SwePub - search: WFRF:(Wang Zhi)

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1.	Klionsky, Daniel J, et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Journal article (peer-reviewed)
2.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
3.	Klionsky, Daniel J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Research review (peer-reviewed)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
4.	2019 Journal article (peer-reviewed)
5.	Kristan, Matej, et al. (author) The Sixth Visual Object Tracking VOT2018 Challenge Results 2019 In: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53 Conference paper (peer-reviewed)abstract The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
6.	You, Xiaohu, et al. (author) Towards 6G wireless communication networks: vision, enabling technologies, and new paradigm shifts 2021 In: Science China Information Sciences. - : Science Press. - 1674-733X .- 1869-1919. ; 64:1 Research review (peer-reviewed)abstract The fifth generation (5G) wireless communication networks are being deployed worldwide from 2020 and more capabilities are in the process of being standardized, such as mass connectivity, ultra-reliability, and guaranteed low latency. However, 5G will not meet all requirements of the future in 2030 and beyond, and sixth generation (6G) wireless communication networks are expected to provide global coverage, enhanced spectral/energy/cost efficiency, better intelligence level and security, etc. To meet these requirements, 6G networks will rely on new enabling technologies, i.e., air interface and transmission technologies and novel network architecture, such as waveform design, multiple access, channel coding schemes, multi-antenna technologies, network slicing, cell-free architecture, and cloud/fog/edge computing. Our vision on 6G is that it will have four new paradigm shifts. First, to satisfy the requirement of global coverage, 6G will not be limited to terrestrial communication networks, which will need to be complemented with non-terrestrial networks such as satellite and unmanned aerial vehicle (UAV) communication networks, thus achieving a space-air-ground-sea integrated communication network. Second, all spectra will be fully explored to further increase data rates and connection density, including the sub-6 GHz, millimeter wave (mmWave), terahertz (THz), and optical frequency bands. Third, facing the big datasets generated by the use of extremely heterogeneous networks, diverse communication scenarios, large numbers of antennas, wide bandwidths, and new service requirements, 6G networks will enable a new range of smart applications with the aid of artificial intelligence (AI) and big data technologies. Fourth, network security will have to be strengthened when developing 6G networks. This article provides a comprehensive survey of recent advances and future trends in these four aspects. Clearly, 6G with additional technical requirements beyond those of 5G will enable faster and further communications to the extent that the boundary between physical and cyber worlds disappears.
7.	Jin, Ying-Hui, et al. (author) Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version) 2020 In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1 Journal article (peer-reviewed)abstract The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
8.	Abbafati, Cristiana, et al. (author) 2020 Journal article (peer-reviewed)
9.	Chen, Zhi, et al. (author) Large-Area Crystalline Zeolitic Imidazolate Framework Thin Films 2021 In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 60:25, s. 14124-14130 Journal article (peer-reviewed)abstract We report that continuous MOF films with highly controlled thickness (from 44 to 5100 nm) can be deposited over length scales greater than 80 centimeters by a facile, fast, and cost-effective spray-coating method. Such success relies on our discovery of unprecedented perfectly dispersed colloidal solutions consisting of amorphous MOF nanoparticles, which we adopted as precursors that readily converted to the crystalline films upon low-temperature in situ heating. The colloidal solutions allow for the fabrication of compact and uniform MOF films on a great deal of substrates such as fluorine-doped tin oxide, glass, SiO2, Al2O3, Si, Cu, and even flexible polycarbonate, widening their technological applications where substrates are essential. Despite the present work focuses on the fabrication of uniform cobalt-(2-methylimidazole)2 and zinc-(2-methylimidazole)2 films, our findings mark a great possibility in producing other high-quality MOF thin films on a large scale.
10.	Ding, Xue Bing, et al. (author) Impaired meningeal lymphatic drainage in patients with idiopathic Parkinson’s disease 2021 In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 411-418 Journal article (peer-reviewed)abstract Animal studies implicate meningeal lymphatic dysfunction in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease (PD). However, there is no direct evidence in humans to support this role1–5. In this study, we used dynamic contrast-enhanced magnetic resonance imaging to assess meningeal lymphatic flow in cognitively normal controls and patients with idiopathic PD (iPD) or atypical Parkinsonian (AP) disorders. We found that patients with iPD exhibited significantly reduced flow through the meningeal lymphatic vessels (mLVs) along the superior sagittal sinus and sigmoid sinus, as well as a notable delay in deep cervical lymph node perfusion, compared to patients with AP. There was no significant difference in the size (cross-sectional area) of mLVs in patients with iPD or AP versus controls. In mice injected with α-synuclein (α-syn) preformed fibrils, we showed that the emergence of α-syn pathology was followed by delayed meningeal lymphatic drainage, loss of tight junctions among meningeal lymphatic endothelial cells and increased inflammation of the meninges. Finally, blocking flow through the mLVs in mice treated with α-syn preformed fibrils increased α-syn pathology and exacerbated motor and memory deficits. These results suggest that meningeal lymphatic drainage dysfunction aggravates α-syn pathology and contributes to the progression of PD.
