bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation
Authors: Joron Khalil , Viegas Juliane Oliveira , Haas-Neill Liam , Bier Sariel , Drori Paz , Dvir Shani , Lim Patrick Siang Lin , Rauscher Sarah , Meshorer Eran , Lerner Eitan 
Published: August 2023

AbstractFluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
Authors: Lee Lindsay , Yu Hongyu , Jia Bojing Blair , Jussila Adam , Zhu Chenxu , Chen Jiawen , Xie Liangqi , Hafner Antonina , Mishra Shreya , Wang Duan Dennis , Strambio-De-Castillia Caterina , Boettiger Alistair , Ren Bing , Li Yun , Hu Ming 
Published: August 2023

AbstractMultiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH.
Anxious individuals shift emotion control from lateral frontal pole to dorsolateral prefrontal cortex
Authors: Bramson Bob , Meijer Sjoerd , van Nuland Annelies , Toni Ivan , Roelofs Karin 
Published: August 2023

AbstractAnxious individuals consistently fail in controlling emotional behavior, leading to excessive avoidance, a trait that prevents learning through exposure. Although the origin of this failure is unclear, one candidate system involves control of emotional actions, coordinated through lateral frontopolar cortex (FPl) via amygdala and sensorimotor connections. Using structural, functional, and neurochemical evidence, we show how FPl-based emotional action control fails in highly-anxious individuals. Their FPl is overexcitable, as indexed by GABA/glutamate ratio at rest, and receives stronger amygdalofugal projections than non-anxious male participants. Yet, high-anxious individuals fail to recruit FPl during emotional action control, relying instead on dorsolateral and medial prefrontal areas. This functional anatomical shift is proportional to FPl excitability and amygdalofugal projections strength. The findings characterize circuit-level vulnerabilities in anxious individuals, showing that even mild emotional challenges can saturate FPl neural range, leading to a neural bottleneck in the control of emotional action tendencies.
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia
Authors: Dwiyanto J. , Huët M. A. L. , Hussain M. H. , Su T. T. , Tan J. B. L. , Toh K. Y. , Lee J. W. J. , Rahman S. , Chong C. W. 
Published: August 2023

AbstractThe prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community’s health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.
Aberrant cortico-thalamo-cerebellar network interactions and their association with impaired cognitive functioning in patients with schizophrenia
Authors: Ha Minji , Park Soo Hwan , Park Inkyung , Kim Taekwan , Lee Jungha , Kim Minah , Kwon Jun Soo 
Published: August 2023

AbstractEvidence indicating abnormal functional connectivity (FC) among the cortex, thalamus, and cerebellum in schizophrenia patients has increased. However, the role of the thalamus and cerebellum when integrated into intrinsic networks and how those integrated networks interact in schizophrenia patients are largely unknown. We generated an integrative network map by merging thalamic and cerebellar network maps, which were parcellated using a winner-take-all approach, onto a cortical network map. Using cognitive networks, the default mode network (DMN), the dorsal attention network (DAN), the salience network (SAL), and the central executive network (CEN) as regions of interest, the FC of 48 schizophrenia patients was compared with that of 57 healthy controls (HCs). The association between abnormal FC and cognitive impairment was also investigated in patients. FC was lower between the SAL-CEN, SAL-DMN, and DMN-CEN and within-CEN in schizophrenia patients than in HCs. Hypoconnectivity between the DMN-CEN was correlated with impaired cognition in schizophrenia patients. Our findings broadly suggest the plausible role of the thalamus and cerebellum in integrative intrinsic networks in patients, which may contribute to the disrupted triple network and cognitive dysmetria in schizophrenia.
Resting-state perfusion in motor and fronto-limbic areas is linked to diminished expression of emotion and speech in schizophrenia
Authors: Gangl Nicole , Conring Frauke , Federspiel Andrea , Wiest Roland , Walther Sebastian , Stegmayer Katharina 
Published: August 2023

AbstractNegative symptoms (NS) are a core component of schizophrenia affecting community functioning and quality of life. We tested neural correlates of NS considering NS factors and consensus subdomains. We assessed NS using the Clinical Assessment Interview for Negative Symptoms and the Scale for Assessment of Negative Symptoms. Arterial spin labeling was applied to measure resting-state cerebral blood flow (rCBF) in 47 schizophrenia patients and 44 healthy controls. Multiple regression analyses calculated the relationship between rCBF and NS severity. We found an association between diminished expression (DE) and brain perfusion within the cerebellar anterior lobe and vermis, and the pre-, and supplementary motor area. Blunted affect was linked to fusiform gyrus and alogia to fronto-striatal rCBF. In contrast, motivation and pleasure was not associated with rCBF. These results highlight the key role of motor areas for DE. Considering NS factors and consensus subdomains may help identifying specific pathophysiological pathways of NS.
Optimization of an alum-anchored clinical HIV vaccine candidate
Authors: Rodrigues Kristen A. , Cottrell Christopher A. , Steichen Jon M. , Groschel Bettina , Abraham Wuhbet , Suh Heikyung , Agarwal Yash , Ni Kaiyuan , Chang Jason Y. H. , Yousefpour Parisa , Melo Mariane B. , Schief William R. , Irvine Darrell J. 
Published: August 2023

