Miracle-dz/UniFAR-FTUs huggingface dataset:
Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
The Deinococcus radiodurans DR1245 Protein, a DdrB Partner Homologous to YbjN Proteins and Reminiscent of Type III Secretion System Chaperones

The bacterium Deinococcus radiodurans exhibits an extreme resistance to ionizing radiation. A small subset of Deinococcus genus-specific genes were shown to be up-regulated upon exposure to ionizing radiation and to play a role in genome reconstitution. These genes include an SSB-like protein called DdrB. Here, we identified a novel protein encoded by the dr1245 gene as an interacting partner of DdrB. A strain devoid of the DR1245 protein is impaired in growth, exhibiting a generation time approximately threefold that of the wild type strain while radioresistance is not affected. We determined the three-dimensional structure of DR1245, revealing a relationship with type III secretion system chaperones and YbjN family proteins. Thus, DR1245 may display some chaperone activity towards DdrB and possibly other substrates.
MiR-155 Alleviates Septic Lung Injury by Inducing Autophagy Via Inhibition of Transforming Growth Factor-&bgr;-Activated Binding Protein 2

Background: The anti-inflammatory effect of miR-155 was closely linked to transforming growth factor-&bgr;-activated kinase-1-binding protein 2 (TAB2) and autophagy. This study investigated the role of miR-155 in attenuation of septic lung injury through TAB2 and autophagy in mouse model and in vitro. Methods: Patients who underwent fiberoptic bronchoscope examination with or without septic lung injury were recruited for the collection of bronchoalveolar lavage fluid (BALF) samples. Mouse model of septic lung injury was established by cecal ligation puncture, while alveolar macrophage cell line was treated with lipopolysaccharide (LPS). Agomir miR-155 transfection into the mouse airways was performed to induce miR-155 expression, while miR-155 mimic, miR-155 inhibitor, or TAB2-siRNA was transfected into NR8383 macrophages. Mouse BALF and cell cytokine levels, lung tissue pathology and wet/dry ratio, numbers of autophagy bodies, miR-155, gene and protein expressions were also examined accordingly. Results: Expression of miR-155 was increased in the BALF of septic lung injury patients, in mouse model and NR8383 macrophages after LPS treatment. Increased numbers of autophagy bodies were also observed in mouse and macrophage models. MiR-155-transfected mice showed alleviation of inflammation, lower water content in lung tissues, increased number of autophagy bodies, increased expression of microtubule-associated protein 1 light chain 3 (LC3 II/I), reduced expressions of cysteinyl aspartate-specific protease-1 (Caspase-1), and TAB2, and decreased cytokines levels. Similar results were obtained in macrophages after LPS treatment. Cells transfected with miR-155 inhibitor showed increased expression of TAB2 and Caspase-1, fewer autophagy bodies, lower LC3 II/I expression, and higher cytokine levels. Conclusion: The current study observed a higher level of miR-155 in the BALF from sepsis patients with acute respiratory distress syndrome and demonstrated that miR-155 alleviated inflammation in septic lung injury in mouse and cell models by inducing autophagy via inhibition of TAB2.
Mesenchymal stem cells support growth and organization of host-liver colorectal-tumor organoids and possibly resistance to chemotherapy

Despite having yielded extensive breakthroughs in cancer research, traditional 2D cell cultures have limitations in studying cancer progression and metastasis and screening therapeutic candidates. 3D systems can allow cells to grow, migrate, and interact with each other and the surrounding matrix, resulting in more realistic constructs. Furthermore, interactions between host tissue and developing tumors influence the susceptibility of tumors to drug treatments. Host-liver colorectal-tumor spheroids composed of primary human hepatocytes, mesenchymal stem cells (MSC) and colon carcinoma HCT116 cells were created in simulated microgravity rotating wall vessel (RWV) bioreactors. The cells were seeded on hyaluronic acid-based microcarriers, loaded with liver-specific growth factors and ECM components. Only in the presence of MSC, large tumor foci rapidly formed inside the spheroids and increased in size steadily over time, while not greatly impacting albumin secretion from hepatocytes. The presence of MSC appeared to drive self-organization and formation of a stroma-like tissue surrounding the tumor foci and hepatocytes. Exposure to a commonly used chemotherapeutic 5-FU showed a dose-dependent cytotoxicity. However, if tumor organoids were allowed to mature in the RWV, they were less sensitive to the drug treatment. These data demonstrate the potential utility of liver tumor organoids for cancer progression and drug response modeling.
Experimental Investigation for the Development and Validation of Atomistic Models in Construction

