Evolution and customisation of the RegCM model for urban climate studies:Addressing multifaceted challenges and advancing climate science

The Regional Climate Model(RegCM)proves valuable for climate analysis and has been applied to a wide range of climate change aspects and other environmental issues at a regional scale.The model also demonstrated success in diverse areas of urban research,including urban heat island studies,extreme climate events analysis,assessing urban resilience,and evaluating urbanization impacts on climate and air quality.Recently,more studies have been conducted in utilizing RegCM to address climate change in cities,due to its enhanced ability over the years to capture meteorological phenomena at city scales.However,there are many challenges associated with its implementation in meso-scale research,which are attributed to various shortcomings and thus create room for further improvement in the model.This paper presents a comprehensive overview of the evolution of the RegCM over the years and its customisation across various parameters,demonstrating its versatility in urban climate studies and underscoring the model’s pivotal role in addressing multifaceted challenges in urban environments.By addressing these aspects,the paper offers valuable insights and recommendations for researchers seeking to enhance the accuracy and efficacy of urban climate simulations using the RegCM system,thereby contributing to the advancement of urban climate science and sustainability.

Fabrication and Applications of Micro/Nanostructured Devices for Tissue Engineering

Nanotechnology allows the realization of new materials and devices with basic structural unit in the range of1–100 nm and characterized by gaining control at the atomic, molecular, and supramolecular level. Reducing the dimensions of a material into the nanoscale range usually results in the change of its physiochemical properties such as reactivity,crystallinity, and solubility. This review treats the convergence of last research news at the interface of nanostructured biomaterials and tissue engineering for emerging biomedical technologies such as scaffolding and tissue regeneration. The present review is organized into three main sections. The introduction concerns an overview of the increasing utility of nanostructured materials in the field of tissue engineering. It elucidates how nanotechnology, by working in the submicron length scale, assures the realization of a biocompatible interface that is able to reproduce the physiological cell–matrix interaction. The second, more technical section, concerns the design and fabrication of biocompatible surface characterized by micro- and submicroscale features, using microfabrication, nanolithography, and miscellaneous nanolithographic techniques.In the last part, we review the ongoing tissue engineering application of nanostructured materials and scaffolds in different fields such as neurology, cardiology, orthopedics, and skin tissue regeneration.

Untargeted metabolomics analysis of four date palm(Phoenix dactylifera L.)cultivars using MS and NMR

Since ancient times,the inhabitants of dry areas have depended on the date palm(Phoenix dactylifera L.)as a staple food and means of economic security.For example,dates have been a staple diet for the inhabitants of the Arabian Peninsula and Sahara Desert in North Africa for millennia and the local culture is rich in knowledge and experience with the benefits of dates,suggesting that dates contain many substances essential for the human body.Madinah dates are considered one of the most important types of dates in the Arabian Peninsula,with Ajwa being one of the most famous types and grown only in Madinah,Saudi Arabia.Date seeds are traditionally used for animal feed,seed oil production,cosmetics,and as a coffee substitute.Phytochemical compounds that have been detected in date fruits and date seeds include phenolic acids,carotenoids,and flavonoids.Phenolic acids are the most prevalent bioactive constituents that contribute to the antioxidant activity of date fruits.The bioactive properties of these phytochemicals are believed to promote human health by reducing the risk of diseases such as chronic inflammation.Ajwa dates especially are thought to have superior bioactivity properties.To investigate these claims,in this study,we compare the metabolic profiles of Ajwa with different types of dates collected from Saudi Arabia and Tunisia.We show by UHPLC-MS that date seeds contain several classes of flavonoids,phenolic acids,and amino acid derivatives,including citric acid,malic acid,lactic acid,and hydroxyadipic acid.Additionally,GC-MS profiling showed that date seeds are richer in metabolite classes,such as hydrocinnamic acids(caffeic,ferulic and sinapic acids),than flesh samples.Deglet N fruit extract(minimum inhibitory concentration:27 MIC/μM)and Sukkari fruit extract(IC_(50):479±0.58μg/mL)have higher levels of antibacterial and antioxidative activity than Ajwa fruits.However,the seed analysis showed that seed extracts have better bioactivity effects than fruit extracts.Specifically,Ajwa extract showed the best MIC and strongest ABTS radical-scavenging activity among examined seed extracts(minimum inhibitory concentration:20μM;IC_(50):54±3.61μg/mL).Our assays are a starting point for more advanced in vitro antibacterial models and investigation into the specific molecules that are responsible for the antioxidative and anti-bacterial activities of dates.

