bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional, Post-Transcriptional, and Post-Translational Mechanisms Rewrite the Tubulin Code During Cardiac Hypertrophy and Failure
Authors: Phyo Sai Aung , Uchida Keita , Chen Christina Yingxian , Caporizzo Matthew A. , Bedi Kenneth , Griffin Joanna , Margulies Kenneth , Prosser Benjamin L.
Published: April 2022

A proliferated and post-translationally modified microtubule network underlies cellular growth in cardiac hypertrophy and contributes to contractile dysfunction in heart failure. Yet how the heart achieves this modified network is poorly understood. Determining how the “tubulin code”—the permutations of tubulin isoforms and post-translational modifications—is rewritten upon cardiac stress may provide new targets to modulate cardiac remodeling. Further, while tubulin can autoregulate its own expression, it is unknown if autoregulation is operant in the heart or tuned in response to stress. Here we use heart failure patient samples and murine models of cardiac remodeling to interrogate transcriptional, autoregulatory, and post-translational mechanisms that contribute to microtubule network remodeling at different stages of heart disease. We find that autoregulation is operant across tubulin isoforms in the heart and leads to an apparent disconnect in tubulin mRNA and protein levels in heart failure. We also find that within 4 h of a hypertrophic stimulus and prior to cardiac growth, microtubule detyrosination is rapidly induced to help stabilize the network. This occurs concomitant with rapid transcriptional and autoregulatory activation of specific tubulin isoforms and microtubule motors. Upon continued hypertrophic stimulation, there is an increase in post-translationally modified microtubule tracks and anterograde motors to support cardiac growth, while total tubulin content increases through progressive transcriptional and autoregulatory induction of tubulin isoforms. Our work provides a new model for how the tubulin code is rapidly rewritten to establish a proliferated, stable microtubule network that drives cardiac remodeling, and provides the first evidence of tunable tubulin autoregulation during pathological progression.
The Emerging Role of the Serine Incorporator Protein Family in Regulating Viral Infection
Authors: Xu Shaofen , Zheng Zhichao , Pathak Janak L. , Cheng Haoyu , Zhou Ziliang , Chen Yanping , Wu Qiuyu , Wang Lijing , Zeng Mingtao , Wu Lihong
Published: April 2022

Serine incorporator (SERINC) proteins 1–5 (SERINC1-5) are involved in the progression of several diseases. SERINC2-4 are carrier proteins that incorporate the polar amino acid serine into membranes to facilitate the synthesis of phosphatidylserine and sphingolipids. SERINC genes are also differentially expressed in tumors. Abnormal expression of SERINC proteins occurs in human cancers of the breast, lung, colon, liver, and various glands, as well as in mouse testes. SERINC proteins also affect cleft lip and palate and nerve-related diseases, such as seizure Parkinsonism and borderline personality. Moreover, SERINC proteins have garnered significant interest as retroviral restriction factors, spurring efforts to define their function and elucidate the mechanisms through which they operate when associated with viruses. Human SERINC proteins possess antiviral potential against human immunodeficiency virus (HIV), SARS-COV-2, murine leukemia virus (MLV), equine infectious anemia virus (EIAV), and hepatitis B virus (HBV). Furthermore, the crystal structure is known, and the critical residues of SERINC5 that act against HIV have been identified. In this review, we discuss the most prevalent mechanisms by which SERINC3 and SERINC5 antagonize viruses and focus on the potential therapeutic applications of SERINC5/3 against HIV.
Multiscale Transcriptomic Integration Reveals B-Cell Depletion and T-Cell Mistrafficking in Nasopharyngeal Carcinoma Progression
Authors: Shi Xiaojie , Pan Junyan , Qiu Fufang , Wu Liqin , Zhang Xuyan , Feng Yan , Gu Xiaoyi , Zhao Jikuang , Zheng Wenwei
Published: April 2022

Nasopharyngeal carcinoma (NPC), featured by Epstein-Barr virus (EBV) infection and regional epidemiology, is curable when detected early, but highly lethal at an advanced stage. The molecular mechanism of NPC progression toward a clinically uncontrollable stage remains elusive. In this study, we developed a novel computational framework to conduct multiscale transcriptomic analysis during NPC progression. The framework consists of four modules enabling transcriptomic analyses spanning from single-cell, bulk, microenvironment, to cohort scales. The bulk-transcriptomic analysis of 133 NPC or normal samples unraveled leading functional enrichments of cell-cycle acceleration, epithelial-mesenchymal transition, and chemokine-modulated inflammatory response during NPC progression. The chemokine CXCL10 in the NPC microenvironment, discovered by single-cell RNA sequencing data analysis, recruits cytotoxic T cells through interacting with its receptor CXCR3 at early but late stages. This T-cell mistrafficking was featured by the decline of cytotoxic T cells and the increase of regulatory T cells, accompanied with B-cell depletion confirmed by immunohistochemistry staining. The featured immunomodulatory chemokines were commonly upregulated in the majority of cancers associated with viral or bacterial infections.
Glucocorticoid Exposure of Preimplantation Embryos Increases Offspring Anxiety-Like Behavior by Upregulating miR-211-5p via Trpm1 Demethylation
Authors: Yuan Hong-Jie , Han Xiao , Wang Guo-Liang , Wu Jia-Shun , He Nan , Zhang Jie , Kong Qiao-Qiao , Gong Shuai , Luo Ming-Jiu , Tan Jing-He
Published: April 2022

