A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Birds maintain complex and intimate associations with a diverse community of microbes in their intestine.Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses.However,the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings.Through performing a network meta-analysis for 13 published bird gut microbiome studies,here we attempt to investigate the comparability of these invasive and non-invasive sampling methods.The two most used non-invasive sampling methods(cloacal swabs and fecal samples)showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples.Overall,non-invasive samples showed decreased alpha diversity compared to intestinal samples,but the alpha diversities of fecal samples were more comparable to the intestinal samples.On the contrary,the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples,but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples.Phylogenetic status,diet,and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples.Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa,while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions.The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.

Future of non-invasive graft evaluation:A systematic review of proteomics in kidney transplantation

BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered insufficient.Protein biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant recipients.AIM To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft assessment.METHODS A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus databases.The primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related com-plications.Eligibility criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity methods.The selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and extracted.Functional and network analysis of the selected proteins was performed.RESULTS In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most investigated.Biological pathways related to immune response and fibrosis have shown to be enriched.Applications of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were reported.Overall,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is concerned.CONCLUSION Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.

Advancements in non-invasive diagnosis of gastric cancer

Gastric cancer(GC),a multifaceted and highly aggressive malignancy,represents challenging healthcare burdens globally,with a high incidence and mortality rate.Although endoscopy,combined with histological examination,is the gold stan-dard for GC diagnosis,its high cost,invasiveness,and specialized requirements hinder widespread use for screening.With the emergence of innovative techno-logies such as advanced imaging,liquid biopsy,and breath tests,the landscape of GC diagnosis is poised for radical transformation,becoming more accessible,less invasive,and more efficient.As the non-invasive diagnostic techniques continue to advance and undergo rigorous clinical validation,they hold the promise of sig-nificantly impacting patient outcomes,ultimately leading to better treatment results and improved quality of life for patients with GC.

Exploring non-invasive diagnostics for metabolic dysfunctionassociated fatty liver disease

The population with metabolic dysfunction-associated fatty liver disease(MAFLD)is increasingly common worldwide.Identification of people at risk of progression to advanced stages is necessary to timely offer interventions and appropriate care.Liver biopsy is currently considered the gold standard for the diagnosis and staging of MAFLD,but it has associated risks and limitations.This has spurred the exploration of non-invasive diagnostics for MAFLD,especially for steatohepatitis and fibrosis.These non-invasive approaches mostly include biomarkers and algorithms derived from anthropometric measurements,serum tests,imaging or stool metagenome profiling.However,they still need rigorous and widespread clinical validation for the diagnostic performance.

Functional near-infrared spectroscopy in non-invasive neuromodulation

Non-invasive cerebral neuromodulation technologies are essential for the reorganization of cerebral neural networks,which have been widely applied in the field of central neurological diseases,such as stroke,Parkinson’s disease,and mental disorders.Although significant advances have been made in neuromodulation technologies,the identification of optimal neurostimulation paramete rs including the co rtical target,duration,and inhibition or excitation pattern is still limited due to the lack of guidance for neural circuits.Moreove r,the neural mechanism unde rlying neuromodulation for improved behavioral performance remains poorly understood.Recently,advancements in neuroimaging have provided insight into neuromodulation techniques.Functional near-infrared spectroscopy,as a novel non-invasive optical brain imaging method,can detect brain activity by measuring cerebral hemodynamics with the advantages of portability,high motion tole rance,and anti-electromagnetic interference.Coupling functional near-infra red spectroscopy with neuromodulation technologies offe rs an opportunity to monitor the cortical response,provide realtime feedbac k,and establish a closed-loop strategy integrating evaluation,feedbac k,and intervention for neurostimulation,which provides a theoretical basis for development of individualized precise neuro rehabilitation.We aimed to summarize the advantages of functional near-infra red spectroscopy and provide an ove rview of the current research on functional near-infrared spectroscopy in transcranial magnetic stimulation,transcranial electrical stimulation,neurofeedback,and braincomputer interfaces.Furthermore,the future perspectives and directions for the application of functional near-infrared spectroscopy in neuromodulation are summarized.In conclusion,functional near-infrared spectroscopy combined with neuromodulation may promote the optimization of central pellral reorganization to achieve better functional recovery form central nervous system diseases.

