bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
Authors: Broeckaert Nand , Longin Hannelore , Hendrix Hanne , De Smet Jeroen , Franz-Wachtel Mirita , Maček Boris , van Noort Vera , Lavigne Rob 
Published: September 2024

Abstract
Bacteria employ a myriad of regulatory mechanisms to adapt to the continuously changing environments that they face. They can, for example, use post-translational modifications, such as Nε-lysine acetylation, to alter enzyme activity. Although a lot of progress has been made, the extent and role of lysine acetylation in many bacterial strains remains uncharted. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) in combination with the immunoprecipitation of acetylated peptides and LC-MS/MS to measure the first Pseudomonas aeruginosa PAO1 acetylome, revealing 1076 unique acetylation sites in 508 proteins. Next, we assessed interstrain acetylome differences within P. aeruginosa by comparing our PAO1 acetylome with two publicly available PA14 acetylomes, and postulate that the overall acetylation patterns are not driven by strain-specific factors. In addition, the comparison of the P. aeruginosa acetylome to 30 other bacterial acetylomes revealed that a high percentage of transcription related proteins are acetylated in the majority of bacterial species. This conservation could help prioritize the characterization of functional consequences of individual acetylation sites.
Internal deformation of the North Andean Sliver in Ecuador-southern Colombia observed by InSAR
Authors: Marconato L , Audin L , Doin M-P , Nocquet J-M , Jarrin P , Rolandone F , Harrichhausen N , Mothes P , Mora-Páez H , Cisneros D 
Published: September 2024

Summary
In the Northern Andes, partitioning of oblique subduction of the Nazca plate beneath the South American continent induces a northeastward motion of the North Andean Sliver. The strain resulting from this motion is absorbed by crustal faults, which have produced magnitude 7 + earthquakes historically in the Andean Cordillera of Ecuador and southern Colombia. In order to quantify the strain in that area, we derive a high-resolution surface velocity map using InSAR time-series processing. We analyzed 6 to 8 years of Sentinel-1 data and combined different satellite line-of-sight directions to produce a reliable velocity map in the East direction. We use interpolated GNSS data to express the velocity map with respect to Stable South America and remove the long-wavelength pattern due to the post-seismic deformation following the 2016 Mw 7.8 Pedernales earthquake. The InSAR velocity map finds high E-W shortening strain rates along N-S trending structures within the Western Cordillera and the Interandean valley, with little deformation taking place east of them. This result strengthens the previous proposition of a ∼350 km long Quito-Latacunga tectonic block, forming a restraining bend in the overall right-lateral strike-slip fault system accommodating the northeastward escape motion of the North Andean Sliver. However, the high spatial resolution provided by InSAR indicates that previously proposed boundaries for this block need to be revised. In particular, InSAR results highlight high strain rate (&gt;300 nstrain/yr) along undescribed active structures, south and west of the proposed limits for the Quito-Latacunga block, respectively in Peltetec and Ibarra regions. Interestingly, the two areas with the largest strain rates spatially correlate with the proposed areas of large historical earthquakes. Modeling of the InSAR and GNSS velocities in these areas suggests shallow coupling and high slip rates on structures which, previously, were not identified as active. We also demonstrate a slow-down of the shallow aseismic slip on the Quito fault after the Pedernales earthquake, suggesting that stress changes following large megathrust events might trigger transient slip behaviors on crustal faults. The high-resolution strain map provided by this work provides a new basis for future tectonic models in the Ecuadorian and southern Colombian Andes, and will contribute to the seismic hazard assessment in this highly populated area of the Andes.
Modeling antisense oligonucleotide therapy in MECP2 duplication syndrome human iPSC-derived neurons reveals gene expression programs responsive to MeCP2 levels
Authors: Bajikar Sameer S , Sztainberg Yehezkel , Trostle Alexander J , Tirumala Harini P , Wan Ying-Wooi , Harrop Caroline L , Bengtsson Jesse D , Carvalho Claudia M B , Pehlivan Davut , Suter Bernhard , Neul Jeffrey L , Liu Zhandong , Jafar-Nejad Paymaan , Rigo Frank , Zoghbi Huda Y 
Published: September 2024

