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Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 295-307 doi: 10.15302/J-FASE-2016126

摘要： Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

关键词： cassava     comparative transcriptomics     energy transport     photosynthesis     starch synthesis    

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Transcriptomics and proteomics in stem cell research

null

《医学前沿（英文）》 2014年 第8卷 第4期   页码 433-444 doi: 10.1007/s11684-014-0336-0

摘要：

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

关键词： embryonic stem cells     transcriptomics     proteomics    

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Sepsis biomarkers: an omics perspective

null

《医学前沿（英文）》 2014年 第8卷 第1期   页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 72-88 doi: 10.1007/s11705-016-1580-4

摘要： Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of overexpression in an industrial strain of WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that , and were upregulated in all conditions. Then the three genes were over-expressed in WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.

关键词： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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The Development and Comparative Analysis of Engineering Project Management Modes

Ji-wei Zhu,Li-nan Zhou,Ming-yuan Yu,Zhao Zhai

《工程管理前沿（英文）》 2015年 第2卷 第4期   页码 351-358 doi: 10.15302/J-FEM-2015060

摘要： Engineering project management is the whole process of project construction management activities up to the point of achieving the goals of engineering construction, which adopts the means of planning, organizing, leading, and controlling. In addition, engineering project management modes are the works of project management and the technical guarantee of project success. For the quality and efficient transformation demands of the Chinese construction industry in the process of marketization, internationalization and informatization, based on the connotation and development path of engineering project management modes, the 16 main and new kinds of project management modes both domestically and abroad are divided into trading mode, financing mode and management mode. These have led to comparative analysis and brief commentary. Finally, it will be pointed out that the engineering project management modes move throughout the whole management process, the combined model and the expansion development of financing model. This work will provide reference for project participants to choose the appropriate project management modes and better understand building company transformation.

关键词： engineering projects     management mode     comparative analysis     development trend    

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Last Planner System and Scrum: Comparative analysis and suggestions for adjustments

Roshan POUDEL, Borja GARCIA de SOTO, Eder MARTINEZ

《工程管理前沿（英文）》 2020年 第7卷 第3期   页码 359-372 doi: 10.1007/s42524-020-0117-1

摘要： This study provides a critical review of the concepts of Agile, Lean, Scrum, and Last Planner System (LPS). A comparative analysis is conducted between LPS and Scrum to expand LPS by considering Scrum’s best practices. Eight dimensions, namely, 1) origins, 2) main purpose, 3) overall system/framework process, 4) tools or artifacts maintained by the team, 5) team composition and main roles, 6) regular events or team meetings, 7) metrics/dashboards, and 8) approach to learning, are evaluated. After analyzing side by side the eight dimensions, it was found that many aspects from Scrum already exist in LPS in the same or similar form. However, the authors identify four main elements from Scrum that can be leveraged to improve the LPS benchmark, such as considering the Scrum “Increment” concept into LPS, having a clear definition of roles and responsibilities, or adding an equivalent to a Scrum Master to have a designated “rule keeper” in LPS. These opportunities to be considered in new LPS benchmarks need to be tested and validated with real applications. To the best of the authors’ knowledge, this work is the first to comprehensively compare Scrum (Agile) and LPS (Lean) and could be seen as a contribution toward the evolution of the Last Planner System for the academic and industrial environments.

关键词： Lean Construction     Last Planner System     Agile     Scrum     comparative analysis     AEC projects     project teams    

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Comparative lipidomic analysis of

Bin QIAO, Hong-Chi TIAN, Ying-Jin YUAN

《化学科学与工程前沿（英文）》 2012年 第6卷 第4期   页码 461-469 doi: 10.1007/s11705-012-1223-3

摘要： Variations in the composition and level of phospholipids (PLs) in yeast cells during industrial ethanol fermentation processes were analyzed. A comparative lipidomic method was used to investigate the changes in total cellular PLs during continuous and fed-batch/batch processes. The phospholipid metabolism in yeast changed during both processes, mainly due to the presence of long-chain poly unsaturated fatty acids (PUFA) that contained phosphatidyglycerol (PG), phosphatidylethanolamine (PE) and phosphatidylserine (PS). The complexity of the media affected the growth of the yeast and the membrane composition. Yeast incorporated lots of exogenous saturated and PUFAs from the feedstock during the fermentations. During the continuous fermentation, there was an increase in PLs with shorter chains as the fermentation progressed and early in process there were more long-chains. During the fed-batch/batch process, the PG species increased as the fermentation progressed. This is probably due to an inositol deficiency in the earlier part of the fermentation.

