bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression study in monocytes: evidence of inflammatory dysregulation in early-onset obsessive-compulsive disorder
Authors: Rodríguez Natalia , Lázaro Luisa , Ortiz Ana E. , Morer Astrid , Martínez-Pinteño Albert , Segura Alex G. , Gassó Patricia , Mas Sergi 
Published: March 2022

AbstractObsessive-compulsive disorder (OCD) has a complex etiology that seems to include immune dysfunction and alterations in circulating monocytes. To investigate the immune basis and the functional dysregulation of monocytes in this disease, we analyzed gene expression in the peripheral monocytes of pediatric patients with OCD (N = 102) compared to controls (N = 47). We examined gene expression in primary cultures of peripheral monocytes from participants, under basal conditions and under exposure to lipopolysaccharide (LPS) to stimulate immune response. Whole-genome expression was assessed in 8 patients and 8 controls. Differentially expressed genes were identified followed by protein-protein interaction network construction and functional annotation analysis to identify the genes and biological processes that are altered in the monocytes of OCD patients. We also explored the expression levels of selected genes in monocytes from the other participants using qPCR. Several changes in gene expression were observed in the monocytes of OCD patients, with several immune processes involved under basal conditions (antigen processing and presentation, regulation of immune system and leukocyte cell adhesion) and after LPS stimulation (immune and inflammatory response, cytokine production and leukocyte activation). Despite the qPCR analysis provided no significant differences between patients and controls, high correlations were observed between the expression levels of some of the genes and inflammatory markers (i.e., T helper 17 and regulatory T cell levels, total monocyte and proinflammatory monocyte subset levels, and the cytokine production by resting and stimulated monocytes) of the study participants. Our findings provide more evidence of the involvement of monocyte dysregulation in early-onset OCD, indicating a proinflammatory predisposition and an enhanced immune response to environmental triggers.
Tctp regulates the level and localization of Foxo for cell growth in Drosophila
Authors: Nam Sujin , Le Thao Phuong , Chung SeYeon , Choi Kwang-Wook 
Published: March 2022

AbstractRegulation of cell size is crucial for organ development. Insulin signaling regulates organ size by antagonizing the subgroup O of forkhead box transcription factor (Foxo) through 14-3-3 in Drosophila. However, mechanisms for controlling the level and the nuclear localization of Foxo in developing organs are not well understood. Here, we investigate the role of Drosophila Translationally controlled tumor protein (Tctp) and its interacting partner 14-3-3 in Foxo regulation during organ development. Foxo overexpression in the developing eye disc results in growth inhibition. We show that Tctp overexpression antagonizes the Foxo effect by downregulating the Foxo level in the eye disc. Foxo overexpression or knockdown of Tctp in the larval salivary gland results in reduced gland size, mainly due to reduced cell size by defects in endoreplication. Whereas 14-3-3ζ knockdown has a negligible effect, knockdown of 14-3-3ε mimics the effect of Foxo overexpression or Tctp knockdown, suggesting an isoform-specific role of 14-3-3. Unlike nuclear enrichment of the endogenous Foxo in the salivary gland, overexpressed Foxo protein is largely distributed in the cytoplasm, and this mislocalization is restored by Tctp overexpression. Opposite to the effect of Tctp overexpression, Tctp knockdown increases cytoplasmic Foxo levels while decreasing nuclear Foxo levels. Together, our data suggest that Tctp and 14-3-3ε play critical roles in cell growth by reducing cytoplasmic Foxo levels. Knockdown of human TCTP also elevates the level of cytoplasmic FOXO1 in HeLa cells, suggesting that human TCTP may have a conserved role in downregulating FOXO in human cells.
Fibre optic distributed acoustic sensing of volcanic events
Authors: Jousset Philippe , Currenti Gilda , Schwarz Benjamin , Chalari Athena , Tilmann Frederik , Reinsch Thomas , Zuccarello Luciano , Privitera Eugenio , Krawczyk Charlotte M. 
Published: March 2022

