bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity
Authors: Aldrovandi Silvia , Fajardo Castro Johana , Ullrich Kristian , Karger Amir , Luria Victor , Tautz Diethard 
Published: December 2024

Abstract
Proteins that emerge de novo from noncoding DNA could negatively or positively influence cellular physiology in the sense of providing a possible adaptive advantage. Here, we employ two approaches to study such effects in a human cell line by expressing random sequences and mouse de novo genes that lack homologs in the human genome. We show that both approaches lead to differential growth effects of the cell clones dependent on the sequences they express. For the random sequences, 53% of the clones decreased in frequency, and about 8% increased in frequency in a joint growth experiment. Of the 14 mouse de novo genes tested in a similar joint growth experiment, 10 decreased, and 3 increased in frequency. When individually analysed, each mouse de novo gene triggers a unique transcriptomic response in the human cells, indicating mostly specific rather than generalized effects. Structural analysis of the de novo gene open reading frames (ORFs) reveals a range of intrinsic disorder scores and/or foldability into alpha-helices or beta sheets, but these do not correlate with their effects on the growth of the cells. Our results indicate that de novo evolved ORFs could easily become integrated into cellular regulatory pathways, since most interact with components of these pathways and could therefore become directly subject to positive selection if the general conditions allow this.
Genome Assembly and Winged fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses
Authors: Geng Fangdong , Zhang Xuedong , Ma Jiayu , Liu Hengzhao , Ye Hang , Hao Fan , Liu Miaoqing , Dang Meng , Zhou Huijuan , Li Mengdi , Zhao Peng 
Published: December 2024

Abstract
The genomic basis and biology of winged fruit are interesting issues in ecological and evolutionary biology. Chinese wingnut (Pterocarya stenoptera) is an important garden and economic tree species in China. The genomic resources of this hardwood tree could provide advanced genomic studies of Juglandaceae and their evolutionary relationships. Here, we reported a high-quality reference genome of P. stenoptera (N50 = 35.15 Mb) and provided a comparative analysis of Juglandaceae genomes. Paralogous relationships among the 16 chromosomes of the Chinese wingnut genome revealed eight main duplications representing the subgenome. Molecular dating suggested that the most recent common ancestor of P. stenopetera and Cyclocarya paliurus diverged from Juglans around 56.7 million years ago (Mya). The expanded and contracted gene families were associated with cutin, suberine, and wax biosynthesis, cytochrome P450, and anthocyanin biosynthesis. We identified large inversion blocks between the P. stenoptera genome and its relatives, which are enriched in genes related lipid biosynthesis and metabolism, and starch and sucrose metabolism. The twenty-eight individuals were clearly clustered into three groups responding to three species, namely Pterocarya macroptera, Pterocarya hupehensis, and P. stenoptera, based on whole genome resequencing data. Morphological and gene expression analysis showed that CAD, COMT, LOX, and MADS-box play important roles during the five developmental stages of wingnuts. Our study highlights the evolutionary history of the P. stenoptera genome and supports P. stenoptera as an appropriate Juglandaceae model for studying winged fruits. These results provide a theoretical basis for the evolution, development, and diversity of woody plant winged fruits.
Design and analysis of a hydrogen production system using hybrid concentrated photovoltaic thermal system integrated with an organic Rankine cycle
Authors: AL-Zoubi Omar H , Dhaliwal Arshdeep Singh , Trivedi Tapankumar , Shomurotova Shirin , Foladi Ali 
Published: December 2024

Abstract
This study evaluates an improved organic Rankine cycle (ORC) with a solar energy source for hydrogen production and presents functional results, validation, and sensitivity analysis. The increase in condenser outlet temperature causes a decrease in the total thermal efficiency, a decrease in the efficiency of the ORC, a decrease in the total electrical efficiency, and a decrease in hydrogen production. The most striking result is that the net generating power of the system is equal to 4200 W, which is equivalent to producing 0.02372 g/s of hydrogen and 0.0810 g/s of oxygen.
Weather Shocks in The Gambia: Macroeconomic Effects and Households Vulnerability
Authors: Bayo Ebrima , Busato Francesco , Cisco Gianluigi , Ferrara Maria 
Published: December 2024

