bluuebunny/crossref_metadata_2025 huggingface dataset:
MUSTANG: MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance
Authors: Niyakan Seyednami , Sheng Jianting , Cao Yuliang , Zhang Xiang , Xu Zhan , Wu Ling , Wong Stephen T.C. , Qian Xiaoning
Published: September 2023

Abstract

Spatially resolved transcriptomics has revolutionized genome-scale transcriptomic profiling by providing high-resolution characterization of transcriptional patterns. We here present our spatial transcriptomics analysis framework,MUSTANG(MUlti-sampleSpatialTranscriptomics dataANalysis with cross-sample transcriptional similarityGuidance), which is capable of performing multi-sample spatial transcriptomics spot cellular deconvolution by allowing both cross-sample expression based similarity information sharing as well as spatial correlation in gene expression patterns within samples. Experiments on two real-world spatial transcriptomics datasets demonstrate the effectiveness ofMUSTANGin revealing biological insights inherent in cellular characterization of tissue samples under the study. MUSTANG is publicly available at athttps://github.com/namini94/MUSTANG
Next-generation sequencing-based liquid biopsy can be used for detection of residual disease and cancer recurrence monitoring in dogs
Authors: McCleary-Wheeler Angela L. , Fiaux Patrick C. , Ruiz-Perez Carlos A. , McLennan Lisa M. , Tynan John A. , Hicks Susan C. , Rafalko Jill M. , Grosu Daniel S. , Chibuk Jason , O’Kell Allison L. , Cohen Todd A. , Flesner Brian K. , Chorny Ilya , Tsui Dana W.Y. , Kruglyak Kristina M. , Flory Andi
Published: September 2023

Objective

The purpose of this study was to evaluate the performance of a next-generation sequencing-based liquid biopsy test for cancer monitoring in dogs.

Samples

Pre- and post-operative blood samples were collected prospectively from dogs with confirmed cancer diagnoses originally enrolled in the CANcer Detection in Dogs (CANDiD) study. A subset of these dogs also had longitudinal blood samples collected for recurrence monitoring.

Methods

All patients had a pre-operative blood sample collected (after diagnosis but prior to surgical intervention) in which a cancer signal was detected, and had at least one post-operative sample collected. Clinical data were collected for all patients and used to assign a clinical disease status for each follow-up visit.

Results

Following excisional surgery, in the absence of clinical residual disease at the post-operative visit, patients withCancer Signal Detectedresults at that visit were 1.95-times as likely to have clinical recurrence within 6 months compared to patients withCancer Signal Not Detectedresults. In the subset of patients with longitudinal liquid biopsy samples that had clinical recurrence documented during the study period, 73% (8/11; 95% CI: 39 – 93%) of patients hadCancer Signal Detectedin blood prior to or concomitant with clinical recurrence; in the 6 patients where molecular recurrence was detected prior to clinical recurrence, the median lead time was 168 days (range: 47 – 238).

Clinical Relevance

Next-generation sequencing-based liquid biopsy is a non-invasive tool for cancer monitoring in dogs that can be used as an adjunct to current standard-of-care clinical assessment methods.
A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)
Authors: Wang Cankun , Acosta Diana , McNutt Megan , Bian Jiang , Ma Anjun , Fu Hongjun , Ma Qin
Published: September 2023

Alzheimer’s Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability. The database encompasses 1,053 samples (277 integrated datasets) from 67 AD-related scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells. Additionally, it archives 381 ST datasets from 18 human and mouse brain studies. Each dataset is annotated with details such as species, gender, brain region, disease/control status, age, and AD Braak stages. ssREAD also provides an analysis suite for cell clustering, identification of differentially expressed and spatially variable genes, cell-type-specific marker genes and regulons, and spot deconvolution for integrative analysis. ssREAD is freely available athttps://bmblx.bmi.osumc.edu/ssread/.
Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis
Authors: Wu Hsin-Yen Larry , Ai Qiaoyun , Teixeira Rita Teresa , Song Gaoyuan , Montes Christian , Elmore J. Mitch , Walley Justin W. , Hsu Polly Yingshan
Published: September 2023

A crucial step in functional genomics is identifying actively translated open reading frames (ORFs) that link biological functions. The challenge lies in identifying short ORFs, as they are greatly impacted by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis, revealing uncharacterized translation events in nucleus-, chloroplast-, and mitochondria-encoded genes. We identified 7,751 unconventional translation events, including 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ncORFs on presumed non-coding RNAs. Proteomics data confirmed the production of stable proteins from some of the unannotated translation events. We present evidence of active translation on primary transcripts of tasiRNAs (TAS1-4) and microRNAs (pri-miR163, pri-miR169), and periodic ribosome stalling supporting co-translational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORF (AUG-stop), and 2,984 tiny uORFs (2-10 aa), as well as 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
Comparison of the microbiome and mycobiome in tissues of the tropical carnivorous epiphytic herbUtricularia jamesoniana
Authors: Naranjo-Aguilar Valeria , Mora-Castro Rebeca , Morera-Huertas Jessica , Acuña-Castillo Rafael H. , Rojas-Jimenez Keilor
Published: September 2023

