Elevational and temporal patterns of pollination success in distylous and homostylous buckwheats(Fagopyrum)in the Hengduan Mountains

Reproductive strategies of sexually dimorphic plants vary in response to the environment.Here,we ask whether the sexual systems of Fagopyrum species(i.e.,selfing homostylous and out-crossing distylous)represent distinct adaptive strategies to increase reproductive success in changing alpine environments.To answer this question,we determined how spatial and temporal factors(e.g.,elevation and peak flowering time)affect reproductive success(i.e.,stigmatic pollen load)in nine wild Fagopyrum species(seven distylous and two homostylous)among 28 populations along an elevation gradient of 1299-3315 m in the Hengduan Mountains,southwestern China.We also observed pollinators and conducted hundreds of hand pollinations to investigate inter/intra-morph compatibility,self-compatibility and pollen limitation in four Fagopyrum species(two distylous and two homostylous).We found that Fagopyrum species at higher elevation generally had bigger flowers and more stigmatic pollen loads;lateflowering individuals had smaller flowers and lower pollen deposition.Stigmatic pollen deposition was more variable in distylous species than in homostylous species.Although seed set was not pollenlimited in all species,we found that fruit set was much lower in distylous species,which rely on frequent pollinator visits,than in homostylous species capable of autonomous self-pollination.Our findings that pollination success increases at high elevations and decreases during the flowering season suggest that distylous and homostylous species have spatially and temporally distinct reproductive strategies related to environment-dependent pollinator activity.

GOMA:functional enrichment analysis tool based on GO modules

Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel enrichment analysis method based on the new concept of enriched functional Gene Ontology (GO) modules. With this method, we systematically revealed functional GO modules, i.e., groups of functionally similar GO terms, via an optimization model and then ranked them by enrichment scores. Our new method simplifies enrichment analysis results by reducing redundancy, thereby preventing inconsistent enrichment results among functionally similar terms and providing more biologically meaningful results.

Effect of prior malignancy on the prognosis of gastric cancer and somatic mutation

BACKGROUND Cancer survivors have a higher risk of developing secondary cancer,with previous studies showing heterogeneous effects of prior cancer on cancer survivors.AIM To describe the features and clinical significance of a prior malignancy in patients with gastric cancer(GC).METHODS We identified eligible patients from the Surveillance,Epidemiology,and End Results(SEER)database,and compared the clinical features of GC patients with/without prior cancer.Kaplan-Meier curves and Cox analyses were used to assess the prognostic impact of prior cancer on overall survival(OS)and cancerspecific survival(CSS)outcomes.We also validated our results in The Cancer Genome Atlas(TCGA)cohort and compared mutation patterns.RESULTS In the SEER dataset,of the 35492 patients newly diagnosed with GC between 2004 and 2011,4,001(11.3%)had at least one prior cancer,including 576(1.62%)patients with multiple cancers.Patients with a prior cancer history tended to be elderly,with a more localized stage and less positive lymph nodes.The prostate(32%)was the most common initial cancer site.The median interval from initial cancer diagnosis to secondary GC was 68 mo.By using multivariable Cox analyses,we found that a prior cancer history was not significantly associated with OS(hazard ratio[HR]:1.01,95%confidence interval[CI]:0.97–1.05).However,a prior cancer history was significantly associated with better GCspecific survival(HR:0.82,95%CI:0.78–0.85).In TCGA cohort,no significant difference in OS was observed for GC patients with or without prior cancer.Also,no significant differences in somatic mutations were observed between groups.CONCLUSION The prognosis of GC patients with previous diagnosis of cancer was not inferior to that of primary GC patients.

Construction and Control of Genetic Regulatory Networks:A Multivariate Markov Chain Approach

In the post-genomic era, the construction and control of genetic regulatory networks using gene expression data is a hot research topic. Boolean networks (BNs) and its extension Probabilistic Boolean Networks (PBNs) have been served as an effective tool for this purpose. However, PBNs are difficult to be used in practice when the number of genes is large because of the huge computational cost. In this paper, we propose a simplified multivariate Markov model for approximating a PBN The new model can preserve the strength of PBNs, the ability to capture the inter-dependence of the genes in the network, qnd at the same time reduce the complexity of the network and therefore the computational cost. We then present an optimal control model with hard constraints for the purpose of control/intervention of a genetic regulatory network. Numerical experimental examples based on the yeast data are given to demonstrate the effectiveness of our proposed model and control policy.

