Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Comparative Orotomy of the Archean Superior,North China,and Phanerozoic Altaid Orogenic Systems Architecture

Geological maps encode vast amounts of data about rock types,ages,chemistry,orogenic architecture and deep-time history or different tectonic units,yet these are often difficult to extract because of the way different geologists portray their results at various scales.To understand orogenesis in 4D,it is essential to uniformly integrate map data,together with geophysical data and deep geochemical mapping(Wang et al.,2023).

Rice-wheat comparative genomics:Gains and gaps

Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits.Several wheat genes and gene families have been characterized based on their rice orthologs.Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops.Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.

Comparative proteomics analysis reveals the domesticated Lepista sordida primordium differentiation regulation mechanism and the subsequent different development patterns in the pileus and stipe

The wild Lepista sordida is a kind of precious and rare edible fungus.An excellent strain of it by artificial domestication was obtained,which was high-yield and high in iron content.In this study,high-throughput comparative proteomics was used to reveal the regulatory mechanism of its primordium differentiation in the early fruiting body formation.The mycelium before the primordium differentiation mainly expressed high levels of mitochondrial functional proteins and carbon dioxide concentration regulatory proteins.In young mushrooms,the highly expressed proteins were mainly involved in cell component generation,cell proliferation,nitrogen compound metabolism,nucleotide metabolism,glutathione metabolism,and purine metabolism.The differential regulation patterns of pileus and stipe growth to maturity were also revealed.The highly expressed proteins related to transcription,RNA splicing,the production of various organelles,DNA conformational change,nucleosome organization,protein processing,maturation and transport,and cell detoxification regulated the pileus development and maturity.The proteins related to carbohydrate and energy metabolism,large amounts of obsolete cytoplasmic parts,nutrient deprivation,and external stimuli regulated the stipe development and maturity.Multiple CAZymes regulated nutrient absorption,morphogenesis,spore production,stress response,and other life activities at different growth and development stages.

Comparative genomic analysis revealed that dietary habits affected the adaptation of Bifidobacterium bifidum to the intestinal tract in different geographic populations

Recent research on the genome of Bifidobacterium bifidum has mainly focused on the isolation sources(intestinal tract niche)recently,but reports on the isolation region are limited.This study analyzed the differences in the genome of B.bifidum isolated from different geographical populations by comparative genomic analysis.Results at the genome level indicated that the GC content of American isolates was significantly higher than that of Chinese and Russian isolates.The phylogenetic tree,based on 919 core genes showed that B.bifidum might be related to the geographical characteristics of isolation region.Furthermore,functional annotation analysis demonstrated that copy numbers of carbohydrate-active enzymes(CAZys)involved in the degradation of polysaccharide from plant and host sources in B.bifidum were high,and 18 CAZys showed significant differences across different geographical populations,indicating that B.bifidum had adapted to the human intestinal environment,especially in the groups with diets rich in fiber.Dietary habits were one of the main reasons for the differences of B.bifidum across different geographical populations.Additionally,B.bifidum exhibited high diversity,evident in glycoside hydrolases,the CRISPR-Cas system,and prophages.This study provides a genetic basis for further research and development of B.bifidum.

The relationship between compartment models and their stochastic counterparts:A comparative study with examples of the COVID-19 epidemic modeling

Deterministic compartment models(CMs)and stochastic models,including stochastic CMs and agent-based models,are widely utilized in epidemic modeling.However,the relationship between CMs and their corresponding stochastic models is not well understood.The present study aimed to address this gap by conducting a comparative study using the susceptible,exposed,infectious,and recovered(SEIR)model and its extended CMs from the coronavirus disease 2019 modeling literature.We demonstrated the equivalence of the numerical solution of CMs using the Euler scheme and their stochastic counterparts through theoretical analysis and simulations.Based on this equivalence,we proposed an efficient model calibration method that could replicate the exact solution of CMs in the corresponding stochastic models through parameter adjustment.The advancement in calibration techniques enhanced the accuracy of stochastic modeling in capturing the dynamics of epidemics.However,it should be noted that discrete-time stochastic models cannot perfectly reproduce the exact solution of continuous-time CMs.Additionally,we proposed a new stochastic compartment and agent mixed model as an alternative to agent-based models for large-scale population simulations with a limited number of agents.This model offered a balance between computational efficiency and accuracy.The results of this research contributed to the comparison and unification of deterministic CMs and stochastic models in epidemic modeling.Furthermore,the results had implications for the development of hybrid models that integrated the strengths of both frameworks.Overall,the present study has provided valuable epidemic modeling techniques and their practical applications for understanding and controlling the spread of infectious diseases.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.

