bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review on imaging techniques and quantitative measurements for dynamic imaging of cerebral aneurysm pulsations
Authors: Stam L. B. , Aquarius R. , de Jong G. A. , Slump C. H. , Meijer F. J. A. , Boogaarts H. D. 
Published: January 2021

AbstractMeasurement of intracranial aneurysm wall motion may refine the current rupture risk estimation. A golden standard for measuring aneurysm pulsation is lacking. The aim is to evaluate magnitudes of aneurysm pulsation as published in current literature. Embase and PubMed were searched for publications containing quantitative measures of cardiac-cycle related cerebral aneurysm pulsation (no date or language restrictions). Eleven studies were included, covering 197 unruptured and untreated cerebral aneurysms. Quantitative pulsation measurements were extracted from the studies. Characteristics of the study population and aneurysms were taken into account, as well as the imaging modality, scanning technique and data processing methods used. A meta-analysis was performed of studies with similar methodologies and individual IA measures and locations. The magnitude of the absolute volume pulsations varied between 14 ± 9 mm3 and 106 ± 123 mm3 and the mean relative volume change varied between 5 and 36%. The meta-analysis revealed a positive correlation between size and absolute volume change. The relative volume change in Basilar artery aneurysms seems smaller. No authors were contacted for original study data and articles only describing visual pulsations were excluded. The variation in methodologies impedes an accurate estimation of the magnitude of IA pulsations. Validation of aneurysm pulsation measurement is crucial prior to clinical studies evaluating IA pulsatility in relation to IA rupture risk. Prerequisite is a reliable and robust imaging method with high spatial and temporal resolution and standardization of the image analysis methods.
Liraglutide, 7,8-DHF and their co-treatment prevents loss of vision and cognitive decline in a Wolfram syndrome rat model
Authors: Seppa Kadri , Jagomäe Toomas , Kukker Kaia Grete , Reimets Riin , Pastak Marko , Vasar Eero , Terasmaa Anton , Plaas Mario 
Published: January 2021

AbstractWolfram syndrome (WS) is a monogenic progressive neurodegenerative disease and is characterized by various neurological symptoms, such as optic nerve atrophy, loss of vision, cognitive decline, memory impairment, and learning difficulties. GLP1 receptor agonist liraglutide and BDNF mimetic 7,8-dihydroxyflavone (7,8-DHF) have had protective effect to visual pathway and to learning and memory in different rat models of neurodegenerative disorders. Although synergistic co-treatment effect has not been reported before and therefore the aim of the current study was to investigate liraglutide, 7,8-DHF and most importantly for the first time their co-treatment effect on degenerative processes in WS rat model. We took 9 months old WS rats and their wild-type (WT) control animals and treated them daily with liraglutide, 7,8-DHF or with the combination of liraglutide and 7,8-DHF up to the age of 12.5 months (n = 47, 5–8 per group). We found that liraglutide, 7,8-DHF and their co-treatment all prevented lateral ventricle enlargement, improved learning in Morris Water maze, reduced neuronal inflammation, delayed the progression of optic nerve atrophy, had remyelinating effect on optic nerve and thereby improved visual acuity in WS rats compared to WT controls. Thus, the use of the liraglutide, 7,8-DHF and their co-treatment could potentially be used as a therapeutic intervention to induce neuroprotection or even neuronal regeneration.
Pre- and postmenopausal women have different core urinary microbiota
Authors: Ammitzbøll Nadia , Bau Benedikt Paul Josef , Bundgaard-Nielsen Caspar , Villadsen Annemarie Brusen , Jensen Ann-Maria , Leutscher Peter Derek Christian , Glavind Karin , Hagstrøm Søren , Arenholt Louise Thomsen Schmidt , Sørensen Suzette 
Published: January 2021