Utricularia jamesoniana, a small epiphytic plant found in wet tropical forests, stands out for its carnivorous habit, intricate trap system, and small but beautiful and complex flowers. This species remains relatively understudied despite its wide geographical distribution and curious adaptations. In this study, we employed 16S rRNA and ITS sequencing to compare the prokaryotic and fungal communities within leaves and traps ofU. jamesoniana. The analysis of amplicon sequence variants (ASVs) unveiled notable differences in community composition depending on the plant tissue and type of microorganism. Prokaryotic communities predominantly comprised Proteobacteria and Actinobacteriota, featuring genera such asAcidocella, Bradyrhizobium, Ferritrophicum, andFerrovum. Fungal communities were dominated by Ascomycota and Basidiomycota, encompassing representatives of Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Agaricomycetes, as well as ASVs related to Mycosphaerellaceae,Colletotrichum, Aspergillus, andThanatephorus. We determined that the prokaryotic diversity has higher in the bladders with respect to the leaves. Fungal communities, in turn, were more diverse in leaves than in bladders. This study sheds light on the microbial communities associated with this carnivorous epiphyte and provides valuable insights into the intricate relationships between the plant and its microbial inhabitants across different tissues.
Effects of a high cholesterol diet onDrosophilachill tolerance are highly context-dependent
Authors: Allen Mitchell C. , Ritchie Marshall W. , El-Saadi Mahmoud I. , MacMillan Heath A.
Published: September 2023

Chill susceptible insects are thought to be injured through different mechanisms depending on the duration and severity of chilling. While chronic chilling causes “indirect” injury through disruption of metabolic and ion homeostasis, acute chilling is suspected to cause “direct” injury, in part through phase transitions of cell membrane lipids. Dietary supplementation of cholesterol can reduce acute chilling injury inDrosophila melanogaster, but the generality of this effect and the mechanisms underlying it remain unclear. To better understand how and why cholesterol has this effect, we assessed how a high cholesterol diet and thermal acclimation independently and interactively impact several measures of chill tolerance in both male and female flies. Cholesterol supplementation positively affected tolerance to acute chilling in warm-acclimated flies (as reported previously). Conversely, feeding on the high-cholesterol diet negatively affected tolerance to chronic chilling in both cold and warm acclimated flies, as well as tolerance to acute chilling in cold acclimated flies. Cholesterol had no effect on the ability of flies to remain active in the cold or recover movement after a cold stress. Our findings support the idea that dietary cholesterol reduces mechanical injury to membranes caused by direct chilling injury, and that acute and chronic chilling are associated with distinct mechanisms of injury. Feeding on a high-cholesterol diet may interfere with mechanisms involved in cold acclimation, leaving cholesterol augmented flies more susceptible to chilling injury under some conditions.

Highlights

Cholesterol improves cold shock tolerance of warm-acclimated flies

Cold acclimation and chronic cold instead lead to negative effects of cholesterol on chill tolerance

Cholesterol did not affect the ability of flies to remain active in the cold

Both sexes were similarly affected by a high cholesterol diet
Effectiveness of SGLT2 inhibitor therapy in treatment of Heart failure: A Meta-Analysis
Authors: Albalushi Sarvinoz , Zarif Azmaeen , Karaduman Suheyla , Tran Khoa , Talpeka Alesia
Published: September 2023

Aim

We conducted a meta-analysis on the effectiveness of sodium-glucose co-transporter 2 (SGLT2) inhibitors in heart failure (HF) patients with preserved (HFpEF) and reduced (HFrEF) ejection fraction.

Methods

A comprehensive search of several databases for placebo-controlled randomised controlled trials of SGLT2 inhibitors from inception to September 30 2022, limited to English language and excluding animal studies, was conducted. The databases included Medline, Scopus, Cochrane Central, and ClinicalTrials.gov. Randomised controlled studies were chosen if they included HF patients and reported at least one of the predetermined outcomes. Hazard ratios (HRs) or risk ratios were pooled together with the appropriate 95% confidence intervals using a random-effect model. Fourteen trials met the inclusion criteria, with 42 409 HF patients participating (N = 21 678 in the SGLT2 inhibitor arms and N = 20 731 in the placebo arms).

Results

SGLT2 inhibitors significantly reduced the composite of HF hospitalisation or cardiovascular death [HR: 0.75 (0.71–0.79);P< 0.001;I2= 0%], total hospitalisations for heart failure [HR: 0.70 (0.66– 0.75);P< 0.001;I2= 0%], and reduced the occurrence of cardiovascular death [HR: 0.86 (0.81–0.92);P< 0.001;I2= 43%]. Sub-group analysis was conducted based on HF status at baseline, EF, diabetes status at baseline, and sex. SGLT2 inhibitors significantly reduced the composite heart failure hospitalisation and cardiovascular death for all the subgroups except for patients with HFpEF at baseline [HR: 0.87 (0.74– 1.03);P= 0.11;I2= 60%] and no diabetes status at baseline [HR: 0.92 (0.73–1.16);P= 0.50;I2= 78%].

