Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines

The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.

Word sense disambiguation using semantic relatedness measurement

All human languages have words that can mean different things in different contexts, such words with multiple meanings are potentially “ambiguous”. The process of “deciding which of several meanings of a term is intended in a given context” is known as “word sense disambiguation (WSD)”. This paper presents a method of WSD that assigns a target word the sense that is most related to the senses of its neighbor words. We explore the use of measures of relatedness between word senses based on a novel hybrid approach. First, we investigate how to “literally” and “regularly” express a “concept”. We apply set algebra to WordNet’s synsets cooperating with WordNet’s word ontology. In this way we establish regular rules for constructing various representations (lexical notations) of a concept using Boolean operators and word forms in various synset(s) defined in WordNet. Then we establish a formal mechanism for quantifying and estimating the semantic relatedness between concepts—we facilitate “concept distribution statistics” to determine the degree of semantic relatedness between two lexically expressed con- cepts. The experimental results showed good performance on Semcor, a subset of Brown corpus. We observe that measures of semantic relatedness are useful sources of information for WSD.

A study on the psychological needs of nurses caring for patients with coronavirus disease 2019 from the perspective of the existence,relatedness, and growth theory

Objective:This study aimed to explore the psychological needs of nurses caring for patients with coronavirus disease 2019(COVID-19)and to propose corresponding interventions.Methods:In-depth interviews were conducted with 10 nurses who cared for patients with COVID-19.Interview data were analyzed by category analysis from the perspective of the existence,relatedness,and growth theory(ERG).Results:The existence needs were mainly reflected in health and security needs,whereas the relatedness needs consisting mainly of interpersonal needs,humanistic concern needs,and family needs;further,the growth needs were mainly reflected as a strong need for knowledge.Existence needs were the main needs during the epidemic,with health and security needs influencing each other.Humanistic concern needs were the most important of the relatedness needs;interpersonal and family needs were also growing.Conclusion:It is found that the existence,relatedness,and growth needs coexist in clinical nurses.It is helpful to take effective interventions to meet their needs if the needs of nurses caring for COVID-19 patients could be perceived well.

The genetic diversity, individual relatedness and possible mating system of an isolated population of the Cyprinid species Megalobrama pellgrini in upper reaches of the Changjiang (Yangtze) River, China

Megalobrama pellegrini is a cyprinid fish endemic to upper reaches of the Changjiang(Yangtze)River,China,which is also an important economic species in the local area.In recent years,resources of this species have decreased sharply and its conservation has drawn great attention.In the present study,we collected 120 individuals from the Longxi River,a tributary isolated from the main channel of the Changjiang River,where M.pellegrini is still relatively abundant.Using two different molecular markers,mitochondrial cytochrome b(cyt b)gene,and nuclear microsatellite(simple sequence repeat,SSR),we analyzed the genetic diversity of this isolated population.The results show that sequence genetic diversity was low(Hd:0.290 and P i:0.000 77 for cyt b gene),while the SSR genetic diversity was high(Ho:0.824 4±0.147 2,He:0.823 5±0.145 1).Analysis indicated that this population had experienced a bottleneck,with inbreeding and small effective population size(around 50).Based on SSR data,relatedness analyzing revealed that the 120 samples were grouped into 10 completely independent clusters.It was inferred that the mating system of M.pellegrini was polygamy.We suggested that the low genetic diversity could be induced by the overfishing and inbreeding depression.Therefore,we suggested that the urgent conservation measures should be taken to control the overfi shing and give better conditions for the fish to grow and spawn,then to restore population size.

Intercontinental comparison of phylogenetic relatedness in introduced plants at the transition from naturalization to invasion:A case study on the floras of South Africa and China

Invasive species may pose significant threats to biodiversity and ecosystem structure and functioning.The number of introduced species that have become invasive is substantial and is rapidly increasing.Identifying potentially invasive species and preventing their expansion are of critical importance in invasion ecology.Phylogenetic relatedness between invasive and native species has been used in predicting invasion success.Previous studies on the phylogenetic relatedness of plants at the transition from naturalization to invasion have shown mixed results,which may be because different methods were used in different studies.Here,I use the same method to analyze two comprehensive data sets from South Africa and China,using two phylogenetic metrics reflecting deep and shallow evolutionary histories,to address the question whether the probability of becoming invasive is higher for naturalized species distantly related to the native flora.My study suggests that the probability of becoming invasive is higher for naturalized species closely related to the native flora.The finding of my study is consistent with Darwin's preadaptation hypothesis.

