bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo
Authors: Benetti Natalia , Gouil Quentin , Tapia del Fierro Andres , Beck Tamara , Breslin Kelsey , Keniry Andrew , McGlinn Edwina , Blewitt Marnie E. 
Published: July 2022

AbstractParents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect onHoxgene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation ofHoxgenes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo.Hoxgenes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriateHoxgene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.
Prediction of elevation of substantial fluctuation in coal seam floor based on surface spline function and its derivative
Authors: Yang Zhenwei , Xu Junyi , Xu Zhaofeng , Chen Jiangfeng 
Published: July 2022

AbstractWith the increasing depth of coal mining, the geological stress and structure becomes more and more complex. The elevation of No.8 coal floor significantly undulates in the studied coal mine. Even though a lot of boreholes have been drilled, it remains difficult to predict the spatial distribution features and it becomes challenging to plan the tunnel for the working face. Consequently, there has been a great loss of production in the coal mine, therefore, it is of great significance to study the prediction method for coal floor elevation of the working face. The surface spline function can be regarded as an infinite flat plate deformation in pure bending. The fluctuation of the coal floor can be considered to be the result of multi-period tectonic stress applied on the coal seam, so, the prediction of elevation of the coal floor with surface spline method is feasible. An advantage of surface spline method is that any order differentiable smooth surface can be obtained without regular known lattice and boundary derivatives. In the paper, the complete expression of surface spline function is derived, which is used to predict the elevation of No.8 coal floor of the coal mine. The results show that the trend of elevation of the coal floor can be extrapolated by known data, and the maximum error is 20 m, the minimum error is 0 m, and the error of 80% of the data is less than 3 m. The general trend of the coal floor has been predicted well. However, local peaks and valleys could not be predicted correctly, therefore, the first and second order derivative are projected to predict the peaks and valleys in the head of the tunneling.
Ascent of the conus medullaris in human foetuses: a systematic review and meta-analysis
Authors: Costa Almeida Lucas , de Souza Figueiredo Yasmin Juliany , Pinheiro Zylberman André , Garção Diogo Costa 
Published: July 2022

AbstractThe aim of the present systematic review and meta-analysis was to identify when the ascent of the conus medullaris occurs in human foetuses considering differences in evaluation methods and sample characteristics. Five databases were searched for relevant articles using different combinations of keywords. Article selection and data extraction were performed independently by two reviewers. Disagreements were resolved by a third reviewer. The variables were distributed into four groups according to the gestational age of the specimens: I (13–18 weeks); II (19–25 weeks); III (26–32 weeks); IV (33 weeks to the probable date of birth). Eighteen articles were included. The majority used imaging exams as the evaluation method. Cadaveric dissections were reported in the remaining articles. Only morphological studies were included in the meta-analysis. Significant ascent occurs between groups I and III as well as groups II and IV. Despite the considerable heterogeneity among the studies included in the present review, the findings enabled the determination that the conus medullaris reaches its normal birth level by the 26th week. Further analyses should be performed based on nationality and ethnicity to diminish the heterogeneity of the data.
Altered genome-wide hippocampal gene expression profiles following early life lead exposure and their potential for reversal by environmental enrichment
Authors: Singh G. , Singh V. , Kim T. , Ertel A. , Fu W. , Schneider J. S. 
Published: July 2022