AbstractRecent studies suggest that alterations in the female urinary microbiota is associated to development of bladder disease. However, the normal microbiota composition and variation in healthy women are poorly described. Moreover, the effects of hormonal changes on microbiota during menopause is not well understood. The aim of our study was to investigate the urinary microbiota in healthy pre- and postmenopausal women without urinary tract symptoms. Microbiota composition in catheterized urine samples was mapped using 16S rRNA gene sequencing. In total, 41 premenopausal and 42 postmenopausal women were initially included. Samples with first PCR amplification concentration below level of the negative control were excluded, resulting in 34 premenopausal and 20 postmenopausal women included in data analysis. Urine from postmenopausal women showed significantly higher alpha diversity compared to premenopausal women.Lactobacilluswas the most abundant bacteria in both groups, however the relative abundance ofLactobacillusaccounted for 77.8% in premenopausal versus 42.0% in postmenopausal women. In conclusion, urine from premenopausal mostly presented withLactobacillusdominated urotypes,whereas urine from postmenopausal women presented a more diverse urinary microbiota with higher abundance of the generaGardnerellaandPrevotella. The clinical and pathophysiological implications of this difference remain to be elucidated.
Interannual and seasonal asymmetries in Gulf Stream Ring Formations from 1980 to 2019
Authors: Silver Adrienne , Gangopadhyay Avijit , Gawarkiewicz Glen , Silva E. Nishchitha S. , Clark Jenifer 
Published: January 2021

AbstractAs the Gulf Stream separates from the coast, it sheds both Warm and Cold Core Rings between $$75^\circ$$

75
∘

and $$55^\circ \,\hbox {W}$$

55
∘

W

. We present evidence that this ring formation behavior has been asymmetric over both interannual and seasonal time-scales. After a previously reported regime-shift in 2000, 15 more Warm Core Rings have been forming yearly compared to 1980–1999. In contrast, there have been no changes in the annual formation rate of the Cold Core Rings. This increase in Warm Core Ring production leads to an excess heat transfer of 0.10 PW to the Slope Sea, amounting to 7.7–12.4% of the total Gulf Stream heat transport, or 5.4–7.3% of the global oceanic heat budget at $$30^\circ \,\hbox {N}$$

30
∘

N

. Seasonally, more Cold Core Rings are produced in the winter and spring and more Warm Core Rings are produced in the summer and fall leading to more summertime heat transfer to the north of the Stream. The seasonal cycle of relative ring formation numbers is strongly correlated (r = 0.82) with that of the difference in upper layer temperatures between the Sargasso and Slope seas. This quantification motivates future efforts to understand the recent increasing influence of the Gulf Stream on the circulation and ecosystem in the western North Atlantic.
Abnormal promoter DNA hypermethylation of the integrin, nidogen, and dystroglycan genes in breast cancer
Authors: Strelnikov Vladimir V. , Kuznetsova Ekaterina B. , Tanas Alexander S. , Rudenko Viktoria V. , Kalinkin Alexey I. , Poddubskaya Elena V. , Kekeeva Tatiana V. , Chesnokova Galina G. , Trotsenko Ivan D. , Larin Sergey S. , Kutsev Sergey I. , Zaletaev Dmitry V. , Nemtsova Marina V. , Simonova Olga A. 
Published: January 2021

AbstractCell transmembrane receptors and extracellular matrix components play a pivotal role in regulating cell activity and providing for the concerted integration of cells in the tissue structures. We have assessed DNA methylation in the promoter regions of eight integrin genes, two nidogen genes, and the dystroglycan gene in normal breast tissues and breast carcinomas (BC). The protein products of these genes interact with the basement membrane proteins LAMA1, LAMA2, and LAMB1; abnormal hypermethylation of the LAMA1, LAMA2, and LAMB1 promoters in BC has been described in our previous publications. In the present study, the frequencies of abnormal promoter hypermethylation in BC were 13% for ITGA1, 31% for ITGA4, 4% for ITGA7, 39% for ITGA9, 38% for NID1, and 41% for NID2. ITGA2, ITGA3, ITGA6, ITGB1, and DAG1 promoters were nonmethylated in normal and BC samples. ITGA4, ITGA9, and NID1 promoter hypermethylation was associated with the HER2 positive tumors, and promoter hypermethylation of ITGA1, ITGA9, NID1 and NID2 was associated with a genome-wide CpG island hypermethylated BC subtype. Given that ITGA4 is not expressed in normal breast, one might suggest that its abnormal promoter hypermethylation in cancer is non-functional and is thus merely a passenger epimutation. Yet, this assumption is not supported by our finding that it is not associated with a hypermethylated BC subtype. ITGA4 acquires expression in a subset of breast carcinomas, and methylation of its promoter may be preventive against expression in some tumors. Strong association of abnormal ITGA4 hypermethylation with the HER2 positive tumors (p = 0.0025) suggests that simultaneous presence of both HER2 and integrin α4 receptors is not beneficial for tumor cells. This may imply HER2 and integrin α4 signaling pathways interactions that are yet to be discovered.
Freshwater mussels (Unionidae) brought into captivity exhibit up-regulation of genes involved in stress and energy metabolism
Authors: Roznere Ieva , Sinn Brandon T. , Daly Marymegan , Watters G. Thomas 
Published: January 2021