AbstractUnderstanding physical processes prior to and during volcanic eruptions has improved significantly in recent years. However, uncertainties about subsurface structures distorting observed signals and undetected processes within the volcano prevent volcanologists to infer subtle triggering mechanisms of volcanic phenomena. Here, we demonstrate that distributed acoustic sensing (DAS) with optical fibres allows us to identify volcanic events remotely and image hidden near-surface volcanic structural features. We detect and characterize strain signals associated with explosions and locate their origin using a 2D-template matching between picked and theoretical wave arrival times. We find evidence for non-linear grain interactions in a scoria layer of spatially variable thickness. We demonstrate that wavefield separation allows us to incrementally investigate the ground response to various excitation mechanisms. We identify very small volcanic events, which we relate to fluid migration and degassing. Those results provide the basis for improved volcano monitoring and hazard assessment using DAS.
Northwestern Pacific tropical cyclone activity enhanced by increased Asian dust emissions during the Little Ice Age
Authors: Yang Yang , Piper David J. W. , Xu Min , Gao Jianhua , Jia Jianjun , Normandeau Alexandre , Chu Dongdong , Zhou Liang , Wang Ya Ping , Gao Shu 
Published: March 2022

AbstractInstrumental records reveal that intense tropical cyclone (TC) activity varies with tropical sea surface temperature (SST) on annual-decadal scales. Drivers of intense TC activity at the centennial-millennial scale are less clear, due to the sparseness of pre-observational reconstructions. Here, we present a new 2 kyr continuous activity record of intense TCs from offshore eastern China. Our reconstruction indicates that this site witnessed enhanced TC activity during relatively warm periods, with a widespread increase in TC activity during the later part of the Little Ice Age. This latter observation reveals that enhanced TC activity was synchronized with increased Asian dust emissions during the Little Ice Age. TC activity was also lower in the late Roman Warm Period, when SST was higher but Asian dust emissions were lower than in the early phase. Such patterns suggest a centennial-millennial link between TC climatology and a combination of SST changes and Asian dust levels.
Double helical π-aggregate nanoarchitectonics for amplified circularly polarized luminescence
Authors: Wang Yuan , Niu Dian , Ouyang Guanghui , Liu Minghua 
Published: March 2022

AbstractThe canonical double helical π-stacked array of base pairs within DNA interior has inspired the interest in supramolecular double helical architectures with advanced electronic, magnetic and optical functions. Here, we report a selective-recognized and chirality-matched co-assembly strategy for the fabrication of fluorescent π-amino acids into double helical π-aggregates, which show exceptional strong circularly polarized luminescence (CPL). The single crystal structure of the optimal combination of co-assemblies shows that the double-stranded helical organization of these π-amino acids is cooperatively assisted by both CH-π and hydrogen-bond arrays with chirality match. The well-defined spatial arrangement of the π-chromophores could effectively suppress the non-radiative decay pathways and facilitate chiral exciton couplings, leading to superior CPL with a strong figure of merit (glum = 0.14 and QY = 0.76). Our findings might open a new door for developing DNA-inspired chiroptical materials with prominent properties by enantioselective co-assembly initiated double helical π-aggregation.
SHAPE-guided RNA structure homology search and motif discovery
Authors: Morandi Edoardo , van Hemert Martijn J. , Incarnato Danny 
Published: March 2022

AbstractThe rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.
Associations with response to Poly(ADP-ribose) Polymerase (PARP) inhibitors in patients with metastatic breast cancer
Authors: Desnoyers A. , Nadler M. , Wilson B. E. , Stajer S. , Amir E. 
Published: March 2022

