Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat(Triticum aestivum L.)

Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

Projecting Wintertime Newly Formed Arctic Sea Ice through Weighting CMIP6 Model Performance and Independence

Precipitous Arctic sea-ice decline and the corresponding increase in Arctic open-water areas in summer months give more space for sea-ice growth in the subsequent cold seasons. Compared to the decline of the entire Arctic multiyear sea ice,changes in newly formed sea ice indicate more thermodynamic and dynamic information on Arctic atmosphere–ocean–ice interaction and northern mid–high latitude atmospheric teleconnections. Here, we use a large multimodel ensemble from phase 6 of the Coupled Model Intercomparison Project(CMIP6) to investigate future changes in wintertime newly formed Arctic sea ice. The commonly used model-democracy approach that gives equal weight to each model essentially assumes that all models are independent and equally plausible, which contradicts with the fact that there are large interdependencies in the ensemble and discrepancies in models' performances in reproducing observations. Therefore, instead of using the arithmetic mean of well-performing models or all available models for projections like in previous studies, we employ a newly developed model weighting scheme that weights all models in the ensemble with consideration of their performance and independence to provide more reliable projections. Model democracy leads to evident bias and large intermodel spread in CMIP6 projections of newly formed Arctic sea ice. However, we show that both the bias and the intermodel spread can be effectively reduced by the weighting scheme. Projections from the weighted models indicate that wintertime newly formed Arctic sea ice is likely to increase dramatically until the middle of this century regardless of the emissions scenario.Thereafter, it may decrease(or remain stable) if the Arctic warming crosses a threshold(or is extensively constrained).

Longitudinal changes in body weight of breastfeeding mothers in the first year after delivery and its relationship with human milk composition:a combined longitudinal and cross-sectional cohort study

Objective:Postpartum weight retention(PPWR)is a common problem among women after childbirth.The main objectives of this study are to understand the changes in body weight of breastfeeding mothers during long-term follow-up and preliminarily explore the relationship between maternal body weight and human milk composition,including macronutrients,leptin,and adiponectin.Methods:The study included a longitudinal cohort(122 mothers),and a cross-sectional cohort(37 mothers).The human milk,maternal weight,and dietary surveys were collected in the longitudinal cohort at different follow-up time points(1-14 days postpartum,2-4 months postpartum,5-7 months postpartum,and 12-17 months postpartum).The maternal body weight was analyzed using the responses in the survey questionnaires.A milk analyzer based on the mid-infrared spectroscopy(MIRS)was used to determine milk composition,and nutrition analysis software evaluated dietary intakes.In the cross-sectional cohort,participating mothers were asked to provide blood and human milk samples and pertinent information related to maternal body composition.Maternal body composition was measured by bioelectrical impedance analysis(BIA),while ELISA analyzed leptin and adiponectin in milk and serum.Results:At 5-7 months postpartum,the PPWR of breastfeeding mothers was(2.46±3.59)kg.At 12-17 months postpartum,the PPWR was(0.98±4.06)kg.PPWR was found to be negatively correlated with milk fat content within 14 days postpartum and positively correlated at 2-4 months postpartum.In addition,the maternal weight and body muscle mass were positively correlated with leptin and adiponectin in milk.Plasma leptin was positively correlated with the mother’s body weight,body mass index(BMI),FAT percentage,and body fat mass,while plasma adiponectin did not correlate with any parameter.The results also indicate that the PPWR did not correlate with leptin and adiponectin in plasma or milk.Conclusions:Breastfeeding mothers may retain considerable weight gain one year after delivery.Human milk composition may be related to changes in maternal body weight.Leptin and adiponectin in breast milk and leptin in plasma are associated with the maternal body composition.This study supports the notion that maternal nutritional status may affect offspring health through lactation,and future research should focus on exploring weight management of postpartum mothers.

TOEPLITZ OPERATORS BETWEEN WEIGHTED BERGMAN SPACES OVER THE HALF-PLANE

In this paper,by characterizing Carleson measures,we investigate a class of bounded Toeplitz operator between weighted Bergman spaces with Békolléweights over the half-plane for all index choices.