AbstractIn the ongoing effort to develop a vaccine against HIV, vaccine approaches that promote strong germinal center (GC) responses may be critical to enable the selection and affinity maturation of rare B cell clones capable of evolving to produce broadly neutralizing antibodies. We previously demonstrated an approach for enhancing GC responses and overall humoral immunity elicited by alum-adjuvanted protein immunization via the use of phosphoserine (pSer) peptide-tagged immunogens that stably anchor to alum particles via ligand exchange with the alum particle surface. Here, using a clinically relevant stabilized HIV Env trimer termed MD39, we systematically evaluated the impact of several parameters relevant to pSer tag composition and trimer immunogen design to optimize this approach, including phosphate valency, amino acid sequence of the trimer C-terminus used for pSer tag conjugation, and structure of the pSer tag. We also tested the impact of co-administering a potent saponin/monophosphoryl lipid A (MPLA) nanoparticle co-adjuvant with alum-bound trimers. We identified MD39 trimer sequences bearing an optimized positively-charged C-terminal amino acid sequence, which, when conjugated to a pSer tag with four phosphates and a polypeptide spacer, bound very tightly to alum particles while retaining a native Env-like antigenicity profile. This optimized pSer-trimer design elicited robust antigen-specific GC B cell and serum IgG responses in mice. Through this optimization, we present a favorable MD39-pSer immunogen construct for clinical translation.
C5aR+ dendritic cells fine-tune the Peyer’s patch microenvironment to induce antigen-specific CD8+ T cells
Authors: Kim Sae-Hae , Shim Eun-Hyeon , Kim Doo-Jin , Jang Yong-Suk 
Published: August 2023

AbstractThe mucosal delivery route is considered ideal for immunization. However, induction of antigen-specific mucosal immunity is difficult due to the tolerogenic environment. Therefore, developing an immunogenic mucosal dendritic cell (DC)-targeting strategy is required. Herein, we investigated the characteristics and immunogenic potential of Peyer’s patch (PP) DCs as an oral vaccination-targeting strategy. Single-cell RNA sequencing analysis of the PP DCs showed that complement C5a receptor- and lysozyme-expressing DCs exhibit increased expression of genes related to chemotaxis. Administration of the Co1 peptide, a C5aR ligand, increased CD8+ T cell infiltration and response to the co-delivered model antigen in mice. Furthermore, in the SARS-CoV-2 vaccine model, vaccination with Co1 elicited both systemic and mucosal immunity. Collectively, these findings demonstrate that C5aR signaling in mucosal DCs plays a role in regulating adjuvant activity by modulating the tissue microenvironment.
Interferometric imaging of amplitude and phase of spatial biphoton states
Authors: Zia Danilo , Dehghan Nazanin , D’Errico Alessio , Sciarrino Fabio , Karimi Ebrahim 
Published: August 2023

AbstractHigh-dimensional biphoton states are promising resources for quantum applications, ranging from high-dimensional quantum communications to quantum imaging. A pivotal task is fully characterizing these states, which is generally time-consuming and not scalable when projective measurement approaches are adopted; however, new advances in coincidence imaging technologies allow for overcoming these limitations by parallelizing multiple measurements. Here we introduce biphoton digital holography, in analogy to off-axis digital holography, where coincidence imaging of the superposition of an unknown state with a reference state is used to perform quantum state tomography. We apply this approach to single photons emitted by spontaneous parametric down-conversion in a nonlinear crystal when the pump photons possess various quantum states. The proposed reconstruction technique allows for a more efficient (three orders of magnitude faster) and reliable (an average fidelity of 87%) characterization of states in arbitrary spatial modes bases, compared with previously performed experiments. Multiphoton digital holography may pave the route toward efficient and accurate computational ghost imaging and high-dimensional quantum information processing.
On reliability of annotations in contextual emotion imagery
Authors: Martínez-Miwa Carlos A. , Castelán Mario 
Published: August 2023