How do the landslide and non-landslide sampling strategies impact landslide susceptibility assessment? d A catchment-scale case study from China

The aim of this study is to investigate the impacts of the sampling strategy of landslide and non-landslide on the performance of landslide susceptibility assessment(LSA).The study area is the Feiyun catchment in Wenzhou City,Southeast China.Two types of landslides samples,combined with seven non-landslide sampling strategies,resulted in a total of 14 scenarios.The corresponding landslide susceptibility map(LSM)for each scenario was generated using the random forest model.The receiver operating characteristic(ROC)curve and statistical indicators were calculated and used to assess the impact of the dataset sampling strategy.The results showed that higher accuracies were achieved when using the landslide core as positive samples,combined with non-landslide sampling from the very low zone or buffer zone.The results reveal the influence of landslide and non-landslide sampling strategies on the accuracy of LSA,which provides a reference for subsequent researchers aiming to obtain a more reasonable LSM.

Research on a Monte Carlo global variance reduction method based on an automatic importance sampling method

Global variance reduction is a bottleneck in Monte Carlo shielding calculations.The global variance reduction problem requires that the statistical error of the entire space is uniform.This study proposed a grid-AIS method for the global variance reduction problem based on the AIS method,which was implemented in the Monte Carlo program MCShield.The proposed method was validated using the VENUS-Ⅲ international benchmark problem and a self-shielding calculation example.The results from the VENUS-Ⅲ benchmark problem showed that the grid-AIS method achieved a significant reduction in the variance of the statistical errors of the MESH grids,decreasing from 1.08×10^(-2) to 3.84×10^(-3),representing a 64.00% reduction.This demonstrates that the grid-AIS method is effective in addressing global issues.The results of the selfshielding calculation demonstrate that the grid-AIS method produced accurate computational results.Moreover,the grid-AIS method exhibited a computational efficiency approximately one order of magnitude higher than that of the AIS method and approximately two orders of magnitude higher than that of the conventional Monte Carlo method.

FibroScan-aspartate transaminase:A superior non-invasive model for diagnosing high-risk metabolic dysfunction-associated steatohepatitis

BACKGROUND Non-alcoholic fatty liver disease(NAFLD)with hepatic histological NAFLD activity score≥4 and fibrosis stage F≥2 is regarded as“at risk”non-alcoholic steatohepatitis(NASH).Based on an international consensus,NAFLD and NASH were renamed as metabolic dysfunction-associated steatotic liver disease(MASLD)and metabolic dysfunction-associated steatohepatitis(MASH),respectively;hence,we introduced the term“high-risk MASH”.Diagnostic values of seven non-invasive models,including FibroScan-aspartate transaminase(FAST),fibrosis-4(FIB-4),aspartate transaminase to platelet ratio index(APRI),etc.for high-risk MASH have rarely been studied and compared in MASLD.AIM To assess the clinical value of seven non-invasive models as alternatives to liver biopsy for diagnosing high-risk MASH.METHODS A retrospective analysis was conducted on 309 patients diagnosed with NAFLD via liver biopsy at Beijing Ditan Hospital,between January 2012 and December 2020.After screening for MASLD and the exclusion criteria,279 patients wereincluded and categorized into high-risk and non-high-risk MASH groups.Utilizing threshold values of each model,sensitivity,specificity,positive predictive value(PPV),and negative predictive values(NPV),were calculated.Receiver operating characteristic curves were constructed to evaluate their diagnostic efficacy based on the area under the curve(AUROC).RESULTS MASLD diagnostic criteria were met by 99.4%patients with NAFLD.The MASLD population was analyzed in two cohorts:Overall population(279 patients)and the subgroup(117 patients)who underwent liver transient elastography(FibroScan).In the overall population,FIB-4 showed better diagnostic efficacy and higher PPV,with sensitivity,specificity,PPV,NPV,and AUROC of 26.9%,95.2%,73.5%,72.2%,and 0.75.APRI,Forns index,and aspartate transaminase to alanine transaminase ratio(ARR)showed moderate diagnostic efficacy,whereas S index and gamma-glutamyl transpeptidase to platelet ratio(GPR)were relatively weaker.In the subgroup,FAST had the highest diagnostic efficacy,its sensitivity,specificity,PPV,NPV,and AUROC were 44.2%,92.3%,82.1%,67.4%,and 0.82.The FIB-4 AUROC was 0.76.S index and GPR exhibited almost no diagnostic value for high-risk MASH.CONCLUSION FAST and FIB-4 could replace liver biopsy as more effectively diagnostic methods for high-risk MASH compared to APRI,Forns index,ARR,S index,and GPR;FAST is superior to FIB-4.