11.	Pecunia, Vincenzo, et al. (author) Roadmap on energy harvesting materials 2023 In: Journal of Physics. - : IOP Publishing. - 2515-7639. ; 6:4 Journal article (peer-reviewed)abstract Ambient energy harvesting has great potential to contribute to sustainable development and address growing environmental challenges. Converting waste energy from energy-intensive processes and systems (e.g. combustion engines and furnaces) is crucial to reducing their environmental impact and achieving net-zero emissions. Compact energy harvesters will also be key to powering the exponentially growing smart devices ecosystem that is part of the Internet of Things, thus enabling futuristic applications that can improve our quality of life (e.g. smart homes, smart cities, smart manufacturing, and smart healthcare). To achieve these goals, innovative materials are needed to efficiently convert ambient energy into electricity through various physical mechanisms, such as the photovoltaic effect, thermoelectricity, piezoelectricity, triboelectricity, and radiofrequency wireless power transfer. By bringing together the perspectives of experts in various types of energy harvesting materials, this Roadmap provides extensive insights into recent advances and present challenges in the field. Additionally, the Roadmap analyses the key performance metrics of these technologies in relation to their ultimate energy conversion limits. Building on these insights, the Roadmap outlines promising directions for future research to fully harness the potential of energy harvesting materials for green energy anytime, anywhere.
12.	Wang, Peng, et al. (author) Depression-like behavior in rat: Involvement of galanin receptor subtype 1 in the ventral periaqueductal gray 2016 In: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 113:32, s. E4726-E4735 Journal article (peer-reviewed)abstract The neuropeptide galanin coexists in rat brain with serotonin in the dorsal raphe nucleus and with noradrenaline in the locus coeruleus (LC), and it has been suggested to be involved in depression. We studied rats exposed to chronic mild stress (CMS), a rodent model of depression. As expected, these rats showed several endophenotypes relevant to depression-like behavior compared with controls. All these endophenotypes were normalized after administration of a selective serotonin reuptake inhibitor. The transcripts for galanin and two of its receptors, galanin receptor 1 (GALR1) and GALR2, were analyzed with quantitative real-time PCR using laser capture microdissection in the following brain regions: the hippocampal formation, LC, and ventral periaqueductal gray (vPAG). Only Galr1 mRNA levels were significantly increased, and only in the latter region. After knocking down Galr1 in the vPAG with an siRNA technique, all parameters of the depressive behavioral phenotype were similar to controls. Thus, the depression-like behavior in rats exposed to CMS is likely related to an elevated expression of Galr1 in the vPAG, suggesting that a GALR1 antagonist could have antidepressant effects.
13.	He, Wei, et al. (author) China's Terrestrial Carbon Sink Over 2010–2015 Constrained by Satellite Observations of Atmospheric CO2 and Land Surface Variables 2022 In: Journal of Geophysical Research: Biogeosciences. - 2169-8953. ; 127:2 Journal article (peer-reviewed)abstract The magnitude and distribution of China's terrestrial carbon sink remain uncertain due to insufficient constraints at large scales, whereby satellite data offer great potential for reducing the uncertainty. Here, we present two carbon sink estimates for China constrained either by satellite CO2 column concentrations (XCO2) within the Global Carbon Assimilation System or by remotely sensed soil moisture and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) in addition to in situ CO2 observations within the Carbon Cycle Data Assimilation System. They point to a moderate size of carbon sinks of 0.34 ± 0.14 (mean ± unc.) and 0.43 ± 0.09 PgC/yr during 2010–2015, which are supported by an inventory-based estimate for forest and soil carbon sink (0.26 PgC/yr) and fall in the range of contemporary ensemble atmospheric inversions (0.25–0.48 PgC/yr). They also agree reasonably well on interannual variations, which reflect the carbon sink anomalies induced by regional droughts in southwest China. Furthermore, their spatial distributions are broadly consistent that of the forest inventory-based estimate, indicating that the largest carbon sinks locate in central and eastern China. Their estimates for forest carbon sink coincide fairly well with the inventory-based estimate across different regions, especially when aggregated to the north and south of China. Although enhanced recently by afforestation, China's carbon sink was also significantly weakened by regional droughts, which were often not fully represented in previous in situ CO2-based inversions due to insufficient observations. Our results suggest that satellite-based atmospheric CO2 and land surface observations are vital in characterizing terrestrial net carbon fluxes at regional scales.
14.	Liang, Lin, et al. (author) Non-Interpenetrated Single-Crystal Covalent Organic Frameworks 2020 In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 59:41, s. 17991-17995 Journal article (peer-reviewed)abstract Growth of covalent organic frameworks (COFs) as single crystals is extremely challenging. Inaccessibility of open-structured single-crystal COFs prevents the exploration of structure-oriented applications. Herein we report for the first time a non-interpenetrated single-crystal COF, LZU-306, which possesses the open structure constructed exclusively via covalent assembly. With a high void volume of 80 %, LZU-306 was applied to investigate the intrinsic dynamics of reticulated tetraphenylethylene (TPE) as the individual aggregation-induced-emission moiety. Solid-state(2)H NMR investigation has determined that the rotation of benzene rings in TPE, being the freest among the reported cases, is as fast as 1.0x10(4) Hz at 203 K to 1.5x10(7) Hz at 293 K. This research not only explores a new paradigm for single-crystal growth of open frameworks, but also provides a unique matrix-isolation platform to reticulate functional moieties into a well-defined and isolated state.
