Array Database Research Articles

Unraveling the role of lipid droplets and perilipin 2 in bovine luteal cells.

Steroidogenic tissues contain cytosolic lipid droplets that are important for steroidogenesis. Perilipin 2 (PLIN2), a structural coat protein located on the surface of lipid droplets in mammalian cells, plays a crucial role in regulating lipid droplet formation and contributing to various cellular processes such as lipid storage and energy homeostasis. Herein, we examine the role that PLIN2 plays in regulating progesterone synthesis in the bovine corpus luteum. Utilizing gene array databases and Western blotting, we have delineated the expression pattern of PLIN2 throughout the follicular to luteal transition. Our findings reveal the presence of PLIN2 in both ovarian follicular and steroidogenic luteal cells, demonstrating an increase in its levels as follicular cells transition into the luteal phase. Moreover, the depletion of PLIN2 via siRNA enhanced progesterone production in small luteal cells, whereas adenovirus-mediated overexpression of both PLIN2 and Perilipin 3 (PLIN3) induced an increase in cytosolic lipid droplet accumulation and decreased hormone-induced progesterone synthesis in these cells. Lastly, invivo administration of the luteolytic hormone prostaglandin F2α resulted in an upregulation of PLIN2 mRNA and protein expression, accompanied by a decline in serum progesterone. Our findings highlight the pivotal role of PLIN2 in regulating progesterone synthesis in the bovine corpus luteum, as supported by its dynamic expression pattern during the follicular to luteal transition and its responsiveness to luteotropic and luteolytic hormones. We suggest PLIN2 as a potential therapeutic target for modulating luteal function.

Discovery and technical validation of high-performance methylated DNA markers for the detection of cervical lesions at risk of malignant progression in low- and middle-income countries

BackgroundCervical cancer remains a leading cause of death, particularly in developing countries. WHO screening guidelines recommend human papilloma virus (HPV) detection as a means to identify women at risk of developing cervical cancer. While HPV testing identifies those at risk, it does not specifically distinguish individuals with neoplasia. We investigated whether a quantitative molecular test that measures methylated DNA markers could identify high-risk lesions in the cervix with accuracy.ResultsMarker discovery was performed in TCGA-CESC Infinium Methylation 450 K Array database and verified in three other public datasets. The panel was technically validated using Quantitative Multiplex-Methylation-Specific PCR in tissue sections (N = 252) and cervical smears (N = 244) from the USA, South Africa, and Vietnam. The gene panel consisted of FMN2, EDNRB, ZNF671, TBXT, and MOS. Cervical tissue samples from all three countries showed highly significant differential methylation in squamous cell carcinoma (SCC) with a sensitivity of 100% [95% CI 74.12–100.00], and specificity of 91% [95% CI 62.26–99.53] to 96% [95% CI 79.01–99.78], and receiver operating characteristic area under the curve (ROC AUC) = 1.000 [95% CI 1.00–1.00] compared to benign cervical tissue, and cervical intraepithelial neoplasia 2/3 with sensitivity of 55% [95% CI 37.77–70.84] to 89% [95% CI 67.20–98.03], specificity of 93% [95% CI 84.07–97.38] to 96% [95% CI 79.01–99.78], and a ROC AUC ranging from 0.793 [95% CI 0.68–0.89] to 0.99 [95% CI 0.97–1.00] compared to CIN1. In cervical smears, the marker panel detected SCC with a sensitivity of 87% [95% CI 77.45–92.69], specificity 95% [95% CI 88.64–98.18], and ROC AUC = 0.925 [95% CI 0.878–0.974] compared to normal, and high-grade squamous intraepithelial lesion (HSIL) at a sensitivity of 70% (95% CI 58.11–80.44), specificity of 94% (95% CI 88.30–97.40), and ROC AUC = 0.884 (95% CI 0.822–0.945) compared to low-grade intraepithelial lesion (LSIL)/normal in an analysis of pooled data from the three countries. Similar to HPV-positive, HPV-negative cervical carcinomas were frequently hypermethylated for these markers.ConclusionsThis 5-marker panel detected SCC and HSIL in cervical smears with a high level of sensitivity and specificity. Molecular tests with the ability to rapidly detect high-risk HSIL will lead to timely treatment for those in need and prevent unnecessary procedures in women with low-risk lesions throughout the world. Validation of these markers in prospectively collected cervical smear cells followed by the development of a hypermethylated marker-based cervical cancer detection test is warranted.

