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Population survey and conservation assessment of the globally threa- tened cheer pheasant （Catreus wallicht） in Jhelum Valley, Azad Kas- hmir, Pakistan

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Zoological Research 2014年第4期35卷 338-345页

作者： Muhammad Naeem AWAN Hassan ALI David charles lee WWF Pakistan Regional Office Azad Kashmir Muzaffarabad Pakistan WWF Pakistan Feroze Pur Road Lahore Pakistan School of Applied Sciences the University of South Wales Pontypridd UK

The cheer pheasant Catreus wallichi is a globally threatened species that inhabits the western Himalayas. Though it is well established that the species is threatened and its numbers declining, updated definitive estimates are lacking, so in 2011, we conducted a survey to assess the density, population size, and threats to the species in Jhelum valley, Azad Kashmir, which holds the largest known population of cheer pheasants in Pakistan. We conducted dawn call count surveys at 17 points clustered in three survey zones of the valley, 11 of which had earlier been used for a 2002-2003 survey of the birds. Over the course of our survey, 113 birds were recorded. Mean density of cheer pheasant in the valley was estimated at 11.8±6.47 pairs per km2, with significant differences in terms of both counts and estimated density of cheer were significantly different across the three survey zones, with the highest in the Chinari region and the lowest, that is the area with no recorded sightings of the pheasants, in Gari Doppata. The total breeding population of cheer pheasants is estimated to be some 2 490 pairs, though this does not consider the actual area of occupancy in the study area. On the whole, more cheer pheasants were recorded in this survey than from the same points in 2002-2003, indicating some success in population growth. Unfortunately, increasing human settlement, fires, livestock grazing, hunting, and the collection of non-timber forest products continue to threaten the population of cheer in the Jhelum valley. To mitigate these potential impacts, some degree of site protection should be required for the conservation of cheer pheasants in Pakistan, and more effective monitoring of the species is clearly needed.

关键词： Abundance Habitat analysis Cheer Pheasant Jhelum valley Pakistan

JAX-CNV:A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1197-1206页

作者： Wan-Ping lee Qihui Zhu Xiaofei Yang Silvia Liu Eliza Cerveira Mallory Ryan Adam Mil-Homens Lauren Bellfy Kai Ye charles lee Chengsheng Zhang Precision Medicine Center The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA School of Cyber Science and Engineering Xi’an Jiaotong UniversityXi’an 710049China Department of Pathology and Laboratory Medicine Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Department of Life Sciences Ewha Womans UniversitySeoul 03760South Korea

We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical ***-CNV is thus developed for CNV detection from WGS *** performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 *** result showed that JAX-CNV recalled 100%of these ***,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated *** validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×*** CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to ***-CNV is available at https://***/TheJacksonLaboratory/JAX-CNV.

关键词： Copy number variant Chromosomal microarray assay Whole-genome sequencing JAX-CNV Genetic testing

基于生存模型的沥青路面预防性养护经济性评价

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华南理工大学学报（自然科学版） 2012年第11期40卷 133-137页

作者：虞将苗 charles lee 陈磊磊华南理工大学土木与交通学院广东广州510640 加利福尼亚大学路面研究中心东南大学智能运输系统研究中心江苏南京210096

为探索经济、有效的沥青路面养护方法,降低沥青路面的养护费用,对沥青路面的预防性养护进行了全寿命经济性评价.首先根据美国加利福尼亚州交通部门的路面观测数据,采用生存模型建立了沥青路面在裂缝类预防性养护情况下的全寿命周期的性... 详细信息

为探索经济、有效的沥青路面养护方法,降低沥青路面的养护费用,对沥青路面的预防性养护进行了全寿命经济性评价.首先根据美国加利福尼亚州交通部门的路面观测数据,采用生存模型建立了沥青路面在裂缝类预防性养护情况下的全寿命周期的性能模型;进而,通过概率分析建立了路面的性能-成本模型,分析了不同破坏准则下预防性养护措施的经济性,并与矫正性修复措施的经济性进行了对比.结果表明,在沥青路面的寿命周期内,一直采用预防性养护的成本较采用矫正性修复的成本平均节约了27%,采用每两次矫正性修复间加入两次预防性养护的成本较一直使用矫正性修复的成本平均节约了17%.分析结果还表明,越早进行预防性养护,沥青路面的寿命周期成本越低.

