bluuebunny/crossref_metadata_2025_split huggingface dataset:
Populations of Bemisia tabaci Mediterranean in São Paulo state are inefficient vectors of Brazilian begomoviruses
Authors: Nogueira Angélica Maria , de Oliveira Cíntia Sabino , Bello Vinicius Henrique , Favara Gabriel Madoglio , Vicentin Eduardo , Marubayashi Julio Massaharu , da Cruz Martines Caroline , Watanabe Luis Fernando Maranho , Barbosa Tarsiane Mara Carneiro , de Lima Alvarez Daniel , de Oliveira Regiane Cristina , Zerbini Francisco Murilo , Rezende Jorge Alberto Marques , Krause‐Sakate Renate 
Published: July 2024

AbstractBegomoviruses cause losses in several crops around the world. Whiteflies of the Bemisia tabaci cryptic species MEAM1 and MED are efficient vectors of begomoviruses. MEAM1 has been the predominant species in Brazil since the mid‐1990s. MED was detected in Brazil in 2014, and since then, high insect infestations have been reported, mainly in greenhouse production of solanaceous crops. In this study, we compared the transmission efficiency of the begomoviruses tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV) to tomato (Solanum lycopersicum) and bean golden mosaic virus (BGMV) to common bean (Phaseolus vulgaris) by a population of MEAM1 and four populations of MED. B. tabaci MEAM1 efficiently transmitted ToSRV and ToRMV to tomato and BGMV to common bean. B. tabaci MED populations did not transmit ToSRV and ToRMV to tomato. Only one population of B. tabaci MED transmitted BGMV with an efficiency of 3%. PCR analysis indicated that B. tabaci MED can acquire ToSRV, ToRMV and BGMV after a 24 h acquisition access period. Furthermore, some greenhouse tomato plantings from São Paulo state were surveyed for the presence of viruses and whiteflies, and B. tabaci MED were predominant, whereas begomoviruses were absent. Our results demonstrate that populations of MED from São Paulo state are inefficient vectors of begomoviruses, being able to acquire the virus but not transmit it to plants. Understanding this interaction is important and suggests that the spread of B. tabaci MED could change the epidemiological scenario of begomoviruses in areas where this insect predominates.
Climate‐controlled conservation: Remaking ‘the botanical metropolis of the world’
Authors: Rutherford Jonathan , Marvin Simon 
Published: July 2024

AbstractThis paper examines the understudied relationship between nature conservation and climate control in botanic gardens. Drawing on research conducted at Kew Gardens in West London, we analyse how the relations between climate control, techniques that allow the creation of particular microclimatic conditions in volumetric enclosures, and ex‐situ—out of nature—botanical management have changed over time. The paper shows how climate‐controlled conservation works through three spatial‐technological modes—acclimatisation, climate simulation, and climate security—that reconfigure in‐situ and ex‐situ relations. These modes increasingly transcend local environmental conditions, creating the possibility of conservation without natural climate. The paper extends existing geographies of climate control by focusing on the role of technology in permitting plant life to be moved between different geographical contexts, in enabling ex‐situ and in‐situ natures to become increasingly entwined, and in constructing enclosed conditions decoupled from local climate. Secure climate‐controlled conservation now strategically transforms ex‐situ botanic gardens into the actual sites, and in some cases the last remaining sites, of these natures.
IDENTIFYING KEY FACTORS OF COMMUTER TRAIN SERVICE QUALITY:AN EMPIRICAL ANALYSIS FOR DHAKA CITY
Authors: Nowshin Mowrin Anika , Hadiuzzaman Md. , Barua Saurav , Rahman Md. Mizanur 
Published: July 2024

Commuter train is a viable alternative to road transport to ease the traffic congestion which requires appropriate planning by concerned authorities. The research is aimed to assess passengersâ€™ perception about commuter train service running in areas near Dhaka city. An Adaptive Neuro Fuzzy Inference System (ANFIS) model has been developed to evaluate service quality (SQ) of commuter train. Field survey data has been conducted among 802 respondents who were the regular user of commuter train and 12 attributes have been selected for model development. ANFIS was developed by the training and then tested by 80% and 20% of the total sample respectively. After that, model performance has been evaluated by (i) Confusion Matrix (ii) Root Mean Square Error (RMSE) and attributes are ranked based on their relative importance. The proposed ANFIS model has 61.50% accuracy in training and 47.80% accuracy in testing.Â From the results, it is found that 'Bogie condition', 'Cleanliness', â€˜Female harassmentâ€™, 'Behavior of staff' and 'Toilet facility' are the most significant attributes. This indicates that some necessary measures should be taken immediately to recover the effects of these attributes to improve the SQ of commuter train.Â
A Perspective on Democratizing Mechanical Testing: Harnessing Artificial Intelligence to Advance Sustainable Material Adoption and Decentralized Manufacturing
Authors: Athanasiou Christos E. , Liu Xing , Gao Huajian 
Published: July 2024

