bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanded chromosomal microarray comprising screening for spinal muscular atrophy and monogenic diseases3
Authors: Luan Xiaorui , Xu Naixin , Xie Yaojun , Shi Weihui , Cao Xianling , Zhou Xuanyou , Chen Songchang , Xu Chenming 
Published: November 2024

AbstractBackgroundCopy number variants platforms, as critical supports for genetic diagnosis, have been well implemented in prenatal diagnosis. However, numerous severe conditions with underlying single-gene defects are not included in current invasive prenatal screening. To bridge this gap, an expanded chromosomal microarray analysis was developed, employing a meticulous designed single nucleotide polymorphism chip. This chip incorporated additional probes to augment its efficacy in screening for spinal muscular atrophy and diagnosing monogenic disorders.Objective(s)This study aimed to evaluate the accuracy, efficacy, and incremental yield of expanded chromosomal microarray, compared with karyotype analysis and low-depth genome sequencing for routine prenatal diagnosis.Study DesignIn this prospective study, total of 512 fetuses were included in this study. In this study three distinct diagnostic techniques-karyotype analysis, low-depth genome sequencing, and expanded chromosomal microarray-were processed to evaluate each sample. Aneuploidies and multigene copy number variations were detected and analyzed in a blinded fashion.SMN1exonic copy number variations were confirmed by multiplex ligation-dependent probe amplification and single nucleotide variations were confirmed by sanger sequencing.ResultsOverall, expanded chromosomal microarray identified genetic abnormalities in 91 out of 512 cases (17.6%). The encountered rate was significantly higher than the rates observed with low-depth genome sequencing (66 out of 512 cases, 12.9%) and conventional chromosome karyotyping (42 out of 512 cases, 8.2%). Expanded chromosomal microarray not only detected all these non-mosaic aneuploidies and copy number variations in 62(12.1%) diagnosed cases identified by low-depth genome sequencing (low-depth genome sequencing), but also detected 9 cases with regions of homozygosity, 10(2.0%) cases with exonic deletions (SMN1andDMD), and 13(2.5%) cases with single nucleotide variations.ConclusionsCompared with low-depth GS, expanded chromosomal microarray increased the additional detection rate by 4.7% (24/512). Compared with traditional chromosomal microarray, expanded chromosomal microarray increased the additional detection rate by 3.9% (20/512) in 512 fetuses. Although the expanded chromosomal microarray (ECMA) has limited accuracy for detecting single nucleotide variations, its screening capacity is significantly enhanced when complemented with Sanger sequencing validation. Using expanded chromosomal microarray, we detected not only copy number variations, but also exonic deletions, regions of homozygosity with high accuracy in an acceptable turnaround time (2-3 weeks). Our results suggest that expanded chromosomal microarray has the potential to be a promising prenatal diagnostic tool with incremental yield of screening exonic copy number variations inSMN1.
Modulatory effect of plasma-activated water on arbuscular mycorrhizal symbiosis inLotus japonicus
Authors: Cortese Enrico , Binci Filippo , Nouri Erfan , Capparotto Arianna , Settimi Alessio G. , Dabalà Manuele , Antoni Vanni , Squartini Andrea , Giovannetti Marco , Navazio Lorella 
Published: November 2024

AbstractPlasma-activated water (PAW) is a recently developed cutting-edge technology that is increasingly gaining interest for its applications in medicine, food industry and agriculture. In plant biology, PAW has been shown to promote seed germination, plant growth, and plant resistance to biotic and abiotic stresses. Despite increasing knowledge of the beneficial effects exerted by PAW on plants, little information is currently available about how this emerging technology may affect the mutualistic plant-microbe interactions in the rhizosphere. In this work we have investigated the impact of irrigation with PAW, generated by a plasma torch, on arbuscular mycorrhizal (AM) symbiosis between the model legumeLotus japonicusand the AM fungusRhizophagus irregularis.Since PAW sensing by plants has recently been demonstrated to occur through calcium-mediated signalling, we monitored early cellular responses to different doses of PAW inL. japonicusroots expressing the Ca2+-sensitive photoprotein aequorin targeted to either the cytosol or nucleus. Quantitative analyses of AM fungal accommodation in host roots along with phosphate accumulation in leaves, as well as chemical analysis of N, C, S in shoots, showed that treatments with PAW play a modulatory role on plant AM symbiotic performance, in a manner dependent on the time interval of water exposure to the plasma and on the duration of plant irrigation treatment with PAW. Establishing a solid scientific ground for plasma-related technology may provide key elements to develop tools and treatments aimed to increase crop plant yield in a sustainable manner.
Expectation Violations as an Effective Alternative to Complex Mentalizing in Novel Communication
Authors: Buidze Tatia , Yao Yuan-Wei , Gläscher Jan 
Published: November 2024

