Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally c...Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental conditions.Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production type.Results We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important traits.Most candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment analysis.Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.展开更多
Colorectal cancer(CRC)belongs to the class of significantly malignant tumors found in humans.Recently,dysregulated fatty acid metabolism(FAM)has been a topic of attention due to its modulation in cancer,specifically C...Colorectal cancer(CRC)belongs to the class of significantly malignant tumors found in humans.Recently,dysregulated fatty acid metabolism(FAM)has been a topic of attention due to its modulation in cancer,specifically CRC.However,the regulatory FAM pathways in CRC require comprehensive elucidation.Methods:The clinical and gene expression data of 175 fatty acid metabolic genes(FAMGs)linked with colon adenocarcinoma(COAD)and normal cornerstone genes were gathered through The Cancer Genome Atlas(TCGA)-COAD corroborating with the Molecular Signature Database v7.2(MSigDB).Initially,crucial prognostic genes were selected by uni-and multi-variate Cox proportional regression analyses;then,depending upon these identified signature genes and clinical variables,a nomogram was generated.Lastly,to assess tumor immune characteristics,concomitant evaluation of tumor immune evasion/risk scoring were elucidated.Results:A 8-gene signature,including ACBD4,ACOX1,CD36,CPT2,ELOVL3,ELOVL6,ENO3,and SUCLG2,was generated,and depending upon this,CRC patients were categorized within high-risk(H-R)and low-risk(L-R)cohorts.Furthermore,risk and age-based nomograms indicated moderate discrimination and good calibration.The data confirmed that the 8-gene model efficiently predicted CRC patients’prognosis.Moreover,according to the conjoint analysis of tumor immune evasion and the risk scorings,the H-R cohort had an immunosuppressive tumor microenvironment,which caused a substandard prognosis.Conclusion:This investigation established a FAMGs-based prognostic model with substantially high predictive value,providing the possibility for improved individualized treatment for CRC individuals.展开更多
A metropolitan city such as Los Angeles (LA) is an ideal study site with a very high population density, and it houses at least 3 treatment plants where sewage is treated preliminarily and then progressing to tertiary...A metropolitan city such as Los Angeles (LA) is an ideal study site with a very high population density, and it houses at least 3 treatment plants where sewage is treated preliminarily and then progressing to tertiary treatment before discharging into the LA River. We will gain a better understanding of the water quality in the LA River and the nitrate load in the watershed system by examining the influence of waste water treatment plants (WWTPs). The goal of this study is to pinpoint the exact source of nitrate in the LA River using the isotope signatures. We have selected sampling locations both upstream and downstream of the WWTP. This serves to monitor nitrate levels, aiding in the assessment of treatment plant effectiveness, pinpointing nitrate pollution sources, and ensuring compliance with environmental regulations. The research explores the isotopic composition of NO3 in relation to atmospheric nitrogen and Vienna Standard Mean Ocean Water, shedding light on the contributions from various sources such as manure, sewage, soil organic nitrogen, and nitrogen fertilizers. Specifically, there is a change in the δ15NAir value between the dry and wet seasons. The isotope values in the Tillman WWTP sample changed between dry and wet seasons. Notably, the presence of nitrate originating from manure and sewage is consistent across seasons, emphasizing the significant impact of anthropogenic and agricultural activities on water quality. This investigation contributes to the broader understanding of nitrogen cycling in urban water bodies, particularly in the context of wastewater effluent discharge. The findings hold implications for water quality management and highlight the need for targeted interventions to mitigate the impact of nitrogen-containing compounds on aquatic ecosystems. Overall, the study provides a valuable framework for future research and environmental stewardship efforts aimed at preserving the health and sustainability of urban water resources. This data informs decisions regarding additional treatment or mitigation actions to safeguard downstream water quality and ecosystem health.展开更多
Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence ...Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study,we sequenced 149 largemouth bass fish, including protospecies(imported from the US) and improved breeds(four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection,including several associated with growth(psst1 and grb10), early development(klf9, sp4, and sp8), and immune traits(pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.展开更多
Understanding the sensitivity of tidal flats to environmental changes is challenging.Currently,most studies rely on process-based models to systematically explain the morphodynamic evolution of tidal flats.In this stu...Understanding the sensitivity of tidal flats to environmental changes is challenging.Currently,most studies rely on process-based models to systematically explain the morphodynamic evolution of tidal flats.In this study,we proposed an alternative empirical approach to explore tidal flat dynamics using statistical indices based on long-term time series of daily surface elevation development.Surface elevation dynamic(SED)indices focus on the magnitude and period of surface elevation changes,while morphodynamic signature(MDS)indices relate sediment dynamics to environmental drivers.The statistical analyses were applied to an intervention site in the Netherlands to determine the effect of recently constructed groynes on the tidal flat.Using these analyses,we were able to(1)detect a reduction in the daily SED and(2)determine that the changes in the daily SED were predominantly caused by the reduction in wave impact between the groynes rather than the reduction in tidal currents.Overall,the presented results showed that the combination of novel statistical indices provides new insights into the trajectories of tidal flats,ecosystem functioning,and sensitivity to physical drivers(wind and tides).Finally,we suggested how the SED and MDS indices may help to explore the future trajectories and climate resilience of intertidal habitats.展开更多