Shortened anther-stigma distance reduces compatible pollination in two distylous Primula species

Aims Distyly has been regarded as an adaptation to improve compatible pollination between two floral morphs with reciprocal herkogamy.The hypothesis that the different positions of anthers and stigmas within flowers as well as their reciprocal position between morphs,reduce the probability of self pollination raised by Darwin has been rarely tested.in this study,we measured stigmatic pollen loads in response to reduced reciprocal herkogamy in two Primula species.Methods To see whether reciprocal herkogamy can increase compatible and/or reduce incompatible pollen deposition,thus promoting compat-ible pollination,we shortened the distance between anthers and stigmas within the flowers by changing the position of the corolla tube,to which the anthers were fused,i.e.reduced herkogamy in natural populations of Primula secundiflora and P.poissonii and quantified stigmatic pollen loads in the field over 2 years.Important Findingsin both species,stigmatic pollen loads were significantly higher in the long-styled(l-morph)than in the short-styled morph(s-morph)in both control and manipulated flowers,but percentage of compatible pollen in s-morph were higher.Flowers manipulated to halve the anther-stigma distance showed a similar pattern for 2 years:total pollen grain counts on stigmas did not differ significantly but compatible pollen grains in l-and s-morphs were significantly decreased in both species.The percentage of compatible pollen loads was decreased by 68.7%in P.secundiflora and 65.3%in P.poissonii in l-morphs,while it decreased by 30.6%and 2.9%in s-morphs,respectively.our manipulation of the relative position of anthers and stigmas in the two distylous species indicated that a lower degree of herkogamy reduced compatible but incompatible pollen transfer was likely to increase.The higher proportion of compatible pollen in the s-morph than in the l-morph in the two Primula species could be attributed to the accessibility of two-level sexual organs,floral orientations and pollinator behaviors.This is a first attempt to manipulate intraflower herkogamy for understanding adaptation of heterostyly,shedding insights into how the reciprocal herkogamy promotes compatible pollination.

A Dynamic Programming Algorithm for the κ-Haplotyping Problem

The Minimum Fragments Removal （MFR） problem is one of the haplotyping problems： given a set of fragments, remove the minimum number of fragments so that the resulting fragments can be partitioned into k classes of non-conflicting subsets. In this paper, we formulate the κ-MFR problem as an integer linear programming problem, and develop a dynamic programming approach to solve the κ-MFR problem for both the gapless and gap eases.

Operations Research in the Blockchain Technology

In the past decade,as a decentralized distributed database technology blockchain has developed rapidly at an unprecedented speed and been applied to a wide range of scenarios far beyond cryptocurrencies,for example,insurance,energy,risk management,and Internet of things(IoT).The blockchain technology combines the achievements from cryptography,computer science,economics,and operations research and has increasingly attracted attention from both academia and industry.Though the operations research has been widely adopted in the blockchain technology,there is a lack of comprehensive survey on the operations research in blockchain-related issues.In order to fill the gap,we analyze the blockchain technology through the perspective of operations research and present a comprehensive review of the operations research problems from the aspects of security and stability,efficiency and performance,and resource allocation.This paper aimed to help the relevant readers in the field of operations research find their own points of interest and conduct in-depth research on the blockchain technology,hoping to promote the rapid development and wider application of the blockchain technology in the near future.

Preface:Special Issue on New Developments in Mathematical Programming and Operations Research

COVID-19 has brought us an abnormal environment,which caused a great deal of inconvenience to every aspect of life,including academic interchange.In response to this,the Operations Research Society of China(ORSC)organized an OR Road-to-Future Forum(运筹千里纵横论坛).As of April 30,2020,this series forum has held more than 100 talks from globally outstanding operational researchers,including the IFORS President Professor M.Grazia Speranza from University of Brescia(Italy),Professor Yin-Yu Ye from Stanford University(USA),Professor Zhi-Quan Luo from the Chinese University of Hong Kong(Shenzhen,China),and Professor De-Feng Sun from the Hong Kong Polytechnic University(Hong Kong,China).At the same time,OR Road-to-Future Forum also invites some outstanding junior speakers to share their latest works.These talks cover a wide range of areas in mathematical programming and operations research,such as graph theory,computational mathematics,bioinformatics,machine learning,artificial intelligence,engineering problems,as well as their applications.