关键词： lipidomics     systems biology     phospholipids     stirred-tank     saccharomyces cerevisiae     biorefinery engineering    

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Layer-like FAU-type zeolites: A comparative view on different preparation routes

Bastian Reiprich, Tobias Weissenberger, Wilhelm Schwieger, Alexandra Inayat

《化学科学与工程前沿（英文）》 2020年 第14卷 第2期   页码 127-142 doi: 10.1007/s11705-019-1883-3

摘要： The creation of intergrown layer-like zeolite crystals is one route to form hierarchical zeolites. Faujasite-type (FAU-type) zeolites are among the industrially most important zeolites and the implementation of hierarchical porosity is a promising way to optimise their catalytic and adsorptive performance. After a short general survey into routes for the preparation of hierarchical pore systems in FAU, we will review the currently existing strategies for the synthesis of FAU with layer-like morphology. Those strategies are mainly based on the presence of morphology modifying agents in the synthesis mixture. However, a very recent approach is the synthesis of layer-like FAU-type zeolite crystals assembled in an intergrown manner in the absence of such additives, just by finely adjusting the crystallization temperature. This additive-free preparation route for layer-like FAU, which appears very attractive from an ecological as well as economic point of view, is highlighted in this review. Concluding, a comparison, including powder X-ray diffraction, scanning and transmission electron microscopy, nitrogen physisorption and elemental analysis, between conventional FAU and three layer-like FAU obtained by different synthesis routes was carried out to show the structural, morphological and textural differences and similarities of these materials.

关键词： FAU     hierarchical zeolite     layer-like morphology    

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Robotic distal pancreatectomy versus conventional laparoscopic distal pancreatectomy: a comparative study

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 356-360 doi: 10.1007/s11684-015-0404-0

摘要：

Robotic system has been increasingly used in pancreatectomy. However, the effectiveness of this method remains uncertain. This study compared the surgical outcomes between robot-assisted laparoscopic distal pancreatectomy and conventional laparoscopic distal pancreatectomy. During a 15-year period, 35 patients underwent minimally invasive approach of distal pancreatectomy in our center. Seventeen of these patients had robot-assisted laparoscopic approach, and the remaining 18 had conventional laparoscopic approach. Their operative parameters and perioperative outcomes were analyzed retrospectively in a prospective database. The mean operating time in the robotic group (221.4 min) was significantly longer than that in the laparoscopic group (173.6 min) (P = 0.026). Both robotic and conventional laparoscopic groups presented no significant difference in spleen-preservation rate (52.9% vs. 38.9%) (P = 0.505), operative blood loss (100.3 ml vs. 268.3 ml) (P = 0.29), overall morbidity rate (47.1% vs. 38.9%) (P = 0.73), and post-operative hospital stay (11.4 days vs. 14.2 days) (P = 0.46). Both groups also showed no perioperative mortality. Similar outcomes were observed in robotic distal pancreatectomy and conventional laparoscopic approach. However, robotic approach tended to have the advantages of less blood loss and shorter hospital stay. Further studies are necessary to determine the clinical position of robotic distal pancreatectomy.

关键词： distal pancreatectomy     pancreatic neoplasm     robotic surgery    

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The current phosphate recycling situation in China and Germany: a comparative review

null

《农业科学与工程前沿（英文）》 2019年 第6卷 第4期   页码 403-418 doi: 10.15302/J-FASE-2019287

摘要：

Phosphorus (P) is an indispensable element for organisms but the primary source of P—mineral phosphate resources—are non-renewable. Agricultural production has a high demand for fossil phosphate resources, but the resulting phosphate-rich residues are lack of management. This leads to rapid reserves depletion and severe phosphate pollution risks. One sustainable way is to reuse the phosphate dispersed in various residues such as sewage sludge and livestock manure. Diverse techniques have emerged to recover phosphate from wastes to close the phosphate cycle. While it is a global issue, the regional situations regarding potential phosphate scarcity and its management differ strongly. China is rich in phosphate resources, but over-exploitation has greatly increased the risk of phosphate rocks depletion, while in Germany the P resources depend on imports, but there is commitment to keep a balance between import and utilization. This had led to great differences in the way the two countries deal with the “re-use” of phosphate in waste. China is now in a transition phase from the simple terminal pollution control to “waste” reuse and nutrient resources recycling. One sign of this tendency is the mandatory garbage classification and preparation for further processing and recycling. This was first implemented in Shanghai in 2019, whereas Germany has been following the legal framework for waste management since the 19th century. There are a series of laws to control the nutrient loss from municipal and agricultural activities, as for instance with sewage sludge ordinance and fertilizer legislation. Many of these laws have been newly revised recently. Sewage sludge cannot be directly utilized on farmland as organic fertilizer any more. Alternatively, phosphate and other nutrients should be recovered from sewage sludge. Advanced phosphate recovery technologies and related nutrient recycling schemes are proceeding. This review summarizes the current situation of phosphate-containing residues management and phosphate reuse in China and Germany. The state legislation and policies, which would affect the phosphate recycling concept are presented as well. As there are various kinds of phosphate-containing residues, different phosphate recovery technologies can be applied. Those technologies are discussed from their mechanism and suitability.