考虑融雪及土壤冻融的新安江模型及其应用——以雅砻江上游径流模拟为例

寒区为中国大江大河的主要产流区,其径流预报精度直接影响下游水利工程调度和水资源科学管理。针对传统概念性水文模型较少考虑积雪融雪及土壤冻融过程对径流的叠加影响这一问题,以新安江模型为基础,以降水量和气温为驱动数据,提出了基于“等效土壤温度”和“土壤冻融特征曲线”的概念性土壤冻融模块来刻画积雪融雪及土壤冻融共同影响下的流域产流过程,构建了考虑融雪产流和土壤冻融的新安江模型。以雅砻江甘孜水文站以上流域为典型研究区,开展了流域2017—2022年冰雪消融期逐小时的径流模拟分析。结果表明,相比于HBV模型,考虑融雪产流和土壤冻融的模型可以显著提升流域冰雪消融期的水文模拟精度,各年份消融期径流的纳什效率系数中位数由0.69提升至0.83,相关系数中位数由0.88上升至0.92。本研究所提出的考虑融雪及土壤冻融的新安江模型可以为寒区的水文业务预报提供科学支撑。

Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection

Currently,the most cost-effective and efficient method for phosphorus(P)removal from wastewater is enhanced biological P removal(EPBR)via polyphosphate-accumulating organisms(PAOs).This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment.The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment.Notably,Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates,possess specific enzymes for ATP production from polyphosphate,and have electrochemical transporters for acetate and C4-dicarboxylates.In contrast,Tetrasphaera,Candidatus Phosphoribacter,Knoellia,and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids.Additionally,this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants.Notably,FISH-Raman spectroscopy emerges as one of the most advanced detection techniques.Overall,this review provides critical insights into PAO research,underscoring the need for enhanced strategies in biological phosphorus removal.

The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

基于多源数据的黄河源区降雪比变化及其影响因素

黄河源区是黄河流域关键产流区域,对气候变化十分敏感。在气候变暖背景下,降水形态转变及其影响因素的研究依然不足。围绕这一重要科学问题,本研究基于地面气象站点观测和多源高分辨率气象数据集[China Meteorological Forcing Dataset(CMFD)、ECWMF ERA5-Land(ERA5-Land)、Multi-Source Weather(MSWX)],采用湿球温度参数化模型对1980—2015年黄河源区降水形态进行区分,并对降雪比长期变化趋势及其影响因素进行了综合研究。结果表明,1980—2015年黄河源区降水量整体呈增加趋势,降水形态向降雨转变,降雪量减少,平均降雪比呈显著下降趋势(P<0.05),四套数据源的降雪比平均下降速率为0.002 a^(-1)(P<0.05)。降雪比呈显著下降趋势(P<0.05)的格点占比分别为98.31%(ERA5-Land)、96.87%(MSWX)、67.62%(CMFD)。黄河源区中西部降雪比下降速率较快,下降速率最大的地区为玛多、达日等地。三套格点产品中CMFD能够较好地呈现降雪比变化趋势的空间差异,MSWX次之,而ERA5-Land降雪比变化趋势空间变异较小。源区降雪比与年平均气温、降水量相关性较高(P<0.05),相关系数r分别为-0.42和-0.48,亦受到西风的影响(r=-0.31,P=0.07)。研究结果有助于加深气候变暖对黄河源区水文气象过程影响的科学认识,为黄河流域区域水资源管理提供理论支撑。

Lactate-mediated medium-chain fatty acid production from expired dairy and beverage waste