AbstractEarly life lead (Pb) exposure is detrimental to neurobehavioral development. The quality of the environment can modify negative influences from Pb exposure, impacting the developmental trajectory following Pb exposure. Little is known about the molecular underpinnings in the brain of the interaction between Pb and the quality of the environment. We examined relationships between early life Pb exposure and living in an enriched versus a non-enriched postnatal environment on genome-wide transcription profiles in hippocampus CA1. RNA-seq identified differences in the transcriptome of enriched vs. non-enriched Pb-exposed animals. Most of the gene expression changes associated with Pb exposure were reversed by enrichment. This was also true for changes in upstream regulators, splicing events and long noncoding RNAs. Non-enriched rats also had memory impairments; enriched rats had no deficits. The results demonstrate that an enriched environment has a profound impact on behavior and the Pb-modified CA1 transcriptome. These findings show the potential for interactions between Pb exposure and the environment to result in significant transcriptional changes in the brain and, to the extent that this may occur in Pb-exposed children, could influence neuropsychological/educational outcomes, underscoring the importance for early intervention and environmental enrichment for Pb-exposed children.
Polarimetric biomarkers of peri-tumoral stroma can correlate with 5-year survival in patients with left-sided colorectal cancer
Authors: Lad Jigar , Serra Stefano , Quereshy Fayez , Khorasani Mohammadali , Vitkin Alex 
Published: July 2022

AbstractUsing a novel variant of polarized light microscopy for high-contrast imaging and quantification of unstained histology slides, the current study assesses the prognostic potential of peri-tumoral collagenous stroma architecture in 32 human stage III colorectal cancer (CRC) patient samples. We analyze three distinct polarimetrically-derived images and their associated texture features, explore different unsupervised clustering algorithm models to group the data, and compare the resultant groupings with patient survival. The results demonstrate an appreciable total accuracy of ~ 78% with significant separation (p < 0.05) across all approaches for the binary classification of 5-year patient survival outcomes. Surviving patients preferentially belonged to Cluster 1 irrespective of model approach, suggesting similar stromal microstructural characteristics in this sub-population. The results suggest that polarimetrically-derived stromal biomarkers may possess prognostic value that could improve clinical management/treatment stratification in CRC patients.
High-throughput screening of stable and efficient double inorganic halide perovskite materials by DFT
Authors: Diao Xinfeng , Diao Yongxin , Tang Yanlin , Zhao Gangling , Gu Qinzhong , Xie Yu , Shi Yebai , Zhu Ping , Zhang Liang 
Published: July 2022

AbstractPerovskite solar cells have become the most promising third-generation solar cells because of their superior physical–chemical properties and high photoelectric conversion efficiency. However, the current obstacles to commercialization of perovskite solar cells are their poor stability and harmful elements. How to find high-efficiency, high-stability and non-toxic perovskite materials from thousands of possible perovskite crystals is the key to solve this problem. In this paper, the inorganic halide double perovskite A2BX6 and its crystal structure are considered, and the data mining algorithm in informatics is introduced into the high-throughput computing data to analyze various elements in nature to study the perovskite materials that can meet the requirements of high performance. The photoelectric conversion properties and stability of 42 inorganic double perovskite materials are studied based on density functional theory (DFT). The results show that the tolerance factors of 39 crystals are between 0.8 and 1.10, indicating that these crystals have stable perovskite structure. In addition, the dielectric function, PDOS, elastic modulus, shear modulus and poison’s ratio of these crystals are analyzed. According to the above theoretical simulation results, three candidate materials for ideal light absorption are presented. This can provide a theoretical basis for the industrial application of perovskite solar cells.
Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation
Authors: Anamizu Kotaro , Takase Ryuichi , Hio Mamoru , Watanabe Daisuke , Mikami Bunzo , Hashimoto Wataru 
Published: July 2022

AbstractGram-negative Sphingomonas sp. strain A1 exhibits positive chemotaxis toward acidic polysaccharide pectin. SPH1118 has been identified as a pectin-binding protein involved in both pectin chemotaxis and assimilation. Here we show tertiary structures of SPH1118 with six different conformations as determined by X-ray crystallography. SPH1118 consisted of two domains with a large cleft between the domains and substrates bound to positively charged and aromatic residues in the cleft through hydrogen bond and stacking interactions. Substrate-free SPH1118 adopted three different conformations in the open form. On the other hand, the two domains were closed in substrate-bound form and the domain closure ratio was changed in response to the substrate size, suggesting that the conformational change upon binding to the substrate triggered the expression of pectin chemotaxis and assimilation. This study first clarified that the solute-binding protein with dual functions recognized the substrate through flexible conformational changes in response to the substrate size.
A pilot study to understand the relationship between cortical arousals and leg movements during sleep
Authors: Bansal Kanika , Garcia Javier , Feltch Cody , Earley Christopher , Robucci Ryan , Banerjee Nilanjan , Brooks Justin 
Published: July 2022