Abstract
Democratized mechanical testing offers a promising solution for enabling the widespread adoption of recycled and renewably sourced feedstocks. Locally sourced, sustainable materials often exhibit variable mechanical properties, which limit their large-scale use due to tight manufacturing specifications. Wider access to mechanical testing at the local level can address this challenge by collecting data on the variable properties of sustainable feedstocks, allowing for the development of appropriate, uncertainty-aware mechanics frameworks. These frameworks are essential for designing custom manufacturing approaches that accommodate variable local feedstocks, while ensuring product quality and reliability through post-manufacturing testing. However, traditional mechanical testing apparatuses are too costly and complex for widespread local use by individuals or small, community-based facilities. Despite promising efforts over the past decade to develop more affordable and versatile testing hardware, significant limitations remain in their reliability, adaptability, and ease–of-use. Recent advances in artificial intelligence (AI) present an opportunity to overcome these limitations by reducing human intervention, enhancing instrument reliability, and facilitating data interpretation. AI can thus enable the creation of low-cost, user-friendly mechanical testing infrastructure. Future efforts to democratize mechanical testing are expected to be closely linked with advancements in manufacturing and materials mechanics. This perspective paper highlights the need to embrace AI advancements to facilitate local production from sustainable feedstocks and enhance the development of decentralized, low-/zero-waste supply chains.
Electromechanical Responses of a Piezoelectric Semiconducting Nanoplate With the Steigmann–Ogden Surface
Authors: Li Xiaobao , Zhan Chunxiao , Xu Yang 
Published: July 2024

Abstract
Piezoelectric semiconductors (PSCs) find widespread applications in smart electronic devices due to their unique combination of piezoelectric and semiconductive properties. With the increasing demand for smaller and more efficient electronic devices, the performance of their components needs to be carefully optimized, especially when they are scaled down to nanoscale sizes. Pioneering studies have demonstrated that surface elastic properties play a significant role in determining the mechanical performance of nanoscale materials and structures. Therefore, it is important to comprehensively investigate the effects of surface elasticity, including surface residual stress, surface membrane stiffness, and surface bending stiffness, on the electromechanical responses of a PSC nanoplate. Additionally, it is crucial to examine the influence of flexoelectricity at the nanoscale. Our results demonstrate that surface elastic properties predominantly impact mechanical performance, while the flexoelectric effect plays a more prominent role in electric field and redistribution of charge carriers. In particular, the significance of surface bending rigidity, which was often overlooked in previous literature, becomes pronounced when the thickness of a PSC nanoplate is less than 7 nm. Furthermore, the dependence of natural vibration frequency on surface elastic moduli, flexoelectricity, and size is, respectively, explored. The redistributions of electric potential and charge carriers across the cross section are also evidently affected. Our findings provide valuable insights for improving the performance of electronic devices that utilize nanoscale PSCs.
A host of issues: pseudoreplication in host–microbiota studies
Authors: McKinnon Reish Hannah , Dewey Lindsey , Kirschman Lucas J. 
Published: July 2024

ABSTRACT

Pseudoreplication compromises the validity of research by treating non-independent samples as independent replicates. This review examines the prevalence of pseudoreplication in host–microbiota studies, highlighting the critical need for rigorous experimental design and appropriate statistical analysis. We systematically reviewed 115 manuscripts on host–microbiota interactions. Our analysis revealed that 22% of the papers contained pseudoreplication, primarily due to co-housed organisms, whereas 52% lacked sufficient methodological details. The remaining 26% adequately addressed pseudoreplication through proper experimental design or statistical analysis. The high incidence of pseudoreplication and insufficient information underscores the importance of methodological reporting and statistical rigor to ensure reproducibility of host–microbiota research.
ORC1 enhances repressive epigenetic modifications on HIV-1 LTR to promote HIV-1 latency
Authors: Zhou Mo , Yang Tao , Yuan Ming , Li Xinyu , Deng Jieyi , Wu Shiyu , Zhong Zhihan , Lin Yingtong , Zhang Wanying , Xia Baijin , Wu Yating , Wang Lilin , Chen Tao , Liu Ruxin , Pan Ting , Ma Xiancai , Li Linghua , Liu Bingfeng , Zhang Hui 
Published: July 2024