Hazelnut(Corylus spp.)is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits.However,hazelnut promotion worldwide is increasingly challenged by global climate chan...Hazelnut(Corylus spp.)is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits.However,hazelnut promotion worldwide is increasingly challenged by global climate change,limiting its production to a few regions.Focusing on the eurytopic Section Phyllochlamys,we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement.Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background,and highlighted the differentiation between European and Asian lineages.Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns,and multiple environmental factors have contributed to the lineage divergence.Whole-genome scans identified 279,111,and 164 selective sweeps that underlie local adaptation in Corylus heterophylla,Corylus kweichowensis,and Corylus yunnanensis,respectively.Relevant positively selected genes were mainly involved in regulating signaling pathways,growth and development,and stress resistance.The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes,when compared to C.heterophylla and Corylus avellana,respectively,including those that regulate protein polymerization,photosynthesis,and response to water deprivation.Among these loci,22 candidate genes were highly associated with the regulation of biological quality.Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments,and offers valuable resources for future climate-resilient breeding.展开更多
The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some ...The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits.In the present study,we performed extended haplotype homozygosity(EHH)tests to identify significant core regions in 202 Jinhua pigs.A total of 26161 core regions spanning 636.42 Mb were identified,which occupied approximately 28%of the genome across all autosomes,and 1158 significant(P<0.01)core haplotypes were selected.Genes in these regions were related to several economically important traits,including meat quality,reproduction,immune responses and exterior traits.A panel of genes including ssc-mir-365-2,KDM8,RABEP2,GSG1L,RHEB,RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values.The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome,and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.展开更多
Humans can sense, weigh and grasp different objects, deduce their physical properties at the same time, and exert appropriate forces – a challenging task for modern robots. Studying the mechanics of human grasping ob...Humans can sense, weigh and grasp different objects, deduce their physical properties at the same time, and exert appropriate forces – a challenging task for modern robots. Studying the mechanics of human grasping objects will play a supplementary role in visual-based robot object processing. These tools require large-scale tactile data sets with high spatial resolution. However, there is no large human-grasped tactile data set covering the whole hand, because dense coverage of the human hand with tactile sensors is challenging. Hence, the capability of observing and learning from successful daily humanobject interactions is the long-term goal of aiding the development of robots and prosthetics.展开更多
The intricate “orchestered molecular conversation” between the host and gut microbiome is one of the most dynamic research areas in recent years. The rhythmic chemical cross talk in the form of bioactive metabolites...The intricate “orchestered molecular conversation” between the host and gut microbiome is one of the most dynamic research areas in recent years. The rhythmic chemical cross talk in the form of bioactive metabolites and signalling molecules synthesized by gut microbiome plays a significant role for the modulation of human health in diversified ways. They are recognized as low molecular weight (LMW) molecules having versatile chemical attributes. They possess magnificent capability of interacting with surrounding environment and controlling the genes for various genetic, biochemical and physiological functions for maintaining the homeostasis that is now-a-days termed as “small molecules microbes originated (SMOM) homeostasis” in the host. These metabolic signatures have close structural and functional resemblance with small molecules synthesized by host eukaryotic cells and dietary components. Therefore, they may be considered as universalized metabolites contributing to the remarkable phenomenon of epigenetic regulation, cell to cell communication and stability of genome manifesting the overall growth and development of the host and known as “metabiotics”. The wide panorama of utilization of probiotics is continuously expanding and conferring the major health benefits through metabiotic components are gaining tremendous momentum therefore recognized as “hidden soldiers” of the body. Therefore firstly, we outline the need and types of metabiotic molecules and depicting their role in human health. Then, we summarize their preventive and therapeutic avenues in various diseases and finally, we propose the current technological interventions, bottlenecks and future perspectives in this field that are implied for accelerating their comprehensive understanding and utilization at industrial scale.展开更多