AbstractApproximately two thirds of freshwater mussel species in the United States and Canada are imperiled, and populations are declining rapidly. Translocation and captive management are commonly used to mitigate losses of freshwater mussel biodiversity, but these conservation tools may result in decreased growth and increased mortality. This study uses RNA-Seq to determine how translocation into captivity affects gene expression inAmblema plicata. Mussels were collected from the Muskingum River in Ohio, USA and brought into a captive holding facility. RNA was extracted from gill tissue 11 months post translocation from mussels in captivity and the Muskingum River on the same day. RNA was sequenced on an Illumina HiSeq 2500, and differential expression analysis was performed on de novo assembled transcripts. More than 1200 transcripts were up-regulated in captive mussels, and 246 were assigned functional annotations. Many up-regulated transcripts were involved in energy metabolism and the stress response, such as heat shock proteins and antioxidants. More than 500 transcripts were down-regulated in captive mussels, and 41 were assigned functional annotations. We observed an over-representation of down-regulated transcripts associated with immune response. Our work suggests thatA. plicataexperienced moderate levels of stress and altered energy metabolism and immune response for at least 11 months post translocation into captivity.
Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Authors: Middelkamp H. H. T. , Verboven A. H. A. , De Sá Vivas A. G. , Schoenmaker C. , Klein Gunnewiek T. M. , Passier R. , Albers C. A. , ‘t Hoen P. A. C. , Nadif Kasri N. , van der Meer A. D. 
Published: January 2021

AbstractIn vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.
Acyl-CoA thioesterase activity of peroxisomal ABC protein ABCD1 is required for the transport of very long-chain acyl-CoA into peroxisomes
Authors: Kawaguchi Kosuke , Mukai Emi , Watanabe Shiro , Yamashita Atsushi , Morita Masashi , So Takanori , Imanaka Tsuneo 
Published: January 2021

AbstractThe ABCD1 protein, one of the four ATP-binding cassette (ABC) proteins in subfamily D, is located on the peroxisomal membrane and is involved in the transport of very long chain fatty acid (VLCFA)-CoA into peroxisomes. Its mutation causes X-linked adrenoleukodystophy (X-ALD): an inborn error of peroxisomal β-oxidation of VLCFA. Whether ABCD1 transports VLCFA-CoA as a CoA ester or free fatty acid is controversial. Recently, Comatose (CTS), a plant homologue of human ABCD1, has been shown to possess acyl-CoA thioesterase (ACOT) activity, and it is suggested that this activity is required for transport of acyl-CoA into peroxisomes. However, the precise transport mechanism is unknown. Here, we expressed human His-tagged ABCD1 in methylotrophic yeast, and characterized its ACOT activity and transport mechanism. The expressed ABCD1 possessed both ATPase and ACOT activities. The ACOT activity of ABCD1 was inhibited by p-chloromercuribenzoic acid (pCMB), a cysteine-reactive compound. Furthermore, we performed a transport assay with ABCD1-containing liposomes using 7-nitro-2–1,3-benzoxadiazol-4-yl (NBD)-labeled acyl-CoA as the substrate. The results showed that the fatty acid produced from VLCFA-CoA by ABCD1 is transported into liposomes and that ACOT activity is essential during this transport process. We propose a detailed mechanism of VLCFA-CoA transport by ABCD1.
Application of green tea catechins, polysaccharides, and flavonol prevent fine dust induced bronchial damage by modulating inflammation and airway cilia
Authors: Kim Juewon , Choi Hyunjung , Choi Dong-Hwa , Park Kyuhee , Kim Hyung-June , Park Miyoung 
Published: January 2021