15.	Liu, Wei, et al. (author) Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride 2022 In: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1 Journal article (peer-reviewed)abstract Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
16.	Tang, Shi, et al. (author) Aggregation-Induced Emission by Molecular Design: A Route to High-Performance Light-Emitting Electrochemical Cells 2023 In: Angewandte Chemie - International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 62:23 Journal article (peer-reviewed)abstract The emission efficiency of organic semiconductors (OSCs) often suffers from aggregation caused quenching (ACQ). An elegant solution is aggregation-induced emission (AIE), which constitutes the design of the OSC so that its morphology inhibits quenching π–π interactions and non-radiative motional deactivation. The light-emitting electrochemical cell (LEC) can be sustainably fabricated, but its function depends on motion of bulky ions in proximity of the OSC. It is therefore questionable whether the AIE morphology can be retained during LEC operation. Here, we synthesize two structurally similar OSCs, which are distinguished by that 1 features ACQ while 2 delivers AIE. Interestingly, we find that the AIE-LEC significantly outperforms the ACQ-LEC. We rationalize our finding by showing that the AIE morphology remains intact during LEC operation, and that it can feature appropriately sized free-volume voids for facile ion transport and suppressed non-radiative excitonic deactivation.
17.	Wang, Jun-Zhi, et al. (author) An analytical study on artesian flow conditions in unconfined-aquifer drainage basins 2015 In: Water resources research. - : American Geophysical Union (AGU). - 0043-1397 .- 1944-7973. ; 51:10, s. 8658-8667 Journal article (peer-reviewed)abstract Although it has been reported that flowing artesian wells could be topographically controlled, there is no quantitative research on artesian flow conditions in unconfined aquifers. In this study, the water table, which has a lower amplitude than the land surface, is damped from the topography and used as the boundary condition to obtain the analytical solution of hydraulic head of a unit basin with a single flow system. The term artesian head is defined to characterize the condition of flowing artesian wells. The zone with positive artesian head is called artesian zone while with negative artesian head is nonartesian zone. The maximum artesian head and the size of artesian zones are found to increase with the damping factor and the anisotropy ratio, and decrease with the ratio of basin width to depth and the depth-decay exponent of hydraulic conductivity. Moreover, the artesian head increases with depth nearby the valley and decreases with depth near by the divide, and the variation rates are influenced by the decay exponent and the anisotropy ratio. Finally, the distribution of flowing artesian wells and the artesian head measurements in different depths of a borehole in a small catchment in the Ordos Plateau, Northwestern China is used to illustrate the theoretical findings. The change in artesian head with depth was used to estimate the anisotropy ratio and the decay exponent. This study opens up a new door to analyze basin-scale groundwater flow.
18.	Wang, Shi Zhi, et al. (author) Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds 2024 In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7 Journal article (peer-reviewed)abstract The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
19.	Wang, Yu-Cheng, et al. (author) Porous Carbon Membrane-Supported Atomically Dispersed Pyrrole-Type Fe-N-4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction 2020 In: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 16:31 Journal article (peer-reviewed)abstract The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-N-x sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-N-x single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type Fe-N-4 structure is identified as the real catalytic site in HzOR.
20.	Wuttke, Matthias, et al. (author) A catalog of genetic loci associated with kidney function from analyses of a million individuals 2019 In: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 51:6, s. 957-972 Journal article (peer-reviewed)abstract Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
21.	Zhang, Xiao-Jie, et al. (author) Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation 2024 In: Nature Structural & Molecular Biology. - : NATURE PORTFOLIO. - 1545-9993 .- 1545-9985. ; 31:1 Journal article (peer-reviewed)abstract DNA cytosine methylation plays a vital role in repressing retrotransposons, and such derepression is linked with developmental failure, tumorigenesis and aging. DNA methylation patterns are formed by precisely regulated actions of DNA methylation writers (DNA methyltransferases) and erasers (TET, ten-eleven translocation dioxygenases). However, the mechanisms underlying target-specific oxidation of 5mC by TET dioxygenases remain largely unexplored. Here we show that a large low-complexity domain (LCD), located in the catalytic part of Tet enzymes, negatively regulates the dioxygenase activity. Recombinant Tet3 lacking LCD is shown to be hyperactive in converting 5mC into oxidized species in vitro. Endogenous expression of the hyperactive Tet3 mutant in mouse oocytes results in genome-wide 5mC oxidation. Notably, the occurrence of aberrant 5mC oxidation correlates with a consequent loss of the repressive histone mark H3K9me3 at ERVK retrotransposons. The erosion of both 5mC and H3K9me3 causes ERVK derepression along with upregulation of their neighboring genes, potentially leading to the impairment of oocyte development. These findings suggest that Tet dioxygenases use an intrinsic auto-regulatory mechanism to tightly regulate their enzymatic activity, thus achieving spatiotemporal specificity of methylome reprogramming, and highlight the importance of methylome integrity for development. Here the authors show that TET dioxygenases, the erasers of DNA methylation, use a self-limiting mechanism via their LCD domain to ensure adaptable methylome status and protect the genome from excessive oxidative methylation.
