Miracle-dz/UniFAR-FTUs huggingface dataset:
Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifactorial disorders’ growth and incidence. Numerous studies have emphasized its significance and alterations in PCOS. We used bioinformatic methods to find novel dysregulated lncRNAs in PCOS. To achieve this objective, the gene expression profile of GSE48301, comprising PCOS patients and normal control tissue samples, was evaluated using the R limma package with the following cut-off criterion: p-value < 0.05. Firstly, weighted gene co-expression network analysis (WGCNA) was used to determine the co-expression genes of lncRNAs; subsequently, hub gene identification and pathway enrichment analysis were used. With the defined criteria, nine novel dysregulated lncRNAs were identified. In WGCNA, different colors represent different modules. In the current study, WGCNA resulted in turquoise, gray, blue, and black co-expression modules with dysregulated lncRNAs. The pathway enrichment analysis of these co-expressed modules revealed enrichment in PCOS-associated pathways, including gene expression, signal transduction, metabolism, and apoptosis. In addition, CCT7, EFTUD2, ESR1, JUN, NDUFAB1, CTTNB1, GRB2, and CTNNB1 were identified as hub genes, and some of them have been investigated in PCOS. This study uncovered nine novel PCOS-related lncRNAs. To confirm how these lncRNAs control translational modification in PCOS, functional studies are required.
Osteoblasts and Fibroblasts Interaction with a Porcine Acellular Dermal Matrix Membrane

The use of collagen membranes has remained the gold standard in GTR/GBR. In this study, the features and the biological activities of an acellular porcine dermis collagen matrix membrane applicable during dental surgery were investigated, and also by applying hydration with NaCl. Thus, two tested membranes were distinguished, the H-Membrane and Membrane, compared to the control cell culture plastic. The characterization was performed by SEM and histological analyses. In contrast, the biocompatibility was investigated on HGF and HOB cells at 3, 7, and 14 days by MTT for proliferation study; by SEM and histology for cell interaction study; and by RT-PCR for function-related genes study. In HOBs seeded on membranes, mineralization functions by ALP assay and Alizarin Red staining were also investigated. Results indicated that the tested membranes, especially when hydrated, can promote the proliferation and attachment of cells at each time. Furthermore, membranes significantly increased ALP and mineralization activities in HOBs as well as the osteoblastic-related genes ALP and OCN. Similarly, membranes significantly increased ECM-related and MMP8 gene expression in HGFs. In conclusion, the tested acellular porcine dermis collagen matrix membrane, mainly when it is hydrated, behaved as a suitable microenvironment for oral cells.
Sequential one-sample grouped signed rank tests for symmetry: Monte carlo studies

Monte Carlo studies of sequential, one-sample, signed rank tests developed earlier by the authors are reported. The basic tests are the ssr-test based on the sums of signed ranks and the csr-test based on the observed configurations of singed ranks in both of which groups of N observations are obtained a new for the totality of observations available at each stage of the sequential process. The alternative hypothesis in each case is stated in the class of Lehmann alternatives. The main Monte Carlo studies are for the ssr-test with α=β=0.05, N =2(1)10, and K(d)=2(1)5,k(d) indexing the alternative hypotheses. Studies are conducted for the L-model and the Φ-model respectively involving a Lehmann class of populations and classical normal populations with location changes. The parameter k* associated with k 1* describes the L-model while μ(k*) for the Φ-model is associated with it. Limited studies are made for the csr-test and the mcsr-test for comparisons. Average sample numbers and power functions are estima.
Identification of shared gene signatures and molecular mechanisms between chronic kidney disease and ulcerative colitis