SummaryEffective communication in the absence of a shared language is a fundamental challenge, often addressed through complex cognitive mechanisms such as Theory of Mind, which allows individuals to infer others’ intentions and beliefs. However, this process is cognitively demanding and may not always be necessary. In this study, we propose that a more parsimonious cognitive mechanism—expectancy violations—can serve as an efficient alternative for communication in novel interactions. We tested this in the Tacit Communication Game, where we simulated Sender behavior using four computational models: the Surprise model based on expectancy violations and three levels of Theory of mind. After human Receivers interacted with these simulated Senders, we assessed the effectiveness of communication by analyzing accuracy and reaction times. Our results revealed that Receivers paired with the Surprise model achieved accuracy rates comparable to those interacting with the most complex Theory of mind model and exhibited more human-like message patterns. Additionally, models associated with higher accuracies also resulted in faster reaction times, indicating a reduced cognitive load. These findings challenge the necessity of complex mentalizing strategies in novel human interactions and suggest that an intuitive mechanism of expectancy violation may be a more plausible cognitive mechanism, while also providing quick responses.
Model-Driven Elucidation of Lactose and Galactose Metabolism via Oxidoreductive Pathway inSungouiella intermediafor Cell Factory Applications
Authors: Peri Kameshwara. V. R. , Domenzain Ivan , Alalam Hanna D , Valverde Rascon Abril , Nielsen Jens , Geijer Cecilia 
Published: November 2024

AbstractConverting industrial side streams into value-added chemicals using microbial cell factories is of increasing interest, as such processes offer solutions to reduce waste and production costs. However, developing new, efficient cell factories for precision fermentation remains challenging due to limited knowledge about their metabolic capabilities. Here, we investigate the lactose and galactose metabolism of the non-conventional yeastSungouiella intermedia(formerlyCandida intermedia), using knowledge-matching of high-quality genome-scale metabolic model (GEM) with extensive experimental analysis and determine its potential as a future cell factory on lactose-rich industrial side-streams. We show that this yeast possesses the conserved Leloir pathway as well as an oxidoreductive galactose catabolic route. Contextualization of RNAseq data intoSint-GEMhighlights the regulatory mechanisms on the oxidoreductive pathway and how this pathway can enable adaptation to diverse environments. Model simulations, together with experimental data from continuous and batch bioreactors, indicate thatS. intermediauses upstream enzymes of the oxidoreductive pathway, in a condition-dependent manner, and produce the sugar alcohol galactitol as a carbon overflow metabolite, coupled to redox co-factor balancing during both lactose and galactose growth. Furthermore, the new metabolic insights facilitated the development of an improved bioprocess design, where an engineeredS. intermediastrain could achieve galactitol yields of >90% of the theoretical maximum at improved production rates using the industrial side-stream cheese whey permeate as feedstock. Additional strain engineering resulted in galactitol-to-tagatose conversion, proving the versatility of the future production host. Overall, this work sheds new light on the intrinsic interplay between parallel metabolic pathways that shape the lactose and galactose catabolism inS. intermedia. It also demonstrates how a GEM combined with experimental analysis can work in synergy to fast-forward metabolic characterization and development of new, non-conventional yeast cell factories.HighlightsAn oxidoreductive pathway functions in concert with the Leloir pathway for galactose catabolism.GEM predicts that galactitol secretion enables efficient carbon overflow metabolism and maintains redox balance.Knowledge-matching of GEM with experimental results highlights cell factory potential.High galactitol yields and proof-of-concept tagatose production using whey permeate as feedstock.
Building a robust backbone forAstragalus(Fabaceae) using a clade-specific target enrichment bait set
Authors: Buono Daniele , Kadereit Gudrun , Liston Aaron , Zarre Shahin , Morales-Briones Diego F. 
Published: November 2024

