Circular Profile Research Articles

Parameter based definition of eccentric cycloid gearings

Current challenges for today’s industry are an increase in gear ratio in one stage, an increase in load capacity as well as an increase in efficiency compared to standard gears. The standard tooth profile for cylindrical gears is an involute. This tooth profile has certain limits for external gearings regarding its geometry, e.g., undercutting and a small radius of curvature near the base circle. Special gearings overcome these limits and offer an enormous potential in gear design through their adapted profile geometries. New manufacturing possibilities for gears, such as additive manufacturing or 5‑axis milling, mean that special gears can also be produced economically.In comparison to involute gears the description of non-involute gears is often not standardized and parameters describing the geometry are not commonly defined. Thus, it is not possible to adequately determine the corresponding properties. One of these special tooth profiles is the eccentric cycloid gearing (EC gearing), in which a circular profile rolls with a profile of a trochoid equidistant. This flank geometry can provide advantages over the standard involute in certain applications.This study introduces a geometric description of the EC gearing, which is based on a defined set of parameters. Besides the geometrical parameters, parameters describing the characteristics of the gearing are proposed in accordance with the description of involute gears. This parametric description of the EC gearing enables an analytical determination of the flank, the contact geometry and load-free characteristics. With the parametric description shown and the variation of the geometry possible with it, gearings suitable for practical applications can be generated.

Experimental Assessment of the Behavior of Tubular Truss Girder Joints Fabricated with Laser Cutting Technology

Directly welded truss girder joints result in high-stress development on the tube wall, which leads to increased chord thicknesses, requires extra welding, and presents detailing difficulties. Laser cutting technology (LCT) allows us to make precise cuts and pass through the truss members, welding the connection on the two sides. This can reduce geometrical imperfections, and, as a result, it increases joint strength. This paper presents truss girder joints developed with LCT that can develop higher resistance to static gravity loads with respect to conventional connections thanks to the pass-through solution. An extensive experimental campaign (31 specimens) has been carried out involving the monotonic gravity loading of several truss specimens to simulate their in-service conditions. Different truss typologies are tested (Warren and Pratt) using circular and square hollow section profiles, at different scales (full-scale and small-scale). The results showed that Warren-type structures with LCT connection solutions had a 20% higher strength with respect to the equivalent structures with directly welded joints. Furthermore, the correlation between the different failure modes and joint parameters (e.g., angles and distance between brace members) has been discussed.

Experimental Demonstration of an Easy-to-Fabricate 1.3-μm Directly Modulated DFB Laser With Improved Beam Profile

The integration of a directly modulated laser with a spot-size-converter can greatly reduce packaging requirements thereby reducing costs and promoting applications of these devices. However, most of the reported spot-size-converters integrated directly modulated laser need complex fabrication process which will increase cost and may degrade modulation bandwidth. We report a 1.3-μm directly modulated laser with ridge waveguide distributed feedback region and buried waveguide spot-size-converter region to improve beam profile and increase coupling efficiency with low fabrication cost. The core layer with high refractive index is simply tapered into a 500-nm-wide waveguide before regrowth and after the regrowth process, the buried heterojunction spot-size-converter is formed. The ridge waveguide distributed feedback with conventional high reflection coating is replaced by active-distributed-reflector is applied to prevent the aluminium-containing multi quantum wells from the risk of oxidation and further reduce fabrication cost. The fabricated device realized a nearly circular beam profile and more than 70% improvement of power coupling into a 5-μm lensed-fiber compared to normal ridge waveguide lasers. The fabricated laser also demonstrated a 3-dB modulation bandwidth of ∼19 GHz with good single mode stability. Key parameters are extracted to prove that integration of this spot-size-converter does not degrade the modulation performance and the modulation bandwidth is limited by the material gain as the estimated D factor of the tested device is 2.32 GHz/mA close to that extracted from the material parameters.