AbstractWe documented the relabeling process for a subset of a renowned database for emotion-in-context recognition, with the aim of promoting reliability in final labels. To this end, emotion categories were organized into eight groups, while a large number of participants was requested for tagging. A strict control strategy was performed along the experiments, whose duration was 13.45 minutes average per day. Annotators were free to participate in any of the daily experiments (the average number of participants was 28), and a Z-Score filtering technique was implemented to keep trustworthiness of annotations. As a result, the value of the agreement parameter Fleiss’ Kapa increasingly varied from slight to almost perfect, revealing a coherent diversity of the experiments. Our results support the hypothesis that a small number of categories and a large number of voters benefit reliability of annotations in contextual emotion imagery.
Effects of plant growth regulators and sucrose on proliferation and quality of embryogenic tissue in Picea pungens
Authors: Gao Fang , Cao Xi , Qin Caiyun , Chen Shigang , Cai Jufeng , Sun Changbin , Kong Lisheng , Tao Jing 
Published: August 2023

AbstractEmbryogenic tissue (ET) is important for genetic modification and plant re-generation. The proliferation ability and vigor of ET are crucial for plant propagation via somatic embryogenesis. In this study, ET was induced from mature zygotic embryos in blue spruce (Picea pungens Engelm.). There were significant differences in ET induction between two provenances, i.e. 78.8 ± 12.5% and 62.50 ± 12.8% respectively. Effects of 2,4-Dichlorophenoxy acetic acid (2,4-D), 6-Benzyl amino-purine (6-BA) and/or sucrose on ET proliferation and somatic embryo (SE) maturation were further investigated with four cell lines. The highest ET proliferation rate reached 1473.7 ± 556.0% biweekly. Concentrations of 2,4-D or 6-BA applied at tissue proliferation stage impacted SE maturation among the cell lines, whereas sucrose showed less effects. The highest rate, 408 ± 230 mature SEs/g FW, was achieved in SE maturation cultures. This research demonstrated that the culture conditions, i.e. the specific concentrations of 2,4-D and BA, at ET proliferation stage affected not only ET growth, but also the quality of ET for SE maturation. This study revealed the necessity and benefit in developing both the general and the genotype-specific protocols for efficient production of mature SEs, or somatic plants in blue spruce.
Both cell autonomous and non-autonomous processes modulate the association between replication timing and mutation rate
Authors: Vardi-Yaacov Oriya , Yaacov Adar , Rosenberg Shai , Simon Itamar 
Published: August 2023

AbstractCancer somatic mutations are the product of multiple mutational and repair processes, some of which are tightly associated with DNA replication. Mutation rates (MR) are known to be higher in late replication timing (RT) regions, but different processes can affect this association. Systematic analysis of the mutational landscape of 2787 tumors from 32 tumor types revealed that approximately one third of the tumor samples show weak association between replication timing and mutation rate. Further analyses revealed that those samples have unique mutational signatures and are enriched with mutations in genes involved in DNA replication, DNA repair and chromatin structure. Surprisingly, analysis of differentially expressed genes between weak and strong RT-MR association groups revealed that tumors with weak association are enriched with genes associated with cell–cell communication and the immune system, suggesting a non-autonomous response to DNA damage.
Monthly runoff prediction based on a coupled VMD-SSA-BiLSTM model
Authors: Zhang Xianqi , Wang Xin , Li Haiyang , Sun Shifeng , Liu Fang 
Published: August 2023

AbstractThe accurate prediction of monthly runoff in the lower reaches of the Yellow River is crucial for the rational utilization of regional water resources, optimal allocation, and flood prevention. This study proposes a VMD-SSA-BiLSTM coupled model for monthly runoff volume prediction, which combines the advantages of Variational Modal Decomposition (VMD) for signal decomposition and preprocessing, Sparrow Search Algorithm (SSA) for BiLSTM model parameter optimization, and Bi-directional Long and Short-Term Memory Neural Network (BiLSTM) for exploiting the bi-directional linkage and advanced characteristics of the runoff process. The proposed model was applied to predict monthly runoff at GaoCun hydrological station in the lower Yellow River. The results demonstrate that the VMD-SSA-BiLSTM model outperforms both the BiLSTM model and the VMD-BiLSTM model in terms of prediction accuracy during both the training and validation periods. The Root-mean-square deviation of VMD-SSA-BiLSTM model is 30.6601, which is 242.5124 and 39.9835 lower compared to the BiLSTM model and the VMD-BiLSTM model respectively; the mean absolute percentage error is 5.6832%, which is 35.5937% and 6.3856% lower compared to the other two models, respectively; the mean absolute error was 19.8992, which decreased by 136.7288 and 25.7274 respectively; the square of the correlation coefficient (R2) is 0.93775, which increases by 0.53059 and 0.14739 respectively; the Nash–Sutcliffe efficiency coefficient was 0.9886, which increased by 0.4994 and 0.1122 respectively. In conclusion, the proposed VMD-SSA-BiLSTM model, utilizing the sparrow search algorithm and bidirectional long and short-term memory neural network, enhances the smoothness of the monthly runoff series and improves the accuracy of point predictions. This model holds promise for the effective prediction of monthly runoff in the lower Yellow River.
Ecobiology of Haemagogus leucocelaenus arbovirus vector in the golden lion tamarin translocation area of Rio de Janeiro, Brazil
Authors: Machado Sergio Lisboa , de Mello Cecilia Ferreira , Silva Shayenne Olsson Freitas , Alencar Jeronimo 
Published: August 2023