Recent advances in computing power allow for increasingly accurate atomistic modelling in the study of complex chemical processes in a variety of applications. Atomistic modelling has the potential to elucidate the nature of minerals and mechanisms of reactions occurring in the manufacture and use of construction materials such as the decomposition of carbonates. The research described in this paper explores the application of atomistic modelling applied to the materials used in the construction industry by investigating the decomposition process of dolomite. The paper, in particular, describes the results of experimental investigations that are subsequently used to validate computational models. Studies undertaken using thermal gravimetric analysis, X-ray diffraction and Raman spectroscopy suggest that under specific conditions, dolomite (MgCa(CO3)2) decomposes through the formation of periclase (MgO) and calcite phases (CaCO3; first step) with the latter in turn decomposing to lime (CaO; second step) and carbon dioxide (CO2). Our modelling is in agreement with results from previous authors who describe the decomposition of dolomite through the formation of phase separated calcium and magnesium minerals. Consequently, computational efforts focus on pure phases of minerals and their reactions rather than complex mixed-phase models of dolomitic lime.
Changes in dietary patterns and body composition within 12 months of liver transplantation.

Background Cardiometabolic risk factors are increasing in liver transplant recipients (LTR). Influencing dietary factors have not been assessed. The aim of this observational study was to assess changes in weight, metabolic function, dietary intake and eating behaviours in the first year after orthotopic liver transplantation (OLT). Methods Consecutive recruitment of 17 patients (14 males) awaiting OLT at a single tertiary hospital. Dietary intake, food behaviours and anthropometry were recorded at baseline, and 6 and 12 months post-transplant. Results By 12 months, patients had gained on average 7.3% of body weight. The prevalence of overweight or obesity increased from baseline 53% to 77% (P=0.001). By 6 months, 65% (n=11/17) of patients had altered glucose metabolism. Dietary intake was consistent with a Western-style dietary pattern with high saturated fat. Over half of the patients (69%, n=11/16) reported low to no depressive feelings and rated their self-esteem as good (53%, n=9/16). The Power of Food Scale increased between pre and post-transplant, indicating a stronger appetitive drive. Conclusions Weight gain occurs early post-transplant, with significant metabolic dysfunction present within 6 months, however is not associated with significant psychological distress. Early dietary intervention designed to limit weight gain and target cardiometabolic health is recommended for this unique patient population.
MicroRNA-499a-5p inhibits osteosarcoma cell proliferation and differentiation by targeting protein phosphatase 1D through protein kinase B/glycogen synthase kinase 3β signaling

A number of studies have attempted to elucidate the association between mircoRNAs (miRNAs/miRs) and cancer-associated processes. The aim of the present study was to determine how miR-499a-5p intervenes in human osteosarcoma cell proliferation and differentiation. The cancerous tissues and adjacent non-cancerous tissues of 62 patients with osteosarcoma (OS) were collected. miRNA microarray analysis revealed that 29 miRNAs were upregulated while 26 were downregulated, among which miR-499a-5p expression was the most decreased. Western blot analysis and reverse transcription-quantitative polymerase chain reaction demonstrated that the mRNA and protein expression of miR-499a-5p was lower, while that of protein phosphatase 1D (PPM1D) was higher in OS tissues compared with expression levels in normal tissues. Furthermore, miR-499a-5p expression was markedly decreased in the metastatic tumors and in those at stage III+IV compared with the non-metastatic tumors and those at stage I, respectively. In addition, following transfection of the human OS MG-63 cell line with an miR-499a-5p mimic, the expression of miR-499a-5p was elevated while the protein and mRNA expression of PPM1D was decreased. When combining these findings with the information obtained from the Targetscan predictive software, it was confirmed that PPM1D was targeted by miR-499a-5p. In MG-63 cells transfected with an miR-499a-5p mimic, PPM1D-associated downstream proteins phosphorylated protein kinase B (p-Akt) and phosphorylated glycogen synthase kinase 3β (p-GSK-3β) were significantly downregulated compared with the negative control (NC) group, while the expression of p-Akt and p-GSK-3β were significantly elevated in the tumor tissues compared with the adjacent non-tumor tissues. Simultaneously, the growth and proliferation activity of MG-63 cells were notably reduced when transfected with the miR-499a-5p mimic, compared with the NC group. Therefore, it may be concluded that miR-499a-5p suppresses OS cell proliferation and differentiation by targeting PPM1D through modulation of Akt/GSK-3β signaling.
Cooperative Data Scheduling in Hybrid Vehicular Ad Hoc Networks: VANET as a Software Defined Network