AbstractPARP inhibitors (PARPi) have modest antitumor activity in patients with advanced breast cancer and mutation in BRCA. It is unclear whether some subgroups derive greater benefit from treatment. MEDLINE and EMBASE were searched from inception to March 2021 to identify trials of PARPi in patients with metastatic breast cancer. Objective response rate (ORR) and clinical benefit rate (CBR) to PARPi were extracted and pooled in a meta-analysis using the Mantel Haenszel random effects model. Meta-regression explored the influence of patient and tumor characteristics on ORR and CBR. For randomized trials, hazard ratio comparing PARPi to control therapy were pooled using inverse variance and random effects. Analysis included 43 studies comprising 2409 patients. Among these, 1798 (75%) patients had BRCA mutations and 1146 (48%) were triple negative. In 10 studies (28%; n = 680 patients), the PARPi was given in combination with platinum-based chemotherapy. Weighted mean ORR was 45%; 64% when combined with platinum vs 37% with PARPi monotherapy (p < 0.001). Previous platinum-based chemotherapy was associated with lower ORR (p = 0.02). Compared to standard chemotherapy, progression-free survival was improved (HR 0.64, p < 0.001), but there was no difference in overall survival (HR 0.87, p = 0.06). There were no differences in ORR or CBR between BRCA1 and BRCA2 mutations. PARPi are more active in combination with platinum than as monotherapy, with lower response if given as monotherapy after platinum exposure. Significant improvements in ORR translated to modest improvement in progression-free, but not overall survival. There was no association between ORR and BRCA mutations.
Surrounding road density of child care centers in Australia
Authors: Han Chunlei , Xu Rongbin , Wei Xiaoyan , Zhang Yajuan , Liu Jiahui , Zhang Yuguo , Ye Tingting , Wang Siwei , Yu Wenhua , Guo Suying , Han Kun , Ding Yimin , Wang Jinfeng , Guo Yuming , Li Shanshan 
Published: March 2022

AbstractHigh surrounding road density could increase traffic-related air pollution, noise and the risk of traffic injuries, which are major public health concerns for children. We collected geographical data for all childcare centers (16,146) in Australia and provided the data on the road density surrounding them. The road density was represented by the child care center’s nearest distance to main road and motorway, and the length of main road/motor way within 100~1000-meter buffer zone surrounding the child care center. We also got the data of PM2.5 concentration from 2013 to 2018 and standard Normalized Difference Vegetation Index (NDVI) data from 2013 to 2019 according to the longitude and latitude of the child care centers. This data might help researchers to evaluate the health impacts of road density on child health, and help policy makers to make transportation, educational and environmental planning decisions to protect children from exposure to traffic-related hazards in Australia.
A residential labeled dataset for smart meter data analytics
Authors: Pereira Lucas , Costa Donovan , Ribeiro Miguel 
Published: March 2022

AbstractSmart meter data is a cornerstone for the realization of next-generation electrical power grids by enabling the creation of novel energy data-based services like providing recommendations on how to save energy or predictive maintenance of electric appliances. Most of these services are developed on top of advanced machine-learning algorithms, which rely heavily on datasets for training, testing, and validation purposes. A limitation of most existing datasets, however, is the scarcity of labels. The SustDataED2 dataset described in this paper contains 96 days of aggregated and individual appliance consumption from one household in Portugal. The current and voltage waveforms were sampled at 12.8 kHz, and the individual consumption of 18 appliances was sampled at 0.5 Hz. The dataset also contains the timestamps of the ON-OFF transitions of the monitored appliances for the entire deployment duration, providing the necessary ground truth for the evaluation of machine learning problems, particularly Non-Intrusive Load Monitoring. The data is accessible in easy-to-use audio and comma-separated formats.
Tissue-engineered collagenous fibrous cap models to systematically elucidate atherosclerotic plaque rupture
Authors: Wissing T. B. , Van der Heiden K. , Serra S. M. , Smits A. I. P. M. , Bouten C. V. C. , Gijsen F. J. H. 
Published: March 2022