AbstractSignificant pathogens that have resurfaced in humans originate from transmission from animal to human populations. In the Americas, yellow fever cases in humans are usually associated with spillover from non-human primates via mosquitoes. The present study characterized the prevalence of the yellow fever vector Haemagogus leucocelaenus in Rio de Janeiro, Brazil. The Atlantic Forest fragment chosen is an area of translocation of the golden lion tamarin (Leontopithecus rosalia), where 10 ovitraps were installed to collect mosquito eggs in Fazenda Três Irmãos, at Silva Jardim city, from March 2020 to October 2022. A total of 1514 eggs were collected, of which 1153 were viable; 50% belonged to medically important mosquito species and 24% to the yellow fever vector species, Hg. leucocelaenus. The months of December 2020 (n = 252), November 2021 (n = 188), and January 2022 (n = 252) had the highest densities of this vector. Haemagogus leucocelaenus was positively correlated with temperature (r = 0.303) and humidity (r = 0.48), with eggs hatching up to the 15th immersion with higher abundance of females. Implementing mosquito monitoring for arbovirus activity can help protect both the golden lion tamarin and human populations from the threat of arbovirus transmission.
Micro-mechanical and tribological behavior of Al/SiC/B4C/CNT hybrid nanocomposite
Authors: Nirala A. , Soren S. , Kumar Navneet , Khan Mohammad Amir , Islam Saiful , Khan Nadeem A 
Published: August 2023

AbstractThe aluminum nanocomposite is fabricated through squeeze stir casting method where CNT, SiC/B4C powder has been used as a reinforcement in an aluminum matrix. Squeeze action in stir casting opted due to proper reinforcement of 2 vol% of CNT in the matrix. The boron carbide and silicon carbide have been added by 8 and 12 vol% in the matrix. Uniform distribution of reinforcement and phase analysis has been shown by scanning electron microscopy (SEM) and XRD analysis. The formation of intermetallic compounds like Al3BC and Al4C3, dislocation forests, and the interaction of the reinforcement with the matrix are all confirmed by transmission electron microscopy (TEM). The micro-mechanical behavior of aluminum nanocomposites was investigated using nano indentation. The nano hardness, Vickers hardness, and Young's modulus of 12 vol% B4C compared with 12 vol% of SiC are increased by 12%, 23%, and 16%, respectively, and the same trend has been observed for the 8 vol% B4C reinforced composite. The model analysis for Young's modulus has been done and the experimental value for the modulus of elasticity of the composite are validated and not find such differences significantly. The surface topography was determined, furrow scratches and wear scars, and it was discovered that B4C reinforced composites have reduced stripping pits inside the wear marks, as well as lower wear width and depth. Wear analysis is essential because abrasive encounters result in substantial damage owing to larger pits and bigger wear scars.
Reduced brain connectivity along the autism spectrum controlled for familial confounding by co-twin design
Authors: Neufeld Janina , Maier Simon , Revers Mirian , Reisert Marco , Kuja-Halkola Ralf , Tebartz van Elst Ludger , Bölte Sven 
Published: August 2023

AbstractPrevious studies on brain connectivity correlates of autism have often focused on selective connections and yielded inconsistent results. By applying global fiber tracking and utilizing a within-twin pair design, we aimed to contribute to a more unbiased picture of white matter connectivity in association with clinical autism and autistic traits. Eighty-seven twin pairs (n = 174; 55% monozygotic; 24 with clinical autism) underwent diffusion tensor imaging. Linear regressions assessed within-twin pair associations between structural brain connectivity of anatomically defined brain regions and both clinical autism and autistic traits. These were explicitly adjusted for IQ, other neurodevelopmental/psychiatric conditions and multiple testing, and implicitly for biological sex, age, and all genetic and environmental factors shared by twins. Both clinical autism and autistic traits were associated with reductions in structural connectivity. Twins fulfilling diagnostic criteria for clinical autism had decreased brainstem-cuneus connectivity compared to their co-twins without clinical autism. Further, twins with higher autistic traits had decreased connectivity of the left hippocampus with the left fusiform and parahippocampal areas. These associations were also significant in dizygotic twins alone. Reduced brainstem-cuneus connectivity might point towards alterations in low-level visual processing in clinical autism while higher autistic traits seemed to be more associated with reduced connectivity in networks involving the hippocampus and the fusiform gyrus, crucial especially for processing of faces and other (higher order) visual processing. The observed associations were likely influenced by both genes and environment.