bluuebunny/crossref_metadata_2025 huggingface dataset:
uniLIVER: a Human Liver Cell Atlas for Data-Driven Cellular State Mapping
Authors: Wu Yanhong , Fan Yuhan , Miao Yuxin , Li Yuman , Du Guifang , Chen Zeyu , Diao Jinmei , Chen Yu-Ann , Ye Mingli , You Renke , Chen Amin , Chen Yixin , Li Wenrui , Guo Wenbo , Dong Jiahong , Zhang Xuegong , Wang Yunfang , Gu Jin
Published: December 2023

The liver performs several vital functions such as metabolism, toxin removal and glucose storage through the coordination of various cell types. The cell type compositions and cellular states undergo significant changes in abnormal conditions such as fatty liver, cirrhosis and liver cancer. As the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of liver at single cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER by integrative analyzing a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Besides the hierarchical cell type annotations, uniLIVER also proposed a novel data-driven strategy to map any query dataset to the normal reference map by developing a machine learning based framework named LiverCT. Applying LiverCT on the datasets from multiple abnormal conditions (1,867,641 cells and 439 samples from 12 datasets), the alterations of cell type compositions and cellular states were systematically investigated in liver cancer.
Astrocytes regulate neuronal network burst frequency through NMDA receptors species- and donor-specifically
Authors: Räsänen Noora , Tiihonen Jari , Koskuvi Marja , Lehtonen Šárka , Jalkanen Nelli , Karmila Nelli , Weert Isabelle , Vaurio Olli , Ojansuu Ilkka , Lähteenvuo Markku , Pietiläinen Olli , Koistinaho Jari
Published: December 2023

Background

Development of synaptic activity is a neuronal key characteristic that relies largely on interactions between neurons and astrocytes. Although astrocytes have known roles in regulating synaptic function and malfunction, the use of human or donor-specific astrocytes in disease models is still rare. Rodent astrocytes are routinely used to enhance neuronal activity in cell cultures, but less is known how human astrocytes influence neuronal activity.

Methods

We established human induced pluripotent stem cell (hiPSC)-derived neuron-astrocyte co-cultures and studied their functional development on microelectrode array (MEA). We used cell lines from 5 neurotypical control individuals and 3 pairs of monozygotic twins discordant for schizophrenia. A method combining Ngn2 overexpression and dual SMAD inhibition was used for neuronal differentiation. The neurons were co-cultured with hiPSC-derived astrocytes differentiated from 6-month-old astrospheres or rat astrocytes.

Results

We found that the hiPSC-derived co-cultures develop complex network bursting activity similarly to neuronal co-cultures with rat astrocytes. However, the effect of NMDA receptors on neuronal network burst frequency (NBF) differed between co-cultures containing human or rat astrocytes. By using co-cultures derived from patients with schizophrenia and unaffected individuals, we found lowered NBF in the affected cells. We continued to demonstrate how astrocytes from an unaffected individual rescue the lowered NBF in the affected neurons by increasing NMDA receptor activity.

Conclusions

Our results indicate that astrocytes participate in the regulation of neuronal NBF through a mechanism involving NMDA receptors. These findings shed light on the importance of using human and donor-specific astrocytes in disease modeling.
A novel thermostable and processive reverse transcriptase from a group II intron ofAnoxybacillus flavithermus
Authors: Oscorbin Igor P. , Filipenko Maxim L.
Published: December 2023

Reverse transcriptases (RTs) are a family of enzymes synthesizing DNA using an RNA template and participating in retrovirus propagation and telomere lengthening. In vitro, RTs are widely applied in various methods, including RNA-seq, RT-PCR and RT-LAMP. Thermostable RTs from bacterial group II introns are promising tools for biotechnology; they showed higher thermostability, fidelity and processivity comparing to commonly using M-MuLV RT and its mutants. However, the diversity of group II intron-encoded RTs is still insufficiently studied. Here, we biochemically characterized a novel RT from a thermophilic bacterium Anoxybacillus flavithermus, isolated from a hot spring in New Zealand with an optimal temperature for growth around 60°C. The cloned RT, named Afl RT, retained around 40% of the specific activity after 45 min incubation at 50°C. Optimal pH was 8.5, temperature — 45-50 °C and Mn2+ions were an optimal cofactor. In a processivity analysis with MS2 phage gRNA (3569 b), Afl RT elongated fully up to 36% of template molecules. In reverse transcription and RT-qLAMP, the enzyme allowed to detect up to 10 copies of MS2 phage genomic RNA per reaction. Thus, Afl RT is a promising enzyme for practical applications requiring thermostable processive RTs.
Recovering short DNA fragments from minerals and marine sediments: a comparative study evaluating lysis and isolation approaches
Authors: Gande Darjan , Hassenrück Christiane , Žure Marina , Richter-Heitmann Tim , Willerslev Eske , Friedrich Michael W.
Published: December 2023