Genetic relatedness and association mapping of horticulturally valuable traits for the Ceiba plants using ddRAD sequencing

Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.

An estimation of genetic parameters of growth traits in juvenile turbot (Scophthalmus maximus L.) using parental molecular relatedness

The estimation of genetic parameters has played an important role in animal selective breeding for growth traits.Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to improve the performance of an incomplete pedigree（i.e, only parents are known） in the genetic evaluations, 12 microsatellite markers have been applied in the estimation of the genetic parameters for body weight in a farmed population（n=1 890） of juvenile turbot（Scophthalmus maximus L.）. A new relatedness called parental molecular relatedness（PMR） is estimated based on results of genotyping of 48 parents（31 males, 17 females） with microsatellites markers. The feasibility of PMR in estimation of genetic parameters is verified by comparison with pedigree related（PR） which is obtained from a complete pedigree. The results demonstrate that a high correlation（0.872） between them is found. Heritabilities are estimated using the PMR（0.52±0.13） and PR（0.55±0.22） with the same animal model. A cross-validation shows that the predictive abilities of models using the PMR and the PR are identical（0.81）. From that, a conclusion can be made that PMR and PR predicted genetic values equally well in a population of juvenile turbot. Therefore PMR can be applied as an alternative of the PR when only parents are known. However, for a better performance, more markers and more families should be included in a further study.

Antimicrobial Resistance Profiles and Clonal Relatedness of <i>Pseudomonas aeruginosa</i>Strains Recovered from Wounds Infections of Outpatient Population Presenting in a Rural Hospital in Kenya

Pseudomonas aeruginosa is a leading cause of hospital infections and is intrinsically resistant to most antibiotics. Emergence of multidrug resistant (MDR) strains has been reported in the world and poses a great challenge in the management of infections associated with this species. While a substantial amount of research has been done on strains from most of other infection caused by this species in developed countries, little is known about the susceptibility profiles of strains recovered from African countries in general and Kenya in particular. Furthermore, there is paucity of data regarding strain, phenotype and genetic diversity of strains recoverable from wounds among patients in Kenya. The possible risk factors for acquisition of MDR strains and possible factors that could fuel clonal expansion in hospital and community settings remain undetermined. This cross-sectional study conducted in Tigoni Hospital, a rural area in Central Kenya sought to determine risk factors associated with carriage of MDR Pseudomonas aeruginosa in wounds among rural population. We also analyzed antimicrobial resistance profiles among these isolates. Prevalence of P. aeruginosa in wounds was 28% with 85 isolates recovered from wounds of 299 participants. Most antimicrobial resistance prevalence was recorded towards Ceftazidime (64%) and Cefepime (52%) while Piperacillin-tazobactam was the most effective antimicrobial agent with a resistance prevalence rate of 20%. Resistance towards new classes of aminoglycosides such as Gentamicin was at 45% while that towards Amikacin was at 40%. Compared to other related studies, relatively lower resistance towards Ciprofloxacin (25%) and Meropenem (40%) were recorded. Some of the risk factors identified for carriages of MDR strains were self-medication (p: 0.001, C.I: 3.01 - 8.86, O.R: 5.17) and non-completion of dosage (p: 0.12, C.I: 0.9 - 2.5, O.R: 1.5).

A New Metric for Measuring Relatedness of ScientificPapers Based on Non-Textual Features

Measuring relatedness of two papers is an issue which arises in many applications, e.g., recommendation, clustering and classification of papers. In this paper, a digital library is modeled as a directed graph;each node representing three different types of entities: papers, authors, and venues, and each edge representing relationships between these entities. Based on this graph model, six different types of relations are considered between two papers, and a new metric is proposed for evaluating relatedness of the papers. This metric only focuses on the relational features, and does not consider textual features. We have used it in combination with a textual similarity measure in the context of citation recommendation systems. Experimental results show that using this metric can successfully improve the quality of the recommendations.

MethylGenotyper:Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data

Epigenome-wide association studies(EWAS)are susceptible to widespread confounding caused by population structure and genetic relatedness.Nevertheless,kinship estimation is challenging in EWAS without genotyping data.Here,we proposed MethylGenotyper,a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms(SNPs)directly from commercial DNA methylation microarrays.We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm.We conducted extensive simulations to demonstrate the performance of the method.When applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples,we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%,enabling the identification of 255 pairs of close relatedness.Furthermore,we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry.We also implemented MethylGenotyper in a publicly available R package(https://github.com/Yi-Jiang/MethylGenotyper)to facilitate future large-scale EWAS.

