DescFold: A web server for protein fold recognition

<p>Abstract</p> <p>Background</p> <p>Machine learning-based methods have been proven to be powerful in developing new fold recognition tools. In our previous work [Zhang, Kochhar and Grigorov (2005) <it>Protein Science</it>, <b>14</b>: 431-444], a machine learning-based method called DescFold was established by using Support Vector Machines (SVMs) to combine the following four descriptors: a profile-sequence-alignment-based descriptor using Psi-blast <it>e</it>-values and bit scores, a sequence-profile-alignment-based descriptor using Rps-blast <it>e</it>-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. In this work, we focus on the improvement of DescFold by incorporating more powerful descriptors and setting up a user-friendly web server.</p> <p>Results</p> <p>In seeking more powerful descriptors, the profile-profile alignment score generated from the COMPASS algorithm was first considered as a new descriptor (i.e., PPA). When considering a profile-profile alignment between two proteins in the context of fold recognition, one protein is regarded as a template (i.e., its 3D structure is known). Instead of a sequence profile derived from a Psi-blast search, a structure-seeded profile for the template protein was generated by searching its structural neighbors with the assistance of the TM-align structural alignment algorithm. Moreover, the COMPASS algorithm was used again to derive a profile-structural-profile-alignment-based descriptor (i.e., PSPA). We trained and tested the new DescFold in a total of 1,835 highly diverse proteins extracted from the SCOP 1.73 version. When the PPA and PSPA descriptors were introduced, the new DescFold boosts the performance of fold recognition substantially. Using the SCOP_1.73_40% dataset as the fold library, the DescFold web server based on the trained SVM models was further constructed. To provide a large-scale test for the new DescFold, a stringent test set of 1,866 proteins were selected from the SCOP 1.75 version. At a less than 5% false positive rate control, the new DescFold is able to correctly recognize structural homologs at the fold level for nearly 46% test proteins. Additionally, we also benchmarked the DescFold method against several well-established fold recognition algorithms through the LiveBench targets and Lindahl dataset.</p> <p>Conclusions</p> <p>The new DescFold method was intensively benchmarked to have very competitive performance compared with some well-established fold recognition methods, suggesting that it can serve as a useful tool to assist in template-based protein structure prediction. The DescFold server is freely accessible at <url>http://202.112.170.199/DescFold/index.html</url>.</p

TIM-Finder: A new method for identifying TIM-barrel proteins

<p>Abstract</p> <p>Background</p> <p>The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.</p> <p>Results</p> <p>To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of <it>Bacillus subtilis</it>, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.</p> <p>Conclusions</p> <p>TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at <url>http://202.112.170.199/TIM-Finder/</url>.</p

Three-level Back-to-Back Converter Simulation for Wind Turbine Energy Source

AbstractThis paper presents the simulation of three-level back-to-back converter for wind turbine energy source. For this paper, it will be focused on wind turbine energy source and determined the voltage from wind turbine energy source being regular value. The operation of the converter can be simulated by using MATLAB/SIMULINK program. Moreover, the voltage and current of the converter can be properly controlled by SVPWM. The simulation results shown that the output current waveform have signal distortion less than the input current waveform, and also the output voltage waveform is more than the input as well. Therefore, this converter can convert the voltage and current from the AC to DC and from the DC to AC for more performance, and it can be connected to the grid

Spatiotemporal Variation in Driving Factors of Vegetation Dynamics in the Yellow River Delta Estuarine Wetlands from 2000 to 2020

© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).Natural Science Foundation of Shandong Province (grant number ZR2022QD118) and the National Natural Science Foundation of China (grant numbers 42201312 and 32271678)Peer ReviewedPrevious studies of vegetation dynamics in the Yellow River Delta (YRD) predominantly relied on sparse time series or coarse-resolution images, which not only overlooked the rapid and spatially heterogeneous changes, but also limited our understanding of driving mechanisms. Here, employing spatiotemporal data fusion methods, we constructed a novel fused enhanced vegetation index (EVI) dataset with a high spatiotemporal resolution (30-meter and 8-day resolution) for the YRD from 2000 to 2020, and we analyzed the vegetation variations and their driving factors within and outside the YRD Nation Natural Reserve (YRDNRR). The fused EVI effectively captured spatiotemporal vegetation dynamics. Notably, within the YRDNRR core area, the fused EVI showed no significant trend before 2010, while a significant increase emerged post-2010, with an annual growth of 7%, the invasion of Spartina alterniflora explained 78% of this EVI increment. In the YRDNRR experimental area, the fused EVI exhibited a distinct interannual trend, which was characterized by an initial increase (2000–2006, p 0.05); the dynamics of the fused EVI were mainly affected by the spring runoff (R2 = 0.71), while in years with lower runoff, it was also affected by the spring precipitation (R2 = 0.70). Outside of the protected area, the fused EVI demonstrated a substantial increase from 2000 to 2010 due to agricultural land expansion and human management practices, followed by stabilization post-2010. These findings enhance our comprehension of intricate vegetation dynamics in the YRD, holding significant relevance in terms of wetland preservation and management