Marine sediments as excellent climate archives, contain among other biomolecules substantial amounts of extracellular DNA. Through mechanisms of binding to various minerals, some of the DNA stays protected from degradation and remains preserved. While this pool of DNA represents genomic ecosystem fingerprints spanning over millions of years, the capability of current DNA extraction methods in recovering mineral-bound DNA remains poorly understood. We evaluated current sedimentary DNA extraction approaches and their ability to desorb and extract short DNA fragments from pure clay and quartz minerals as well as from different types of marine sediments. We separately investigated lysis (DNA release) and isolation steps (purification of DNA) comparing five different types of lysis buffers across two commonly used DNA isolation approaches: silica magnetic beads and liquid-phase organic extraction and purification. The choice of lysis buffer significantly impacted the amount of recovered mineral-bound DNA and facilitated selective desorption of DNA fragments. High molarity EDTA and phosphate lysis buffers recovered on average an order of magnitude more DNA from clay than other tested buffers, while both isolation approaches recovered comparable amounts of DNA. However, organic extraction caused an inhibitory effect in subsequent downstream applications (e.g., PCR), across all assessed sediment DNA extracts while silica magnetic beads induced inhibition only in half of the tested DNA extracts. Furthermore, we demonstrate that both, the isolation approach and the lysis buffer play a decisive role in successful library preparation and that lysis buffer choice impacted the final library fragment distribution. With this study, we underscore the critical importance of lysis buffer selection to maximize the recovery of mineral-bound DNA in sedimentary DNA extractions and show its profound impact on recovered fragment lengths, a crucial factor alongside existing isolation approaches in facilitating high-quality DNA extracts for downstream analysis related to ancient environmental (aeDNA) research.
Dynamics of AdultAxin2Cell Lineage Integration in Granule Neurons of the Dentate Gyrus
Authors: Sharifi Khadijeh A. , Farzad Faraz , Soldozy Sauson , Price Richard J. , Kalani M. Yashar S. , Tvrdik Petr
Published: December 2023

The Wnt pathway plays critical roles in neurogenesis. The expression ofAxin2is induced by Wnt/β-catenin signaling, making this gene a sensitive indicator of canonical Wnt activity. We employed pulse-chase genetic lineage tracing with theAxin2-CreERT2allele to follow the fate ofAxin2-positive cells in the adult hippocampal formation. We foundAxin2expressed in astrocytes, neurons and endothelial cells, as well as in the choroid plexus epithelia. Simultaneously with tamoxifen induction ofAxin2fate mapping, the dividing cells were marked with 5-ethynyl-2’-deoxyuridine (EdU). Tamoxifen induction resulted in significant increase of dentate gyrus granule cells three months later; however, none of these neurons contained EdU signal. Conversely, six months after the tamoxifen/EdU pulse-chase labeling, EdU-positive granule neurons were identified in each animal. Our data imply thatAxin2is expressed at several different stages of adult granule neuron differentiation and suggest that the process of integration of the adult-born neurons from certain cell lineages may take longer than previously thought.
Estrogenic control of reward prediction errors and reinforcement learning
Authors: Golden Carla E. M. , Martin Audrey C. , Kaur Daljit , Mah Andrew , Levy Diana H. , Yamaguchi Takashi , Lasek Amy W. , Lin Dayu , Aoki Chiye , Constantinople Christine M.
Published: December 2023

Gonadal hormones act throughout the brain1, and neuropsychiatric disorders vary in symptom severity over the reproductive cycle, pregnancy, and perimenopause2–4. Yet how hormones influence cognitive processes is unclear. Exogenous 17β-estradiol modulates dopamine signaling in the nucleus accumbens core (NAcc)5,6, which instantiates reward prediction errors (RPEs) for reinforcement learning7–16. Here we show that endogenous 17β-estradiol enhances RPEs and sensitivity to previous rewards by reducing dopamine reuptake proteins in the NAcc. Rats performed a task with different reward states; they adjusted how quickly they initiated trials across states, balancing effort against expected rewards. NAcc dopamine reflected RPEs that predicted and causally influenced initiation times. Elevated endogenous 17β-estradiol increased sensitivity to reward states by enhancing dopaminergic RPEs in the NAcc. Proteomics revealed reduced dopamine transporter expression. Finally, knockdown of midbrain estrogen receptors suppressed reinforcement learning. 17β-estradiol therefore controls RPEs via dopamine reuptake, mechanistically revealing how hormones influence neural dynamics for motivation and learning.
Brain-wide activity-identity mapping of neural networks associated with prosocial motivation in rats
Authors: Ruzal Keren , Trachtenberg Estherina , Kantor Ben , Flumin Hila , Roemer Adin , Crespo Andres , Kohl Johannes , Bartal Inbal Ben-Ami
Published: December 2023

