed genotypes G and P in infected children.

Method
The cross-sectional study included children with acute gastroenteritis ≤ 5 years old from January 2023 till March 2024 recruited from Mansoura University Children’s Hospital, Egypt based upon laboratory diagnosis by exclusion of bacterial and protozoa pathogens. The stool samples were obtained from each child and subjected to detection of rotavirus antigen by enzyme-linked immunosorbent assay (ELISA) followed by genotypes identification of G and P genotypes by nested polymerase chain reaction (PCR).

Result
A nested PCR study for rotavirus genotypes revealed that G1 was the most common genotype (24.7%) followed by G2 (21.1%), G3 (20%), G9 (20%), and G4 (14.1%). The genotyping of the P genotype revealed that P9 was the commonest genotype (24.7%), followed by P4 (21.2%), P10 (20%), P8 (17.6%) and P6 (16.5%). The commonest combined genotypes of G and P were G1P4 (85.7%), G3P8(88.2%), followed by G2P6 (77.8%) and G9P9(76.5%) and G4P9 (66.7%) followed by G4P10 (33.3%), G9P10(23.5%), G2P10(22.2%), G1P10 (14.3%), G3P10(11.8%). The distribution was significant (P = 0.001). The positive rotavirus antigen was more frequently detected in females (55.3%) than males (44.7%, Odd ratio 0.2, 95% CI 0.22–0.71, P = 0.001). There was a significant association between the summer season and positive rotavirus antigen (P = 0.001) and rural residence of the patients (Odd ratio 6,9 95%CI 3,5-13.5, P = 0.001). The significant associated clinical sign with positive rotavirus antigen was fever (Odd ratio 3,3, 95%CI 1,8-6.05, P = 0.001). The genotypes G and P were significantly associated with positive rotavirus antigen as all cases positive by antigen had been detected by nested PCR with the commonest genotypes G4 (24.7%, P = 0.001) and genotype P9 (24.7%, P = 0.001).

Conclusion
The present study highlights the common genotypes of rotavirus at one center in Egypt, G1, G2, and G3 were the commonest G genotypes. As regard genotype P the commonest genotypes were P9, P4, and P10. The commonest combined genotypes were G1P4, G3P8, G2P6. There was no effect of the practice of rotavirus vaccination at limited rates at private health sections as the rotavirus is still a major pathogen of acute gastroenteritis in children. There is a need for the inclusion of rotavirus vaccination in the national program of children vaccination in Egypt.
Analysis of variable metabolites in preterm infants with bronchopulmonary dysplasia: a systematic review and meta-analysis
Authors: Guo Yanping , Liu Ying , Zhang Ruolin , Xu Songzhou , Guo Xin , Yu Zhangbin , Chen Guobing 
Published: November 2024

AbstractNumerous studies have attempted to identify potential biomarkers for early detection of bronchopulmonary dysplasia (BPD) in preterm infants using metabolomics techniques. However, the presence of consistent evidence remains elusive. Our study aimed to conduct a systematic review and meta-analysis to identify differences in small-molecule metabolites between BPD and non-BPD preterm infants. Through meticulous screening of numerous samples, we identified promising candidates, providing valuable insights for future research. We searched PubMed, the Cochrane Library, Embase, Web of Science, China National Knowledge Internet, Wan-fang database, Chinese Science and Technique Journal Database and Chinese Biomedical Literature Database from inception until January 16, 2024. Studies were comprehensively reviewed against inclusion criteria. We included case-control studies and adhered to Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Study quality was assessed with the Newcastle-Ottawa scale. We compared the changes in metabolite levels between the BPD and non-BPD preterm infants. A meta-analysis was conducted on targeted metabolomics research data based on the strategy of standardized mean differences (MD) and 95% confidence intervals (CI).Fifteen studies (1357 participants) were included. These clinical-based metabolomics studies clarified 110 differential metabolites between BPD and non-BPD preterm infants. The meta-analysis revealed higher glutamate concentration in the BPD group compared to the non-BPD group (MD = 1, 95% CI 0.59 to 1.41, p < 0.00001). Amino acids were identified as the key metabolites distinguishing preterm infants with and without BPD, with glutamate potentially serving as a BPD predictor in this population.
Breast cancer and ATM mutations: treatment implications
Authors: Seca Marta , Narod Steven A. 
Published: November 2024