Therapeutic effect of microRNA-21 on differentially expressed hub genes in gastric cancer based on systems biology

Gastric cancer (GC) is a leading cause of mortality for many people. Cancer’s initiating factors are poorly understood. miR-21 has a crucial function in several malignancies, particularly GC. Furthermore, it has been shown that miR-21 is critical for the emergence and advancement of GC. This work intends to identify new genes which expression is associated with the activity of mir-21 in GC and to investigate the effect of downregulation of mir-21 on these genes and gastric tumorigenesis. We utilized the gene expression profiles of GCs from an Array database (GSE13911) from the Gene Expression Omnibus (GEO) dataset to find differentially expressed genes (DEGs) between control and gastric cancer groups. Using weighted gene correlation network analysis (WGCNA) in R, the Gene co-expression network was reconstructed. The microRNA–mRNA network was then reconstructed using the miRWalk database, and by investigating the microRNA–mRNA network, the genes that have an association with mir-21 were found. To implement the functional investigation, MKN and AGS cell lines were transfected with anti-miR-21 next. Subsequently, MTT proliferation was utilized to assess the cell's vitality. qRT-PCR was then used to evaluate the anticipated levels of gene expression in both GC cell lines. This study discovered and predicted CCL28, NR3C2, and SNYPO2 as the targets of miR-21 (GC), which are downregulated through gastric tumorigenesis, showing great potential as therapeutic and diagnostic targets. The suppression of miR-21 in gastric GC cells led to the inhibition of cell proliferation and decreased expression of CCL28, NR3C2, and SNYPO2 genes. This study established that miR-21, via downregulating these genes, contributes significantly to the development of GC. In addition, systems biology techniques identified CCL28, NR3C2, and SNYPO2 genes as possible GC surveillance and therapy components.

NARFL deficiency caused mitochondrial dysfunction in lung cancer cells by HIF-1α–DNMT1 axis

NARFL was reported to be a component of cytosolic iron–sulfur cluster assembly pathway and a causative gene of the diffused pulmonary arteriovenous malformations (dPAVMs). NARFL knockout dramatically impaired mitochondrial integrity in mice, which might promote mitochondrial dysfunction and lead to worse survival rate of lung cancer. However, the underlying molecular mechanism of NARFL deficiency in non-small cell lung cancer (NSCLC) is unknown. Knockdown assay was performed in A549 and H1299 cells. The protein levels of HIF-1α and DNMT1 were measured, and then Complex I activity, mtDNA copy numbers and mRNA levels of mtND genes were determined. Cisplatin resistance and cell proliferation were conducted using CCK8 assay. Cell migration and invasion were detected using wound heal assay and transwell assay. Survival analysis of lung cancer patients and KM plotter database were used for evaluating the potential value of NARFL deficiency. NARFL protein was expressed in two cell lines and knockdown assay significantly reduced its levels. Knockdown NARFL increased the protein levels of HIF-1α and DNMT1, and downregulated the mRNA levels of ND genes, mitochondrial Complex I activity, mtDNA copy number, and ATP levels. The mitochondrial dysfunction caused by NARFL deficiency were ameliorated by siHIF-1α and DNMT1 inhibitor. Knockdown NARFL increased the drug resistance and cell migration, and siHIF-1α reversed this effect. Moreover, NSCLC patients with NARFL deficiency had a poor survival rate using a tissue array and KM plotter database, and it would be a target for cancer prognosis and treatment. NARFL deficiency caused dysregulation of energy metabolism in lung cancer cells via HIF-1α–DNMT1 axis, which promoted drug resistance and cell migration. It provided a potential target for treatment and prognosis of lung cancer.