A prosocial response to others in distress is an important driver of behavior across social species. To investigate the neurobiological mechanism leading to prosocial behavior, we use a helping behavior test wherein rats may release a trapped conspecific by opening a restrainer door. To ensure rats were not acting for social interaction, a separation divider prevented post-release contact (“separated” test). Despite the divider, most rats consistently opened the restrainer, demonstrating prosocial motivation. Brain-wide c-Fos analysis conducted via our opensource software "Brainways", revealed activity in empathy-related regions, including the anterior cingulate and insular cortices. Nucleus accumbens activity, previously recorded during helping, was not significant in the“separated” test. Chemogenetic manipulations of the accumbens did not prevent helping, suggesting that its activity reflects contact seeking. Mapping of oxytocin and dopamine receptors on active cells revealed region-specific recruitment of these subpopulations, depending on the social context. Network connectivity analysis highlights context-dependent functional subcircuits.
Nuclear cytoophidia assembly represses transcriptional activity to control skeletal development and homeostasis
Authors: Xu Cheng , Wei Zhixin , Lv Longfei , Dong Xiaoyu , Xia Wenwen , Xing Junqiao , Liu Hongni , Zhao Xue , Liu Yuan , Wang Weihua , Jiang Haochen , Gong Yeli , Liu Cong , Xu Kai , Wang Siyuan , Akimoto Yoshie , Hu Zhangfeng
Published: December 2023

Compartmentation via filamentation is an evolutionarily conserved subcellular structure that fine-tunes the inherent activity of proteins. Cytoophidia represent a typical class of filamentous structures controlling enzymatic activities. Despite eukaryotic cells containing both cytoplasmic cytoophidia and nuclear cytoophidia, the physiological significance of nuclear cytoophidia is largely unknown. Here we show that nuclear filamentation inhibits the transcriptional activity of Impdh2 required for limb formation and bone resorption. Impdh2 deletion in mouse limb mesenchymal progenitors causes severe skeletal dysplasia by impairing endochondral ossification and chondrocyte differentiation. Additionally, Impdh2 deficiency in myeloid lineages leads to an increased bone mass via impeding osteoclast differentiation. Furthermore, Impdh2 regulates osteoclastic mitochondrial biogenesis and function. We propose that the nuclear compartmentalization of Impdh2 regulates the transcriptional activity during skeletal development and homeostasis.
Profiling age and body fluid DNA methylation markers using nanopore adaptive sampling
Authors: Yuen Zaka Wing-Sze , Shanmuganandam Somasundhari , Stanley Maurice , Jiang Simon , Hein Nadine , Daniel Runa , McNevin Dennis , Jack Cameron , Eyras Eduardo
Published: December 2023

DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites, as part of a multiplexed assay, rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.
Subthalamic nucleus neurons encode syllable sequence and phonetic characteristics during speech
Authors: Lipski W.J. , Bush A. , Chrabaszcz A. , Crammond D.J. , Fiez J.A. , Turner R.S. , Richardson R.M.
Published: December 2023

Speech is a complex behavior that can be used to study unique contributions of the basal ganglia to motor control in the human brain. Computational models suggest that the basal ganglia encodes either the phonetic content or the sequence of speech elements. To explore this question, we investigated the relationship between phoneme and sequence features of a spoken syllable triplet and the firing rate of subthalamic nucleus (STN) neurons recorded during the implantation of deep brain stimulation (DBS) electrodes in individuals with Parkinson’s disease. Patients repeated aloud a random sequence of three consonant-vowel (CV) syllables in response to audio cues. Single-unit extracellular potentials were sampled from the sensorimotor STN; a total of 227 unit recordings were obtained from the left STN of 25 subjects (4 female). Of these, 113 (50%) units showed significant task-related increased firing and 53 (23%) showed decreased firing (t-test relative to inter-trial period baseline, p<0.05). Linear regression analysis revealed that both populations of STN neurons encode phoneme and sequence features of produced speech. Maximal phoneme encoding occurred at the time of phoneme production, suggesting efference copyor sensory-related processing, rather than speech motor planning (-50ms and +175ms relative to CV transition for consonant and vowel encoding, respectively). These findings demonstrate that involvement of the basal ganglia in speaking includes separate single unit representations of speech sequencing and phoneme selection in the STN.
Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development
Authors: Cao Xuan , Ma Terry , Fan Rong , Yuan Guo-Cheng
Published: December 2023