This paper presents two systems for recognizing static signs (digits) from American Sign Language (ASL). These systems avoid the use color marks, or gloves, using instead, low-pass and high-pass filters in space and f...This paper presents two systems for recognizing static signs (digits) from American Sign Language (ASL). These systems avoid the use color marks, or gloves, using instead, low-pass and high-pass filters in space and frequency domains, and color space transformations. First system used rotational signatures based on a correlation operator;minimum distance was used for the classification task. Second system computed the seven Hu invariants from binary images;these descriptors fed to a Multi-Layer Perceptron (MLP) in order to recognize the 9 different classes. First system achieves 100% of recognition rate with leaving-one-out validation and second experiment performs 96.7% of recognition rate with Hu moments and 100% using 36 normalized moments and k-fold cross validation.展开更多
Information on rare earth elements(REEs)in soils and plants of the Qinghai-Tibet Plateau is very limited.Therefore,in this study,we performed field sampling to explore the geochemical signatures and human health risk ...Information on rare earth elements(REEs)in soils and plants of the Qinghai-Tibet Plateau is very limited.Therefore,in this study,we performed field sampling to explore the geochemical signatures and human health risk of REEs in soils and plants of the northeastern Qinghai-Tibet Plateau,China.A total of 127 soil samples and 127 plant samples were collected from the northeastern Qinghai-Tibet Plateau to acquire the geochemical signatures and related human health risks of REEs.The mean total concentrations of REEs in soils and plants of the study area reached 178.55 and 10.06 mg/kg,respectively.The light REEs in soils and plants accounted for 76%and 77%of the total REEs,respectively.REEs showed significantly homogenous distribution in soils but inhomogeneous distribution in plants of the study area.Characteristic parameters indicated that light REEs were enriched and fractionated significantly,while heavy REEs were moderately fractionated in soils and plants.REEs in soils and plants showed significantly negative Europium anomaly.Cerium showed slightly positive anomaly in plants and slight anomaly in soils.The normalized distribution patterns of REEs were generally similar in the analyzed soils and the corresponding plants of the study area.The average bio-concentration factor of REEs ranged from 0.0478(Scandium)to 0.0604(Europium),confirming a small accumulation of REEs by plants.Health risks caused by REEs in soils and plants were negligible,while risks for adults were lower than those for children.This study provides important information on REEs in soils and plants of the northeastern Qinghai-Tibet Plateau.展开更多
Several generations of mafic dyke swarms(2.7 to 0.8Ga),highlighted by aeromagnetic data,petrography,geochemistry,isotope geology and mostly U-Pb baddeleyite ages,crosscut the Archean
While the mutational processes that subsume biological diversity can be revealed in great detail through phylogenetic inferencing using plastid markers, few studies document their use. Accurate phylogenic inference ca...While the mutational processes that subsume biological diversity can be revealed in great detail through phylogenetic inferencing using plastid markers, few studies document their use. Accurate phylogenic inference can provide a framework for addressing a host of important evolutionary questions including a context to reconstruct molecular evolution of an organism. Despite the obvious utility of plastid markers in illuminating biological enquiry, many important questions still abound. The use of cp-DNA gene sequence data for phylogenetic inference can have an enormous impact on plant phylogenetics and systematics. The repertoire of genetic diversity of Kenya’s Gene Bank repositories can be explored based on cp-genome signatures. This is because cp-DNA-based mutational changes are an important additional tool to the previous evidence available on plant evolution yet to be explored in biodiversity studies in Kenya. Taken together, these evolutionary changes can inspire development of realistic algorithms for phylogenetic inferencing based on molecular data. Phylogenetic reconstructions are at the very core of molecular evolution. Comparative sequence analyses of plastid markers can have utility beyond the study of phylogeny. The pattern of nucleotide substitution observed over evolutionary time can reflect functional constraints imposed due to natural selection. In line with this, it is possible to detect subtle anatomical variations associated with small fitness effects that can account for genetic diversity at varietal level. The lack of sequence information in Kenyan cowpea has limited the robust advancement of molecular markers use in dissecting diversity based on the putative plastid markers?[1]. The present study sought to generate and upscale novel technologies such as genomics, DNA barcoding and bio-informatics in understanding molecular diversity of cowpea accessions from the Gene Bank of Kenya and ecotypes. A total of 298 sequences of cowpea germplasm conserved as in situ and ex situ in Kenya but sourced from phylogeographically diverse settings were examined and their genetic profiles were characterized and evaluated using molecular tools. The Gene Bank materials were purposefully sampled to develop subsets representative of the diversity in the genepool’s collection. We present an extensive study on characterizing the genetic diversity of cp-DNA gene sequence data for the cowpea accessions from the Nation Gene Bank of Kenya. The comparative sequence analyses and phylogenetic clustering of seven plastid markers widely used in the DNA barcoding of land plants provide insights on the molecular evolution of this vascular plant. The detailed and in-depth genome characterization herein greatly enriches the genetic profile of this important crop, which can help in reconstructing realistic models of mutational process during plant evolutionary history. This study addressed this gap by employing a DNA barcode library for cowpea to determine the loci that yield the best species resolution. As well, this study examined the efficacy of custom DNA barcode loci for identification success, and compared phylogenetic diversity measures between sites and among variants.展开更多