This paper presents the first study on scheduling for cooperative data dissemination in a hybrid infrastructure-to-vehicle (I2V) and vehicle-to-vehicle (V2V) communication environment. We formulate the novel problem of cooperative data scheduling (CDS). Each vehicle informs the road-side unit (RSU) the list of its current neighboring vehicles and the identifiers of the retrieved and newly requested data. The RSU then selects sender and receiver vehicles and corresponding data for V2V communication, while it simultaneously broadcasts a data item to vehicles that are instructed to tune into the I2V channel. The goal is to maximize the number of vehicles that retrieve their requested data. We prove that CDS is NP-hard by constructing a polynomial-time reduction from the Maximum Weighted Independent Set (MWIS) problem. Scheduling decisions are made by transforming CDS to MWIS and using a greedy method to approximately solve MWIS. We build a simulation model based on realistic traffic and communication characteristics and demonstrate the superiority and scalability of the proposed solution. The proposed model and solution, which are based on the centralized scheduler at the RSU, represent the first known vehicular ad hoc network (VANET) implementation of software defined network (SDN) concept.
In situ analysis of lignins in transgenic tobacco reveals a differential impact of individual transformations on the spatial patterns of lignin deposition at the cellular and subcellular levels.

Using tobacco transgenic lines altered in the monolignol biosynthetic pathway and which differ in their lignin profiles we have evaluated lignin deposition at the cellular and subcellular levels using several microanalytical techniques. Surprisingly, whereas a Cinnamoyl CoA reductase (CCR) down-regulated line with a strong decrease in lignin content exhibited an overall reduction in lignin deposition in the walls of the different xylem cell types, this reduction was selectively targeted to the fibers in a double transformant (down-regulated for both CCR and Cinnamyl alcohol dehydrogenase (CAD)) displaying a similar degree of global lignin content decrease. Fiber and vessel secondary walls of the transgenic tobacco line homozygous for the ccr antisense gene (CCR.H) down-regulated plants were dramatically destructured, particularly in the S2 sublayer, whereas the deposition of lignins in the S1 sublayer was not significantly modified. In contrast, cell wall organization was slightly altered in xylem cells of the double transformant. The relative distribution of non-condensed and condensed units in lignin, evaluated microscopically with specific antibodies, was differentially affected in the transgenics studied and, in a general way, a drop in non-condensed lignin units (beta- 0-4 interunit linkages) was associated with a loss of cohesion and extensive disorganization of the secondary wall. These results demonstrate that lignification is tightly and independently regulated in individual cell types and cell wall sublayers. They also show that down-regulation of specific genes may induce targeted changes in lignin structure and in spatial deposition patterns of the polymer.
The effect of graphene oxide on UV curing kinetics and properties of SU8 nanocomposites

In the present study SU8 nanocomposites were prepared by incorporating graphene oxide (GO), and its effect on the UV curing kinetics, morphology, electrical, hardness and thermal properties of the nanocomposites were investigated at different loading levels of GO (0.1 − 3 wt%). Studying the reaction kinetics of the UV curing process by means of real-time infrared spectroscopy showed that the polymerization rate and the final conversion of epoxy groups was related to the loading level of GO in the nanocomposites. An autocatalytic kinetics model of the curing reaction confirmed the effect of GO nanoparticles on the curing rate constant (k), the order of the initiation reaction (m) and the ultimate conversion of the UV-cured nanocomposites. Appropriate experimental observations indicated that dispersion of GO within the resin plays a critical role on the cure kinetics and final conversion. The results of the kinetics modeling and morphological observations showed that the curing rate constant of the nanocomposites is highly dependent on the GO content and its dispersion state, indicating that GO prevents epoxy resin crosslinking by photoinitator deactivation. Moreover, oxygen functionalities, such as hydroxyl and carboxyl groups, on the surface of GO facilitate interfacial interactions between epoxy groups from the matrix and GO. Electrical conductivity measurements demonstrated that the UV-induced photo-cured GO filled resins are conductive SU8 nanocomposites. It was observed that the thermal stability of the nanocomposites is enhanced due to the dispersion of GO in the matrix. Moreover, the microhardness analysis showed that addition of GO to neat SU8 increases the mechanical hardness of the nanocomposite. © 2016 Society of Chemical Industry
Induction of cytokines , MMP 9 , TIMPs , RANKL and OPG during orthodontic tooth movement

This controlled longitudinal intervention study investigated changes in cytokines and biomarkers of bone and tissue metabolism within gingival crevicular fluid (GCF) from patients undergoing orthodontic treatment. GCF was collected on PeriopaperTM strips (Oraflow Inc., USA) from 20 volunteers at baseline, before tooth extraction and appliance placement and then at intervals during orthodontic treatment. Samples were taken 10 weeks following first appliance placement: at four hours; 7 days; and 42 days after application of distalising forces to maxillary canine teeth. Cytokines (GM-CSF, interferon-gamma, IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10 and TNFalpha), tissue biomarkers (MMP-9, TIMP-1 & 2) and bone metabolism indicators (RANKL and OPG) were measured in GCF using multiplex assays. Tension sites adjacent to canines showed significant increases in IL-1beta, IL-8, TNFalpha, MMP-9 and TIMPs 1 and 2 across all time points following force application, while compression sites exhibited increases in IL-1beta and IL-8 after 4 hours, MMP-9 after 7 and 42 days and RANKL after 42 days. These data demonstrate that high levels of pro-inflammatory cytokines and biomarkers of tissue and bone metabolism in GCF are associated with orthodontic force application. Elevated levels were evident at 4 hours but continued for periods of up to 6 weeks. The data suggest that GCF biomarker analysis may help optimise orthodontic forces for individual patients.
Early workplace dialogue in physiotherapy practice improved work ability at 1-year follow-up—WorkUp, a randomised controlled trial in primary care