Conclusions

In patients with HF, SGLT2 inhibitors may significantly improve clinical outcomes, including all-cause and cardiovascular mortality. In this meta-analysis, SGLT2 inhibitors did not show a reduction in composite heart failure in patients with heart failure with preserved ejection fraction at baseline.
Myosin-binding protein C forms C-links and stabilizes OFF states of myosin
Authors: Hessel Anthony L. , Engels Nichlas M. , Kuehn Michel , Nissen Devin , Sadler Rachel L. , Ma Weikang , Irving Thomas C. , Linke Wolfgang A. , Harris Samantha P.
Published: September 2023

Contraction force in muscle is produced by the interaction of myosin motors in the thick filaments and actin in the thin filaments and is fine-tuned by other proteins such as myosin-binding protein C (MyBP-C). One form of control is through the regulation of myosin heads between an ON and OFF state in passive sarcomeres, which leads to their ability or inability to interact with the thin filaments during contraction, respectively. MyBP-C is a flexible and long protein that is tightly bound to the thick filament at its C-terminal end but may be loosely bound at its middle- and N-terminal end (MyBP-CC1C7). Under considerable debate is whether the MyBP-CC1C7domains directly regulate myosin head ON/OFF states, and/or link thin filaments (“C-links”). Here, we used a combination of mechanics and small-angle X-ray diffraction to study the immediate and selective removal of the MyBP-CC1C7domains of fast MyBP-C in permeabilized skeletal muscle. After cleavage, the thin filaments were significantly shorter, a result consistent with direct interactions of MyBP-C with thin filaments thus confirming C-links. Ca2+sensitivity was reduced at shorter sarcomere lengths, and crossbridge kinetics were increased across sarcomere lengths at submaximal activation levels, demonstrating a role in crossbridge kinetics. Structural signatures of the thick filaments suggest that cleavage also shifted myosin heads towards the ON state – a marker that typically indicates increased Ca2+sensitivity but that may account for increased crossbridge kinetics at submaximal Ca2+and/or a change in the force transmission pathway. Taken together, we conclude that MyBP-CC1C7domains play an important role in contractile performance which helps explain why mutations in these domains often lead to debilitating diseases.
Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae
Authors: Talkah Nurul Shakina Mohd , Jasim Jasim Haider Mahmod , Nordin Farah Alia , Othman Ahmad Sofiman
Published: September 2023

The yellow–floweredSpathoglottis aurea(tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship betweenS. aureaand the geographically isolatedS. microchilinafrom Borneo that has encouraged further study of theS. aureapopulations, but the genomic resource forS. aureahas not yet been reported. The present study reports the first work to characterize a chloroplast genome among theSpathoglottisgenus. The complete chloroplast (cp) genome ofS. aureawas assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome ofS. aureais 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite chloroplast genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of theS. aureacp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed thatS. aureahas a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such asPhaiusandCephalantheropsis.
Genetics of Congenitally Corrected Transposition of the Great Arteries: next generation sequencing shows a mutation load effect for 156 genes involved in cardiac patterning
Authors: Benadjaoud Yasmine , Benko Sabina , Hanin Fabienne Jabot , Audain Enrique , Deleuze Jean François , Boland Anne , Bole Christine , Bras Marc , Bajolle Fanny , Derouk Morgan , Gordon Christopher T. , Hitz Marc Phillip , Bonnet Damien , Lyonnet Stanislas
Published: September 2023

Congenital heart disease (CHD) is a major public health issue. It is considered as a major cause of infant mortality today.

We focused on a complex and rare CHD, the congenitally corrected transposition of the great arteries (CCTGA).

The aim of this study was to identify the genes that control the alignment of cardiac chambers that are abnormal in CCTGA to further understand the mechanism of this CHD.

We analyzed a cohort of 43 CCTGA cases (41 sporadic cases and 2 familial cases) of isolated CCTGA by next generation sequencing analysis (whole-genome sequencing and whole-exome sequencing).

Under the hypothesis of Mendelian model includingde novogenomic alterations, no major gene effect involved in the disease could be identified.

Under the hypothesis of a complex model of inheritance, we highlighted a group of 156 cardiac mutated genes in our patients, in which we found a significant enrichment of rare variants in patients compared to controls in a replication cohort. The highly heterogeneous combinations of susceptibility rare variants, mostly inherited from the healthy mother and father respectively, are correlated with the CCTGA phenotype, any given deleterious variant combination within the CCTGA gene set being specific to the affected individual.