Abstract
Climate change is increasing the frequency of weather shocks, which poses a significant challenge for agriculture-dependent economies such as those of sub-Saharan African countries. In this study, we present an innovative framework that combines empirical and theoretical procedures to investigate the propagation mechanism of weather shocks in The Gambia. We first document the propagation mechanism of a weather shock using a Structural Vector Auto-regressive (SVAR) model on the Gambia data. We construct and estimate a Dynamic Stochastic General Equilibrium (DSGE) model to elucidate this mechanism. This model is enhanced to encapsulate the weather-dependent agricultural sector, the heterogeneity of households in terms of access to financial markets and the inflow of remittances. Our findings reveal that weather shocks in The Gambia (i) account for approximately 10% of GDP and agricultural output in the short run, (ii) significantly contribute to long-term consumption volatility,(iii) critically increase the volatility of Ricardian households’ consumption and (iv) stimulate an increase in the direct inflow of remittances to vulnerable households.
Moult cycle and setal development of the Atlantic ditch shrimp Palaemon varians Leach, 1814 (Decapoda: Caridea: Palaemonidae)
Authors: Kim Kenneth , Antcliffe Jonathan , Daley Allison C , Robinson-Rechavi Marc 
Published: December 2024

Abstract
The Atlantic ditch shrimp Palaemon varians Leach, 1814 is a common estuarine and brackish water species on Northern Atlantic coasts. Palaemon varians is an appealing model organism for studying arthropod developmental processes, such as moulting (ecdysis). Detailed morphological information on its moult cycle is still lacking, hence we have characterised the changes in the setal features corresponding to the moult stages of P. varians grown under laboratory conditions. The stages of the moult cycle were differentiated and described using microscopic analysis of the setae in the uropods of P. varians based on Drach’s classification system. Moult stages were defined as early and late post-moult (A and B), inter-moult (C), early-, mid- and late pre-moult (D0, D1, and D2), as well as ecdysis stage (E), the actual shedding of the exuvia. Average moult cycle duration was 8.7 days, where pre-moult accounted for the longest duration of 4.4 days on average. This study provides a morphological reference for determining the moult stage of P. varians without the use of invasive techniques, and thus it is well suited for repetitive observations of an individual to track the entire moulting process.
Characterizing hip joint morphology using a multitask deep learning model
Authors: Khosravi Bardia , Bukowiec Lainey G , Mickley John P , Oeding Jacob F , Rouzrokh Pouria , Erickson Bradley J , Sierra Rafael J , Taunton Michael J , Grigoriou Emmanouil , Wyles Cody C 
Published: December 2024

Abstract
Deep learning is revolutionizing medical imaging analysis by enabling the classification of various pathoanatomical conditions at scale. Unfortunately, there have been a limited number of accurate and efficient machine learning (ML) algorithms that have been developed for the diagnostic workup of morphological hip pathologies, including developmental dysplasia of the hip and femoroacetabular impingement. The current study reports on the performance of a novel ML model with YOLOv5 and ConvNeXt-Tiny architecture in predicting the morphological features of these conditions, including cam deformity, ischial spine sign, dysplastic appearance, and other abnormalities. The model achieved 78.0% accuracy for detecting cam deformity, 87.2% for ischial spine sign, 76.6% for dysplasia, and 71.6% for all abnormalities combined. The model achieved an Area under the Receiver Operating Curve of 0.89 for ischial spine sign, 0.80 for cam deformity, 0.80 for dysplasia, and 0.81 for all abnormalities combined. Inter-rater agreement among surgeons, assessed using Gwet’s AC1, was substantial for dysplasia (0.83) and all abnormalities (0.88), and moderate for ischial spine sign (0.75) and cam deformity (0.61).
Patents, gendered bodies and innovation: a case study on contraceptives
Authors: Lai Jessica C 
Published: December 2024

