bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pooled-sample draft genome assembly provides insights into host plant-specific transcriptional responses of a Solanaceae-specializing pest,Tupiocoris notatus(Hemiptera: Miridae)
Authors: Goldberg Jay K , Allan Carson W. , Copetti Dario , Matzkin Luciano M. , Bronstein Judith 
Published: October 2023

AbstractThe assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study we show that high-quality genome assemblies can be produced from samples of multiple wild-caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae:Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30-100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short-read assembly standards (N50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome-guided differential expression study of host-plant specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding onDatura wrightii(Solanaceae) and existing RNA-seq data fromNicotiana attenuata(Solanaceae) fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione-S-transferases, cytochrome P450s, UDP-glucosyltransferases. Together our results show that long-read sequencing of pooled samples can provide a cost-effective genome assembly option for small insects and provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
Colloidal aggregation confounds cell-based Covid-19 antiviral screens
Authors: Glenn Isabella S. , Hall Lauren N. , Khalid Mir M. , Ott Melanie , Shoichet Brian K. 
Published: October 2023

AbstractColloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
Genome-wide evidence of the role of Paf1C in transcription elongation and histone H2B monoubiquitination inArabidopsis
Authors: Blanco-Touriñán Noel , Pérez-Alemany Jaime , Bourbousse Clara , Latrasse David , Ait-Mohamed Ouardia , Benhamed Moussa , Barneche Fredy , Blázquez Miguel A. , Gallego-Bartolomé Javier , Alabadí David 
Published: October 2023

AbstractThe evolutionarily conserved Paf1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNAPII progression through chromatin remodeling. To obtain evidence that Paf1C acts in transcription elongation inArabidopsis, we examined the genomic distribution of the ELF7 and VIP3 subunits of Paf1C. The occupancy of both subunits was confined to thousands of gene bodies and positively correlated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome-wide inelf7seedlings. Genome-wide profiling of RNAPII revealed that inelf7mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest that there is a direct functional link between Paf1C activity, mono-ubiquitination of histone H2B, and the transition of RNPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stably than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.
Association of the LIfestyle for BRAin Health Score and Brain Vascular Damage in a Community-Dwelling Adults Cohort
Authors: Li Hang , Zhou Qi , Cai Xueli , Wang Yicong , Yang Yingying , Wang Suying , Meng Xia , Jing Jing , Liu Dandan , Zhang Yanli , Wang Yongjun , Pan Yuesong , Wang Yilong 
Published: October 2023

AbstractOBJECTIVETo investigate the association of brain vascular damage and the LIfestyle for BRAin Health (LIBRA) dementia risk scores.METHODSThis cross-sectional study was based on the baseline survey from a population-based prospective cohort study. The Polyvascular Evaluation for Cognitive Impairment and Vascular Events (PRECISE) study recruited community-dwelling adults aged 50–75 years based on cluster sampling from Lishui city in China. Eleven modifiable risk or protective factors for dementia collected at baseline survey were combined in the LIBRA score. Eligible participants were scanned by a 3.0T Magnetic resonance imaging scanner. Intracranial atherosclerosis and cerebral small vessel disease (CSVD) burden were assessed.RESULTSIn a total of 3059 individuals, the mean (SD) age was 61.2 (6.7) years; 1630 (53.5%) being women. Compared with the first tertile, subjects with the third tertile of LIBRA score were associated with increased odds of the presence of intracranial atherosclerotic plaque (adj. OR 2.22, 95% CI 1.75 to 2.82,P<0.001). A similar association was observed for intracranial atherosclerotic burden (adj. cOR 2.26, 95% CI 1.79 to 2.87,P<0.001). Whereas, subjects with the third tertile of LIBRA score were not associated with the presence of CSVD (adj. OR 1.05, 95% CI 0.86 to 1.29,P=0.63) or higher CSVD burden (adj. cOR 1.06, 95% CI 0.87 to 1.29,P=0.55). Multivariable binary logistic regression analysis for the association between the LIBRA score and the presence of coexistent atherosclerotic plaque and CSVD was also significant adjusting for the nonmodifiable factors age, sex, education, married or cohabiting status, socioeconomic status, and history of stroke (adj. OR 1.70, 95% CI 1.21 to 2.39,P= 0.002).CONCLUSIONSIn this study, LIBRA scores were positively associated with the presence and burden of intracranial atherosclerosis, coexistence of atherosclerotic plaque and CSVD. These findings suggested that modifiable dementia score maybe useful in identifying individuals at high risk of brain vascular damage.
Fluid Uptake Pathways Are Differentially Modified in Rice (Oryza sativaL.) in Response to Drought and Salinity
Authors: Chowdery Rukaya Amin , Shashidhar H E , Mathew M K 
Published: October 2023

