bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription modulates chromatin dynamics and locus configuration sampling
Authors: Forte Giada , Buckle Adam , Boyle Shelagh , Marenduzzo Davide , Gilbert Nick , Brackley Chris A. 
Published: August 2023

AbstractIn living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we applied the highly predictive heteromorphic polymer (HiP-HoP) model to determine chromatin fiber mobility at the Pax6 locus in three mouse cell lines with different transcription states. While transcriptional activity minimally affects movement of 40-kbp regions, we observed that motion of smaller 1-kbp regions depends strongly on local disruption to chromatin fiber structure marked by H3K27 acetylation. This also substantially influenced locus configuration dynamics by modulating protein-mediated promoter-enhancer loops. Importantly, these simulations indicate that chromatin dynamics are sufficiently fast to sample all possible locus conformations within minutes, generating wide dynamic variability within single cells. This combination of simulation and experimental validation provides insight into how transcriptional activity influences chromatin structure and gene dynamics.
DIPS-Plus: The enhanced database of interacting protein structures for interface prediction
Authors: Morehead Alex , Chen Chen , Sedova Ada , Cheng Jianlin 
Published: August 2023

AbstractIn this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for machine learning of protein interfaces. While the original DIPS dataset contains only the Cartesian coordinates for atoms contained in the protein complex along with their types, DIPS-Plus contains multiple residue-level features including surface proximities, half-sphere amino acid compositions, and new profile hidden Markov model (HMM)-based sequence features for each amino acid, providing researchers a curated feature bank for training protein interface prediction methods. We demonstrate through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.
Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)
Authors: Sahu Sunil Kumar , Liu Min , Chen Yewen , Gui Jinshan , Fang Dongming , Chen Xiaoli , Yang Ting , He Chengzhong , Cheng Le , Yang Jinlong , Sahu Durgesh Nandini , Li Linzhou , Wang Hongli , Mu Weixue , Wei Jinpu , Liu Jie , Zhao Yuxian , Zhang Shouzhou , Lisby Michael , Liu Xin , Xu Xun , Li Laigeng , Wang Sibo , Liu Huan 
Published: August 2023

AbstractWood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.
Seafood label quality and mislabelling rates hamper consumer choices for sustainability in Australia
Authors: Cundy Megan E. , Santana-Garcon Julia , McLennan Alexander G. , Ayad Marcelle E. , Bayer Philipp E. , Cooper Madalyn , Corrigan Shannon , Harrison Emily , Wilcox Chris 
Published: August 2023

AbstractSeafood mislabelling and species substitution, compounded by a convoluted seafood supply chain with significant traceability challenges, hinder efforts towards more sustainable, responsible, and ethical fishing and business practices. We conducted the largest evaluation of the quality and accuracy of labels for 672 seafood products sold in Australia, assessing six seafood groups (i.e., hoki, prawns, sharks and rays, snapper, squid and cuttlefish, and tuna) from fishmongers, restaurants, and supermarkets, including domestically caught and imported products. DNA barcoding revealed 11.8% of seafood tested did not match their label with sharks and rays, and snappers, having the highest mislabelling rate. Moreover, only 25.5% of products were labelled at a species-level, while most labels used vague common names or umbrella terms such as ‘flake’ and ‘snapper’. These poor-quality labels had higher rates of mislabelling than species-specific labels and concealed the sale of threatened or overfished taxa, as well as products with lower nutritional quality, reduced economic value, or potential health risks. Our results highlight Australia’s weak seafood labelling regulations and ambiguous non-mandatory naming conventions, which impede consumer choice for accurately represented, sustainable, and responsibly sourced seafood. We recommend strengthening labelling regulations to mitigate seafood mislabelling and substitution, ultimately improving consumer confidence when purchasing seafood.
An examination of the design for a prefabricated housing unit in Cyprus in terms of energy, daylighting and cost
Authors: Savvides Andreas , Michael Aimilios , Vassiliades Constantinos , Parpa Despina , Triantafyllidou Elina , Englezou Maria 
Published: August 2023

