bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS‐CoV‐2 pathway
Authors: Pramanik Debabrata , Pawar Aiswarya B. , Roy Sudip , Singh Jayant Kumar 
Published: May 2022

AbstractThe emergence of pandemic situations originated from severe acute respiratory syndrome (SARS)‐CoV‐2 and its new variants created worldwide medical emergencies. Due to the non‐availability of efficient drugs and vaccines at these emergency hours, repurposing existing drugs can effectively treat patients critically infected by SARS‐CoV‐2. Finding a suitable repurposing drug with inhibitory efficacy to a host‐protein is challenging. A detailed mechanistic understanding of the kinetics, (dis)association pathways, key protein residues facilitating the entry–exit of the drugs with targets are fundamental in selecting these repurposed drugs. Keeping this target as the goal of the paper, the potential repurposing drugs, Nafamostat, Camostat, Silmitasertib, Valproic acid, and Zotatifin with host‐proteins HDAC2, CSK22, eIF4E2 are studied to elucidate energetics, kinetics, and dissociation pathways. From an ensemble of independent simulations, we observed the presence of single or multiple dissociation pathways with varying host‐proteins‐drug systems and quantitatively estimated the probability of unbinding through these specific pathways. We also explored the crucial gateway residues facilitating these dissociation mechanisms. Interestingly, the residues we obtained for HDAC2 and CSK22 are also involved in the catalytic activity. Our results demonstrate how these potential drugs interact with the host machinery and the specific target residues, showing involvement in the mechanism. Most of these drugs are in the preclinical phase, and some are already being used to treat severe COVID‐19 patients. Hence, the mechanistic insight presented in this study is envisaged to support further findings of clinical studies and eventually develop efficient inhibitors to treat SARS‐CoV‐2.
Photoperiodic regulation of avian physiology: From external coincidence to seasonal reproduction
Authors: Liddle Timothy Adam , Stevenson Tyler John , Majumdar Gaurav 
Published: May 2022

AbstractSeasonal cycles of environmental cues generate variation in the timing of life‐history transition events across taxa. It is through the entrainment of internal, endogenous rhythms of organisms to these external, exogenous rhythms in environment, such as cycling temperature and daylight, by which organisms can regulate and time life history transitions. Here, we review the current understanding of how photoperiod both stimulates and terminates seasonal reproduction in birds. The review describes the role of external coincidence timing, the process by which photoperiod is proposed to stimulate reproductive development. Then, the molecular basis of light detection and the photoperiodic regulation of neuroendocrine timing of seasonal reproduction in birds is presented. Current data indicates that vertebrate ancient opsin is the predominant photoreceptor for light detection by the hypothalamus, compared to neuropsin and rhodopsin. The review then connects light detection to well‐characterized hypothalamic and pituitary gland molecules involved in the photoperiodic regulation of reproduction. In birds, Gonadotropin‐releasing hormone synthesis and release are controlled by photoperiodic cues via thyrotropin‐stimulating hormone‐β (TSHβ) independent and dependent pathways, respectively. The review then highlights the role of D‐box and E‐box binding motifs in the promoter regions of photoperiodic genes, in particular Eyes‐absent 3, as the key link between circadian clock function and photoperiodic time measurement. Based on the available evidence, the review proposes that at least two molecular programs form the basis for external coincidence timing in birds: photoperiodic responsiveness by TSHβ pathways and endogenous internal timing by gonadotropin synthesis.
Real‐world long‐term analysis of daclatasvir plus asunaprevir in patients with hepatitis C virus infection
Authors: Fujii Hideki , Kimura Hiroyuki , Hasebe Chitomi , Akahane Takehiro , Satou Takashi , Kusakabe Atsunori , Kojima Yuji , Kondo Masahiko , Marusawa Hiroyuki , Kobashi Haruhiko , Tsuji Keiji , Ogawa Chikara , Uchida Yasushi , Joko Kouji , Mitsuda Akeri , Kurosaki Masayuki , Izumi Namiki 
Published: May 2022