AbstractAirborne fine dust particles (FDPs) have been identified as major toxins in air pollution that threaten human respiratory health. While searching for an anti-FDP reagent, we found that green tea extract (GTE) and fractions rich in flavonol glycosides (FLGs) and crude tea polysaccharides (CTPs) had protective effects against FDP-stimulated cellular damage in the BEAS-2B airway epithelial cell line. The GTE, FLGs, and CTPs significantly increased viability and lowered oxidative stress levels in FDP-treated cells. Combined treatment with GTE, FLGs, and CTPs also exerted synergistic protective effects on cells and attenuated FDP-induced elevations in inflammatory gene expression. Moreover, the green tea components increased the proportion of ciliated cells and upregulated ciliogenesis in the airway in FDP-stimulated BEAS-2B cells. Our findings provide insights into how natural phytochemicals protect the airway and suggest that green tea could be used to reduce FDP-induced airway damage as an ingredient in pharmaceutical, nutraceutical, and also cosmeceutical products.
Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
Authors: Lee Jeong Hoon , Kweon Solbi , Park Yu Rang 
Published: January 2021

AbstractGenetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
Identification of sulforaphane regulatory network in hepatocytes by microarray data analysis based on GEO database
Authors: Gao Lei , Wang Jinshen , Zhao Yuhua , Liu Junhua , Cai Da , Zhang Xiao , Wang Yutao , Zhang Shuqiu 
Published: January 2021

Abstract
For the past several years, more and more attention has been paid to the exploration of traditional medicinal plants. Further studies have shown that more dietary consumption of cruciferous vegetables can prevent the occurrence of tumor, indicating the potential applications in the chemoprevention of cancer. Sulforaphane (SFN) has been identified by the National Cancer Institute as a candidate for chemopreventive research; it is one of several compounds selected by the National Cancer Institute’s Rapid Access to Preventive Intervention Development Program and is currently in use. In the present study, based on the data of Gene Expression Omnibus database (GEO), the gene expression profile of hepatocytes that were treated with SFN was analyzed. The ANOVA and Limma packets in R were used to analyze the differentially expressed genes (DEGs). On this basis, gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment were further analyzed. The core gene HSP90-α (cytosolic), class A member 1 (HSP90AA1) was screened by protein–protein interaction (PPI) network established by STRING and Cytoscape software for further study. Finally, miRNAs targeted HSP90AA1 were predicted by miRanda. All in all, based on the data of GSE20479 chip, the molecular mechanism of SFN on hepatocytes was studied by a series of bioinformatics analysis methods, and it indicated that SFN might effect on the hepatocyte by regulating HSP90AA1.
Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer
Authors: Yu Jie , Zhang QianYun , Wang MengChuan , Liang SiJia , Huang HongYun , Xie Lang , Cui ChunHui , Yu JinLong 
Published: January 2021

Abstract
Tumor mutation burden (TMB) was a promising marker for immunotherapy. We aimed to investigate the prognostic role of TMB and its relationship with immune cells infiltration in gastric cancer (GC). We analyzed the mutation landscape of all GC cases and TMB of each GC patient was calculated and patients were divided into TMB-high and TMB-low group. Differentially expressed genes (DEGs) between the two groups were identified and pathway analysis was performed. The immune cells infiltration in each GC patient was evaluated and Kaplan–Meier analysis was performed to investigate the prognostic role of immune cells infiltration. At last, hub immune genes were identified and a TMB prognostic risk score (TMBPRS) was constructed to predict the survival outcome of GC patients. The relationships between mutants of hub immune genes and immune infiltration level in GC was investigated. We found higher TMB was correlated with better survival outcome and female patients, patients with T1-2 and N0 had higher TMB score. Altogether 816 DEGs were harvested and pathway analysis demonstrated that patients in TMB-high group were associated with neuroactive ligand–receptor interaction, cAMP signaling pathway, calcium signaling pathway. The infiltration of activated CD4+ memory T cells, follicular helper T cells, resting NK cells, M0 and M1 macrophages and neutrophils in TMB-high group were higher compared than that in TMB-low group and high macrophage infiltration was correlated with inferior survival outcome of GC patients. Lastly, the TMBPRS was constructed and GC patients with high TMBPRS had poor prognosis.
Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT)
Authors: Craig Jonathan M. , Laszlo Andrew H. , Nova Ian C. , Gundlach Jens H. 
Published: January 2021

Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT’s spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT’s ability to discern an enzyme’s nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.