Abstract
The Anthropocene, while a recently popularized term, is part of a long history theorizing human impact globally. Since the 1970s, a chief focus of modulating this impact was population control. While the Anthropocene is about the human impact on the Earth, to date, the contraceptive burden lies with women, using invasive technologies that can have highly detrimental side effects. This article uses patent records to consider the sources of this disparity, including how post-grant patent law theories based on incentives to innovate ignore gender narratives and the varying ways in which society evaluates different bodies, and how this has different consequences for invention and innovation. As we are not yet in a post-gender world, it is important that our post-grant patent theory considers gender. This is necessary if we are to meet the challenges that face all of humankind.
Treatise on International Criminal Law
Authors: Ambos Kai 
Published: December 2024

Abstract
Since the adoption of the Rome Statute of the International Criminal Court (ICC) in 1998, international criminal law has rapidly grown in importance. This fully updated new edition of the third volume of a Treatise on International Criminal Law offers a comprehensive analysis of the procedures and implementation of international law by international criminal tribunals and the ICC. Through analysis of the framework of international criminal procedure, this volume considers each stage in the process of proceedings before the ICC, including the role of legal participants, the scope of jurisdiction, and the enforcement of sentences. This new edition has been expanded to include updated case law and relevant scholarly literature. Among others, it contains new (sub)sections on non-judicial investigative mechanisms, special forms of digital evidence, the ‘submission approach’ to material and information, trial management, and political elements within the ‘interests of justice’. The full three-volume Treatise addresses the entirety of international criminal law, re-stating and re-examining the fundamental principles upon which it rests, the manner in which it is enacted, and the key issues that are shaping its future. It is essential reading for practitioners, scholars, and students of international criminal law alike.
Why Wooden Artifacts of Historical and Cultural Importance Remain Well Preserved for Millennia in Waterlogged Buried Environments: Microscopy Provides a Clue
Authors: Singh Adya P , Chavan Ramesh R , Singh Shruti , Bari Ehsan 
Published: December 2024

Abstract
Prehistoric and man-made ancient wooden artifacts are continually being uncovered from anoxic waterlogged burial environments where they are protected from highly destructive oxygen-dependent wood-degrading fungi. Microscopy has played a crucial role in understanding why such valuable buried objects remain well preserved for millennia. Suitable microscopy techniques have revealed that under anoxic burial conditions, wood is attacked mainly by erosion bacteria, which are well adapted to functioning in such environments, but the speed of wood degradation is extremely slow, in most cases resulting only in surface deterioration even after thousands of years of burial of wooden objects. The information emerging from microscopy studies is also proving crucial in more precise targeting of technology development to adequately conserve/restore the excavated precious wooden artifacts for human benefit.
The Impact of Image Quality on Reliable and Specific Colocalization Analysis
Authors: Pelle Robin A , Ram Michel , Hemmerich Peter , Bottomley Amy L , Cole Louise , Berlinguer-Palmini Rolando , van der Voort Hans T M , van der Voort Nicolaas T M , Schoonderwoert Vincent T G 
Published: December 2024

Abstract
Colocalization analysis is a well-established method to quantify the extent to which fluorescent signal of two different objects or molecule populations are related. Irrespective of the chosen colocalization approach (correlation, co-occurrence, or object-based), the results are fiercely affected by factors such as image background, noise, crosstalk, chromatic aberration, and the diffraction barrier of the optical microscope. Diffraction leads to a blurry appearance of the captured image as each point emitter is represented by the point spread function (PSF) in the image. The PSF structure is also highly dependent on the wavelength of the fluorophore and the type of microscope used for imaging. For example, confocal imaging would show two-point emitting fluorophores as colocalized within its 200 nm lateral resolution limit due to its relatively large PSF, whereas array detector, SMLM, or STED imaging may resolve these same objects as two distinct points. With its capacity to increase the resolution of both super-resolution and conventional microscopy data, deconvolution offers similarly more defined colocalization results by improving resolution, correcting out-of-focus signal, and reducing noise. In this article, we summarize the imaging conditions affecting colocalization analysis with a strong focus on image deconvolution and restoration. We present a range of tools in Huygens Software™ to correct for these imaging aberrations so that, when collectively applied, the fidelity of colocalization analysis is significantly enhanced.
A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation
Authors: Bian Peipei , Li Jiaxin , Zhou Shishuo , Wang Xingquan , Gong Mian , Guo Xi , Cai Yudong , Yang Qimeng , Fu Jiaqi , Li Rongrong , Huang Shuhong , Luo Funong , Shah Ali Mujtaba , Lenstra Johannes A , Mwacharo Joram M , Li Ran , Ren Gang , Wang Xiaolong , Li Cong , Zheng Wenxin , Jiang Yu , Wang Xihong 
Published: December 2024