Abstract
Genomic copy-number variations (CNVs) that can cause neurodevelopmental disorders often encompass many genes, which complicates our understanding of how individual genes within a CNV contribute to pathology. MECP2 duplication syndrome (MDS or MRXSL in OMIM; OMIM#300260) is one such CNV disorder caused by duplications spanning methyl CpG-binding protein 2 (MECP2) and other genes on Xq28. Using an antisense oligonucleotide (ASO) to normalize MECP2 dosage is sufficient to rescue abnormal neurological phenotypes in mouse models overexpressing MECP2 alone, implicating the importance of increased MECP2 dosage within CNVs of Xq28. However, because MDS CNVs span MECP2 and additional genes, we generated human neurons from multiple MDS patient-derived induced pluripotent cells (iPSCs) to evaluate the benefit of using an ASO against MECP2 in a MDS human neuronal context. Importantly, we identified a signature of genes that is partially and qualitatively modulated upon ASO treatment, pinpointed genes sensitive to MeCP2 function, and altered in a model of Rett syndrome, a neurological disorder caused by loss of MeCP2 function. Furthermore, the signature contained genes that are aberrantly altered in unaffected control human neurons upon MeCP2 depletion, revealing gene expression programs qualitatively sensitive to MeCP2 levels in human neurons. Lastly, ASO treatment led to a partial rescue of abnormal neuronal morphology in MDS neurons. All together, these data demonstrate that ASOs targeting MECP2 benefit human MDS neurons. Moreover, our study establishes a paradigm by which to evaluate the contribution of individual genes within a CNV to pathogenesis and to assess their potential as a therapeutic target.
Pathomechanisms of Monoallelic variants in TTN causing skeletal muscle disease
Authors: Gohlke Jochen , Lindqvist Johan , Hourani Zaynab , Rich Kelly , Arnold W David , Heintzman Sarah , Tonino Paola , Elsheikh Bakri , Morales Ana , Vatta Matteo , Burghes Arthur , Granzier Henk , Roggenbuck Jennifer 
Published: September 2024

Abstract
Pathogenic variants in the titin gene (TTN) are known to cause a wide range of cardiac and musculoskeletal disorders, with skeletal myopathy mostly attributed to biallelic variants. We identified monoallelic truncating variants (TTNtv), splice site or internal deletions in TTN in probands with mild, progressive axial and proximal weakness, with dilated cardiomyopathy frequently developing with age. These variants segregated in an autosomal dominant pattern in 7 out of 8 studied families. We investigated the impact of these variants on mRNA, protein levels, and skeletal muscle structure and function. Results reveal that nonsense-mediated decay likely prevents accumulation of harmful truncated protein in skeletal muscle in patients with TTNtvs. Splice variants and an out-of-frame deletion induce aberrant exon skipping, while an in-frame deletion produces shortened titin with intact N- and C-termini, resulting in disrupted sarcomeric structure. All variant types were associated with genome-wide changes in splicing patterns, which represent a hallmark of disease progression. Lastly, RNA-seq studies revealed that GDF11, a member of the TGF-β superfamily, is upregulated in diseased tissue, indicating that it might be a useful therapeutic target in skeletal muscle titinopathies.
Deciphering single-cell gene expression variability and its role in drug response
Authors: Liu Sizhe , Chen Liang 
Published: September 2024

Abstract
The effectiveness of drug treatments is profoundly influenced by individual responses, which are shaped by gene expression variability, particularly within pharmacogenes. Leveraging single-cell RNA sequencing (scRNA-seq) data, our study explores the extent of expression variability among pharmacogenes in a wide array of cell types across eight different human tissues, shedding light on their impact on drug responses. Our findings broaden the established link between variability in pharmacogene expression and drug efficacy to encompass variability at the cellular level. Moreover, we unveil a promising approach to enhance drug efficacy prediction. This is achieved by leveraging a combination of cross-cell and cross-individual pharmacogene expression variation measurements. Our study opens avenues for more precise forecasting of drug performance, facilitating tailored and more effective treatments in the future.
Can there be responsible AI without AI liability? Incentivizing generative AI safety through ex-post tort liability under the EU AI liability directive
Authors: Noto La Diega Guido , Bezerra Leonardo C T 
Published: September 2024

