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| 1 | Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the singlecell level显示文摘Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level. | Andrew Farmer Sandra Thibivilliers Kook Hui Ryu John Schiefelbein Marc Libault | 2021 | Molecular Plant2021，14，3： | 9 |
| 2 | Detection of dietary plant-based small RNAs in animals显示文摘 | Jian Yang Lisa M Farmer Abia AA Agyekum Kendal D Hirschi | 2015 | Cell Research2015，25，4： | 9 |
| 3 | NICE指南概要:共病状态的临床评估和管理显示文摘大多数慢性疾病患者患有一种或多种慢性疾病,共病状态在老年人中十分常见(图1和图2)。共病状态的重要性在于其与降低生活质量、高死亡率、多重用药、更高药物不良事件几率、更多计划外医疗服务耗费均相关。共病患者需要频繁前往初级医疗保健机构和各个专科就诊,这些机构的医师之间可能缺乏有效沟通交流。 | Caroline Farmer Elisabetta Fenu Norma O'Flynn Bruce Guthrie 符天旭 | 2017 | 中国医院院长2017，13，5： | 8 |
| 4 | Probiotic metabolites from Bacillus coagulans GanedenBC30^(TM) support maturation of antigen-presenting cells in vitro显示文摘AIM:To study the effects of probiotic metabolites on maturation stage of antigen-presenting immune cells.METHODS:Ganeden Bacillus coagulans 30(GBC30) bacterial cultures in log phase were used to isolate the secreted metabolite(MET) fraction.A second fraction was made to generate a crude cell-wall-enriched fraction,by centrifugation and lysis,followed by washing.A preparation of MET was subjected to size exclusion centrifugation,generating three fractions:< 3 kDa,3-30 kDa,and 30-200 kDa and activities were tested in comparison to crude MET and cell wall in primary cultures of human peripheral blood mononuclear cell(PBMC) as a source of antigen-presenting mononuclear phagocytes.The maturation status of mononuclear phagocytes was evaluated by staining with monoclonal antibodies towards CD14,CD16,CD80 and CD86 and analyzed by flow cytometry.RESULTS:Treatment of PBMC with MET supported maturation of mononuclear phagocytes toward both macrophage and dendritic cell phenotypes.The biological activity unique to the metabolites included a reduction of CD14+ CD16+ pro-inflammatory cells,and this property was associated with the high molecular weight metabolite fraction.Changes were also seen for the dendritic cell maturation markers CD80 and CD86.On CD14dim cells,an increase in both CD80 and CD86 expression was seen,in contrast to a selective increase in CD86 expression on CD14bright cells.The co-expression of CD80 and CD86 indicates effective antigen presentation to T cells and support of T helper cell differentiation.The selective expression of CD86 in the absence of CD80 points to a role in generating T regulatory cells.CONCLUSION:The data show that a primary mechanism of action of GBC30 metabolites involves support of more mature phenotypes of antigen-presenting cells,important for immunological decision-making. | Kathleen F Benson Kimberlee A Redman Steve G Carter David Keller Sean Farmer John R Endres Gitte S Jensen | 2012 | World Journal of Gastroenterology2012，18，16： | 8 |
| 5 | 双参数混合正则化方法及在电导率反演成像中的应用显示文摘通过引入带有二阶正则算子的正则化项,建立了一种双参数混合正则化方法.为确定最佳正则化参数,这里主要应用L-曲线法、偏差原理和广义交叉校验准则的优化组合来确定.首先对理论模型进行了数值模拟,通过与截断奇异值分解法、共轭梯度法及标准Tikhonov正则化法的结果比较,表明该方法不仅精度高,而且对于数据的随机扰动具有稳定性.然后将此方法应用于对电导率反演成像的计算中,得到的电导率反演成像精确细致可靠,也符合实际情况.这表明该方法求解地球物理反问题时,在增强反演的稳定性及减少多解性的同时,还能进一步提高反演计算速度. | 王文娟 Chris Farmer John Ockendon 冯宝宾 曹俊兴 谭永基 | 2011 | 地球物理学报2011，54，8： | 5 |