Comparative efficacy of proximal femoral nail vs dynamic condylar screw in treating unstable intertrochanteric fractures

BACKGROUND Among the most frequent hip fractures are trochanteric fractures,which usually occur from low-energy trauma like minor falls,especially in older people with osteoporotic bones.AIM To evaluate the treatment efficacy of dynamic condylar screws(DCS)and proximal femoral nails(PFN)for unstable intertrochanteric fractures.METHODS To find pertinent randomized controlled trials and retrospective observational studies comparing PFN with DCS for the management of unstable femoral intertrochanteric fractures,a thorough search was carried out.For research studies published between January 1996 and April 2024,PubMed,EMBASE,Scopus,Web of Science,Cochrane Library,and Google Scholar were all searched.The complete texts of the papers were retrieved,vetted,and independently examined by two investigators.Disputes were settled by consensus,and any disagreements that persisted were arbitrated by a third author.RESULTS This study included six articles,comprising a total of 173 patients.Compared to the DCS,the PFN had a shorter operation time[mean difference(MD):-41.7 min,95%confidence interval(95%CI):-63.04 to-20.35,P=0.0001],higher success rates with closed reduction techniques[risk ratio(RR):34.05,95%CI:11.12-104.31,P<0.00001],and required less intraoperative blood transfusion(MD:-1.4 units,95%CI:-1.80 to-1.00,P<0.00001).Additionally,the PFN showed shorter fracture union time(MD:-6.92 wk,95%CI:-10.27 to-3.57,P<0.0001)and a lower incidence of reoperation(RR:0.37,95%CI:0.17-0.82,P=0.01).However,there was no discernible variation regarding hospital stay,implant-related complications,and infections.CONCLUSION Compared to DCS,PFN offers shorter operative times,reduces the blood transfusions requirements,achieves higher closed reduction success,enables faster fracture healing,and lowers reoperation incidence.

Exploring Nominalization in English Abstracts of Applied Linguistics Research Articles:A Comparative Study Between Chinese and International Journals

Researchers around the world strive to communicate new knowledge,primarily via publication,with the abstract being crucial in conveying core insights.Previous research has generally analyzed the discourse features of abstracts from a macro perspective and often employed either outdated texts,such as those over a decade old,or papers written by authors with lower English academic writing proficiency as research material.In this study,we analyzed forty abstracts from leading journals in applied linguistics,evenly split between Chinese and international journals.It revealed that the use of nominalization in abstracts by Chinese and international scholars showed similarities due to the universal academic requirement for conciseness.However,due to cultural and educational differences,each group differed in their respective language choices and nominalization usage.By analyzing the application of nominalization in different cultural contexts,the results of our study offered practical suggestions for crafting abstracts that effectively convey information,thereby,contributing to the broader academic community.

Descriptive and Comparative Histology of the Urinary System of the Hematophagous Bats Desmodus rotundus and Diphylla ecaudata

Desmodus rotundus and Diphylla ecaudata, both of which are mammals of the order Chiroptera, Desmodontidae family, their diet consisting exclusively of blood. D. rotundus is the main vector and transmitter of the rabies virus, which affects human beings as well as several livestock species so the study of this bat species is of high importance within the fields of animal agriculture and public health. The present study describes and compares the histologic characteristics of the urinary system of two hematophagous bat species. A total of 5 bats from each species were captured in the municipalities of Progreso de Obregón, Hidalgo (D. rotundus), and Huayacocotla, Veracruz (D. ecaudata). Organs belonging to the urinary system were extracted: kidneys, ureters, urinary bladder, and urethra;samples were fixed using 10% formalin and processed by the paraffin embedding technique, obtaining sections of 5 µm thickness, which in turn were stained using hematoxylin-eosin (H-E) and Gomori trichrome (GT) stains. From the obtained histologic preparations, a descriptive and comparative analysis of the structural organography of the urinary system of both species was made, and no noteworthy histological differences between samples were noted. The present research is intended to provide a framework for future studies of these species’ currently understudied microscopic anatomy.

A Comparative Study on Factors Influencing Food Security in China and India

This paper analyzes and compares the key factors influencing food security in two populous countries(China and India),and cate-gorizes them into three types:agricultural production,economic development and income level,and income distribution.Using the prevalence of undernourishment as an indicator of food security,the paper empirically tests the degree of impact of various factors on food security in both countries using Tobit regression and Newey regression methods.The study finds that improving the level of economic development can significantly enhance food security in both countriesꎻreducing the Gini coefficient has a significant impact on India,but not on Chinaꎻincreasing the agricultural production per capita has a much greater effect on China than on India.Therefore,both countries should take measures that are both similar and different according to their national conditions to improve their food security level.

