bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the visualization of viruses in soil
Authors: Parvate Amar D. , Alfaro Trinidad , McDearis Regan , Zimmerman Amy , Hofmockel Kirsten , Nelson William C. , Evans James E. 
Published: October 2024

ABSTRACTViruses are numerically the most abundant forms on Earth, and most are present in soil. Scientific study is usually restricted to viruses or phages which are known to either positively or negatively impact human activities, livestock or crops. Visualizing the diverse morphotypes within native soil virus populations has been challenging even though viruses are highly abundant in soil and critical to rhizosphere function; primarily due to a lack of an established and reliable method of performing high-resolution structural studies on viruses natively isolated from soil. Suspensions of viruses natively isolated from soil contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and makes sample prep for cryo-TEM extremely challenging. Conventional TEM provides only low-resolution structural information. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method is agnostic to isolation approaches as it is a physical biochemical separation to remove large and small debris that hinders high-resolution imaging. In addition to improving image quality and preservation of structural features, the method visualizes morphotypes not typically seen with conventional TEM imaging and enables capturing a particle library with both 2D and 3D information. In addition to tailed and non-tailed polyhedral phages, our study reports several other under reported or novel morphotypes of soil viruses.
Polar bodies serve as a landmark for anteroposterior axis formation in spiders
Authors: Wang Ruixun , Pechmann Matthias 
Published: October 2024

AbstractThe early embryogenesis of many spiders involves the formation of a radially symmetric germ disc. While the cells of the rim of this germ disc develops into anterior structures, the center of the disc will form the posteriorly located segment addition zone of the embryo. Therefore, germ disc formation sets the anterior-posterior (AP) body axis of spider embryos. The early spider egg is a spherical structure with no apparent asymmetry, and it is believed that germ disc formation is a stochastic process.For this study, we have re-analyzed early spider embryogenesis and found a strong correlation of the position of the polar bodies and the formation of the germ disc. Our results suggest that germ disc formation in the common house spiderParasteatoda tepidariorumis not a stochastic but a pre-determined process. Furthermore, we provide evidence that this correlation might be conserved between araneomorph and mygalomorph spider species.
PlasmidGPT: a generative framework for plasmid design and annotation
Authors: Shao Bin 
Published: October 2024

AbstractWe introduce PlasmidGPT, a generative language model pretrained on 153k engineered plasmid sequences from Addgene. PlasmidGPT generatesde novosequences that share similar characteristics with engineered plasmids but show low sequence identity to the training data. We demonstrate its ability to generate plasmids in a controlled manner based on the input sequence or specific design constraint. Moreover, our model learns informative embeddings of both engineered and natural plasmids, allowing for efficient prediction of a wide range of sequence-related attributes.
Mechanism of NPC1L1 mediated 27-hydroxycholesterol metabolisms in the occurrence and development of osteoporosis
Authors: Li Bohao , Lv Zhicheng , Chen Boyu , Zhang Tieqi , Yu Yueming , Sun Shiwei , Huang Haitian , Zhou Lei , Wang Minghai 
Published: October 2024

AbstractCholesterol metabolism is closely related to the occurrence and development of osteoporosis, but the exact mechanism remains unclear. Niemann-Pick C1-like 1 (NPC1L1) is one of the key cholesterol transporter proteins, however, there are few reports on the functions of NPC1L1 besides regulating cholesterol transport, let alone bone homeostasis. Our preliminary research indicated that NPC1L1 may play a negative regulatory role in osteogenic differentiation. In this study, using in vitro osteogenic differentiation experiment and mouse osteoporosis model, we showed here that NPC1L1 expression was downregulated during osteogenesis, and NPC1L1 knockdown significantly enhanced osteogenic differentiation ability of osteoblasts and delayed progress of osteoporosis. Mechanistically, through RNA sequencing, NPC1L1 was found regulate cholesterol metabolism rather than transportation. It increased 27-Hydroxycholesterol (27-OHC) level through activating 27-hydroxylase (Cyp27a1), resulting in 27-OHC accumulation in osteoblasts and inhibition of osteogenesis. Moreover, C/EBPα was proved mediated NPC1L1 promotes production of 27-OHC by Cyp27a1. These findings reveal that NPC1L1 inhibits osteogenesis and promotes osteoporosis via regulate cholesterol metabolism.Graphical AbstractNPC1L1 inhibits osteogenic differentiation and promotes the progression of OP through the C/EBPα/Cyp27a1/27-OHC axis.
Cytosolic Enhanced Dark Epac-Based FRET Sensors for Intracellular cAMP detection in live cells via FLIM
Authors: Zanetti Giulia , Klarenbeek Jeffrey B. , Jalink Kees 
Published: October 2024

