bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework
Authors: Singh Vikram , Singh Vikram 
Published: July 2022

Abstract
Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart (RWR) and graphlet degree vectors (GDV) to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network (TulsiPIN) was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.
Gradient variations of cellulose supramolecular structures in moso bamboo culm: from nano to micro horizons
Authors: Ling Zhe , Jin Zhi , Dai Linxin , Ma Jianfeng , Chen Qian 
Published: July 2022

Abstract
The radially gradient variation in the cellulose supramolecular structures of bamboo culm were systematically studied by XRD and the confocal Raman microspectroscopy. XRD analysis indicated that bamboo yellow (By) has the isotropic crystallite arrangements, while outer bamboo timber (Bt) and bamboo green (Bg) display preferred orientation of crystals. Moreover, both the crystallinity and crystallite sizes notably grow from the inner By to the outer Bg. Raman band ratio (I1095/I2939) was used to predict microfibrils angle (MFA) in different cell wall types, semi-qualitatively. The results showed that the ratio was the highest in parenchyma, followed by narrow layer of fiber wall, and the lowest in the broad layer, which indicated the higher MFA in the parenchyma. Interestingly, the ratio decreased along the successive and alternating broad and narrow lamellae of fiber wall, in accordance with cell wall micromechanical trend. The findings will favor the large-scale utilization for the bamboo-based flexible composites.
Off-Brand: A Six-Year Study of Medication Brand and Generic Name Usage in a Multi-Facility Academic Healthcare System
Authors: Steinkamp Jackson , Hecht Todd , Hennessy Sean , Leonard Charles , Shu Di , Airan-Javia Subha L. 
Published: July 2022

Abstract
Background:
Usage of medication brand names in electronic health records may introduce conflicts of interest, perpetuate false perceptions of brand superiority, alter prescribing practices, and cause confusion leading to errors. We sought to identify the frequency of brand name medication usage in clinical documentation, as well as factors associated with increased usage.
Methods:
We conducted a descriptive analysis to identify generic and brand names for 518 medications in all clinical notes written at our healthcare system between 2015 and 2020. We used string-matching and regular expressions to identify medication mentions. We conducted bivariate analyses to identify associations between brand name usage and author-, note-, and medication-level factors, and a multivariate logistic regression to clarify independent associations between individual factors and brand usage.
Results:
A total of 104,456,653 notes from 37,285 unique authors were included in our analysis. 162,906,009 medication mentions were identified, of which 36.0% were brand name mentions with a steady year-over-year decrease. Factors associated with usage of brand name included: author role, years since release, length and syllabic complexity of the generic name, service type, and encounter context. Over-the-counter availability did not affect usage. There was sizable individual variation between note writers.
Conclusions:
Usage of brand names in documentation is a multifaceted phenomenon involving ease-of-writing and pronunciation, author role and training, and time since medication approval. Our findings indicate potential avenues to reduce usage frequency, including individual clinician education and system-level changes to reduce the difference in complexity between brand names and generic names.
Modelling and estimation of COVID-19 pandemic with the face mask and vaccination
Authors: Bai Zhongtian , Ma Zhihui , Jing Libaihe , Li Yonghong , Wang Shufan , Wang Bin-Guo , Wu Yan , Zhang Jiangqian , Wang Haoyang 
Published: July 2022