Background There is a complex interaction between chronic kidney disease (CKD) and ulcerative colitis (UC), but the pathophysiological mechanisms underlying the coexistence of CKD and UC are unclear. This study aimed to investigate the key molecules and pathways that may mediate the co-occurrence of CKD and UC through quantitative bioinformatics analysis based on a public RNA-sequencing database. Methods The discovery datasets of CKD (GSE66494) and UC (GSE4183), as well as validation datasets of CKD (GSE115857) and UC (GSE10616), were downloaded from the Gene Expression Omnibus (GEO) database. After identifying differentially expressed genes (DEGs) with GEO2R online tool, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for the DEGs were performed. Next, protein-protein interaction network was constructed with Search Tool for the Retrieval of Interacting Genes (STRING) and visualized by Cytoscape. Gene modules were identified by the plug-in MCODE and hub genes were screened using the plug-in CytoHubba. Then, correlation between immune cell infiltration and hub genes was analyzed, and the receiver operating characteristic curves were used to assess the predictive value of hub genes. Finally, immunostaining of human specimens was used to validate the relevant findings. Results A total of 462 common DEGs were identified and selected for further analyses. GO and KEGG enrichment analyses indicated that these DEGs were primarily enriched in immune- and inflammation-related pathways. Among them, the PI3K-Akt signaling pathway ranked top in both discovery and validation cohorts, and the key signal molecule phosphorylated Akt (p-Akt) was shown to be significantly overexpressed in human CKD kidneys and UC colons, and further elevated in CKD-UC comorbidity specimens. Moreover, nine candidate hub genes, including CXCL8, CCL2, CD44, ICAM1, IL1A, CXCR2, PTPRC, ITGAX, and CSF3, were identified, of which ICAM1 was validated as a common hub gene. Besides, immune infiltration analysis revealed that neutrophils, macrophages, and CD4+ T memory cells significantly accumulated in both diseases, and ICAM1 was remarkably associated with neutrophil infiltration. Furthermore, intercellular adhesion molecule1 (ICAM1)-mediated neutrophil infiltration was validated to be upregulated in kidney and colon biopsies of CKD and UC patients, and further increased in patients diagnosed with both CKD and UC. Finally, ICAM1 had shown critical value as a diagnostic marker for the co-occurrence of CKD and UC. Conclusions Our study elucidated that immune response, PI3K-Akt signaling pathway, and ICAM1-mediated neutrophil infiltration might be the common pathogenesis of CKD and UC, and identified ICAM1 as a key potential biomarker and therapeutic target for the comorbidity of these two diseases.
A New Digital Analysis Technique for the Mechanical Aperture and Contact Area of Rock Fractures

In this study, a new digital technique for the analysis of the mechanical aperture and contact area of rock fractures under various normal stresses is proposed. The technique requires point cloud data of the upper and lower fracture surfaces, pressure film image data of the fracture, and normal deformation data of the fracture as input data. Three steps of algorithms were constructed using these input data: (1) a primary matching algorithm that considers the shape of the fracture surfaces; (2) a secondary matching algorithm that uses pressure film images; and (3) a translation algorithm that considers the normal deformation of a fracture. The applicability of the proposed technique was investigated using natural fracture specimens sampled at an underground research facility in Korea. In this process, the technique was validated through a comparison with the empirical equation suggested in a previous study. The proposed technique has the advantage of being able to analyze changes in the mechanical aperture and contact area under various normal stresses without multiple experiments. In addition, the change in the contact area on the fracture surface according to the normal stress can be analyzed in detail.
Bi‐directional electron pitch angle anisotropy in the plasma sheet

Analysis of low-energy particle measurement on Imp 6 satellite have revealed the occurrence of bi-directional electron pitch angle anisotropy (enhanced flux in field-aligned directions) in the magnetotail at the energy range of several hundreds to several keV. The bi-directional anisotropy was observed most commonly near the neutral sheet, with a parallel and perpendicular temperature ratio of 2–3, and they appeared also just inside of the magnetopause and in the boundary layer. The anisotropy of this extent was not an unusual phenomenon in the plasma sheet; in about 10% of the total of ∼200-hour interval that we examined electrons had bi-directional anisotropy. On the other hand, more sharply field-aligned electron flux enhancements, which cannot be represented by a Maxwellian distribution, are sometimes observed at radial distances of ∼10 RE, near the inner edge of the plasma sheet. The small pitch angle (less than ∼10°) observed in such cases suggests coupling of the enhanced field-aligned component with the ionosphere. In this paper we describe the observed characteristics of these anisotropic distributions and attempt to explain their formation by Fermi acceleration process in the plasma sheet. Owing to this process, electrons are more accelerated in parallel than perpendicular directions to the magnetic field as they traverse the neutral sheet. The effect of static electric field along the field line caused by the difference in pitch angle anisotropy of protons and electrons is also discussed.
Promoting customer advocacy in the ride-hailing sector: A generational cohort perspective

The days of the sharing economy being considered a niche market have long passed, as the sharing economy has become a profitable and budding market, attracting large investments and a multitude of customers (Möhlmann 2015:193). Since their rapid growth in popularity following the 2008 financial crisis (Kuswanto et al. 2020:76), the sharing economy and platform business models have become part of many consumers’ daily existence in terms of accommodation-, entertainmentand transportation-related services (Lee et al. 2018:829; Wang et al. 2022:197). Of particular interest to this study are Transportation Network Companies (TNCs) and their ridehailing platform business models. Typically, TNCs use smartphone application platforms to link drivers and customers requiring ride-hailing services. Drivers (fellow community members) cooperating with TNCs transfer customers (service recipients), using their own cars, receive payment by card or in cash, as is the case in some developing countries (Wadud 2020).
Correlations of ionospheric electric fields and energetic particle precipitation