AbstractPremise of the studyWith over 3100 species,Astragalus(Fabaceae) has long fascinated botanists as the largest genus of flowering plants. With an origin in the Middle Miocene,Astragalushas one of the highest diversification rates known in flowering plants. Comprehensive taxonomic treatments exist, and the genus is currently subdivided into 136 sections in the Old World and 93 sections in the New World based on morphological characters. Despite considerable efforts, a comprehensive and well-resolved phylogeny of the genus is still lacking.MethodsHere, we reconstruct the backbone phylogeny ofAstragalususing a custom bait set capturing 819 loci specifically designed for a target enrichment approach in the Astragalean clade. We carefully selected a set of 107 taxa representing all major clades currently recognized inAstragalus. Of those, 80 newly sequenced taxa were obtained from herbarium specimens as old as 110 years.Key resultsWe retrieved all the targeted loci and additional off-target plastome sequences for all samples, including the 80 herbarium specimens. Our phylogenetic analysis reinforced the currently accepted backbone phylogeny ofAstragaluswith high support and unprecedented details, additionally providing insights into cytonuclear phylogenetic conflicts in the genus. Evidence for potential reticulate evolution was found, providing a possible explanation for the conflicts observed.ConclusionsThis work represents an important milestone in obtaining a comprehensive, herbarium-based phylogeny ofAstragalus, which will constitute the base to study a wealth of relevant biological questions, for example, the still unanswered question of what drove the rapid diversification ofAstragalus, with important repercussions on our understanding of diversification in natural contexts.
The effects of running shoe stack height on running style and stability during level running at different running speeds
Authors: Kettner Cagla , Stetter Bernd , Stein Thorsten 
Published: November 2024

AbstractThe footwear market contains a wide variety of running shoe solutions aiming at optimizing performance and minimizing injuries. Stack height is one of the most highly discussed design features of running shoes, but its effects are not yet well understood. This study investigated the effects of different shoes differing mainly in their stack heights (High: 50 mm, Medium: 35 mm & Low: 27 mm) on running style and stability during treadmill running at 10 and 15 km/h. A total of 17 healthy experienced runners participated in this study. The kinematic data were recorded with a 3D motion capturing system. The running style was investigated by a dual-axis framework with duty factor (DF) and leg length normalized to step frequency (SFnorm). Additionally, the ratio of landing to take-off duration, the lower body joint angle time series in the sagittal and frontal planes, the vertical center of mass oscillation (COMosc), and the stiffness parameters (kver & kleg) were compared for different conditions. The stability was analyzed using linear (i.e. discrete frontal ankle parameters) and nonlinear methods (i.e. Maximum Lyapunov Exponent for local dynamic stability of head, trunk, hip, and foot, and detrended fluctuation analysis of stride time). High resulted in longer ground contact relative to stride time (DF) compared to Low. The higher the stack height, the higher was the COMosc. Furthermore, High led to a longer foot eversion during stance compared to Medium. In addition, the local dynamic stability of the hip decreased with High in comparison with Low. The higher stack heights (≥ 35 mm) led to a lower SFnorm at 15 km/h but not at 10 km/h. The remaining shoe effects were independent of the running speed. Findings showed that changes in stack height can affect running style. Furthermore, the highest stack height resulted in changes related with instabilities (i.e., longer foot eversion and lower hip dynamic stability) which may be a critical issue in terms of injuries and performance. However, this study did not include joint load analysis or running performance measures such as VO2. Future studies may benefit from the combination of analysis approaches to better understand stack height effects on running injuries and performance.
Molecular determinant of sterol recognition by sterol cleavage activatory protein
Authors: Khiewdee Charal , Ounjai Puey , Pipatpolkai Tanadet 
Published: November 2024