Hypidone hydrochloride(YL-0919)ameliorates functional deficits after traumatic brain injury in mice by activating the sigma-1 receptor for antioxidation

Traumatic brain injury involves complex pathophysiological mechanisms,among which oxidative stress significantly contributes to the occurrence of secondary injury.In this study,we evaluated hypidone hydrochloride(YL-0919),a self-developed antidepressant with selective sigma-1 receptor agonist properties,and its associated mechanisms and targets in traumatic brain injury.Behavioral experiments to assess functional deficits were followed by assessment of neuronal damage through histological analyses and examination of blood-brain barrier permeability and brain edema.Next,we investigated the antioxidative effects of YL-0919 by assessing the levels of traditional markers of oxidative stress in vivo in mice and in vitro in HT22 cells.Finally,the targeted action of YL-0919 was verified by employing a sigma-1 receptor antagonist(BD-1047).Our findings demonstrated that YL-0919 markedly improved deficits in motor function and spatial cognition on day 3 post traumatic brain injury,while also decreasing neuronal mortality and reversing blood-brain barrier disruption and brain edema.Furthermore,YL-0919 effectively combated oxidative stress both in vivo and in vitro.The protective effects of YL-0919 were partially inhibited by BD-1047.These results indicated that YL-0919 relieved impairments in motor and spatial cognition by restraining oxidative stress,a neuroprotective effect that was partially reversed by the sigma-1 receptor antagonist BD-1047.YL-0919 may have potential as a new treatment for traumatic brain injury.

Autophagy-targeting modulation to promote peripheral nerve regeneration

Nerve regeneration following traumatic peripheral nerve injuries and neuropathies is a complex process modulated by diverse factors and intricate molecular mechanisms.Past studies have focused on factors that stimulate axonal outgrowth and myelin regeneration.However,recent studies have highlighted the pivotal role of autophagy in peripheral nerve regeneration,particularly in the context of traumatic injuries.Consequently,autophagy-targeting modulation has emerged as a promising therapeutic approach to enhancing peripheral nerve regeneration.Our current understanding suggests that activating autophagy facilitates the rapid clearance of damaged axons and myelin sheaths,thereby enhancing neuronal survival and mitigating injury-induced oxidative stress and inflammation.These actions collectively contribute to creating a favorable microenvironment for structural and functional nerve regeneration.A range of autophagyinducing drugs and interventions have demonstrated beneficial effects in alleviating peripheral neuropathy and promoting nerve regeneration in preclinical models of traumatic peripheral nerve injuries.This review delves into the regulation of autophagy in cell types involved in peripheral nerve regeneration,summarizing the potential drugs and interventions that can be harnessed to promote this process.We hope that our review will offer novel insights and perspectives on the exploitation of autophagy pathways in the treatment of peripheral nerve injuries and neuropathies.

Nest composition and worker relatedness in three slave-making ants of the genus Rossomyrmex Arnoldi and their Proformica Ruzsky hosts （Hymenoptera, Formicidae）

In this paper, we analyze and compare nest composition and architecture as well as worker relatedness in three related species of slave-making ants： Rossomyrmex anatolicus, R. minuchae, and R. quandratinodum. Colony structure within nests is an important trait in ants, especially in the case of mixed societies, when host and parasite coexist in the same nest. Data for their respective free-living hosts, Proformica korbi, P.. longiseta and P. sp., are also provided. For our study, we integrated a meticulous excava- tion procedure with a genetic method. We conclude that the average number of parasites, as well as of slaves, is species-specific, whereas nest depth depends on the nest archi- tecture of the host. The genus Rossomyrmex seems to be monogynous and monandrous, whereas Proformica shows differences in the number of queens and mating frequency. R. quandratinodum shows different traits in nest composition （host/parasite ratio： P/R） and architecture. The difference in traits may account for some differences in parasitism： raid process or avoidance of parasitism.

Degenerate slave-makers,but nevertheless slave-makers?Host worker relatedness in the ant Myrmoxenus kraussei

Socially parasitic ants of the formicoxenine genus Myrmoxenus exhibit considerable diversity in colony structure and life history.While some species are active slave-makers with many workers and others are workerless‘murder-parasites,’Myrmoxenus kraussei is considered as a‘degenerate slave-maker’because of its very low worker numbers.Here,we document that Temnothorax recedens host workers in single colonies of M.kraussei from Lago di Garda,Italy,exhibit significantly more genetic diversity than workers in unparasitized colonies.This raises the possibility that,despite its low worker numbers,M.kraussei may actively engage in slave raids in nature.