AbstractSalinity and drought adversely affect rice production globally. Here we have examined physiological responses to drought and salinity across four rice cultivars with varying sensitivity to these stresses. The salt tolerant Pokkali restricts fluid entry to limit Na+uptake under saline stress, while the drought-tolerant ARB6 needs to enhance fluid uptake under drought. Surprisingly, Pokkali does reasonably well when subjected to drought as does ARB6 under saline stress - in contrast to the stress-sensitive but high yielding varieties IR-20 and Jaya. Both tolerant varieties use long roots to mine water under deficit conditions, increasing aerenchyma and suberization of the exodermis to provide oxygen to deep-reaching roots. Major alterations in patterns of suberization in both exodermis and endodermis are undertaken, the patterns being dramatically different under the two stresses. Genes implicated in suberin biosynthesis also showed variation in transcript levels under stress, corresponding with the observed suberization patterns. Osmolyte accumulation drives uptake of water under deficit conditions, while restricting fluid flow to symplastic routes minimizes Na+entry. Overall, the morphological and physiological responses of the tolerant varieties ensure adequate fluid flow through the transpiration stream without excessive salt uptake, thereby promoting growth under both drought and salinity.
Associations between Maternal Sucrose-stimulated Salivary pH and Early Childhood Caries Diagnosis and Severity: An Observational Study
Authors: Okuji David , Lin Amy , Odusanwo Olutayo , Wu Yinxiang 
Published: October 2023

ABSTRACTBackgroundMultiple studies indicate that maternal sucrose-stimulated salivary pH has the potential to signal higher risk for diagnoses of early childhood caries and severity categories from the vertical transmission of bacteria from mother to child.AimThis study primarily investigated the relationship between maternal sucrose-stimulated salivary pH and child caries diagnosis and severity. It secondarily validated associations between 1) child and maternal sucrose-stimulated salivary pH, and 2) child sucrose-stimulated salivary pH and caries diagnosis and severity.DesignSalivary pH levels were measured from 440 mother-child dyads. Early childhood caries diagnoses and severity levels were recorded. The analysis of variance test identified the associations between child and maternal sucrose-stimulated salivary pH and regression models were derived to show that maternal and child salivary pH were estimators for children’s caries diagnosis and severity.ResultsMaternal salivary pH <= 5.6, compared to maternal salivary pH = 7, had 7.58 times higher odds for the child’s ECC diagnosis and 5.61 times higher odds for moderate-extensive caries severity. Similar results were found for child salivary pH <= 5.6, compared to child salivary pH = 7. Maternal and child salivary pH were positively associated. When maternal salivary pH, compared to child salivary pH, was included with age, gender, and race/ethnicity as predictors for early childhood caries, the median interquartile ranges for sensitivity increased from 58.8 to 64.7 percent and specificity decreased from 84.6 to 80.8 percent.ConclusionDentists should understand that both maternal and child sucrose-stimulated salivary pH can signal the diagnosis and severity of early childhood caries.
Human DDX6 regulates translation and decay of inefficiently translated mRNAs
Authors: Weber Ramona , Wohlbold Lara , Chang Chung-Te 
Published: October 2023

ABSTRACTRecent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
Functional and structural analysis of a cyclization domain in a cyclic β-1,2-glucan synthase
Authors: Tanaka Nobukiyo , Saito Ryotaro , Kobayashi Kaito , Nakai Hiroyuki , Kamo Shogo , Kuramochi Kouji , Taguchi Hayao , Nakajima Masahiro , Masaike Tomoko 
Published: October 2023