Orbit Weighting Scheme in the Context of Vector Space Information Retrieval

This study introduces the Orbit Weighting Scheme(OWS),a novel approach aimed at enhancing the precision and efficiency of Vector Space information retrieval(IR)models,which have traditionally relied on weighting schemes like tf-idf and BM25.These conventional methods often struggle with accurately capturing document relevance,leading to inefficiencies in both retrieval performance and index size management.OWS proposes a dynamic weighting mechanism that evaluates the significance of terms based on their orbital position within the vector space,emphasizing term relationships and distribution patterns overlooked by existing models.Our research focuses on evaluating OWS’s impact on model accuracy using Information Retrieval metrics like Recall,Precision,InterpolatedAverage Precision(IAP),andMeanAverage Precision(MAP).Additionally,we assessOWS’s effectiveness in reducing the inverted index size,crucial for model efficiency.We compare OWS-based retrieval models against others using different schemes,including tf-idf variations and BM25Delta.Results reveal OWS’s superiority,achieving a 54%Recall and 81%MAP,and a notable 38%reduction in the inverted index size.This highlights OWS’s potential in optimizing retrieval processes and underscores the need for further research in this underrepresented area to fully leverage OWS’s capabilities in information retrieval methodologies.

qGW11a/OsCAT8,encoding an amino acid permease,negatively regulates grain size and weight in rice

Grain size is a key factor influencing grain weight in rice.In this study,a chromosome segment substitution line(CSSL9-17)was identified,that exhibits a significant reduction in both grain size and weight compared to its donor parent 93-11.Further investigation identified two quantitative trait loci(QTL)on chromosome 11,designated qGW11a and qGW11b,which contribute to 1000-grain weight with an additive effect.LOC_Os11g05690,encoding the amino acid permease OsCAT8,is the target gene of qGW11a.Overexpression of OsCAT8 resulted in decreased grain weight,while OsCAT8 knockout mutants exhibited increased grain weight.The 287-bp located within the OsCAT8 promoter region of 93-11 negatively regulates its activity,which is subsequently correlated with an increase in grain size and weight.These results suggest that OsCAT8 functions as a negative regulator of grain size and grain weight in rice.

Chemical modification of barite for improving the performance of weighting materials for water-based drilling fluids

With increasing drilling depth and large dosage of weighting materials,drilling fluids with high solid content are characterized by poor stability,high viscosity,large water loss,and thick mud cake,easier leading to reservoir damage and wellbore instability.In this paper,micronized barite(MB)was modified(mMB)by grafting with hydrophilic polymer onto the surface through the free radical polymerization to displace conventional API barite partly.The suspension stability of water-based drilling fluids(WBDFs)weighted with API barite:mMB=2:1 in 600 g was significantly enhanced compared with that with API barite/WBDFs,exhibiting the static sag factor within 0.54 and the whole stability index of 2.The viscosity and yield point reached the minimum,with a reduction of more than 40%compared with API barite only at the same density.Through multi-stage filling and dense accumulation of weighting materials and clays,filtration loss was decreased,mud cake quality was improved,and simultaneously it had great reservoir protection performance,and the permeability recovery rate reached 87%.In addition,it also effectively improved the lubricity of WBDFs.The sticking coefficient of mud cake was reduced by 53.4%,and the friction coefficient was 0.2603.Therefore,mMB can serve as a versatile additive to control the density,rheology,filtration,and stability of WBDFs weighted with API barite,thus regulating comprehensive performance and achieving reservoir protection capacity.This work opened up a new path for the productive drilling of extremely deep and intricate wells by providing an efficient method for managing the performance of high-density WBDFs.