AbstractFluorescence Resonance Energy Transfer (FRET)-based biosensors are powerful tools for studying second messengers with high temporal and spatial resolution. FRET is commonly detected by ratio-imaging, but Fluorescence Lifetime Imaging Microscopy (FLIM), which measures the donor fluorophore’s lifetime, offers a robust and more quantitative alternative. We have introduced and optimized four generations of FRET sensors for cAMP, based on the effector molecule Epac1, including variants for either ratio-imaging or FLIM detection. Recently, Massengill and colleagues introduced additional mutations that improve cytosolic localization in these sensors, focusing on constructs optimized for ratio-imaging. Here we present and briefly characterize these mutations in our dedicated FLIM sensors, finding they enhance cytosolic localization while maintaining performance comparable to original constructs.
The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12
Authors: Thoben Corinna , Pucker Boas , Winter Stephan , Econopouly Bethany Fallon , Sheat Samar 
Published: October 2024

AbstractCassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary source of food and income. However, cassava production is threatened by several viral diseases, including cassava brown streak disease, which causes severe damage to the edible storage roots. Current cassava varieties in Africa lack effective resistance to this disease, leading to significant crop losses. We investigated the genetic diversity of cassava and identifed new sources of resistance to the viruses causing cassava brown streak disease. The cassava line, COL40, from a South American germplasm collection showed broad-spectrum resistance against all known strains of the viruses that cause this disease. To further understand the genetic basis of this resistance, we sequenced the genome of COL40 and produced a high-quality, haplotype-resolved genome assembly. This genomic resource provides new insights into cassava’s genetic architecture, particularly in regions associated with disease resistance. The sequence reveals significant structural variation, including transposable elements, inversions, and deletions, which may contribute to the resistance phenotype. The reference genome assembly presented here will provide a valuable genomic resource for studying the cassava brown streak resistance and will help in accelerating breeding efforts to introduce virus resistance into African cassava varieties. By identifying genetic variants linked to resistance, future breeding programs can develop cassava cultivars that are more resilient to viral threats, enhancing food security and livelihoods for smallholder farmers across regions affected by the disease.
Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization inAnophelesmosquitos while reducing their lifespan and malaria parasite burden
Authors: Camacho Emma , Dong Yuemei , Chrissian Christine , Cordero Radames J.B. , Saravia Raúl G. , Anglero-Rodriguez Yessenia , Smith Daniel F.Q. , Jacobs Ella , Hartshorn Isabelle , Patiño-Medina Jose Alberto , DePasquale Michael , Dziedzic Amanda , Jedlicka Anne , Smith Barbara , Mlambo Godfree , Tripathi Abhai , Broderick Nichole A. , Stark Ruth E. , Dimopoulos George , Casadevall Arturo 
Published: October 2024

ABSTRACTL-3,4-dihydroxyphenylalanine (L-DOPA), a naturally occurring tyrosine derivative, is prevalent in environments that include mosquito habitats, potentially serving as part of their diet. Given its role as a precursor for melanin synthesis we investigated the effect of dietary L-DOPA on mosquito physiology and immunity toPlasmodium falciparumandCryptococcus neoformansinfection. Dietary L-DOPA was incorporated into mosquito melanin via a non-canonical pathway and had profound transcriptional effects that were associated with enhanced immunity, increased pigmentation, and reduced lifespan. Increased melanization resulted in an enhanced capacity to absorb electromagnetic radiation that affected mosquito temperatures. Bacteria in the mosquito microbiome were sources of dopamine, which is a substrate for melanization. Our results illustrate how an environmentally abundant amino acid analogue can affect mosquito physiology and suggest its potential usefulness as an environmentally friendly vector control agent to reduce malaria transmission, warranting further research and field studies.
Band-selective IR PRESS for brain tumor spectroscopy allows robust detection of lactate
Authors: Kishimoto Shun , Kim Olga , Munasinghe Jeeva , Yasunori Otowa , Kota Yamashita , Yamamoto Kazutoshi , Linehan W. Marston , Wu Jing , Krishna Murali C , Brender Jeffrey R 
Published: October 2024