关键词：道路工程沥青路面预防性养护生存模型全寿命周期经济性评价

Population assessment and habitat associations of the Visayan Hornbill(Penelopides panini)in Northwest Panay,Philippines

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Avian Research 2021年第4期12卷 612-622页

作者： Holly Isabelle Mynott David charles lee Rhea Aranas Santillan Christian Jürgen Schwarz Benjamin Tacud Arcel Dryden Fernandez Daphne Kerhoas Bristol Zoological Society Bristol Zoo GardensCollege RoadCliftonBristol BS83HAUK School of Applied Sciences University of South WalesAlfred Russel Wallace BuildingUpper Glyntaff CampusPontypridd CF374BBUK PhilinCon L.A.Dioso Memorial Public LibraryIloilo-Antique Road5712 PandanPhilippines PhilinCon Germany Ruhr-Universität BochumUniversitätsstraße 150ND 1/3144801 BochumGermany

Background:Seven out of ten hornbill species in the Philippines are threatened with *** these is the endangered Visayan Hornbill(Penelopides panini),found on the islands of Panay and *** by habitat loss and hunting,its population size is thought to have declined from 1800 individuals 20 years ago to less than ***,a recent study on Negros estimated 3564 individuals across three core forest *** study aims to quantify the Visayan Hornbill population size in and around the Northwest Panay Peninsula Natural Park(NWPPNP)on Panay,the largest contiguous low-elevation forest landscape remaining across its range,and its broad habitat associations across a gradient of environmental ***:Hornbills were surveyed using 10-min distance sampling point counts(n=367)along transects(average length 1.1 km).Environmental variables were recorded along transects,while habitat was classified into primary forest,secondary forest,plantation,or open *** software was used to estimate population densities stratified by habitat,with the overall population estimate taken as a mean of habitat density estimates weighted by habitat *** generalized linear mixed models,hornbill occurrence was modelled using combinations of nine environmental variables as main and two-way fixed ***:Surveys covered 204.4 km^(2) of the 374.8 km^(2) Northwest Panay *** were not recorded in plantations or open *** density was significantly higher in primary forest(17.8 individuals/km~2±26.9%CV)than in secondary forest(3.7 individuals/km^(2)±33.2%CV;z=15.212,P<0.001).The overall population estimate for the NWPPNP and environs is 2109 individuals,and 2673 individuals for the entire Northwest Panay *** presence was best explained by a model including distance from the Park boundary alongside five interaction effects and transect as a random ***,and the interaction between distance

关键词： Distance sampling Endangered species GLMM Hornbill Point count Population size Protected area

Scalable fabrication of sub-10 nm polymernanopores for DNA analysis

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Microsystems & Nanoengineering 2019年第1期5卷 532-541页

作者： Junseo Choi charles C.lee Sunggook Park Department of Mechanical&Industrial Engineering and Center for BioModular Multiscale Systems for Precision Medicine Louisiana State UniversityBaton RougeLA 70803USA Department of Comparative Biomedical Sciences School of Veterinary MedicineLouisiana State UniversityBaton RougeLA 70803USA

We present the first fabrication of sub-10 nm nanopores in freestanding polymer membranes via a simple,costeffective,high-throughput but deterministic fabrication *** in the range of 10 nm were initially produced via a single-step nanoimprinting process,which was further reduced to sub-10 nm pores via a post-NIL polymer reflow *** low shrinkage rate of 2.7 nm/min obtained under the conditions used for the reflow process was the key to achieving sub-10 nm pores with a controllable pore *** fabricated SU-8 nanopore membranes were successfully employed for transient current measurements during the translocation of DNA molecules through the nanopores.

关键词： process. polymer pores

Differential Expression of mGluR2 in the Developing Cerebral Cortex of the Mouse

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Journal of Biomedical Science and Engineering 2014年第13期7卷 1030-1037页

作者： Pooja S. Venkatadri charles C. lee Department of Comparative Biomedical Sciences School of Veterinary Medicine Louisiana State University Baton Rouge USA

Glutamatergic synaptic transmission is an essential component of neural circuits in the central nervous system. Glutamate exerts its effects by binding to various types of glutamate receptors, which are found distributed on neurons throughout the central nervous system. These receptors are broadly classified into two main groups, ionotropic glutamate receptors (iGluRs) and metabo-tropic glutamate receptors (mGluRs). Unlike iGluRs, the mGluRs are G-protein coupled receptors that exert their effects on postsynaptic membrane conductance indirectly through the downstream modification of ion channels. A subtype of mGluRs, the Group II mGluRs, are particularly interesting since their activation by glutamate results in a hyperpolarizing response. Thus, glutamate can act potentially as an inhibitory neurotransmitter, by binding to postsynaptic Group II mGluRs. Given the potential importance of these receptors in synaptic processing, the development of the central nervous system, and neurological disorders, we sought to characterize the expression of mGluR2 in the developing neocortex of the mouse. Therefore, we examined the distribution of mGluR2 in the developing cerebral cortex. We found a general caudal to rostral gradient in the expression of these receptors, with ventral cortical regions labeled caudally and dorsal regions labeled rostrally. Limbic regions highly expressed mGluR2 throughout the brain, as did sensory and motor cortical areas. Finally, other non-cortical structures, such as the thalamic reticular nucleus, amygdala, and mammillary bodies were found to have significant expression of the receptor. These results suggest that mGluR2 may play important roles in mediating glutamatergic inhibition in these structures and also could have a role in shaping the development of mature neural networks in the forebrain.