Multivariate form of Hermite sampling series

In this paper,we establish a new multivariate Hermite sampling series involving samples from the function itself and its mixed and non-mixed partial derivatives of arbitrary order.This multivariate form of Hermite sampling will be valid for some classes of multivariate entire functions,satisfying certain growth conditions.We will show that many known results included in Commun Korean Math Soc,2002,17:731-740,Turk J Math,2017,41:387-403 and Filomat,2020,34:3339-3347 are special cases of our results.Moreover,we estimate the truncation error of this sampling based on localized sampling without decay assumption.Illustrative examples are also presented.

A Review on Combined Strategy of Non-invasive Brain Stimulation and Robotic Therapy

Stroke is a major cause of death and disability among adults in China,and an efficient rehabilitation strategy has been an urgent demand for post-stroke rehabilitation.The non-invasive brain stimulation(NBS)can modulate the excitability of the cerebral cortex and provide after-effects apart from immediate effects to regain extremity motor functions,whereas robotic therapy provides high-intensity and long-duration repetitive movements to stimulate the cerebral cortex backward.The combined strategy of the two techniques is widely regarded as a promising application for stroke patients with dyskinesia.Transcranial magnetic stimulation(TMS)and transcranial electrical stimulation(TES)are important methods of NBS.Their recovery principles,stimulation parameters,and clinical applications have been summarized.The combined treatments of rTMS/tDCS and robotic therapy are analyzed and discussed to overcome the application barriers of the two techniques.The future development trend and the key technical problems are expounded for the clinical applications.

Modified DS np Chart Using Generalized Multiple Dependent State Sampling under Time Truncated Life Test

This study presents the design of a modified attributed control chart based on a double sampling(DS)np chart applied in combination with generalized multiple dependent state(GMDS)sampling to monitor the mean life of the product based on the time truncated life test employing theWeibull distribution.The control chart developed supports the examination of the mean lifespan variation for a particular product in the process of manufacturing.Three control limit levels are used:the warning control limit,inner control limit,and outer control limit.Together,they enhance the capability for variation detection.A genetic algorithm can be used for optimization during the in-control process,whereby the optimal parameters can be established for the proposed control chart.The control chart performance is assessed using the average run length,while the influence of the model parameters upon the control chart solution is assessed via sensitivity analysis based on an orthogonal experimental design withmultiple linear regression.A comparative study was conducted based on the out-of-control average run length,in which the developed control chart offered greater sensitivity in the detection of process shifts while making use of smaller samples on average than is the case for existing control charts.Finally,to exhibit the utility of the developed control chart,this paper presents its application using simulated data with parameters drawn from the real set of data.

RE-SMOTE:A Novel Imbalanced Sampling Method Based on SMOTE with Radius Estimation

Imbalance is a distinctive feature of many datasets,and how to make the dataset balanced become a hot topic in the machine learning field.The Synthetic Minority Oversampling Technique(SMOTE)is the classical method to solve this problem.Although much research has been conducted on SMOTE,there is still the problem of synthetic sample singularity.To solve the issues of class imbalance and diversity of generated samples,this paper proposes a hybrid resampling method for binary imbalanced data sets,RE-SMOTE,which is designed based on the improvements of two oversampling methods parameter-free SMOTE(PF-SMOTE)and SMOTE-Weighted Ensemble Nearest Neighbor(SMOTE-WENN).Initially,minority class samples are divided into safe and boundary minority categories.Boundary minority samples are regenerated through linear interpolation with the nearest majority class samples.In contrast,safe minority samples are randomly generated within a circular range centered on the initial safe minority samples with a radius determined by the distance to the nearest majority class samples.Furthermore,we use Weighted Edited Nearest Neighbor(WENN)and relative density methods to clean the generated samples and remove the low-quality samples.Relative density is calculated based on the ratio of majority to minority samples among the reverse k-nearest neighbor samples.To verify the effectiveness and robustness of the proposed model,we conducted a comprehensive experimental study on 40 datasets selected from real applications.The experimental results show the superiority of radius estimation-SMOTE(RE-SMOTE)over other state-of-the-art methods.Code is available at:https://github.com/blue9792/RE-SMOTE(accessed on 30 September 2024).