Most studies on mechanisms by which prenatal stress affects offspring behavior were conducted during late pregnancy using in vivo models; studies on the effect of preimplantation stress are rare. In vivo models do not allow accurate specification of the roles of different hormones and cells within the complicated living organism, and cannot verify whether hormones act directly on embryos or indirectly to alter progeny behavior. Furthermore, the number of anxiety-related miRNAs identified are limited. This study showed that both mouse embryculture with corticosterone (ECC) and maternal preimplantation restraint stress (PIRS) increased anxiety-like behavior (ALB) while decreasing hippocampal expression of glucocorticoid receptor (GR) and brain-derived neurotrophic factor (BDNF) in offspring. ECC/PIRS downregulated GR and BDNF expression by increasing miR-211-5p expression via promoter demethylation of its host gene Trpm1, and this epigenetic cell fate determination was exclusively perpetuated during development into mature hippocampus. Transfection with miR-211-5p mimic/inhibitor in cultured hippocampal cell lines confirmed that miR-211-5p downregulated Gr and Bdnf. Intrahippocampal injection of miR-211-5p agomir/antagomir validated that miR-211-5p dose-dependently increased ALB while decreasing hippocampal GR/BDNF expression. In conclusion, preimplantation exposure to glucocorticoids increased ALB by upregulating miR-211-5p via Trpm1 demethylation, and miR-211-5p may be used as therapeutic targets and biomarkers for anxiety-related diseases.
Co-creation of a Scalable Climate Service for Kenyan Smallholder Farmers
Authors: van der Horst Sophie , Goosen Hasse , van Selm Merlijn , Koomen Irene , Matsaba Emmanuel Ochola , Wesonga John , Koge Jessica , klein Holkenborg Marjel
Published: April 2022

Climate change is already impacting the horticulture sector in Kenya. Even though the effects of climate change will be severe, adaptation to climate change still has little priority at the local and county level. This paper discusses the development of the agricultural climate atlas for Kajiado and Kiambu counties in Kenya as a climate information service to support the horticulture sector. This climate service for smallholder farmers aims to bridge the gap between climate research and data provision and the uptake by farmers and farmer organizations on the ground. Rather than developing a generic service for the whole of the country, we followed a local, bottom-up approach. Working at the county level, we tried to capture local needs. The result is a co-created atlas for two counties, for specific crops. The approach can be scaled up to other counties and other crops. We elaborate on our approach, and discuss lessons learned, challenges, and future work opportunities. The development of the climate atlas shows the importance of co-creation and user engagement. In addition, flexibility in the output and process was crucial. The main challenge remains to keep engagement high after completion of the project.
Gene Pool Boundaries for the Yosemite Toad (Anaxyrus canorus) Reveal Asymmetrical Migration Within Meadow Neighborhoods
Authors: Maier Paul A. , Vandergast Amy G. , Ostoja Steven M. , Aguilar Andres , Bohonak Andrew J.
Published: April 2022

The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well-documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat “hub” meadows that experience net immigration, surrounded by smaller and topographically rugged “satellite” meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts.
Numerical Study on Heat Transfer and Enhancement Mechanism in PCM-Filled Shell-and-Tube Heat Exchangers
Authors: Fang Jiabin , Han Tao , Bi Yixin , Yan Haobing , Wei Jinjia
Published: April 2022

A numerical model was established using the enthalpy-porosity approach to study the heat transfer characteristics of a shell-and-tube phase change heat exchanger filled with paraffin wax RT50. The influence of exchanger placement forms, tube diameters and fin structures on the phase change process of RT50 was analyzed. The results depicted that the vertical heat exchanger has a faster melting rate than the horizontal one as the tube diameter is large. However, the opposite results were obtained in case the tube diameter is small. For the horizontal exchanger, the heat conduction is dominant at the beginning and end of the melting process, while the natural convection plays a more important role at the intermediate stage of melting. Besides, the duration of the melting is mainly determined by the natural convection. In addition, adopting fins on the outer of the tube can significantly improve the heat transfer and therefore shorten the melting time. Compared with finless tube, the use of annular-fin tube can reduce the melting time by 31.6% mainly because of the intensifying of heat conduction, while the use of straight-fin tube can shorten the melting time by 42.1% attributed to the enhancement of both natural convection and heat conduction during the melting process.
Epidermolysis Bullosa With Congenital Absence of Skin: Congenital Corneal Cloudiness and Esophagogastric Obstruction Including Extended Genotypic Spectrum of PLEC, LAMC2, ITGB4 and COL7A1
Authors: Pongmee Pharuhad , Wittayakornrerk Sanchawan , Lekwuttikarn Ramrada , Pakdeeto Sasikarn , Watcharakuldilok Piangor , Prempunpong Chatchay , Tim-Aroon Thipwimol , Puttanapitak Chawintee , Wattanasoontornsakul Piyawan , Junhasavasdikul Thitiporn , Wongkittichote Parith , Noojarern Saisuda , Wattanasirichaigoon Duangrurdee
Published: April 2022

