Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of the secretory proteome of human adipose stromal vascular fraction cells during adipogenesis

Adipogenesis is a complex process that is accompanied by a number of molecular events. In this study, a proteomic approach was adopted to identify secretory factors associated with adipogenesis. A label‐free shotgun proteomic strategy was implemented to analyze proteins secreted by human adipose stromal vascular fraction cells and differentiated adipocytes. A total of 474 proteins were finally identified and classified according to quantitative changes and statistical significances. Briefly, 177 proteins were significantly upregulated during adipogenesis (Class I), whereas 60 proteins were significantly downregulated (Class II). Changes in the expressions of several proteins were confirmed by quantitative RT‐PCR and immunoblotting. One obvious finding based on proteomic data was that the amounts of several extracellular modulators of Wnt and transforming growth factor‐β (TGF‐β) signaling changed during adipogenesis. The expressions of secreted frizzled‐related proteins, dickkopf‐related proteins, and latent TGF‐β‐binding proteins were found to be altered during adipogenesis, which suggests that they participate in the fine regulation of Wnt and TGF‐β signaling. This study provides useful tools and important clues regarding the roles of secretory factors during adipogenic differentiation, and provides information related to obesity and obesity‐related metabolic diseases.
First Draft Genome Sequence of a Member of the Genus Mangrovibacter, Isolated from an Aquaculture Farm in India

ABSTRACT Mangrovibacter sp. MFB070, a Gram-negative, facultatively anaerobic, nitrogen-fixing bacterium, was isolated from an aquaculture farm in Cochin, India. Here, we report the first draft genome sequence of a member of the genus Mangrovibacter, which may help us to elucidate the evolutionary status of this genus. The draft genome sequence of the Mangrovibacter sp. consists of 5,361,682 bp, encoding 4,971 predicted coding sequences in 57 contigs.
N-terminal Sequences Contained in the Src Homology 2 and 3 Domains of p120 GTPase-activating Protein Are Required for Full Catalytic Activity Toward Ras (*)

The p120 GTPase-activating protein (GAP) is a negative regulator of Ras, which has a central role in signal transduction pathways that control cell proliferation. p120 GAP accelerates the conversion of activated Ras-GTP to its inactive form, Ras-GDP, thereby inhibiting mitogenic signaling. To examine potential contributions of p120 N-terminal sequences to regulation of its C-terminal catalytic domain, we constructed deletion mutants lacking defined regions, including the variable hydrophobic region as well as the Src homology 2 (SH2) and 3 (SH3) domains. These mutant proteins were expressed in infected Sf9 insect cells from recombinant baculoviruses and assayed in vitro for their ability to stimulate the intrinsic GTPase activity of purified Ras. While deletion of the variable hydrophobic region had no effect on p120 GAP activity, deletion of the entire SH2/SH3/SH2 region severely impaired catalytic activity toward Ras. Deletion of individual SH2 and SH3 domains within this region partially inhibited p120 GAP activity. Moreover, p120 N-terminal sequences enhanced the Ras GTPase-stimulating activity of the neurofibromin GAP-related domain. These results demonstrate that sequences in the SH2/SH3/SH2 region of p120 GAP are required for full catalytic activity toward Ras. Together with earlier findings that the p120 GAP SH2 domains mediate interactions with several GAP-associated proteins, our results suggest multiple roles for the N-terminal sequences in regulating p120 GAP catalytic activity and mitogenic signaling pathways. In addition, our results raise the possibility that SH2 domain point mutations in p120 GAP detected in some basal cell carcinomas reduce catalytic activity toward Ras and thereby contribute to oncogenesis.
Coordinated reactive power control for static synchronous compensators under unbalanced voltage sags