A Research Conception on Indigenous Chinese Leadership:Based on Comparative Case Studies on Political Elites in Ancient China

Due to the complexity of leadership and its variability across situations,it is suggested that research on leadership should focus on attempts to understand leadership in specific situations or roles,and develop local knowledge about leadership in each situation or role.This paper validates the possibility and importance of building indigenous leadership theories from historical perspective.We demonstrated how to carry out research on indigenous Chinese leadership from a historical perspective by comparative case studies using historical data.Based on the principles of typicalness,representativeness,and comparativeness,we selected six counterparts of political elites in ancient China as comparative cases,which includes Guan Zhong&Shang Yang(organizational reformer),Liu Bang&Xiang Yu(entrepreneur),Li Shimin&Qin Shihuang(intergenerational transition successor),Zhuge Liang&Zeng Guofan(professional manager),Lu Su&Zhang Juzheng(mess-to-order maker),and Zuo Zongtang&Wang Anshi(national dream driver).The paper aims to develop indigenous leadership theory specific to Chinese mental states and culture.

Integrated Machine Learning and Deep Learning Models for Cardiovascular Disease Risk Prediction: A Comprehensive Comparative Study

Cardiovascular Diseases (CVDs) pose a significant global health challenge, necessitating accurate risk prediction for effective preventive measures. This comprehensive comparative study explores the performance of traditional Machine Learning (ML) and Deep Learning (DL) models in predicting CVD risk, utilizing a meticulously curated dataset derived from health records. Rigorous preprocessing, including normalization and outlier removal, enhances model robustness. Diverse ML models (Logistic Regression, Random Forest, Support Vector Machine, K-Nearest Neighbor, Decision Tree, and Gradient Boosting) are compared with a Long Short-Term Memory (LSTM) neural network for DL. Evaluation metrics include accuracy, ROC AUC, computation time, and memory usage. Results identify the Gradient Boosting Classifier and LSTM as top performers, demonstrating high accuracy and ROC AUC scores. Comparative analyses highlight model strengths and limitations, contributing valuable insights for optimizing predictive strategies. This study advances predictive analytics for cardiovascular health, with implications for personalized medicine. The findings underscore the versatility of intelligent systems in addressing health challenges, emphasizing the broader applications of ML and DL in disease identification beyond cardiovascular health.

Quantitative Comparative Study of the Performance of Lossless Compression Methods Based on a Text Data Model

Data compression plays a key role in optimizing the use of memory storage space and also reducing latency in data transmission. In this paper, we are interested in lossless compression techniques because their performance is exploited with lossy compression techniques for images and videos generally using a mixed approach. To achieve our intended objective, which is to study the performance of lossless compression methods, we first carried out a literature review, a summary of which enabled us to select the most relevant, namely the following: arithmetic coding, LZW, Tunstall’s algorithm, RLE, BWT, Huffman coding and Shannon-Fano. Secondly, we designed a purposive text dataset with a repeating pattern in order to test the behavior and effectiveness of the selected compression techniques. Thirdly, we designed the compression algorithms and developed the programs (scripts) in Matlab in order to test their performance. Finally, following the tests conducted on relevant data that we constructed according to a deliberate model, the results show that these methods presented in order of performance are very satisfactory:- LZW- Arithmetic coding- Tunstall algorithm- BWT + RLELikewise, it appears that on the one hand, the performance of certain techniques relative to others is strongly linked to the sequencing and/or recurrence of symbols that make up the message, and on the other hand, to the cumulative time of encoding and decoding.

Comparative Study of the Reliability and Complexity of Symmetrical and Asymmetrical Cryptosystems for the Protection of Academic Data in the Democratic Republic of Congo

In the digital age, the data exchanged within a company is a wealth of knowledge. The survival, growth and influence of a company in the short, medium and long term depend on it. Indeed, it is the lifeblood of any modern company. A companys operational and historical data contains strategic and operational knowledge of ever-increasing added value. The emergence of a new paradigm: big data. Today, the value of the data scattered throughout this mother of knowledge is calculated in billions of dollars, depending on its size, scope and area of intervention. With the rise of computer networks and distributed systems, the threats to these sensitive resources have steadily increased, jeopardizing the existence of the company itself by drying up production and losing the interest of customers and suppliers. These threats range from sabotage to bankruptcy. For several decades now, most companies have been using encryption algorithms to protect and secure their information systems against the threats and dangers posed by the inherent vulnerabilities of their infrastructure and the current economic climate. This vulnerability requires companies to make the right choice of algorithms to implement in their management systems. For this reason, the present work aims to carry out a comparative study of the reliability and effectiveness of symmetrical and asymmetrical cryptosystems, in order to identify one or more suitable for securing academic data in the DRC. The analysis of the robustness of commonly used symmetric and asymmetric cryptosystems will be the subject of simulations in this article.