22.	Zhao, Sen, et al. (author) Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders 2022 In: NPJ genomic medicine. - : Nature Publishing Group. - 2056-7944. ; 7:1 Journal article (peer-reviewed)abstract Pathogenic variants in MYH3 cause distal arthrogryposis type 2A and type 2B3 as well as contractures, pterygia and spondylocarpotarsal fusion syndromes types 1A and 1B. These disorders are ultra-rare and their natural course and phenotypic variability are not well described. In this study, we summarize the clinical features and genetic findings of 17 patients from 10 unrelated families with vertebral malformations caused by dominant or recessive pathogenic variants in MYH3. Twelve novel pathogenic variants in MYH3 (NM_002470.4) were identified: three of them were de novo or inherited in autosomal dominant way and nine were inherited in autosomal recessive way. The patients had vertebral segmentation anomalies accompanied with variable joint contractures, short stature and dysmorphic facial features. There was a significant phenotypic overlap between dominant and recessive MYH3-associated conditions regarding the degree of short stature as well as the number of vertebral fusions. All monoallelic variants caused significantly decreased SMAD3 phosphorylation, which is consistent with the previously proposed pathogenic mechanism of impaired canonical TGF-β signaling. Most of the biallelic variants were predicted to be protein-truncating, while one missense variant c.4244T>G,p.(Leu1415Arg), which was inherited in an autosomal recessive way, was found to alter the phosphorylation level of p38, suggesting an inhibition of the non-canonical pathway of TGF-β signaling. In conclusion, the identification of 12 novel pathogenic variants and overlapping phenotypes in 17 affected individuals from 10 unrelated families expands the mutation and phenotype spectrum of MYH3-associated skeletal disorders. We show that disturbances of canonical or non-canonical TGF-β signaling pathways are involved in pathogenesis of MYH3-associated skeletal fusion (MASF) syndrome.
23.	Zhao, ZH, et al. (author) Rapidly rising incidence of childhood type 1 diabetes in Chinese population: epidemiology in Shanghai during 1997-2011 2014 In: Acta diabetologica. - : Springer Science and Business Media LLC. - 1432-5233 .- 0940-5429. ; 51:6, s. 947-953 Journal article (peer-reviewed)
24.	Berndt, Sonja I., et al. (author) Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia 2016 In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7 Journal article (peer-reviewed)abstract Chronic lymphocytic leukemia (CLL) is a common lymphoid malignancy with strong heritability. To further understand the genetic susceptibility for CLL and identify common loci associated with risk, we conducted a meta-analysis of four genome-wide association studies (GWAS) composed of 3,100 cases and 7,667 controls with follow-up replication in 1,958 cases and 5,530 controls. Here we report three new loci at 3p24.1 (rs9880772, EOMES, P = 2.55 x 10(-11)), 6p25.2 (rs73718779, SERPINB6, P = 1.97 x 10(-8)) and 3q28 (rs9815073, LPP, P = 3.62 x 10(-8)), as well as a new independent SNP at the known 2q13 locus (rs9308731, BCL2L11, P = 1.00 x 10(-11)) in the combined analysis. We find suggestive evidence (P<5 x 10(-7)) for two additional new loci at 4q24 (rs10028805, BANK1, P = 7.19 x 10(-8)) and 3p22.2 (rs1274963, CSRNP1, P = 2.12 x 10(-7)). Pathway analyses of new and known CLL loci consistently show a strong role for apoptosis, providing further evidence for the importance of this biological pathway in CLL susceptibility.
25.	Bi, Zenghui, et al. (author) Highly dispersed La−O/N−C sites anchored in hierarchically porous nitrogen-doped carbon as bifunctional catalysts for high-performance rechargeable Zn−air batteries 2023 In: Energy Storage Materials. - : Elsevier. - 2405-8289 .- 2405-8297. ; 54, s. 313-322 Journal article (peer-reviewed)abstract Inexpensive, high-activity bifunctional catalysts for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are imperative for the development of energy storage and conversion systems. A nitrogen-doped carbon material with a micro−meso−macroporous structure doped with La (LaPNC) containing La−O/N−C active sites is prepared using SiO2 particle templating of carbon and a metal node exchange strategy. The coordination environment of La sites stabilized by two oxygen and four nitrogen atoms (LaO2N4), is further verified by X-ray absorption spectroscopy. The ORR half-wave potential reaches 0.852 V, and the OER overpotential reaches 263 mV at 10 mA cm−2. The Zn−air battery, with LaPNC as the air cathode, has a maximum power density of 202 mW cm−2 and achieves stable charge−discharge for at least 100 h without a significant increase or decrease in the charge or discharge voltages, respectively. Density functional theory calculations suggest that LaO2N4 sites exhibit the lowest activation free energy and the most easily desorbed oxygen capacity. This study provides new insights into the design of efficient, durable bifunctional catalysts as alternatives to precious-metal-based catalysts.
26.	Cao, Zhi, et al. (author) Adherence to a healthy lifestyle counteracts the negative effects of risk factors on all-cause mortality in the oldest-old 2019 In: Aging. - : Impact Journals, LLC. - 1945-4589. ; 11:18, s. 7605-7619 Journal article (peer-reviewed)abstract In the study, we examined the extent to which the harmful effects of risk factors on all-cause mortality can be counteracted by healthy lifestyle practices in the oldest-old (80 years of age and older). A total of 17,660 oldest-old from China were followed up for up to 10 years. The data were analyzed using the Cox proportional hazard model with adjustment for potential confounders. We found that having a rural residence, not being married, having lower economic status, physical disability, impaired cognitive function, or comorbidity were all associated with an elevated risk of mortality. Using these factors, we computed a weighted risk score. Because never smoking, never drinking, doing physical exercise, having an ideal diet, and a normal weight were independently associated with lower mortality, we also combined them to compute a weighted protection score. Both scores were divided into lowest, middle, and highest groups using their tertiles. In joint effect analyses, participants with the combined highest-risk score and lowest-protection score profile had a nearly threefold higher joint death risk. These analyses show that adherence to a healthy lifestyle counteracts the negative effect of risk factors on all-cause mortality in the oldest-old by more than 20%.