GeSn/Ge Multiquantum-Well Vertical-Cavity Surface-Emitting p-i-n Structures and Diode Emitters on a 200 mm Ge-on-Insulator Platform

An efficient monolithically integrated light source with complementary metal-oxide-semiconductor (CMOS) compatibility remains the missing component to enable Si photonics for various applications. In particular, vertical-cavity-surface-emitting (VCSE) light sources, such as resonant cavity light-emitting diodes (RCLEDs) and vertical-cavity surface-emitting lasers (VCSELs), are strong contenders due to their compact size, circular emission profile with low beam divergence, wafer-scale fabrication compatibility, high bandwidth, and high coupling efficiency to fiber optic cables. We report the first demonstration of 8-in. wafer-scale GeSn/Ge multiple-quantum-well VCSE p-i-n structures and diodes for laser or light-emitting diode (LED) applications in Si photonics by wafer bonding and layer transfer techniques, which are challenging for all-epitaxy routes. The wafer could be 12 in. (300 mm) since the MQW gain medium is grown on a 300 mm Si wafer, and the bonding is wafer-scale. Alternative dielectric layers (SiO2/SiN/SiO2), introduced by wafer bonding, under the emitting structure, serve as the bottom mirror for the vertical cavity. The Ge0.92Sn0.08/Ge MQW layer is utilized to improve the material quality and to confine injected carriers. As a result, more than 8× enhancement of light emission due to the vertical cavity resonance was demonstrated by photoluminescence spectroscopy. Besides, the spectral purity is enhanced by the single-longitudinal-mode cavity. The intensity of light emission is insensitive to the temperature range from 4 to 300 K and even becomes stronger at higher temperatures since the stronger resonant cavity effect at higher temperatures compensates for the drop in light emission efficiency caused by nonradiative centers. The vertical cavity effect on the light emission is further verified by reflectivity spectroscopy and optical simulations. A positive gain can be achieved as indicated by optical gain calculations. Room-temperature electroluminescence and an excellent carrier injection efficiency of the MQW VCSE diode are observed, showing its potential for electrically injected RCLEDs and VCSELs.

The Magnetic Sensitivity of the (250–278 nm) Fe ii Polarization Spectrum

This paper presents a theoretical investigation of the polarization and magnetic sensitivity of the near-ultraviolet (near-UV) solar spectral lines of Fe ii between 250 and 278 nm. In recent years, UV spectropolarimetry has become key to uncovering the magnetism of the upper layers of the solar chromosphere. The unprecedented data obtained by the CLASP2 suborbital space experiment across the Mg ii h and k lines around 280 nm are a clear example of the capabilities of near-UV spectropolarimetry for magnetic field diagnostics throughout the whole solar chromosphere. Recent works have pointed out the possible complementary diagnostic potential of the many Fe ii lines in the unexplored spectral region between 250 and 278 nm, but no quantitative analysis of the polarization and magnetic sensitivity of those spectral lines has been carried out yet. To study the polarization signals in these spectral lines, we create a comprehensive atomic model including all the atomic transitions resulting in strong spectral lines. We then study the magnetic sensitivity of the linear and circular polarization profiles in a semiempirical model representative of the quiet Sun. We present a selection of Fe ii spectral lines with significant linear and circular polarization signals and evaluate their diagnostic capabilities by studying their formation heights and magnetic sensitivity through the action of the Hanle and Zeeman effects. We conclude that when combined with the CLASP2 spectral region these Fe ii lines are of interest for the inference of magnetic fields throughout the solar chromosphere, up to near the base of the corona.

Transcriptome sequencing reveals the effects of circRNA on testicular development and spermatogenesis in Qianbei Ma goats.