Effect of Molecular Weight on Thermoelectric Performance of P3HT Analogues with 2-Propoxyethyl Side Chains

By replacing hexyl chains in poly(3-hexylthiophene)(P3HT)with 2-propoxyethyls,four poly(3-(2-propoxyethyl)thiophene)(P3POET)homopolymers with comparable polydispersity indexes(PDI)and regioregularities were prepared herein in addition with step increment of about 7 kDa on numberaverage molecular weight(M_(n))from around 11 to 32 kDa(accordingly denoted as P11k,P18k,P25k,and P32k).When doped in film by FeCl_(3)at the optimized conditions,the maximum power factor(PF_(max))increases greatly from 4.3μW·m^(-1)·K^(-2)for P11k to 8.8μW·m^(-1)·K^(-2)for P18k,and further to 9.7μW·m^(-1)·K^(-2)for P25k,followed by a slight decrease to 9.2μW·m^(-1)·K^(-2)for P32k.The close Seebeck coefficients(S)at PF_(max)are observed in these doped polymer films due to their consistent frontier orbital energy levels and Fermi levels.The main contribution to this PF_(max)evolution thus comes from the corresponding conductivities(σ).Theσvariation of the doped films can be rationally correlated with their microstructure evolution.

A redundant subspace weighting procedure for clock ensemble

A redundant-subspace-weighting(RSW)-based approach is proposed to enhance the frequency stability on a time scale of a clock ensemble.In this method,multiple overlapping subspaces are constructed in the clock ensemble,and the weight of each clock in this ensemble is defined by using the spatial covariance matrix.The superimposition average of covariances in different subspaces reduces the correlations between clocks in the same laboratory to some extent.After optimizing the parameters of this weighting procedure,the frequency stabilities of virtual clock ensembles are significantly improved in most cases.

Optimal investment based on relative performance and weighted utility

This paper studies the optimal portfolio allocation of a fund manager when he bases decisions on both the absolute level of terminal relative performance and the change value of terminal relative performance comparison to a predefined reference point. We find the optimal investment strategy by maximizing a weighted average utility of a concave utility and an Sshaped utility via a concavification technique and the martingale method. Numerical results are carried out to show the impact of the extent to which the manager pays attention to the change of relative performance related to the reference point on the optimal terminal relative performance.

Algorithms and statistical analysis for linear structured weighted total least squares problem

Weighted total least squares(WTLS)have been regarded as the standard tool for the errors-in-variables(EIV)model in which all the elements in the observation vector and the coefficient matrix are contaminated with random errors.However,in many geodetic applications,some elements are error-free and some random observations appear repeatedly in different positions in the augmented coefficient matrix.It is called the linear structured EIV(LSEIV)model.Two kinds of methods are proposed for the LSEIV model from functional and stochastic modifications.On the one hand,the functional part of the LSEIV model is modified into the errors-in-observations(EIO)model.On the other hand,the stochastic model is modified by applying the Moore-Penrose inverse of the cofactor matrix.The algorithms are derived through the Lagrange multipliers method and linear approximation.The estimation principles and iterative formula of the parameters are proven to be consistent.The first-order approximate variance-covariance matrix(VCM)of the parameters is also derived.A numerical example is given to compare the performances of our proposed three algorithms with the STLS approach.Afterwards,the least squares(LS),total least squares(TLS)and linear structured weighted total least squares(LSWTLS)solutions are compared and the accuracy evaluation formula is proven to be feasible and effective.Finally,the LSWTLS is applied to the field of deformation analysis,which yields a better result than the traditional LS and TLS estimations.

Transcriptomic and metabolomic analysis of changes in grain weight potential induced by water stress in wheat

The sink strength of developing ovaries in wheat determines the grain weight potential.The period from booting to the grain setting stage is critical for ovary growth and development and potential sink capacity determination.However,the underlying regulatory mechanism during this period by which the wheat plant balances and coordinates the floret number and ovary/grain weight under water stress has not been clarified.Therefore,we designed two irrigation treatments of W0(no seasonal irrigation)and W1(additional 75 mm of irrigation at the jointing stage)and analyzed the responses of the ovary/grain weight to water stress at the phenotypic,metabolomic,and transcriptomic levels.The results showed that the W0 irrigation treatment reduced the soil water content,plant height,and green area of the flag leaf,thus reducing grain number,especially for the inferior grains.However,it improved the grain weight of the superior and inferior grains as well as average grain weight at maturity,while the average ovary/grain weight and volume during–3 to 10 days after anthesis(DAA)also increased.Transcriptomic analysis indicated that the genes involved in both sucrose metabolism and phytohormone signal transduction were prominently accelerated by the W0 treatment,accompanied by greater enzymatic activities of soluble acid invertase(SAI)and sucrose synthase(Sus)and elevated abscisic acid(ABA)and indole-3-acetic acid(IAA)levels.Thus,the sucrose content decreased,while the glucose and fructose contents increased.In addition,several TaTPP genes(especially TaTPP-6)were down-regulated and the IAA biosynthesis genes TaTAR1 and TaTAR2 were up-regulated under the W0 treatment before anthesis,which further increased the IAA level.Collectively,water stress reduced the growth of vegetative organs and eliminated most of the inferior grains,but increased the ABA and IAA levels of the surviving ovaries/grains,promoting the enzymatic activity of Sus and degrading sucrose into glucose and fructose.As a result,the strong sucrose utilization ability,the enhanced enzymatic activity of SAI and the ABA-and IAA-mediated signaling jointly increased the weight and volume of the surviving ovaries/grains,and ultimately achieved the tradeoff between ovary/grain weight and number in wheat under water stress.