27.	Cerhan, James R., et al. (author) Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma 2014 In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:11, s. 1233-1238 Journal article (peer-reviewed)abstract Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 x 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 x 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 x 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 x 10(-13) and 3.63 x 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.
28.	Chen, Shi-Peng, et al. (author) Guanidine-based protic ionic liquids as highly efficient intermolecular scissors for dissolving natural cellulose 2023 In: Green Chemistry. - : Royal Society of Chemistry. - 1463-9262 .- 1463-9270. ; 25:22, s. 9322-9334 Journal article (peer-reviewed)abstract The development of highly efficient and environmentally friendly solvents for dissolving cellulose, which is the most abundant natural polymer on Earth, remains a challenge, hindering its full utilization. Herein, a green protic ionic liquid, 1,1,3,3-tetramethylguanidinium methoxyacetate ([TMGH][MAA]), was found to exhibit attractive capacity to dissolve natural cellulose with an appropriate TMG/MAA molar ratio of 7 : 3 at 80 degrees C. The solubility of cotton linter and ultra-high molecular weight cotton fibers reached 13% (w/w) and 3% (w/w), respectively, surpassing that of most solvent systems currently used for the dissolution of cellulose. The experimental and simulation results verified that the excellent dissolution ability of [TMGH][MAA] for cellulose is mainly attributed to the destruction of the intrinsic hydrogen-bond networks in cellulose by the synergistic interactions of the [TMGH] cations and [MAA] anions with the hydroxyl groups in the cellulose chains, acting as highly efficient "intermolecular scissors". The superiority of this novel dissolution system was further demonstrated by the remarkable comprehensive properties of the regenerated cellulose film including satisfactory thermostability, high transparency, and excellent mechanical properties. Furthermore, the satisfactory recovery performance of this solvent highlights its significant feasibility for large-scale industrial manufacturing. The proposed [TMGH][MAA] in this study exhibits great potential as a next-generation processing solvent for dissolving, and thus processing cellulose, promoting the sustainable development of high-value-added cellulose materials.
29.	Chen, Zhi-Hui, et al. (author) Enhanced normal-direction excitation and emission of dual-emitting quantum dots on a cascaded photonic crystal surface 2014 In: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:24, s. 14708-14715 Journal article (peer-reviewed)abstract Large normal-direction excitation and emission of dual-emitting quantum dots (QDs) are essential for practical application of QD sensors based on the ratiometric fluorescence response. We have numerically demonstrated an all-dielectric four-layer cascaded photonic crystal (CPC) structure (alternating TiO2 and SiO2/SU8 layers with two dimensional nanoscale patterns in each layer) which is capable of providing normal-direction high Q-factor leaky modes at excitation wavelengths of QDs and two low Q-factor leaky modes coinciding with the two emission peaks of a dual-emitting QD. Normal-direction excitation and far-field emission of the dual-emitting QDs are enhanced significantly when QDs are distributed on/in the top TiO2 layer of the CPC structure, especially in the spatial distribution areas of the resonant leaky modes. QDs can be positioned differently depending on the applications. Positioning QDs on the top TiO2 layer will improve the signal-to-noise ratios of QD biomedical/chemical/temperature sensors, while embedding QDs in the top TiO2 layer will increase the light extraction from the QD light emitting device, making our CPC a versatile optical coupling structure. Our CPC-QD structure is experimentally feasible and robust against the parameter perturbation in real fabrication.
30.	Cheng, Shi-Ping, et al. (author) Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger 2021 In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1 Journal article (peer-reviewed)abstract Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
31.	Chi, Zhi-Hong, et al. (author) Zinc transporter 7 is located in the cis-Golgi apparatus of mouse choroid epithelial cells. 2006 In: Neuroreport. - : Ovid Technologies (Wolters Kluwer Health). - 0959-4965. ; 17:17, s. 1807-11 Journal article (peer-reviewed)abstract The cellular localization of zinc transporter 7 protein in the mouse choroid plexus was examined in this study. Zinc transporter 7 immunoreactive cells were detected in the third, lateral, and fourth ventricles of CD-1 mouse brain. Distinct zinc transporter 7 immunoreactivity was concentrated in the perinuclear regions of the positive cells. The results from zinc autometallography showed that zinc-positive grains were also predominantly located in the perinuclear areas. Ultrastructural localization showed that zinc transporter 7 immunostaining was predominantly present in the membrane and cisternae of the cis-Golgi networks and some vesicle compartments. The results support the notion that zinc transporter 7 may participate in the transport of the cytoplasmic zinc into the Golgi apparatus, and may be involved in local packaging of zinc-binding proteins in the mouse choroid plexus.
32.	Feng, Dawei, et al. (author) Stable metal-organic frameworks containing single-molecule traps for enzyme encapsulation 2015 In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6, s. 5979- Journal article (peer-reviewed)abstract Enzymatic catalytic processes possess great potential in chemical manufacturing, including pharmaceuticals, fuel production and food processing. However, the engineering of enzymes is severely hampered due to their low operational stability and difficulty of reuse. Here, we develop a series of stable metal-organic frameworks with rationally designed ultra-large mesoporous cages as single-molecule traps (SMTs) for enzyme encapsulation. With a high concentration of mesoporous cages as SMTs, PCN-333(Al) encapsulates three enzymes with record-high loadings and recyclability. Immobilized enzymes that most likely undergo single-enzyme encapsulation (SEE) show smaller Km than free enzymes while maintaining comparable catalytic efficiency. Under harsh conditions, the enzyme in SEE exhibits better performance than free enzyme, showing the effectiveness of SEE in preventing enzyme aggregation or denaturation. With extraordinarily large pore size and excellent chemical stability, PCN-333 may be of interest not only for enzyme encapsulation, but also for entrapment of other nanoscaled functional moieties.