Genetic diversity and relatedness inferred from microsatellite loci as a tool for broodstock management of fine flounder Paralichthys adspersus

Paralichthys adspersus is a native species from the Pacific coast of South America that is of great economic importance for Peruvian aquaculture.Even though establishing sustainable farming depends on avoiding irreversible damage to the population gene pool due to processes such as inbreeding,studies focusing on genetically characterizing farmed stocks are yet to be documented.By using ten microsatellite loci on captive and wild individuals of P.adspersus,we successfully characterized the only commercial broodstock of this species in Peru by means of determining the genetic diversity and inferring relatedness.Although most microsatellite loci showed deviations from Hardy-Weinberg equilibrium,the genetic diversity levels in the commercial broodstock were considered healthy compared to those obtained for a wild population,with an average number of alleles of 17.40,an effective number of alleles of 9.14,and an observed and expected heterozygosity of 0.49 and 0.87.No significant differences between the broodstock and the wild population in terms of genetic diversity were observed.The fixation index and analysis of molecular variance also indicated a low rate of differentiation between both populations.In relatedness estimation,the analysis based on five method-of-moment estimators and a maximum-likelihood estimator showed the category“unrelated”as being the most probable relationship among the individuals within the commercial broodstock.Our findings reveal the conservation of genetic diversity in this population and outline potential breeding strategies that hatchery managers could use to minimize the loss of genetic diversity and long-term inbreeding.This could help establish proper genetic management in captive populations of P.adspersus and should apply to other captive stocks where pedigree information is lacking.

An unprotected vulnerable relict subtropical conifer-Keteleeria evelyniana: Its forests, populations, growth and endangerment by invasive alien plant species in China

Relict subtropical coniferous forests in China face severe fragmentation,resulting in declining populations,and some are under significant threat from invasive alien species.Despite the crucial importance of understanding forest dynamics,knowledge gaps persist,particularly regarding the impact of invasive plants on vulnerable natives like Keteleeria evelyniana.In this study,we investigated the impact of invasive plants on the regeneration of forests dominated by K.evelyniana,a subtropical relict species in southwestern China.For this purpose,we characterized forest dynamics of 160 forest plots featuring K.evelyniana as the primary dominant species and determined whether the presence of invasive plants was correlated with regeneration of K.evelyniana.We identified four distinct forest types in which K.evelyniana was dominant.We found that radial growth of K.evelyniana trees is faster in younger ageclasses today than it was for older trees at the same age.The population structure of K.evelyniana in each forest type exhibited a multimodal age-class distribution.However,three forest types lacked established saplings younger than 10 years old,a situation attributed to the dense coverage of the invasive alien Ageratina adenophora.This invasive species resulted in a reduction of understory species diversity.Additionally,our analysis uncovered a significant negative correlation in phylogenetic relatedness(net relatedness index)between native and invasive alien plant species in eastern Yunnan.This suggests closely related invasive species face heightened competition,hindering successful invasion.Taken together,our findings indicate that successful establishment and habitat restoration of K.evelyniana seedling/saplings require effective measures to control invasive plants.

Hard life for sons in the nest?Sex-dependent offspring mortality in Great Tits in urban and forest areas

Sex-biased mortality can occur in birds during development,for example due to sexual differences in energy requirement and/or environmental sensitivity,or the effects of sex hormones or sex differences in the expression of mutations linked to sex chromosomes.The extent of sex-bias in mortality may also be related to environmental conditions that influence offspring development and survival.Urban areas often provide poorer conditions for nestling development resulting in higher offspring mortality compared to natural areas,which may accelerate sex differences in offspring mortality in cities.To test this hypothesis,we examined the sex ratio of dead offspring in Great Tits(Parus major),using 427 samples of unhatched eggs and dead nestlings collected in two urban and two forest sites between 2013 and 2019.The ratio of males in the whole sample of dead offspring(56.9%)was significantly higher than expected by an 1:1 ratio,and the strongest sex biases were detected in urban areas(57.6%males)and in young nestlings(<14 days old,59.0%males).However,the sex ratios of dead offspring did not differ significantly among study sites and between offspring developmental stages.29.3%of unhatched eggs contained a visible embryo,and the proportion of embryo-containing unhatched eggs did not differ significantly between urban and forest study sites.These results suggest male-biased offspring mortality in Great Tits,and highlight the need of large datasets to detect subtle differences between habitats and developmental stages.