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) reservoir consists of latently infected cells which present a major obstacle to achieving a functional cure for HIV-1. The formation and maintenance of HIV-1 latency have been extensively studied, and latency-reversing agents (LRAs) that can reactivate latent HIV-1 by targeting the involved host factors are developed; however, their clinical efficacies remain unsatisfactory. Therefore, it is imperative to identify novel targets for more potential candidates or better combinations for LRAs. In this study, we utilized CRISPR affinity purification
in situ
of regulatory elements system to screen for host factors associated with the HIV-1 long terminal repeat region that could potentially be involved in HIV-1 latency. We successfully identified that origin recognition complex 1 (ORC1), the largest subunit of the origin recognition complex, contributes to HIV-1 latency in addition to its function in DNA replication initiation. Notably, ORC1 is enriched on the HIV-1 promoter and recruits a series of repressive epigenetic elements, including DNMT1 and HDAC1/2, and histone modifiers, such as H3K9me3 and H3K27me3, thereby facilitating the establishment and maintenance of HIV-1 latency. Moreover, the reactivation of latent HIV-1 through ORC1 depletion has been confirmed across various latency cell models and primary CD4
+
T cells from people living with HIV-1. Additionally, we comprehensively validated the properties of liquid-liquid phase separation (LLPS) of ORC1 from multiple perspectives and identified the key regions that promote the formation of LLPS. This property is important for the recruitment of ORC1 to the HIV-1 promoter. Collectively, these findings highlight ORC1 as a potential novel target implicated in HIV-1 latency and position it as a promising candidate for the development of novel LRAs.

IMPORTANCE
Identifying host factors involved in maintaining human immunodeficiency virus type 1 (HIV-1) latency and understanding their mechanisms prepares the groundwork to discover novel targets for HIV-1 latent infection and provides further options for the selection of latency-reversing agents in the “shock” strategy. In this study, we identified a novel role of the DNA replication factor origin recognition complex 1 (ORC1) in maintaining repressive chromatin structures surrounding the HIV-1 promoter region, thereby contributing to HIV-1 latency. This discovery expands our understanding of the non-replicative functions of the ORC complex and provides a potential therapeutic strategy for HIV-1 cure.
Sub-genomic flaviviral RNA elements increase the stability and abundance of recombinant AAV vector transcripts
Authors: Meganck Rita M. , Ogurlu Roza , Liu Jiacheng , Moller-Tank Sven , Tse Victor , Blondel Leo O. , Rosales Alan , Hall Aaron C. , Vincent Heather A. , Moorman Nathaniel J. , Marzluff William F. , Asokan Aravind 
Published: July 2024

ABSTRACT

Many viruses have evolved structured RNA elements that can influence transcript abundance and translational efficiency, and help evade host immune factors by hijacking cellular machinery during replication. Here, we evaluated the functional impact of sub-genomic flaviviral RNAs (sfRNAs) known to stall exoribonuclease activity, by incorporating these elements into recombinant adeno-associated viral (AAV) genome cassettes. Specifically, sfRNAs from Dengue, Zika, Japanese Encephalitis, Yellow Fever, Murray Valley Encephalitis, and West Nile viruses increased transcript stability and transgene expression compared to a conventional woodchuck hepatitis virus element (WPRE). Further dissection of engineered transcripts revealed that sfRNA elements (i) require incorporation in
cis
within the 3′ untranslated region (UTR) of AAV genomes, (ii) require minimal dumbbell structures to exert the observed effects, and (iii) can stabilize AAV transcripts independent of 5′−3′ exoribonuclease 1 (XRN1)-mediated decay. Additionally, preliminary
in vivo
assessment of AAV vectors bearing sfRNA elements in mice achieved increased transcript abundance and expression in cardiac tissue. Leveraging the functional versatility of engineered viral RNA elements may help improve the potency of AAV vector-based gene therapies.

IMPORTANCE
Viral RNA elements can hijack host cell machinery to control stability of transcripts and consequently, infection. Studies that help better understand such viral elements can provide insights into antiviral strategies and also potentially leverage these features for therapeutic applications. In this study, by incorporating structured flaviviral RNA elements into recombinant adeno-associated viral (AAV) vector genomes, we show improved AAV transcript stability and transgene expression can be achieved, with implications for gene transfer.
Bis-benzylisoquinoline alkaloids inhibit African swine fever virus internalization and replication by impairing late endosomal/lysosomal function
Authors: Zhu Junhai , Chen Huahan , Gao Fei , Jian Weijun , Huang Guangyu , Sunkang Yongjie , Chen Xiaona , Liao Ming , Zhang Kehui , Qi Wenbao , Huang Lihong 
Published: July 2024