Fruits,vegetables,and dairy products are typically the primary sources of household food waste.Currently,anaerobic digestion is the most used bioprocess for the treatment of food waste with concomitant generation of biogas.However,to achieve a circular carbon economy,the organics in food waste should be converted to new chemicals with higher value than energy.Here we demonstrate the feasibility of medium-chain carboxylic acid(MCCA)production from expired dairy and beverage waste via a chain elongation platform mediated by lactate.In a two-stage fermentation process,the first stage with optimized operational conditions,including varying temperatures and organic loading rates,transformed expired dairy and beverage waste into lactate at a concentration higher than 900 mM C at 43℃.This lactate was then used to produce>500 mM C caproate and>300 mM C butyrate via microbial chain elongation.Predominantly,lactate-producing microbes such as Lactobacillus and Lacticaseibacillus were regulated by temperature and could be highly enriched under mesophilic conditions in the firststage reactor.In the second-stage chain elongation reactor,the dominating microbes were primarily from the genera Megasphaera and Caproiciproducens,shaped by varying feed and inoculum sources.Cooccurrence network analysis revealed positive correlations among species from the genera Caproiciproducens,Ruminococcus,and CAG-352,as well as Megasphaera,Bacteroides,and Solobacterium,indicating strong microbial interactions that enhance caproate production.These findings suggest that producing MCCAs from expired dairy and beverage waste via lactate-mediated chain elongation is a viable method for sustainable waste management and could serve as a chemical production platform in the context of building a circular bioeconomy.

Environmental Stress and Pre-mRNA Splicing

Pre-mRNA splicing is an important step for gene expression regulation in plants in response to abiotic stress. In recent years, RNA sequencing （RNA-seq） based on various next-generation sequencing technologies has been used to study dynamic changes of pre-mRNA splicing under conditions of diverse abiotic stress in several plant species. Accumulating results indi- cate that alternative splicing （AS） of pre-mRNA is closely linked with environmental stress response in plants.

Compliant lightweight non-invasive standalone“Marine Skin”tagging system

Current marine research primarily depends on weighty and invasive sensory equipment and telemetric network to understand the marine environment,including the diverse fauna it contains,as a function of animal behavior and size,as well as equipment longevity.To match animal morphology and activity within the surrounding marine environment,here we show a physically flexible and stretchable skin-like and waterproof autonomous multifunctional system,integrating Bluetooth,memory chip,and high performance physical sensors.The sensory tag is mounted on a swimming crab(Portunus pelagicus)and is capable of continuous logging of depth,temperature,and salinity within the harsh ocean environment.The fully packaged,ultra-lightweight(<2.4 g in water),and compliant“Marine Skin”system does not have any wired connection enabling safe and weightless cuttingedge approach to monitor and assess marine life and the ecosystem’s health to support conservation and management of marine ecosystems.

Alkaloids as potential antivirals.A comprehensive review

Alkaloids are a diverse group of natural phytochemicals.These phytochemicals in plants provide them protection against pests,and herbivorous organisms and also control their development.Numerous of these alkaloids have a variety of biological effects,and some have even been developed into medications with different medicinal properties.This review aims to provide a broad overview of the numerous naturally occurring alkaloids(isolated from both terrestrial and aquatic species)along with synthetically produced alkaloid compounds having prominent antiviral properties.Previous reviews on this subject have focused on the biological actions of both natural and synthetic alkaloids,but they have not gone into comprehensive detail about their antiviral properties.We reviewed here several antiviral alkaloids that have been described in the literature in different investigational environments i.e.(in-vivo,in-ovo,in-vitro,and in-silico),and found that these alkaloid compounds have significant antiviral properties against several infectious viruses.These alkaloids repressed and targeted various important stages of viral infection at non-toxic doses while some of the alkaloids reported here also exhibited comparable inhibitory activities to commercially used drugs.Overall,these anti-viral effects of alkaloids point to a high degree of specificity,implying that they could serve as effective and safe antiviral medicines if further pursued in medicinal and pharmacological investigations.