AbstractGenetic testing for breast cancer predisposing genes has expanded beyond BRCA1 and BRCA2 and now includes panels of 20 or more genes. It is now recommended that all women diagnosed with breast cancer at age 65 or below be offered testing for an extended gene panel. The rationale for testing includes personalizing the management of breast cancer according to the mutation found. For BRCA1 and BRCA2 carriers, the finding of a mutation has clear implications for cancer management, but for other genes, such as ATM, the management implications are less clear. Women with an ATM mutation have a lifetime risk of breast cancer of approximately 25%, the majority of which are ER-positive. The risk of ovarian cancer is approximately 5%. It is not yet clear how the identification of an ATM mutation in a patient newly diagnosed with breast cancer should impact on her treatment and follow-up. At present, these women are treated in the same way as women without a mutation. It is important that large prospective studies be conducted looking at various treatment modalities in women with breast cancer and an ATM mutation in order to optimize outcomes.
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Authors: Yuan Tianyu , Yan Hao , Li Kevin C. , Surovtsev Ivan , King Megan C. , Mochrie Simon G. J. 
Published: November 2024

Abstract
Background
Inhomogeneous patterns of chromatin-chromatin contacts within 10–100-kb-sized regions of the genome are a generic feature of chromatin spatial organization. These features, termed topologically associating domains (TADs), have led to the loop extrusion factor (LEF) model. Currently, our ability to model TADs relies on the observation that in vertebrates TAD boundaries are correlated with DNA sequences that bind CTCF, which therefore is inferred to block loop extrusion. However, although TADs feature prominently in their Hi-C maps, non-vertebrate eukaryotes either do not express CTCF or show few TAD boundaries that correlate with CTCF sites. In all of these organisms, the counterparts of CTCF remain unknown, frustrating comparisons between Hi-C data and simulations.

Results
To extend the LEF model across the tree of life, here, we propose the conserved-current loop extrusion (CCLE) model that interprets loop-extruding cohesin as a nearly conserved probability current. From cohesin ChIP-seq data alone, we derive a position-dependent loop extrusion rate, allowing for a modified paradigm for loop extrusion, that goes beyond solely localized barriers to also include loop extrusion rates that vary continuously. We show that CCLE accurately predicts the TAD-scale Hi-C maps of interphase Schizosaccharomyces pombe, as well as those of meiotic and mitotic Saccharomyces cerevisiae, demonstrating its utility in organisms lacking CTCF.

Conclusions
The success of CCLE in yeasts suggests that loop extrusion by cohesin is indeed the primary mechanism underlying TADs in these systems. CCLE allows us to obtain loop extrusion parameters such as the LEF density and processivity, which compare well to independent estimates.
Identification and transfer to stepped care of depressed and psychosocially stressed parents during peri- and postpartum—UPlusE: study protocol for cluster randomized trial of a screening intervention
Authors: Stentzel Ulrike , van den Berg Neeltje , Lanczik Freya , Gehrmann Andrea , Nehring Ina , Mall Volker , Friedmann Anna , Seivert Carolin , Schade Stefanie , Fusch Christoph ,   UPlusE-group, Bauer Ines , Emgenbroich Anke , Radau Tilo , Jonas-Dieke Sebastian , Monks Sean , Kittel-Schneider Sarah , Simen Susanne 
Published: November 2024

Abstract
Background
Perinatal depression affects 10–15% of mothers and approximately 5% of fathers. However, only a small number of affected individuals seek treatment. If left unrecognized and untreated, it can have negative long-term consequences for the family’s health, leading to subsequent high costs. Early treatment is crucial, yet there is a notable underdiagnosis and undertreatment. Affected individuals are often seen during this time, e.g. in paediatric practices, but not by specialists in mental health. Consequently, this study aims to increase detection and treatment rates of affected individuals by implementing a screening for depression and psychosocial stress in perinatal and postpartum parents within routine obstetric and paediatric care with subsequent advice and—if necessary—further referral to a mental health specialist.