Epidermolysis bullosa (EB) is a rare and genetically heterogeneous disorder characterized by skin fragility and blister formation occurring spontaneously or after minor trauma. EB is accompanied by congenital absence of skin (EB with CAS) in some patients. Pathogenic variants of COL7A1 are responsible for EB with CAS in the vast majority of cases. Type and subtype diagnosis of EB with CAS generally requires specific immunohistological examinations that are not widely available plus targeted gene analysis. The present study aimed to determine the clinical features of five patients affected by EB with CAS and to identify the underlying genetic defects using whole exome sequencing (WES) followed by focused analysis of the target genes. Four patients had generalized skin involvement and one had localized defects. Two patients exhibited extremely severe skin manifestations and congenital cloudy cornea along with pyloric atresia, and one had partial esophagogastric obstruction and anuria due to vesicoureteric obstruction. In the WES analysis, the average coverage of the target exons was 99.05% (726 of 733 exons), with a range of 96.4–100% for individual genes. We identified four novel and two known pathogenic/likely pathogenic variants of five distinct genes in the examined families: PLEC:c.2536G > T (p.Glu846Ter); LAMC2:c.3385C > T (p.Arg1129Ter); KRT5:c.429G > A (p.Glu477Lys); ITGB4:c.794dupC (p.Ala266SerfsTer5); COL7A1:c.5440C > T (p.Arg1814Cys); and COL7A1:c.6103delG. All alleles were inherited from the parents, except for the KRT5 variant as a de novo finding. The findings reveal extremely rare phenotypes found in EB with CAS, namely congenital cloudy cornea, esophagogastric obstruction, and anuria, and extend the genotypic spectrum of EB-related genes. The data confirm that WES provides very high coverage of coding exons/genes and support its use as a reasonable alternative method for diagnosis of EB. The present data from an underrepresented population in Southeast Asia could further broaden the knowledge and research on EB.
SLAMF8 Participates in Acute Renal Transplant Rejection via TLR4 Pathway on Pro-Inflammatory Macrophages
Authors: Teng Lisha , Shen Lingling , Zhao Wenjun , Wang Cuili , Feng Shi , Wang Yucheng , Bi Yan , Rong Song , Shushakova Nelli , Haller Hermann , Chen Jianghua , Jiang Hong
Published: April 2022

Background

Acute rejection (AR) in kidney transplantation is an established risk factor that reduces the survival rate of allografts. Despite standard immunosuppression, molecules with regulatory control in the immune pathway of AR can be used as important targets for therapeutic operations to prevent rejection.

Methods

We downloaded the microarray data of 15 AR patients and 37 non-acute rejection (NAR) patients from Gene Expression Omnibus (GEO). Gene network was constructed, and genes were classified into different modules using weighted gene co-expression network analysis (WGCNA). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cytoscape were applied for the hub genes in the most related module to AR. Different cell types were explored by xCell online database and single-cell RNA sequencing. We also validated the SLAMF8 and TLR4 levels in Raw264.7 and human kidney tissues of TCMR.

Results

A total of 1,561 differentially expressed genes were filtered. WGCNA was constructed, and genes were classified into 12 modules. Among them, the green module was most closely associated with AR. These genes were significantly enriched in 20 pathway terms, such as cytokine–cytokine receptor interaction, chemokine signaling pathway, and other important regulatory processes. Intersection with GS > 0.4, MM > 0.9, the top 10 MCC values and DEGs in the green module, and six hub genes (DOCK2, NCKAP1L, IL2RG, SLAMF8, CD180, and PTPRE) were identified. Their expression levels were all confirmed to be significantly elevated in AR patients in GEO, Nephroseq, and quantitative real-time PCR (qRT-PCR). Single-cell RNA sequencing showed that AR patient had a higher percentage of native T, CD1C+_B DC, NKT, NK, and monocytes in peripheral blood mononuclear cells (PBMCs). Xcell enrichment scores of 20 cell types were significantly different (p<0.01), mostly immune cells, such as B cells, CD4+ Tem, CD8+ T cells, CD8+ Tcm, macrophages, M1, and monocytes. GSEA suggests that highly expressed six hub genes are correlated with allograft rejection, interferon γ response, interferon α response, and inflammatory response. In addition, SLAMF8 is highly expressed in human kidney tissues of TCMR and in M1 phenotype macrophages of Raw264.7 cell line WGCNA accompanied by high expression of TLR4.