Simultaneous dual-contrast three-dimensional imaging in live cells via optical diffraction tomography and fluorescence

We report a dual-contrast method of simultaneously measuring and visualizing the volumetric structural information in live biological samples in three-dimensional(3D) space. By introducing a direct way of deriving the 3D scattering potential of the object from the synthesized angular spectra, we obtain the quantitative subcellular morphology in refractive indices(RIs) side-by-side with its fluorescence signals. The additional contrast in RI complements the fluorescent signal, providing additional information of the targeted zones. The simultaneous dual-contrast 3D mechanism unveiled interesting information inaccessible with previous methods, as we demonstrated in the human immune cell(T cell) experiment. Further validation has been demonstrated using a Monte Carlo model.

抽油泵固定凡尔球运动规律的数值模拟

固定凡尔是抽油泵的主要部件之一,其中固定凡尔球的运动规律决定了泵内流体的吸入过程。为研究固定凡尔球的运动规律,采用COMSOL Multiphysics数值模拟软件,建立了多物理场耦合模型;运用动网格技术和接触压力方法,解决了固定凡尔球运动、启闭引起的网格质量和触壁反弹的问题。分析了冲次、泵内流体粘度对固定凡尔球运动规律的影响。结果表明:冲次对固定凡尔球上升的稳定性有较大影响,黏度对固定凡尔球升程影响更为显著。

QAUST:Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.

ROS and Lipid Droplet accumulation induced by high glucose exposure in healthy colon and Colorectal Cancer Stem Cells

Lipid Droplets(LDs)are emerging as crucial players in colon cancer development and maintenance.Their expression has been associated with high tumorigenicity in Cancer Stem Cells(CSCs),so that they have been proposed as a new functional marker in Colorectal Cancer Stem Cells(CR-CSCs).They are also indirectly involved in the modulation of the tumor microenvironment through the production of pro-inflammatory molecules.There is growing evidence that a possible connection between metabolic alterations and malignant transformation exists,although the effects of nutrients,primarily glucose,on the CSC behavior are still mostly unexplored.Glucose is an essential fuel for cancer cells,and the connections with LDs in the healthy and CSC populations merit to be more deeply investigated.Here,we showed that a high glucose concentration activated the PI3K/AKT pathway and increased the expression of CD133 and CD44v6 CSC markers.Additionally,glucose was responsible for the increased amount of Reactive Oxygen Species(ROS)and LDs in both healthy and CR-CSC samples.We also investigated the gene modulations following the HG treatment and found out that the healthy cell gene profile was the most affected.Lastly,Atorvastatin,a lipidlowering drug,induced the highest mortality on CR-CSCs without affecting the healthy counterpart.

有杆抽油泵固定凡尔球开启时间规律研究

有杆抽油泵的固定凡尔控制抽油泵的吸入过程,其固定凡尔球的打开程度与开启时间对合理调整抽油机工作制度有至关重要的作用。为此建立抽油泵固定凡尔球的流固耦合模型,运用动网格技术和接触压力方法,实现了上冲程阶段固定凡尔球的运动过程,解决了凡尔球在流体域中接触其他固体壁面产生的拓扑结构变化问题,并在此基础上得到了各影响因素下固定凡尔球的打开程度与所需开启时间的变化规律曲线。数值模拟的结果为抽油机工作制度的合理优化提供了理论参考。

Installing the neurospora carotenoid pathway in plants enables cytosolic formation of provitamin A and its sequestration in lipid droplets