Improving the operational stability of perovskite solar cells with cesium-doped graphene oxide interlayer

Perovskite solar cells(PSCs)have made great advances in terms of power conversion efficiency(PCE),yet their subpar stability continues to hinder their commercialization.The interface between the perovskite layer and the charge-carrier transporting layers plays a crucial role in undermining the stability of PSCs.In this work,we propose a strategy to stabilize high-performance PSCs with PCE over 23%by introducing a cesium-doped graphene oxide(GO-Cs)as an interlayer between the perovskite and hole-transporting material.The GO-Cs treated PSCs exhibit excellent operational stability with a projected T80(the time where the device PCE reduces to 80%of its initial value)of 2143 h of operation at the maximum powering point under one sun illumination.

Immunoglobulin G4-related spinal pachymeningitis:A case report

BACKGROUND Immunoglobulin G4-related disease(IgG4-RD)is a complex immune-mediated condition that causes fibrotic inflammation in several organs.A significant clinical feature of IgG4-RD is hypertrophic pachymeningitis,which manifests as inflammation of the dura mater in intracranial or spinal regions.Although IgG4-RD can affect multiple areas,the spine is a relatively rare site compared to the more frequent involvement of intracranial structures.CASE SUMMARY A 70-year-old male presented to our hospital with a two-day history of fever,altered mental status,and generalized weakness.The initial brain magnetic resonance imaging(MRI)revealed multiple small infarcts across various cerebral regions.On the second day after admission,a physical examination revealed motor weakness in both lower extremities and diminished sensation in the right lower extremity.Electromyographic evaluation revealed findings consistent with acute motor sensory neuropathy.Despite initial management with intravenous immunoglobulin for presumed Guillain-Barrésyndrome,the patient exhibited progressive worsening of motor deficits.On the 45th day of hospitalization,an enhanced MRI of the entire spine,focusing specifically on the thoracic 9 to lumbar 1 vertebral level,raised the suspicion of IgG4-related spinal pachymeningitis.Subsequently,the patient was administered oral prednisolone and participated in a comprehensive rehabilitation program that included gait training and lower extremity strengthening exercises.CONCLUSION IgG4-related spinal pachymeningitis,diagnosed on MRI,was treated with corticosteroids and a structured rehabilitation regimen,leading to significant improvement.

Application value of machine learning models in predicting intraoperative hypothermia in laparoscopic surgery for polytrauma patients

BACKGROUND Hypothermia during laparoscopic surgery in patients with multiple trauma is a significant concern owing to its potential complications.Machine learning models offer a promising approach to predict the occurrence of intraoperative hypothermia.AIM To investigate the value of machine learning model to predict hypothermia during laparoscopic surgery in patients with multiple trauma.METHODS This retrospective study enrolled 220 patients who were admitted with multiple injuries between June 2018 and December 2023.Of these,154 patients were allocated to a training set and the remaining 66 were allocated to a validation set in a 7:3 ratio.In the training set,53 cases experienced intraoperative hypothermia and 101 did not.Logistic regression analysis was used to construct a predictive model of intraoperative hypothermia in patients with polytrauma undergoing laparoscopic surgery.The area under the curve(AUC),sensitivity,and specificity were calculated.RESULTS Comparison of the hypothermia and non-hypothermia groups found significant differences in sex,age,baseline temperature,intraoperative temperature,duration of anesthesia,duration of surgery,intraoperative fluid infusion,crystalloid infusion,colloid infusion,and pneumoperitoneum volume(P<0.05).Differences between other characteristics were not significant(P>0.05).The results of the logistic regression analysis showed that age,baseline temperature,intraoperative temperature,duration of anesthesia,and duration of surgery were independent influencing factors for intraoperative hypothermia during laparoscopic surgery(P<0.05).Calibration curve analysis showed good consistency between the predicted occurrence of intraoperative hypothermia and the actual occurrence(P>0.05).The predictive model had AUCs of 0.850 and 0.829 for the training and validation sets,respectively.CONCLUSION Machine learning effectively predicted intraoperative hypothermia in polytrauma patients undergoing laparoscopic surgery,which improved surgical safety and patient recovery.