Looking for evidence of high-mass star formation at core scale in a massive molecular clump

Context. High-mass stars are formed as a result of the fragmentation of massive molecular clumps. However, what it is not clear is whether this fragmentation gives rise to stable prestellar cores massive enough to directly form high-mass stars or leads to prestellar cores of low masses that, by acquiring material from the environment, generate high-mass stars. Several recent observational studies focused on the characterisation of prestellar massive clump candidates. Nevertheless, studies of active massive clumps at different evolutionary stages are still needed to gain a complete understanding of how high-mass stars form. Aims. We present a comprehensive physical and chemical study of the fragmentation and star formation activity towards the massive clump AGAL G338.9188+0.5494, which harbours the extended green object EGO 338.92+0.55(b). The presence of an EGO embedded in a massive clump suggests that high-mass star formation is occurring at clump scale. The main goal of this work is to find evidence of such high-mass star formation, but at core scale. Methods. Using millimetre observations of continuum and molecular lines obtained from the Atacama Large Millimeter Array database at Bands 6 and 7, we study the substructure of the massive clump AGAL G338.9188+0.5494. The angular resolution of the data at Band 7 is about 0″.5, which allows us to resolve structures of about 0.01 pc (~2000 au) at the distance of 4.4 kpc. Results. The continuum emission at 340 GHz reveals that the molecular clump is fragmented into five cores, labelled C1 to C5. The 12CO J = 3−2 emission shows the presence of molecular outflows related to three of them. The molecular outflow related to core C1 is among the most massive (from 0.25 to 0.77 M⊙) and energetic (from 0.4 × 1046 to 1.2 × 1046 erg), considering studies carried out with similar observations towards this type of source. Rotational diagrams for the CH3CN and CH3CCH yield temperatures of about 340 and 72 K, respectively, for the core C1. The different temperatures show that the methyl cyanide would trace a gas layer closer to the protostar than the methyl acetylene, which would trace outermost layers. Using a range of temperatures going from 120 K (about the typical molecular desorption temperature in hot cores) to the temperature derived from CH3CN (about 340 K), the mass of core C1 ranges from 3 to 10 M⊙. The mid-IR 4.5 µm extended emission related to the EGO coincides in position and inclination with the discovered molecular outflow arising from core C1, which indicates that it should be the main source responsible for the 4.5 µm brightness. The average mass and energy of such a molecular outflow is about 0.5 M⊙ and 1046 erg, respectively, which suggest that 10 M⊙ is the most likely mass value for core C1. Additionally, we find that the region is chemically very rich with several complex molecular species. In particular, from an analysis of the CN emission, we find strong evidence that this radical is indirectly tracing the molecular outflows, or, more precisely, the border of the cavity walls carved out by such outflows, and therefore we point out that this is probably one of the first clear detection of CN as a tracer of molecular outflows in star-forming regions.

EFEMP2 upregulates PD-L1 expression via EGFR/ERK1/2/c-Jun signaling to promote the invasion of ovarian cancer cells