AbstractIntracellular cholesterol homeostasis is regulated by the sterol response element-binding protein (SREBP) pathway through the SREBP cleavage-activating protein (SCAP) and the insulin-induced gene protein (INSIG). Previous studies highlighted that high concentrations of cholesterol mediated the dimerisation between INSIG and SCAP, which led to an inhibition of cholesterol uptake and biogenesis. However, the molecular understanding of SCAP-INSIG and cholesterol interactions remains elusive. Here, we used coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulation to determine interactions between INSIG, SCAP and cholesterol. Our work highlighted the novel binding pocket in the luminal domain at the atomistic resolution. Using a combination of the AlphaFold3 model and Gō-martini forcefield, we showed that loop 7 dynamics are crucial for cholesterol binding and are able to highlight conserved residues, which lead to INSIG-SCAP dimerisation. Together, our work highlights novel mechanisms of cholesterol sensor pathways and will benefit the development of novel therapeutic strategies for diseases, such as neuroinflammatory disease, caused by irregular cholesterol homeostasis.
The sequence and structural integrity of the SARS-CoV-2 Spike protein transmembrane domain is crucial for viral entry
Authors: Ortiz-Mateu J , Belda D , Avilés-Alía AI , Alonso-Romero J , García-Murria MJ , Mingarro I , Geller R , Martinez-Gil L 
Published: November 2024

AbstractThe Spike protein of SARS-CoV-2 is a type I membrane protein that mediates target cell recognition and membrane fusion. Its transmembrane domain (TMD) is usually considered a passive physical anchor that attaches the protein to the viral envelope. However, current knowledge of the dynamics and biogenesis of integral membrane proteins indicates that TMDs generally play key functions beyond membrane anchoring. Here, we explored the role of the SARS-CoV-2 Spike protein TMD during viral entry. To do so, we generated a series of amino acid substitutions and insertions within the hydrophobic core of the TMD and analyzed their impact on protein function. Our results indicate that the SARS-CoV-2 Spike protein is highly susceptible to changes in its TMD. Furthermore, the TMD sequence and structural parameters relevant for viral entry are distributed across the entire segment, albeit with a stronger implication of the N-terminal portion. The relative orientation of the regions before and after the TMD was also found to be relevant for particle entry. Finally, our results suggest that the SARS-CoV-2 Spike protein TMD can form homo-oligomers through a motif in which small residues are necessary.
Microbial dysbiosis is evident in oral squamous cell carcinoma (OSCC) tissues of a group of Sri Lankan male patients with oral risk habits
Authors: Perera Manosha Lakmali , Perera Irosha Rukmali 
Published: November 2024

AbstractBackgroundMetagenomic investigations into components of the oral microbiome in a single study remain scarce.ObjectiveTo ascertain the microbiome profile of oral squamous cell carcinoma (OSCC) tissues in a group of Sri Lankan male patients.MethodsFrom the main sample of an unmatched case-control study, a sub-sample consisting of 29 OSCC cases and 25 Fibroepithelial polyp (FEP) controls were selected. OSCC incisional and FEP excisional biopsies were collected and stored at -800C. DNA was extracted from frozen specimens using Gentra Puregene Tissue kit (Qiagen, Germany), solid tissue protocol. The DNA extracts were stored at -800C. Extracted DNA samples were sequenced by Illumina’s 2×300 bp chemistry. High quality non-chimeric merged reads were classified to the species level by prioritized BLASTN-algorithm for bacteriome and BLASTN-algorithm with UNITE’s named species sequences as reference for mycobiome.ResultsOur study identifies several potential periodontal pathogens, includingCampylobacter concisus, Prevotella salivae, Prevotella loeschii, andFusobacterium oral taxon 204. Additionally,Candida albicansis frequently associated with oral potentially malignant disorders (OPMDs) and oral cancers. Notably, we found a significant association betweenCandida etchelliiand oral cancer for the first time. Furthermore, Capnocytophaga, Atopobium, and Candida were the most abundant microbial genera present in oral squamous cell carcinoma (OSCC) tissues.ConclusionsA dysbiotic microbiome was discovered in the tumor microenvironment of a group of OSCC male patients with oral risk habits. Validation of these biomarkers indifferent cohorts to supplement inadequacy in the diagnosis of epithelial dysplasia histologically is much warranted in the golden era ofmicrobiome-first-medicine
Long-lasting, subtype-specific regulation of somatostatin interneurons during sensory learning
Authors: Zhu Mo , Mosso Matthew B. , Ma Xiaoyang , Park Eunsol , Barth Alison L. 
Published: November 2024