Circular RNAs (circRNAs) play an important role in regulating the mammalian reproductive system, especially testicular development and spermatogenesis. However, their functions in testicular development and spermatogenesis in the Qianbei Ma goat, the Guizhou endemic breed are still unclear. In this study, tissue sectioning and circRNAs transcriptome analysis were conducted to compare the changes of morphology and circular RNAs gene expression profile at four different developmental stages (0Y, 0-month-old; 6Y, 6-month-old; 12Y, 12-month-old; 18Y, 18-month-old). The results showed that the circumferences and area of the seminiferous tubule gradually increased with age, and the lumen of the seminiferous tubule in the testis differentiated significantly. 12,784 circRNAs were detected from testicular tissues at four different developmental stages by RNA sequencing, and 8,140 DEcircRNAs (differentially expressed circRNAs) were found in 0Y vs. 6Y, 6Y vs. 12Y, 12Y vs. 18Y and 0Y vs. 18Y, 0Y vs. 12Y, 6Y vs. 18Y Functional enrichment analysis of the source genes showed that they were mainly enriched in testicular development and spermatogenesis. In addition, the miRNAs and mRNAs associated with DECircRNAs in 6 control groups were predicted by bioinformatics, and 81 highly expressed DECircRNAs and their associated miRNAs and mRNAs were selected to construct the ceRNA network. Through functional enrichment analysis of the target genes of circRNAs in the network, some candidate circRNAs related to testicular development and spermatogenesis were obtained. Such as circRNA_07172, circRNA_04859, circRNA_07832, circRNA_00032 and circRNA_07510. These results will help to reveal the mechanism of circRNAs in testicular development and spermatogenesis, and also provide some guidance for goat reproduction.

Endosidin 5 disruption of the Golgi Apparatus and extracellular matrix secretion in the unicellular charophyte, Penium margaritaceum.

Endosidins are a group of small molecular weight compounds, first identified by "chemical biology" screening assays, that have been used to target specific components of the endomembrane system. In this study, we employed multiple microscopy-based screening techniques to elucidate effects of Endosidin 5 (ES5) on the Golgi Apparatus and the secretion of extracellular matrix (ECM) components, Penium margaritaceum. These effects were compared with those caused by treatments with brefeldin A and concanamycin A. Penium margaritaceum's extensive Golgi Apparatus and endomembrane system make it an outstanding model organism for screening changes to the endomembrane system. Here we detail changes to the Golgi Apparatus and secretion of ECM material caused by Endosidin 5. Changes to extracellular polymeric substance (EPS) secretion and cell wall expansion were screened using fluorescence microscopy. Confocal laser scanning microscopy, and transmission electron microscopy were used to assess changes to the Golgi Apparatus, the cell wall and the vesicular network. Electron tomography was also performed in order to detail the changes to the Golgi Apparatus. While other endosidins were able to impact EPS secretion and cell wall expansion only ES5 completely inhibited EPS secretion and cell wall expansion over 24h. Short treatments of ES5 resulted in displacement of the Golgi bodies from their typical linear alignment. The number of cisternae decreased per Golgi stack and trans face cisternae in-curled to form distinct elongate circular profiles. Longer treatment resulted in a transformation of the Golgi body to an irregular aggregate of cisternae. These alterations could be reversed by removal of ES5 and returning cells to culture. ES5 alters secretion of ECM material in Penium by affecting the Golgi apparatus and does so in a markedly different way than other endomembrane inhibitors such as Brefeldin A and Concanamycin A.

Modelling of a semi-active vibration absorber featuring variable stiffness and variable damping using magnetorheological materials

This study focuses on vibration control and presents an innovative hybrid shock absorber with variable damping and stiffness. The simultaneous control over damping and stiffness is achieved using the Magnetorheological (MR) fluid and MR elastomer, respectively. A mathematical and Simulink model is developed by adding the four-parametric fluid model with the Bouc-Wen model. Two different road profiles, circular bump road and trapezoidal bump road profiles, are considered to analyze the performance of vibration absorbers. The compared results show the superiority of the proposed isolator over the passive system and reveal that the vehicle stability is improved by 87.5% to 92% and ride comfort is improved by 84.85% to 85.99% for circular and trapezoidal bump road profiles, respectively.

Screening differential circular RNA expression profiles and the potential role of hsa_circ_0085465 in liver cancer.

This study aimed to screen the circular RNAs (circRNAs) that are differentially expressed between liver cancer and paired paracarcinoma tissues and then elucidate their role in cancer progression. High-throughput sequencing of cancer and paired paracarcinoma tissues was followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the parental genes of the differentially expressed circRNAs, which were also verified via real-time quantitative polymerase chain reaction analysis of the tissues. In addition, the function of selected circRNAs was determined using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulfophenyl)-2H-tetrazolium (MTS) and transwell assays. Total 218 and 121 circRNAs were differentially upregulated and downregulated, respectively; these were mainly enriched with GO and KEGG terms related to biological functions. From five representatives of the differentially expressed circRNAs, we selected hsa_circ_0085465 for further analysis, discovering that its overexpression promoted the proliferation, migration, and invasion of 97 L cells. Taken together, our results suggest that hsa_circ_0085465 is relevant to liver cancer progression.