MicroRNAs have emerged as one of the major classes of non-coding RNAs. Recent reports have placed them in high abundance in the nervous system, having key roles in development. Neurological disorders such as Parkinson...MicroRNAs have emerged as one of the major classes of non-coding RNAs. Recent reports have placed them in high abundance in the nervous system, having key roles in development. Neurological disorders such as Parkinson’s disease, Alzheimer’s disease as well as Huntington disease have also been studied and several microRNAs associated with diseases pathogenesis have been identified. Various such findings indicate differential expression levels of many of these microRNAs. Such changes in the expression levels not only indicate towards a control of the biogenesis of these microRNAs but also indicate towards critical yet unelucidated roles of regulatory proteins, which probably act in concert to control the production or maturation of these molecules. In this work, a collection of overrepresented regulatory motif signatures were identified in the DNA and RNA sequences of the precursor microRNAs. The identification of such regulatory sequence signatures promises to provide new insights into many facets of microRNA regulation and neurological disorders.展开更多
This paper presents a new algorithm for generation of attack signatures based on sequence alignment. The algorithm is composed of two parts: a local alignment algorithm-GASBSLA (Generation of Attack Signatures Based o...This paper presents a new algorithm for generation of attack signatures based on sequence alignment. The algorithm is composed of two parts: a local alignment algorithm-GASBSLA (Generation of Attack Signatures Based on Sequence Local Alignment) and a multi-sequence alignment algorithm-TGMSA (Tri-stage Gradual Multi-Sequence Alignment). With the inspiration of sequence alignment used in Bioinformatics, GASBSLA replaces global alignment and constant weight penalty model by local alignment and affine penalty model to improve the generality of attack signatures. TGMSA presents a new pruning policy to make the algorithm more insensitive to noises in the generation of attack signatures. In this paper, GASBSLA and TGMSA are described in detail and validated by experiments.展开更多
We communicate many difficulties that we encounter when attempting to pinpoint a common origin for the several observed anomalies[1;2] or assessing their tension with existing exclusion limits. These include systemati...We communicate many difficulties that we encounter when attempting to pinpoint a common origin for the several observed anomalies[1;2] or assessing their tension with existing exclusion limits. These include systematics affecting the operation of the detectors, our knowledge of their response, astrophysical uncertainties, and the broad range of particle couplings that can mediate the interaction with a detector target. The interesting astrophysical evidence[2] that motivates a search for dark-photon and focuses our attention on a Hidden Valleys model with a GeV-scale dark sector that produces exciting signatures. Results from the recent underground experiments[1] are also considered.展开更多
We present a new fair blind signature scheme based on the fundamental properties of quantum mechanics.In addition,we analyse the security of this scheme,and show that it is not possible to forge valid blind signatures...We present a new fair blind signature scheme based on the fundamental properties of quantum mechanics.In addition,we analyse the security of this scheme,and show that it is not possible to forge valid blind signatures.Moreover,comparisons between this scheme and public key blind signature schemes are also discussed.展开更多
Fourier-transform infrared(FTIR) spectroscopy has emerged as a viable alternative to biochemical and molecular biology techniques for bacterial typing with advantages such as short analysis time, low cost and laborato...Fourier-transform infrared(FTIR) spectroscopy has emerged as a viable alternative to biochemical and molecular biology techniques for bacterial typing with advantages such as short analysis time, low cost and laboratorial simplicity. In this study, synchrotron radiationbased FTIR(SR-FTIR) spectroscopy with higher spectral quality was successfully applied to type 16 foodborne pathogenic bacterial strains. Combined with principal component analysis(PCA) and hierarchical cluster analysis(HCA), we found that the specific spectral region1300-1000 cm^(-1), which reflects the information of phosphate compounds and polysaccharides, can be used as the signature region to cluster the strains into groups similar with genetic taxonomic method. These findings demonstrated that FTIR spectra combined with HCA have a great potential in quickly typing bacteria depending on their biochemical signatures.展开更多
We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotate...We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.展开更多
基金supported by Croatian Science Foundation project IP-2018–01-8708-Application of NGS methods in the assessment of genomic variability in ruminants–“ANAGRAMS”the EU Operational Program Competitiveness and Cohesion 2014–2020 project KK.01.1.1.04.0058—Potential of microencapsulation in cheese productionthe project No.QK1919156 of the Ministry of Agriculture,Czech Republic.