AbstractSomatostatin (SST)-expressing inhibitory neurons are a major class of neocortical γ-amino butyric acid (GABA) neurons, where morphological, electrophysiological, and transcriptomic analyses indicate more than a dozen different subtypes. However, whether this diversity is related to specific roles in cortical computations and plasticity remains unclear. Here we identify learning-dependent, subtype-specific plasticity in layer 2/3 SST neurons of the mouse somatosensory cortex. Martinotti-type, SST neurons expressing calbindin-2 show a selective decrease in excitatory synaptic input and stimulus-evoked calcium responses as mice learn a stimulus-reward association. Using these insights, we develop a label-free classifier using basal activity fromin vivoimaging that accurately predicts learning-associated response plasticity. Our data indicate that molecularly-defined SST neuron subtypes play specific and highly-regulated roles in sensory information processing and learning.
Cross-species Comparison of Ultramafic Rock Bio-accelerated Weathering Performance
Authors: Plante Luke , Klug Jacob D. , Lee Joseph , Hornby Adrian , Adair James , Marecos Sabrina , Reid Matthew C. , Gazel Esteban , Barstow Buz 
Published: November 2024

AbstractCarbon mineralization is a natural process that sequesters atmospheric CO2by reacting it with cations (e.g., Mg2+, Ca2+) released by weathering of rocks to form solid carbonates. However, this process is too slow to capture the excess CO2resulting from anthropogenic emissions in time to prevent significant warming of the atmosphere1–3. Additionally, accelerating carbon mineralization process by chemical or mechanical methods has proven prohibitively expensive to date4. Microbial rock-dissolution processes, including acidolysis, redoxolysis, and complexolysis, have the potential to accelerate weathering with low energy input5. However, there is no industrially useful microbe capable of dissolving ultramafic (rich in ferromagnesian minerals) rocks, suggesting that one will need to be discovered or built with synthetic biology. While microbes are known to dissolve ultramafic minerals6,7, the performance envelopes for these processes remain uncharacterized, and significant gaps exist in our knowledge of microbe-mineral interaction processes. Here, we make a normalized performance comparison of the dissolution of the ultramafic rock dunite (> 90% olivine ((Mg, Fe)2SiO4)) by three well-known mineral-dissolving microbes:Gluconobacter oxydans7–9,Sphingomonas desiccabilis10,11, andPenicillium simplicissimum12–14. We show thatG. oxydansoutperformedP. simplicissimumandS. desiccabilis, producing the most acidic biolixiviant (pH 2.15 when leaching 1% pulp density), and extracting the most magnesium (3,130 mg/L when leaching at 3% pulp density). Additionally,G. oxydansco-dissolves nine other metals, eight of which are critical for energy technologies (Cr, Mn, Co, Ni, Cu, and Zn)15,16with a maximum dissolved concentration of 33 mg/L for Ni. While increasing the pulp density of the dunite (solid to liquid ratio) resulted in higher metal dissolution byG. oxydansandS. desiccabilis, notably pulp densities above 2% inhibited mineral dissolution byP. simplicissimum. Our results provide evidence that the gap in performance betweenG. oxydansand the other two microbes increases with pulp density, and thus,G. oxydansis best suited for process and genetic engineering to maximize performance and minimize costs and environmental impacts of bio-accelerated weathering. Finally, we propose thatG. oxydansandP. simplicissimumcan use cellulosic hydrolysate as a cost-effective substitute for glucose for biolixiviant production.