AbstractA significant amount of vascular thrombotic events are associated with rupture of the fibrous cap that overlie atherosclerotic plaques. Cap rupture is however difficult to predict due to the heterogenous composition of the plaque, unknown material properties, and the stochastic nature of the event. Here, we aim to create tissue engineered human fibrous cap models with a variable but controllable collagen composition, suitable for mechanical testing, to scrutinize the reciprocal relationships between composition and mechanical properties. Myofibroblasts were cultured in 1 × 1.5 cm-sized fibrin-based constrained gels for 21 days according to established (dynamic) culture protocols (i.e. static, intermittent or continuous loading) to vary collagen composition (e.g. amount, type and organization). At day 7, a soft 2 mm ∅ fibrin inclusion was introduced in the centre of each tissue to mimic the soft lipid core, simulating the heterogeneity of a plaque. Results demonstrate reproducible collagenous tissues, that mimic the bulk mechanical properties of human caps and vary in collagen composition due to the presence of a successfully integrated soft inclusion and the culture protocol applied. The models can be deployed to assess tissue mechanics, evolution and failure of fibrous caps or complex heterogeneous tissues in general.
Tomato (Solanum lycopersicum L.) accumulation and allergenicity in response to nickel stress
Authors: Roccotiello Enrica , Nicosia Elena , Pierdonà Lorenzo , Marescotti Pietro , Ciardiello Maria Antonietta , Giangrieco Ivana , Mari Adriano , Zennaro Danila , Dozza Denise , Brancucci Michele , Mariotti Mauro 
Published: March 2022

AbstractVegetables represent a major source of Ni exposure. Environmental contamination and cultural practices can increase Ni amount in tomato posing significant risk for human health. This work assesses the tomato (Solanum lycopersicum L.) response to Ni on the agronomic yield of fruits and the related production of allergens. Two cultivars were grown in pots amended with Ni 0, 30, 60, 120, and 300 mg kg−1, respectively. XRF and ICP-MS analyses highlighted the direct increase of fruit Ni content compared to soil Ni, maintaining a stable biomass. Leaf water content increased at Ni 300 mg kg−1. Total protein content and individual allergenic components were investigated using biochemical (RP-HPLC and N-terminal amino acid sequencing) and immunological (inhibition tests of IgE binding by SPHIAa assay on the FABER testing system) methodologies. Ni affected the fruit tissue concentration of pathogenesis-related proteins and relevant allergens (LTP, profilin, Bet v 1-like protein and TLP). This study elucidates for the first time that tomato reacts to exogenous Ni, uptaking the metal while changing its allergenic profiles, with potential double increasing of exposure risks for consumers. This evidence highlighted the importance of adequate choice of low-Ni tomato cultivars and practices to reduce Ni uptake by potentially contaminated matrices.
A machine learning model to estimate myocardial stiffness from EDPVR
Authors: Babaei Hamed , Mendiola Emilio A. , Neelakantan Sunder , Xiang Qian , Vang Alexander , Dixon Richard A. F. , Shah Dipan J. , Vanderslice Peter , Choudhary Gaurav , Avazmohammadi Reza 
Published: March 2022

AbstractIn-vivo estimation of mechanical properties of the myocardium is essential for patient-specific diagnosis and prognosis of cardiac disease involving myocardial remodeling, including myocardial infarction and heart failure with preserved ejection fraction. Current approaches use time-consuming finite-element (FE) inverse methods that involve reconstructing and meshing the heart geometry, imposing measured loading, and conducting computationally expensive iterative FE simulations. In this paper, we propose a machine learning (ML) model that feasibly and accurately predicts passive myocardial properties directly from select geometric, architectural, and hemodynamic measures, thus bypassing exhaustive steps commonly required in cardiac FE inverse problems. Geometric and fiber-orientation features were chosen to be readily obtainable from standard cardiac imaging protocols. The end-diastolic pressure-volume relationship (EDPVR), which can be obtained using a single-point pressure-volume measurement, was used as a hemodynamic (loading) feature. A comprehensive ML training dataset in the geometry-architecture-loading space was generated, including a wide variety of partially synthesized rodent heart geometry and myofiber helicity possibilities, and a broad range of EDPVRs obtained using forward FE simulations. Latin hypercube sampling was used to create 2500 examples for training, validation, and testing. A multi-layer feed-forward neural network (MFNN) was used as a deep learning agent to train the ML model. The model showed excellent performance in predicting stiffness parameters$$a_f$$afand$$b_f$$bfassociated with fiber direction ($$R^2_{a_f}=99.471\%$$Raf2=99.471%and$$R^2_{b_f}=92.837\%$$Rbf2=92.837%). After conducting permutation feature importance analysis, the ML performance further improved for$$b_f$$bf($$R^2_{b_f}=96.240\%$$Rbf2=96.240%), and the left ventricular volume and endocardial area were found to be the most critical geometric features for accurate predictions. The ML model predictions were evaluated further in two cases: (i) rat-specific stiffness data measured using ex-vivo mechanical testing, and (ii) patient-specific estimation using FE inverse modeling. Excellent agreements with ML predictions were found for both cases. The trained ML model offers a feasible technology to estimate patient-specific myocardial properties, thus, bridging the gap between EDPVR, as a confounded organ-level metric for tissue stiffness, and intrinsic tissue-level properties. These properties provide incremental information relative to traditional organ-level indices for cardiac function, improving the clinical assessment and prognosis of cardiac diseases.
Identification, analysis of deleterious SNPs of the human GSR gene and their effects on the structure and functions of associated proteins and other diseases
Authors: Vyas Bharti , Bhowmik Ratul , Akhter Mymoona , Ahmad Farhan Jalees 
Published: March 2022