Vitamin A deficiency remains a severe global health issue,which creates a need to biofortify crops with provitamin A carotenoids(PACs).Expanding plant cell capacity for synthesis and storing of PACs outside the plastids is a promising biofortification strategy that has been little explored.Here,we engineered PAC formation and sequestration in the cytosol of Nicotiana benthamiana leaves,Arabidopsis seeds,and citrus callus cells,using a fungal(Neurospora crassa)carotenoid pathway that consists of only three enzymes converting C5 isopentenyl building blocks formed from mevalonic acid into PACs,including β-carotene.This strategy led to the accumulation of significant amounts of phytoene and γ-and β-carotene,in addition to fungal,health-promoting carotenes with 13 conjugated double bonds,such as the PAC torulene,in the cytosol.Increasing the isopentenyl diphosphate pool by adding a truncated Arabidopsis hydroxymethylglutaryl-coenzyme A reductase substantially increased cytosolic carotene production.Engineered carotenes accumulate in cytosolic lipid droplets(CLDs),which represent a novel sequestering sink for storing these pigments in plant cytosol.Importantly,β-carotene accumulated in the cytosol of citrus callus cells was more light stable compared to compared with plastidialβ-carotene.Moreover,engineering cytosolic carotene formation increased the number of large-sized CLDs and the levels of β-apocarotenoids,including retinal,the aldehyde corresponding to vitamin A.Collectively,our study opens up the possibility of exploiting the high-flux mevalonic acid pathway for PAC biosynthesis and enhancing carotenoid sink capacity in green and non-green plant tissues,especially in lipid-storing seeds,and thus paves the way for further optimization of carotenoid biofortification in crops.

Efficient Mimics for Elucidating Zaxinone Biology and Promoting Agricultural Applications

Zaxinone is an apocarotenoid regulatory metabolite required for normal rice growth and development.In addition,zaxinone has a large application potential in agriculture,due to its growth-promoting activity and capability to alleviate infestation by the root parasitic plant Striga through decreasing strigolactone(SL)production.However,zaxinone is poorly accessible to the scientific community because of its laborious organic synthesis that impedes its further investigation and utilization.In this study,we developed easy-to-synthesize and highly efficient mimics of zaxinone(MiZax).We performed a structure-activity relationship study using a series of apocarotenoids distinguished from zaxinone by different structural features.Using the obtained results,we designed several phenyl-based compounds synthesized with a high-yield through a simple method.Activity tests showed that MiZax3 and MiZax5 exert zaxinone activity in rescuing root growth of a zaxinone-deficient rice mutant,promoting growth,and reducing SL content in roots and root exudates of wild-type plants.Moreover,these compounds were at least as efficient as zaxinone in suppressing transcript level of SL biosynthesis genes and in alleviating Striga infestation under greenhouse conditions,and did not negatively impact mycorrhization.Taken together,MiZax are a promising tool for elucidating zaxinone biology and investigating rice development,and suitable candidates for combating Striga and increasing crop growth.

Astroglial anatomy in the times of connectomics

In contrast to neurons, the role of astro-cytes has been matter of debate since their discovery, and mostly because of misconceptions about their role. As a consequence, technologies to study brain physiology have been designed around neurons, to answer one specifc question, leaving glia experts with the only possibility to “hack” these techniques to describe astrocytes. As questions to answer about astrocytic functioning are based on factual observations, conclusions are often vague and cryptic, no matter how technically sound the work is. For instance, compelling evidence on calcium elevations has been provided, their dynamics have been studied in detail, but their role is still open for interpretation. Another as-trocytic feature that carries a lot of mysteries is their com-plex morphology. The use of three-dimensional electron microscopy （3DEM） would most certainly be the best approach to unveil hidden features of such complex cells, nevertheless so far 3DEM hasn’t been fully exploited in that sense, nor techniques has been adapted for astrocytic observations in particular. One of the most ambitious neuroscience projects, the connectome, is pushing to their limits electron microscopy, image segmentation and 3D reconstruction and analysis, making it a very good candi-date to adapt pipelines and methodologies to the study of astrocytic morphology. Here, we briefy review our current knowledge and technical state of art on 3D glia morphology, and speculate about its future directions.

Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics:An Engineering Head Start

Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multidisciplinary nature of the field.To facilitate their use,here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput.First,a device encapsulating single cells in droplets at a rate of~250 Hz is described considering droplet size and cell growth.Then,we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers(i.e.,405,488,561,and 637 nm)in a single platform to make it compatible with different fluorescence-emitting biosensors.For this sorter,both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz.Then,a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz.Finally,we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools.Because of the overall integration and the technical details presented here,our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability(>50,000 cells/day)for mining and bioprospecting metagenomic data.