Abstract
COVID-19 is a public health emergency for human beings and brings some very harmful consequences in social and economic fields. In order to model COVID-19 and develop the effective controlling measures, this paper proposes an SEIR-type epidemic model with the mask wearing and the vaccination. Firstly, the effective reproduction number and the threshold conditions are obtained by analyzing the dynamical behaviors of the proposed epidemic model. Secondly, selecting the data of South Korea from January 20, 2022 to March 21, 2022, all model parameters are defined and estimated. Finally, based on the estimated parameters, the numerical simulations are conducted and the simulation suitably fit with the presented model. The results show that the mask wearing ratio, the effectiveness of the certain face mask, the vaccination rate and effectiveness of vaccination for the susceptible individuals play an important role in preventing and controlling COVID-19 pandemic. The face mask wearing is associated with 83% and 90% reductions in the numbers of the cumulative cases and the newly confirmed cases respectively after sixty days while the face mask wearing rate increases 15%, and the vaccination rate is associated with 75% and 80% reductions in the numbers of the cumulative cases and the newly confirmed cases respectively after sixty days while the vaccination rate augments 15\%. Therefore, the effect of the mask wearing on reducing the cumulative cases and the newly confirmed cases is more remarkable than that of the vaccination, this means the disease control departments should strongly recommended that peoples should wear the face mask to prevent themselves from becoming infected when the vaccination willingness of individuals is relative low. The face mask wearing still the primary measure to prevent and control the transmission of COVID-19 pandemic.
Space Discretization-based Optimal Trajectory Planning for Automated Vehicles in Narrow Corridor Scenes
Authors: Xu Biao , Lin Xuerong , Hu Manjiang , Bian Yougang , Qin ZhaoBo 
Published: July 2022

Abstract
The narrow corridor is a common working scene for automated vehicles, where it is pretty challenging to plan a safe, feasible, and smooth trajectory due to the narrow passable area constraints. This paper presents a space discretization-based optimal trajectory planning method for automated vehicles in a narrow corridor scene with the consideration of travel time minimization and boundary collision avoidance. In this method, we firstly design a driving corridor model to describe the reference path and the feasible areas mathematically. Then, we build a space discretization-based trajectory optimization model in which the objective function is travel efficiency, and the vehicle-kinematics constraints, collision-avoidance constraints, and several other constraints are proposed to ensure the feasibility and comfortability of the planned trajectory. Finally, the proposed method is verified with both simulations and field tests. The test results demonstrate the enhanced smoothness and effectiveness of the trajectories compared with the baseline algorithm.
Effects of let-7a microRNA and C-C chemokine receptor type 7 expression on cellular function and prognosis in esophageal squamous cell carcinoma
Authors: Yura Masahiro , Fukuda Kazumasa , Matsuda Satoru , Irino Tomoyuki , Nakamura Rieko , Kawakubo Hirofumi , Takeuchi Hiroya , Kitagawa Yuko 
Published: July 2022

Abstract
Background
The C-C chemokine receptor type 7 (CCR7) plays an important role in chemotactic and metastatic responses in various cancers, including esophageal squamous cell carcinoma (ESCC). Several studies have reported that let-7a microRNA (miRNA) suppresses migration and invasion of various types of cancer cells by downregulating CCR7 expression.
Methods
The expression of CCR7 and let-7a was measured in the cell lines, tumor tissues, and peritumoral tissues of ESCC patients. KYSE cell lines were transfected with synthetic let-7a miRNA and a let-7a miRNA inhibitor, and their CCR7 expression and invasive ability were evaluated. A highly invasive cell line was established via an invasion assay, and CCR7 and let-7a expression was subsequently evaluated. In vivo, cancer cells overexpressing CCR7 were injected subcutaneously into mice and monitored for tumor growth and lymph node metastasis.
Results
A negative correlation between CCR7 and let-7a expression was observed in ESCC cell lines and patient tissue samples. Synthetic let-7a decreased CCR7 expression, while the let-7a inhibitor increased it. In vitro, the established highly invasive cancer cells with high and low levels of CCR7 and let-7a expression, respectively, exhibited a greater invasive ability than the wild-type cell line. In vivo, the highly invasive cells were associated with tumor growth and lymph node metastasis in mice. Patients in the high-CCR7/low-let-7a group had the worst prognosis with five-year recurrence free survival (5-RFS) at 37.5%, followed by the high-CCR7/high-let-7a (5-RFS: 60.0%) and low-CCR7 (5-RFS: 85.7%; p = 0.038) groups.
Conclusions
The expression of CCR7 was downregulated by let-7a miRNA in esophageal cancer cells. The decrease in let-7a expression led to the increased expression of CCR7 in ESCC cells, consequently increasing their invasive ability and malignancy, and resulted in a worse prognosis for ESCC patients.
Trial registration:
Retrospectively registered.
COVID-19 Vaccination Induced Corneal Graft Rejection Does Not Exist: Results of a Large Multi-country Population Based Study
Authors: Roberts Harry , Wilkins Mark , Malik Mohsan , Langroudi Melody , Myerscough James , Pellegrini Marco , Yu Angeli Christy , Busin Massimo 
Published: July 2022

Abstract
PURPOSE: The aim of the study was to present the rates of corneal transplant rejection from 2018 to 2022 at both Moorfields Eye Hospital UK, and Ospedali Privati Forli (OPF) “Villa Igea”, Italy and evaluate the purported association between COVID-19 vaccination and rejection. METHODS: We performed a retrospective review of rejection cases presenting to the two units. Monthly rates were correlated against regional vaccination program rates. At OPF, conditional Poisson regression model was employed to estimate the incidence risk ratio (IRR) of graft rejection following COVID-19 vaccination risk period compared with the control period. RESULTS: Between January 2018 and March 2022, there were 471 (Moorfields), 95 (OPF) episodes of rejection. From the start of vaccination programme in the UK in late January 2021, the median number of graft rejections per month at Moorfields was 6 (range: 5 – 9), which was not significantly different to post-lockdown, pre-vaccination programme (March 2020 – January 2021), p=0.367. At OPF, the median rates of rejection before and after initiation of the vaccination program were not significantly different (p=0.124). No significant increase in incidence rate of rejection in the risk period following COVID-19 vaccination was found (IRR=0.53, p=0.71). CONCLUSION: No notable increase in rates of transplant rejection was noted in year 2021 when COVID-19 vaccination was broadly implemented. The apparent temporal relationship between COVID-19 vaccination and corneal graft rejection highlighted in several case reports may not represent a causative association
Two novel mgCas12a proteins from the human gut metagenome exhibit reduced collateral DNase activity
Authors: Kim Han Seong , Kim Dongwook , Choe Sunghwa 
Published: July 2022

Abstract
CRISPR/Cas9 and CRISPR/Cas12a are characterized by a single-component effector protein. Despite unique features like DNA cleavage with 5′ staggered ends and a single crRNA, Cas12a has not been adopted in therapeutics to the same extent as Cas9. To address the pressing therapeutic needs for effective CRISPR/Cas12 systems, we selected two candidates, designated mgCas12a-1 and mgCas12a-2, from an analysis of the human microbiome metagenome (mg) for biochemical characterization. These new Cas12 proteins shared about 37% identity with FnCas12a from Francisella novicida and showed preference for Mn2+ and Mg2+ over Ca2+ or Fe2+ as divalent metal ions. The new Cas12 proteins also tolerated pH values from 5 to 8 and temperatures from 30°C to 50°C and had lower non-specific nuclease activity upon prolonged incubation than did FnCas12a. Considering their biochemical characteristics and greater purification yield, the novel mgCas12a proteins may expedite the application of Cas12a proteins in genomics research as well as human therapeutics.
Functional transcriptomic landscape informs novel therapeutic strategies in multiple myeloma
Authors: Sudalagunta Praneeth Reddy , Canevarolo Rafael , Meads Mark , Silva Ariosto , zhao Xiaohong , Cubitt Christopher , DeAvila Gabriel , Alugubelli Raghunandan Reddy , Logothetis Constantine , Tungesvik Alexandre , Zhang Qi , Hampton Oliver , Teer Jamie , Welsh Eric , Yoder Sean , Shah Bijal , Hazlehurst Lori , Gatenby Robert , Domelen Dane Van , Chai Yi , Wang Feng , DeCastro Andrew , Bloomer Amanda , Seigel Erin , Sullivan Daniel , Alsina Melissa , Nishihori Taiga , Brayer Jason , Cleveland John L. , Dalton William , Gillies Robert , Walker Christopher , Landesman Yosef , Baz Rachid , Silva Ariosto Siqueira , Shain Kenneth 
Published: July 2022

Abstract
We present a unique database of tumor samples from 399 multiple myeloma (MM) patients, whose functional genomic landscape was assessed by integrating ex vivo drug sensitivity to 138 drugs, clinical variables, cytogenetics, mutational profiles and transcriptomes. These analyses revealed a novel MM transcriptomic topology that, when associated with ex vivo drug sensitivity, generates “footprints” having both mechanistic and predictive applications. We validated the transcriptomic footprint for the nuclear export inhibitor selinexor in two clinical trials, BOSTON and MCC17814, and showed such a gene signature can accurately classify clinical response and suggest mechanism of resistance. Finally, we propose a novel evolutionary-based therapeutic strategy involving sequential therapy of monoclonal antibody daratumumab and selinexor, based on anti-correlative transcriptomic footprints, which was validated in two clinical trials (STOMP and XPORT-MM-028). Collectively, this database and computational framework can be leveraged to inform underlying biology, and to identify novel therapeutic strategies to improve treatment of MM.
Design and CNFET Implementation of the GDI Based Ternary Prefix Adders
Authors: Shanmugam Kavitha , C Kumar 
Published: July 2022

Abstract
Ternary adders have produced more benefits compared to the binary adders (i.e.) the ternary adder occupies less amount of area as well as produces less interconnect complexity. But the CMOS implementation of the ternary adders are failed to perform the process when the channel length is taken as 32nm. At 32nm technology, the CMOS transistors are exhibited undesired effects such as SCE, mobility degradation, etc., These issues are overcome by multi-gate devices. CNFETs (Carbon Nano-tube Field Effect Transistors) are the one of the technology to work efficiently when channel length is 32nm. In this paper, CNFETs based ternary prefix adders are designed. The power consumption is the most needed requirement for the VLSI system. So, this can be achieved by reducing the number of transistors. The reduction approach is called as the GDI (Gate Diffusion Input) logic is also included in the proposed prefix adder design. The proposed adder improved by reducing the power upto 83%, Energy upto 83%, current upto 78%, delay upto 96%. Finally, the PDP (Power Delay product) also reduced by 84% compared to existing ternary adders.
Automated Estimation of Hepatorenal Index: a Biomarker for Hepatic Steatosis
Authors: Wang Shuhang , Kumar Viksit , Hu Szu-Yeu , Wang Xiaohong , Chen Lei , Wang Jingchao , Ozturk Arinc , Li Qian , Pierce Theodore T. , Tsymbalenko Yelena , O’Dea Paul , Washburn Michael J. , Samir Anthony E. 
Published: July 2022

Abstract
Steatosis is the most common cause of chronic liver disease worldwide. Ultrasound helps diagnose steatosis due to its wide availability, non-invasiveness, and safety. The hepatorenal index (HRI) is a clinically used biomarker for diagnosing steatosis. To study the automated calculation of HRI from ultrasound images, we identified a retrospective cohort undergoing abdominal ultrasound with 1320 images, one image per patient. The patients were divided into training (n=1166) and test (n=154) sets. The test set consists of 48 patients without steatosis (S0) and 106 patients with steatosis (S1-S3). An automated method was proposed to calculate HRI using four steps (a) segment the liver and the renal cortex, (b) remove pixels associated with ducts, vessels, masses, cysts, and shadowing artifacts, (c) place two regions of interest (ROIs), one each in the liver and the renal cortex, and (d) calculate the HRI as the ratio of the mean pixel value of the liver ROI to the renal cortex ROI. We explored several sets of rules for ROI placement. The method minimizing the Euclidean distance between the two ROIs, the best performer, had an area under the ROC (AUROC) curve of 0.87 compared to physicians with an AUROC of 0.82 (p=0.159). In addition, the Euclidean distance constraint showed no dependence on depth for ROI placement. The proposed automated method can be translated into clinical care without modifying existing imaging protocols to optimize the diagnostic capability of ultrasound for hepatic steatosis and assist with triaging patients.
Aesthetic Reconstruction of Onco-surgical Maxillary Defects Using Free Scapular Flap with and without CAD/CAM Customized Osteotomy Guide
Authors: Alwadeai Mohamed Salah , aroomi Lina Ali Al , Shindy Mostafa Ibrahim , Amin Ayman Abdel-Wahab , Zedan Mohamed Hamdallah 
Published: July 2022

Abstract
Background: Reconstruction of the maxillary defects following tumor ablation remains to be a challenge for surgeons. Virtual Surgical Planning (VSP), intraoperative cutting guides and stereolithographic models provides the head and neck reconstructive surgeon with powerful tools for complex reconstruction planning. Despite its use in fibular osteocutaneous reconstruction, application to the scapular free flap has not been as widely reported. The aim of this study was to compare aesthetic results and operation time of free scapular flap, with and without computer-aided design and computer-aided manufacturing (CAD/CAM) customized osteotomy guide, for reconstruction of maxillary defects.Methods: In this prospective randomized controlled clinical trial study, we randomly assigned 22 patients with maxillary defects who were scheduled to undergo maxillary reconstruction with either free scapular flap with CAD/CAM customized osteotomy guide; study group (n = 11) or free scapular flap without CAD/CAM customized osteotomy guide; control group (n =11). All patients were followed up for 3 months. The aesthetic outcome, operation and ischemic times were evaluated and compared.Results: Aesthetic outcomes were evaluated objectively by means of differential surface area (sagittal and axial) measurement, which showed improved aesthetic outcome (contour symmetry) in the study group with a mean of (241.39±113.74), compared to patients in control group with a mean of (358.70±143.99). There were significant differences between the two groups (P< 0.05). Aesthetic outcomes were also evaluated subjectively by means of visual analogue scale (VAS) and patient’s satisfaction score (PSS). The postoperative aesthetic appearance was better in the study group with more patients satisfied than that in control group and there were statistically significant differences (P=0.039). The mean total operative time was 678.81 minutes and 777.18 minutes in the study group and control group respectively (P<0.05) and the mean ischemia time was 133.18 minutes and 195.72 minutes for study group and control group respectively (P<0.05).The ischemia time and total operative time were shorter in the study group compared to those in the control group and there were no flap losses in both groups.Conclusion: The use of CAD/CAM prefabricated cutting guides facilitates scapular flap molding and placement, minimizes ischemic time and operating time as well as improves aesthetic outcomes.Trial registration: This trial was registered at ClinicalTrials.gov. Registration number: NCT03757286. Registration date: 28/11/ 2018.
Using 5A’s model for lifestyle counseling on psychological symptoms in women with polycystic ovary syndrome: a randomized field trial
Authors: ZareMobini Fatemeh , Farajzadegan Ziba , Kazemi Ashraf , Salehi Mehrdad 
Published: July 2022

Abstract
Lifestyle modification in women with polycystic ovary syndrome (PCOS) could be associated with an increase in psychological symptoms. The aim of this study was to evaluate the effect of lifestyle modification counseling through using 5As Model on the psychological symptoms of women with PCOS. This double-blind randomized field trial was performed on 70 women with PCOS in two groups of lifestyle modification counseling based on 5A’s model and counseling without using the model. The intervention was performed based on five stages of the 5A’s model including ask, advise, assess, assist, and arrange during a week, and psychological symptoms were assessed using Symptom Checklist-90-R before the intervention and one and three months after the intervention. The results showed that one and three months after the intervention, the level of psychological symptoms, except obsessive-compulsive, were significantly lower in the intervention group than the control group (p <0.05). Moreover, the level of these symptoms decreased over time in the intervention group (p <0.0001). Using of 5A’s model in lifestyle modification counseling is associated with the promotion of mental health in women with PCOS and the 5 A’s model is recommended for using lifestyle counseling in women with polycystic ovary syndrome.
Dual-Channel P-Type Ternary DNTT–Graphene Barristor
Authors: Lee Yongsu , Kim Seung-Mo , Kim Kiyung , Kim So-Young , Lee Ho-In , Kwon Heejin , Lee Hae-Won , Kim Chaeeun , Some Surajit , Hwang Hyeon Jun , Lee Byoung Hun 
Published: July 2022

Abstract
P-type ternary switch devices are crucial elements for the practical implementation of complementary ternary circuits. This report demonstrates a p-type ternary device showing three distinct electrical output states with controllable threshold voltage values using a dual-channel dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]-thiophene–graphene barristor structure. To obtain transfer characteristics with distinctively separated ternary states, novel structures called contact-resistive and contact-doping layers were developed. The feasibility of a complementary standard ternary inverter design around 1 V was demonstrated using the experimentally calibrated ternary device model.