关键词： Metabotropic Glutamate Receptor Mouse Cortex mGluR2 Group II mGluR

Mako:A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 205-218页

作者： Jiadong Lin Xiaofei Yang Walter Kosters Tun Xu Yanyan Jia Songbo Wang Qihui Zhu Mallory Ryan Li Guo Chengsheng Zhang The Human Genome Structural Variation Consortium charles lee Scott E.Devine Evan E.Eichler Kai Ye School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Leiden Institute of Advanced Computer Science Faculty of ScienceLeiden UniversityLeiden 2311EZNetherland School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Precision Medicine Center the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Institute for Genome Sciences University of Maryland School of MedicineBaltimoreMD 21201USA Department of Genome Sciences University of Washington School of MedicineSeattleWA 98119USA Howard Hughes Medical Institute University of WashingtonSeattleWA 98195USA The School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China 不详

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural ***,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match *** a result,there has been limited progress for CSV discovery compared with simple structural ***,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read ***,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined *** evaluations on both simulated and real datasets revealed that Mako outperformed other ***,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,***,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed *** analysis of these CSVs also revealed the impact of sequence homology on the formation of *** is publicly available at https://***/xjtu-omics/Mako.

关键词： Next-generation sequencing Complex structural variant Pattern growth Graph mining Formation mechanism

Recent development and challenges in enhancing fire performance on wood and wood-based composites:A 10-year review from 2012 to 2021

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Journal of Bioresources and Bioproducts 2024年第1期9卷 27-42页

作者： charles Michael Albert Kang Chiang Liew Faculty of Tropical Forestry Universiti Malaysia SabahKota Kinabalu 88400Kota KinabaluSabah 88400Malaysia

Due to their durability,versatility,and aesthetic value,wood and wood-based composites are widely used as building *** fact that these materials are flammable,however,raises a major worry since they might cause fire hazards and significant loss of life and *** article investigates the variables that affect fire performance as well as the various fire-retardant treatments and their *** current developments and challenges in improving the fire performance of wood and wood-based composites treated with fire-retardant materials are summarized in this ***,organic chemicals,and densification are some recent developments in fire-retardant treatments that are also *** points from the review are summarized,along with potential areas for further research and development.

关键词： Fire performance Fire-retardant materials Wood Wood-based composite Nanoparticles coating Surface charring Bio-based fire retardant Densification

Efficacy of Autologous Cultured Fibroblast Cells as a Treatment for Patients with Facial Contour Defects: A Clinical Replication Study

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Journal of Cosmetics, Dermatological Sciences and Applications 2017年第4期7卷 306-317页

作者： Edward charles R. lee Kim Siea lee Jezamine Lim Jason Yip Cheng Zhang Xu Zhang Han Bin To Lim Sabah Medical Centre Sabah Malaysia Loh Guan Lye Specialists Centre Pinang Malaysia Tissue Engineering Centre University Kebangsaan Kuala Lumpur Malaysia Astute Clinic Kuala Lumpur Malaysia Beijing Cell Technology Inc. Beijing China SB Clinical Research Malaysia

Background: The US FDA has recently approved autologous cultured fibroblast cells (ACF) as treatment for cutaneous contour defects. ACF provides an alternative to synthetic fillers or fat grafting with the significant advantage of producing longer lasting effect. Methods: This was a prospective open label single group clinical study to demonstrate the clinical efficacy of ACF that we have replicated in our lab. The study enrolled 18 patients with nasolabial folds from 2 centres in Malaysia in 2011-2012. ACF at dose of 23 or 92 million cells were injected on 3 occasions at 4 weeks interval. Efficacy at 6- and 12-month post treatment was assessed using a standardized 7-point scale which was performed by the 2 investigators as well as a panel of 7 independent evaluators. Results: We obtained a successful outcome (primary endpoint), defined as improvement in the appearance of the nasolabial fold of at least 2 points on the 7-point scale, in 33% of patients as assessed by investigators at 12-month follow-up and in 22% of patients assessed by independent evaluators. Investigators also found 78% of patients having had a 1-point improvement from baseline while independent evaluators found 83% of patients having improved by as much. Patients were uniformly (100%) satisfied with the improvement in their appearance. No treatment-related adverse event was reported. Baseline score and follow-up duration had significant effect on treatment response. The greater the baseline severity and the longer the post-treatment follow-up, the better the response to ACF. Larger dose of cells (92 million cells) has little additional effect suggesting that the 1 mL dose (23 million cells) is near optimal. Older patients showed a trend towards poorer response but this was not statistically significant. Conclusions: We have successfully replicated the laboratory method and clinical procedure to perform ACF treatment which was effective in improving the appearance of nasolabial folds in some patie

关键词： Facial Contour Defect Nasolabial Fold Wrinkle Autologous Cultured Fibroblast Cell Autologous Cell Therapy