AbstractHousing prefabrication emerged as an energy and cost-saving solution, which can also be linked to the reduction of environmental impacts, as well as to the development of green construction practices. In the first part of this study, a comprehensive literature review of the prefabricated assembly methods and their inherent potential, in terms of both design and construction are presented. Design strategies that incorporate the integration of environmental systems are also considered. A classification and taxonomy of archetypes is included, based on key design principles pertaining to environmental design. Based on the conclusions drawn from the assessment of these considerations, this paper revisits the realm of design and construction techniques used in energy efficient and environmentally compatible prefabricated housing unit in a Cypriot context. Cost-saving strategies are proposed, as well as architectural design and fabrication recommendations. Consequently, the research aims to contribute to existing literature by drawing results from an actual demonstration project in Cyprus. It goes on to outline considerations affecting the front end of the design and construction processes based on criteria for efficient prefabrication and modular construction. Findings are then related to simulations for energy and daylighting performance supplemented by a techno-economic analysis, aiming to demonstrate the viability of this enterprise. In this way it is hoped that stakeholders considering the adoption of this approach to design and construction may make better informed and more appropriate decisions.
Ramifications of POU4F3 variants associated with autosomal dominant hearing loss in various molecular aspects
Authors: Lee Sang-Yeon , Kim Min Young , Han Jin Hee , Park Sang Soo , Yun Yejin , Jee Seung-Cheol , Han Jae Joon , Lee Jun Ho , Seok Heeyoung , Choi Byung Yoon 
Published: August 2023

AbstractPOU4F3, a member of the POU family of transcription factors, commonly causes autosomal dominant deafness. Exome sequencing was used to identify four novel variants in POU4F3 (NM_002700.2), including c.564dupA: p.Ala189SerfsTer26, c.743T > C:p.Leu248Pro, c.879C > A:p.Phe293Leu, and c.952G > A:p.Val318Met, and diverse aspects of the molecular consequences of their protein expression, stability, subcellular localization, and transcriptional activity were investigated. The expression of three mutant proteins, encoded by missense variants, was reduced compared to the wild-type protein, demonstrating that the mutants were unstable and vulnerable to degradation. Additionally, all the mutant proteins had distinct subcellular localization patterns. A mutant protein carrying p.Ala189SerfsTer26, in which both mono- and bi-partite nuclear localization signals were disrupted, showed abnormal subcellular localization. Resultantly, all the mutant proteins significantly reduced the transcriptional activity required to regulate the downstream target gene expression. Furthermore, we identified the altered expression of 14 downstream target genes associated with inner ear development using patient-derived lymphoblastoid cell lines. There was a significant correlation of the expression profile between patient-derived cells and the cochlear hair cells, which provided a breakthrough for cases where the collection of human cochlear samples for transcriptome studies was unfeasible. This study expanded the genotypic spectrum of POU4F3 in DFNA15, and further refined the molecular mechanisms underlying POU4F3-associated DFNA15.
Delhi urbanization footprint and its effect on the earth’s subsurface state-of-stress through decadal seismicity modulation
Authors: Tiwari Deepak K. , Hari Manoj , Kundu Bhaskar , Jha Birendra , Tyagi Bhishma , Malik Kapil 
Published: August 2023

AbstractUrban land and its expansion have profoundly impacted the global environment, including the stress change in the earth’s subsurface, even though urban land is a small fraction of the global land surface. Divulging such effects has never been more important, given the role of stress in determining the safety of the urban population against earthquakes. However, knowledge of this time-dependent non-linear effect of urbanization on the subsurface remains in the gray area. This study focuses on the area surrounding Delhi, the capital city of India, to understand the relative contribution of the building load created by rapid urbanization in exacerbating the subsurface state-of-stress. The results highlight that, since 2010, the modulation in the seismicity rate and the stability of basement thrust faults is linked not only to urbanization but also to decadal groundwater storage. Mounting evidence suggests that the rapid urbanization, and the resulting non-tectonic horizontal compression, stabilize faults in the Aravalli Delhi belt, which are destabilized due to the extensive groundwater extraction. This affects the decadal seismicity trend around the Aravalli Delhi fold belt. Nonetheless, the magnitude of this time-dependent deformation influence on the seismicity modulation remains uncertain. The findings from this study quantify the geomechanical impacts of urbanization in the Delhi area for the first time.
Phase field modelling of hopper crystal growth in alloys
Authors: Bollada P. C. , Jimack P. K. , Mullis A. M. 
Published: August 2023

AbstractHere we use phase field to model and simulate “hopper” crystals, so named because of their underlying cubic structure but with a hopper-like depression on each of the six faces. Over the past three decades simulations of single phase solidification have successfully explored dendritic structures, in two and three dimensions, formed under high undercooling from a slight perturbation in anisotropy. More recently we see the modelling of faceted structures at near equilibrium, and also, under high undercooling, the formation of dendritic-like structures in two dimensions which retain some faceting in the dendrite arms. A cubic hopper crystal appears to be a hybrid structure, somewhere between a perfect cube and a dendrite, and, to date, has not appeared in the modelling literature. In this paper we describe a model for faceted cubic growth and explore results, necessarily in three dimensions, that include perfect cube, hopper and dendritic. We also touch briefly on one other morphology—octahedral.
Effects of repeated sprinting on hamstring shear modulus pattern and knee flexor neuromuscular parameters
Authors: Pimenta Ricardo , Lopes Tomás , Correia José Pedro , Veloso António Prieto 
Published: August 2023