Systemic Lupus Erythematosus Patients with DNASE1L3·Deficiency Have a Distinctive and Specific Genic Circular DNA Profile in Plasma

Cell-free (cf) extrachromosomal circular DNA (eccDNA) has a potential clinical application as a biomarker. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a complex immunological pathogenesis, associated with autoantibody synthesis. A previous study found that SLE patients with deoxyribonuclease 1-like 3 (DNASE1L3) deficiency exhibit changes in the frequency of short and long eccDNA in plasma compared to controls. Here, using the DifCir method for differential analysis of short-read sequenced purified eccDNA data based on the split-read signal of the eccDNA on circulomics data, we show that SLE patients with DNASE1L3 deficiency have a distinctive profile of eccDNA excised by gene regions compared to controls. Moreover, this profile is specific; cf-eccDNA from the top 93 genes is detected in all SLE with DNASE1L3 deficiency samples, and none in the control plasma. The top protein coding gene producing eccDNA-carrying gene fragments is the transcription factor BARX2, which is involved in skeletal muscle morphogenesis and connective tissue development. The top gene ontology terms are 'positive regulation of torc1 signaling' and 'chondrocyte development'. The top Harmonizome terms are 'lymphopenia', 'metabolic syndrome x', 'asthma', 'cardiovascular system disease', 'leukemia', and 'immune system disease'. Here, we show that gene associations of cf-eccDNA can serve as a biomarker in the autoimmune rheumatic diseases.

An Experimental Study On Friction Stir Welding Of Aluminum-Magnesium Alloys For Improved Mechanical Properties Of Tailor Welded Blanks.

Tailor welded blanks (TWB) are used in automotive and aerospace industries as they offer weight saving followed by cost saving and improved fuel economy. Being light in weight and having low cost, Aluminum alloys have piqued the interest of scientists. Friction Stir Welding (FSW) is a well-known accepted technique used since 1991 worldwide for Aluminum and its alloys. Due to friction stir welding, mechanical changes occur due to stirring action at the joint. Also the inter-metallic compounds, kissing bond formation, onion ring formation etc. are defects encountered in the nugget zone of welding. Hence, a novel technique is suggested to carry out the friction stir welding using a blend of techniques viz. double sided friction stir welding and multi objective optimization of process parameters. For experimentation, AA 5182 and AA 5754-Aluminum Magnesium alloys of 5000 series are used with sheet size of 1.5 mm thickness. Experimentation was carried out on a vertical machining center, with circular, square, and triangular tool pin profiles with a tool rotational speed range between 1500 -1800 rpm and a welding speed range of 40 mm/min.-60 mm/min. For the analysis purpose, L9 orthogonal array was used and Grey Relational Analysis(GRA) was employed and ASTM standards were used for tensile testing. Base sample materials of AA 5182 and AA5754 are having ultimate tensile strengths of 289.58 N/mm2 and 220.75N/mm2respectively. The designed welded blank of the two materials recorded maximum ultimate tensile strength of 268.11N/mm2which was remarkable for FSW. Welded joint efficiency was found to be 92.73% and percentage elongation of TWB was found to be 44% as compared to the base metals.

Porthole die extrusion of aluminum 6063 industrial scrap by shear assisted processing and extrusion

Shear Assisted Processing and Extrusion (ShAPE) is presented as a new manufacturing technology for converting aluminum scrap directly into extruded products. In this work, a porthole die configuration is integrated within the rotating ShAPE process to extrude circular, square, trapezoidal, and two-cell trapezoidal profiles from aluminum alloy 6063 industrial scrap. Microstructural characterization is presented for a trapezoidal profile having an average grain size of 6.7 µm in the as-extruded condition. Round tubes achieved yield strength (246.9 ± 10.4 MPa), ultimate tensile strength (270.8 ± 9.6 MPa), and uniform elongation (16.5 ± 2.4%) exceeding industry standards.