AbstractHereditary glutathione reductase deficiency, caused by mutations of the GSR gene, is an autosomal recessive disorder characterized by decreased glutathione disulfide (GSSG) reduction activity and increased thermal instability. This study implemented computational analysis to screen the most likely mutation that might be associated with hereditary glutathione reductase deficiency and other diseases. Using ten online computational tools, the study revealed four nsSNPs among the 17 nsSNPs identified as most deleterious and disease associated. Structural analyses and evolutionary confirmation study of native and mutant GSR proteins using the HOPE project and ConSruf. HOPE revealed more flexibility in the native GSR structure than in the mutant structure. The mutation in GSR might be responsible for changes in the structural conformation and function of the GSR protein and might also play a significant role in inducing hereditary glutathione reductase deficiency. LD and haplotype studies of the gene revealed that the identified variations rs2978663 and rs8190955 may be responsible for obstructive heart defects (OHDs) and hereditary anemia, respectively. These interethnic differences in the frequencies of SNPs and haplotypes might help explain the unpredictability that has been reported in association studies and can contribute to predicting the pharmacokinetics and pharmacodynamics of drugs that make use of GSR.
Variant landscape of the RYR1 gene based on whole genome sequencing of the Singaporean population
Authors: Foo Claribel Tian Yu , To Yi Hui , Irwanto Astrid , Ng Alvin Yu-Jin , Yan Benedict , Chew Sophia Tsong Huey , Liu Jianjun , Ti Lian Kah 
Published: March 2022

AbstractThe RYR1 gene codes for a ryanodine receptor which is a calcium release channel in the skeletal muscle sarcoplasmic reticulum. It is associated with Malignant Hyperthermia (MH) and congenital myopathies including Central Core Disease (CCD), Multiminicore Disease (MMD) and Congenital Fibre-Type Disproportion (CFTD). There is currently little information on the epidemiology of RYR1 variants in Asians. Our study aims to describe the RYR1 variant landscape in a Singapore cohort unselected for RYR1-associated conditions. Data was retrieved from the SG10K pilot project, where whole genome sequencing was performed on volunteers unselected and undetermined for RYR1-associated conditions. Variants were classified based on pathogenicity using databases ClinVar and InterVar. Allele frequencies of pathogenic variants were compared between Chinese, Indians and Malays. Using databases ExAC, GnomAD and GenomeAsia 100k study, we further compared local allele frequencies to those in Europe, America and Asia. Data was analysed using R Commander. Significant P value was set at p < 0.05. Majority of the RYR1 variants were missense mutations. We identified four pathogenic and four likely pathogenic RYR1 variants. All were related to the aforementioned RYR1-associated conditions. There were 6 carriers of RYR1 pathogenic variants amongst 4810 individuals, corresponding to an allele frequency of 0.06%. The prevalence of pathogenic variants was the highest amongst Indians (4 in 1127 individuals) (p = 0.030). Majority of pathogenic and likely pathogenic mutations were missense and located in mutational hotspots. These variants also occurred at higher frequencies in Asians than globally. This study describes the variant landscape of the RYR1 gene in Singapore. This knowledge will facilitate genetic screening for RYR1-related conditions.