AbstractLactate plays a critical role in the tumor microenvironment, driving tumor progression, metastasis, and immune evasion. Despite its importance, in vivo quantification of lactate using magnetic resonance spectroscopy (MRS) has faced challenges, primarily due to the overlapping lipid signal at 1.3 ppm. Current clinical practice employs a long echo time to exploit differences in T2 relaxation between lactate and lipids; however, this approach significantly suppresses signals from other metabolites. Lipid has a notably different T1 relaxation time than lactate and other metabolites, which may be exploited by an inversion recovery sequence to better distinguish them. However, this method has not found wide use because of the loss of signal in other metabolites. Here we introduce a selective inversion pulse with a short echo time MRS method (SPIR-PRESS), which mitigates this issue. In phantom experiments, SPIR-PRESS successfully suppressed lipid signals that could be misinterpreted as lactate in short TE PRESS spectra, while maintaining sensitivity to the full metabolite profile. SPIR-PRESS demonstrated superior performance in quantifying lactate compared to long echo time PRESS, with ∼ 60 % increase in sensitivity for lactate detection compared to conventional PRESS with a 288 ms TE. In a mouse glioma model, SPIR-PRESS clearly detected lactate and other key tumor metabolites (choline, creatine, NAA) in the tumor, which were not detectable in conventional long TE PRESS. These findings highlight SPIR-PRESS as a promising technique for improved lactate quantification and comprehensive metabolite profiling in tumor environments.
Genome Report: Diploid assembly of the Mexican lime genome reveals extensive heterozygosity
Authors: Massaro Isabelle , Thomson James , Leichty Aaron R. 
Published: October 2024

ABSTRACTClonally propagated crops have long been recognized for their high levels of heterozygosity both between subgenomes within a somatic cell and between cells within an individual clone. Recent developments in long read sequencing technologies have accelerated our ability to identify this diversity and it is increasingly clear that these sources of diversity are abundant in clonal varieties and can contribute to variation in traits of interest to breeders. In this work, we assemble both subgenomes of Mexican lime (Citrusxaurantifolia), an interspecific hybrid betweenC. hystrixvar.micranthaandC. medica. Using this chromosome-level assembly, we find extensive divergence between haplotypes, with at least 89% of the annotated genes harboring polymorphisms at an average rate of 13 per kilobase of coding sequence. Additionally, using high coverage PacBio HiFi libraries from leaf tissue of four individuals we identified multiple large structural variants differing between thorned and thornless lineages, and evidence for mosaicism at hundreds of loci. Many of these variants are found in the promoters and bodies of genes and may act as standing variation for continued improvement of this cultivar.
Modular representations emerge in neural networks trained to perform context-dependent tasks
Authors: Johnston W. Jeffrey , Fusi Stefano 
Published: October 2024

AbstractThe brain has large-scale modular structure in the form of brain regions, which are thought to arise from constraints on connectivity and the physical geometry of the cortical sheet. In contrast, experimental and theoretical work has argued both for and against the existence of specialized sub-populations of neurons (modules) within single brain regions. By studying artificial neural networks, we show that this local modularity emerges to support context-dependent behavior, but only when the input is low-dimensional. No anatomical constraints are required. We also show when modular specialization emerges at the population level (different modules correspond to orthogonal subspaces). Modularity yields abstract representations, allows for rapid learning and generalization on novel tasks, and facilitates the rapid learning of related contexts. Non-modular representations facilitate the rapid learning of unrelated contexts. Our findings reconcile conflicting experimental results and make predictions for future experiments.
Dynamic functional adaptations during touch observation in autism: Connectivity strength is linked to attitudes towards social touch and social responsiveness
Authors: Masson Haemy Lee 
Published: October 2024

AbstractAutistic adults often experience differences in social interactions involving physical contact. Brain imaging studies suggest that these differences may be related to atypical brain responses to social-affective cues, affecting both the experience of receiving touch and observing it in others. However, it remains unclear whether these atypical responses are limited to specific brain regions or represent broader alterations in brain connectivity. The current study investigated how the functional network architecture is modulated during touch observation associated with autism and explored the extent to which changes in this architecture are associated with individual differences in social touch preferences and social responsiveness. By integrating generalized psychophysiological interaction (gPPI) analysis with independent component analysis (ICA), the current study analyzed existing fMRI datasets, in which 21 autistic and 21 non-autistic male adults viewed videos of social and nonsocial touch while undergoing MRI scans. A gPPI analysis of pre-defined regions of interest revealed that autistic adults exhibited increased connectivity between sensory and social brain regions. The strength of some of these connections was positively associated with a higher preference for social touch and greater social responsiveness, suggesting neural compensatory mechanisms that may help autistic adults better understand the meaning of touch. At the level of large-scale brain networks extracted using ICA, atypical connectivity was predominantly observed between the sensorimotor network and other networks involved in social-emotional processing. Increased connectivity was observed in the sensorimotor network during nonsocial touch, suggesting that embodied simulation, the process by which individuals internally simulate touch experience of others in this context, may be more engaged when observing human-object interactions than during human-to-human touch in autism. This study reveals atypical context-dependent modulation of functional brain architecture associated with autism during touch observation, suggesting that challenges in recognizing and using affective touch in social interactions may be associated with altered brain connectivity. Neural compensatory mechanisms in autistic individuals who enjoy social touch and show higher social responsiveness may function as adaptive social responses. However, these compensations appear to be limited to specific brain regions, rather than occurring at the level of large-scale brain networks.
RO8191, a new compound for initiating embryo implantation in mice
Authors: Shu Junlan , Terakawa Jumpei , Osuka Satoko , Muraoka Ayako , Ruan Jiali , Ito Junya , Iida Atsuo , Hondo Eiichi 
Published: October 2024