Conclusion

This study demonstrates six hub genes and functionally enriched pathways related to AR. SLAMF8 is involved in the M1 macrophages via TLR4, which contributed to AR process.
CD8+ T Cells in SARS-CoV-2 Induced Disease and Cancer—Clinical Perspectives
Authors: Mortezaee Keywan , Majidpoor Jamal
Published: April 2022

Dysregulated innate and adaptive immunity is a sign of SARS-CoV-2-induced disease and cancer. CD8+ T cells are important cells of the immune system. The cells belong to the adaptive immunity and take a front-line defense against viral infections and cancer. Extreme CD8+ T-cell activities in the lung of patients with a SARS-CoV-2-induced disease and within the tumor microenvironment (TME) will change their functionality into exhausted state and undergo apoptosis. Such diminished immunity will put cancer cases at a high-risk group for SARS-CoV-2-induced disease, rendering viral sepsis and a more severe condition which will finally cause a higher rate of mortality. Recovering responses from CD8+ T cells is a purpose of vaccination against SARS-CoV-2. The aim of this review is to discuss the CD8+ T cellular state in SARS-CoV-2-induced disease and in cancer and to present some strategies for recovering the functionality of these critical cells.
Antarctic Krill Biomass and Flux Measured Using Wideband Echosounders and Acoustic Doppler Current Profilers on Submerged Moorings
Authors: Cutter George R. , Reiss Christian S. , Nylund Sven , Watters George M.
Published: April 2022

During austral summer 2018/2019, we deployed an array of six submerged moorings equipped with Nortek Signature100 integrated wideband echosounder and acoustic Doppler current profilers (ADCPs) on the continental shelf of the northern Antarctic Peninsula. Acoustic data from these instruments were used to classify targets, estimate water flow and the biomass of Antarctic krill (Euphausia superba), and quantify krill flux (biomass transport). We differentiated krill from other target aggregations using a supervised classification of data from the echosounder representing five wideband frequency bins spanning 68–113 kHz and two narrowband frequencies at 70 and 120 kHz. We estimated krill biomass using echosounder data collected at 120 kHz and water flow using the ADCP data. We estimated the biomass flux from the product of mean volumetric krill density and flow speed over a depth-integration range of 150 m. The overall mean krill areal biomass density based on hourly averages was 174 g⋅m–2 during the austral summer (December–March). Mean daily biomass decreased by an order of magnitude, from 300 to 31 g⋅m–2, over the sampling period, and fluctuated by nearly a factor of 4 above and below the local trend within weekly intervals. Mean current direction was along-shelf toward the west, and mean flow speed increased from ∼0.10 to 0.14 m⋅s–1 during the season. Krill flux was correlated with biomass variation, and the grand mean flux was 0.13 g⋅m–2⋅s–1. During the study period and in our approximately 1,300 km2 study area, average total biomass of krill was 116265 metric tons, and total cumulative krill biomass was 2.5 million tons. Our results demonstrate the utility of integrated echosounder-ADCP systems for quantifying krill flux in an important foraging area used by krill-dependent predators (seabirds and marine mammals) that breed nearby and highlight the scales of variability in a key prey resource required by these predators.
Differential Responses of Eelgrass and Macroalgae in Pacific Northwest Estuaries Following an Unprecedented NE Pacific Ocean Marine Heatwave
Authors: Magel Caitlin L. , Chan Francis , Hessing-Lewis Margot , Hacker Sally D.
Published: April 2022

The 2013-2016 northeast Pacific Ocean marine heatwave (MHW) had myriad impacts on marine communities, but little is known about how this event affected coastal estuaries. We examined the extent to which elevated temperatures associated with the offshore MHW were observed in four estuaries (Willapa Bay, Washington and Netarts Bay, Yaquina Bay, and Coos Bay, Oregon) and the responses of macrophytes at marine dominated sites within these estuaries. Records of eelgrass (Zostera marina), ulvoid macroalgae (Ulva and Enteromorpha spp.), and environmental characteristics, including water temperature, were analyzed over three periods: before (2006-2010), during (2015-2016), and after (2017-2019) the MHW. During the MHW, all four estuaries experienced “estuarine heatwaves” (anomalous warm water events) at monitoring stations and there was an associated decline in macroalgae biomass. In northern estuaries (Willapa and Netarts bays) where water temperatures are normally higher and estuaries are shallower, aboveground eelgrass biomass declined and did not recover for at least three years after the MHW. In southern estuaries (Yaquina and Coos bays), where water temperatures are normally colder and estuaries are deeper, the MHW was associated with a neutral, or temporarily positive, change in aboveground eelgrass biomass. Our analysis supports the hypothesis that upwelling intensity and estuarine depth determined the severity of MHW impacts on macrophytes at marine dominated sites, and that the colder and deeper estuaries in the south may serve as refuges for eelgrass but not macroalgae. We suggest that estuary-specific responses were predictable given the drivers of macrophyte abundance at marine dominated sites, and that baseline ocean upwelling and estuarine temperature can be used to anticipate macrophyte responses at marine dominated sites to MHWs in the future.
Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection
Authors: Li Yaoguang , Jiao Mengfan , Liu Ying , Ren Zhigang , Li Ang
Published: April 2022

The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.
Do the Reclaimed Fungal Communities Succeed Toward the Original Structure in Eco-Fragile Regions of Coal Mining Disturbances? A Case Study in North China Loess—Aeolian Sand Area
Authors: Ji Chuning , Huang Jiu , Yu Haochen , Tian Yu , Rao Xunzheng , Zhang Xin
Published: April 2022