Enhancing Deep Learning Semantics:The Diffusion Sampling and Label-Driven Co-Attention Approach

The advent of self-attention mechanisms within Transformer models has significantly propelled the advancement of deep learning algorithms,yielding outstanding achievements across diverse domains.Nonetheless,self-attention mechanisms falter when applied to datasets with intricate semantic content and extensive dependency structures.In response,this paper introduces a Diffusion Sampling and Label-Driven Co-attention Neural Network(DSLD),which adopts a diffusion sampling method to capture more comprehensive semantic information of the data.Additionally,themodel leverages the joint correlation information of labels and data to introduce the computation of text representation,correcting semantic representationbiases in thedata,andincreasing the accuracyof semantic representation.Ultimately,the model computes the corresponding classification results by synthesizing these rich data semantic representations.Experiments on seven benchmark datasets show that our proposed model achieves competitive results compared to state-of-the-art methods.

Recent advances in protein conformation sampling by combining machine learning with molecular simulation

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

FPSblo:A Blockchain Network Transmission Model Utilizing Farthest Point Sampling

Peer-to-peer(P2P)overlay networks provide message transmission capabilities for blockchain systems.Improving data transmission efficiency in P2P networks can greatly enhance the performance of blockchain systems.However,traditional blockchain P2P networks face a common challenge where there is often a mismatch between the upper-layer traffic requirements and the underlying physical network topology.This mismatch results in redundant data transmission and inefficient routing,severely constraining the scalability of blockchain systems.To address these pressing issues,we propose FPSblo,an efficient transmission method for blockchain networks.Our inspiration for FPSblo stems from the Farthest Point Sampling(FPS)algorithm,a well-established technique widely utilized in point cloud image processing.In this work,we analogize blockchain nodes to points in a point cloud image and select a representative set of nodes to prioritize message forwarding so that messages reach the network edge quickly and are evenly distributed.Moreover,we compare our model with the Kadcast transmission model,which is a classic improvement model for blockchain P2P transmission networks,the experimental findings show that the FPSblo model reduces 34.8%of transmission redundancy and reduces the overload rate by 37.6%.By conducting experimental analysis,the FPS-BT model enhances the transmission capabilities of the P2P network in blockchain.

Aggregation‑Value‑Based Active Sampling Method for Multi‑sensor Freeform Surface Measurement and Reconstruction

Freeform surface measurement is a key basic technology for product quality control and reverse engineering in aerospace field.Surface measurement technology based on multi-sensor fusion such as laser scanner and contact probe can combine the complementary characteristics of different sensors,and has been widely concerned in industry and academia.The number and distribution of measurement points will significantly affect the efficiency of multisensor fusion and the accuracy of surface reconstruction.An aggregation‑value‑based active sampling method for multisensor freeform surface measurement and reconstruction is proposed.Based on game theory iteration,probe measurement points are generated actively,and the importance of each measurement point on freeform surface to multi-sensor fusion is clearly defined as Shapley value of the measurement point.Thus,the problem of obtaining the optimal measurement point set is transformed into the problem of maximizing the aggregation value of the sample set.Simulation and real measurement results verify that the proposed method can significantly reduce the required probe sample size while ensuring the measurement accuracy of multi-sensor fusion.

A Path Planning Algorithm Based on Improved RRT Sampling Region

For the problem of slow search and tortuous paths in the Rapidly Exploring Random Tree(RRT)algorithm,a feedback-biased sampling RRT,called FS-RRT,is proposedbasedon RRT.Firstly,toimprove the samplingefficiency of RRT to shorten the search time,the search area of the randomtree is restricted to improve the sampling efficiency.Secondly,to obtain better information about obstacles to shorten the path length,a feedback-biased sampling strategy is used instead of the traditional random sampling,the collision of the expanding node with an obstacle generates feedback information so that the next expanding node avoids expanding within a specific angle range.Thirdly,this paper proposes using the inverse optimization strategy to remove redundancy points from the initial path,making the path shorter and more accurate.Finally,to satisfy the smooth operation of the robot in practice,auxiliary points are used to optimize the cubic Bezier curve to avoid path-crossing obstacles when using the Bezier curve optimization.The experimental results demonstrate that,compared to the traditional RRT algorithm,the proposed FS-RRT algorithm performs favorably against mainstream algorithms regarding running time,number of search iterations,and path length.Moreover,the improved algorithm also performs well in a narrow obstacle environment,and its effectiveness is further confirmed by experimental verification.