Taken together, the cases could be explained by a mutation load of segregated alleles at loci mostly involved in heart tubelooping, outflow tract morphogenesis and establishment of left-right asymmetry. Our data suggest that CHD are not Mendelian traits, but rather of polygenic origin. In the majority of cases, both parents harbour a set of susceptibility alleles for the CHD that are inherited by the offspring in a combination that confers the risk of CCTGA.
Multimodal mental health assessment with remote interviews using facial, vocal, linguistic, and cardiovascular patterns
Authors: Jiang Zifan , Seyedi Salman , Griner Emily , Abbasi Ahmed , Bahrami Rad Ali , Kwon Hyeokhyen , Cotes Robert O. , Clifford Gari D.
Published: September 2023

Objective

The current clinical practice of psychiatric evaluation suffers from subjectivity and bias, and requires highly skilled professionals that are often unavailable or unaffordable. Objective digital biomarkers have shown the potential to address these issues. In this work, we investigated whether behavioral and physiological signals, extracted from remote interviews, provided complimentary information for assessing psychiatric disorders.

Methods

Time series of multimodal features were derived from four conceptual modes: facial expression, vocal expression, linguistic expression, and cardiovascular modulation. The features were extracted from simultaneously recorded audio and video of remote interviews using task-specific and foundation models. Averages, standard deviations, and hidden Markov model-derived statistics of these features were computed from 73 subjects. Four binary classification tasks were defined: detecting 1) any clinically-diagnosed psychiatric disorder, 2) major depressive disorder, 3) self-rated depression, and 4) self-rated anxiety. Each modality was evaluated individually and in combination.

Results

Statistically significant feature differences were found between controls and subjects with mental health conditions. Correlations were found between features and self-rated depression and anxiety scores. Visual heart rate dynamics achieved the best unimodal performance with areas under the receiver-operator curve (AUROCs) of 0.68-0.75 (depending on the classification task). Combining multiple modalities achieved AUROCs of 0.72-0.82. Features from task-specific models outperformed features from foundation models.

Conclusion

Multimodal features extracted from remote interviews revealed informative characteristics of clinically diagnosed and self-rated mental health status.

Significance

The proposed multimodal approach has the potential to facilitate objective, remote, and low-cost assessment for low-burden automated mental health services.
Finding Long-COVID: Temporal Topic Modeling of Electronic Health Records from the N3C and RECOVER Programs
Authors: O’Neil Shawn T. , Madlock-Brown Charisse , Wilkins Kenneth J. , McGrath Brenda M. , Davis Hannah E. , Assaf Gina S. , Wei Hannah , Zareie Parya , French Evan T. , Loomba Johanna , McMurry Julie A. , Zhou Andrea , Chute Christopher G. , Moffitt Richard A. , Pfaff Emily R , Yoo Yun Jae , Leese Peter , Chew Robert F. , Lieberman Michael , Haendel Melissa A.
Published: September 2023

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), also known as Long-COVID, encompasses a variety of complex and varied outcomes following COVID-19 infection that are still poorly understood. We clustered over 600 million condition diagnoses from 14 million patients available through the National COVID Cohort Collaborative (N3C), generating hundreds of highly detailed clinical phenotypes. Assessing patient clinical trajectories using these clusters allowed us to identify individual conditions and phenotypes strongly increased after acute infection. We found many conditions increased in COVID-19 patients compared to controls, and using a novel method to associate patients with clusters over time, we additionally found phenotypes specific to patient sex, age, wave of infection, and PASC diagnosis status. While many of these results reflect known PASC symptoms, the resolution provided by this unprecedented data scale suggests avenues for improved diagnostics and mechanistic understanding of this multifaceted disease.
Single-cell analysis of psoriasis resolution reveals an inflammatory fibroblast state targeted by IL-23 blockade
Authors: Francis Luc , McCluskey Daniel , Ganier Clarisse , Jiang Treasa , Du-Harpur Xinyi , Gabriel Jeyrroy , Dhami Pawan , Kamra Yogesh , Visvanathan Sudha , Barker Jonathan N. , Smith Catherine H. , Capon Francesca , Mahil Satveer K.
Published: September 2023

Biologics targeting the IL-23/IL-17 axis have transformed the treatment of psoriasis. However, the early mechanisms of action of these drugs remain poorly understood. Here, we performed longitudinal single-cell RNA-sequencing in affected individuals receiving IL-23 inhibitor therapy. By profiling skin at baseline, day 3 and day 14 of treatment, we demonstrated that IL-23 blockade causes marked gene expression shifts, with fibroblast and myeloid populations displaying the most extensive changes at day 3. We also identified a transientWNT5A+/IL24+fibroblast state, which was only detectable in lesional skin.In-silicoandin-vitrostudies indicated that signals stemming from theseWNT5A+/IL24+fibroblasts upregulated multiple inflammatory genes in keratinocytes. Importantly, the abundance ofWNT5A+/IL24+fibroblasts was significantly reduced after treatment. This observation was validatedin-silico, by deconvolution of multiple transcriptomic datasets, and experimentally, by RNAin-situhybridization. These findings demonstrate that the evolution of inflammatory fibroblast states is a key feature of resolving psoriasis skin.
Spatial and temporal pattern of structure-function coupling of human brain connectome with development
Authors: Feng Guozheng , Wang Yiwen , Huang Weijie , Chen Haojie , Cheng Jian , Shu Ni
Published: September 2023