It is well known that the chromatin states play a major role in cell-fate decision and cell-identity maintenance; however, the spatial variation of chromatin statesin situremains poorly characterized. Here, by leveraging recently available spatial-CUT&Tag data, we systematically characterized the global spatial organization of the H3K4me3 profiles in a mouse embryo. Our analysis identified a subset of genes with spatially coherent H3K4me3 patterns, which together delineate the tissue boundaries. The spatially coherent genes are strongly enriched with tissue-specific transcriptional regulators. Remarkably, their corresponding genomic loci are marked by broad H3K4me3 domains, which is distinct from the typical H3K4me3 signature. Spatial transition across tissue boundaries is associated with continuous shortening of the broad H3K4me3 domains as well as expansion of H3K27me3 domains. Our analysis reveals a strong connection between the genomic and spatial variation of chromatin states, which may play an important role in embryonic development.
Structural mechanism of angiogenin activation by the ribosome
Authors: Loveland Anna B. , Koh Cha San , Ganesan Robin , Jacobson Allan , Korostelev Andrei A.
Published: December 2023

Angiogenin, an RNase A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases, and epigenetic inheritance. Upon activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, producing nicked tRNA (also known as tRNA halves, tiRNAs or tsRNAs) and resulting in translation repression. The catalytic activity of isolated angiogenin, however, is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here, we uncover these mechanisms using biochemical assays and cryogenic electron microscopy. Our work reveals that the cytosolic ribosome is the long-sought activator of angiogenin. A 2.8-Å resolution cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic center, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S•angiogenin structures capture how the tRNA substrate is directed by the ribosome next to angiogenin’s active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, whose abundance increases during cellular stresses.
Unveiling interactions of spatial-temporal information in tactile motion perception
Authors: Qu Boyi , Tan Xiaojun , Tang Zheng , Friedman Robert M. , Wang Haiming , Lan Lan , Schriver Kenneth E , Pan Gang , Lai Hsin-Yi
Published: December 2023

The intricate interplay of spatial and temporal information in tactile-motion perception remains elusive. Despite strides in decoding neural signals for direction, speed and texture in tactile perception, nuanced interactions persist as challenges. Addressing this, we investigated direction and speed tactile perception, exploring the intricate spatial-temporal dynamics. Psychophysical experiments manipulated direction and speed parameters using a laboratory-designed fingerpad ball-stimulator. A pivotal discovery includes quadrant-dependent anisotropic distortion in perceived motion direction, expanding the well-known notion of a specific preferred orientation. Spatial features primarily influence inherent responses, while temporal features impact stimulus-specific responses, shedding light on dynamic directional perception. The introduction of a psychometric function improved the modeling of tactile-motion speed perception, incorporating both linear and nonlinear components for a more accurate representation. This study provides intriguing insights into the neural mechanisms in tactile-motion perception, with potential applications for somatosensation in brain-machine interfaces.

Teaser

This study unveils the intricate interplay of perceiving tactile motion, shedding light on the mysteries of tactile sensations.
Live microscopy of multicellular spheroids with the multi-modal near-infrared nanoparticles reveals differences in oxygenation gradients
Authors: Debruyne Angela C. , Okkelman Irina A. , Heymans Nina , Pinheiro Cláudio , Hendrix An , Nobis Max , Borisov Sergey M. , Dmitriev Ruslan I.
Published: December 2023

Assessment of hypoxia, nutrients, metabolite gradients, and other hallmarks of the tumor microenvironment within 3D multicellular spheroid and organoid models represents a challenging analytical task. Here, we report red/near-infrared emitting cell staining O2-sensitive nanoparticles, which enable measurements of spheroid oxygenation on a conventional fluorescence microscope. Nanosensor probes, termed ’MMIR’ (multi-modal infrared), incorporate a near-infrared O2-sensitive metalloporphyrin (PtTPTBPF) and a deep red aza-BODIPY reference dyes within a biocompatible polymer shell, allowing oxygen gradients quantificationviafluorescence ratio and phosphorescence lifetime readouts. We optimized staining techniques and evaluated nanosensor probe characteristics and cytotoxicity. Subsequently, we applied nanosensors to the live spheroid models based on HCT116, DPSCs, and SKOV3 cells, at rest and treated with drugs affecting cell respiration. We found that the growth medium viscosity, spheroids size, and formation method influenced spheroid oxygenation.