AbstractCyclic β-1,2-glucan synthase (CGS) is a key enzyme in production of cyclic β-1,2-glucans (CβGs) which are involved in bacterial infection or symbiosis to host organisms. Nevertheless, a mechanism of cyclization, the final step in the CGS reaction, has not been fully understood. Here we performed functional and structural analyses of the cyclization domain of CGS alone fromThermoanaerobacter italicus(TiCGSCy). We first found that β-glucosidase-resistant compounds are produced by TiCGSCywith linear β-1,2-glucans as substrates. The1H-NMR analysis revealed that these products are CβGs. Next, action pattern analyses using β-1,2-glucooligosaccharides revealed a unique reaction pattern: exclusive transglycosylation without hydrolysis and a hexasaccharide as the minimum length of the substrate. Nevertheless, longer substrate β-1,2-glucooligosaccharides are preferred, being consistent with the fact that CGSs generally produce CβGs with degrees of polymerization of around 20. Finally, the overall structure of the cyclization domain of TiCGSCywas found to be similar to those of β-1,2-glucanases in phylogenetically different groups. Meanwhile, the identified catalytic residues indicated clear difference in the reaction pathways between these enzymes. Therefore, we propose a novel reaction mechanism of TiCGSCy. Thus, we propose that the present group of CGSs should be defined as a new glycoside hydrolase family, GHxxx.Statements and DeclarationsCompeting Interests: The authors declare no competing interests.Key PointsIt was clearly evidenced that cyclization domain alone produces cyclic β-1,2-glucans.The domain exclusively catalyzes transglycosylation without hydrolysis.The present catalytic domain should be defined as a new glycoside hydrolase family.
Discrete somatotopic representation and neural response properties in hummingbird and zebra finch forebrain nuclei
Authors: Gaede Andrea H. , Wu Pei-Hsuan , Leitch Duncan B. 
Published: October 2023

SummarySomatosensation allows animals to perceive the external world through touch, providing critical information about physical contact, temperature, pain, and body position. Somatosensory pathways, particularly those related to the rodent vibrissae, have been well-studied in mammals, illuminating principles of cortical organization and sensory processing1,2. However, comparative studies across diverse vertebrate species are imperative to understand how somatosensory systems are shaped by evolutionary pressures and specialized ecological needs.Birds provide an excellent model for studying the evolution of somatosensation, as they exhibit remarkable diversity in body plans, sensory capabilities, and behavior. Prior work in pigeons3-6, parrots7, and finches8have identified general tactile-responsive regions within the avian telencephalon. Yet how somatosensory maps and response properties vary across key avian groups remains unclear. Here, we aimed to elucidate somatotopic organization and neural coding in the telencephalon of Anna’s hummingbirds (Calypte anna) and zebra finches (Taeniopygia guttata).Usingin vivoextracellular electrophysiological techniques, we recorded single and multi-unit activity in telencephalic regions of anesthetized hummingbirds and finches. We stimulated the beak, face, trunk, wings, and hindlimbs with controlled tactile stimuli and mapped somatosensory receptive fields. We found distinct representations of body regions distributed across multiple somatosensory zones, with surprising differences in relative areas devoted to key body surfaces, potentially as related to behavioral significance.Highlights□Somatosensation provides birds with critical information for behaviors necessary to survival including foraging and flight.□In vivoextracellular physiological recordings were used to monitor tactile responses in contralateral forebrain nuclei corresponding to the feather deflection in hummingbirds and finches including to air puff stimuli.□Both hummingbirds and finches show distinct separation of body and head receptive field representation in different nuclei.□A continuous somatotopic arrangement can be found in both the rostral Wulst (corresponding to the wings and body) and in nucleus basorostralis (corresponding to the head and beak), with particularly enlarged representations of the wing leading edge and the foot.
PDZD8 promotes autophagy at ER-Lysosome contact sites to regulate synaptogenesis
Authors: Thakur Rajan S. , O’Connor-Giles Kate M. 
Published: October 2023