33.	Fu, Yifeng, 1984, et al. (author) Graphene related materials for thermal management 2020 In: 2D Materials. - : IOP Publishing. - 2053-1583. ; 7:1 Journal article (peer-reviewed)abstract Almost 15 years have gone ever since the discovery of graphene as a single atom layer. Numerous papers have been published to demonstrate its high electron mobility, excellent thermal and mechanical as well as optical properties. We have recently seen more and more applications towards using graphene in commercial products. This paper is an attempt to review and summarize the current status of the research of the thermal properties of graphene and other 2D based materials including the manufacturing and characterization techniques and their applications, especially in electronics and power modules. It is obvious from the review that graphene has penetrated the market and gets more and more applications in commercial electronics thermal management context. In the paper, we also made a critical analysis of how mature the manufacturing processes are; what are the accuracies and challenges with the various characterization techniques and what are the remaining questions and issues left before we see further more applications in this exciting and fascinating field.
34.	Gao, Zhi xin, et al. (author) Progress of passive enhanced heat transfer tubes 2017 In: Xiandai Huagong/Modern Chemical Industry. - 0253-4320. ; 37:3, s. 24-30 Research review (peer-reviewed)abstract A review of several typical enhanced heat transfer tubes such as corrugated tube, transversally corrugated tube, twisted tube and spiral fluted tube, is carried out. Compared with smooth wall tube, these enhanced tubes have higher heat exchange capacity and better anti - fouling ability. Besides, the heat transfer efficiency can be promoted to a higher level if the objects that can disturb flow are put in the tubes. However, higher heat transfer efficiency of such enhanced heat transfer tubes can only be achieved under certain conditions. Therefore, new heat transfer tubes that could avoid the formation of mobile dead-zone should be designed to meet the broad applications or facilitate better heat transfer effect.
35.	Guo, Junji, et al. (author) Prominent Electrochromism Achieved Using Aluminum Ion Insertion/Extraction in Amorphous WO3 Films 2018 In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 122:33, s. 19037-19043 Journal article (peer-reviewed)abstract Although monovalent lithium has been successfully used as a coloring ion in electrochromic applications, it still faces the challenges of low safety, high cost, and limited reserves. Herein, we demonstrate that the amorphous WO3 films intercalated with Al3+ ions could exhibit desired wide optical modulation (similar to 63.0%) and high coloration efficiency (similar to 72.0 cm(2) A(-1), which is >100% higher than that with Li+ or Na+), benefiting from the three-electron redox properties of aluminum. Due to the strong electrostatic force and large atomic weight, the charge exchange processes for Al3+ ions are limited only to the near-surface region and consequently bring about enhanced electrochromic stability. Our findings provide in-depth insights into the nature of electrochromism and also open up a new route toward scalable electrochromic devices using sputtering techniques and earth-abundant materials.
36.	Guo, Junji, et al. (author) Vacancy dependent electrochromic behaviors of NiOx anodes : As a single layer and in devices 2018 In: Solar Energy Materials and Solar Cells. - : ELSEVIER SCIENCE BV. - 0927-0248 .- 1879-3398. ; 178, s. 193-199 Journal article (peer-reviewed)abstract Electrochromic(EC), nonstoichiometric NiOx thin films were made by reactive magnetron sputtering at low oxygen flow ratio(i.e., P = O-2/Ar + O-2 < 10%). The results of optical spectral, x-ray diffraction spectrum, and x-ray photoelectron spectroscopy analyses indicate that the samples are oxygen(nickel)-deficient as P <= %4(>=%6), resulting in sub(over)-stoichiometry films. Spectroelectrochemical measurements show that the EC effect of NiOx in nonaqueous PC - LiClO4 electrolyte is direct correlation with the nickel vacancy concentration in films, while that in the aqueous KOH solution is nearly uninfluenced upon the change in stoichiometry as P >= %4. The films deposited at P = 6% exhibit higher coloration efficiency of - 25.3 cm(2)C(-1), larger ionic diffusion coefficient of - 2.84 x 10(-14) m(2)s(-1), and broader EC modulation span of 24% in PC - LiClO4 than the other ones. Based upon these values, EC devices featuring a WO3/PMMA - PC - LiClO4/NiOx structure and excellent performances were fabricated. We demonstrated that the nickel anodization should be responsible for the initial "activation" phenomena, which decreases(increases) the number of oxygen(nickel) vacancies. Moreover, the cause of degradation resulting from Li+-ion trapping in the IS layer was also clarified. This work provides a general framework for studying and designing superior EC devices, experimentally as well as theoretically.