Methods
UPlusE is a prospective, cluster-randomized controlled trial conducted in an outpatient setting. Obstetric and paediatric practices will be randomized into an intervention and control group (1:1 ratio). Practices and enrolling patients will be required to use specific smartphone apps (practice apps) for interaction. The screening will occur with the apps at each paediatric checkup up to the child’s age of 12 months, using the Edinburgh Postnatal Depression Scale (EPDS), KID-PROTEKT questionnaire, and the scale 1 (impaired bonding) of the Postpartum Bonding Questionnaire (PBQ-1). The goal is to screen 10,000 patients across Germany. Gynaecologists and paediatricians will receive certified training on peripartum depression. Participants in the intervention group with scores above cut-offs (EPDS ≥ 10, KID-PROTEKT ≥ 1, PBQ-1 ≥ 12) will receive counselling through their treating gynaecologists/paediatricians and will be provided with regional addresses for psychiatrists, psychotherapists, and “Frühe Hilfen” (early prevention) as well as family counselling centres, depending on symptom severity. At each screening, participants will be asked whether they sought support, where, and with whom (utilization). Utilization is the primary outcome.

Discussion
The screening is designed to reduce underdiagnosis to enable suitable support at an early stage (especially for those often overlooked, such as individuals with “high-functioning depression”) and hence to avoid manifestation of mental health problems in the whole family, especially infants who are exceptionally dependent on their parents and their well-being will benefit from this program.

Trial registration
German Clinical Trials Register, DRKS00033385. Registered on 15 January 2024.
Targeted dsRNA-mediated suppression of Phytophthora infestans infection via Avr3a
Authors: Lee Hyeonmin , Park Minsu , Kweon Yujin , Lee Dowhan , Shin Chanseok 
Published: November 2024

AbstractPhytophthora infestans (P. infestans) is a highly destructive oomycete that causes the late blight in Solanaceous crops, such as potatoes and tomatoes, reducing crop yield. Although many pesticides are used to control P. infestans, the pathogen has evolved resistance to these chemical pesticides over time. In this study, we employed RNAi technology as an alternative strategy to suppress P. infestans infection. We designed and synthesized two dsRNAs targeting 5' and 3' regions of the Avirulence Protein 3a (Avr3a) gene, a key effector essential for the virulence of P. infestans. Interestingly, the dsRNA targeting the 5' region which contains the conserved RxLR-EER motif of Avr3a exhibited more substantial suppression of P. infestans infection and Avr3a expression level compared to the 3' region targeting dsRNA. Additionally, we identified changes in the expression of genes related to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants treated with these dsRNAs. In leaves treated with dsRNAs targeting Avr3a, the expression of PTI-related genes was restored, while ETI-related genes showed lower expression levels compared to the mock-treated leaves. These results suggest that dsRNAs targeting Avr3a effectively suppress P. infestans infection, enabling plants to achieve balanced immunity and enhanced defense.
Cardiac arrhythmias during and after thoracic irradiation for malignancies
Authors: Heckmann Markus B. , Münster Jan P. , Finke Daniel , Hund Hauke , Schunn Fabian , Debus Jürgen , Mages Christine , Frey Norbert , Rahm Ann-Kathrin , Lehmann Lorenz H. 
Published: November 2024

Abstract
Background
Cardiac arrhythmia has been reported as a significant complication of thoracic radiotherapy. Both bradyarrhythmias and tachyarrhythmias have been reported, highlighting the arrhythmia-modulating potential of radiation in certain oncologic therapies. This study aimed to analyse the arrhythmic burden in patients with cardiac implantable electrical devices (CIEDs) undergoing thoracic irradiation, examining both immediate effects of radiotherapy and long-term sequelae post-therapy.

Methods and results
A retrospective cohort study was conducted involving patients with CIEDs who received thoracic radiotherapy between January 2012 and December 2022. Two distinct analyses were performed involving (1) daily CIED follow-ups during radiotherapy and (2) long-term arrhythmic outcomes post-therapy. For long-term outcomes, Patients were matched in a 1:2 ratio with non-irradiated controls based on age, sex, cardiovascular risk factors, cardiac disease, and beta-blocker use. Statistical analyses included negative binomial regression and propensity score matching. A total of 186 patients underwent daily CIED monitoring during radiotherapy, with 79 receiving thoracic irradiation. Thoracic irradiation was negatively associated with atrial arrhythmia (OR 0.11 [0.02;0.70, 95% CI], adjusted p = 0.0498) and there was a tendency towards less ventricular events (OR 0.14 [0.02;1.41, 95% CI], adjusted p = 0.3572) during radiotherapy in a univariate regression analysis. This association was not significant in the multivariate (OR 0.44 [0.10;1.80, 95%-CI], p = 0.16) model including a history of atrial fibrillation, diabetes and beta-blocker use. Coronary artery disease was associated with an increase in atrial and ventricular arrhythmia. For the long-term analysis, 122 patients were followed up after thoracic (N = 33) and non-thoracic radiation (N = 89) and compared to 244 matched controls drawn from approximately 10.000 CIED-patients. There was no significant increase in arrhythmic events compared to controls over a median follow-up of 6.6 months. A previous history of ventricular or atrial arrhythmic events was the strongest predictor for events during the follow-up.