Research on the Policy Evolution of Inclusive Education from an International Comparative Perspective

In recent years,thanks to the vigorous promotion by UNESCO,inclusive education has rapidly developed and spread worldwide.Governments across various nations have responded and implemented this approach,successively introducing laws and policies to ensure that children with special needs are better integrated into society and receive a comprehensive education.This paper begins by exploring the concept and connotation of inclusive education.Through an international comparative perspective,it conducts a comparative analysis of the policy evolution of inclusive education in China and the United Kingdom.Furthermore,it investigates the implications that advanced international policy experiences have for the development of inclusive education in China.

A comparative study of the main factors controlling geohazards induced by 10 strong earthquakes in Western China since the Wenchuan earthquake in 2008

Determining the main controlling factors of earthquake-triggered geohazards is a prerequisite for studying earthquake geohazards and post-disaster emergency response.By studying these factors,the geomorphic and geological factors controlling the nature,condition,and distribution of earthquake-induced geohazards can be analyzed.Such insights facilitate earthquake disaster prediction and emergency response planning.The authors combined field investigations and spatial data analysis to examine geohazards induced by seismic events,examining ten earthquakes including the Wenchuan,Yushu,Lushan events,to elucidate the main control factors of seismic geohazard.The authors observed that seismic geohazard occurrence is usually affected by many factors,among which active nature of the seismogenic fault,seismic peak ground acceleration(PGA),topographic slope and geomorphic height differences,and distance from the fault zone and river system are the most important.Compared with strike-slip earthquakes,thrust earthquakes induce more high-altitude and high-speed remote landslides,which can cause great harm.Slopes of 0°–40°are prone to secondary seismic geohazards,which are mainly concentrated 0–6 km from the river system.Secondary geohazards are not only related to seismogenic fault but also influenced by the associated faults in the earthquake area.The maximum seismic PGA and secondary seismic geohazard number are positively correlated,and the horizontal and vertical ground motions play leading and promoting roles in secondary geohazard formation,respectively.Through the research,the spatial distribution of seismic geohazards is predicted,providing a basis for the formulation of emergency response plans following disasters.

Comparative transcriptomes reveal the disjunction adaptive strategy of Thuja species in East Asia and North America

The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.

Structural characterization of four Rhododendron spp.chloroplast genomes and comparative analyses with other azaleas

Azalea is a general designation of Rhododendron in the Ericaceae family.Rhododendron not only has high ornamental value but also has application value in ecological protection,medicine,and scientific research.In this study,we used Illumina and PacBio sequencing to assemble and annotate the entire chloroplast genomes(cp genomes)of four Rhododendron species.The chloroplast genomes of R.concinnum,R.henanense subsp.lingbaoense,R.micranthum,and R.simsii were assembled into 207,236,208,015,207,233,and 206,912 bp,respectively.All chloroplast genomes contain eight rRNA genes,with either 88 or 89 protein-coding genes.The four cp genomes were compared and analyzed by bioinformatics,and the phylogenetic analysis based on chloroplast genomes of 26 species of Ericaceae,Actinidiaceae,and Primulaceae under Ericales was conducted.A comparison of the linear structure of cp genomes of four Rhododendron showed that there were substantial sequence similarities in coding regions,but high differences in non-coding regions.A phylogenetic analysis,based on chloroplast whole genome sequences,showed that all Rhododendron species are in the clade Ericaceae.This study provides valuable genetic information for the study of population genetics and evolutionary relationships in Rhododendron and other azalea species.

Understanding Poison:Study of a Word Du from the Perspective of Comparative History

This article investigates the word Du(毒)in premodern Chinese medicine and culture.It highlights the paradoxical meaning of the word that served as a foundation for the therapeutic use of poisons in traditional Chinese medicine.The article then situates the study in a comparative framework.By comparing the Chinese notion of Du with the Greek concept of pharmakon,it demonstrates significant similarities on the medical use of poisons in the two cultures.It further identifies a striking difference:While the European pharmacy started to separate poisons from medicines in the medieval era,poisons remained an integral part of healing repertoire throughout imperial China.The article ends with offering some cultural explanations for this divergence,and more broadly,a distinct worldview as revealed by the intimate relationship between poisons and medicines in traditional Chinese pharmacy.