Spatial search weighting information contained in cell velocity distribution

Cell migration plays a significant role in physiological and pathological processes.Understanding the characteristics of cell movement is crucial for comprehending biological processes such as cell functionality,cell migration,and cell–cell interactions.One of the fundamental characteristics of cell movement is the specific distribution of cell speed,containing valuable information that still requires comprehensive understanding.This article investigates the distribution of mean velocities along cell trajectories,with a focus on optimizing the efficiency of cell food search in the context of the entire colony.We confirm that the specific velocity distribution in the experiments corresponds to an optimal search efficiency when spatial weighting is considered.The simulation results indicate that the distribution of average velocity does not align with the optimal search efficiency when employing average spatial weighting.However,when considering the distribution of central spatial weighting,the specific velocity distribution in the experiment is shown to correspond to the optimal search efficiency.Our simulations reveal that for any given distribution of average velocity,a specific central spatial weighting can be identified among the possible central spatial weighting that aligns with the optimal search strategy.Additionally,our work presents a method for determining the spatial weights embedded in the velocity distribution of cell movement.Our results have provided new avenues for further investigation of significant topics,such as relationship between cell behavior and environmental conditions throughout their evolutionary history,and how cells achieve collective cooperation through cell-cell communication.

PRODUCT TYPE OPERATORS ACTING BETWEEN WEIGHTED BERGMAN SPACES AND BLOCH TYPE SPACES

For analytic functions u,ψin the unit disk D in the complex plane and an analytic self-mapφof D,we describe in this paper the boundedness and compactness of product type operators T_(u,ψ,φ)f(z)=u(z)f(φ(z))+ψ(z)f'(φ(z)),z∈D,acting between weighted Bergman spaces induced by a doubling weight and a Bloch type space with a radial weight.

Curve Classification Based onMean-Variance Feature Weighting and Its Application

The classification of functional data has drawn much attention in recent years.The main challenge is representing infinite-dimensional functional data by finite-dimensional features while utilizing those features to achieve better classification accuracy.In this paper,we propose a mean-variance-based(MV)feature weighting method for classifying functional data or functional curves.In the feature extraction stage,each sample curve is approximated by B-splines to transfer features to the coefficients of the spline basis.After that,a feature weighting approach based on statistical principles is introduced by comprehensively considering the between-class differences and within-class variations of the coefficients.We also introduce a scaling parameter to adjust the gap between the weights of features.The new feature weighting approach can adaptively enhance noteworthy local features while mitigating the impact of confusing features.The algorithms for feature weighted K-nearest neighbor and support vector machine classifiers are both provided.Moreover,the new approach can be well integrated into existing functional data classifiers,such as the generalized functional linear model and functional linear discriminant analysis,resulting in a more accurate classification.The performance of the mean-variance-based classifiers is evaluated by simulation studies and real data.The results show that the newfeatureweighting approach significantly improves the classification accuracy for complex functional data.