AbstractDuring early pregnancy in mice, leukemia inhibitory factor (LIF) regulates embryo implantation by activating the JAK/STAT3 signaling pathway. The STAT3 pathway has been recognized to play a critical role in embryo implantation. However, it is not clear whether STAT3 activation itself can cause induction of embryo implantation. In this study, the effects of RO8191, a potential STAT3 activator, on embryo implantation were investigated through a series of studies with different mouse models. We found that the injection of RO8191 can induce embryo implantation by activating the STAT3 pathway in delayed implantation mice. Furthermore, RO8191 can initiate decidualization, which is essential for embryo implantation, in uterine epithelial-specificStat3, Gp130, orLifrconditional knockout (cKO) mice, which shows infertility due to embryo implantation failure. Histomorphological observations revealed that successful embryo implantation and embryonic development was seen inLifrcKO mice. Increased epithelial detachment and vascularization were observed inStat3cKO mice, and excessive inflammatory response and embryo death were observed inGp130cKO mice. These results suggest that STAT3, Gp130 and LIFR each play a distinct role in embryo implantation and development. Although the specific mechanisms of RO8191 are not fully understood, the present study will provide insights to support the application of RO8191 in treating recuurent implantation failure.
Harmonizing Maqasid al-Shari’ah with sustainable waste management practices: a conceptual framework for principles and implementation
Authors: Azmin Shompa Zohora , Akbar Mohamed Aslam , Mohd Mohadis Hazwani 
Published: October 2024

Purpose
This paper aims to investigate the principles guiding sustainable waste management practices within the framework of Maqasid al-Shari’ah. The purpose is to address the environmental challenges arising from economic expansion, population growth and resource consumption, which often lead to unsustainable waste management practices and hinder economic growth. The focus is on aligning waste management principles with the ethical objectives outlined in Shari’ah.

Design/methodology/approach
Adopting a qualitative content analysis method and an inductive approach to outline the constituent elements that formulate the framework, this study investigates the objectives of Maqasid al-Shari’ah to identify underlying elements crucial for sustainable waste management.

Findings
The study reveals how the principles embedded in Maqasid al-Shari’ah provide a foundation for effective waste management practices. The findings emphasize the importance of integrating these principles into human behavior to ensure that waste management aligns with the Shari’ah viewpoint. The insights shed light on the role of Maqasid al-Shari’ah in managing waste sustainably and contributing to environmental conservation efforts.

Originality/value
This research contributes to the field by offering a unique perspective on waste management practices through the lens of Maqasid al-Shari’ah. The study’s originality lies in its exploration of how Islamic ethical objectives can guide sustainable waste management, providing a framework that goes beyond conventional approaches. The incorporation of a comprehensive literature review enhances the authenticity and novelty of the proposed waste management framework.
Enhancing supply chain resilience through the supply network approach
Authors: Cinti Alessandro , Marcone Maria Rosaria , Sabatini Andrea , Temperini Valerio 
Published: October 2024

Purpose
This study aims to investigate the efficacy of the supply network approach in bolstering supply chain resilience amidst escalating global uncertainty. With enterprises worldwide facing increasing threats that disrupt supply chains, this research explores how firms enhance supply network resilience during crises.

Design/methodology/approach
Using a multi-case study design, this research thoroughly examines interactions within firms’ supply networks to uncover new insights on supply network approach and how firms enhance supply network resilience against global uncertainty. The selection of cases was methodologically aligned to represent diverse industries and geographical locations to ensure a comprehensive analysis.

Findings
This study’s findings reveal how firms develop supply network resilience during global crises. The supply network perspective provides a deeper understanding of how firms manage supply chain interactions, interdependencies and strategic positions to survive and thrive during crises. The conceptual framework developed here provides insights that can foster improved coordination and facilitate effective temporary organising. The framework highlights the need for firms to proactively seize opportunities and mitigate risks within their global supply chains during crises to boost overall resilience.

Originality/value
Offering novel insights into the domain of supply chain networks, this study underscores novel perspectives of the supply network approach when firms develop supply chain resilience during global crises. Highlighting the adaptive responses of firms that integrate these approaches enriches the understanding of strategic manoeuvres firms can use to navigate global uncertainty and secure supply chain continuity.