Brain structural circuitry shapes a richly patterned functional synchronization, supporting for complex cognitive and behavioural abilities. However, how coupling of structural connectome (SC) and functional connectome (FC) develops and its relationships with cognitive functions and transcriptomic architecture remain unclear. We used multimodal magnetic resonance imaging data from 439 participants aged 5.7 to 21.9 years to predict functional connectivity by incorporating intracortical and extracortical structural connectivity, characterizing SC-FC coupling. Our findings revealed that SC-FC coupling was strongest in the visual and somatomotor networks, consistent with evolutionary expansion, myelin content, and functional principal gradient. As development progressed, SC-FC coupling exhibited heterogeneous alterations dominated by an increase in cortical regions, broadly distributed across the somatomotor, frontoparietal, dorsal attention, and default mode networks. Moreover, we discovered that SC-FC coupling significantly predicted individual variability in general intelligence, mainly influencing frontoparietal and default mode networks. Finally, our results demonstrated that the heterogeneous development of SC-FC coupling is positively associated with genes in oligodendrocyte-related pathways and negatively associated with astrocyte-related genes. This study offers insight into the maturational principles of SC-FC coupling in typical development.
Syntaxin 17 recruitment to mature autophagosomes is temporally regulated by PI4P accumulation
Authors: Shinoda Saori , Sakai Yuji , Matsui Takahide , Uematsu Masaaki , Koyama-Honda Ikuko , Sakamaki Jun-ichi , Yamamoto Hayashi , Mizushima Noboru
Published: September 2023

During macroautophagy, cytoplasmic constituents are engulfed by autophagosomes. Lysosomes fuse with closed autophagosomes but not with unclosed intermediate structures. This is achieved in part by the late recruitment of the autophagosomal SNARE syntaxin 17 (STX17) to mature autophagosomes. However, how STX17 recognizes autophagosome maturation is not known. Here, we show that this temporally regulated recruitment of STX17 depends on the positively charged C-terminal region of STX17. Consistent with this finding, mature autophagosomes are more negatively charged compared with unclosed intermediate structures. This electrostatic maturation of autophagosomes is likely driven by the accumulation of phosphatidylinositol 4-phosphate (PI4P) in the autophagosomal membrane. Accordingly, dephosphorylation of autophagosomal PI4P prevents the association of STX17 to autophagosomes. Furthermore, molecular dynamics simulations support PI4P-dependent membrane insertion of the transmembrane helices of STX17. Based on these findings, we propose a model in which STX17 recruitment to mature autophagosomes is temporally regulated by a PI4P-driven change in the surface charge of autophagosomes.
Of mice and men: Dendritic architecture differentiates human from mice neuronal networks
Authors: Kanari Lida , Shi Ying , Arnaudon Alexis , Barros-Zulaica Natalí , Benavides-Piccione Ruth , Coggan Jay S. , DeFelipe Javier , Hess Kathryn , Mansvelder Huib D. , Mertens Eline J. , Meystre Julie , de Campos Perin Rodrigo , Pezzoli Maurizio , Daniel Roy Thomas , Stoop Ron , Segev Idan , Markram Henry , de Kock Christiaan P.J.
Published: September 2023

The organizational principles that distinguish the human brain from other species have been a long-standing enigma in neuroscience. Focusing on the uniquely evolved human cortical layers 2 and 3, we computationally reconstruct the cortical architecture for mice and humans. We show that human pyramidal cells form highly complex networks, demonstrated by the increased number and simplex dimension compared to mice. This is surprising because human pyramidal cells are much sparser in the cortex. We show that the number and size of neurons fail to account for this increased network complexity, suggesting that another morphological property is a key determinant of network connectivity. Topological comparison of dendritic structure reveals much higher perisomatic (basal and oblique) branching density in human pyramidal cells. Using topological tools we quantitatively show that this neuronal structural property directly impacts network complexity, including the formation of a rich subnetwork structure. We conclude that greater dendritic complexity, a defining attribute of human L2 and 3 neurons, may provide the human cortex with enhanced computational capacity and cognitive flexibility.

Graphical abstract

A. A multiscale analysis was performed to compare the mouse and human brains: from the anatomical properties of brain regions to the morphological details of single neurons. B. Human circuits are larger than mice in terms of size and number of neurons, but present decreased neuron density, resulting in increased distances between neurons, particularly among pyramidal cells. C. Greater network complexity emerges within the human brain. Network complexity is defined by larger groups of neurons forming complex interconnections throughout the network. D. The topological analysis of layer 2/3 pyramidal cells in the temporal cortex reveals an intriguing difference: human neurons exhibit a significantly larger number of dendritic branches, especially near the cell body compared to mice. This phenomenon is termed ”higher topological complexity” in dendrites. Our findings suggest that dendritic complexity wields a more substantial influence on network complexity than neuron density.
Modularity of biological systems: a link between structure and function
Authors: Kadelka Claus , Wheeler Matthew , Veliz-Cuba Alan , Murrugarra David , Laubenbacher Reinhard
Published: September 2023