SUMMARYBuilding synaptic connections, which are often far from the soma, requires coordinating a host of cellular activities from transcription to protein turnover, placing a high demand on intracellular communication. Membrane contact sites (MCSs) formed between cellular organelles have emerged as key signaling hubs for coordinating an array of cellular activities. We have found that the endoplasmic reticulum (ER) MCS tethering protein PDZD8 is required for activity-dependent synaptogenesis. PDZD8 is sufficient to drive ectopic synaptic bouton formation through an autophagy-dependent mechanism and required for basal synapse formation when autophagy biogenesis is limited. PDZD8 functions at ER-late endosome/lysosome (LEL) MCSs to promote lysosome maturation and accelerate autophagic flux. Mutational analysis of PDZD8’s SMP domain further suggests a role for lipid transfer at ER-LEL MCSs. We propose that PDZD8-dependent lipid transfer from ER to LELs promotes lysosome maturation to increase autophagic flux during periods of high demand, including activity-dependent synapse formation.GRAPHICAL ABSTRACT
Sustainable technology development during intellectual property rights commercialisation by university startups
Authors: Shahidan Noor Hidayah , Abdul Latiff Ahmad Shaharudin , Abdul Wahab Sazali 
Published: October 2023

Purpose
The purpse of this study is to examine sustainable technology development (STD) during the “Valley of Death” phase encountered by university startups undertaking intellectual property rights (IPR) commercialisation.

Design/methodology/approach
A comprehensive literature review was conducted after searching for relevant documents across multiple databases. Semi-structured interviews with university startup founders were also conducted as part of a qualitative case study.

Findings
This study resulted in two significant findings. First, the Valley of Death has been redefined in the specific context of IPR commercialisation by university startups. Second, the sustainable technology development framework (STDF) has been conceptualised to enhance the success rate of IPR commercialisation by university startups. The authors also identified three essential components of STD in the context of university startups: market development, technical efficiency and business sustainability.

Research limitations/implications
This exploratory research involved a thorough literature analysis. Given that only one qualitative case study was conducted, data saturation was not achieved. Further empirical research is needed to validate the conceptualised STDF.

Practical implications
The validated STDF will be a useful tool for enhancing the success of IPR commercialisation by university startups.

Originality/value
While others have focused on innovating business models, this study focused on an underexplored area: the sustainability of technology development during the commercialisation of IPR by university startups during the Valley of Death phase.
Role of behavioural abstraction (vs concrete) levels in accepting health technologies
Authors: Taneja Bharat , Bharti Kumkum 
Published: October 2023

Purpose
While attempting to persuade surgeons to accept their health technology, sales representatives for medical devices face daily challenges in the operating room. Surgeons exhibit cognitive complexity (abstractness vs. concreteness) when accepting any form of health technology. Surgeons choose technologies on behalf of their patients, taking patient priorities and expectations into account. Prior research has focused on cognitive complexity in the context of health technology adoption, but the issue of technology acceptance has not been addressed. The purpose of this study to use the construal level (CL) theory to determine the role of behavioural abstraction levels in the acceptance of surgical health technology.

Design/methodology/approach
On the basis of 556 min of seminar-based data and semi-directive interviews, the surgeons’ experiences regarding the acceptance of health technology were analysed. A non-directive observational method was used to permit the spontaneous emergence of CL dimensions in a natural environment. A categorization model was used for data coding, and MAXQDA, in addition to traditional multidimensional scaling and hierarchical cluster analysis, was used to generate results with joint displays.

Findings
Effort expectancy, learning curve, performance risk, habit, patient clinical condition, clinical outcome expectancy, technology setting and social influence were construed at a low construal level (LCL). On the other hand, patient paying capacity, technology cost, price value, financial risk and patient performance expectation were construed at a high construal level (HCL). The study also reveals duality-based factors which showed proximity to HCL but intersected at LCL, and vice versa. Duality-based factors such as effort expectancy, surgical technique, trust and perceived risk intersected at HCL, whereas performance expectancy, relative advantage, time expectancy, perceived value, physical risk and peer group influence intersected at LCL.

Originality/value
This is one of the early studies that presented the impact of behavioural abstraction on behavioural intention to accept health technology for surgeries.