Conclusion
Thoracic radiotherapy can be safely administered in patients with CIEDs. However, patients with a history of arrhythmia are more prone to arrhythmic events during and after radiation. These findings highlight the need for personalized arrhythmia management strategies and further research to understand the mechanisms underlying the antiarrhythmic effects of thoracic radiation.

Graphical Abstract
Fine construction of gene coexpression network analysis using GTOM and RECODE detected a critical module of neuroblastoma stages 4 and 4S
Authors: Nakamura Fumihiko , Nakano Yushi , Yamada Shiro 
Published: November 2024

Abstract
Background
Stage 4 neuroblastoma (NBL), a solid tumor of childhood, has a poor prognosis. Despite intensive molecular genetic studies, no targetable gene abnormalities have been identified. Stage 4S NBL has a characteristic of spontaneous regression, and elucidation of the mechanistic differences between stages 4 and 4S may improve treatment. Conventional NBL studies have mainly focused on the detection of abnormalities in individual genes and have rarely examined abnormalities in gene networks. While the gene coexpression network is expected to contribute to the detection of network abnormalities, the fragility of the network due to data noise and the extraction of arbitrary topological structures for the high-dimensional network are issues.

Results
The present paper concerns the classification method of stages 4 and 4S NBL patients using highly accurate gene coexpression network analysis based on RNA-sequencing data of transcription factors (TFs). In particular, after applying a noise reduction method RECODE, generalized topological overlapping measure (GTOM), which weighs the connections of nodes in the network structure, succeeded in extracting a cluster of TFs that showed high classification performance for stages 4 and 4S. In addition, we investigated how these clusters correspond to clinical information and to TFs which control the normal adrenal tissue and NBL characters.

Conclusions
A clustering method is presented for finding intermediate-scale clusters of TFs that give considerable separation performance for distinguishing between stages 4 and 4S. It is suggested that this method is useful as a way to extract factors that contribute to the separation of groups from multiple pieces of information such as gene expression levels.
Relationship between exercise habits and social isolation in older patients with predialysis CKD: a cross-sectional study
Authors: Tabata Aki , Yabe Hiroki , Katogi Takehide , Mitake Yuya , Oono Shunta , Yamaguchi Tomoya , Fujii Takayuki 
Published: November 2024

Abstract
Background
Maintaining exercise habits in older patients with predialysis chronic kidney disease (CKD) is important to prevent conversion to renal replacement therapy and improve prognosis. This study identified factors influencing exercise habits in older patients with predialysis CKD.

Methods
This cross-sectional study included 113 patients aged ≥ 65 years with stages 3–5 predialysis CKD who were admitted for CKD education purposes. Exercise habits were assessed using the transtheoretical model. Social isolation was assessed using the Lubben Social Network Scale (LSNS-6). Furthermore, the short physical performance battery (SPPB) and grip strength, exercise self-efficacy (SE), hemoglobin, and estimated glomerular filtration rate of the participants were assessed.

Results
Among the 55 patients who maintained exercise habits, 20 (57.1%) were at CKD stage 3, 19 (43.2%) were at CKD stage 4, and 16 (47.1%) were at CKD stage 5. The LSNS-6, SPPB, grip strength, and exercise SE scores significantly differed between the with exercise habits group and without exercise habits group (p < 0.05). The multivariate logistic regression analysis results indicated that the LSNS-6 (OR:1.10; 95%CI:1.022–1.210) and exercise SE (OR:1.10; 95%CI:1.009–1.199) were significantly associated with exercise habits (p < 0.05). Conversely, no significant associations were found between exercise habits and SPPB, grip strength, renal function, or anemia.

Conclusions
Social isolation and SE may be an important factor influencing exercise habits in older patients with predialysis CKD.