文摘Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental conditions.Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production type.Results We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important traits.Most candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment analysis.Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.
基金supported by the Doctoral Fund of Jining No.1 People’s Hospital(2021-BS-002).
文摘Colorectal cancer(CRC)belongs to the class of significantly malignant tumors found in humans.Recently,dysregulated fatty acid metabolism(FAM)has been a topic of attention due to its modulation in cancer,specifically CRC.However,the regulatory FAM pathways in CRC require comprehensive elucidation.Methods:The clinical and gene expression data of 175 fatty acid metabolic genes(FAMGs)linked with colon adenocarcinoma(COAD)and normal cornerstone genes were gathered through The Cancer Genome Atlas(TCGA)-COAD corroborating with the Molecular Signature Database v7.2(MSigDB).Initially,crucial prognostic genes were selected by uni-and multi-variate Cox proportional regression analyses;then,depending upon these identified signature genes and clinical variables,a nomogram was generated.Lastly,to assess tumor immune characteristics,concomitant evaluation of tumor immune evasion/risk scoring were elucidated.Results:A 8-gene signature,including ACBD4,ACOX1,CD36,CPT2,ELOVL3,ELOVL6,ENO3,and SUCLG2,was generated,and depending upon this,CRC patients were categorized within high-risk(H-R)and low-risk(L-R)cohorts.Furthermore,risk and age-based nomograms indicated moderate discrimination and good calibration.The data confirmed that the 8-gene model efficiently predicted CRC patients’prognosis.Moreover,according to the conjoint analysis of tumor immune evasion and the risk scorings,the H-R cohort had an immunosuppressive tumor microenvironment,which caused a substandard prognosis.Conclusion:This investigation established a FAMGs-based prognostic model with substantially high predictive value,providing the possibility for improved individualized treatment for CRC individuals.
文摘A metropolitan city such as Los Angeles (LA) is an ideal study site with a very high population density, and it houses at least 3 treatment plants where sewage is treated preliminarily and then progressing to tertiary treatment before discharging into the LA River. We will gain a better understanding of the water quality in the LA River and the nitrate load in the watershed system by examining the influence of waste water treatment plants (WWTPs). The goal of this study is to pinpoint the exact source of nitrate in the LA River using the isotope signatures. We have selected sampling locations both upstream and downstream of the WWTP. This serves to monitor nitrate levels, aiding in the assessment of treatment plant effectiveness, pinpointing nitrate pollution sources, and ensuring compliance with environmental regulations. The research explores the isotopic composition of NO3 in relation to atmospheric nitrogen and Vienna Standard Mean Ocean Water, shedding light on the contributions from various sources such as manure, sewage, soil organic nitrogen, and nitrogen fertilizers. Specifically, there is a change in the δ15NAir value between the dry and wet seasons. The isotope values in the Tillman WWTP sample changed between dry and wet seasons. Notably, the presence of nitrate originating from manure and sewage is consistent across seasons, emphasizing the significant impact of anthropogenic and agricultural activities on water quality. This investigation contributes to the broader understanding of nitrogen cycling in urban water bodies, particularly in the context of wastewater effluent discharge. The findings hold implications for water quality management and highlight the need for targeted interventions to mitigate the impact of nitrogen-containing compounds on aquatic ecosystems. Overall, the study provides a valuable framework for future research and environmental stewardship efforts aimed at preserving the health and sustainability of urban water resources. This data informs decisions regarding additional treatment or mitigation actions to safeguard downstream water quality and ecosystem health.
基金supported by the Key-Area Research and Development Program of Guangdong Province(2021B0202020001)China Agriculture Research System of MOF and MARA(CARS-46)+2 种基金Central Public-interest Scientific Institution Basal Research Fund of CAFS(2020TD23,2020ZJTD-02)Project of Construction of Guangdong Aquatic Seed Industry Demonstration Base 2021Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(KJYF202101-02)。
文摘Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study,we sequenced 149 largemouth bass fish, including protospecies(imported from the US) and improved breeds(four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection,including several associated with growth(psst1 and grb10), early development(klf9, sp4, and sp8), and immune traits(pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
基金supported by the Royal Netherlands Academy of Arts and Sciences(KNAW)(Grant No.PSA-SA-E-02)the Province of Zeeland,the Netherlands(Grant No.CoE-Buitendijks)。
文摘Understanding the sensitivity of tidal flats to environmental changes is challenging.Currently,most studies rely on process-based models to systematically explain the morphodynamic evolution of tidal flats.In this study,we proposed an alternative empirical approach to explore tidal flat dynamics using statistical indices based on long-term time series of daily surface elevation development.Surface elevation dynamic(SED)indices focus on the magnitude and period of surface elevation changes,while morphodynamic signature(MDS)indices relate sediment dynamics to environmental drivers.The statistical analyses were applied to an intervention site in the Netherlands to determine the effect of recently constructed groynes on the tidal flat.Using these analyses,we were able to(1)detect a reduction in the daily SED and(2)determine that the changes in the daily SED were predominantly caused by the reduction in wave impact between the groynes rather than the reduction in tidal currents.Overall,the presented results showed that the combination of novel statistical indices provides new insights into the trajectories of tidal flats,ecosystem functioning,and sensitivity to physical drivers(wind and tides).Finally,we suggested how the SED and MDS indices may help to explore the future trajectories and climate resilience of intertidal habitats.