AbstractLeg movements during sleep occur in patients with sleep pathology and healthy individuals. Some (but not all) leg movements during sleep are related to cortical arousals which occur without conscious awareness but have a significant effect of sleep fragmentation. Detecting leg movements during sleep that are associated with cortical arousals can provide unique insight into the nature and quality of sleep. In this study, a novel leg movement monitor that uses a unique capacitive displacement sensor and 6-axis inertial measurement unit, is used in conjunction with polysomnography to understand the relationship between leg movement and electroencephalogram (EEG) defined cortical arousals. In an approach that we call neuro-extremity analysis, directed connectivity metrics are used to interrogate causal linkages between EEG and leg movements measured by the leg movement sensors. The capacitive displacement measures were more closely related to EEG-defined cortical arousals than inertial measurements. Second, the neuro-extremity analysis reveals a temporally evolving connectivity pattern that is consistent with a model of cortical arousals in which brainstem dysfunction leads to near-instantaneous leg movements and a delayed, filtered signal to the cortex leading to the cortical arousal during sleep.
The prognostic value of neutrophil-to-lymphocyte ratio in cholangiocarcinoma: a systematic review and meta-analysis
Authors: Liu Dong , Heij Lara R. , Czigany Zoltan , Dahl Edgar , Dulk Marcel den , Lang Sven A. , Ulmer Tom F. , Neumann Ulf P. , Bednarsch Jan 
Published: July 2022

AbstractThe neutrophil-to-lymphocyte ratio (NLR) is used as biomarker in malignant diseases showing significant association with poor oncological outcomes. The main research question of the present study was whether NLR has also prognostic value in cholangiocarcinoma patients (CCA). A systematic review was carried out to identify studies related to NLR and clinical outcomes in CCA evaluating the literature from 01/2000 to 09/2021. A random-effects model, pooled hazard ratios (HR) and 95% confidence interval (CI) were used to investigate the statistical association between NLR and overall survival (OS) as well as disease-free survival (DFS). Subgroup analyses, evaluation of sensitivity and risk of bias were further carried out. 32 studies comprising 8572 patients were eligible for this systematic review and meta-analysis. The pooled outcomes revealed that high NLR prior to treatment is prognostic for poor OS (HR 1.28, 95% CI 1.18–1.38, p < 0.01) and DFS (HR 1.39, 95% CI 1.17–1.66, p < 0.01) with meaningful HR values. Subgroup analysis revealed that this association is not significantly affected by the treatment modality (surgical vs. non-surgical), NLR cut-off values, age and sample size of the included studies. Given the likelihood of NLR to be prognostic for reduced OS and DFS, pre-treatment NLR might serve as a useful biomarker for poor prognosis in patients with CCA and therefore facilitate clinical management.
Catulin reporter marks a heterogeneous population of invasive breast cancer cells with some demonstrating plasticity and participating in vascular mimicry
Authors: Gielata Mateusz , Karpińska Kamila , Gwiazdowska Aleksandra , Boryń Łukasz , Kobielak Agnieszka 
Published: July 2022