37.	Han, Xin-Bao, et al. (author) Fe-substituted cobalt-phosphate polyoxometalates as enhanced oxygen evolution catalysts in acidic media 2020 In: Cuihuà xuébào. - : Science Press. - 0253-9837 .- 1872-2067. ; 41:5, s. 853-857 Journal article (peer-reviewed)abstract All-inorganic and earth-abundant bi-/trimetallic hydr(oxy)oxides are widely used as oxygen evolution electrocatalysts owing to their remarkable performance. However, their atomically precise structures remain undefined, complicating their optimization and limiting the understanding of their enhanced performance. Here, the underlying structure-property correlation is explored by using a well-defined cobalt-phosphate polyoxometalate cluster [{Co-4(OH)(3)(PO4)}(4)(SiW9O34)(4)](32-) (1), which may serve as a molecular model of multimetal hydr(oxy)oxides. The catalytic activity is enhanced upon replacing Co by Fe in 1, resulting in a reduced overpotential (385 mV) for oxygen evolution (by 66 mV) compared to that of the parent 1 at 10 mA cm(-2) in an acidic medium; this overpotential is comparable to that for the IrO2 catalyst. These abundant-metal-based polyoxometalates exhibit high stability, with no evidence of degradation even after 24 h of operation.
38.	He, Li, et al. (author) Evolutionary origin and establishment of a dioecious diploid-tetraploid complex 2023 In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:11, s. 2732-2749 Journal article (peer-reviewed)abstract Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.
39.	Joshi, Peter K, et al. (author) Directional dominance on stature and cognition in diverse human populations 2015 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 523:7561, s. 459-462 Journal article (peer-reviewed)abstract Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.
40.	Li, Shuqi, et al. (author) Rtt105 functions as a chaperone for replication protein A to preserve genome stability 2018 In: EMBO Journal. - : Wiley-VCH Verlagsgesellschaft. - 0261-4189 .- 1460-2075. ; 37:17 Journal article (peer-reviewed)abstract Generation of single-stranded DNA (ssDNA) is required for the template strand formation during DNA replication. Replication Protein A (RPA) is an ssDNA-binding protein essential for protecting ssDNA at replication forks in eukaryotic cells. While significant progress has been made in characterizing the role of the RPA-ssDNA complex, how RPA is loaded at replication forks remains poorly explored. Here, we show that the Saccharomyces cerevisiae protein regulator of Ty1 transposition 105 (Rtt105) binds RPA and helps load it at replication forks. Cells lacking Rtt105 exhibit a dramatic reduction in RPA loading at replication forks, compromised DNA synthesis under replication stress, and increased genome instability. Mechanistically, we show that Rtt105 mediates the RPA-importin interaction and also promotes RPA binding to ssDNA directly in vitro, but is not present in the final RPA-ssDNA complex. Single-molecule studies reveal that Rtt105 affects the binding mode of RPA to ssDNA These results support a model in which Rtt105 functions as an RPA chaperone that escorts RPA to the nucleus and facilitates its loading onto ssDNA at replication forks.
41.	Li, Youbing, et al. (author) Single-Atom-Thick Active Layers Realized in Nanolaminated Ti-3(AlxCu1-x)C-2 and Its Artificial Enzyme Behavior 2019 In: ACS Nano. - : AMER CHEMICAL SOC. - 1936-0851 .- 1936-086X. ; 13:8, s. 9198-9205 Journal article (peer-reviewed)abstract A Ti-3(AlxCu1-x)C-2 phase with Cu atoms with a degree of ordering in the A plane is synthesized through the A site replacement reaction in CuCl2 molten salt. The weakly bonded single -atom -thick Cu layers in a Ti-3(AlxCu1-x)C-2 MAX phase provide actives sites for catalysis chemistry. As -synthesized Ti-3(AlxCu1-x)C-2 presents unusual peroxidase-like catalytic activity similar to that of natural enzymes. A fabricated Ti-3(AlxCu1-x)C-2/chitosan/glassy carbon electrode biosensor prototype also exhibits a low detection limit in the electrochemical sensing of H2O2. These results have broad implications for property tailoring in a nanolaminated MAX phase by replacing the A site with late transition elements.
42.	Lin, Min-Zhi, et al. (author) A High-Speed Si-Based Power Transistor With Bipolar-Assisted Gate Discharging Behavior 2019 In: IEEE Electron Device Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 0741-3106 .- 1558-0563. ; 40:4, s. 589-592 Journal article (peer-reviewed)
43.	Liu, Chaocheng, et al. (author) Probing the Néel-Type Antiferromagnetic Order and Coherent Magnon–Exciton Coupling in Van Der Waals VPS3 2023 In: Advanced Materials. - 0935-9648. ; 35:30 Journal article (peer-reviewed)abstract 2D van der Waals (vdW) antiferromagnets have received intensive attention due to their terahertz resonance, multilevel magnetic-order states, and ultrafast spin dynamics. However, accurately identifying their magnetic configuration still remains a challenge owing to the lack of net magnetization and insensitivity to external fields. In this work, the Néel-type antiferromagnetic (AFM) order in 2D antiferromagnet VPS3 with the out-of-plane anisotropy, which is demonstrated by the temperature-dependent spin–phonon coupling and second-harmonic generation (SHG), is experimentally probed. This long-range AFM order even persists at the ultrathin limit. Furthermore, strong interlayer exciton–magnon coupling (EMC) upon the Néel-type AFM order is detected based on the monolayer WSe2/VPS3 heterostructure, which induces an enhanced excitonic state and further certifies the Néel-type AFM order of VPS3. The discovery provides optical routes as the novel platform to study 2D antiferromagnets and promotes their potential applications in magneto-optics and opto-spintronic devices.