Unexpectedly, some spheroids (produced from HCT116 and dental pulp stem cells) exhibited ’inverted’ oxygenation gradients, with higher core oxygen levels than the periphery. This contrasted with the frequently encountered ‘normal’ gradient of hypoxia towards the core caused by diffusion. Further microscopy analysis of spheroids with an “inverted” gradient demonstrated metabolic stratification of cells within spheroids: thus, autofluorescence FLIM of NAD(P)H revealed the formation of glycolytic core, and localization of OxPhos-active cells at the periphery. Collectively, we demonstrate a strong potential of NIR-emitting ratiometric nanosensors for advanced microscopy studies targeting live and quantitative real-time monitoring of cell metabolism and hypoxia in complex 3D tissue models.

Graphical abstract
Subcallosal area 25: its responsivity to the stress hormone cortisol and its opposing effects on appetitive motivation in marmosets
Authors: Banai Tizkar Rana , McIver Lauren , Wood Christian Michael , Roberts Angela Charlotte
Published: December 2023

Aberrant activity in caudal subcallosal anterior cingulate cortex (scACC) is implicated in depression and anxiety symptomatology, with its normalisation a putative biomarker of successful treatment response. The function of scACC in emotion processing and mental health is not fully understood despite its known influence on stress-mediated processes through its rich expression of mineralocorticoid and glucocorticoid receptors. Here we examine the causal interaction between area 25 within scACC (scACC-25) and the stress hormone, cortisol, in the context of anhedonia and anxiety-like behaviour. Moreover, the overall role of scACC-25 in hedonic capacity and motivation is investigated under transient pharmacological inactivation and overactivation. The results suggest that a local increase of cortisol in scACC-25 shows a rapid induction of anticipatory anhedonia and increased responsiveness to uncertain threat. Separate inactivation and overactivation of scACC-25 increased and decreased motivation and hedonic capacity, respectively, likely through different underlying mechanisms. Together, these data show that area scACC-25 has a causal role in consummatory and motivational behaviour and produces rapid responses to the stress hormone cortisol, that mediates anhedonia and anxiety-like behaviour.
Learning of object-in-context sequences in freely-moving macaques
Authors: Abbaspoor S. , Rahman K. , Zinke W. , Hoffman K.L.
Published: December 2023

Flexible learning is a hallmark of primate cognition, which arises through interactions with changing environments. Studies of the neural basis for this flexibility are typically limited by laboratory settings that use minimal environmental cues and restrict interactions with the environment, including active sensing and exploration. To address this, we constructed a 3-D enclosure containing touchscreens on its walls, for studying cognition in freely moving macaques. To test flexible learning, two monkeys completed trials consisting of a regular sequence of object selections across four touchscreens. On each screen, the monkeys had to select by touching the sole correct object item (‘target’) among a set of four items, irrespective of their positions on the screen. Each item was the target on exactly one screen of the sequence, making correct performance conditioned on the spatiotemporal sequence rule across screens. Both monkeys successfully learned multiple 4-item sets (N=14 and 22 sets), totaling over 50 and 80 unique, conditional item-context memoranda, with no indication of capacity limits. The enclosure allowed freedom of movements leading up to and following the touchscreen interactions. To determine whether movement economy changed with learning, we reconstructed 3D position and movement dynamics using markerless tracking software and gyroscopic inertial measurements. Whereas general body positions remained consistent across repeated sequences, fine head movements varied as monkeys learned, within and across sequence sets, demonstrating learning set or “learning to learn”. These results demonstrate monkeys’ rapid, capacious, and flexible learning within an integrated, multisensory 3-D space. Furthermore, this approach enables the measurement of continuous behavior while ensuring precise experimental control and behavioral repetition of sequences over time. Overall, this approach harmonizes the design features that are needed for electrophysiological studies with tasks that showcase fully situated, flexible cognition.
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
Authors: Ginatt Alon Avraham , Berihu Maria , Castel Einam , Medina Shlomit , Carmi Gon , Doron-Faigenboim Adi , Sharon Itai , Tal Ofir , Droby Samir , Somera Tracey , Mazzola Mark , Eizenberg Hanan , Freilich Shiri
Published: December 2023

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome-scale metabolic models of bacteria associated with a specific disease suppressive vs disease conductive apple rhizospheres were drafted based on genome resolved metagenomes, comprising anin-siliconative microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.
Rules, hypergraphs, and probabilities: the three-level analysis of chemical reaction systems and other stochastic stoichiometric population processes
Authors: Smith Eric , Smith Harrison B. , Andersen Jakob Lykke
Published: December 2023