This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene regulatory network modularity has focused on network structure, typically represented through either directed or undirected graphs. But since gene regulation is a highly dynamic process as it determines the function of cells over time, it is natural to consider functional modularity as well. One of the main results is that the structural decomposition of a network into modules induces an analogous decomposition of the dynamic structure, exhibiting a strong relationship between network structure and function. An extensive simulation study provides evidence for the hypothesis that modularity might have evolved to increase phenotypic complexity while maintaining maximal dynamic robustness to external perturbations.
Anemonefish are better taxonomists than humans
Authors: Kashimoto Rio , Mercader Manon , Zwahlen Jann , Miura Saori , Tanimoto Miyako , Yanagi Kensuke , Reimer James Davis , Khalturin Konstantin , Laudet Vincent
Published: September 2023

The symbiosis between giant sea anemones, photosynthetic algae of the family Symbiodiniaceae, and anemonefish is an iconic example of a mutualistic “menage à 3”1. Patterns of associations among 28 species of anemonefish and 10 species of giant sea anemone hosts are complex: Some anemonefish species are highly specialized to inhabit only one species of sea anemone (e.g.,Amphiprion frenatuswithEntacmaea quadricolor), whereas others are more generalist and can live in almost any host species (e.g.,Amphiprion clarkii)1,2,3. Reasons for host preferences and the mechanisms involved are obscured, among other things, by the lack of resolution of giant sea anemone phylogeny. Recent molecular analyses have shown that giant sea anemones hosting anemonefish belong to three distinct clades:Entacmaea, Stichodactyla, andHeteractis4,5,6. Inside these clades, however, species delimitation has been impeded by morphological variability of the giant sea anemones and is poorly resolved with classical markers4,5. Here, we employed an extensive transcriptomic dataset from 55 sea anemones collected from southern Japan to build a robust phylogeny. With this dataset, we observed that the bubble-tip sea anemoneE. quadricolor, currently considered to be a single species, can in fact be separated into at least four distinct cryptic lineages (A-D). Moreover, these lineages can be precisely distinguished by their association with anemonefish:A. frenatusis only found associated with lineage D, whereasA. clarkiilives in the other three lineages.
Childhood maltreatment and subsequent risk of hospitalization or death due to COVID-19: a cohort study in the UK Biobank
Authors: Wang Yue , Ge Fenfen , Aspelund Thor , Ask Helga , Hauksdóttir Arna , Hu Kejia , Jakobsdóttir Jóhanna , Zoega Helga , Shen Qing , Whalley Heather C , Vesterager Pedersen Ole Birger , Lehto Kelli , Andreassen Ole A , Fang Fang , Song Huan , Valdimarsdóttir Unnur A
Published: September 2023

Childhood maltreatment has been associated with some infection-related outcomes, yet its potential role in severe COVID-19 outcomes has not been addressed. Therefore, leveraging longitudinal data from the population-based UK Biobank (N=151,427), our study aimed to explore the association between childhood maltreatment and severe COVID-19 outcomes (i.e., hospitalization or death due to COVID-19) and its underlying mechanisms. Our resultssuggestthat childhood maltreatment, particularly physical neglect, is associated with a 54.0% increased risk of severe COVID-19 outcomes (i.e., hospitalization or death due to COVID-19), which was not modified by genetic predisposition to severe COVID-19 outcomes.Wefound that 50.9% of this association was mediated by suboptimal socioeconomic status, lifestyle and prepandemic somatic diseases or psychiatric disorders. These findings highlight the role of early life adversities in severe health consequences across the lifespan and call for increased clinical surveillance of people exposed to childhood maltreatment in COVID-19 outbreaks and future pandemics.
The variation of malaria prevention measures knowledge and their associated factors: A cross-sectional study in East Nusa Tenggara Province Indonesia
Authors: Guntur Robertus Dole , Kleden Maria A. , Kusumaningrum Damai , Amirul Islam Fakir M
Published: September 2023

Objective

Malaria is one of the major public health problems in African and Southeast Asian countries including Indonesia. However, knowledge of malaria prevention measures (MPM) is not well studied, particularly in Indonesia. This study aimed to investigate the level of MPM knowledge and associated factors among rural adults in high, moderate and low endemic settings of East Nusa Tenggara Province (ENTP) Indonesia.

Methods

A community-based cross-sectional study was conducted among a randomly selected 1495 households at rural ENTP. Multistage sampling technique was employed to recruit participants. Univariate and multivariable logistic regression model was used to assess factors affecting knowledge of MPM.