基金Thisworkwas supported by the National Natural Science Foundation of China(32101541)the Key Research and Development Program of Hebei Province(21326804D).
文摘Hazelnut(Corylus spp.)is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits.However,hazelnut promotion worldwide is increasingly challenged by global climate change,limiting its production to a few regions.Focusing on the eurytopic Section Phyllochlamys,we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement.Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background,and highlighted the differentiation between European and Asian lineages.Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns,and multiple environmental factors have contributed to the lineage divergence.Whole-genome scans identified 279,111,and 164 selective sweeps that underlie local adaptation in Corylus heterophylla,Corylus kweichowensis,and Corylus yunnanensis,respectively.Relevant positively selected genes were mainly involved in regulating signaling pathways,growth and development,and stress resistance.The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes,when compared to C.heterophylla and Corylus avellana,respectively,including those that regulate protein polymerization,photosynthesis,and response to water deprivation.Among these loci,22 candidate genes were highly associated with the regulation of biological quality.Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments,and offers valuable resources for future climate-resilient breeding.
基金supported by the Key Technology R&D Program of China(2016C02054-2)the National Natural Science Foundation of China(31872976)。
文摘The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits.In the present study,we performed extended haplotype homozygosity(EHH)tests to identify significant core regions in 202 Jinhua pigs.A total of 26161 core regions spanning 636.42 Mb were identified,which occupied approximately 28%of the genome across all autosomes,and 1158 significant(P<0.01)core haplotypes were selected.Genes in these regions were related to several economically important traits,including meat quality,reproduction,immune responses and exterior traits.A panel of genes including ssc-mir-365-2,KDM8,RABEP2,GSG1L,RHEB,RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values.The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome,and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.
文摘Humans can sense, weigh and grasp different objects, deduce their physical properties at the same time, and exert appropriate forces – a challenging task for modern robots. Studying the mechanics of human grasping objects will play a supplementary role in visual-based robot object processing. These tools require large-scale tactile data sets with high spatial resolution. However, there is no large human-grasped tactile data set covering the whole hand, because dense coverage of the human hand with tactile sensors is challenging. Hence, the capability of observing and learning from successful daily humanobject interactions is the long-term goal of aiding the development of robots and prosthetics.
文摘The intricate “orchestered molecular conversation” between the host and gut microbiome is one of the most dynamic research areas in recent years. The rhythmic chemical cross talk in the form of bioactive metabolites and signalling molecules synthesized by gut microbiome plays a significant role for the modulation of human health in diversified ways. They are recognized as low molecular weight (LMW) molecules having versatile chemical attributes. They possess magnificent capability of interacting with surrounding environment and controlling the genes for various genetic, biochemical and physiological functions for maintaining the homeostasis that is now-a-days termed as “small molecules microbes originated (SMOM) homeostasis” in the host. These metabolic signatures have close structural and functional resemblance with small molecules synthesized by host eukaryotic cells and dietary components. Therefore, they may be considered as universalized metabolites contributing to the remarkable phenomenon of epigenetic regulation, cell to cell communication and stability of genome manifesting the overall growth and development of the host and known as “metabiotics”. The wide panorama of utilization of probiotics is continuously expanding and conferring the major health benefits through metabiotic components are gaining tremendous momentum therefore recognized as “hidden soldiers” of the body. Therefore firstly, we outline the need and types of metabiotic molecules and depicting their role in human health. Then, we summarize their preventive and therapeutic avenues in various diseases and finally, we propose the current technological interventions, bottlenecks and future perspectives in this field that are implied for accelerating their comprehensive understanding and utilization at industrial scale.