Unbalanced voltage sags strongly deteriorate the performance of power converters and electrical machines connected to the distribution network. In particular, a reduction of the power quality is noticed in these equipments, which is caused by a ripple in the output power and an increase of the current harmonic distortion. Several solutions based on reactive power compensation have been introduced to cope with this problem. Among them, static synchronous compensators have confirmed the superior performance due to the possibility of using all rated power exclusively to voltage support. This paper presents a simple reactive power control algorithm for static synchronous compensators operating under unbalanced voltage sags. The main feature of the proposed algorithm is that it allows a fine adjustment of the amount of reactive power injected by the positive- and negative-sequence components. Thus the control algorithm provides voltage support at the output of the static synchronous compensator. Specifically the proposed control conveniently corrects both the positive- and negative-sequence voltage. Selected simulation results are provided to validate the proposal.
Increased copy number of the 5' end of the SPS2 gene inhibits sporulation of Saccharomyces cerevisiae

We found that the introduction into a yeast cell of a high-copy-number plasmid containing the 5' end of the SPS2 gene, a sporulation-specific gene of Saccharomyces cerevisiae, led to a reduction in the efficiency of spore formation. The plasmid pAP290, which contains the sequence from -138 to +152 of the SPS2 gene, caused a fivefold reduction in spore formation; the presence of the plasmid had no effect on transcription of the chromosomal SPS2 gene. A plasmid containing only the sequence upstream of the TATA box of the SPS2 gene (-350 to -68) was unable to inhibit the completion of sporulation, whereas the downstream sequence, from -70 to +404, although unable by itself to inhibit sporulation, could do so when provided with an upstream fragment containing the CYC1 upstream activation sequence. Deletion of 22 base pairs from pAP290, which introduced a frameshift after codon 17 of the SPS2 gene and reduced the open reading frame to 26 amino acids, generated a plasmid (pAP290 delta Pst) which could no longer inhibit sporulation. The SPS2 inserts of pAP290 and pAP290 delta Pst were found to direct equivalent levels of sporulation-specific transcription. We conclude from these results that the presence of both the SPS2 promoter (or a substitute promoter) and the initial coding sequence of the SPS2 gene is required in the high-copy-number plasmid to generate the asporogenous phenotype. We speculate that the accumulation of a protein containing the amino-terminal portion of the SPS2 gene product, synthesized from the transcripts of the truncated plasmid-borne copies of the SPS2 gene, prevents ascus formation.
Free-viewpoint thumbnail for light field compression

This paper proposes a new JPEG-compatible coder of light field data. When viewing a 3D scene using light field data, we usually require a specialized light field viewer. However, the proposed coder produces an output file from which we can see a thumbnail of the light field by using common JPEG viewers. This thumbnail can be a free viewpoint image of the scene which reflects user’s preference or creator’s idea. We can also achieve good compression efficiency by using this thumbnail as a reference image.
Calculating the probability of timing violation of F/F-controlled paths with timing variations

We propose an analytic method to calculate the probability of timing violation of F/F-controlled paths by considering timing variations. We first characterize the timing characteristics of F/Fs and path delays using a generalized canonical delay model. The probability of setup-time violation is then calculated by considering the correlation between F/Fs and logic paths. For the calculation, we used conditional tightness probability equation which reflects the nonlinearity of the process parameters. In experiments, the proposed method exhibited the error less than 7 % with respect to Monte-Carlo (MC) simulation results. Compared to the benchmark method that does not consider the variations of the timing characteristics of F/Fs, the proposed method improved the accuracy by more than 18% on average.
Designing Wideband Tapered-Slot Antennas: A novel method using SIW technology.

In this article, a novel method for the design of wideband tapered-slot antennas (TSAs) using substrate-integrated waveguide (SIW) technology is proposed. The proposed procedure includes modeling of TSAs by step lines, which are terminated in intrinsic impedance of free space, along with applying the theory of small reflections. To provide insight into the radiation mechanism of the designed antennas, the method is discussed in detail. Employing the proposed method, an initial antenna is designed with a central frequency of 37.5 GHz. This antenna, which is implemented on a single-layer substrate, is compact in size and has satisfying radiation characteristics. It provides 75% fractional bandwidth from 25 to over 55 GHz, with the peak gain variations between 2 and 5 dB in its operating band. To further verify the design principle, the proposed antenna is redesigned for a central frequency of 14 GHz, and its prototype is fabricated. The comparison of the simulated and measured results confirms the accuracy of the proposed method.
The influence of physical activity on abdominal fat: a systematic review of the literature