RNA Sequencing Reveals the Differentially Expressed circRNAs between Stable and Unstable Carotid Atherosclerotic Plaques.

This study aimed to identify circular RNA profiles (circRNAs) via high-throughput RNA sequencing and distinguish the differentially expressed (DE) circRNAs between stable and unstable plaques. RNA sequencing was performed on unstable and stable carotid plaque samples obtained from patients with carotid artery stenosis. DE circRNAs were screened, and six DE circRNAs were verified using quantitative real-time PCR (qRT-PCR). Functional evaluation of the DE circRNAs was conducted via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. We screened 344 DE circRNAs in unstable plaques, consisting of 342 upregulated and 2 downregulated circRNAs. GO analysis showed that the host genes of the upregulated circRNAs were related to ER to Golgi transport vesicle membrane, endocytic vesicle membrane, and Ran GTPase binding. KEGG analysis revealed that the host genes of the upregulated circRNAs were primarily associated with protein processing in endoplasmic reticulum, lysine degradation, homologous recombination, epithelial cell signaling in Helicobacter pylori infection, and yersinia infection. The results of qRT-PCR verified three upregulated DE circRNAs and two downregulated DE circRNAs in unstable plaques. Hsa-circ-0001523, hsa-circ-0008950, hsa-circ-0000571, hsa-circ-0001946, and hsa-circ-0000745 may be involved in regulating the stability of atherosclerotic plaques and serves as a therapeutic target for unstable plaques.

Bioinformatic analysis confirms differences in circular RNA expression profiles of cumulus cells between patients with ovarian and peritoneal endometriosis-associated infertility.

Endometriosis has a detrimental effect on oocyte quality, and ovarian endometriosis (OEM) and peritoneal endometriosis (PEM) may have different effects on female fertility. Therefore, we conducted a study to explore the circular RNA (circRNA) expression profiles of cumulus cells (CCs) in patients with OEM (n = 3), PEM (n = 3), and tubal factor infertility (TFI, n = 3) using high-throughput sequencing techniques and attempted to identify common and unique circRNAs in the OEM and PEM groups. The CIRCexplorer2 program was used to identify circRNAs. Seven candidate circRNAs were validated in 30 samples using quantitative real-time polymerase chain reaction (qRT-PCR). Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to annotate the function of circRNA-targeted genes, which were verified by sequencing results and constructed circRNA-miRNA-mRNA networks. A total of 11833 circRNAs were identified in nine samples. The numbers of differentially expressed circRNAs between the OEM and TFI groups, PEM and TFI groups, and OEM and PEM groups were 130, 71, and 191, respectively. After taking intersections, 11 circRNAs were considered common circRNAs in the OEM and PEM groups; 39 circRNAs in the OEM group and 17 circRNAs in the PEM group were identified as unique key circRNAs. During qRT-PCR validation, hsa_circ_0003638 was significantly upregulated in the PEM group compared to that in the OEM and TFI groups. Functional analysis of circRNA-targeted genes revealed that apoptosis, PI3K-AKT, and p53 signaling pathways were enriched in the PEM-TFI comparison groups, whereas the functions of target genes involved in the JAK-STAT and TGF-β signaling pathways were enriched in the PEM-OEM comparison groups. Our findings confirmed differences in circRNA expression profiles of CCs between patients with OEM and PEM infertility and provide new insights into the different effects of various endometriosis phenotypes on oocytes.

Identification of Circular RNA Profiles in the Liver of Diet-Induced Obese Mice and Construction of the ceRNA Network.

Obesity is a major risk factor for cardiovascular, cerebrovascular, metabolic, and respiratory diseases, and it has become an important social health problem affecting the health of the population. Obesity is affected by both genetic and environmental factors. In this study, we constructed a diet-induced obese C57BL/6J mouse model and performed deep RNA sequencing (RNA-seq) on liner-depleted RNA extracted from the liver tissues of the mice to explore the underlying mechanisms of obesity. A total of 7469 circular RNAs (circRNAs) were detected, and 21 were differentially expressed (DE) in the high-fat diet (HFD) and low-fat diet (LFD) groups. We then constructed a comprehensive circRNA-associated competing endogenous RNA (ceRNA) network. Bioinformatic analysis indicated that DE circRNAs associated with lipid metabolic-related pathways may act as miRNA sponges to modulate target gene expression. CircRNA1709 and circRNA4842 may serve as new candidates to regulate the expression of PTEN. This study provides systematic circRNA-associated ceRNA profiling in HFD mouse liver, and the results can aid early diagnosis and the selection of treatment targets for obesity in the future.