| 6 | Assessment of the cardiovascular and gastrointestinal autonomic complications of diabetes显示文摘The global prevalence of diabetes mellitus is increasing; arguably as a consequence of changes in diet, lifestyle and the trend towards urbanization. Unsurprisingly, the incidence of both micro and macrovascular complications of diabetes mirrors this increasing prevalence. Amongst the complications with the highest symptom burden, yet frequently under-diagnosed and sub-optimally treated, is diabetic autonomic neuropathy, itself potentially resulting in cardiovascular autonomic neuropathy and gastrointestinal(GI) tract dysmotility. The aims of this review are fourfold. Firstly to provide an overview of the pathophysiological processes that cause diabetic autonomic neuropathy. Secondly, to discuss both the established and emerging cardiometric methods for evaluating autonomic nervous system function in vivo. Thirdly, to examine the tools for assessing pan-GI and segmental motility and finally, we will provide the reader with a summary of putative non-invasive biomarkers that provide a pathophysiological link between lowgrade neuro inflammation and diabetes, which may allow earlier diagnosis and intervention, which in future may improve patient outcomes. | Christina Brock Birgitte Brock Anne Grave Pedersen Asbjorn Mohr Drewes Niels Jessen Adam D Farmer | 2016 | World Journal of Diabetes2016，7，16： | 5 |
| 7 | 初乳摄入量:影响仔猪生产性能和变化的因素显示文摘初乳摄入不足是仔猪在出生后最初几天内死亡的根本原因。最新的研究发现,据估计每头仔猪在出生后的24 h内摄入200 g初乳,是显著降低其断奶前死亡风险、产生被动免疫力以及能够实现轻微增重的最低摄入量。为使仔猪拥有良好的健康以及在断奶前后取得合理的生长速度,建议让仔猪摄入250 g的初乳。根据这一标准,至少三分之一的母猪不能产生足够满足所有仔猪需求的初乳量。因此,我们必须考虑使用多种可以增加仔猪初乳摄入量的方法,例如增强仔猪吮吸能力、减少窝内仔猪初生重的差异以及提高母猪初乳质量等。对母猪妊娠期间营养的研究已经获得了令人振奋的结果,尤其是在仔猪出生时的活力以及获得被动免疫力方面。侧重于营养或遗传选种的方法,预期也可以提高母猪窝产仔猪初生重的均匀性。最后,很明显,有关提高母猪初乳产量的方法还需要进一步研究。一个已被忽略但还需要更多研究的领域是乳腺发育对初乳产量的潜在影响。未来,研究重点应集中在母猪青春期和孕期最后几天的激素水平和营养状况对初乳产量的影响。 | 唐彩琰 Hélène Quesnel Chantal Farmer Nicolas Devillers | 2017 | 国外畜牧学(猪与禽)2017，0，9： | 5 |
| 8 | 求三维本征声线的一种新方法显示文摘本文采用“自动搜寻”法求海洋中均匀声速背景上有三维声速扰动时的本征声线。与传统方法比较,这种方法计算声线的次数减小约二个数量级。 | 王恕铨 David Farmer | 1992 | 声学学报1992，17，2： | 5 |
| 9 | High efficiency, high power 808nm laser array and stacked arrays optimized for elevated temperature operation显示文摘Operation of 808-nm laser diode pumping at elevated temperature is crucial to many applications. Reliable operation at high power is limited by high thermal load and low catastrophic optical mirror damage (COMD) threshold at elevated temperature range. We demonstrated high efficiency and high power operation at elevated temperature with high COMD power. These results were achieved through device design optimization such as growth conditions, doping profile, and materials composition of the quantum-well and other layers. Electrical-to-optical efficiency as high as 62% was obtained through lowered threshold current, lowered series resistance and increased slope efficiency. The performance of single broad-area laser diodes scales to that of high power single bars on water-cooled copper micro-channel heatsinks or conductively-cooled CS heatsinks. No reduction in bar performance or significant spectral broadening is seen when these micro-channel coolers are assembled into 6-bar and 18-bar CW stacks for the highest power levels. | Crump P A Crum T R DeVito M Farmer J Grimshaw M Huang Z Igl S A Macomber S Thiagarajan P Wise D | 2004 | 光机电信息2004，21，6： | 4 |
| 10 | Brain changes in diabetes mellitus patients withgastrointestinal symptoms显示文摘Diabetes mellitus is a common disease and its prevalence is increasing worldwide. In various studies up to 30%-70% of patients present dysfunction and complications related to the gut. To date several clinical studies have demonstrated that autonomic nervous system neuropathy and generalized neuropathy of the central nervous system(CNS) may play a major role. This systematic review provides an overview of the neurodegenerative changes that occur as a consequence of diabetes with a focus on the CNS changes and gastrointestinal(GI) dysfunction. Animal models where diabetes was induced experimentally support that the disease induces changes in CNS. Recent investigations with