AbstractThe purpose of the present study was to examine the acute effects of a maximum repeated sprint protocol on (1) hamstring shear modulus and (2) knee flexor neuromuscular parameters such as peak torque (PT) and rate of torque development (RTD). Muscle shear modulus was assessed in 18 healthy males using shear wave elastography at rest and during 30° isometric knee flexion at 20% of maximal voluntary isometric contraction, before and after a 10 × 30 m repeated sprint protocol. There was a 9% decrease in average speed between the fastest and slowest sprint (p < 0.001; d = 2.27). A pre-post decrease was observed in PT (p = 0.004; η2p = 0.399) and in the 0–50 ms (p = 0.042; η2p = 0.222), and 50–100 ms (p = 0.028; η2p = 0.254) RTD periods. For the active shear modulus, the only significant change after the sprint task was in the biceps femoris long head (BFlh) with an increase of 10% (Pre: 26.29 ± 8.89 kPa; Post: 28.93 ± 8.31 kPa; p = 0.015; d = 0.31). The present study provides evidence that repeated sprinting leads to significant decreases in average speed, PT, early RTD (0–50 ms; 50–100 ms), and to an increase in BFlh active shear modulus without changing the shear modulus of the other hamstrings muscles.
Transient power equalization control strategy of virtual synchronous generator in isolated island microgrid with heterogeneous power supply
Authors: Gao Changwei , Sun Yongchang , Zheng Weiqiang , Wang Wei 
Published: August 2023

AbstractIn the parallel supply system of synchronous generator and virtual synchronous generator, the physical structure and control structure of the two kinds of power supply are quite different, and it is difficult to distribute the transient power of the two kinds of power supply evenly when the load changes abruptly. Especially in the case of sudden load increase, virtual synchronous generator bears too much load in the transient process because of its fast adjustment speed, and even causes short-term overload, which makes the capacity of virtual synchronous generator can not be fully utilized. In view of this problem, firstly, the mechanism of transient power uneven distribution of two heterogeneous power sources is explained from the differences of frequency modulation, voltage regulation and output impedance. Secondly, virtual speed regulation, virtual excitation and dynamic virtual impedance are added to the traditional virtual synchronous generator control to simulate the speed regulation characteristics and electromagnetic transient characteristics of the synchronous generator, so as to realize the transient and steady-state power equalization between heterogeneous power supplies when the virtual synchronous generator and the synchronous generator run in parallel. Thirdly, in order to ensure the fast dynamic response characteristics of the virtual synchronous generator in independent operation mode, the traditional virtual synchronous generator control algorithm is still maintained in independent operation mode, and the mode switching control link based on state tracking is designed to realize smooth switching between the two working modes. Finally, the hardware in loop experiment results based on RT-LAB show that the proposed control method can realize the transient and steady-state power equalization when the virtual synchronous generator and the synchronous generator operate in parallel, it can keep the fast voltage regulation and frequency modulation ability when the virtual synchronous generator operates independently, and can realize smooth switching between independent and parallel operation modes.
A chlorzoxazone–folic acid combination improves cognitive affective decline in SCA2-58Q mice
Authors: Marinina Ksenia S. , Bezprozvanny Ilya B. , Egorova Polina A. 
Published: August 2023

AbstractSpinocerebellar ataxia type 2 (SCA2) is a polyglutamine disorder caused by a pathological expansion of CAG repeats in ATXN2 gene. SCA2 is accompanied by cerebellar degeneration and progressive motor decline. Cerebellar Purkinje cells (PCs) seem to be primarily affected in this disorder. The majority of the ataxia research is focused on the motor decline observed in ataxic patients and animal models of the disease. However, recent evidence from patients and ataxic mice suggests that SCA2 can also share the symptoms of the cerebellar cognitive affective syndrome. We previously reported that SCA2-58Q PC-specific transgenic mice exhibit anxiolytic behavior, decline in spatial memory, and a depressive-like state. Here we studied the effect of the activation of the small conductance calcium-activated potassium channels (SK channels) by chlorzoxazone (CHZ) combined with the folic acid (FA) on the PC firing and also motor, cognitive and affective symptoms in SCA2-58Q mice. We realized that CHZ-FA combination improved motor and cognitive decline as well as ameliorated mood alterations in SCA2-58Q mice without affecting the firing rate of their cerebellar PCs. Our results support the idea of the combination therapy for both ataxia and non-motor symptoms in ataxic mice without affecting the firing frequency of PCs.
Neuronal correlates of eyeblinks are an expression of primary consciousness phenomena
Authors: Callara Alejandro Luis , Greco Alberto , Scilingo Enzo Pasquale , Bonfiglio Luca 
Published: August 2023