44.	Lu, Shen-ning, et al. (author) Application of an innovative grid-based surveillance strategy to ensure elimination and prevent reintroduction of malaria in high-risk border communities in China 2022 In: BMC Public Health. - : Springer Nature. - 1471-2458. ; 22:1 Journal article (peer-reviewed)abstract Grid management is a grassroots governance strategy widely implemented in China since 2004 to improve the government's efficiency to actively find and solve problems among populated regions. A grid-based strategy surveillancing high-risk groups, including mobile and migrant populations (MMPs), in the China-Myanmar border region has played an indispensable role in promoting and consolidating the malaria elimination efforts by tracking and timely identification of potential importation or re-establishment of malaria among MMPs. A sequential mixed methods was implementated to explore the operational mechanism and best practices of the grid-based strategy including through the focus group discussions (FGDs), comparison of before and after the implementation of a grid-based strategy in the field sites, and data collection from the local health system.This paper distills the implementation mechanism and highlights the role of the grid-based strategy in the elimination and prevention of re-establishment of malaria transmission.
45.	Ma, Yu-Bo, et al. (author) One-pot synthesis of Pd-Au-alloy-nanoparticle-decorated graphene oxide functionalized with dodecahydrododecaborate cluster for rapid and complete reduction of 4-nitrophenol at room temperature 2023 In: Rare Metals. - : Springer Nature. - 1001-0521 .- 1867-7185. ; 42:11, s. 3622-3629 Journal article (peer-reviewed)
46.	Machiela, Mitchell J., et al. (author) Genetically predicted longer telomere length is associated with increased risk of B-cell lymphoma subtypes 2016 In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 25:8, s. 1663-1676 Journal article (peer-reviewed)abstract Evidence from a small number of studies suggests that longer telomere length measured in peripheral leukocytes is associated with an increased risk of non-Hodgkin lymphoma (NHL). However, these studies may be biased by reverse causation, confounded by unmeasured environmental exposures and might miss time points for which prospective telomere measurement would best reveal a relationship between telomere length and NHL risk. We performed an analysis of genetically inferred telomere length and NHL risk in a study of 10 102 NHL cases of the four most common B-cell histologic types and 9562 controls using a genetic risk score (GRS) comprising nine telomere length-associated single-nucleotide polymorphisms. This approach uses existing genotype data and estimates telomere length by weighing the number of telomere length-associated variant alleles an individual carries with the published change in kb of telomere length. The analysis of the telomere length GRS resulted in an association between longer telomere length and increased NHL risk [four B-cell histologic types combined; odds ratio (OR) = 1.49, 95% CI 1.22-1.82, P-value = 8.5 x 10(-5)]. Subtype-specific analyses indicated that chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL/SLL) was the principal NHL subtype contributing to this association (OR = 2.60, 95% CI 1.93-3.51, P-value = 4.0 x 10(-10)). Significant interactions were observed across strata of sex for CLL/SLL and marginal zone lymphoma subtypes as well as age for the follicular lymphoma subtype. Our results indicate that a genetic background that favors longer telomere length may increase NHL risk, particularly risk of CLL/SLL, and are consistent with earlier studies relating longer telomere length with increased NHL risk.
47.	Pan, Jin, et al. (author) Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers 2015 In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 15:4, s. 711-722 Journal article (peer-reviewed)abstract Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11000 and 14751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.
48.	Qian, Jin Yuan, et al. (author) Experimental and numerical analysis of spring stiffness on flow and valve core movement in pilot control globe valve 2017 In: International Journal of Hydrogen Energy. - : Elsevier BV. - 0360-3199. ; 42:27, s. 17192-17201 Journal article (peer-reviewed)abstract Valves are widely used for fluid flow control, not only for conventional fluid like water, gas and oil, but also for hydrogen under high pressure and so forth. Under these new conditions, the response time and energy consumption of valves are closely related to the whole performance of the piping system. Pilot-control globe valve (PCGV) is a novel quick response valve, which can utilize the pressure difference before and after the valve core to control the open/close states of the main valve. In this paper, the effects of spring stiffness inside PCGV on the flow and the valve core movement are carried out, respectively. To begin with, the experimental setup is introduces and the 3D numerical model is established. The simulation is carried out in software FLUENT with RNG k-ε turbulence model, User Defined Function method and dynamic mesh regeneration methods under transmit state. Then, a comparison of steady valve core displacements between experiment and simulation is carried out. After that, the effects of spring stiffness on flow characteristics, valve core movement and response times during opening and closing periods are presented. Finally, a spring chosen correction equation is proposed. This work can benefit the further design work of PCGVs or similar valves with springs, and it can be also referred by someone dealing with novel control valves design or flow control issues.
49.	Qu, Chang, et al. (author) Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex 2024 In: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831. ; 62:1, s. 135-148 Journal article (peer-reviewed)abstract Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.
50.	Rong, Zhi-Hai, et al. (author) Emergence of cooperation through coevolving time scale in spatial prisoner's dilemma 2010 In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1063-651X .- 1095-3787. ; 82:2, s. 026101- Journal article (peer-reviewed)abstract We study evolutionary prisoner’s dilemma game by considering adaptive strategy-selection time scale among individuals according to a “win-slower, lose-faster” rule: if an individual successfully resists the invasion of an opponent, she is prone to hold her strategy for longer time through decreasing her strategy-selection time scale; otherwise, she increases the time scale because of losing. We find that the greater the losers increase their strategy-selection time scales, the better for cooperation. Interestingly, optimal cooperation can be induced by proper adaptive rate in the strategy-selection time scale. Our results may have potential implications in the design of consensus protocol in multiagent systems.

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