Influence of sampling on three-dimensional surface shape measurement

In order to accurately measure an object’s three-dimensional surface shape,the influence of sampling on it was studied.First,on the basis of deriving spectra expressions through the Fourier transform,the generation of CCD pixels was analyzed,and its expression was given.Then,based on the discrete expression of deformation fringes obtained after sampling,its Fourier spectrum expression was derived,resulting in an infinitely repeated"spectra island"in the frequency domain.Finally,on the basis of using a low-pass filter to remove high-order harmonic components and retaining only one fundamental frequency component,the inverse Fourier transform was used to reconstruct the signal strength.A method of reducing the sampling interval,i.e.,reducing the number of sampling points per fringe,was proposed to increase the ratio between the sampling frequency and the fundamental frequency of the grating.This was done to reconstruct the object’s surface shape more accurately under the condition of m>4.The basic principle was verified through simulation and experiment.In the simulation,the sampling intervals were 8 pixels,4 pixels,2 pixels,and 1 pixel,the maximum absolute error values obtained in the last three situations were 88.80%,38.38%,and 31.50%in the first situation,respectively,and the corresponding average absolute error values are 71.84%,43.27%,and 32.26%.It is demonstrated that the smaller the sampling interval,the better the recovery effect.Taking the same four sampling intervals in the experiment as in the simulation can also lead to the same conclusions.The simulated and experimental results show that reducing the sampling interval can improve the accuracy of object surface shape measurement and achieve better reconstruction results.

Improving Generalization for Hyperspectral Image Classification:The Impact of Disjoint Sampling on Deep Models

Disjoint sampling is critical for rigorous and unbiased evaluation of state-of-the-art(SOTA)models e.g.,Attention Graph and Vision Transformer.When training,validation,and test sets overlap or share data,it introduces a bias that inflates performance metrics and prevents accurate assessment of a model’s true ability to generalize to new examples.This paper presents an innovative disjoint sampling approach for training SOTA models for the Hyperspectral Image Classification(HSIC).By separating training,validation,and test data without overlap,the proposed method facilitates a fairer evaluation of how well a model can classify pixels it was not exposed to during training or validation.Experiments demonstrate the approach significantly improves a model’s generalization compared to alternatives that include training and validation data in test data(A trivial approach involves testing the model on the entire Hyperspectral dataset to generate the ground truth maps.This approach produces higher accuracy but ultimately results in low generalization performance).Disjoint sampling eliminates data leakage between sets and provides reliable metrics for benchmarking progress in HSIC.Disjoint sampling is critical for advancing SOTA models and their real-world application to large-scale land mapping with Hyperspectral sensors.Overall,with the disjoint test set,the performance of the deep models achieves 96.36%accuracy on Indian Pines data,99.73%on Pavia University data,98.29%on University of Houston data,99.43%on Botswana data,and 99.88%on Salinas data.

Recent developments in non-invasive methods for assessing metabolic dysfunction-associated fatty liver disease

The prevalence of metabolic dysfunction-associated fatty liver disease(MAFLD)is increasing,affecting over one-third of the global population and contributing to significant morbidity and mortality.Diagnosing MAFLD,especially with advan-ced fibrosis,remains challenging due to the limitations of liver biopsy,the current gold standard.Non-invasive tests are crucial for early detection and management.Among these,the fibrosis-4 index(Fib-4)is widely recommended as a first-line test for screening for liver fibrosis.Advanced imaging techniques,including ultrasound-based elastography and magnetic resonance elastography,offer high accuracy but are limited by cost and availability.Combining biomarkers,such as in the enhanced liver fibrosis score and FibroScan-AST score,enhances diagnostic precision and is recommended to further stratify patients who are considered to be intermediate or high risk from the Fib-4 score.We believe that the future lies in the combined use of biomarkers to improve diagnostic accuracy.