Abstract
In Europe, the governance discourse surrounding artificial intelligence (AI) has been predominantly centred on the AI Act, with a proliferation of books, certification courses, and discussions emerging even before its adoption. This narrow focus has overshadowed other crucial regulatory interventions that promise to fundamentally shape AI. This article highlights the proposed EU AI liability directive (AILD), the first attempt to harmonize general tort law in response to AI-related threats, addressing critical issues such as evidence discovery and causal links. As AI risks proliferate, this article argues for the necessity of a responsive system to adequately address AI harms as they arise. AI safety and responsible AI, central themes in current regulatory discussions, must be prioritized, with ex-post liability in tort playing a crucial role in achieving these objectives. This is particularly pertinent as AI systems become more autonomous and unpredictable, rendering the ex-ante risk assessments mandated by the AI Act insufficient. The AILD’s focus on fault and its limited scope is also inadequate. The proposed easing of the burden of proof for victims of AI, through enhanced discovery rules and presumptions of causal links, is insufficient in a context where Large Language Models exhibit unpredictable behaviours and humans increasingly rely on autonomous agents for complex tasks. Moreover, the AILD’s reliance on the concept of risk, inherited from the AI Act, is misplaced, as tort liability intervenes after the risk has materialized. However, the inherent risks in AI systems could justify EU harmonization of AI torts in the direction of strict liability. Bridging the liability gap will enhance AI safety and responsibility, better protect individuals from AI harms, and ensure that tort law remains a vital regulatory tool.
Actinomycin D reduces virulence factors and biofilms against Aeromonas hydrophila
Authors: Zeng Yuexiang , Liu Junsheng , Wang Wei , Wang Bo , Jia Aiqun 
Published: September 2024

Abstract

Aims
Aeromonas hydrophila, a Gram-negative bacterium, is ubiquitously found in many aquatic habitats, causing septicemia in humans and fishes. Attributed to abuse or misuse of conventional antimicrobial drug usage, antimicrobial resistance is at an alarming rise. There is an available alternative strategy to bacterial resistance to antimicrobials, which is inhibition of virulence and pathogenicity employing quorum sensing inhibitors (QSIs). Hence, actinomycin D’s effectiveness against A. hydrophila SHAe 115 as a QSI was investigated in decreasing virulence factors and preventing biofilm formation.

Methods and results
Actinomycin D, belongs to the QSI combating Pseudomonas aeruginosa PAO1 originally isolated from an entophytic actinomycete (Streptomyces cyaneochromogenes RC1) in Areca catechu L. In the present work, further investigations were carried out to assess the effect of actinomycin D at subminimal inhibitory concentrations (sub-MICs), QS-regulated virulence factors, and biofilm inhibition strategies. Intrinsic properties encompassing inhibition of the production of protease and hemolysin and subsequent activities on biofilm formation and eradication of mature biofilm were established along with weakened swimming and swarming motilities in A. hydrophila SHAe 115. In the Tenebrio molitor survival assay, actinomycin D effectively reduced the virulence and pathogenicity of A. hydrophila, resulting in elimination of mortality. However, the hydrolysate of actinomycin D, 2-hydroxy-4,6-dimethyl-3-oxo-3H-phenoxazine-1,9-dicarboxylic acid (HDPD), had lost the QSI activity in A. hydrophila.