AbstractBackground and AimThis study aimed to evaluate the long‐term clinical course of patients achieving a sustained virologic response (SVR) with daclatasvir plus asunaprevir (DCV/ASV) therapy.MethodsA total of 911 patients who achieved SVR with DCV/ASV were assessed. To evaluate pretreatment factors contributing to hepatocellular carcinoma (HCC) after SVR, univariate and multivariate analyses were performed in all patients, in those with preexisting HCC, and in those without preexisting HCC. We selected a low‐risk group of HCC cases after SVR. Finally, we evaluated liver function after achieving SVR.ResultsIn multivariable analyses, male sex, older age, patients with a history of HCC treatment, excess alcohol use, lower albumin, and low platelet count remained significant in the overall group; male sex and low albumin remained significant in patients with a history of HCC treatment; and male sex, older age, excess alcohol use, low platelet count, high alpha‐fetoprotein (AFP), and high des‐γ‐carboxy prothrombin (DCP) remained significant in those without a history of HCC treatment. Patients who had not received treatment for HCC, females, those under 70 years of age, and those with platelet count ≥13 (×104/μL), AFP <6 ng/mL, and DCP <23 mAU/mL were at low risk of HCC. The process of liver function improvement was different according to the factors.ConclusionsThe incidence rate of HCC, risk factors associated with HCC, group with very low risk of developing HCC, and the clinical course in a real‐world long‐term study were evaluated.
Is the degree of physiological bone remodeling a predictive factor for peri‐implantitis?
Authors: Rodriguez Maria Vera , Ravidà Andrea , Saleh Muhammad H.A. , Basma Hussein S. , Dukka Himabindu , Khurshid Hadiya , Wang Hom‐Lay , Moreno Pablo Galindo 
Published: May 2022

AbstractBackgroundThe amount of initial physiological bone remodeling (IPBR) after implant placement varies and the ways it may play a role in peri‐implantitis development remains unknown. The aim of this retrospective study was to investigate the association between the amount of IPBR during the first year of implant placement and incidence of peri‐implantitis as well as the pattern of progressive bone loss.MethodsClinical and radiographic documentation of implants at the time of implant placement (T0), 1 year ± 6 months after crown placement (T1), and at a ≥2‐year follow‐up from implant placement (T2) were retrospectively collected. IPBR was defined as the bone loss occurring from implant placement to the end of the bone remodeling (T1). Cases were grouped into those diagnosed with (test) or without peri‐implantitis (PIm) (control). Linear regression model under generalized estimation equation approach was estimated to assess correlation between marginal bone loss (MBL) rates in both periods (T1‐T0) and (T2‐T1). Receiver operating characteristics curve was estimated to explore an optimal cut‐off point of T1‐T0 MBL to discriminate between PIm and no‐PIm implants.ResultsA total of 45 patients receiving 57 implants without PIm and 40 with PIm were included. There were no associations between PIm and IPBR (p > 0.05), nor between BML of (T2‐T1) and (T1‐T0). However, arch and total follow‐up showed significant influence on the probability of PIm. Splinted implants showed an MBL rate of 0.60‐mm/year higher than non‐splinted implants (p < 0.001) from T1 to T2.ConclusionNo statistically significant association was found between IPBR and incidence of peri‐implantitis.
Open flap debridement compared to repeated applications of photodynamic therapy in the treatment of residual pockets: A randomized clinical trial
Authors: Andere Naira M. R. B. , Castro dos Santos Nídia C. , Araújo Cássia F. , Paz Hélvis E. S. , Shaddox Luciana M. , Casarin Renato C. V. , Santamaria Mauro P. 
Published: May 2022