Abstract Workplace involvement in rehabilitation for patients with musculoskeletal pain may improve work ability. Convergence Dialogue Meeting (CDM) is a model aimed at helping the patient, the care giver, and the employer to support work ability and return-to-work. Our aim was to study the effect on work ability when adding a workplace dialogue according to CDM in physiotherapy practice for patients with pain in ordinary primary care. We conducted a prospective pairwise cluster randomised controlled trial (ClinicalTrials.gov ID: NCT02609750) in primary care involving 20 primary care rehabilitation units with 1-year follow-up. Adult patients with acute/subacute neck and back pain, worked ≥4 weeks past year and not currently on sick leave or no more than 60 days of sick leave and considered at-risk of sick leave were included (n = 352). All patients received structured physiotherapy and the intervention was the addition of CDM, delivered by the treating physiotherapist. The main confirmatory outcome, work ability (defined as working at least 4 consecutive weeks at follow-up), was assessed by a weekly short text message question on number of sick leave days past week. Work ability was reached by significantly more patients in the intervention group (108/127, 85%) compared with the reference group (127/171, 74%) (P = 0.02). The intervention increased the odds of having work ability at 1-year follow-up, also after adjustment for baseline health-related quality of life (odds ratio 1.85, confidence interval 1.01-3.38). We conclude that an early workplace dialogue in addition to structured physiotherapy improved work ability significantly.
Social capital and mental well-being of older people residing in a residential care facility in Durban, South Africa

Introduction: Global increases in life expectancy are expected to continue, with accompanying physical and mental well-being challenges specifically for older people living in residential care settings. Objective: The aim of the study was to investigate the association between mental well-being and social capital of older residents (60+ years) in an urban residential care facility in South Africa. Method: A descriptive survey was conducted with 103 residents living in a residential care facility in an urban environment in South Africa. The social capital framework from the Canadian Policy Research Initiative, the WHO-5 well-being index, the Kessler-6 measure of psychosocial distress, the OSLO-3 Social Support Scale and the Australian Bureau of Statistics Indigenous Health Questionnaire were used to develop the questionnaire. Results: The WHO-5 showed moderate ratings of mental well-being for the standard scoring (>13) (62, 82.7%), but lower levels when using ‘no negative ratings’ (36; 50.6%). Significant differences in the primary network size, average closeness, self-efficacy and social support as well as the ability to confide in primary network was shown between residents with mentally well and unwell ratings. Logistic regression showed that the strongest predictor for mental well-being was participation in activities outside of the residence and having a primary network. Conclusion: The study confirms the association between social capital and mental well-being.
Automatic Peak Selection by a Benjamini-Hochberg-Based Algorithm

A common issue in bioinformatics is that computational methods often generate a large number of predictions sorted according to certain confidence scores. A key problem is then determining how many predictions must be selected to include most of the true predictions while maintaining reasonably high precision. In nuclear magnetic resonance (NMR)-based protein structure determination, for instance, computational peak picking methods are becoming more and more common, although expert-knowledge remains the method of choice to determine how many peaks among thousands of candidate peaks should be taken into consideration to capture the true peaks. Here, we propose a Benjamini-Hochberg (B-H)-based approach that automatically selects the number of peaks. We formulate the peak selection problem as a multiple testing problem. Given a candidate peak list sorted by either volumes or intensities, we first convert the peaks into -values and then apply the B-H-based algorithm to automatically select the number of peaks. The proposed approach is tested on the state-of-the-art peak picking methods, including WaVPeak [1] and PICKY [2]. Compared with the traditional fixed number-based approach, our approach returns significantly more true peaks. For instance, by combining WaVPeak or PICKY with the proposed method, the missing peak rates are on average reduced by 20% and 26%, respectively, in a benchmark set of 32 spectra extracted from eight proteins. The consensus of the B-H-selected peaks from both WaVPeak and PICKY achieves 88% recall and 83% precision, which significantly outperforms each individual method and the consensus method without using the B-H algorithm. The proposed method can be used as a standard procedure for any peak picking method and straightforwardly applied to some other prediction selection problems in bioinformatics. The source code, documentation and example data of the proposed method is available at http://sfb.kaust. edu.sa/pages/software.aspx.