Mining activity has caused serious environmental damage, particularly for soil ecosystems. How the soil fungal community evolves in mine reclamation and what are the succession patterns of molecular ecological networks still needs to be studied in depth. We used high-throughput sequencing to explore the changes in soil fungal communities, molecular ecological networks, and interactions with soil environmental factors in five different ages (the including control group) during 14 years of reclamation in eco-fragile mines. The results showed that the abundance and diversity of soil fungi after 14 years of reclamation were close to, but still lower than, those in the undisturbed control area, but the dominant phylum was Ascomycota. Soil nitrate-N, C/N ratio, pH, and water content significantly affected the fungal community with increasing reclamation ages. Moreover, we found that Mortierellomycota, despite its high relative abundance, had little significant connectivity with other species in the molecular ecological network. Fungal molecular ecological networks evolve with increasing ages of reclamation, with larger modules, more positive connections, and tighter networks, forming large modules of more than 60 nodes by age 9. The large modules were composed mainly of Ascomycota and Basidiomycota, which can form mycorrhiza with plant roots, and are not only capable of degrading pollution but are also “encouraged” by most (more than 64%) physicochemical factors in the soil environment. The results can provide a basis for scientific mine ecological restoration, especially for eco-fragile regions.
Phylogenetic and Evolutionary Genomic Analysis of Listeria monocytogenes Clinical Strains in the Framework of Foodborne Listeriosis Risk Assessment
Authors: Gattuso Antonietta , Cella Eleonora , Fillo Silvia , Ortoffi Marco Francesco , Angeletti Silvia , Ciccozzi Massimo , De Medici Dario , Lista Florigio , Fiore Alfonsina
Published: April 2022

Listeria monocytogenes is one of the most important foodborne pathogens responsible for listeriosis, a severe disease with symptoms ranging from septicemia, meningoencephalitis, and abortion. Given the strong impact of listeriosis on human health and the difficulty of controlling L. monocytogenes along the food production chain, listeriosis has become a priority subjected to molecular surveillance in European Union/European Economic Area since 2007. From 2018, surveillance is based on whole-genome sequence using the core genome multilocus sequence type. The complete sequences of 132 clinical strains were used to define the evolutionary relatedness among subtypes of L. monocytogenes isolated in Italy from 2010 to 2016, allowing the identification of clades and/or clusters associated with outbreaks or sporadic cases of listeriosis. All the strains analyzed are clustered in lineages I and II, and the majority of the strains were classified as lineage II. A probable epidemic entrance in different years for every clade and cluster from each different region was defined. The persistence of the same specific clonal complexes of L. monocytogenes has been found over long periods; this may be related to the fact that some strains are able to survive better than others in a food production environment. Phylogenic studies, using whole-genome sequence data, are able to identify the emergence of highly persistent pathogenic variants, contributing to improving the hazard characterization of L. monocytogenes.
Contextual Information Modulates Pupil Size in Autistic Children
Authors: Tortelli Chiara , Pomè Antonella , Turi Marco , Igliozzi Roberta , Burr David C. , Binda Paola
Published: April 2022

Recent Bayesian models suggest that perception is more “data-driven” and less dependent on contextual information in autistic individuals than others. However, experimental tests of this hypothesis have given mixed results, possibly due to the lack of objectivity of the self-report methods typically employed. Here we introduce an objective no-report paradigm based on pupillometry to assess the processing of contextual information in autistic children, together with a comparison clinical group. After validating in neurotypical adults a child-friendly pupillometric paradigm, in which we embedded test images within an animation movie that participants watched passively, we compared pupillary response to images of the sun and meaningless control images in children with autism vs. age- and IQ-matched children presenting developmental disorders unrelated to the autistic spectrum. Both clinical groups showed stronger pupillary constriction for the sun images compared with control images, like the neurotypical adults. However, there was no detectable difference between autistic children and the comparison group, despite a significant difference in pupillary light responses, which were enhanced in the autistic group. Our report introduces an objective technique for studying perception in clinical samples and children. The lack of statistically significant group differences in our tests suggests that autistic children and the comparison group do not show large differences in perception of these stimuli. This opens the way to further studies testing contextual processing at other levels of perception.
Radiomics Based on Digital Mammography Helps to Identify Mammographic Masses Suspicious for Cancer
Authors: Wang Guangsong , Shi Dafa , Guo Qiu , Zhang Haoran , Wang Siyuan , Ren Ke
Published: April 2022

Objectives

This study aims to build radiomics model of Breast Imaging Reporting and Data System (BI-RADS) category 4 and 5 mammographic masses extracted from digital mammography (DM) for mammographic masses characterization by using a sensitivity threshold similar to that of biopsy.

Materials and Methods

This retrospective study included 288 female patients (age, 52.41 ± 10.31) who had BI-RADS category 4 or 5 mammographic masses with an indication for biopsy. The patients were divided into two temporal set (training set, 82 malignancies and 110 benign lesions; independent test set, 48 malignancies and 48 benign lesions). A total of 188 radiomics features were extracted from mammographic masses on the combination of craniocaudal (CC) position images and mediolateral oblique (MLO) position images. For the training set, Pearson’s correlation and the least absolute shrinkage and selection operator (LASSO) were used to select non-redundant radiomics features and useful radiomics features, respectively, and support vector machine (SVM) was applied to construct a radiomics model. The receiver operating characteristic curve (ROC) analysis was used to evaluate the classification performance of the radiomics model and to determine a threshold value with a sensitivity higher than 98% to predict the mammographic masses malignancy. For independent test set, identical threshold value was used to validate the classification performance of the radiomics model. The stability of the radiomics model was evaluated by using a fivefold cross-validation method, and two breast radiologists assessed the diagnostic agreement of the radiomics model.