Results

The level of MPM knowledge in low, moderate, and high endemic settings differs significantly with the highest in low settings (57%, 95% CI: 50.5 – 63.5 and the lowest in high settings (19.3%, 95% CI: 11.1 – 27.5). In all settings, good level of MPM knowledge was significantly higher for adults with high SES (Adjusted odds ratio (AOR) = 2.52, 95% CI: 1.20 – 5.30; AOR=20.5,95%CI: 4.64-90.8, AOR=3.31,95%CI: 1.34-8.15 respectively) compared to those having low SES. In high and moderate settings, the likelihood of good MPM knowledge was considerately higher for adults with at least secondary (AOR=2.35, 95% CI= 1.29 – 4.36, AOR=2.66, 95% CI=1.32-5.39 respectively) than those with primary or no education level.

Conclusions

The good level of MPM knowledge was very low in three different malaria endemic settings. Higher level of education and high SES were significantly associated with the good level. Therefore, health education promotion on MPM knowledge is critical to support malaria elimination program in the province.
The neonatal gut microbiota: a role in the encephalopathy of prematurity
Authors: Vaher Kadi , Blesa Cabez Manuel , Parga Paula Lusarreta , Binkowska Justyna , van Beveren Gina J , Odendaal Mari-Lee , Sullivan Gemma , Stoye David Q , Corrigan Amy , Quigley Alan J , Thrippleton Michael J , Bastin Mark E , Bogaert Debby , Boardman James P
Published: September 2023

Preterm birth associates with atypical brain development and neurocognitive impairment. The gut microbiome is implicated in neurobehavioural outcomes of typically developing infants and children, but its relationship with neurodevelopment in preterm infants is unknown. We characterised the faecal microbiome in a cohort of 147 neonates enriched for very preterm birth (<32 weeks’ gestation) using 16S-based and shotgun metagenomic sequencing. Delivery mode had the strongest association with preterm microbiome shortly after birth; low birth gestational age, infant sex and antibiotics significantly associated with microbiome composition at NICU discharge. Thereafter, we integrated these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associated with MRI features of encephalopathy of prematurity. Particularly, abundances ofEscherichia coliandKlebsiellaspp. correlated with microstructural parameters in deep and cortical grey matter. Metagenome functional capacity analyses suggested that these bacteria may interact with brain microstructural development via tryptophan and propionate metabolism. This study indicates that gut microbiome associates with brain development following preterm birth.
The exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth
Authors: Xu Kang , Zeng Haoran , Lin Feiyang , Yumoto Emi , Asahina Masashi , Hayashi Ken-ichiro , Fukaki Hidehiro , Ito Hisashi , Watahiki Masaaki K.
Published: September 2023

Root development is essential for plant survival. The lack of carotenoid biosynthesis in thephytoene desaturase 3(pds3) mutant results in short primary roots (PR) and reduced lateral root (LR) formation. In this study, we show that short-term inhibition of PDS by fluridone suppressed PR growth in WT, but to a lesser extent in auxin mutants. Such an inhibition of PDS activity increased endogenous indole-3-acetic acid (IAA) levels, promoted auxin signaling, and partially complemented the PR growth of auxin deficient mutant,YUCCA 3 5 7 8 9quadruple mutant (yucQ). The exogenous application of retinaldehyde (retinal), an apocarotenoid derived from β-carotene, complemented the fluridone-induced suppression of root growth, as well as the short roots of thepds3mutant. Retinal also partially complemented the auxin-induced suppression of root growth. These results suggest that retinal may play a role in regulating root growth by modulating endogenous auxin levels.

One-sentence summary

The short-term inhibition of carotenoid biosynthesis mediates the production of β-carotene-derived apocarotenoid retinal which negatively regulates auxin levels and signaling to control root growth.
Sterol 3-beta-Glucosyltransferase TRANSPARENT TESTA15 Controls Seed Development and Flavanol Accumulation through its Role in Vacuole Biogenesis and Maintenance in Arabidopsis
Authors: Akary Elodie , Berger Adeline , Perreau François , Frey Anne , To Alexandra , Citerne Sylvie , Schaller Hubert , Vernhettes Samantha , Grandjean Olivier , Nesi Nathalie , Marion-Poll Annie , Lepiniec Loïc , Debeaujon Isabelle
Published: September 2023

The Arabidopsis sterol 3-beta-glucosyltransferase UGT80B1/TRANSPARENT TESTA15 (TT15) catalyzes sterol glucoside biosynthesis. Its loss of function causes reduced seed size, defective flavanol, polysaccharide and lipid polyester deposition at the seed coat and reduced seed dormancy. How TT15 controls seed development and physiology is unknown. Here we show thattt15mutants exhibit seed lethality with incomplete penetrance and maternal determinism that is correlated with endosperm cellularization defects, together with an increased sensitivity of seed germination to exogenous abscisic acid and paclobutrazol. We also reveal that flavanol deposition in the vacuole duringtt15seed development triggers premature endothelium cell death. An autoimmune-like syndrome characterized by callose and H2O2accumulation was detected in endothelium at the seed abaxial pole. Similar phenotypes were observed withtt9/gfs9,a mutant defective in endomembrane trafficking and homotypic vacuole fusion. Double mutant analysis showed thattt9partially rescuedtt15endothelium phenotypes. Consistent with seed mutant phenotypes,TT15promoter activity was detected in endothelium and endosperm and TT15 protein was located mainly at the vacuolar membrane (tonoplast). Using fluorescence recovery after photobleaching, we demonstrated that tonoplast fluidity was increased intt15roots. Altogether our data suggest that TT15 regulates seed development and flavanol accumulation by modulating vacuole biogenesis and maintenance.
Impacts of ethical leadership, innovative climate on project success: the role of innovative behavior and time pressure
Authors: Tran Pham Toan Khanh , Nguyen Le To Quyen Hoang Thuy
Published: September 2023