The relationship between excess abdominal adipose tissue, metabolic and cardiovascular health risk has stimulated interest in the efficacy of physical activity in specifically perturbing this adipose depot. The evolution of imaging techniques has enabled more direct measurement of changes in abdominal and visceral fat. The purpose of this summary was to systematically review the relationship between physical activity and abdominal fat. Methods: Database searches were performed on MEDLINE, CINAHL, SPORT DISCUS and PUBMED, from 1985 to 2005 with keywords ‘exercise’, ‘abdominal fat’ and ‘visceral fat’. Results: Nineteen randomized controlled trials (RCTs) and eight non‐randomized controlled trials were selected. In RCTs using imaging techniques to measure change in abdominal fat in overweight or obese subjects, seven out of 10 studies (including three trials with type 2 diabetics) reported significant reductions compared with controls. Reductions in visceral and total abdominal fat may occur in the absence of changes in body mass and waist circumference. Waist‐to‐hip ratio is not a sensitive measure of change in regional adiposity in exercise studies. No studies fulfil the Consolidated Standards of Reporting Trials (CONSORT) statement's criteria for the highest quality of randomized trial; however, many studies were in progress or published before the opportunity to comply with these recommendations. Therefore, limited evidence from a number of studies suggests a beneficial influence of physical activity on reduction in abdominal and visceral fat in overweight and obese subjects when imaging techniques are used to quantify changes in abdominal adiposity. More rigorous studies are needed to confirm these observations.
Simulation and analysis of MEMS cantilever designs with fractal surface geometry for TG sensing and frequency switching

Surface geometry plays an important role in case of analyte sensing and RF switching using beams and electrodes. In general, rather than simply supported beam and diaphragm, microcantilever beams are widely preferred in BIO-MEMS and RF-MEMS for biosensing and RF switching, respectively. The lower level detection ability and simple structure make these cantilevers more applicable in many applications. The rectangular cantilever beams are most widely used in TG detection. but due to their constant or planner geometry and non-adhesion of analyte they are less sensitive in case of nano or pico level biosensing. This paper introduces the fractal surface geometry concept for increasing the deflection sensitivity corresponding to lower molecular or analyte loading. The rectangular and stepped cantilever beam structures along with fractal surface are simulated and analysed for TG molecular pressure 294.3 Pa. Both the rectangular and stepped microcantilever beams with fractal surface exhibit better free end or tip deflection (nearly 2×) as compare to the planner surface based beam. The proposed fractal concept also reduces the actuation voltage requirement for perfect switching.
Estimation of variable stiffness in flexible robot based on information assimilation

The quick and accurate estimation of variable stiffness in Adjustable Stiffness Joints (ASJ) is very important for the close loop control of the joint. On account of the stiffness is not directly measurable, and the construction of joints is complicated, the method of establishing mathematic model is not accurate enough for control system. Besides the joint models are always nonlinear, with multi-inputs and multi-outputs, and the parameters of which are coupling. All of the above factors throw down a great challenge to the effective estimation methods. Current on-line stiffness identifications are sensitive to the system conditions, the too fast or too slow changing will give rise to a bigger estimation error, and the estimation value is always deviant at the beginning time. For the purposes of establishing an effective method for control the stiffness on-line, we introduce the Extended Kalman Filter to assimilate the two pieces information of on-line identification methods and the system mathematic model, which take advantages of the both methods. As a result, the estimation accuracy of stiffness identification at the beginning time is improved, and the method is robust to the system conditions at the same time. Simulation on the variable joint model validate the approach.
Properties of a novel magnetized alginate for magnetic resonance imaging.

Implanting recombinant cells encapsulated in alginate microcapsules to secrete therapeutic proteins has been proven clinically effective in treating several murine models of human diseases. However, once implanted, these microcapsules cannot be assessed without invasive surgery. We now report the preparation and characterization of a novel ferrofluid to render these microcapsules visible with magnetic resonance imaging (MRI). The ferrofluid was prepared as a colloidal iron oxide stabilized in water by alginate. The presence of iron particles in the ferrofluid was verified with chemical titration, dynamic light scattering, and magnetization measurement. The microcapsules fabricated with various concentrations of the ferrofluid in the core, or on the surface of alginate microcapsules, or both, all produced microcapsules with smooth surfaces as shown with light and scanning electron microscopy. However, at the nanoscale level, as revealed with atomic force microscopy, the ferrofluid-fabricated microcapsules demonstrated increased granularity, particularly when the ferrofluid was used to laminate the surface. From the force spectroscopy measurements, these modified microcapsules showed increasing surface rigidity in the following order: traditional alginate < ferrofluid in the core < ferrofluid on the surface. Although the mechanical stability of low-concentration ferrofluid (0.1%) microcapsules was reduced, increasing concentrations, up to 20%, were able to improve stability. When these ferrofluid microcapsules were examined with MRI, their T(2) relaxation time was reduced, thereby producing increased contrast readily detectable with MRI, whereas the traditional alginate microcapsules showed no difference when compared with water. In conclusion, such ferrofluid-enhanced alginate is suitable for fabricating microcapsules that offer the potential for in vivo tracking of implanted microcapsules without invasive surgery.
Lifetime prediction based on opitimal Loess smoothing and UKF for lithium-ion batteries

Life prediction is the key part of the Prognostics and Health Management for lithium-ion batteries and it is an important means to master the decline tendency of power performance. In this paper, we have established a simplified and effective double exponential distribution capacity attenuation model through the analysis of data from the NASA Ames Center accelerated life test. Based on the model, an infusion method with unscented Kalman filtering algorithm and opitimal Loess smoothing is proposed to predict the life of the lithium-ion battery. The research results show that the presented methods of lithium-ion battery life prediction can effectively estimate the useful life of lithium-ion batteries, thus improving the stability and accuracy of the prediction.
Blood flow quantification with contrast-enhanced US: "entrance in the section" phenomenon--phantom and rabbit study.

PURPOSE To investigate changes in destruction-replenishment curves (in vitro and in vivo) that result from microbubble destruction in feeding vessels that pass through the imaging plane before microbubbles enter the region of interest (ROI). MATERIALS AND METHODS During continuous injections of an ultrasonographic contrast agent, nonlinear gray-scale images were obtained in vitro in the longitudinal plane of a renal dialysis cartridge flow phantom (flow rates of 100, 200, and 400 mL/min) and in vivo in the coronal plane of the left kidneys of two rabbits (two kidneys). Destruction-replenishment curves were obtained for the dialysis cartridge in ROIs located immediately after the entrance of the microbubbles into the image plane and further from the entrance, after microbubbles had traveled across the complete length of the imaging plane. Replenishment curves were also obtained from ROIs in the rabbit kidneys at the level of segmental arteries, distal interlobar arteries, and the cortex. RESULTS The ROIs immediately after the entrance of the microbubbles in the image plane of the dialysis cartridge and in the segmental artery of the kidney followed a typical exponential function, A(1 - e-alphat). Early portions of curves obtained in ROIs filled with microbubbles that had already passed through the image plane of the dialysis cartridge or in the renal cortex were not well described by such a function. The shape of the curve and the variations as a function of flow rate can be explained by means of a mathematical model based on indicator-dilution theory. CONCLUSION When the feeding vessels of an ROI travel across the ultrasound field before they reach the measurement region, the typical shape of the replenishment curve is modified (reduced velocity parameter and plateau).
Folate deficiency inhibits proliferation of adult hippocampal progenitors