Results

In the training set, the radiomics model obtained an area under the receiver operating characteristic curve (AUC) of 0.934 [95% confidence intervals (95% CI), 0.898–0.971], a sensitivity of 98.8% (81/82), a threshold of 0.22, and a specificity of 60% (66/110). In the test set, the radiomics model obtained an AUC of 0.901 (95% CI, 0.835–0.961), a sensitivity of 95.8% (46/48), and a specificity of 66.7% (32/48). The radiomics model had relatively stable sensitivities in fivefold cross-validation (training set, 97.39% ± 3.9%; test set, 98.7% ± 4%).

Conclusion

The radiomics method based on DM may help reduce the temporarily unnecessary invasive biopsies for benign mammographic masses over-classified in BI-RADS category 4 and 5 while providing similar diagnostic performance for malignant mammographic masses as biopsies.
Clinical Epidemiology of Pediatric COVID-19 Delta Variant Cases From North Sumatra, Indonesia
Authors: Kusumawati R. Lia , Lubis Inke Nadia Diniyanti , Kumaheri Meutia Ayuputeri , Pradipta Ariel , Faksri Kiatichai , Mutiara Mutiara , Shankar Anuraj H. , Tania Tryna
Published: April 2022

The Delta variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) dominated the coronavirus disease 2019 (COVID-19) pandemic in 2021. Here we report the Delta variant among pediatric cases in North Sumatra, Indonesia, from June to July 2021. Whole-genome sequencing (WGS) from 18 new COVID-19 pediatric patients showed that six were B.1.459 and six were B.1.466.2, known variants in Indonesia in clade 20A. Six were the Delta variant B.1.617.2 of clade 21A, with five on one branch and one on a distant branch consistent with that patient's geographic separation, suggesting at least two introductions to the region. Variants tended to be spatially clustered, and four children with Delta variant had an adult infected household member, all of whom had lower real-time polymerase chain reaction cycle threshold (Ct) values compared with the child. No temporal trends were observed for Ct. These data support a paradigm shift with children being highly susceptible to the Delta variant and a priority for vaccination.
Meta-Analysis of Vitamin D Receptor Gene Polymorphisms in Childhood Asthma
Authors: Zhou Yong , Li Sheng
Published: April 2022

We conducted the systematic review to investigate the potential relationship between the vitamin polymorphisms of D receptor (VDR) gene and childhood asthma. Relevant studies researching on VDR polymorphisms and asthma susceptibility were searched throughout Embase, PubMed, China Science and technology journal database (CQVIP), etc. till 12 April, 2021. We calculated the pooled odds ratios (OR) and its 95% confidence interval (CI) using RevMan 5.3 software and Stata 11.0. FokI (rs2228570) could significantly affect childhood asthma risk across co dominant model (Ff vs. FF: OR (95%CI) = 0.82 (0.65, 1.02), P = 0.071) and dominant model (ff+Ff vs. FF: OR (95%CI) = 0.77 (0.63, 0.95), P = 0.016), especially among Caucasians in additive model (f vs. F: OR (95%CI) = 0.63 (0.43, 0.92), P = 0.015) and dominant model (ff+Ff vs. FF: OR (95%CI) = 0.67 (0.51, 0.88), P = 0.004). TaqI (rs731236) was significantly related with childhood asthma in additive model (t vs. T: OR (95%CI) = 0.45 (0.23, 0.89), P = 0.022), co dominant model (Tt vs. TT: OR (95%CI) = 0.36 (0.17, 0.77), P = 0.009), and dominant model (tt+Tt vs. TT: OR (95%CI) = 0.36 (0.15, 0.87), P = 0.024) among Asian, as well as population-based subgroup in co dominant model (Tt vs. TT: OR (95%CI) = 0.53 (0.31, 0.94), P = 0.029). However, no evidence supported the role of ApaI (rs7975232) and BsmI (rs1544410) polymorphisms in childhood asthma. FokI and TaqI polymorphisms were found to be related with the susceptibility of childhood asthma. However, it seems that ApaI and BsmI polymorphisms are not related with childhood asthma susceptibility.
Novel Advances in the Evaluation and Treatment of Children With Symptoms of Gastroesophageal Reflux Disease
Authors: Rosen Rachel
Published: April 2022