Evaluation of soil erosion vulnerability in Hubei Province of China using RUSLE model and combination weighting method

Soil erosion has been recognized as a critical environmental issue worldwide.While previous studies have primarily focused on watershed-scale soil erosion vulnerability from a natural factor perspective,there is a notable gap in understanding the intricate interplay between natural and socio-economic factors,especially in the context of spatial heterogeneity and nonlinear impacts of human-land interactions.To address this,our study evaluates the soil erosion vulnerability at a provincial scale,taking Hubei Province as a case study to explore the combined effects of natural and socio-economic factors.We developed an evaluation index system based on 15 indicators of soil erosion vulnerability:exposure,sensitivity,and adaptability.In addition,the combination weighting method was applied to determine index weights,and the spatial interaction was analyzed using spatial autocorrelation,geographical temporally weighted regression and geographical detector.The results showed an overall decreasing soil erosion intensity in Hubei Province during 2000 and 2020.The soil erosion vulnerability increased before 2000 and then.The areas with high soil erosion vulnerability were mainly confined in the central and southern regions of Hubei Province(Xiantao,Tianmen,Qianjiang and Ezhou)with obvious spatial aggregation that intensified over time.Natural factors(habitat quality index)had negative impacts on soil erosion vulnerability,whereas socio-economic factors(population density)showed substantial spatial variability in their influences.There was a positive correlation between soil erosion vulnerability and erosion intensity,with the correlation coefficients ranging from-0.41 and 0.93.The increase of slope was found to enhance the positive correlation between soil erosion vulnerability and intensity.

Hybrid Block Diagonalization Precoding for Multi-User Weighted Sum-Rate Maximization

This paper studies large-scale multi-input multi-output(MIMO)orthogonal frequency division multiplexing(OFDM)communications in a broadband frequency-selective channel,where a massive MIMO base station(BS)communicates with multiple users equipped with multi-antenna.We develop a hybrid precoding design to maximize the weighted sum-rate(WSR)of the users by optimizing the digital and the analog precoders alternately.For the digital part,we employ block-diagonalization to eliminate inter-user interference and apply water-filling power allocation to maximize the WSR.For the analog part,the optimization of the PSN is formulated as an unconstrained problem,which can be efficiently solved by a gradient descent method.Numerical results show that the proposed block-diagonal hybrid precoding algorithm can outperform the existing works.

Effects of low molecular weight polysaccharide from Sargassum thunbergii against palmitic acid-induced intracellular lipid accumulation in 3T3-L1 adipocyte and HepG2 cells

Low molecular weight polysaccharides can be isolated from Sargassum thunbergii(LMPST)and in vitro experiments were conducted to evaluate the inhibitory effects on lipids.Two natures of LMPST were attained from S.thunbergii and appraised their LMPST on palmitic acid(PA)induced lipid accretion in Hep G2,and 3T3-L1 cells.LMPST treatment lessened lipid deposition and intracellular free fatty acid and triglyceride intensities in PA-treated above mentioned cells.The mechanistic study publicized that LMPST2 significantly suppressed adipogenesis and stimulated the PA-treated 3T3-L1 cells occupied in the lipolysis pathway.Furthermore,in PA-treated Hep G2 cells,the free fatty acid oxidation was significantly increased by LMPST2.Given these constructive properties of LMPST2 from S.thunbergii,is a potential candidate for diminishing the intracellular lipids,and for a therapeutic agent in those conditions.

The Weighted Basis for PHT-Splines

PHT-splines are defined as polynomial splines over hierarchical T-meshes with very efficient local refinement properties.The original PHT-spline basis functions constructed by the truncation mechanism have a decay phenomenon,resulting in numerical instability.The non-decay basis functions are constructed as the B-splines that are defined on the 2×2 tensor product meshes associated with basis vertices in Kang et al.,but at the cost of losing the partition of unity.In the field of finite element analysis and topology optimization,forming the partition of unity is the default ingredient for constructing basis functions of approximate spaces.In this paper,we will show that the non-decay PHT-spline basis functions proposed by Kang et al.can be appropriately modified to form a partition of unity.Each non-decay basis function is multiplied by a positive weight to form the weighted basis.The weights are solved such that the sum of weighted bases is equal to 1 on the domain.We provide two methods for calculatingweights,based on geometric information of basis functions and the subdivision of PHT-splines.Weights are given in the form of explicit formulas and can be efficiently calculated.We also prove that the weights on the admissible hierarchical T-meshes are positive.