Direct measurements of the thermal ionospheric ion distribution function made from two sounding rockets launched into the expansive phase of an auroral substorm are discussed. Ion flows perpendicular (convective) and parallel to the geomagnetic field lines are derived from these observations at altitudes from 200 to 840 km. Equivalent convective electric fields were observed to vary between a few tens of millivolts per meter to over 150 mV/m and are shown to be highly correlated with energetic electron precipitation. High-velocity (up to 2 km/s) parallel ion flows were observed at various times and also found to be correlated with auroral electron precipitation. A correlation analysis of perpendicular (or equivalent electric fields E/sub perpendicular/) and parallel ion flow velocities with energetic electron intensities I at various energies is presented. The form of the E/sub perpendicular/ versus the logarithm of I relationship is shown to be approximately linear over most of the observed E/sub perpendicular/ range. Ionospheric ''line-tying'' models are presented and compared with the measured E/ sub perpendicular/ versus I relationship. The model is found to be most consistent with observations when magnetospheric forces are assumed to be independent of the instantaneous values of E/sub perpendicular/ and I rather than viscouslike.more » No evidence was found to suggest that decoupling of magnetospheric and ionospheric convection through parallel electric fields produced the observed anticorrelation of E/sub perpendicular/ and I. (auth)« less
Effect of Energy Level of Photobiomodulation Therapy on Bone Repair in Rats

The aim of this experimental study was to determine the effect of photobiomodulation therapy on bone repair in a rat tibia osteotomy model at 15 and 30 days. The sample consisted of 36 male Holtzman rats that were randomized into 6 equal groups. Groups A1 and A2: osteotomy + 1 J laser energy. Groups B1 and B2: osteotomy + 3 J laser energy. Groups C1 and C2 (controls): osteotomy only. The bone repair was analyzed by histological evaluation of osteoblasts and osteocytes both at 15 days (groups A1, B1, and C1) and at 30 days (groups A2, B2, and C2). Within the results, in all groups a greater number of osteoblasts was found at 15 days vs 30 days (p<0.05), and a greater number of osteocytes in B1 and C2 vs B2 and C1, respectively (p<0.05). When evaluating the 3 groups worked up to 15 days, more osteoblasts were found in A1 and C1 vs B1 (p<0.001); and osteocytes predominated in A1 and B1 vs C1 (p<0.001). At 30 days there was a greater quantity of osteoblasts in C2 vs A2 and B2 (p<0.05) and of osteocytes in C2 vs B2 (p<0.05). It is concluded that 1 J photobiomodulation therapy improved bone repair at 15 days; however, this improvement was not observed at 30 days because there were no differences between the irradiated groups and the control.
Efficient Solution Methods for N-component Condensation

This thesis describes efficient solution methods developed for N-component condensation processes. These methods are aimed at either the reduction of the numerical effort required for solving the equations describing the condensation process or the simplification of the physical description. The models and corresponding algorithms differ in their ability to describe the condensation phenomenon and the required computing times. The equilibrium thermodynamics of real gases is presented and a robust numerical procedure is constructed based on Newton-Raphson iteration. The Jacobian of the system of equations has been determined analytically. The initialization scheme for the iterative procedure for these equilibrium problems uses a pressure-extrapolation scheme. Results are given for a three-phase ternary real-gas mixture. A multigrid method has been developed to enhance the efficiency of implicit numerical methods for solving the N-component Becker-Doring (NBD) equations. The geometrical multigrid method for arbitrary number of grid levels is presented. The multigrid algorithm solves the full set of NBD equations 10 times faster than conventional iterative schemes. The method is restricted to the regime of small cluster sizes due to limited available computational resources. However, the time dependent solution of the NBD equations does provide useful insight in the physics of the initial stages of the nucleation process. For single component condensation the Stationary Diffusion Flux (SDF) model has been derived which is valid in the entire cluster size space. The diffusion flux in the Fokker-Planck equation for unsteady condensation contains an unknown distribution function. This distribution function is approximated by a closed-form expression based on the cluster size distribution function for steady condensation. The resulting Stationary Diffusion Flux model is valid for all cluster sizes, computationally efficient and applicable to various types of cluster formation processes. In the regime of supercritical cluster sizes the diffusion flux is given by an analytical expression. The Phase Path Analysis (PPA) algorithm has been extended to N-component mixtures. For this method the N-component General Dynamic Equation (NGDE) is constructed. This model introduces clusters at a source point in the N-component cluster size space. The model allows for a very fast solution of the approximate Ncomponent cluster size distribution. For validation of the method a nucleation pulse test case involving a binary mixture has been used. Comparison of the numerical results of the NBD equations and those from the NGDE shows excellent agreement for the cluster size, cluster composition and the integral properties of the cluster size distribution. The PPA algorithm applied to the NGDE reduces the computational effort by a factor 105 compared to the effort required for solving the full set of NBD equations.
Francisella tularensis subsp. holarctica wild-type is able to colonize natural aquatic ex vivo biofilms