AbstractBackgroundThe aim of the present study was to compare repeated applications of antimicrobial photodynamic therapy (aPDT) to open flap debridement (OFD) in the treatment of residual periodontal pockets in non‐furcation sites.MethodsForty‐six subjects with a diagnosis of Stage III or IV Grade C periodontitis, that had been previously treated, participated in the study. Residual pockets were divided between two groups: (1) aPDT group: received ultrasonic periodontal debridement followed by immediate application of aPDT, and repeated on1st, 2nd, 7th, and 14th days; and (2) OFD group: treated by modified papilla preservation technique, where granulation tissue and visible calculus were removed with hand curettes and an ultrasonic device. Clinical, immunological, and microbiological parameters were evaluated before and after treatment.ResultsBoth treatments were effective reducing clinical parameters of disease. OFD resulted in a greater mean probing pocket depths (PPD) reduction in deep pockets (p = 0.001). However, aPDT resulted in a lower occurrence of gingival recession (GR), dentin hypersensitivity (DH) and analgesic intake. Reduction in Porphyromonas gingivalis was observed in both groups. Only the OFD group had a significant reduction in Aggregatibacter actinomycetemcomitans. aPDT group had greater increase in interleukin 10 (IL‐10) levels and a greater reduction of interleukin 1 beta (IL‐1β) at 14 days when compared to the OFD group (p < 0.05).ConclusionOFD was superior in reducing PPD in deep pockets compared to the aPDT. However, OFD resulted in greater GR. Both treatments lowered P. gingivalis levels but only OFD reduced levels of A. actinomycemtemcomitans.
Intraoperative pectoral block versus thoracic paravertebral block for postoperative analgesia after breast cancer surgery: A randomized controlled trial
Authors: Sagun Aslinur , Rumeli Sebnem , Ozdemir Levent , Azizoglu Mustafa , Berkesoglu Mustafa , Mutlu Veli 
Published: May 2022

AbstractBackground and MethodsWith the increasing rate of breast cancer surgery, the pain management of these patients gains importance. The aim of this study is to compare the ultrasound (US) guided thoracic paravertebral block (TPV) versus intraoperative pectoral nerve block (PECS) with a low volume local anaesthetic for postoperative analgesia after breast cancer surgery. A total of 41 patients underwent mastectomy and sentinel lymph node biopsy or modified radical mastectomy were included in this randomized controlled, single‐blinded trial. The patients were divided into two groups as PECS and TPV blocks. In the PECS group, 10 ml of 0.5% bupivacaine was administered to the fascial plane by the surgeon. In the TPV group, 25 ml of 0.25% bupivacaine at T3 level was administered by the anaesthetist under US‐guidance. Visual analogue scale (VAS) scores and additional analgesic requirements were recorded at postoperative 0, 6, 12, 24 and 48 h.ResultsIn the TPV group, mean VAS score (VAS0) was significantly lower (p ˂ 0.001). In other time periods, there was no significant difference between the groups.ConclusionsIt was observed that intraoperative PECS block was as effective as TPV in providing postoperative analgesia and additional analgesic requirements were similar. This result suggests PECS block may be a good alternative to TPV.
A metric learning‐based method using graph neural network for pancreatic cystic neoplasm classification from CTs
Authors: Zhang Jiachen , Mao Yishen , Li Ji , Li Yiru , Luo Jianxu 
Published: May 2022

AbstractPurposePancreatic cystic neoplasms (PCNs) are relatively rare neoplasms and difficult to be classified preoperatively. Ordinary deep learning methods have great potential to provide support for doctors in PCNs classification but require a quantity of labeled samples and exact segmentation of neoplasm. The proposed metric learning‐based method using graph neural network (GNN) aims to overcome the limitations brought by small and imbalanced dataset and get fast and accurate PCNs classification result from computed tomography (CT) images.MethodsThe proposed framework applies GNN. GNNs perform well in fusing information and modeling relational data and get better results on dataset with small size. Based on metric learning strategy, model learns distance from the data. The similarity‐based algorithm enhances the classification performance, and more characteristic information is found. We use a convolutional neural network (CNN) to extract features from given images. Then GNN is used to find the similarity between each two feature vectors and complete the classification. Several subtasks consisting of randomly selected images are established to improve generalization of the model. The experiments are carried out on the dataset provided by Huashan Hospital. The dataset is labeled by postoperative pathological analysis and contains region of interest (ROI) information calibrated by experts. We set two tasks based on the dataset: benign or malignant diagnosis of PCNs and classification of specific types.ResultsOur model shows good performance on the two tasks with accuracies of 88.926% and 74.497%. The comparison of different methods' F1 scores in the benign or malignant diagnosis shows that the proposed GNN‐based method effectively reduces the negative impact brought by imbalanced dataset, which is also verified by the macroaverage comparison in the four‐class classification task.ConclusionsCompared with existing models, the proposed GNN‐based model shows better performance in terms of imbalanced dataset with small size while reducing labeling cost. The result provides a possibility for its application into the computer‐aided diagnosis of PCNs.
Finite strip method based on Carrera unified formulation for the free vibration analysis of variable stiffness composite laminates
Authors: Daraei Behnam , Shojaee Saeed , Hamzehei‐Javaran Saleh 
Published: May 2022