Innate resistance to Leishmania amazonensis Infection in rat is dependent on NOS2

Leishmania infection causes diverse clinical manifestations in humans. The disease outcome is complicated by the combination of many host and parasite factors. Inbred mouse strains vary in resistance to Leishmania major but are highly susceptible to Leishmania amazonensis infection. However, rats are highly resistant to L. amazonensis infection due to unknown mechanisms. We use the inducible nitric oxide synthase (Nos2) gene knockout rat model (Nos2−/− rat) to investigate the role of NOS2 against leishmania infection in rats. Our results demonstrated that diversion toward the NOS2 pathway is the key factor explaining the resistance of rats against L. amazonensis infection. Rats deficient in NOS2 are susceptible to L. amazonensis infection even though their immune response to infection is still strong. Moreover, adoptive transfer of NOS2 competent macrophages into Nos2−/− rats significantly reduced disease development and parasite load. Thus, we conclude that the distinct L-arginine metabolism, observed in rat macrophages, is the basis of the strong innate resistance to Leishmania. These data highlight that macrophages from different hosts possess distinctive properties and produce different outcomes in innate immunity to Leishmania infections

A prospective and consecutive study assessing short-term clinical and radiographic outcomes of Chinese domestically manufactured 3D printing trabecular titanium acetabular cup for primary total hip arthroplasty: evaluation of 236 cases

PurposeWe prospectively evaluate the short-term clinical and radiographic outcomes of the only Chinese domestically produced trabecular titanium acetabular cup(3D ACT™ cup) in primary total hip arthroplasty (THA), aiming to provide evidence-based support for its clinical application.MethodsA total of 236 patients, who underwent primary THA using 3D ACT™ cup in the Department of Joint Surgery at our hospital between January 2017 and June 2019, were included in this study. General patient data, imaging information, functional scores, and complications were collected to evaluate the early clinical efficacy.ResultsAll patients were followed up for 33–52 months, with an average of (42.2 ± 9.2) months. At the last follow-up, the preoperative HHS score increased significantly from 43.7 ± 6.8 to 85.6 ± 9.3 points (P &lt; 0.01). Similarly, the preoperative WOMAC scores showed significant improvement from 59.2 ± 5.8 to 13.1 ± 3.5 points (P &lt; 0.01). 92.3% of the patients expressed satisfaction or high satisfaction with the clinical outcome. Furthermore, 87.7% of the acetabular cups were positioned within the Lewinnek safe zone, achieving successful reconstruction of the acetabular rotation center. The cup survival rate at the last follow-up was 100%.ConclusionsThe utilization of the only Chinese domestically manufactured 3D printing trabecular titanium acetabular cup in primary THA demonstrated favorable short-term clinical and radiographic outcomes. The acetabular cup exhibits excellent initial stability, high survival rate, and favorable osseointegration, leading to a significant enhancement in pain relief and functional improvement. In the future, larger sample sizes and multicenter prospective randomized controlled trials will be required to validate the long-term safety and effectiveness of this 3D ACT™ cup

Disc-corona interaction in the heartbeat state of GRS 1915+105

Timing analysis provides information about the dynamics of matter accreting on to neutron stars and black holes, and hence is crucial for studying the physics of the accretion flow around these objects. It is difficult, however, to associate the different variability components with each of the spectral components of the accretion flow. We apply several new methods to two Rossi X-ray Timing Explorer observations of the black hole binary GRS 1915+105 during its heartbeat state to explore the origin of the X-ray variability and the interactions of the accretion-flow components. We offer a promising window into the disc--corona interaction through analysing the formation regions of the disc aperiodic variabilities with different time-scales via comparing the corresponding transition energies of the amplitude-ratio spectra. In a previous paper, we analysed the Fourier power density as a function of energy and frequency to study the origin of the aperiodic variability, and combined that analysis with the phase lag as a function of frequency to derive a picture of the disc--corona interaction in this source. We here, for the first time, investigate the phase lag as a function of energy and frequency, and display some interesting details of the disc--corona interaction. Besides, the results from the shape of amplitude-ratio spectrum and from several other aspects suggest that the quasi-periodic oscillation originates from the corona.Comment: 12 pages, 7 figure

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal