bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of enhanced empirical wavelet transform and correlation kurtosis in bearing fault diagnosis
Authors: Xue Jijun , Xu Hao , Liu Xiaodong , Zhang Di , Xu Yonggang
Published: November 2022

The traditional empirical wavelet transform (EWT) based on the Meyer wavelet and scale-space method can decompose a signal into several empirical modes. However, this method is not effective in dealing with strong noise and non-stationary signals, which may lead to modal mixing or even decompose too many invalid components. For this purpose, a method based on the combination of enhanced empirical wavelet transform (EEWT) and correlation kurtosis (CK) is proposed in this paper. Firstly, the EEWT is used to segment the spectrum based on the characteristics of the spectrum fluctuations. It uses the minimum points of the envelope as the boundaries of the segmented spectrum. Secondly, a filter bank is constructed based on these boundaries and a maximum value order statistics filter segments the Fourier spectrum with the adaptive decomposition of the signals. Finally, the envelope spectrum generated by CK is used to screen the bearing fault information, which belongs to the decomposition of a signal into empirical modes, so that the rolling bearing fault can be accurately diagnosed. The method’s effectiveness is verified by simulated signal experiments and rolling bearing fault signals. The results show that the performance of the proposed method in this paper is better than that of the traditional EWT. Therefore, the method can be applied to the field of bearing faults or other mechanical fault diagnosis directions.
Enhanced neural network model for regional ionospheric modeling and evaluation under different solar-geomagnetic conditions
Authors: Dong Yanfeng , Gao Chengfa , Long Fengyang , Nie Wenfeng , Juan Jose Miguel , Rovira-Garcia Adria , Zhang Ruicheng
Published: November 2022

Monitoring spatiotemporal variations of ionospheric vertical total electron content (VTEC) is crucial for space weather and satellite positioning. In the present study, an enhanced neural network (ENN) model is proposed to capture the changing characteristics of ionospheric VTEC and compared with the traditional mathematical models, i.e. the POLYnomial (POLY) model, generalized trigonometric series function and spherical harmonic function (SHF) model. The ionospheric VTEC data obtained from 31 permanent global positioning system stations in the southwest region of China on 26 August and 8 September, 2017, were used to test the performance of the mentioned models under different Solar-geomagnetic conditions. The ENN model is derived from the ensemble learning method, and the disadvantage that simple backpropagation neural network learners that are not robust enough is weakened by the ENN model. After statistical analysis and single-frequency precise point positioning (SF-PPP) experiments, it is demonstrated that the ENN model is superior to the above three mathematical models, regardless of the solar-geomagnetic conditions. In terms of mean absolute error, root mean square error, standard deviation, and mean absolute percentage error, the ENN model outperforms the SHF model, which is the best mathematical model in the analysis, by 40.7%, 30.20%, 29.88%, 38.04% under quiet solar-geomagnetic conditions, and by 37.66%, 29.93%, 30.96%, 32.01% under active solar-geomagnetic conditions. In addition, the accuracy of the SF-PPP is greatly affected by the error caused by ionosphere. In the static SF-PPP experiment of this study, the ENN model can better correct ionospheric error. Under quiet and active solar-geomagnetic conditions, the SF-PPP accuracy can be improved by 85.1% and 85.2% with the ionosphere delay correction from the ENN model.
Seizure forecasting using machine learning models trained by seizure diaries
Authors: Gleichgerrcht Ezequiel , Dumitru Mircea , Hartmann David A , Munsell Brent C , Kuzniecky Ruben , Bonilha Leonardo , Sameni Reza
Published: November 2022

Objectives. People with refractory epilepsy are overwhelmed by the uncertainty of their next seizures. Accurate prediction of future seizures could greatly improve the quality of life for these patients. New evidence suggests that seizure occurrences can have cyclical patterns for some patients. Even though these cyclicalities are not intuitive, they can be identified by machine learning (ML), to identify patients with predictable vs unpredictable seizure patterns. Approach. Self-reported seizure logs of 153 patients from the Human Epilepsy Project with more than three reported seizures (totaling 8337 seizures) were used to obtain inter-seizure interval time-series for training and evaluation of the forecasting models. Two classes of prediction methods were studied: (1) statistical approaches using Bayesian fusion of population-wise and individual-wise seizure patterns; and (2) ML-based algorithms including least squares, least absolute shrinkage and selection operator, support vector machine (SVM) regression, and long short-term memory regression. Leave-one-person-out cross-validation was used for training and evaluation, by training on seizure diaries of all except one subject and testing on the left-out subject. Main results. The leading forecasting models were the SVM regression and a statistical model that combined the median of population-wise seizure time-intervals with a test subject’s prior seizure intervals. SVM was able to forecast 50%, 70%, 81%, 84%, and 87% of seizures of unseen subjects within 0, 1, 2, 3 to 4 d of mean absolute forecasting error, respectively. The subject-wise performances show that patients with more frequent seizures were generally better predicted. Significance. ML models can leverage non-random patterns within self-reported seizure diaries to forecast future seizures. While diary-based seizure forecasting alone is only one of many aspects of clinical care of patients with epilepsy, studying the level of predictability across seizures and patients paves the path towards a better understanding of predictable vs unpredictable seizures on individualized and population-wise bases.
Characterization of rheumatic heart disease from electrocardiogram recordings
Authors: Asmare Melkamu Hunegnaw , Chuma Amsalu Tomas , Varon Carolina , Woldehanna Frehiwot , Janssens Luc , Vanrumste Bart
Published: November 2022

Objective. Rheumatic Heart Disease (RHD) is one of the highly prevalent heart diseases in developing countries that can affect the pericardium, myocardium, or endocardium. Rheumatic endocarditis is a common RHD variant that gradually deteriorates the normal function of the heart valves. RHD can be diagnosed using standard echocardiography or listened to as a heart murmur using a stethoscope. The electrocardiogram (ECG), on the other hand, is critical in the study and identification of heart rhythms and abnormalities. The effectiveness of ECG to identify distinguishing signs of rheumatic heart problems, however, has not been adequately examined. This study addressed the possible use of ECG recordings for the characterization of problems of the heart in RHD patients. Approach. To this end, an extensive ECG dataset was collected from patients suffering from RHD (PwRHD), and healthy control subjects (HC). Bandpass filtering was used at the preprocessing stage. Each data was then standardized by removing its mean and dividing by its standard deviation. Delineation of the onsets and offsets of waves was performed using KIT-IBT open ECG MATLAB toolbox. PR interval, QRS duration, RR intervals, QT intervals, and QTc intervals were computed for each heartbeat. The median values of the temporal parameters were used to eliminate possible outliers due to missed ECG waves. The data were clustered in different age groups and sex. Another categorization was done based on the time duration since the first RHD diagnosis. Main results. In 47.2% of the cases, a PR elongation was observed, and in 26.4% of the cases, the QRS duration was elongated. QTc was elongated in 44.3% of the cases. It was also observed that 62.2% of the cases had bradycardia. Significance. The end product of this research can lead to new medical devices and services that can screen RHD based on ECG which could somehow assist in the detection and diagnosis of the disease in low-resource settings and alleviate the burden of the disease.
Hysteretic behaviour and structural control performance of a piezoelectric friction damper
Authors: Zhang Xiaolong , Luo Qixing , Han Qinghua , Lu Yan , Wang Yue
Published: November 2022

This study proposes a novel piezoelectric friction damper (PFD). Experiments and numerical simulations are carried out to investigate the mechanical model of the PFD, and the effects of loading speed, displacement amplitude, voltage, friction plate material, piezoelectric stack actuator dimensions, and spring parameters on the hysteretic characteristics of the PFD. Results show that the PFD attains a stable mechanical performance within the design loading speed and displacement amplitude. The piezoelectric stack actuator functioning as a friction control device, can increase friction by 54% at 120 V. In damper design, an appropriate increase of the constraint stiffness of the damper and a piezoelectric stack actuator with the same stiffness as the damper constraint can achieve greater output force, and the preload of the spring should be greater than the friction to prevent residual displacement. The PFD has better seismic performance for large-span cable dome structures than the traditional friction damper. The vertical peak displacement and acceleration reduction ratio reached 45.1% and 67.7% with PFDs, respectively. The PFD with semi-active control is suitable for large-span spatial structures.
Analysis of pulsatile combined electroosmotic and shear-driven flow of generalized Maxwell fluids in a microchannel with slip-dependent zeta potential
Authors: Mahanta Kaushik , Panda Swapnil , Banerjee Debanjan , Pati Sukumar , Biswas Pankaj
Published: November 2022

The present study investigates the flow characteristics for a pulsatile, combined electroosmotic and shear-driven flow of generalized Maxwell fluid through a straight planar microchannel including the effect of hydrodynamic slippage on asymmetric zeta potential. Mathematical expressions have been obtained in dimensionless form for the electrical potential distribution of the electrical double layer (EDL), velocity distribution and the volumetric flow rate after analytically solving the Poisson-Boltzmann and momentum equations. Critical values and critical ranges of time period of oscillating electric field have been obtained for no-slip and slip cases respectively where anomalous behaviour of dimensionless volumetric flow rate is observed. Flow rate magnitude sensitivity on hydrodynamic slippage is also analyzed. Moreover, critical values of the time period of oscillating electric field are obtained where the sensitivity of flow rate magnitude on the relaxation time of Maxwell fluid vanishes. Similarly, pivotal values of the time period of oscillating electric field are obtained at which the sensitivity of flow rate magnitude on the relaxation time of Maxwell fluid becomes invariant with the lower wall velocity.
Triggering of tearing instability by impurity radiation through resistive interchange reversal in a tokamak
Authors: Zeng Shiyong , Zhu Ping , Zhou Ruijie , Escande Dominique Frank
Published: November 2022

Recent MHD simulations find that the reversal of the local resistive interchange parameter

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R

from negative to positive due to impurity radiation cooling is able to linearly destabilize the resistive tearing mode (TM) growth in a tokamak above a threshold in impurity level. A layer of perturbed Pfirsch–Schlüter current density and resistivity are also induced by the impurity radiation, which further govern the TM growth and saturation in the nonlinear stage. The impurity threshold and the TM growth strongly depend on the parallel thermal conductivity, and such a dependence derives from the impact on

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of the fast parallel thermal equilibration along the helical magnetic field lines.
Acousto-optic k-space filtering for multifrequency laser beam shaping
Authors: Yushkov Konstantin B , Kupreychik Maxim I , Obydennov Dmitry V , Molchanov Vladimir Y
Published: November 2022

One of emerging applications of acousto-optic tunable filters (AOTFs) is spatial filtering of optical beams. A noncollinear AOTF has a tunable ring-shaped transfer function determined by geometry of the refractive index surface in a uniaxial crystal. We rigorously derive the geometrical parameters of the AOTF’s elliptic transfer function under noncritical phase matching condition in uniaxial crystals. This basic family of transfer functions can be used for synthesis of axially symmetric transfer functions with the help of multifrequency ultrasonic signals. A two-color tunable optical trap configuration is proposed based on a single AOTF used for laser beam shaping.
Preparation and characterization of Fe3O4 nanoparticles via a hydrothermal process with propanediol as the solvent
Authors: Liu Tao , Zhang Shuting , Xu Yueyang
Published: November 2022

Fe3O4 nanomaterials have received great attention in various technology fields. However, the limitations are Fe3O4 is easy to agglomerate and obtaining Fe3O4 nanoparticles of tunable magnetism and controllable size, and well-dispersed ability remains a challenge. In this study, a simple hydrothermal process with propanediol as the solvent was used to prepare Fe3O4 nanoparticles. In the optimization of preparation conditions, three key factors (hydrothermal temperature, hydrothermal time, and solvent volume) were optimized by x-ray diffraction (XRD) and vibrating sample magnetometer (VSM). The results showed that the magnetism and the phase content of the prepared Fe3O4 were controllable during the optimization process. The optimum hydrothermal temperature was 170 °C, hydrothermal time was 18 h and solvent volume was 40 ml. The elemental composition, surface morphology, and magnetic properties of Fe3O4 nanoparticles were characterized. The prepared Fe3O4 nanoparticles exhibited superparamagnetic properties and high crystallinity, with an average particle size of 20 nm, a specific surface area of 84.756 m2 g−1, a pore volume of 0.265 cm3 g−1, and saturation magnetization (Ms) of 129.38 emu g−1.
Recent progress on the mechanical exfoliation of 2D transition metal dichalcogenides
Authors: Li Yangang , Kuang Guizhi , Jiao Zhongjie , Yao Lin , Duan Ruihuan
Published: November 2022

Two-dimensional (2D) transition metal dichalcogenides (TMDs) have attracted extensive attraction due to their unique properties in novel physical phenomena, such as superconductors, Moiré superlattices, ferromagnetics, Weyl semimetals, which all require the high quality of 2D TMDs. Mechanical exfoliation (ME) as a top-down strategy shows great potential to obtain 2D TMDs with high quality and large scale. This paper reviews the theoretical and experimental details of this method. Subsequently, diverse modified ME methods are introduced. Significantly, the recent progress of the Au-assisted ME method is the highlight. Finally, this review will have an insight into their advantages and limitations, and point out a rational direction for the exfoliation of TMDs with high quality and large size.
Flexible temperature sensor with high sensitivity ranging from liquid nitrogen temperature to 1200 °C
Authors: Liu Zhaojun , Tian Bian , Jiang Zhuangde , Li Shuimin , Lei Jiaming , Zhang Zhongkai , Liu Jiangjiang , Shi Peng , Lin Qijing
Published: November 2022

Flexible temperature sensors have been extensively investigated due to their prospect of wide application in various flexible electronic products. However, most of the current flexible temperature sensors only work well in a narrow temperature range, with their application at high or low temperatures still being a big challenge. This work proposes a flexible thermocouple temperature sensor based on aerogel blanket substrate, the temperature-sensitive layer of which uses the screen-printing technology to prepare indium oxide and indium tin oxide. It has good temperature sensitivity, with the test sensitivity reaching 226.7μV °C−1. Most importantly, it can work in a wide temperature range, from extremely low temperatures down to liquid nitrogen temperature to high temperatures up to 1200 °C, which is difficult to be achieved by other existing flexible temperature sensors. This temperature sensor has huge application potential in biomedicine, aerospace and other fields.
Reduction of mutual coupling in a microstrip array antenna with circular polarization in the C-frequency band using a combination of DGS and EBG methods
Authors: Shirpay A , Rohaninezhad M R , Tavakoli M , Zarezadeh E
Published: November 2022

In this study, in the first stage, an antenna with circular polarization was designed with the technique of cutting the corners of radiation patches. Then a hybrid structure with DGS and EBG methods was presented. For this purpose, the designed structure of the combination of DGS and EBG, which was designed to reduce mutual coupling, was placed between the radiating elements of the antenna. This method is implemented on a microstrip antenna. The reduction of the coupling of this structure is based on the creation of a magnetic band gap. All simulation was performed numerically by CST Microwave Studio software. The simulation results showed that this structure, unlike previous structures, improves all the characteristics of the antenna, such as the antenna gain, antenna radiation efficiency, and antenna envelope correlation coefficient. Also, the resonant frequency of the antenna is 6.35 GHz, which reduces the coupling by 36.5 dB by placing the designed structure between the radiating elements of the antenna.
Representing collective thinking through cognitive networks
Authors: Duarte Denise , Guedes Gilvan R , Pereira Wesley H S , Ribeiro Rodrigo B
Published: November 2022

This article presents a novel quantitative approach using network features to represent community collective thinking. We propose a new function, called the cognitive affinity coefficient that maps individual cognitive links within a graph structure. This function transforms the data generated by the words chosen for an individual regarding a specific subject into an appropriate relational object for analysing cognitive networks. We apply our methodology to novel data on evocations about river floods, which allowed us to find communities inside the network according to their thinking about this subject and identify the most active individuals inside each one and, therefore, explicit their collective thinking. We also present a utility tool implemented in R, which allows the analysis of the data collected as a network.
Controllability of a class of swarm signalling networks
Authors: Sun Peng , Kooij Robert E , Bouffanais Roland
Published: November 2022

In this article, we propose closed-form analytical expressions to determine the minimum number of driver nodes that is needed to control a specific class of networks. We consider swarm signalling networks with regular out-degree distribution where a fraction $p$ of the links is unavailable. We further apply our method to networks with bi-modal out-degree distributions. Our approximations are validated through intensive simulations. Results show that our approximations have high accuracy when compared with simulation results for both types of out-degree distribution.
Impact of a national screening programme on obesity and cardiovascular risk factors
Authors: Nakao Yoko M , Gale Chris P , Miyazaki Kei , Kobayashi Hajime , Matsuda Ayako , Nadarajah Ramesh , Motonishi Taizo
Published: November 2022

Aims

The benefits of nationwide screening and tailored health guidance on improving obesity and cardiovascular risk factors is uncertain. The aim of the present study was to investigate the association of the national health screening and tailored health guidance with population health outcomes.

Methods and results

A fuzzy regression discontinuity design analysed data of men and women aged 40–74 years who participated in a nationwide health screening programme in Japan from 1 April 2008 to 31 March 2019 and were recorded in the Japanese National Database. Exposure was assignment to the national health guidance of counselling on healthy lifestyle and clinical follow-up for individuals found to have waist circumference ≥85 cm for men ≥90 cm for women with one or more cardiovascular risk factors during annual national health screening. The primary outcomes were changes in obesity status and cardiovascular risk factors 1 year after screening. Of 3 490 112 men and 2 328 929 women, the assignment to the health guidance resulted in small reductions in obesity parameters: waist circumference; men, −0.27 cm [95% confidence interval (CI) −0.29 to −0.26]; women −0.34 (−0.41 to −0.27); body mass index, −0.07 kg/m2 (−0.075 to −0.066); −0.11 kg/m2 (−0.13 to −0.10); weight, −0.21 kg (−0.22 to −0.19); −0.28 kg (−0.32 to −0.24) that attenuated over time. Short-term improvements were also observed in blood pressure, haemoglobin A1c, fasting glucose and triglycerides across both sexes.

Conclusion

A nationwide health screening programme was associated with only small, and transient improvements in obesity and cardiovascular risk factors.
Artificial intelligence in gastric cancer: applications and challenges
Authors: Cao Runnan , Tang Lei , Fang Mengjie , Zhong Lianzhen , Wang Siwen , Gong Lixin , Li Jiazheng , Dong Di , Tian Jie
Published: November 2022

Gastric cancer (GC) is one of the most common malignant tumors with high mortality. Accurate diagnosis and treatment decisions for GC rely heavily on human experts' careful judgments on medical images. However, the improvement of the accuracy is hindered by imaging conditions, limited experience, objective criteria, and inter-observer discrepancies. Recently, the developments of machine learning, especially deep-learning algorithms, have been facilitating computers to extract more information from data automatically. Researchers are exploring the far-reaching applications of artificial intelligence (AI) in various clinical practices, including GC. Herein, we aim to provide a broad framework to summarize current research on AI in GC. In the screening of GC, AI can identify precancerous diseases and assist in early cancer detection with endoscopic examination and pathological confirmation. In the diagnosis of GC, AI can support tumor-node-metastasis (TNM) staging and subtype classification. For treatment decisions, AI can help with surgical margin determination and prognosis prediction. Meanwhile, current approaches are challenged by data scarcity and poor interpretability. To tackle these problems, more regulated data, unified processing procedures, and advanced algorithms are urgently needed to build more accurate and robust AI models for GC.
Evolutionary Conservation and Transcriptome Analyses Attribute Perenniality and Flowering to Day-Length Responsive Genes in Bulbous Barley (Hordeum bulbosum)
Authors: Fuerst Dana , Shermeister Bar , Mandel Tali , Hübner Sariel
Published: November 2022

Rapid population growth and dramatic climatic turnovers are challenging global crop production. These challenges are spurring plant breeders to enhance adaptation and sustainability of major crops. One intriguing approach is to turn annual systems into perennial ones, yet long-term classical breeding efforts to induce perenniality have achieved limited success. Here, we report the results of our investigation of the genetic basis of bulb formation in the nonmodel organism Hordeum bulbosum, a perennial species closely related to barley. To identify candidate genes that regulate bulb formation in H. bulbosum, we applied two complementary approaches. First, we explored the evolutionary conservation of expressed genes among annual Poaceae species. Next, we assembled a reference transcriptome for H. bulbosum and conducted a differential expression (DE) analysis before and after stimulating bulb initiation. Low conservation was identified in genes related to perenniality in H. bulbosum compared with other species, including bulb development and sugar accumulation genes. We also inspected these genes using a DE analysis, which enabled identification of additional genes responsible for bulb initiation and flowering regulation. We propose a molecular model for the regulation of bulb formation involving storage organ development and starch biosynthesis genes. The high conservation observed along a major part of the pathway between H. bulbosum and barley suggests a potential for the application of biotechnological techniques to accelerate breeding toward perenniality in barley.
Whole-exome sequencing study identifies four novel gene loci associated with diabetic kidney disease
Authors: Pan Yang , Sun Xiao , Mi Xuenan , Huang Zhijie , Hsu Yenchih , Hixson James E , Munzy Donna , Metcalf Ginger , Franceschini Nora , Tin Adrienne , Köttgen Anna , Francis Michael ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium TOPMed Kidney Function Working Group, Brody Jennifer A , Kestenbaum Bryan , Sitlani Colleen M , Mychaleckyj Josyf C , Kramer Holly , Lange Leslie A , Guo Xiuqing , Hwang Shih-Jen , Irvin Marguerite R , Smith Jennifer A , Yanek Lisa R , Vaidya Dhananjay , Chen Yii-Der Ida , Fornage Myriam , Lloyd-Jones Donald M , Hou Lifang , Mathias Rasika A , Mitchell Braxton D , Peyser Patricia A , Kardia Sharon L R , Arnett Donna K , Correa Adolfo , Raffield Laura M , Vasan Ramachandran S , Cupple L Adrienne , Levy Daniel , Kaplan Robert C , North Kari E , Rotter Jerome I , Kooperberg Charles , Reiner Alexander P , Psaty Bruce M , Tracy Russell P , Gibbs Richard A , Morrison Alanna C , Feldman Harold , Boerwinkle Eric , He Jiang , Kelly Tanika N ,   the CRIC Study Investigators
Published: November 2022

Diabetic kidney disease (DKD) is recognized as an important public health challenge. However, its genomic mechanisms are poorly understood. To identify rare variants for DKD, we conducted a whole-exome sequencing (WES) study leveraging large cohorts well-phenotyped for chronic kidney disease and diabetes. Our two-stage WES study included 4372 European and African ancestry participants from the Chronic Renal Insufficiency Cohort and Atherosclerosis Risk in Communities studies (stage 1) and 11 487 multi-ancestry Trans-Omics for Precision Medicine participants (stage 2). Generalized linear mixed models, which accounted for genetic relatedness and adjusted for age, sex and ancestry, were used to test associations between single variants and DKD. Gene-based aggregate rare variant analyses were conducted using an optimized sequence kernel association test implemented within our mixed model framework. We identified four novel exome-wide significant DKD-related loci through initiating diabetes. In single-variant analyses, participants carrying a rare, in-frame insertion in the DIS3L2 gene (rs141560952) exhibited a 193-fold increased odds [95% confidence interval (CI): 33.6, 1105] of DKD compared with noncarriers (P = 3.59 × 10−9). Likewise, each copy of a low-frequency KRT6B splice-site variant (rs425827) conferred a 5.31-fold higher odds (95% CI: 3.06, 9.21) of DKD (P = 2.72 × 10−9). Aggregate gene-based analyses further identified ERAP2 (P = 4.03 × 10−8) and NPEPPS (P = 1.51 × 10−7), which are both expressed in the kidney and implicated in renin–angiotensin–aldosterone system modulated immune response. In the largest WES study of DKD, we identified novel rare variant loci attaining exome-wide significance. These findings provide new insights into the molecular mechanisms underlying DKD.
In situ digestion of alcohol-fixed cells for quantitative proteomics
Authors: Hatano Atsushi , Takami Tomoyo , Matsumoto Masaki
Published: November 2022

Currently, the bottom-up approach, in which proteins are digested by enzymes such as trypsin prior to mass spectrometry, is the mainstream approach in mass spectrometer-based proteomics. In this approach, the enzymatic digestion process strongly affects the reproducibility of protein identification and quantification. Here, we quantitatively evaluated the enzymatic digestion of proteins under various conditions by quantitative proteomics using data-independent acquisition and found that proteins precipitated with acetone after solubilization with SDS were fully digestible without re-solubilization. This result implies that organic solvent treatment makes cells amenable to trypsin digestion. Direct trypsin digestion of methanol-fixed cells achieved the same digestion efficiency and quantitative reproducibility as the conventional method. Furthermore, this method was found to be equally applicable to mouse liver samples. The establishment of this method indicates that the sample preparation process in bottom-up proteomics can be simplified while maintaining high digestion efficiency and is expected to become a general method for sample preparation in bottom-up proteomics in the future.
Circ_0000253 promotes the progression of osteosarcoma via the miR-1236-3p/SP1 axis
Authors: Xu Lijun , Duan Jun , Li Mingwu , Zhou Cong , Wang Qinzhi
Published: November 2022

Objective

Circular RNAs (circRNAs) play important roles in modulating tumour progression. This study investigated the role of circ_0000253 in osteosarcoma (OS).

Methods

We downloaded the chip dataset GSE140256 from the Gene Expression Omnibus database and the circRNAs differentially expressed in OS tissue and normal tissue samples were analysed. Quantitative real-time PCR (qRT-PCR) was carried out to examine circ_0000253 expression in OS tissues and cells. Cell counting kit-8, BrdU and flow cytometry assays were performed to verify the effects of circ_0000253 on OS cell growth and apoptosis. Bioinformatics analysis was conducted to predict, and RNA immunoprecipitation assay and dual-luciferase reporter gene assay were performed to verify the targeted relationships of miR-1236-3p with circ_0000253 and Sp1 transcription factor (SP1) mRNA 3ʹUTR. The effects of miR-1236-3p and circ_0000253 on SP1 expression in OS cells were detected through Western blot.

Key findings

Circ_0000253 was upregulated in OS tissues and cell lines. Circ_0000253 overexpression facilitated OS cell growth and suppressed apoptosis, whereas knocking down circ_0000253 inhibited OS cell growth and facilitated apoptosis. Circ_0000253 targeted miR-1236-3p directly and negatively modulated its expression. SP1 was miR-1236-3p’s target gene and positively regulated by circ_0000253.

Conclusion

Circ_0000253 promotes OS cell proliferation and suppresses cell apoptosis via regulating the miR-1236-3p/SP1 molecular axis.
Pharos 2023: an integrated resource for the understudied human proteome
Authors: Kelleher Keith J , Sheils Timothy K , Mathias Stephen L , Yang Jeremy J , Metzger Vincent T , Siramshetty Vishal B , Nguyen Dac-Trung , Jensen Lars Juhl , Vidović Dušica , Schürer Stephan C , Holmes Jayme , Sharma Karlie R , Pillai Ajay , Bologa Cristian G , Edwards Jeremy S , Mathé Ewy A , Oprea Tudor I
Published: November 2022

The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for users to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.
Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation
Authors: Ares-Arroyo Manuel , Coluzzi Charles , Rocha Eduardo P C
Published: November 2022

Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.
On a Turán Conjecture and random multiplicative functions
Authors: Angelo Rodrigo , Xu Max Wenqiang
Published: November 2022

We show that if f is the random completely multiplicative function, the probability that $\sum_{n\le x}\frac{f(n)}{n}$ is positive for every x is at least $1-10^{-45}$, while also strictly smaller than 1. For large x, we prove an asymptotic upper bound of $O(\exp(-\exp( \frac{\log x}{C\log \log x })))$ on the exceptional probability that a particular truncation is negative, where C is some positive constant.
Natural annual transcriptome dynamics ofEucalyptusreveal seasonal adaptation of tropical/sub-tropical trees
Authors: Dai Xiaokang , Lin Ying , Zhou Tingting , Li Yue , Liao Xiaoli , Cao Jianbo , Ding Jihua
Published: November 2022

Seasonal environment cues are primary factors that influence a plant’s growth and adaptation. The molecular basis of seasonal phenology has been well studied in trees growing in boreal and temperate ecosystems. However, little is known about the molecular phenology of trees belonging to tropical/sub-tropical regions. Here, we characterize the annual transcriptome dynamics of Eucalyptus dunnii, one of the world’s most widely planted tropical/sub-tropical hardwoods, in natural environments. Our transcriptome analysis combined with the geographical distribution, environmental cues, microscopic observations and heterologous transformation analyses provides a molecular timetable of seasonal regulatory events of E. dunnii and its planting prospects in China. We further investigated the molecular mechanisms of the flowering phenology of E. dunnii. Our results suggest that low temperature is one of environment triggers for its seasonal flowering. In addition, a comparative transcriptome and cell ultrastructure analysis between Eucalyptus and Populus reveals the molecular bases of different shoot apex growth habits of trees originating from tropical/sub-tropical and boreal/temperate regions. Our study will provide cues for further investigating the molecular mechanisms underlying the seasonal phenology of trees from tropical/sub-tropical regions.
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales
Authors: Li Nien-Kung , Corander Jukka , Grad Yonatan H , Chang Hsiao-Han
Published: November 2022

Incomplete selection makes it challenging to infer selection on genes at short time scales, especially for microorganisms, due to stronger linkage between loci. However, in many cases, the selective force changes with environment, time, or other factors, and it is of great interest to understand selective forces at this level to answer relevant biological questions. We developed a new method that uses the change in dN/dS, instead of the absolute value of dN/dS, to infer the dominating selective force based on sequence data across geographical scales. If a gene was under positive selection, dN/dS was expected to increase through time, whereas if a gene was under negative selection, dN/dS was expected to decrease through time. Assuming that the migration rate decreased and the divergence time between samples increased from between-continent, within-continent different-country, to within-country level, dN/dS of a gene dominated by positive selection was expected to increase with increasing geographical scales, and the opposite trend was expected in the case of negative selection. Motivated by the McDonald–Kreitman (MK) test, we developed a pairwise MK test to assess the statistical significance of detected trends in dN/dS. Application of the method to a global sample of dengue virus genomes identified multiple significant signatures of selection in both the structural and non-structural proteins. Because this method does not require allele frequency estimates and uses synonymous mutations for comparison, it is less prone to sampling error, providing a way to infer selection forces within species using publicly available genomic data from locations over broad geographical scales.
The spectrum of foot deformities in Loeys-Dietz syndrome
Authors: Badin Daniel , Dietz Harry C. , Sponseller Paul D.
Published: November 2022

Loeys-Dietz syndrome (LDS) is characterized by a wide spectrum of musculoskeletal manifestations, including foot deformities. The spectrum of foot deformities in LDS has not been previously characterized. Our objective was to describe the incidence and characteristics of foot deformities in LDS. We retrospectively reviewed the demographic, clinical and imaging data for patients diagnosed with LDS who were seen at our Orthopedic surgery department from 2008 to 2021. We performed descriptive analyses and compared distributions of deformities by LDS genetic mutations. Of the 120 patients studied, most presented for evaluation of foot deformities (N = 56, 47%) and scoliosis (N = 45; 38%). Ninety-seven patients (81%) had at least one foot deformity, and 87% of these patients had bilateral foot deformities. The most common deformities were pes planovalgus (53%) and talipes equinovarus (34%). Of patients with foot deformities, 58% presented for evaluation of the feet. Of patients with pes planovalgus, only 17% presented for evaluation of the feet. Among patients with pes planovalgus, 2% underwent surgery and 16% used orthotics compared with 76% and 42%, respectively, for patients with talipes equinovarus. We found no association between deformities and genetic mutations. Bilateral foot deformities are highly prevalent in patients with LDS and are the most common reason for presentation to orthopedic surgeons. Although pes planovalgus is the most common deformity, it rarely prompted surgical treatment. Orthopedic surgeons treating LDS patients should be aware of the unique characteristics of foot deformities in LDS.
Reconstruction of polysyndactyly of the fused fifth toe with the fourth toe
Authors: Du Zijing , Cui Yan , Jiang Hao , Han Dong
Published: November 2022

Polysyndactyly of the fused fifth toe with the fourth toe is a common subtype of postaxial polydactyly. The aim of the study was to present an operative technique for cosmetic improvement and reconstruction of polysyndactyly of the fused fifth toe with the fourth toe. We retrospectively reviewed the details of 22 patients with postaxial polydactyly treated from January 2018 to May 2021. The operation involved medial toe excision and web space reconstruction using a dorsal rectangular flap without skin grafting and simultaneous correction of a valgus deformity by chondroplasty and soft tissue balancing without an osteotomy. The web shape, scar, and aesthetic outcomes were evaluated on the criteria of the D‘Arcangelo, Vancouver Scar Scale score, and satisfactory questionnaire, respectively. The patients were followed up for 7–43 months. At the last follow-up, valgus deformity was completely corrected without recurrence. On the basis of the criterion of D‘Arcangelo, the height and width of the webs were good in 24 of the feet, fair in four of the feet, and poor in none of the feet. The mean Vancouver Scar Scale score was 1.55. All parents and patients were satisfied with the appearance and function. The described medial toe excision technique and reconstruction of the web space without a skin graft corrected the valgus deformity and were able to satisfy functional and cosmetic requirements.
Surgical (over) treatment of pediatric Lyme arthritis: a need for faster Borrelia testing
Authors: Konopka Jaclyn A. , Sacks Hayley A. , Castañeda Pablo G. , Carter Cordelia W.
Published: November 2022

Pediatric Lyme arthritis is described but not well-characterized in urban populations. Similarities in clinical features between Lyme and septic arthritis also results in some patients with Lyme arthritis undergoing surgical treatment. The aims of this study are to (1) characterize Lyme arthritis in an urban population and (2) determine what factors predispose patients with Lyme arthritis to undergoing surgery. We performed a retrospective review of children with Lyme arthritis at a single academic institution in New York City from 2016 to 2021. Inclusion criteria were age ≤18 years, involvement of a major joint, and positive Lyme serology. Patients treated with irrigation and debridement were compared to those treated non-surgically using Chi-squared tests with a significance of P < 0.05. A total of 106 children with Lyme arthritis were included. Mean age was 9.5 years; 61.3% were male, and 71.7% were Caucasian. 46.2% lived in regions with an average household income >$100 000; 70.8% had private insurance. Ten patients (9.4%) underwent surgery for suspected septic arthritis. The operative group was more likely to have an elevated heart rate, white blood cell count, C-reactive protein level, erythrocyte sedimentation rate level and synovial cell count (P < 0.05). Patients were more likely to undergo surgery if they presented to the emergency department than to the clinic (P = 0.03). The average time for a Lyme test to result was 43.5 h, averaging 8.7 h after the surgical start time. Lyme arthritis occurs commonly in an urban pediatric population. Surgery is performed in ~10% of Lyme arthritis patients. More efficient diagnostic tests may reduce this rate.
Analysis of risk factors for nonunion in pediatric lateral column lengthening
Authors: Torrez Timothy W. , Kothari Ezan A. , Andrews Nicholas , Seidenstein Alexandra H , Strom Shane , McGwin Gerald , Gilbert Shawn R. , Shah Ashish , Doyle John S. , Conklin Michael J
Published: November 2022

The lateral column lengthening procedure is a commonly used osteotomy for correction of pes planus performed by inserting a graft in the anterior aspect of the calcaneus through a transverse osteotomy. Though nonunion and calcaneo-cuboid subluxation have been previously reported, these complications have not been extensively studied in pediatric patients. After IRB approval, 111 patients (151 feet) who underwent lateral column lengthening at a single institution were identified. Fifty-three females (70 feet) and 58 males (81 feet) with an average age of 11.4 years (2.6 SD; range 5–17) were analyzed. The primary outcome was nonunion defined as a lack of radiographic evidence of osteotomy healing by 9 months. Underlying diagnosis, pre and postoperative radiographic measurements, age, operative technique, fixation, calcaneo-cuboid subluxation, graft material and concomitant procedures were analyzed for their relationship to nonunion. Nonunion occurred in 7 of 151 feet (4.6%). Patient age at the time of surgery and calcaneo-cuboid subluxation trended toward a significant association with nonunion (P = 0.053, 0.054, respectively). The degree of surgical correction, as determined by radiographic analysis, and the use of calcaneo-cuboid fixation were not significantly associated with nonunion. None of the other factors evaluated were significantly associated with nonunion. There were three cases of postoperative infections (2.0%), two were superficial and 1 (0.7%) was deep. Thirty-five of 151 feet disclosed radiographic evidence of subluxation. Excluding subluxation, the overall complication rate was 8.6%. Nonunion occurred in 4.6% of pediatric feet undergoing lateral column lengthening. Fixation type was not significantly associated with nonunion. Older age at the time of surgery and calcaneocuboid subluxation trended towards significance. The placement of a calcaneo-cuboid pin was not found to be a significant factor in preventing calcaneo-cuboid subluxation or nonunion.
Radiographic foot alignment and morphological features of deltoid ligament in pediatric patients with medial osteochondral lesions of the talus
Authors: Ikuta Yasunari , Nakasa Tomoyuki , Sumii Junichi , Nekomoto Akinori , Adachi Nobuo
Published: November 2022

The cause of osteochondral lesions of the talus (OLT) in patients without a history of trauma remains unclear, and almost all nontraumatic lesions appear to involve the medial talar dome. This study aimed to investigate the relationship between foot alignment, deltoid morphology, and medial OLT in pediatric patients. In total, 28 patients (31 feet) with medial OLT (17 boys, 11 girls, mean age: 14.9 years), and 50 patients without OLT (50 feet, 31 boys, 19 girls, mean age: 14.5 years) were included in this study. The OLT patients were subdivided into traumatic and nontraumatic groups. Radiographic parameters of the foot arch were measured on weight-bearing lateral images. The extent of the OLT was measured on computed tomographic images. The ratio of deep deltoid attachment length of the talus to talar height was examined as deltoid ligament position index (DPI) on coronal magnetic resonance imaging. Nontraumatic medial lesions were frequently observed in pediatric patients (54.8%) compared to traumatic lesions. The depression of the foot arch was commonly identified in pediatric patients with resistant medial lesions. The lesion size was moderately correlated with DPI (rho = 0.48; P = 0.0086). The attachment of the deep deltoid ligament to the medial talar dome was located more proximally in nontraumatic lesions than in traumatic lesions and the control group. Our findings suggest that a combination of foot alignment and the anatomic variations in the attachment of the deep deltoid ligament contributes to the incidence of nontraumatic medial OLT in the pediatric population. Level of evidence: level IV.