We consider problems in the functional analysis and evolution of combinatorial chemical reaction networks as rule-based, or three-level systems. The first level consists of rules, realized here as graph-grammar representations of reaction mechanisms. The second level consists of stoichiometric networks of molecules and reactions, modeled as hypergraphs. At the third level is the stochastic population process on molecule counts, solved for dynamics of population trajectories or probability distributions. Earlier levels in the hierarchy generate later levels combinatorially, and as a result constraints imposed in earlier and smaller layers can propagate to impose order in the architecture or dynamics in later and larger layers. We develop general methods to study rule algebras, emphasizing system consequences of symmetry; decomposition methods of flows on hypergraphs including the stoichiometric counterpart to Kirchhoff’s current decomposition and work/dissipation relations studied in [1]; and the large-deviation theory for currents in a stoichiometric stochastic population process, deriving additive decompositions of the large-deviation function that relate a certain Kirchhoff flow decomposition to the extended Pythagorean theorem from information geometry. The latter result allows us to assign a natural probabilistic cost to topological changes in a reaction network of the kind produced by selection for catalyst-substrate specificity. We develop as an example a model of biological sugar-phosphate chemistry from a rule system published in [2]. It is one of the most potentially combinatorial reaction systems used by biochemistry, yet one in which two ancient, widespread and nearly unique pathways have evolved in the Calvin-Benson cycle and the Pentose Phosphate pathway, which are additionally nearly reverses of one another. We propose a probabilistic accounting in which physiological costs can be traded off against the fitness advantages that select them, and which suggests criteria under which these pathways may be optimal.
Sex-specific behavioral features of juvenile and adult haploinsufficientScn2a+/−female mice, model of Autism Spectrum Disorder
Authors: Marcantonio Wendy , Simonti Martina , Léna Isabelle , Mantegazza Massimo
Published: December 2023

Variants of theSCN2Agene, encoding the NaV1.2 sodium channel, cause a spectrum of neurodevelopmental and epileptic disorders, and are among those that show the strongest association with Autism Spectrum Disorder (ASD). ASD has a male-bias prevalence, but several studies have proposed that female prevalence may be underestimated due to different symptomatic expression compared with males. However, it is unclear whether this is related to actual different pathological features or to greater masking abilities in females.

Studies onScn2a+/−mice, a model ofSCN2Ahaploinsufficiency and ASD, have shown an age-dependent ASD-like phenotype attenuated at adulthood in males. However, little is known about the behavioral features ofScn2a+/−female mice. We performed a battery of behavioral tests that are relevant for assessing ASD-like features, investigating juvenile and adultScn2a+/−female mice.

Our results demonstrate that femaleScn2a+/−mice exhibit an overall milder phenotype than males, showing increased sociability and increased risk taking in juveniles, hyper-reactivity to cold stimuli in adults, altered decision-making related behaviors in both. Thus, this is consistent with the male-bias prevalence of ASD and the existence of different ASD phenotypic features in males and females. Both genders should be investigated in studies of mouse models of ASD.
Evolution of extended-spectrum β-lactamase-producing ST131Escherichia coliat a single hospital over 15 years
Authors: Cho Shu-Ting , Mills Emma G. , Griffith Marissa P. , Nordstrom Hayley R. , McElheny Christi L. , Harrison Lee H. , Doi Yohei , Van Tyne Daria
Published: December 2023

Escherichia colibelonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131E. colifrequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producingE. coliclinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly geneftsI, the LPS biosynthesis genearnC, and the yersiniabactin uptake receptorfyuA.Diverse ESBL genes belonging to theblaCTX-M,blaSHV, andblaTEMfamilies were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.
WITHDRAWN: Cross-species Myocardial Proteomics For Animal Models of Cardiometabolic Heart Failure With Preserved Ejection Fraction
Authors: Guo Alina , Yoo Edwin J.
Published: December 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to insufficient sample size to make conclusions. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies
Authors: Cai Wang , Pichler Maximilian , Biggs Jeremy , Nicolet Pascale , Ewald Naomi , Griffiths Richard A. , Bush Alex , Leibold Mathew A. , Hartig Florian , Yu Douglas W.
Published: December 2023