electroencephalography and functional brain imaging in patients with diabetes confirm these structural and functional brain changes. Encephalographic studies demonstrated that altered insular processing of sensory stimuli seems to be a key player in symptom generation. In fact one study indicated that the more GI symptoms the patients experienced, the deeper the insular electrical source was located. The electroencephalography was often used in combination with quantitative sensory testingmainly showing hyposensitivity to stimulation of GI organs. Imaging studies on patients with diabetes and GI symptoms mainly showed microstructural changes,especially in brain areas involved in visceral sensory processing. As the electrophysiological and imaging changes were associated with GI and autonomic symptoms they may represent a future therapeutic target for treating diabetics either pharmacologically or with neuromodulation. | Anne M Drewes Eirik Søfteland Georg Dimcevski Adam D Farmer Christina Brock Jens B Frøkjær Klaus Krogh Asbjørn M Drewes | 2016 | World Journal of Diabetes2016，7，2： | 4 |
| 11 | Albumin fusion with granulocyte-macrophage colony-stimulating factor acts as an immunotherapy against chronic tuberculosis显示文摘A long duration of treatment and emerging drug resistance pose significant challenges for global tuberculosis(TB)eradication efforts.Therefore,there is an urgent need to develop novel strategies to shorten TB treatment regimens and to treat drug-resistant TB.Using an albumin-fusion strategy,we created a novel albumin-fused granulocyte-macrophage colony-stimulating factor(albGM-CSF)molecule that harnesses albumin’s long half-life and targeting abilities to enhance the biostability of GM-CSF and direct it to the lymph nodes,where the effects of GM-CSF can increase dendritic cell populations crucial for eliciting a potent immune response.In this study,we demonstrate that albGM-CSF serves as a novel immunotherapy for chronic Mycobacterium tuberculosis(Mtb)infections by enhancing GM-CSF biostability in serum.Specifically,albumin is very safe,stable,and has a long half-life,thereby enhancing the biostability of GM-CSF.In the lungs and draining lymph nodes,albGM-CSF is able to increase the numbers of dendritic cells,which are crucial for the activation of naive T cells and for eliciting potent immune responses.Subcutaneous administration of albGM-CSF alone reduced the mean lung bacillary burden in mice with chronic tuberculosis infection.While GM-CSF administration was associated with IL-1βrelease from Mtb-infected dendritic cells and macrophages,higher IL-1βlevels were observed in albGM-CSF-treated mice with chronic tuberculosis infection than in mice receiving GM-CSF.Albumin fusion with GM-CSF represents a promising strategy for the control of chronic lung tuberculosis infections and serves as a novel therapeutic vaccination platform for other infectious diseases and malignancies. | Yu-Min Chuang Liangmei He Michael L.Pinn Ya-Chea Tsai Max A.Cheng Emily Farmer Petros C.Karakousis Chien-Fu Hung | 2021 | Cellular & Molecular Immunology2021，18，10： | 3 |
| 12 | Liver Transplantation Criteria For Hepatocellular Carcinoma Should Be Expanded: A 22-Year Experience With 467 Patients at UCLA显示文摘 | John P. Duffy Andrew Vardanian Elizabeth Benjamin Melissa Watson Douglas G. Farmer Rafik M. Ghobrial Gerald Lipshutz Hasan Yersiz David S. K. Lu Charles Lassman Myron J. Tong Jonathan R. Hiatt Ronald W. Busuttil | 2007 | Annals of Surgery2007，，3： | 3 |
| 13 | Vascular Complications of Orthotopic Liver Transplantation: Experience in More than 4,200 Patients显示文摘 | John P. Duffy Johnny C. Hong Douglas G. Farmer Rafik M. Ghobrial Hasan Yersiz Jonathan R. Hiatt Ronald W. Busuttil | 2009 | Journal of the American College of Surgeons2009，，5： | 3 |