Abstract
Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.
Evolutionary Novelty of Apolipoprotein D Facilitates Metabolic Plasticity in Lepidopteran Wings
Authors: Jia Shunze , Li Rongqiao , Li Yinghui , Huang Yuxin , Liu Minmin , Zhou Yanyan , Liang Yanting , Hao Zhihua , Xu Yusong , Wang Huabing 
Published: December 2024

Abstract
Understanding metabolic plasticity of animal evolution is a fundamental challenge in evolutionary biology. Owing to the diversification of insect wing morphology and dynamic energy requirements, the molecular adaptation mechanisms underlying the metabolic pathways in wing evolution remain largely unknown. This study reveals the pivotal role of the duplicated Apolipoprotein D (ApoD) gene in lipid and energy homeostasis in the lepidopteran wing. ApoD underwent significant expansion in insects, with gene duplication and consistent retention observed in Lepidoptera. Notably, duplicated ApoD2 was highly expressed in lepidopteran wings and encoded a unique C-terminal tail, conferring distinct ligand-binding properties. Using Bombyx mori as a model organism, we integrated evolutionary analysis, multiomics, and in vivo functional experiments to elucidate the way duplicated ApoD2 mediates lipid trafficking and homeostasis via the AMP-activated protein kinase pathway in wings. Moreover, we revealed the specific expression and functional divergence of duplicated ApoD as a key mechanism regulating lipid homeostasis in the lepidopteran wing. These findings highlight an evolutionary scenario in which neofunctionalization conferred a novel role of ApoD in shaping adaptive lipid metabolic regulatory networks during wing phenotypic evolution. Overall, we provide in vivo evidence for the functional differentiation of duplicate genes in shaping adaptive metabolic regulatory networks during phenotypic evolution.
Fetal MRI deep learning segmentation of body and lung in congenital diaphragmatic hernia
Authors: Bischoff Leon M , Nowak Sebastian , Mader Maximilian , Theis Maike , Vollbrecht Thomas , Isaak Alexander , Kuetting Daniel , Pieper Claus C , Geipel Annegret , Kipfmueller Florian , Strizek Brigitte , Sprinkart Alois M , Luetkens Julian A 
Published: December 2024

Abstract

Purpose
To determine if deep learning (DL) segmentation of total fetal body volume (TFBV) and total fetal lung volume (TFLV) in fetuses with congenital diaphragmatic hernia has comparable performance to manual segmentation.

Materials and Methods
A total of 208 fetal MRI studies with congenital diaphragmatic hernia, acquired between August 2007 and September 2023, were retrospectively included. TFBV and TFLV were extracted from manual tissue segmentations in balanced gradient echo and single shot T2-weighted turbo spin echo sequences. MRI studies were split into training (n = 188) and hold-out test data (n = 20). Wilcoxon signed-rank test was used to compare manual and DL-based segmentations by 2 U-Nets. Manual and DL segmentation times were noted and compared using Student’s t-test. The observed/expected ratio of the total lung volume (O/E TLV) as a prognostic marker for postnatal survival was calculated. Outcome predictions of O/E TLV for postnatal death were assessed with univariate regression analysis.