Biofilms are a matrix-associated lifestyle of microbial communities, often enabling survivability and persistence of such bacteria. The objective of this study was to investigate the survival of the wild-type strain A-271 of Francisella tularensis subsp. holarctica (Fth) in a natural aquatic ex vivo biofilm. To that purpose, we allowed Fth A-271 to produce its own biofilm on solid surfaces but also to colonize naturally formed biofilms from aquatic habitats, which were infected with Francisella in the laboratory. The survival rates of the bacteria in biofilms were compared to those of planktonic bacteria as a function of the employed culture condition. It could be shown by light- and electron microscopy that Fth is able to form a complex, matrix-associated biofilm. The biofilm form of Francisella showed longer cultivability on agar plates in natural water when compared to planktonic (free-living) bacteria. Be it as a part of the existing ex vivo biofilm or free-floating above as planktonic bacteria, more than 80% of Francisella were not only able to survive under these conditions for 28 days, but even managed to establish microcolonies and areas with their own exclusive biofilm architecture within the ex vivo biofilm. Here, we can demonstrate for the first time that a Francisella tularensis wild-type strain (Type B) is able to successfully colonize an aquatic multi-species ex vivo biofilm. It is worthwhile to speculate that Fth might become more persistent in the environment when it forms its own biofilm or integrates in an existing one. Multi-species biofilms have been shown to be more resistant against stress compared to single-species biofilms. This may have an important impact on the long-term survival of Francisella in aquatic habitats and infection cycles in nature.
Investigating Hydroclimatic Variables Trends on the Natural Lakes of Western Greece Using Earth Observation Data

Expected global climate change is allegedly becoming more intense, and the impacts on water resources are being tracked in various hydroclimatic regimes. The present research investigates a hydrologically important area of Greece, where four natural lakes are concentrated. It aims to quantify any potential long-term trends in lake water area, precipitation, and temperature timeseries. Water area timeseries spanning four decades are estimated by the mNDWI from Landsat satellite imagery and used as an index of each lake’s water storage. Precipitation and temperature measurements are obtained from the open access datasets Hydroscope and ERA5-Land, respectively. All of the timeseries were tested seasonally and annually with the Pettitt and Mann–Kendal tests for statistically significant breakpoints and trends detection. No timeseries analysis resulted in a statistically significant (at 0.05 or 0.1 levels) annual or seasonal trend. The hydroclimatic regime over the past forty years in western Greece is found to have been relatively stable. Land use was also assessed to have been relatively unchanging, converging to the overall stability of the local water regime. However, the findings of this research should not be interpreted as a reassurance against climate change, but as a call to further research for the detailed regional and local assessment of climate change and hydroclimatic variability with acknowledged statistical approaches.
Encouraging Adults Aged 65 and over to Participate in Resistance Training by Linking Them with a Peer: A Pilot Study

Resistance training (RT) is beneficial for older adults, particularly to support living independently in their home. However, fewer than 25% of older adults in Australia participate in the recommended, twice-weekly sessions. Reasons older adults do not participate in RT include not having anyone to go with or not knowing what to do. Our study linked older adults with a peer (i.e., older person already participating in RT) to help them overcome these barriers. The aim of our study was to determine whether peer support was suitable for older adults participating in RT for the first time in the home or gymnasium setting. Each group (home vs. gymnasium) received a 6 week, twice-weekly program. Twenty-one participants completed the 6 week intervention: 14 in the home group and seven in the gymnasium group. The home group completed significantly more sessions per week (2.7 vs. 1.8) than the gymnasium group. Although both groups significantly improved on many physical assessments, no between-group differences were found. However, it is suitable to link a peer for support with novice older people participating in a RT program for the first time in the home or gymnasium. It is recommended that future studies explore whether peer support improves sustainability.
Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet

Simple Summary Liquid feeding is an alternative practice employed in swine production that allows the recovery of low-cost liquid by-products to reduce environmental impact. This type of feeding can positively affect animal’s gut health, well-being, and performance. Liquid whey is a palatable feed and it can represent a resource to administer ingredients without additional costly processes. Nowadays, the study of the gut microbiome is considered a relevant tool due to the impact of this research field on host health, well-being, and growth. Therefore, this study investigated the fecal microbiota of the autochthonous pig breed Nero Siciliano fed a liquid whey co-feed-supplemented diet using a metagenomics approach. Abstract The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3–V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.