AbstractThis work presents a refinement of the finite strip method (FSM) based on the Carrera unified formulation (CUF) and is applied to free vibration analysis of variable stiffness composite laminated (VSCL) plates. VSCL plates considered here are composed of layers with curvilinear fibers in which their orientation angle changes linearly with respect to one of the in‐plane coordinates. The FSM permits the plate to be divided into some finite strips connected along the so‐called nodal lines. The conventional finite strip method involves an approximation of the solution of a plate problem by using continuously harmonic series in the longitudinal direction along the nodal lines and simple polynomial shape functions (the usual beam shape functions) in the transverse direction of the plate. However, refined finite strip model that presented in this paper allows one to express the unknown variables as a set of thickness functions that only depend on the thickness coordinate and the corresponding variable that depends on the in‐plane coordinates which involve continuously harmonic series and polynomial shape functions. Thanks to this new finite strip model, the shape functions used in the transverse direction can be chosen as 1D bar shape functions, and also, all three components of the displacement field are considered in each nodal line. Moreover, based on this approach, three‐dimensional displacement field is approximated in a compact form as a generic N‐order expansion. Therefore, explicit expressions of fundamental nuclei of finite strip matrices are obtained in a compact form and presented here. The results obtained by the present formulation for VSCL plates are compared with those obtained from published data. The results show that this kind of strip is efficient and useful. Further, several numerical examples are presented, and the effect of the order of expansion, the number of strips, curvilinear fiber angle, and various boundary conditions are examined.
Analysis of an open foam generated from computerized tomography scans of physical foam samples
Authors: Leblanc Christophe , Kilingar Nanda Gopala , Jung Anne , Kamel Karim Ehab Moustafa , Massart Thierry Jacques , Noels Ludovic , Béchet Eric 
Published: May 2022

AbstractThe present article introduces an automated procedure to construct geometrical representative volume elements (RVE) of open‐foam cellular materials from computerized tomography (CT) images, with the final aim of generating meshable geometries usable in the finite element method (FEM) used in order to analyse their mechanical behavior. The methodology consists in growing and fitting a set of ellipsoids to each of the foam cells. These ellipsoids are seeded by local maxima of the distance to the struts obtained from computer tomography images. This methodology is thus fully voxel‐based and does not depend on any assumption about statistical distributions of the foam cells. Therefore, it is able to reproduce an accurate geometrical model of the foam's microstructure and its possible irregularities. Moreover, this procedure allows the processing of large 3D data sets that do not fit the random access memory (RAM) by slicing it into smaller independent chunks. The effectiveness of the proposed approach is illustrated by comparing it to FEM simulations for which meshes are obtained from a feature reconstruction approach. Both FEM simulations are then compared with experimental results of uniaxial compressions of an open foam.
Vibration analysis of piezoelectric Kirchhoff–Love shells based on Catmull–Clark subdivision surfaces
Authors: Liu Zhaowei , McBride Andrew , Saxena Prashant , Heltai Luca , Qu Yilin , Steinmann Paul 
Published: May 2022

AbstractAn isogeometric Galerkin approach for analysing the free vibrations of piezoelectric shells is presented. The shell kinematics is specialized to infinitesimal deformations and follow the Kirchhoff–Love hypothesis. Both the geometry and physical fields are discretized using Catmull–Clark subdivision bases. This provides the required ‐continuous discretization for the Kirchhoff–Love theory. The crystalline structure of piezoelectric materials is described using an anisotropic constitutive relation. Hamilton's variational principle is applied to the dynamic analysis to derive the weak form of the governing equations. The coupled eigenvalue problem is formulated by considering the problem of harmonic vibration in the absence of external load. The formulation for the purely elastic case is verified using a spherical thin shell benchmark. Thereafter, the piezoelectric shell formulation is verified using a one dimensional piezoelectric beam. The piezoelectric effect and vibration modes of a transverse isotropic curved plate are analyzed and evaluated for the Scordelis–Lo roof problem. Finally, the eigenvalue analysis of a CAD model of a piezoelectric speaker shell structure showcases the ability of the proposed method to handle complex geometries.
Trajectory tracking control based on memory data for robots with imprecise dynamic properties and interference
Authors: Wang Zhuo , Fang Mengliang 
Published: May 2022