Technological progress is enabling ecologists to create repeated, large-scale, structured, and standardised community surveys. However, it is unclear how best to extract information from these novel community data. We metabarcoded 48 vertebrate species from their eDNA in 320 ponds in England and applied the ‘internal-structure’ approach, which uses joint species distribution models to explain community compositions as the outcome of four metacommunity assembly processes: environmental filtering, dispersal, species interactions, and stochasticity. We find that the environment plays an important role in community assembly and that the inferred environmental preferences of species are consistent with their ecologies. We also infer negative biotic covariances between fish and amphibians, which is consistent with predator-prey interactions, and high spatial autocorrelation for the palmate newt, which is consistent with its hypothesised relictual distribution. Comparing sites in the metacommunity, environmentally and spatially distinctive sites are better explained by their environmental covariates and geographic locations, respectively, revealing sites where environmental filtering and dispersal limitation act more strongly. Furthermore, species belonging to different trait groups differ in how well environmental covariates, biotic covariances, and geographical locations explain their distributions. Overall, our results highlight the value of a modern interpretation of metacommunity ecology that embraces the fact that assembly processes differ between individual species and sites. We discuss how novel community data make feasible several study-design improvements that will strengthen the inference of metacommunity assembly processes from observational data.
Probabilistic clustering of cells using single-cell RNA-seq data
Authors: Saha Joy , Tanvir Ridwanul Hasan , Hassan Samee Md. Abul , Rahman Atif
Published: December 2023

Single-cell RNA sequencing is a modern technology for analyzing cellular heterogeneity. A key challenge is to cluster a heterogeneous sample of different cell types into multiple different homogeneous groups. Although there exist a number of clustering methods, they do not perform well consistently across various datasets. Moreover, most of them are not based on probabilistic approaches making it difficult to assess uncertainties in their results. Therefore, in spite of having large cell atlases, it is often quite difficult to map cells to types. In addition, many of the methods require prior knowledge such as marker gene information for each type. Also due to technological limitations, dropouts of gene expressions may occur in the data which is not taken into account in other methods. Here we present a probabilistic method named CellHorizon for clustering scRNA-seq data that is based on a generative model, handles dropouts and works without any prior marker gene information. Experiments reveal that our method outperforms current state-of-the-art methods overall on six gold standard datasets.
Efficient boundary-guided scanning for high-resolution X-ray ptychography
Authors: Lin Dergan , Jiang Yi , Deng Junjing , Marin Fabricio S. , Di Zichao Wendy
Published: December 2023

In the realm of X-ray ptychography experiments, a considerable amount of ptychography scans are typically performed within a field of view encompassing the target sample. While it is crucial to obtain overlapping scans in small increments over the region of interest for achieving high-resolution sample reconstruction, a significant number of these scans often redundantly measure the empty background within the wide field of view. To address this inefficiency, an innovative algorithm is proposed that introduces automatic guidance for data acquisition. The algorithm first directs the scan point to actively search for the object of interest within the field of view. Subsequently, it intelligently scans along the perimeter of the sample, strategically acquiring measurements exclusively within the boundary of the region of interest. By employing this approach, a reduction in the number of measurements required to obtain high-resolution reconstruction images is demonstrated, as compared with conventional raster scanning methods. Furthermore, the automatic guidance provided by the algorithm offers the added advantage of saving valuable time during the reconstruction process. Through practical implementation on real experiments, these findings showcase the efficacy of the proposed algorithm in enhancing the efficiency and accuracy of X-ray ptychography experiments. This novel approach holds immense potential for advancing sample analysis and imaging techniques in various scientific disciplines.
Cylindrical electromagnets: modeling, analysis, simulation and implementation
Authors: Hashemi Ali , Yazdanpanah Qaraei Parsa
Published: December 2023

Purpose

This paper aims to present an accurate magnetic equivalent circuit for modeling the cylindrical electromagnet so that by analyzing it, the magnetic flux density in different parts of the electromagnet, as well as its lifting force, can be calculated.

Design/methodology/approach

The structure of the electromagnet is divided into parts that can be modeled by lumped element parameters. Mathematical equations for calculating these elements are presented and proved. The axial symmetry of the cylindrical electromagnet made it possible to use planar circuits for its modeling. To increase the accuracy of the proposed equivalent circuit, attention has been paid to the leakage flux as well as the nonlinear behavior of the ferromagnetic core. Also, the curvature of the magnetic flux path is considered in the calculation of the corner permeances of the core.

Findings

The magnetic flux density in different parts of the electromagnet was calculated using nodal analysis of the circuit and compared to the results of the finite element method. Also, a test bed was established to measure the lifting force of the electromagnet. Comparing the results shows a difference of less than 3% which indicate the good accuracy of the proposed circuit. In addition, due to the curvature of the flux path, there is a no-flux region in the center of the disk, the extent of which depends on the thickness of the disk and the diameter of the middle leg.