Clone particles: A simplified technique to enforce solid boundary conditions in SPH

A simplified technique for the enforcement of boundary conditions along solid profiles is proposed in the framework of the Smoothed Particle Hydrodynamics. The main idea relies on a local definition of the normal and tangent vectors to the solid body, along with a local mirroring of the flow fields. This compound approach allows for a robust and accurate modelling of the fluid–solid interaction close to acute angles and sharp profiles. Numerical benchmarks at increasing complexity are considered to prove the reliability of the proposed technique: hydrostatic test cases, flow past cylinders with elliptic, triangular and spiked circular profile and, finally, a roto-translating motion of a spiked cylinder. The results are compared and validated with other numerical methods.

Tomography of a Solar Plage with the Tenerife Inversion Code

We apply the Tenerife Inversion Code (TIC) to the plage spectropolarimetric observations obtained by the Chromospheric LAyer SpectroPolarimeter (CLASP2). These unprecedented data consist of full Stokes profiles in the spectral region around the Mg ii h and k lines for a single slit position, with around two thirds of the 196″ slit crossing a plage region and the rest crossing an enhanced network. A previous analysis of these data had allowed us to infer the longitudinal component of the magnetic field by applying the weak-field approximation (WFA) to the circular polarization profiles, and to assign the inferred magnetic fields to different layers of the solar atmosphere based on the results of previous theoretical radiative transfer investigations. In this work, we apply the recently developed TIC to the same data. We obtain a stratified model atmosphere that fits the intensity and circular polarization profiles at each position along the spectrograph slit and we compare our results for the longitudinal component of the magnetic field with the previously obtained WFA results, highlighting the generally good agreement in spite of the fact that the WFA is known to produce an underestimation when applied to the outer lobes of the Mg ii h and k circular polarization profiles. Finally, we use the inverted model atmospheres to give a rough estimation of the energy that could be carried by Alfvén waves propagating in the chromosphere in the plage and network regions, showing that it is sufficient to compensate for the estimated energy losses in the chromosphere of solar active regions.

Exact Formulation for the Curvature of Gothic Arch Ball Screw Profiles and New Approximated Solution Based on Simplified Groove Geometry

The correct evaluation of the curvatures of ball screw grooves allows the accurate design of the constructive parameters of this mechanism and enhancing its performance. The formulation commonly used in the literature, however, refers to ball bearing geometry, ignoring the shape of the section’s profile and the helix angle. In this paper, the exact formulae for calculating the principal curvature radii of the screw shaft and the nut grooves are analytically derived and presented. These equations, obtained through a rigorous differential geometry approach, consider the helix angle and a gothic arch profile. An approximated formulation is proposed simplifying the exact solution under the assumption of a circular groove profile. These new simple formulae accurately reproduce the exact curvature radii values with a mean relative error of approximatively 0.51% and 0.40%, respectively, for the screw shaft and nut grooves, against the value of more than 50% obtained by using the literature formulae for common off-the-shelf ball screws, especially those with high helix angles. Furthermore, they allow a computational time saving of 98%, making them suitable for being incorporated in high-fidelity dynamic models of ball. Finally, two MATLAB functions are provided to easily evaluate the complex curvature exact solution.

Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles.