ABSTRACT

African swine fever (ASF), caused by the African swine fever virus (ASFV), is a highly infectious disease afflicting domestic pigs and wild boars. It exhibits an alarming acute infection fatality rate of up to 100%. Regrettably, no commercial vaccines or specific drugs for combating this disease are currently available. This study evaluated the anti-ASFV activities in porcine alveolar macrophages, 3D4/21 cells, and PK-15 cells of four bis-benzylisoquinoline alkaloids (BBAs): cepharanthine (CEP), tetrandrine, fangchinoline, and iso-tetrandrine. Furthermore, we demonstrated that CEP, which exhibited the highest selectivity index (SI = 81.31), alkalized late endosomes/lysosomes, hindered ASFV endosomal transport, disrupted virus uncoating signals, and thereby inhibited ASFV internalization. Additionally, CEP disrupted ASFV DNA synthesis, leading to the inhibition of viral replication. Moreover, berbamine was labeled with NBD to synthesize a fluorescent probe to study the cellular location of these BBAs. By co-staining with Lyso-Tracker and lysosome-associated membrane protein 1, we demonstrated that BBAs target the endolysosomal compartments for the first time. Our data together indicated that BBAs are a class of natural products with significant inhibitory effects against ASFV infection. These findings suggest their potential efficacy as agents for the prevention and control of ASF, offering valuable references for the identification of potential drug targets.

IMPORTANCE
The urgency and severity of African swine fever (ASF) underscore the critical need for effective interventions against this highly infectious disease, which poses a grave threat to domestic pigs and wild boars. Our study reveals the potent anti-African swine fever virus (ASFV) efficacy of bis-benzylisoquinoline alkaloids (BBAs), particularly evident in the absence of progeny virus production under a 5 µM concentration treatment. The structural similarity among cepharanthine, tetrandrine, fangchinoline, and iso-tetrandrine, coupled with their analogous inhibitory stages and comparable selectivity indexes, strongly suggests a shared antiviral mechanism within this drug category. Further investigation revealed that BBAs localize to lysosomes and inhibit the internalization and replication of ASFV by disrupting the endosomal/lysosomal function. These collective results have profound implications for ASF prevention and control, suggesting the potential of the investigated agents as prophylactic and therapeutic measures. Furthermore, our study offers crucial insights into identifying drug targets and laying the groundwork for innovative interventions.
Draft genome for
Pseudomonas alkylphenolica
IMGN1, isolated from soil
Authors: Lee Jaeyeon , Ku Bon-Jin , Kim Yeongjun , Han Jeong A. , Kim Eun Yu , Lee Ho-Seok 
Published: July 2024

ABSTRACT

Biocontrol using organisms like
Pseudomonas alkylphenolica
offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of
Pseudomonas alkylphenolica
IMGN1, a strain known for promoting plant growth, advancing our understanding of biocontrol mechanisms.
Draft genome sequences of four
Corynebacterium amycolatum
strains isolated from female urine samples
Authors: Kula Alex , Chilton Grace , Damaso James , Golzar Yusef , Rushnaiwala Fatima , Appleberry Helen , Wolfe Alan J. , Putonti Catherine 
Published: July 2024

ABSTRACT

Corynebacterium amycolatum
is an emerging pathogen of the urinary tract. Here, we present the draft genomes for four strains isolated from urine collected from symptomatic and asymptomatic female participants.
Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes
Authors: Roager Line , Kempen Paul J. , Bentzon-Tilia Mikkel , Sonnenschein Eva C. , Gram Lone 
Published: July 2024

ABSTRACT

Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte
Isochrysis galbana,
the chlorophyte
Tetraselmis suecica,
and the diatom
Conticribra weissflogii
(previously
Thalassiosira
), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but
I. galbana
microbiomes diverged further from
T. suecica
and
C. weissflogii
microbiomes.
I. galbana
microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of
I. galbana
affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of
I. galbana
microbiomes diverging further from those of
T. suecica
and
C. weissflogii
microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of
C. weissflogii,
which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host.

IMPORTANCE
As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.
Central Afar: An analogue for oceanic plateau development
Authors: Rime Valentin , Keir Derek , Phethean Jordan , Kidane Tesfaye , Foubert Anneleen 
Published: July 2024

Abstract
The structure, composition, and evolution of oceanic plateaus are poorly understood and strongly debated. Here, we compared the magmatic history and crustal structure of Afar with the Greenland–Iceland–Faroe Ridge and other oceanic plateaus. Key similarities indicate that Central Afar represents the early stage of development of a specific type of oceanic plateau: a rifted oceanic magmatic plateau (ROMP). These features begin their formation before continental rifting and develop into wide magmatic rift systems capable of isolating slivers of continental crust within the new igneous crust. Importantly, the anomalous magmatism continues through breakup and for several tens of millions of years afterward. The recognition of Central Afar as a precursor of this type of oceanic plateau allows us to better understand their formation. Increased melt production causes early and voluminous magmatism, ultrathick igneous crust, and repeated reorganization of the extension locus during rift/ridge jumps, which delay the onset of oceanization and Penrose-style crustal production. These factors differentiate ROMPs from many magma-rich rifted continental margins and from other types of oceanic plateaus, highlighting that Central Afar and other ROMPs should neither be considered as conventional magma-rich margins nor be considered as normal oceanic crust.