Conclusions
Actinomycin D was proved as a viable QSI in lessening A. hydrophila’s the virulence and pathogenicity, as evident from our research findings
Large branchiopods (Anostraca, Notostraca, Laevicaudata, Spinicaudata) from the semi-arid regions of western India
Authors: Vanjare Avinash Isaac , Katke Prashant Manohar , Padhye Sameer M 
Published: September 2024

Abstract
Large branchiopod crustaceans are flagship species of temporary water bodies, especially in arid and semi-arid regions. Less information is available about the large branchiopods of tropical Asia compared to other parts of the world such as the Americas. To reduce this disparity, we surveyed large branchiopods from the semi-arid region of Maharashtra state, India. Sampling at 29 sites over four years revealed nine species representing four orders. This is the highest diversity ever reported from a single regional study in India. Anostracans were the most commonly occurring group, whereas the spinicaudatans Leptestheria cf. nobilisSars, 1900, L. jaisalmerensisTiwari, 1962, and Eulimnadia michaeliNayar & Nair, 1968 were very rare. Leptestheria jaisalmerensis had been known previously only from its type locality nearly 1,200 km north of our study region. Congeneric assemblages of the anostracans Streptocephalus dichotomusBaird, 1860 + S. simplexGurney, 1906 and the spinicaudatans Leptestheria cf. nobilis + L. jaisalmerensis were collected. Temporary aquatic habitats are threatened due to adverse anthropogenic activities, especially in developing countries like India. The endemic species of large branchiopods in the Indian subcontinent should be red-listed, as is done elsewhere.
Sustainable aquaculture of West African freshwater prawns Macrobrachium vollenhovenii (Herklots, 1857) and M. macrobrachion (Herklots, 1851) (Decapoda: Caridea: Palaemonidae)
Authors: Taguemount Riyad 
Published: September 2024

Abstract
The river prawn Macrobrachium vollenhovenii (Herklots, 1857) and the brackish river prawn M. macrobrachion (Herklots, 1851) are economically and ecologically significant West African species. Recent molecular studies suggest they might be different ecotypes of the same species, complicating taxonomy and sustainable aquaculture practices. Both species face significant threats from human exploitation, leading to high exploitation rates and smaller average sizes within populations. Seasonal variations affect their abundance, with M. macrobrachion more prevalent during the rainy season and M. vollenhovenii thriving in the dry season. Their omnivorous detritivorous feeding habits involve consuming detritus, diatoms, phytoplankton, and insect larvae during juvenile stages. Aquaculture of M. vollenhovenii and M. macrobrachion encounters difficulties such as limited hatchery technology and low larval survival rates. Efforts to cultivate juveniles or adults in captivity face obstacles like high mortality rates due to moulting stress, handling, feeding, and cannibalism. Reintroducing captive-bred prawns into the wild offers dual benefits: controlling snail populations that host parasite causing schistosomiasis and restoring ecological balance while enhancing local fisheries and providing socio-economic benefits. To achieve sustainable aquaculture, it is crucial to address taxonomic complexities, implement management measures to mitigate overexploitation, improve hatchery technology, optimise feeding strategies, reduce stress during moulting and handling, and engage local communities through capacity building and awareness programs. This review aims to contribute to a better understanding of these prawns, promoting informed decision-making for sustainable management, conservation, and socio-economic benefits in West Africa.
Density-guided and adaptive update strategy for multi-objective particle swarm optimization
Authors: Zhang Xiaoyan , Liu Yanmin , Song Qian , Zhang Yansong , Yang Jie , Wang Xingtao 
Published: September 2024

Abstract
As a powerful optimization technique, multi-objective particle swarm optimization (MOPSO) has been paid more and more attention by scientists. However, in more complex problems, MOPSO faces the challenges of weak global search ability and easy-to-fall-into local optimality. To address these challenges and obtain better solutions, people have proposed many variants. In this study, a density-guided and adaptive update strategy for multi-objective particle swarm optimization (DAMOPSO) is proposed. First, an adaptive grid is used to determine the mutation particles and guides. Then, the Cauchy mutation operator is performed for the poorly distributed particles to expand the search space of the population. Additionally, the strategy of non-dominated sorting and hyper-region density are devised for maintaining external archives, which contribute to the uniform distribution of optimal solutions. Finally, an adaptive detection strategy based on the adjustment coefficient and conversion efficiency is designed to update the flight parameters. These approaches not only speed up the convergence of algorithms, but also balance exploitation and exploration more effectively. The proposed algorithm is compared with several representative multi-objective optimization algorithms on 22 benchmark functions; meanwhile, statistical tests, ablation experiments, analysis of stability, and complexity are also performed. The experimental results demonstrate DAMOPSO is more competitive than other comparison algorithms.
Parental self-efficacy and early language development in deaf and hard-of-hearing children
Authors: Davenport Carrie A , Smolen Elaine , Castellanos Irina , Dirks Evelien , Houston Derek M 
Published: September 2024