AbstractThe blinking rate far exceeds that required for moistening the cornea and changes depending on whether a person is resting or engaged in cognitive tasks. During ecological cognitive tasks (such as speaking, reading, and watching videos), blinks occur at breakpoints of attention suggesting a role in information segmentation, but the close relationship between cognition dynamics and blink timing still escapes a full understanding. The aim of the present study is to seek (1) if there is a temporal relationship between blink events and the consecutive steps of cognitive processing, and (2) if blink timing and the intensity of blink-related EEG responses are affected by task-relevance of stimuli. Our results show that, in a classical visual oddball task, (i) the occurrence of blinks is influenced by stimuli, irrespective of their relevance, (ii) blinks following relevant stimuli are only apparently delayed due to the need of finalizing a behavioural response, and (iii) stimulus relevance does not affect the intensity of the blink-related EEG response. This evidence reinforce the idea that blinks are not emitted until the last step of the processing sequence has been completed and suggests that blink-related EEG responses are generated by primary consciousness phenomena which are considered by their nature non-modulable (all-or-nothing) phenomena.
GlobalUsefulNativeTrees, a database documenting 14,014 tree species, supports synergies between biodiversity recovery and local livelihoods in landscape restoration
Authors: Kindt Roeland , Graudal Lars , Lillesø Jens-Peter B. , Pedercini Fabio , Smith Paul , Jamnadass Ramni 
Published: August 2023

AbstractTree planting has the potential to improve the livelihoods of millions of people as well as to support environmental services such as biodiversity conservation. Planting however needs to be executed wisely if benefits are to be achieved. We have developed the GlobalUsefulNativeTrees (GlobUNT) database to directly support the principles advocated by the ‘golden rules for reforestation’, including planting tree mixtures that maximize the benefits to local livelihoods and the diversity of native trees. Developed primarily by combining data from GlobalTreeSearch with the World Checklist of Useful Plant Species (WCUPS), GlobUNT includes 14,014 tree species that can be filtered for ten major use categories, across 242 countries and territories. The 14,014 species represent roughly a quarter of the tree species from GlobalTreeSearch and a third of the plant species from WCUPS. GlobUNT includes over 8000 species used as materials (9261 species; 68.4% of the total in WCUPS for that use category) or medicines (8283; 31.1%), over 2000 species with environmental uses (3317; 36.9%), used as human food (3310; 47.0%) or fuel (2162; 85.5%), over 1000 species used as gene sources (1552; 29.8%), animal food (1494; 33.7%), social uses (1396; 53.8%) or poisons (1109; 36.8%), and 712 species (68.4%) as insect food.
DNA-based assessment of root lesion nematode infections in cereal roots
Authors: Fatemi Ehsan , Melzer Siegbert , Jung Christian 
Published: August 2023

AbstractRoot lesion nematodes (RLN) of the genus Pratylenchus are causing significant damage in cereal production worldwide. Due to climate change and without efficient and environment-friendly treatments, the damages through RLNs are predicted to increase. Microscopic assessments of RLNs in the field and the greenhouses are time-consuming and laborious. As a result, cereal breeders have mostly ignored this pest. We present a method measuring RLN in infected cereal roots using a standardized PCR approach. Publicly available Pratylenchus neglectus primer combinations were evaluated. An optimal primer combination for RT-qPCR assay was identified to detect and quantify P. neglectus within infected cereal roots. Using the RT-qPCR detection assay, P. neglectus could be clearly distinguished from other plant parasitic nematodes. We could identify P. neglectus DNA in barley and wheat roots as low as 0.863 and 0.916 ng/µl of total DNA, respectively. A single P. neglectus individual was detected in water suspension and within barley and wheat roots. The RT-qPCR detection assay provides a robust and accurate alternative to microscopic nematode identification and quantification. It could be of interest for resistance breeding, where large populations must be screened to detect and quantify P. neglectus in farmer’s fields.