Originality/value

Magnetic equivalent circuit is a new contribution to analyze the cylindrical electromagnet and calculate its lifting force with good accuracy. The circuit lumped elements can be quickly calculated using mathematical equations and software such as MATLAB according to the actual path of the magnetic flux. Compared to other methods, the proposed circuit analyzes the electromagnet in a shorter period of time. This is the most important advantage of the proposed circuit model.
Assessment of the factors for the adoption of Internet of things (IoT) in the logistics: a PLS-SEM (partial least squares structural equation modeling) approach
Authors: Kumar Ankur , Srivastava Ambika , Misra Subhas C.
Published: December 2023

Purpose

The purpose of this study is to investigate the influence that technological, environmental and organizational factors have on the rate of Internet of Things (IoT) adoption within the logistics industry. In addition, the moderating effect that the risk factor has on the technological, environmental and organizational factors regarding the implementation of IoT in logistics.

Design/methodology/approach

For the purpose of testing the models and hypotheses, a survey was carried out in order to collect the responses from currently employed individuals at various companies working in the field of logistics or IoT. For the purpose of analysis, the authors made use of the partial least squares structure equation model (PLS-SEM) technique.

Findings

Findings of this study concluded that technology- and environmental-related factors significantly affect the adoption of IoT in logistics, while risk acts as a moderator for the technological-related factor only in the adoption of IoT in logistics.

Research limitations/implications

The relevance of the authors' study lies in the growing importance of IoT in logistics and the need for logistics companies to understand the factors that impact the adoption of IoT in their operations. By identifying and analyzing the factors that influence IoT adoption in logistics, the authors' study provides valuable insights that can help logistics companies make informed decisions about whether and how to adopt IoT.

Practical implications

The research will help organizations make strategies for the successful adoption of IoT and ease the lives of all the stakeholders.

Originality/value

In this research, the authors attempted to find the factors that influence the adoption of IoT in logistics management. The influence of the technological, environmental, organizational and risk-related factors on the adoption of IoT in logistics management was studied. The moderating effect of risk over these factors on the adoption of IoT in logistics was also analyzed. This is original work and has never been done earlier.
Gender occupational intensity and wages in the Northern Triangle of Central America
Authors: Espino Ilya , Hermeto Ana , Luz Luciana
Published: December 2023

Purpose

This paper aims to explore the relationship between gender occupational intensity and wages in the Northern Triangle of Central America using national surveys carried out in 2014.

Design/methodology/approach

A harmonized occupational classification at the -digit level is built with the objective of analyzing the occupational distribution across countries. Then, quantile regressions (QRs) are estimated to explore in detail which factors are affecting the wages of both females and males; in particular, this paper pays special attention to female occupational intensity (the share of females within each occupation).

Findings

The comparative analysis suggests that women are overrepresented in certain occupations, and they are much more likely to be working in part-time jobs than men in all countries. Furthermore, findings reveal that working in female-dominated occupations has a negative effect on wages along the distribution across countries. However, the effect of this variable is higher at the lower quantile of the distribution for women, especially in El Salvador and Honduras.

Originality/value

This paper first proposes a new typology of occupations, which allows a consistent and comparable analysis of the occupational structure. The results then provide a picture to address gender occupational intensity and its links with wages. Further, the characteristics of the labor market and differences in trends across these countries suggest that this topic requires challenging research for the region.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-03-2021-0165
Toward an extended metadata standard for digital art
Authors: Martynovich Sofia
Published: December 2023

Purpose

The interpretation of any emerging form or period in art history was never a trivial task. However, in the case of digital art, technology, becoming an integral part, multiplied the complexity of describing, systematizing and evaluating it. This article investigates the most common metadata standards for the documentation of art as a broad category and suggests possible next steps toward an extended metadata standard for digital art.

Design/methodology/approach

Describing several techno-cultural phenomena formed in the last decade, manifesting the extendibility of digital art (its ability to be easily extended across multiple modalities), the article, at first, points to the long overdue need to re-evaluate the standards around it. Then it suggests a deeper analysis through a comparative study. In the scope of the study three artworks, The Arnolfini Portrait (Jan van Eyck), an iconic example of the early Renaissance, The World's First Collaborative Sentence (Douglas Davis), a classic example of early Internet art and Fake It Till You Make It (Maya Man), a prominent example of the blockchain art, are examined following the structure of the VRA Core 4.0 standard.

Findings

The comparative study demonstrates that digital art is more multi-semantic than traditional physical art, and requires new taxonomies as well as approaches for data acquisition.

Originality/value

Acknowledging that digital art simply has not yet evolved to the stage of being systematically collected by cultural institutions for documentation, curation and preservation, but otherwise, in the past few years, it has been at the front-center of social, economic and technological trends, the article suggests looking for hints on the future-proof extended metadata standard in some of those trends.