AbstractBreast cancer is the most commonly diagnosed cancer in women worldwide. The activation of partial or more complete epithelial–mesenchymal transition in cancer cells enhances acquisition of invasive behaviors and expands their generation of cancer stem cells. Increased by EMT plasticity of tumor cells could promote vascular mimicry, a newly defined pattern of tumor microvascularization by which aggressive tumor cells can form vessel-like structures themselves. VM is strongly associated with a poor prognosis, but biological features of tumor cells that form VM remains unknown. Here we show that catulin is expressed in human BC samples and its expression correlates with the tumor progression. Ablation of catulin in hBC cell lines decreases their invasive potential in the 3D assays. Using a novel catulin promoter based reporter we tracked and characterized the small population of invasive BC cells in xenograft model. RNAseq analysis revealed enrichment in genes important for cellular movement, invasion and interestingly for tumor-vasculature interactions. Analysis of tumors unveiled that catulin reporter marks not only invasive cancer cells but also rare population of plastic, MCAM positive cancer cells that participate in vascular mimicry. Ablation of catulin in the xenograft model revealed deregulation of genes involved in cellular movement, and adhesive properties with striking decrease in CD44 which may impact stemness potential, and plasticity of breast cancer cells. These findings show directly that some plastic tumor cells can change the fate into endothelial-like, expressing MCAM and emphasize the importance of catulin in this process and breast cancer progression.
Altered resting-state functional connectivity within corticostriatal and subcortical-striatal circuits in chronic pain
Authors: Park Su Hyoun , Baker Anne K. , Krishna Vinit , Mackey Sean C. , Martucci Katherine T. 
Published: July 2022

AbstractBrain corticostriatal circuits are important for understanding chronic pain and highly relevant to motivation and cognitive processes. It has been demonstrated that in patients with chronic back pain, altered nucleus accumbens (NAcc)—medial prefrontal cortex (MPFC) circuit fMRI-based activity is predictive of patient outcome. We evaluated the NAcc-MPFC circuit in patients with another chronic pain condition, fibromyalgia, to extend these important findings. First, we compared fMRI-based NAcc-MPFC resting-state functional connectivity in patients with fibromyalgia (N = 32) vs. healthy controls (N = 37). Compared to controls, the NAcc-MPFC circuit’s connectivity was significantly reduced in fibromyalgia. In addition, within the fibromyalgia group, NAcc-MPFC connectivity was significantly correlated with trait anxiety. Our expanded connectivity analysis of the NAcc to subcortical brain regions showed reduced connectivity of the right NAcc with mesolimbic circuit regions (putamen, thalamus, and ventral pallidum) in fibromyalgia. Lastly, in an exploratory analysis comparing our fibromyalgia and healthy control cohorts to a separate publicly available dataset from patients with chronic back pain, we identified reduced NAcc-MPFC connectivity across both the patient groups with unique alterations in NAcc-mesolimbic connectivity. Together, expanding upon prior observed alterations in brain corticostriatal circuits, our results provide novel evidence of altered corticostriatal and mesolimbic circuits in chronic pain.
Genome-wide variance quantitative trait locus analysis suggests small interaction effects in blood pressure traits
Authors: Shi Gang 
Published: July 2022

AbstractGenome-wide variance quantitative trait loci (vQTL) analysis complements genome-wide association study (GWAS) and has the potential to identify novel variants associated with the trait, explain additional trait variance and lead to the identification of factors that modulate the genetic effects. I conducted genome-wide analysis of the UK Biobank data and identified 27 vQTLs associated with systolic blood pressure (SBP), diastolic blood pressure (DBP) and pulse pressure (PP). The top single-nucleotide polymorphisms (SNPs) are enriched for expression QTLs (eQTLs) or splicing QTLs (sQTLs) annotated by GTEx, suggesting their regulatory roles in mediating the associations with blood pressure (BP). Of the 27 vQTLs, 14 are known BP-associated QTLs discovered by GWASs. The heteroscedasticity effects of the 13 novel vQTLs are larger than their genetic main effects, which were not detected by existing GWASs. The total R-squared of the 27 top SNPs due to variance heteroscedasticity is 0.28%, compared with 0.50% owing to their main effects. The overall effect size of the variance heteroscedasticity is small in GWAS SNPs compared with their main effects. For the 411, 384 and 285 GWAS SNPs associated with SBP, DBP and PP, respectively, their heteroscedasticity effects were 0.52%, 0.43%, and 0.16%, and their main effects were 5.13%, 5.61%, and 3.75%, respectively. The number and effects of the vQTLs are small, which suggests that the effects of gene–environment and gene–gene interactions are small. The main effects of the SNPs remain the major source of genetic variance for BP, which would probably be true for other complex traits as well.
The presence of adjacent others facilitates interpersonal neural synchronization in the left prefrontal cortex during a simple addition task
Authors: Miura Naoki , Noguchi Satsuki 
Published: July 2022