文摘This paper presents two systems for recognizing static signs (digits) from American Sign Language (ASL). These systems avoid the use color marks, or gloves, using instead, low-pass and high-pass filters in space and frequency domains, and color space transformations. First system used rotational signatures based on a correlation operator;minimum distance was used for the classification task. Second system computed the seven Hu invariants from binary images;these descriptors fed to a Multi-Layer Perceptron (MLP) in order to recognize the 9 different classes. First system achieves 100% of recognition rate with leaving-one-out validation and second experiment performs 96.7% of recognition rate with Hu moments and 100% using 36 normalized moments and k-fold cross validation.
基金the One Hundred Talents Program of Chinese Academy of Sciences(Y610061033)the Kunlun Talent Action Plan of Qinghai Province,China(E140WX42)+2 种基金the Science and Technology Plan Protect of Qinghai Province,China(2021-ZJ-T07)the Taishan Scholar Program of Shandong Province,China(tsqn201812116)the Two-Hundred Talents Plan of Yantai City of Shandong Province,China。
文摘Information on rare earth elements(REEs)in soils and plants of the Qinghai-Tibet Plateau is very limited.Therefore,in this study,we performed field sampling to explore the geochemical signatures and human health risk of REEs in soils and plants of the northeastern Qinghai-Tibet Plateau,China.A total of 127 soil samples and 127 plant samples were collected from the northeastern Qinghai-Tibet Plateau to acquire the geochemical signatures and related human health risks of REEs.The mean total concentrations of REEs in soils and plants of the study area reached 178.55 and 10.06 mg/kg,respectively.The light REEs in soils and plants accounted for 76%and 77%of the total REEs,respectively.REEs showed significantly homogenous distribution in soils but inhomogeneous distribution in plants of the study area.Characteristic parameters indicated that light REEs were enriched and fractionated significantly,while heavy REEs were moderately fractionated in soils and plants.REEs in soils and plants showed significantly negative Europium anomaly.Cerium showed slightly positive anomaly in plants and slight anomaly in soils.The normalized distribution patterns of REEs were generally similar in the analyzed soils and the corresponding plants of the study area.The average bio-concentration factor of REEs ranged from 0.0478(Scandium)to 0.0604(Europium),confirming a small accumulation of REEs by plants.Health risks caused by REEs in soils and plants were negligible,while risks for adults were lower than those for children.This study provides important information on REEs in soils and plants of the northeastern Qinghai-Tibet Plateau.
文摘Several generations of mafic dyke swarms(2.7 to 0.8Ga),highlighted by aeromagnetic data,petrography,geochemistry,isotope geology and mostly U-Pb baddeleyite ages,crosscut the Archean
文摘While the mutational processes that subsume biological diversity can be revealed in great detail through phylogenetic inferencing using plastid markers, few studies document their use. Accurate phylogenic inference can provide a framework for addressing a host of important evolutionary questions including a context to reconstruct molecular evolution of an organism. Despite the obvious utility of plastid markers in illuminating biological enquiry, many important questions still abound. The use of cp-DNA gene sequence data for phylogenetic inference can have an enormous impact on plant phylogenetics and systematics. The repertoire of genetic diversity of Kenya’s Gene Bank repositories can be explored based on cp-genome signatures. This is because cp-DNA-based mutational changes are an important additional tool to the previous evidence available on plant evolution yet to be explored in biodiversity studies in Kenya. Taken together, these evolutionary changes can inspire development of realistic algorithms for phylogenetic inferencing based on molecular data. Phylogenetic reconstructions are at the very core of molecular evolution. Comparative sequence analyses of plastid markers can have utility beyond the study of phylogeny. The pattern of nucleotide substitution observed over evolutionary time can reflect functional constraints imposed due to natural selection. In line with this, it is possible to detect subtle anatomical variations associated with small fitness effects that can account for genetic diversity at varietal level. The lack of sequence information in Kenyan cowpea has limited the robust advancement of molecular markers use in dissecting diversity based on the putative plastid markers?[1]. The present study sought to generate and upscale novel technologies such as genomics, DNA barcoding and bio-informatics in understanding molecular diversity of cowpea accessions from the Gene Bank of Kenya and ecotypes. A total of 298 sequences of cowpea germplasm conserved as in situ and ex situ in Kenya but sourced from phylogeographically diverse settings were examined and their genetic profiles were characterized and evaluated using molecular tools. The Gene Bank materials were purposefully sampled to develop subsets representative of the diversity in the genepool’s collection. We present an extensive study on characterizing the genetic diversity of cp-DNA gene sequence data for the cowpea accessions from the Nation Gene Bank of Kenya. The comparative sequence analyses and phylogenetic clustering of seven plastid markers widely used in the DNA barcoding of land plants provide insights on the molecular evolution of this vascular plant. The detailed and in-depth genome characterization herein greatly enriches the genetic profile of this important crop, which can help in reconstructing realistic models of mutational process during plant evolutionary history. This study addressed this gap by employing a DNA barcode library for cowpea to determine the loci that yield the best species resolution. As well, this study examined the efficacy of custom DNA barcode loci for identification success, and compared phylogenetic diversity measures between sites and among variants.