BackgroundFibulin-like extracellular matrix protein 2 (EFEMP2) has been reported to be related to the progression of various cancers. We have previously reported that EFEMP2 was highly expressed in ovarian cancer and was strongly associated with poor prognosis in patients. This study intends to further explore its interacting proteins and possible downstream signaling pathways.MethodThe expression of EFEMP2 was detected by RT-qPCR, ICC and western blot in 4 kinds of ovarian cancer cells with different migration and invasion ability. Cell models with strong or weak EFEMP2 expression were constructed by lentivirus transfection. The effects of the down-regulation and up-regulation of EFEMP2 on the biological behavior of ovarian cancer cells were studied through in-vitro and in-vivo functional tests. The phosphorylation pathway profiling array and KEGG database analyses identified the downstream EGFR/ERK1/2/c-Jun signaling pathway and the programmed death-1 (PD-L1) pathway enrichment. Additionally, the protein interaction between EFEMP2 and EGFR was detected by immunoprecipitation.ResultEFEMP2 was positively correlated with the invasion ability of ovarian cancer cells, its down-regulation inhibited the migrative, invasive and cloning capacity of cancer cells in vitro and suppressed the tumor proliferation and intraperitoneal diffusion in vivo, while its up-regulation did the opposite. Moreover, EFEMP2 could bind to EGFR to induce PD-L1 regulation in ovarian cancer, which was caused by the activation of EGFR/ERK1/2/c-Jun signaling. Similar to EFEMP2, PD-L1 was also highly expressed in aggressive cells and had the ability to promote the invasion and metastasis of ovarian cancer cells both in vitro and in vivo, and PD-L1 upregulation was partly caused by EFEMP2 activation. Afatinib combined with trametinib had an obvious effect of inhibiting the intraperitoneal diffusion of ovarian cancer cells, especially in the group with low expression of EFEMP2, while overexpression of PD-L1 could reverse this phenomenon.ConclusionEFEMP2 could bind to EGFR to activate ERK1/2/c-Jun pathway and regulate PD-L1 expression, furthermore PD-L1 was extremely essential for EFEMP2 to promote ovarian cancer cells invasion and dissemination in vitro and in vivo. Targeted therapy against the source gene EFEMP2 is our future research direction, which may better inhibit the invasion and metastasis of ovarian cancer cells.

EpEX, the soluble extracellular domain of EpCAM, resists cetuximab treatment of EGFR-high head and neck squamous cell carcinoma

ObjectivesCetuximab (Cmab) is a molecularly targeted monoclonal antibody drug for head and neck squamous cell carcinoma (HNSC), although cetuximab resistance is a serious challenge. Epithelial cell adhesion molecule (EpCAM) is an established marker for many epithelial tumors, while the soluble EpCAM extracellular domain (EpEX) functions as a ligand for epidermal growth factor receptor (EGFR). We investigated the expression of EpCAM in HNSC, its involvement in Cmab action, and the mechanism by which soluble EpEX activated EGFR and played key roles in Cmab resistance. Materials and methodsWe first examined EPCAM expression in HNSCs and its clinical significance by searching gene expression array databases. We then examined the effects of soluble EpEX and Cmab on intracellular signaling and Cmab efficacy in HNSC cell lines (HSC-3 and SAS). ResultsEPCAM expression was found to be enhanced in HNSC tumor tissues compared to normal tissues, and the enhancement was correlated with stage progression and prognosis. Soluble EpEX activated the EGFR-ERK signaling pathway and nuclear translocation of EpCAM intracellular domains (EpICDs) in HNSC cells. EpEX resisted the antitumor effect of Cmab in an EGFR expression-dependent manner. ConclusionSoluble EpEX activates EGFR to increase Cmab resistance in HNSC cells. The EpEX-activated Cmab resistance in HNSC is potentially mediated by the EGFR-ERK signaling pathway and the EpCAM cleavage-induced nuclear translocation of EpICD. High expression and cleavage of EpCAM are potential biomarkers for predicting the clinical efficacy and resistance to Cmab.

New eruptive variable(s) in the RAFGL 7009S H ii region

ABSTRACT Eruptions of young stellar objects (YSOs) are rare events, therefore a new outburst is always noteworthy. We present two new high-amplitude variable YSOs, J183421.85−055951.0 (#1) and J183421.39−055937.7 (#2), in the RAFGL 7009S star-forming region. We find them in the United Kingdom Infrared Telescope Infrared Deep Sky Survey Galactic Plane Survey data base, and supplement these data with archived infrared and millimetre photometric and spectral images and data from the Spitzer Infrared Array Camera, the K-band Multi-Object Spectrograph, and the Atacama Large Millimeter/submillimeter Array data bases. The outburst in #1 occurred in the period 2007–2011, during which the brightness increased by ∼2.7 mag in the K band and by ∼2.5 mag in the 3.6 μm band. The colour indices indicate a YSO in Class I/II evolutionary stage. After outburst, the K-band spectrum shows the CO band, Brγ, Mg i in absorption and H2 in emission – characteristics associated with a FU Orionis (FUors)-type eruptive variable. Object #1 is associated with an outflow detected in the near-infrared and millimetre ranges, mainly in the H2, SiO, HCO+, and HCN lines. Object #2 only shows high-amplitude variability in the K band (ΔK = 2.0 mag) while its colour indices before outburst indicate a YSO at an early evolutionary stage. There is no obvious outflow activity associated with this object. We classify #1 as a FUor-type eruptive variable based on the obtained data. The limited information on #2 makes it difficult to draw definite conclusions about the nature of its variability.