Neurogenesis in the adult hippocampus may play important roles in learning and memory, and in recovery from injury. As recent findings suggest, the perturbance of homocysteine/folate or one-carbon metabolism can adversely affect both the developing and the adult brain, and increase the risk of neural tube defects and Alzheimer's disease. We report that dietary folic acid deficiency dramatically increased blood homocysteine levels and significantly reduced the number of proliferating cells in the dentate gyrus of the hippocampus in adult mice. In vitro, the perturbance of one-carbon metabolism repressed proliferation of cultured embryonic multipotent neuroepithelial progenitor cells and affected cell cycle distribution. Our results suggest that dietary folate deficiency inhibits proliferation of neuronal progenitor cells in the adult brain and thereby affects neurogenesis.
Mutations in the Chromodomain-like Insertion of Translation Elongation Factor 3 Compromise Protein Synthesis through Reduced ATPase Activity*

Background: Eukaryotic translation elongation factor 3 (eEF3) is a ribosome binding ATPase essential for fungal protein synthesis. Results: Mutations in the chromodomain-like insertion in an ATPase domain of eEF3 reduce ATPase activity but not ribosome binding. Conclusion: The chromodomain-like insertion affects the ATPase activity of eEF3 and translation. Significance: The chromodomain-like insertion of eEF3 may be targeted to develop new antifungal compounds. Translation elongation is mediated by ribosomes and multiple soluble factors, many of which are conserved across bacteria and eukaryotes. During elongation, eukaryotic elongation factor 1A (eEF1A; EF-Tu in bacteria) delivers aminoacylated-tRNA to the A-site of the ribosome, whereas eEF2 (EF-G in bacteria) translocates the ribosome along the mRNA. Fungal translation elongation is striking in its absolute requirement for a third factor, the ATPase eEF3. eEF3 binds close to the E-site of the ribosome and has been proposed to facilitate the removal of deacylated tRNA from the E-site. eEF3 has two ATP binding cassette (ABC) domains, the second of which carries a unique chromodomain-like insertion hypothesized to play a significant role in its binding to the ribosome. This model was tested in the current study using a mutational analysis of the Sac7d region of the chromodomain-like insertion. Specific mutations in this domain result in reduced growth rate as well as slower translation elongation. In vitro analysis demonstrates that these mutations do not affect the ability of eEF3 to interact with the ribosome. Kinetic analysis revealed a larger turnover number for ribosomes in comparison to eEF3, indicating that the partial reactions involving the ribosome are significantly faster than that of eEF3. Mutations in the chromodomain-like insertion severely compromise the ribosome stimulated ATPase of eEF3, strongly suggesting that it exerts an allosteric effect on the hydrolytic activity of eEF3. The chromodomain-like insertion is, therefore, vital to eEF3 function and may be targeted for developing novel antifungal drugs.
Development of an antigen-capture monoclonal antibody–based enzyme-linked immunosorbent assay and comparison with culture for detection of Salmonella enterica serovar Enteritidis in poultry hatchery environmental samples

An antigen-capture enzyme-linked immunosorbent assay (ELISA) was developed for use as a presumptive screening test for detection of Salmonella enterica serovar Enteritidis and other group D Salmonella in poultry hatchery environments. A mixture of 2 monoclonal antibodies that recognize different forms of the lipopolysaccharide O-antigen was used for specific detection of group D Salmonella. The performance of the ELISA was evaluated in comparison to standard Salmonella culture procedures. Culture for each sample included nonselective enrichment with buffered peptone water and primary selective enrichment and delayed secondary enrichment with both tetrathionate and Rappaport–Vassiliadis broths. One thousand fifty-seven samples were collected from poultry hatcheries over a 5-year period (received in 85 submissions), and S. Enteritidis was recovered from 106 (10%) of them. The diagnostic sensitivity and specificity of the ELISA relative to culture were 97.2% and 99.6%, respectively, on a sample basis and were both 100% on a submission basis. Delayed secondary enrichment increased the number of S. Enteritidis culture and ELISA-positive samples as compared to nonselective enrichment and primary selective enrichment by 25%. A significantly higher (P < 0.05) number of S. Enteritidis culture- and ELISA-positive results were obtained from Rappaport–Vassiliadis broth than from tetrathionate broth or buffered peptone water cultures. The results indicate that this ELISA procedure may be useful for screening poultry hatchery environmental samples for the presence of S. Enteritidis.