AbstractThe hyperscanning technique, that is, simultaneous measurement of neural signals in more than one person, is a powerful research tool for understanding humans’ social interactions. In recent years, many studies have investigated interpersonal neural synchronization during various types of communication processes. However, there has been little focus on the impact of the presence of others without explicit social interaction, despite the mere presence of others having been suggested as influencing behavior. In this study, we clarify whether neural signals during a self-paced, repeated, addition task are synchronized when another individual is adjacent without direct interaction. Twenty pairs of participants were measured using a hyperscanning approach with near-infrared spectroscopy. The results show that interpersonal neural synchronization of the task-related signal in the left forehead region was enhanced under the condition of being adjacent to another participant. By contrast, a significant decrease in neural synchronization in the center of the forehead region, where increased neural synchronization is often reported in explicit communication, was observed. Thus, the results indicate that the adjacency of others modulates interpersonal neural synchronization in the task-related signal, and the effect on cognitive processing is different from that of explicit social interaction.
Density estimates reveal that fragmented landscapes provide important habitat for conserving an endangered mesopredator, the spotted-tailed quoll
Authors: Henderson T. , Fancourt B. A. , Rajaratnam R. , Vernes K. , Ballard G. 
Published: July 2022

AbstractNative predators are increasingly exposed to habitat loss and fragmentation globally. When developing conservation and management strategies, it is important to determine whether fragmented landscapes can still support similar predator densities to intact areas, and thereby constitute important habitat for these species. The spotted-tailed quoll (Dasyurus maculatus) is an endangered Australian mesopredator that is often considered to be forest-dependent. While quolls are known to occur in some fragmented forest landscapes, it is unclear whether these areas represent sub-optimal habitat where quolls merely persist, or whether quolls can still occur at densities similar to those observed in intact forest landscapes. We used camera traps to detect quolls in both a fragmented and intact forested site, over three years. We used each quoll’s unique pelage pattern to identify individual quolls and estimate population density at each site. We were able to assign more than 94% of quoll image sequences across both sites to identify 173 individuals during the study. Density estimates of 0.13–0.66 quolls per km2at the fragmented site were comparable to estimates of 0.28–0.48 quolls per km2at the intact site. Our results highlight the importance of retaining and protecting forest fragments for the conservation of endangered quoll populations.
Increased temporal stride variability contributes to impaired gait coordination after stroke
Authors: Patel Prakruti , Enzastiga Diana , Casamento-Moran Agostina , Christou Evangelos A. , Lodha Neha 
Published: July 2022

AbstractHeightened motor variability is a prominent impairment after stroke. During walking, stroke survivors show increased spatial and temporal variability; however, the functional implications of increased gait variability are not well understood. Here, we determine the effect of gait variability on the coordination between lower limbs during overground walking in stroke survivors. Ambulatory stroke survivors and controls walked at a preferred pace. We measured stride length and stride time variability, and accuracy and consistency of anti-phase gait coordination with phase coordination index (PCI). Stroke survivors showed increased stride length variability, stride time variability, and PCI compared with controls. Stride time variability but not stride length variability predicted 43% of the variance in PCI in the stroke group. Stride time variability emerged as a significant predictor of error and consistency of phase. Despite impaired spatial and temporal gait variability following stroke, increased temporal variability contributes to disrupted accuracy and consistency of gait coordination. We provide novel evidence that decline in gait coordination after stroke is associated with exacerbated stride time variability, but not stride length variability. Temporal gait variability may be a robust indicator of the decline in locomotor function and an ideal target for motor interventions that promote stable walking after stroke.