CA916798 predicts poor prognosis and promotes Gefitinib resistance for lung adenocarcinoma

BackgroundOur previous studies have identified CA916798 as a chemotherapy resistance-associated gene in lung cancer. However, the histopathological relevance and biological function of CA916798 in lung adenocarcinoma (LUAD) remains to be delineated. In this study, we further investigated and explored the clinical and biological significance of CA916798 in LUAD.MethodsThe relationship between CA916798 and clinical features of LUAD was analyzed by tissue array and online database. CCK8 and flow cytometry were used to measure cell proliferation and cell cycle of LUAD after knockdown of CA916798 gene. qRT-PCR and western blotting were used to detect the changes of cell cycle-related genes after knockdown or overexpression of CA916798. The tumorigenesis of LUAD cells was evaluated with or without engineering manipulation of CA916798 gene expression. Response to Gefitinib was evaluated using LUAD cells with forced expression or knockdown of CA916798.ResultsThe analysis on LUAD samples showed that high expression of CA916798 was tightly correlated with pathological progression and poor prognosis of LUAD patients. A critical methylation site in promoter region of CA916798 gene was identified to be related with CA916798 gene expression. Forced expression of CA916798 relieved the inhibitory effects of WEE1 on CDK1 and facilitated cell cycle progression from G2 phase to M phase. However, knockdown of CA916798 enhanced WEE1 function and resulted in G2/M phase arrest. Consistently, chemical suppression of CDK1 dramatically inhibited G2/M phase transition in LUAD cells with high expression of CA916798. Finally, we found that CA916798 was highly expressed in Gefitinib-resistant LUAD cells. Exogenous expression of CA916798 was sufficient to endow Gefitinib resistance with tumor cells, but interference of CA916798 expression largely rescued response of tumor cells to Gefitinib.ConclusionsCA916798 played oncogenic roles and was correlated with the development of Gefitinib resistance in LUAD cells. Therefore, CA916798 could be considered as a promising prognostic marker and a therapeutic target for LUAD.

Investigation of Hippo pathway-related prognostic lncRNAs and molecular subtypes in liver hepatocellular carcinoma

This study aimed to investigate Hippo pathway-related prognostic long noncoding RNAs (lncRNAs) and their prognostic value in liver hepatocellular carcinoma (LIHC). Expression and clinical data regarding LIHC were acquired from The Cancer Genome Atlas and European Bioinformatics Institute array databases. Hippo pathway-related lncRNAs and their prognostic value were revealed, followed by molecular subtype investigations. Differences in survival, clinical characteristics, immune cell infiltration, and checkpoint expression between the subtypes were explored. LASSO regression was used to determine the most valuable prognostic lncRNAs, followed by the establishment of a prognostic model. Survival and differential expression analyses were conducted between two groups (high- and low-risk). A total of 313 Hippo pathway-related lncRNAs were identified from LIHC, of which 88 were associated with prognosis, and two molecular subtypes were identified based on their expression patterns. These two subtypes showed significant differences in overall survival, pathological stage and grade, vascular invasion, infiltration abundance of seven immune cells, and expression of several checkpoints, such as CTLA-4 and PD-1/L1 (P < 0.05). LASSO regression identified the six most valuable independent prognostic lncRNAs for establishing a prognosis risk model. Risk scores calculated by the risk model assigned patients into two risk groups with an AUC of 0.913 and 0.731, respectively, indicating that the high-risk group had poor survival. The risk score had an independent prognostic value with an HR of 2.198. In total, 3007 genes were dysregulated between the two risk groups, and the expression of most genes was elevated in the high-risk group, involving the cell cycle and pathways in cancers. Hippo pathway-related lncRNAs could stratify patients for personalized treatment and predict the prognosis of patients with LIHC.