关键词： phosphate recovery     manure     sewage sludge     ordinances     technologies    

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医学专业目录设置的国际比较及对策研究

余中光,张鹏俊,张知新,王辰

《中国工程科学》 2020年 第22卷 第1期   页码 139-145 doi: 10.15302/J-SSCAE-2020.01.018

摘要：

医学专业目录设置对于促进医学学科发展、培养合格的医学人才具有重要意义，在高等院校实施一流学科建设的背景下，健全、科学的专业目录显得尤为重要。为助力我国医学学科发展，本文运用文献分析法梳理了我国医学专业设置现状，系统比较了中国、美国、英国的医学专业目录类别与特点。研究发现，当前我国医学专业目录设置存在专业目录不统一、专业设置数量和内容相对滞后、临床医学专业过早专科化、与住院医师规范化培训专业目录衔接不畅等问题；建议采取统一医学专业目录、丰富学科内涵、体现交叉学科特点、建立规范的医学专业准入和退出机制等举措，推进医学专业目录与国际接轨，为培养合格、规范的医学人才提供路径指引。

关键词： 医学     专业目录     临床医学     比较分析    

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A comparative study of electroacupuncture at Zhongliao (BL33) and other acupoints for overactive bladder

null

《医学前沿（英文）》 2017年 第11卷 第1期   页码 129-136 doi: 10.1007/s11684-016-0491-6

摘要：

Electroacupuncture (EA) at Zhongliao (BL33) can improve the symptoms of overactive bladder (OAB), such as urinary frequency, urgency, and incontinence. However, its performance compared with other acupoints remains unclear. This study investigated the effects of EA at BL33 with deep needling on rats with OAB by detecting urodynamics in eight groups: no intervention group, D-BL33 group (deep needling at BL33), S-BL33 group (shallow needling at BL33), non-acupoint group (needling at the non-acupoint next to BL33), Weizhong (BL40) group, Sanyinjiao (SP6) group, Tongtian (BL7) group, and Hegu (LI4) group. Results revealed that EA at BL33 with deep needling, BL40, and SP6 prolonged the intercontraction interval (ICI) of rats with OAB (P=0.001, P=0.005, P=0.046, respectively, post-treatment vs. post-modeling). Furthermore, the change in ICI from post-modeling in the D-BL33 group was significantly greater than those of the no intervention and other EA groups (all P<0.01). Significantly shortened vesical micturition time (VMT) and elevated maximum detrusor pressure (MDP) were also observed in the D-BL33 group (P=0.017 and P=0.024, respectively, post-treatment vs. post-modeling). However, no statistically significant differences in the changes of VMT and MDP from post-modeling were observed between D-BL33 and the other EA groups. In conclusion, EA at BL33 with deep needling may inhibit acetic-acid-induced OAB more effectively.

关键词： overactive bladder     electroacupuncture     acupuncture points    

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Experimental investigation and comparative study of inter-turn short-circuits and unbalanced voltage

Fatima BABAA, Abdelmalek KHEZZAR, Mohamed el kamel OUMAAMAR

《能源前沿（英文）》 2013年 第7卷 第3期   页码 271-278 doi: 10.1007/s11708-013-0258-6

摘要： A transient model for an induction machine with stator winding turn faults on a single phase is derived using reference frame transformation theory. The negative sequence component and the 3rd harmonic are often considered as accurate indicators. However, small unbalance in the supply voltage and/or in the machine structure that exists in any real system engenders the same harmonics components. In this case, it is too difficult to distinguish between the current harmonics due to the supply voltage and those originated by inter-turn short-circuit faults. For that, to have the correct diagnosis and to increase the sensitivity and the reliability of the diagnostic system, it is crucial to provide the relationship between the inter-turn short-circuits in the stator winding and the supply voltage imbalance through an accurate mathematical model and via a series of experimental essays.