Results
Manual segmentation times were higher compared to DL segmentations (30 ± 7 minutes versus 0.25 ± 0.05 minutes, P &lt; .001). Manual and DL-based TFBV were similar (1317 ± 498 mL versus 1306 ± 491 mL; P = .04; Dice score: 0.98 ± 0.01). TFLV (19.4 ± 11.5 mL versus 18.7 ± 12.4 mL; P = .11; Dice score: 0.84 ± 0.09) and O/E TLV (39.3 ± 18.1 mL versus 37.7 ± 19.1 mL, P = .13) were not significantly different. Postnatal mortality was negatively associated with higher manual O/E TLV (odds ratio: 0.97; 95% confidence interval [CI], 0.96–0.98; P &lt; .001) and DL O/E TLV (odds ratio: 0.97; 95% CI, 0.96–0.98; P &lt; .001).

Conclusion
DL for body and lung segmentation in fetuses with congenital diaphragmatic hernia allows reliable and rapid calculations of the observed/expected ratio and equally predicts prognostic outcome.
On modes of disease transmission and the hidden shape of pandemics: A review of Asymptomatic by Joshua Weitz
Authors: Ogbunugafor C. Brandon 
Published: December 2024

Abstract
The importance of asymptomatic transmission was a key discovery in our efforts to study and intervene in the COVID-19 pandemic. In Asymptomatic (Johns Hopkins University Press, 2024), Joshua Weitz uses this aspect of SARS-CoV-2 natural history to discuss many counterintuitive characteristics of the pandemic. In this essay, I engage the arguments in the book, and discuss why asymptomatic transmission is such a critical dimension of the study of infectious diseases. I explore ideas contained within Asymptomatic and connect them to related issues in evolutionary virology and disease ecology, including epistemic uncertainty and the evolution of virulence. Furthermore, I comment on the broader messages in the text, including the gap between scientific knowledge and social understanding.
Retinal Racemosal Hemangioma Associated with Intracranial Vascular Malformation (Wyburn -Mason Syndrome) – Case Report
Authors: Arredondo-Cardona Susan D. , Contreras-Duque Natalia , Martínez-Blanco Alexander M. , Bonilla-Escobar Francisco J. 
Published: December 2024

Purpose:
To describe a case of Wyburn-Mason syndrome in a young child with initially declined treatment leading to delayed intervention.

Methodology:
Case report.

Results:
We report a 6-year-old boy with mild periocular trauma following a fall, who was incidentally found to have a retinal arteriovenous malformation (AVM) associated with a brain AVM, indicative of Wyburn-Mason Syndrome. The patient's visual exam was unremarkable except for a visual acuity of 20/150 in the right eye, corrected to 20/60, and 20/30 in the left eye, along with mild proptosis and facial asymmetry. Radiosurgical management was proposed but declined by the caregivers due to fear of complications. Eighteen months later, the patient presented with neurological deterioration, manifesting as left hemiparesis. The patient received antiangiogenic therapy with sirolimus (inhibitor of the mammalian target of rapamycin, mTOR) and underwent a catheter-based embolization procedure that partially occluded the brain AVM without complications. The patient showed partial recovery of strength but experienced a deterioration in visual acuity in the right eye to 20/400.

Conclusion:
This report highlights an extremely rare malformation that associates ocular and cerebral vascular malformations. It underscores the importance of correlating various signs and symptoms to suspect it and emphasizes the need for adherence and follow-up.
An Infiltrative Choroidal Lesion
Authors: Li Yanliang , Gabr Hesham , Mieler William F 
Published: December 2024

Purpose:
To present a distinctive case of primary choroidal lymphoma diagnosed by choroidal biopsy with MYD88 testing

Methods:
We describe the case of a 55-year-old male with unilateral progressive blurry vision. Fundus examination found a whitish/yellowish infiltrative lesion in the posterior pole with macular edema, which had interval improvement with oral prednisone, followed by worsening on OCT with persistent subretinal hyper-reflective materials.

Results:
As the initial Pars plana vitrectomy/vitreous biopsy and choroidal fine needle aspiration biopsy (FNAB) were inconclusive, the second FNAB was performed with an additional MYD88 genetic test and revealed a rare in-frame deletion of MYD88 (p.D288_T294del) in the choroidal sample.

Conclusion:
The diagnosis of PCL was eventually established. After treatment with methotrexate, followed by external beam radiotherapy, the choroidal infiltrate was normalized on B scan.