Gastroesophageal reflux disease has long been implicated as a cause for multiple pediatric symptoms ranging from abdominal pain and regurgitation to cough and dental erosions. Diagnostic testing has evolved greatly over the last 20 years; initial testing with pH-metry to measure esophageal acid reflux burden has evolved into measurement of both acid and non-acid reflux and liquid and gas reflux. However, measuring reflux burden alone only tells a small part of the GERD story and many symptoms originally thought to be reflux related are, in fact, related to other disorder which mimic reflux. The current paradigm which involves empiric treatment of symptoms with acid suppression has been replaced with early testing for not only gastroesophageal reflux but also for other diagnostic masqueraders. The focus for interventions has shifted away from acid suppression toward motility interventions and includes a greater recognition of both functional and motility disorders which present with reflux symptoms.
High Expression of RAI14 in Triple-Negative Breast Cancer Participates in Immune Recruitment and Implies Poor Prognosis Through Bioinformatics Analyses
Authors: Cui Ranliang , Zhao Ting , Bai Changsen , Ji Ning , Hua Jialei , Ren Li , Li Yueguo
Published: April 2022

Objective: The purpose of current research is to explore the function of retinoic acid-induced protein 14 (RAI14), being a reciprocal protein of carboxypeptidase N1 (CPN1), and as a biomarker for prognosis and immunoregulatory effects in breast cancers.

Methods: Interacting proteins of CPN1 were characterized by co-immunoprecipitation (CO-IP) and mass spectrometry. We evaluated RAI14 expression and related clinical prognosis based on bioinformatics methods. The level of relevance between RAI14 and infiltrating immune cells biomarkers was investigated by using TIMER and certificated by immunohistochemical staining and cytology experiments.

Results: RAI14 is an interacting protein of CPN1. Higher RAI14 expression in TNBC was significantly correlated with poor prognosis in TNBC, especially (RFS: HR = 1.32, p = 0.015; DFS: HR = 1.18, p = 0.035). The estrogen receptor (ER), P53 status, and histological types and triple-negative status were observed and correlated with RAI14 expression. Moreover, the level of RAI14 was positive in relation with the expression of CD163 (M2 macrophages marker, r = 0.393, p = 1.89e-06) and PD-1 (T-cell exhaustion marker, r = 0.626, p = 4.82e-03), indicating RAI14 levels were mainly related to M2 macrophages and T-cell exhaustion infiltration in TNBC. Furthermore, CPN1 overexpression was accompanied by RAI14 and PD-L1 upregulation, and a correlation was found among them.

Conclusions: RAI14 is a potential downstream molecule of CPN1, which may be a potential prognostic biomarker and identification of an immunosuppressive tumor microenvironment in TNBC.
Premature Beats Rejection Strategy on Paroxysmal Atrial Fibrillation Detection
Authors: Zhang Xiangyu , Li Jianqing , Cai Zhipeng , Zhao Lina , Liu Chengyu
Published: April 2022

Paroxysmal atrial fibrillation (PAF) may related to the risk of thromboembolism and is the most common cardiac risk factor of cryptogenic stroke (CS). Due to its paroxysmal characteristics, it is usually diagnosed by continuous long-term ECG. Patients with paroxysmal atrial fibrillation usually have premature beats at the same time which is easy to be confused with the rhythm of atrial fibrillation. Therefore, in this article, we designed a screening algorithm for single premature beat, multi premature beats, bigeminy and trigeminy premature beats, according to their rhythm characteristics to reduce false detection caused by premature beats during the PAF detection process. The proposed elimination method was verified on ECG segments with different types of premature beats, and tested on long-term ECG data of PAF patients. ECG segments of different kinds of premature beats were selected from MIT Atrial Fibrillation database (MIT-AFDB), MIT-BIH Arrhythmia database (MIT-AR) and wearable ECG data from the China Physiological Signal Challenge 2021 (CPSC 2021). The proposed method can effectively eliminate single premature beat segments with 99.5% accuracy, and it also can eliminate more than 95% of ECG segments with other types of premature beats. We designed PAF-score as a new index to evaluate the accuracy of detection, and we also calculate the misjudged and missed segments to comprehensively evaluate the PAF detection algorithm. The proposed method get a PAF-score of 0.912 on MIT-AFDB. The proposed method also has the potential to implant low computing power wearable devices for real-time analysis.
Facilitating Text Production in Fourth Graders: Effects of Script-Based Knowledge and Writing Prompts
Authors: Bourdin Béatrice , Fayol Michel
Published: April 2022

This study aimed at providing evidence that prior knowledge (semantic relatedness) and its organization (scripted versus not related) prompted either through pictures alone, pictures and associated words, words only have different impacts on several components of text produced by fourth graders. The results showed that the semantic relatedness affected three dependent measures: prompt words recalled, coherence and quality of texts. The nature of the prompts impacted on planning (number of ideas) and translating (number of propositions and length of texts) processes. Findings, instructional applications, limitations, and proposals for future research are discussed.
The Brain Is Adaptive Not Triune: How the Brain Responds to Threat, Challenge, and Change
Authors: Steffen Patrick R. , Hedges Dawson , Matheson Rebekka
Published: April 2022