Purpose

This study aims to explore how ethical leadership and innovative climate impact project success through employees innovative behavior. In addition, based on the conservation of resources theory, this study also examines whether time pressure moderates the innovative work behavior and project success nexus.

Design/methodology/approach

Data were collected from 403 employees working in Vietnam's information technology (IT) companies. The partial least squares structural equation modeling was used to investigate the impact of ethical leadership and innovative climate on project success, the mediating effect of innovative behavior and the moderating role of time pressure.

Findings

Empirical findings indicate that ethical leadership and innovative climate positively impact on project success. Moreover, employees' innovative behavior has a complementary effect on these relationships. In addition, time pressure moderates the nexus between innovative work behavior and project success.

Practical implications

The findings suggest that IT companies can promote innovative work behavior among employees by building ethical leadership and enhancing an innovative climate. Moreover, when designing and implementing a project, project managers should take care to allow enough time for innovative behavior within the team.

Originality/value

This inquiry is probably the first attempt to explore the mechanism linking ethical leadership and innovative climate to project success, with the mediating role of employees' innovative behavior. Additionally, time pressure is an increasingly relevant factor in contemporary business, but so far little explored in research. This study extends the current knowledge by considering the moderating role of time pressure in the innovative behavior and project success nexus.
How does platform certification affect the marketing performance of sellers in food e-commerce? Interaction with reputation mechanisms
Authors: Xue Hu , Jin Shanshan , Wu Qianrong , Geng Xianhui
Published: September 2023

Purpose

Platform certification constitutes an effective mechanism for managing the lemon problem concerning food e-commerce. This work aims to evaluate the market effect of platform certification and analyzes its correction mechanism for lemon problem combined with reputation mechanism.

Design/methodology/approach

Utilizing the Gold Seller certification of Taobao.com to serve as an illustration, the authors conducted an empirical study based on the sales data of hairy crabs among 2,239 sample sites over six points in time from October to December 2019, systematically examining the market effect of food e-commerce platform certification along with the interaction between food e-commerce platform certification and reputation mechanisms, followed by a heterogeneity test by product price.

Findings

This study finds that sellers with platform certification can significantly increase their sales. The market effect of platform certification is more easily observed in the low-price product market. In addition, platform certification and reputation mechanisms have complementary effects. In a low-price product market, the complementary effect of platform certification and product reputation diminishes, while the complementary effect of platform certification and seller reputation disappears.

Originality/value

This study explores the market effect of food e-commerce platform certification, reveals the market effect of certification mechanism when multiple signaling mechanisms exist simultaneously and conducts an empirical test based on real market data. It provides a better comprehension of how platform certifications work in food e-commerce.
Integrating blockchain with building information modelling (BIM): a systematic review based on a sociotechnical system perspective
Authors: Yu Jiyang , Zhong Hua , Bolpagni Marzia
Published: September 2023

Purpose

The purpose of this paper is to analyse the current state of research on the integration of blockchain and building information modelling (BIM) in the Architecture, Engineering, Construction and Operations (AECO) industry as a means of identifying gaps between the existing paradigm and practical applications for determining future research directions and improving the industry. The study aims to provide clear guidance on areas that need attention for further research and funding and to draw academic attention to factors beyond the technical dimension.

Design/methodology/approach

A mixed-method systematic review is used, considering multiple literature types and using a sociotechnical perspective-based framework that covers three dimensions (technic, process and context) and three research elements (why, what and how). Data are retrieved and analysed from the Web of Science and Scopus databases for the 2017–2023 period.

Findings

While blockchain has the potential to address security, traceability and transparency and complement the system by integrating supporting applications, significant gaps still exist between these potentials and widespread industry adoption. Current limitations and further research needs are identified, including designing fully integrated prototypes, empirical research to identify operational processes, testing and analysing operational-level models or applications and developing and applying a technology acceptance model for the integration paradigm. Previous research lacks contextual settings, real-world tests or empirical investigations and is primarily conceptual.

Originality/value

This paper provides a comprehensive, critical systematic review of the integration of blockchain with BIM in the construction industry, using a sociotechnical perspective-based framework which can be applied in future reviews. The study provides insight into the current state and future opportunities for policymakers and practitioners in the AECO industry to prepare for the transition in this disruptive paradigm. It also provides a phased plan along with a clear direction for the transition to more advanced applications.