关键词： induction machines     fault indicator     inter-turn short-circuit fault     unbalance supply voltage    

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Peridynamics versus XFEM: a comparative study for quasi-static crack problems

Jinhai ZHAO, Hesheng TANG, Songtao XUE

《结构与土木工程前沿（英文）》 2018年 第12卷 第4期   页码 548-557 doi: 10.1007/s11709-017-0434-6

摘要： Peridynamics (PD) is a nonlocal continuum theory based on integro-differential equations without spatial derivatives. The fracture criterion is implicitly incorporated in the PD theory and fracture is a natural outcome of the simulation. However, capturing of complex mixed-mode crack patterns has been proven to be difficult with PD. On the other hand, the extended finite element method (XFEM) is one of the most popular methods for fracture which allows crack propagation with minimal remeshing. It requires a fracture criterion which is independent of the underlying discretization though a certain refinement is needed in order to obtain suitable results. This article presents a comparative study between XFEM and PD. Therefore, two examples are studied. The first example is crack propagation in a double notched specimen under uniaxial tension with different crack spacings in loading direction. The second example is the specimens with two center cracks. The results show that PD as well as XFEM are well suited to capture this type of behaviour.

关键词： XFEM     peridynamic     bilateral crack     parallel double cracks     nonlocal theory    

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The comparative study of dwelling houses in the southwest multi-ethnic region, taking Fugong county for

Fang WANG, Jiaping LIU

《结构与土木工程前沿（英文）》 2010年 第4卷 第4期   页码 474-482 doi: 10.1007/s11709-010-0089-z

摘要： A number of ethnic minorities are being distributed in southwest China. Yunnan Province is an area inhabited by multi-ethnic groups. For a long time, the ethnic groups have been interacted by others in the cultural aspect, while retaining their own ethnic traditions. The performances of ethnic groups’ dwelling houses are similar as determined by natural and cultural elements of the same area. This paper mainly analyzes decisive factors behind similar appearances by the way of field research on two minorities, Nu ethnic group and Li-su ethnic group, in the Fugong county, Nujiang Li-su autonomous prefecture. Moreover, the paper tries to summarize the commonality and individuality of the minorities in order to provide useful theoretical reference for the minorities building of new socialist countryside in the future.

关键词： Nu ethnic group     Li-su ethnic group     mixed region     living culture     living mode     living acts    

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标题 作者 时间 类型 操作

Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

期刊论文

Transcriptomics and proteomics in stem cell research

null

期刊论文

Sepsis biomarkers: an omics perspective

null

期刊论文

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

期刊论文

The Development and Comparative Analysis of Engineering Project Management Modes

Ji-wei Zhu,Li-nan Zhou,Ming-yuan Yu,Zhao Zhai

期刊论文

Last Planner System and Scrum: Comparative analysis and suggestions for adjustments

Roshan POUDEL, Borja GARCIA de SOTO, Eder MARTINEZ

期刊论文

Comparative lipidomic analysis of

Bin QIAO, Hong-Chi TIAN, Ying-Jin YUAN

期刊论文

Layer-like FAU-type zeolites: A comparative view on different preparation routes

Bastian Reiprich, Tobias Weissenberger, Wilhelm Schwieger, Alexandra Inayat

期刊论文

Robotic distal pancreatectomy versus conventional laparoscopic distal pancreatectomy: a comparative study

null

期刊论文

The current phosphate recycling situation in China and Germany: a comparative review

null

期刊论文

医学专业目录设置的国际比较及对策研究

余中光,张鹏俊,张知新,王辰

期刊论文

A comparative study of electroacupuncture at Zhongliao (BL33) and other acupoints for overactive bladder

null

期刊论文

Experimental investigation and comparative study of inter-turn short-circuits and unbalanced voltage

Fatima BABAA, Abdelmalek KHEZZAR, Mohamed el kamel OUMAAMAR

期刊论文

Peridynamics versus XFEM: a comparative study for quasi-static crack problems

Jinhai ZHAO, Hesheng TANG, Songtao XUE

期刊论文

The comparative study of dwelling houses in the southwest multi-ethnic region, taking Fugong county for

Fang WANG, Jiaping LIU

期刊论文