Abstract
This study examined the relationship between parental self-efficacy in parents of young deaf and hard-of-hearing (DHH) children and children’s spoken language skills. A retrospective within-subjects study design was used that included 24 mother–child dyads with DHH children. Parental self-efficacy was assessed using the Scale of Parental Involvement and Self-Efficacy–Revised. Children’s language abilities were assessed using the Preschool Language Scale–5th edition. Our data revealed no significant associations between global measures of parental self-efficacy and children’s auditory comprehension, expressive communication, and total language scores. However, positive correlations were found between child language skills and specific parents’ beliefs about their ability to support their child’s spoken language development, their ability to use strategies to help their child communicate, and their active involvement in intervention. Findings highlight the importance of examining discrete aspects of parental self-efficacy as it specifically relates to parents supporting their DHH child’s spoken language development. Future directions and implications are provided.
Language and executive function in Mandarin-speaking deaf and hard-of-hearing children aged 3–5
Authors: Pan Yuchen , Xiao Yongtao 
Published: September 2024

Abstract
The study aimed to explore spoken language and executive function (EF) characteristics in 3–5-year-old prelingually deaf and hard-of-hearing (DHH) children, and evaluate the impact of demographic variables and EF on spoken language skills. 48 DHH children and 48 typically developing children who use auditory-oral communication were recruited. All participants underwent EF tests, including auditory working memory (WM), inhibitory control, cognitive flexibility, and the EF performance reported by parents. Using Mandarin Clinical Evaluation of Language for Preschoolers (MCELP), vocabulary comprehension, sentence comprehension, vocabulary naming, sentence structure imitation, and story narration were evaluated only in the DHH group, and their results were compared with the typical developmental level provided by MCELP. Results showed that DHH children exhibit deficiencies in different spoken language domains and EF components. While the spoken language skills of DHH children tend to improve as they age, a growing proportion of individuals fail to reach the typical developmental level. The spoken language ability in DHH children was positively correlated with age and EFs, and negatively correlated with aided hearing threshold, while auditory WM could positively predict their spoken language performance.
Dispersal of the Golden-mantled Ground Squirrel (Callospermophilus lateralis)
Authors: Nguyen Nhan T T , Wells Caitlin P , Van Vuren Dirk H 
Published: September 2024

Abstract
Dispersal is common in mammals and can have an important role in shaping demography, genetics, distribution, and social structure. Dispersal entails potential costs but also potential benefits, and the dispersal decision is thought to be conditional; the potential disperser assesses prospects for success at its current location and disperses to improve its fitness. However, the costs and benefits of dispersal, as well as factors influencing the dispersal decision, are not well known. We used trapping and observation to study dispersal in the Golden-mantled Ground Squirrel (Callospermophilus lateralis), a species for which dispersal is largely unknown. We characterized the dispersal process by evaluating dispersal timing and distance, assessed factors that might influence the dispersal decision, and analyzed the fitness cost of dispersal after settlement. We found that most dispersal occurred during the summer of birth, as is expected for a small-bodied sciurid. However, some squirrels delayed dispersal until early in their yearling summer. Dispersal was male-biased in dispersal tendency, and it was also male-biased in dispersal distance, but only over shorter dispersal distances. The dispersal decision for juvenile females appeared to originate as soon as 10 days after they emerged from the natal burrow, and the decision was not associated with body mass or several measures of competition. Instead, dispersal of juvenile females was associated with the number of littermate sisters, with each sister present increasing the likelihood of dispersal by 26%. Littermate sisters might be a cue foretelling the effects of kin competition the following year. We did not find a significant difference in lifetime reproductive success between philopatric and dispersing females after settlement, suggesting that for golden-mantled ground squirrels, any cost of dispersal is experienced primarily during the transience phase.