AbstractIn this article, a new controller design method is proposed for the trajectory tracking problem of robots with imprecise dynamic properties and interference. By using the tracking error memory data of state variables to construct control law, the tracking errors caused by the system interference and inaccurate system modeling can be eliminated, and interference compensation can be realized, so that the system has the desired dynamic performance. The proposed method comes from the tracking control design of an affine nonlinear system. The controller is based on the error function of the control input in the ideal state and the actual state. According to the Lyapunov stability principle, it is proved that the proposed controller has good robustness under the conditions of bounded interference and inaccurate modeling. MATLAB was used to establish the controller and dynamic equation of the two‐joint planar robot for trajectory tracking simulation. Simulation results are presented to illustrate the performance of the proposed controller.
Mechanical and thermal analysis of coir fiber reinforced jute/bamboo hybrid epoxy composites
Authors: Sathish Thanikodi , Jagadeesh Praveenkumara , Rangappa Sanjay Mavinkere , Siengchin Suchart 
Published: May 2022

AbstractIn this current research study, nine different combinations of coir, jute, and bamboo reinforced epoxy composites were fabricated using casting technique. These composites were employed to mechanical tests such as flexural and impact tests, and analyzed the thermal stability through Thermogravimetric analysis (TGA) and Differential Scanning Calorimetry (DSC). Moreover, the thermal conductivity and surface morphology was also studied for hybrid composites. The hybridization of more than one fiber with epoxy matrix resulted in better mechanical and thermal properties as compared to individual reinforcements, and this statement is agreed with the present research work as well as the research works reported in the literature. The hybrid composite with the maximum amount of jute fibers reinforcement with bamboo fiber (B2C0J8) exhibited maximum flexural and impact strengths of 92.521 MPa and 82.4 kJ/m2respectively, which is due to the higher modulus and energy‐absorbing behavior of jute fibers, also it was an advantage of coir fibers absence having lower modulus and strength values. In thermal conductivity analysis, the marginal variations of values were observed with different volume fractions of fibers, and the maximum conductivity (0.317 W/m‐K) was obtained for B2C8J Composite having only coir and bamboo fiber reinforcements with epoxy matrix. The Thermogravimetric analysis results reveal that all nine types of hybrid composites possess nearly equal thermal stability, and slight variations in degradation temperatures were observed in the thermographs. The B2C1J7 hybrid composite was recommended for better mechanical and thermal properties, where it has 89.06 MPa of flexural strength, 78.6 kJ/m2of impact strength, 0.233 W/m‐K of thermal conductivity and exhibited better surface morphology.
Improvement of mechanical and antibacterial properties of silica‐filled styrene butadiene rubber composite by using cinnamaldehyde
Authors: Kandil Heba , Nour Shaimaa A. 
Published: May 2022

AbstractIn this study, cinnamaldehyde (CAD) was used as a filler modifier and antimicrobial material for silica‐filled styrene butadiene rubber (SBR) composite. CAD was used in different amounts to modify the silica surface. Fourier‐transform infrared spectroscopy (FTIR) was used to characterize the obtained CAD modified silicas. The modified silicas were mixed with SBR matrices using a laboratory two‐roll mill to produce modified silica‐filled SBR composites. The curing, mechanical, swelling and antibacterial properties of the resulting composites were studied and compared with those of the unmodified silica‐filled SBR composite. The surface morphologies of the obtained composites were also studied. The mechanical results showed that the use of 3 g of CAD resulted in a significant improvement in the mechanical properties of the resulting composite as its tensile strength, elongation at break and modulus at 100% increased by 144.9%, 105.1%, and 37.5%; respectively; compared to the unmodified composite. Furthermore, the antibacterial results showed that all the modified composites had a high activity against Gram+ and Gram− bacteria compared to the unmodified one, and this activity increased by increasing the amount of CAD. Accordingly, it is expected that these prepared composites can be used for medicinal purposes in the future.