60 років базам даних (заключна частина)

The article provides an overview of research and development of databases since their appearance in the 60s of the last century to the present time. The following stages are distinguished: the emergence formation and rapid development, the era of relational databases, extended relational databases, post-relational databases and big data. At the stage of formation, the systems IDS, IMS, Total and Adabas are described. At the stage of rapid development, issues of ANSI/X3/ SPARC database architecture, CODASYL proposals, concepts and languages of conceptual modeling are highlighted. At the stage of the era of relational databases, the results of E. Codd’s scientific activities, the theory of dependencies and normal forms, query languages, experimental research and development, optimization and standardization, and transaction management are revealed. The extended relational databases phase is devoted to describing temporal, spatial, deductive, active, object, distributed and statistical databases, array databases, and database machines and data warehouses. At the next stage, the problems of post-relational databases are disclosed, namely, NOSQL-, NewSQL- and ontological databases. The sixth stage is devoted to the disclosure of the causes of occurrence, characteristic properties, classification, principles of work, methods and technologies of big data. Finally, the last section provides a brief overview of database research and development in the Soviet Union.

HN1L/AP-2γ/PLK1 signaling drives tumor progression and chemotherapy resistance in esophageal squamous cell carcinoma

Hematological and neurological expressed 1 like (HN1L) is a newly identified oncogene in lung cancer and hepatocellular carcinoma recently identified by our team, but its roles in the development and treatment of esophageal squamous cell carcinoma (ESCC) remain incompletely cataloged. Here, using ESCC tissue array and public database analysis, we demonstrated that HN1L was highly expressed in ESCC tissues, which was associated with tumor tissue invasion, poor clinical stage and short survival for ESCC patients. Loss- and gain-of-function studies in ESCC cells revealed that HN1L enhances ESCC cell metastasis and proliferation in vitro and in mice models. Moreover, high level of HN1L reduces the sensibility of ESCC cells to chemotherapeutic drugs, such as Docetaxel. Mechanism studies revealed that HN1L activated the transcription of polo-like kinase 1 (PLK1) by interacting with transcription factor AP-2γ, which increased the expression of malignancy related proteins Cyclin D1 and Slug in ESCC cells. Blocking PLK1 with inhibitor BI-2356 abrogated the oncogenic function of HN1L and significantly suppressed ESCC progression by combining with chemotherapy. Therefore, this study demonstrates the vital pro-tumor role of HN1L/AP-2γ/PLK1 signaling axis in ESCC, offering a potential therapeutic strategy for ESCC patients with high HN1L by blocking PLK1.

A survey on machine learning in array databases

This paper provides an in-depth survey on the integration of machine learning and array databases. First,machine learning support in modern database management systems is introduced. From straightforward implementations of linear algebra operations in SQL to machine learning capabilities of specialized database managers designed to process specific types of data, a number of different approaches are overviewed. Then, the paper covers the database features already implemented in current machine learning systems. Features such as rewriting, compression, and caching allow users to implement more efficient machine learning applications. The underlying linear algebra computations in some of the most used machine learning algorithms are studied in order to determine which linear algebra operations should be efficiently implemented by array databases. An exhaustive overview of array data and relevant array database managers is also provided. Those database features that have been proven of special importance for efficient execution of machine learning algorithms are analyzed in detail for each relevant array database management system. Finally, current state of array databases capabilities for machine learning implementation is shown through two example implementations in Rasdaman and SciDB.

60 років базам даних (частина четверта)

The article provides an overview of research and development of databases since their appearance in the 60s of the last century to the present time. The following stages are distinguished: the emer- gence formation and rapid development, the era of relational databases, extended relational data- bases, post-relational databases and big data. At the stage of formation, the systems IDS, IMS, Total and Adabas are described. At the stage of rapid development, issues of ANSI/X3/SPARC database architecture, CODASYL proposals, concepts and languages of conceptual modeling are highlighted. At the stage of the era of relation-al databases, the results of E. Codd’s scientific activities, the theory of dependencies and normal forms, query languages, experimental research and development, optimization and standardiza- tion, and transaction management are revealed. The extended relational databases phase is devot- ed to describing temporal, spatial, deductive, ac- tive, object, distributed and statistical databases, array databases, and database machines and data warehouses. At the next stage, the problems of post-relational databases are disclosed, namely, NOSQL-, NewSQL- and ontological databases. The sixth stage is devoted to the disclosure of the causes of occurrence, characteristic properties, classification, principles of work, methods and technologies of big data. Finally, the last section provides a brief overview of database research and development in the former Soviet Union.

60 років базам даних (частина третя)

The article provides an overview of research and development of databases since their appearance in the 60s of the last century to the present time. The following stages are distinguished: the emergence formation and rapid development, the era of relational databases, extended relational databases, post-relational databases and big data. At the stage of formation, the systems IDS, IMS, Total and Adabas are described. At the stage of rapid development, issues of ANSI/X3/SPARC database architecture, CODASYL proposals, concepts and languages of conceptual modeling are highlighted. At the stage of the era of relational databases, the results of E. Codd’s scientific activities, the theory of dependencies and normal forms, query languages, experimental research and development, optimization and standardization, and transaction management are revealed. The extended relational databases phase is devoted to describing temporal, spatial, deductive, active, object, distributed and statistical databases, array databases, and database machines and data warehouses. At the next stage, the problems of post-relational databases are disclosed, namely, NOSQL-, NewSQL- and ontological databases. The sixth stage is devoted to the disclosure of the causes of occurrence, characteristic properties, classification, principles of work, methods and technologies of big data. Finally, the last section provides a brief overview of database research and development in the Soviet Union.

CMTM Family Genes Affect Prognosis and Modulate Immunocytes Infiltration in Grade II/III Glioma Patients by Influencing the Tumor Immune Landscape and Activating Associated Immunosuppressing Pathways.

Lower-grade glioma (LGG) is one of the most common primary tumor types in adults. The chemokine-like factor (CKLF)-like Marvel transmembrane domain-containing (CMTM) family is widely expressed in the immune system and can modulate tumor progression. However, the role of the CMTM family in LGG remains unknown. A total of 508 LGG patients from The Cancer Genome Atlas (TCGA) database were used as a training cohort, and 155 LGG patients from the Chinese Glioma Genome Atlas (CGGA) array database, 142 LGG patients from the CGGA RNA-sequencing database, and 168 LGG patients from the GSE108474 database were used as the validation cohorts. Patients were subdivided into two groups using consensus clustering. The ENET algorithm was applied to build a scoring model based on the cluster model. Finally, ESTIMATE, CIBERSORT, and xCell algorithms were performed to define the tumor immune landscape. The expression levels of the CMTM family genes were associated with glioma grades and isocitrate dehydrogenase (IDH) status. Patients in cluster 2 and the high-risk score group exhibited a poor prognosis and were enriched with higher grade, wild-type IDH (IDH-WT), 1p19q non-codeletion, MGMT promoter unmethylation, and IDH-WT subtype. Patients in cluster 1 and low-risk score group were associated with high tumor purity and reduced immune cell infiltration. Enrichment pathways analysis indicated that several essential pathways involved in tumor progression were associated with the expression of CMTM family genes. Importantly, PD-1, PD-L1, and PD-L2 expression levels were increased in cluster 2 and high-risk groups. Therefore, the CMTM family contributes to LGG progression through modulating tumor immune landscape.

Unveiling the substructure of the massive clump AGAL G035.1330−00.7450

Context. It is known that high-mass stars form as the result of the fragmentation of massive molecular clumps. However, it is not clear whether this fragmentation gives rise to cores that are massive enough to directly form high-mass stars, or if leads to cores of low and intermediate masses that generate high-mass stars by acquiring material from their environment. Aims. Detailed studies of massive clumps at the early stage of star formation are needed to collect observational evidence that sheds light on the fragmentation processes from clump to core scales. The infrared-quiet massive clump AGAL G035.1330−00.7450 (AGAL35) located at a distance of 2.1 kpc is a promising object for studying the fragmentation and the star formation activity at early stages. Methods. Using millimeter observations of continuum and molecular lines obtained from the Atacama Large Millimeter Array database at Bands 6 and 7, we studied the substructure of the source AGAL35. The angular resolution of the data at Band 7 is about 0.′′7, which allowed us to resolve structures of about 0.007 pc (~1500 au). Results. The continuum emission at Bands 6 and 7 shows that AGAL35 harbors four dust cores, labeled C1 to C4, with masses lower than 3 M⊙. Cores C3 and C4 exhibit well-collimated, young, and low-mass molecular outflows related to molecular hydrogen emission-line objects that were previously detected. Cores C1 and C2 present CH3CN J = 13–12 emission, from which we derive rotational temperatures of about 180 and 100 K, respectively. These temperatures allow us to estimate masses of about 1.4 and 0.9 M⊙ for C1 and C2, respectively, which are about an order of magnitude lower than those estimated in previous works and agree with the Jeans mass of this clump. In particular, the moment 1 map of CH3CN emission suggests the presence of a rotating disk towards C1, which is confirmed by the CH3OH and CH3OCHO (20–19) emissions. On the other hand, the CN N = 2–1 emission shows a clumpy and filamentary structure that seems to connect all the cores. These filaments might be tracing the remnant gas of the fragmentation processes taking place within the massive clump AGAL35 or the gas that is being transported toward the cores, which would imply a competitive accretion scenario. Conclusions. The massive clump AGAL35 harbors four low- to intermediate-mass cores with masses lower than 3 M⊙, which is about an order of magnitude smaller than the masses estimated in previous works. This study shows that in addition to the importance of high-resolution and sensitivity observations for a complete detection of all fragments, it is very important to accurately determine the temperature of these cores for a correct mass estimation. Finally, although no high-mass cores were detected toward AGAL35, the filamentary structure connecting all the cores means that high-mass stars might form through the competitive accretion mechanism.

On the performance limits of thread placement for array databases in non-uniform memory architectures

On the performance limits of thread placement for array databases in non-uniform memory architectures

GeoSPARQL query support for scientific raster array data

This paper presents the design of a GeoSPARQL query processing solution for scientific raster array data, called GeoLD. The solution enables the implementation of SPARQL endpoints on top of OGC standard Web Coverage Processing Services (WCPS). Thus, the semantic querying of scientific raster data is supported without the need of specific raster array functions in the language. To achieve this, first Coverage to RDF mapping solutions were defined, based on the well-known W3C standard mappings for relational data. Next, the SPARQL algebra is extended with a new operator that delegates part of the GeoSPARQL query in WCPS services. Query optimization replaces those parts of the SPARQL query plan that may be delegated to a WCPS service by instances of such new WCPS operator. A first prototype has been implemented by extending the ARQ SPARQL query engine of Apache Jena. Petascope was used as the WCPS implementation on top of the Rasdaman raster array database. An initial evaluation with real meteorological data shows, as it was initially expected, that the approach outperforms an existing reference relational database based GeoSPARQL implementation.

Multi-Dimensional Data Compression and Query Processing in Array Databases

In recent times, the production of multidimensional data in various domains and their storage in array databases has witnessed a sharp increase; this rapid growth in data volumes necessitates compression in array databases. However, existing compression schemes used in array databases are general-purpose and not designed specifically for the databases. They could degrade query performance with complex analytical tasks, which incur huge computing costs. Thus, a compression scheme that considers the workflow of array databases is required. This study presents a compression scheme, SEACOW, for storing and querying multidimensional array data. The scheme is specially designed to be efficient for both dimension-based and value-based exploration. It considers data access patterns for exploration queries and embeds a synopsis, which can be utilized as an index, in the compressed array. In addition, we implement an array storage system, namely MSDB, to perform experiments. We evaluate query performance on real scientific datasets and compared it with those of existing compression schemes. Finally, our experiments demonstrate that SEACOW provides high compression rates compared to existing compression schemes, and the synopsis improves analytical query processing performance.