To bring new extrachromosomal circular DNA (eccDNA) enrichment technologies closer to the clinic, specifically for screening, early diagnosis, and monitoring of diseases or lifestyle conditions, it is paramount to identify the differential pattern of the genic eccDNA signal between two states. Current studies using short-read sequenced purified eccDNA data are based on absolute numbers of unique eccDNAs per sample or per gene, length distributions, or standard methods for RNA-seq differential analysis. Previous analyses of RNA-seq data found significant transcriptomics difference between sedentary and active life style skeletal muscle (SkM) in young people but very few in old. The first attempt using circulomics data from SkM and blood of aged lifelong sedentary and physically active males found no difference at eccDNA level. To improve the capability of finding differences between circulomics data groups, we designed a computational method to identify Differentially Produced per Gene Circles (DPpGCs) from short-read sequenced purified eccDNA data based on the circular junction, split-read signal, of the eccDNA, and implemented it into a software tool DifCir in Matlab. We employed DifCir to find to the distinctive features of the influence of the physical activity or inactivity in the aged SkM that would have remained undetected by transcriptomics methods. We mapped the data from tissue from SkM and blood from two groups of aged lifelong sedentary and physically active males using Circle_finder and subsequent merging and filtering, to find the number and length distribution of the unique eccDNA. Next, we used DifCir to find up-DPpGCs in the SkM of the sedentary and active groups. We assessed the functional enrichment of the DPpGCs using Disease Gene Network and Gene Set Enrichment Analysis. To find genes that produce eccDNA in a group without comparison with another group, we introduced a method to find Common PpGCs (CPpGCs) and used it to find CPpGCs in the SkM of the sedentary and active group. Finally, we found the eccDNA that carries whole genes. We discovered that the eccDNA in the SkM of the sedentary group is not statistically different from that of physically active aged men in terms of number and length distribution of eccDNA. In contrast, with DifCir we found distinctive gene-associated eccDNA fingerprints. We identified statistically significant up-DPpGCs in the two groups, with the top up-DPpGCs shed by the genes AGBL4, RNF213, DNAH7, MED13, and WWTR1 in the sedentary group, and ZBTB7C, TBCD, ITPR2, and DDX11-AS1 in the active group. The up-DPpGCs in both groups carry mostly gene fragments rather than whole genes. Though the subtle transcriptomics difference, we found RYR1 to be both transcriptionally up-regulated and up-DPpGCs gene in sedentary SkM. DifCir emphasizes the high sensitivity of the circulome compared to the transcriptome to detect the molecular fingerprints of exercise in aged SkM. It allows efficient identification of gene hotspots that excise more eccDNA in a health state or disease compared to a control condition.

Differential Circular RNA Expression Profiles in Induced Sputum of Patients with Asthma

Introduction: circRNA played a role in a variety of diseases. This paper aimed to explore the differentially expressed circRNA in induced sputum cells of asthma patients, so as to provide new potential biomarkers and new ideas for the study of asthma. Methods: All subjects were from the First Affiliated Hospital of Sun Yat-sen University. Differentially expressed circRNAs of asthma patients were screened by high-throughput sequencing. qRT-PCR was used to verify the expression of differential circRNAs. The association between circRNA and asthma was explored by analyzing the correlation between circRNA and clinical data and some cytokines of asthma patients. The possible ceRNA network was analyzed and predicted by online software, and the expression of each molecule in the network was preliminary verified by qRT-PCR in induced sputum cells and 16HBE cell. Results: We screened a total of 49 circRNAs differentially expressed in asthma patients (including 12 circRNAs with elevated expression and 37 circRNAs with decreased expression), among which has_circSORT1 and has_circSERPINB1 were significantly elevated. Correlation analysis showed that has_circSORT1 was correlated with FeNO, EOS%, IL-17A, IFN-γ, and PC20, and has_circSERPINB1 was correlated with IL-6, IL-17A, IFN-γ, FEV1%, and FVC%. The possible existence of has_circSORT1/has-miR-185-3p/ZNFX1, a ceRNA regulatory network, in induced sputum cells of asthma patients was hypothesized by online software prediction and qRT-PCR in sputum cells and 16HBE. Conclusion: Differentially expressed circRNAs existed in induced sputum cells of asthma patients, among which has_circSORT1 and has_circSERPINB1 were significantly upregulated and may be involved in the process of asthma disease, which could be expected to be a potential biomarker for asthma diagnosis. In addition, a ceRNA regulatory network, has_circSORT1/has-miR-185-3p/ZNFX1, may exist in asthma.