文摘MicroRNAs have emerged as one of the major classes of non-coding RNAs. Recent reports have placed them in high abundance in the nervous system, having key roles in development. Neurological disorders such as Parkinson’s disease, Alzheimer’s disease as well as Huntington disease have also been studied and several microRNAs associated with diseases pathogenesis have been identified. Various such findings indicate differential expression levels of many of these microRNAs. Such changes in the expression levels not only indicate towards a control of the biogenesis of these microRNAs but also indicate towards critical yet unelucidated roles of regulatory proteins, which probably act in concert to control the production or maturation of these molecules. In this work, a collection of overrepresented regulatory motif signatures were identified in the DNA and RNA sequences of the precursor microRNAs. The identification of such regulatory sequence signatures promises to provide new insights into many facets of microRNA regulation and neurological disorders.
文摘This paper presents a new algorithm for generation of attack signatures based on sequence alignment. The algorithm is composed of two parts: a local alignment algorithm-GASBSLA (Generation of Attack Signatures Based on Sequence Local Alignment) and a multi-sequence alignment algorithm-TGMSA (Tri-stage Gradual Multi-Sequence Alignment). With the inspiration of sequence alignment used in Bioinformatics, GASBSLA replaces global alignment and constant weight penalty model by local alignment and affine penalty model to improve the generality of attack signatures. TGMSA presents a new pruning policy to make the algorithm more insensitive to noises in the generation of attack signatures. In this paper, GASBSLA and TGMSA are described in detail and validated by experiments.
文摘We communicate many difficulties that we encounter when attempting to pinpoint a common origin for the several observed anomalies[1;2] or assessing their tension with existing exclusion limits. These include systematics affecting the operation of the detectors, our knowledge of their response, astrophysical uncertainties, and the broad range of particle couplings that can mediate the interaction with a detector target. The interesting astrophysical evidence[2] that motivates a search for dark-photon and focuses our attention on a Hidden Valleys model with a GeV-scale dark sector that produces exciting signatures. Results from the recent underground experiments[1] are also considered.
基金Project supported by the National Natural Science Foundation of China (Grant Nos.60873191,60903152 and 60821001)the Specialized Research Fund for the Doctoral Program of Higher Education (Grant No.200800131016)+5 种基金Beijing Nova Program (Grant No.2008B51)Key Project of the Chinese Ministry of Education (Grant No.109014)the Natural Science Foundation of Beijing (Grant No.4072020)China Postdoctoral Science Foundation (Grant No.20090450018)the Natural Science Foundation of the Education Bureau of Henan Province of China (Grant No.2010B120008)the Youth Foundation of Luoyang Normal University
文摘We present a new fair blind signature scheme based on the fundamental properties of quantum mechanics.In addition,we analyse the security of this scheme,and show that it is not possible to forge valid blind signatures.Moreover,comparisons between this scheme and public key blind signature schemes are also discussed.
基金supported by the National Natural Science Foundation of China(Nos.U1732130 and 11474298)Key Research Program of Frontier Sciences of the Chinese Academy Sciences(No.QYZDJSSW-SLH019)
文摘Fourier-transform infrared(FTIR) spectroscopy has emerged as a viable alternative to biochemical and molecular biology techniques for bacterial typing with advantages such as short analysis time, low cost and laboratorial simplicity. In this study, synchrotron radiationbased FTIR(SR-FTIR) spectroscopy with higher spectral quality was successfully applied to type 16 foodborne pathogenic bacterial strains. Combined with principal component analysis(PCA) and hierarchical cluster analysis(HCA), we found that the specific spectral region1300-1000 cm^(-1), which reflects the information of phosphate compounds and polysaccharides, can be used as the signature region to cluster the strains into groups similar with genetic taxonomic method. These findings demonstrated that FTIR spectra combined with HCA have a great potential in quickly typing bacteria depending on their biochemical signatures.
基金supported by the grants from the Sichuan Science and Technology Program,China(2020YFN0024)the earmarked fund for the China Agriculture Research System(CARS-35-01A)+2 种基金the National Key R&D Program of China(2018YFD0501204)the National Natural Science Foundation of China(C170102)the Sichuan Innovation Team of Pig,China(sccxtd-2021-08)。
文摘We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.