Theory impacts how research is conducted. A popular theory used to conceptualize brain functioning is the triune brain theory. The triune brain theory is an evolutionary theory of brain development that emphasizes three key brain regions consisting of the brainstem, the limbic system, and the cortex that function relatively independently in coping with stress via fight or flight, emotion, and cognition, respectively. However, modern neuroscience research demonstrates that the triune brain theory does not accurately explain how the brain functions in everyday life or during the stress response. Specifically, emotion and cognition are interdependent and work together, the limbic system is not a purely emotional center nor are there purely emotional circuits in the brain, and the cortex is not a purely cognitive center nor are there purely cognitive circuits in the brain. We propose a new evolutionarily based model, the adaptive brain, that is founded on adaptive prediction resulting from interdependent brain networks using interoception and exteroception to balance current needs, and the interconnections among homeostasis, allostasis, emotion, cognition, and strong social bonds in accomplishing adaptive goals.
Threats and Interventions on Wellbeing in Asylum Seekers in the Netherlands: A Scoping Review
Authors: Pluck Ferdy , Ettema Roelof , Vermetten Eric
Published: April 2022

Background

Most asylum seekers experience stress, not only due to the reason for fleeing and their travel but also due to their compulsory stay in the asylum seeker center in the Netherlands and the asylum procedure. This often leads to self-medication and addiction which causes lower self-esteem and lower quality of life. Adverse life events, forced migration, and prolonged asylum procedures, in addition to the complexity of the acculturation process, can all contribute to higher levels of psychopathology.

Objective

What are the threats to wellbeing in terms of mental health, psychosocial, and addiction problems, and what are the effective interventions for wellbeing for asylum seekers in asylum seeker centers in the Netherlands, reported in the literature?

Method

Following the descriptive nature of the research question and the need for identifying knowledge gaps, an overview of existing knowledge was created by executing a scoping review on influencing factors on the mental health of asylum seekers. The Neuman system model was used as a guiding framework to understand the complexity of the issues this population experience and to identify the stressors and the factors which cause the imbalance and also the disease.

Results

The literature review resulted in 26 articles that met the criteria for inclusion. The threats included the influence of staying in the environment of an asylum seekers center, drug abuse among asylum seekers, health-care professionals and employees who do not detect or underestimate the underlying suffering of asylum seekers, and frequent relocations of asylum seekers. The two assessment instruments used were the Rapid-Assessment-Response method (RAR method) and the Health Information Assessment Tool Asylum Seeker tool (HIATUS tool). Finally, the five interventions were identified: therapy for asylum seekers diagnosed with post-traumatic stress disorder (PSTD), art therapy, education focused on prevention as intervention, cultural interview, and mindspring.

Conclusion

The knowledge on identifying and reducing threats, assessment, and treatment interventions for asylum seekers living in an asylum seekers center found in the literature provided perspectives on improving their wellbeing. The great diversity of cultural aspects and continuous changes in the number and origin of refugees in the Dutch asylum seekers centers disrupted the continuity of care.
Affordances of School Ground Environments for Physical Activity: A Case Study on 10- and 12-Year-Old Children in a Norwegian Primary School
Authors: Kjønniksen Lise , Wiium Nora , Fjørtoft Ingunn
Published: April 2022

Several studies have focused on how different school ground environments can stimulate physical activity (PA) in children. This study aimed to investigate the contributions of two school ground environments (a constructed schoolyard and a natural forest) in moderate to vigorous physical activity (MVPA) of Norwegian school children in the 5th and 7th grades. This study described two school ground environments that provided large and multifunctional spaces, giving the children several affordances for being physically active during the school day. The constructed schoolyard afforded a space of 44 m2 per child and had an access to sports and game courts and various types of equipment for PA. The natural forest provided a space of 50.6 m2 per child and had a varied landscape for activities that afforded a wide range of PA. On average, the children engaged in 50% of the 60-min period of MVPA when playing in the natural and constructed play settings. The two different environments, thus, contributed equally to the daily MVPA of the school children. The findings can inform policies and programs aiming at promoting recommended levels of PA among children using school outdoor environments that may eventually have implications for the physical and mental health of school children during the current pandemic.
Reliability of the Evidence to Guide Decision-Making in Acupuncture for Functional Dyspepsia
Authors: Huang Jinke , Liu Jiali , Liu Zhihong , Ma Jing , Ma Jinxin , Lv Mi , Wang Fengyun , Tang Xudong
Published: April 2022

Background and Aims

There has been a significant increase in the number of systematic reviews (SRs)/meta-analyses (MAs) investigating the effects of acupuncture for functional dyspepsia (FD). To systematically collate, appraise, and synthesize the current evidence, we carried out an umbrella review of SRs/MAs.

Methods

Systemic reviews/meta-analyses on acupuncture for FD were collected by searching major medical databases. The included studies were evaluated in terms of methodological quality, reporting quality, and evidence quality using the criteria from the Assessment of Multiple Systematic Reviews 2 (AMSTAR-2) tool, the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, and the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) system, respectively.

Results

Ten SRs/MAs were analyzed for this study. The methodological quality, reporting quality, and evidence quality of the included SRs/MAs were generally unsatisfactory. Lack of protocol registration, no list of excluded trials, or lack of a comprehensive search strategy were the main limitations. No high-quality evidence was found to support the effects of acupuncture for FD; the qualitative data synthesis relied on low quality trials with small sample sizes and was the main factor for evidence degradation.

Conclusions

Acupuncture seems to have a promising efficacy in the treatment of FD. It provides a new and prospective therapeutic method for FD. Although the quality of the included SRs/MAs was generally low and defects were frequent, this umbrella review highlights areas where improvement in methodology is required.