| 14 | Long-Term Patient Outcome and Quality of Life After Liver Transplantation: Analysis of 20-Year Survivors显示文摘 | John P. Duffy Kenneth Kao Clifford Y. Ko Douglas G. Farmer Sue V. McDiarmid Johnny C. Hong Robert S. Venick Susan Feist Leonard Goldstein Sammy Saab Jonathan R. Hiatt Ronald W. Busuttil | 2010 | Annals of Surgery2010，，4： | 3 |
| 15 | Clonal isolation of endothelial colony-forming cells from early gestation chorionic villi of human placenta for fetal tissue regeneration显示文摘BACKGROUND Endothelial colony-forming cells(ECFCs)have been implicated in the process of vascularization,which includes vasculogenesis and angiogenesis.Vasculogenesis is a de novo formation of blood vessels,and is an essential physiological process that occurs during embryonic development and tissue regeneration.Angiogenesis is the growth of new capillaries from pre-existing blood vessels,which is observed both prenatally and postnatally.The placenta is an organ composed of a variety of fetal-derived cells,including ECFCs,and therefore has significant potential as a source of fetal ECFCs for tissue engineering.AIM To investigate the possibility of isolating clonal ECFCs from human early gestation chorionic villi(CV-ECFCs)of the placenta,and assess their potential for tissue engineering.METHODS The early gestation chorionic villus tissue was dissociated by enzyme digestion.Cells expressing CD31 were selected using magnetic-activated cell sorting,and plated in endothelial-specific growth medium.After 2-3 wks in culture,colonies displaying cobblestone-like morphology were manually picked using cloning cylinders.We characterized CV-ECFCs by flow cytometry,immunophenotyping,tube formation assay,and Dil-Ac-LDL uptake assay.Viral transduction of CVECFCs was performed using a Luciferase/tdTomato-containing lentiviral vector,and transduction efficiency was tested by fluorescent microscopy and flow cytometry.Compatibility of CV-ECFCs with a delivery vehicle was determined using an FDA approved,small intestinal submucosa extracellular matrix scaffold.RESULTS After four passages in 6-8 wks of culture,we obtained a total number of 1.8×107 CV-ECFCs using 100 mg of early gestational chorionic villus tissue.Immunophenotypic analyses by flow cytometry demonstrated that CV-ECFCs highly expressed the endothelial markers CD31,CD144,CD146,CD105,CD309,only partially expressed CD34,and did not express CD45 and CD90.CV-ECFCs were capable of acetylated low-density lipoprotein uptake and tube formation,similar to cord blood-derived ECFCs(CB-ECFCs).CV-ECFCs can be transduced with a Luciferase/tdTomato-containing lentiviral vector at a transduction efficiency of 85.1%.Seeding CV-ECFCs on a small intestinal submucosa extracellular matrix scaffold confirmed that CV-ECFCs were compatible with the biomaterial scaffold.CONCLUSION In summary,we established a magnetic sorting-assisted clonal isolation approach to derive CV-ECFCs.A substantial number of CV-ECFCs can be obtained within a short time frame,representing a promising novel source of ECFCs for fetal treatments. | Kewa Gao Siqi He Priyadarsini Kumar Diana Farmer Jianda Zhou Aijun Wang | 2020 | World Journal of Stem Cells2020，12，2： | 2 |
| 16 | Liver Transplantation in Highest Acuity Recipients: Identifying Factors to Avoid Futility显示文摘 | Henrik Petrowsky Abbas Rana Fady M. Kaldas Anuj Sharma Johnny C. Hong Vatche G. Agopian Francisco Durazo Henry Honda Jeffrey Gornbein Victor Wu Douglas G. Farmer Jonathan R. Hiatt Ronald W. Busuttil | 2014 | Annals of Surgery2014，，6： | 2 |
| 17 | Liver Transplantation for Nonalcoholic Steatohepatitis: The New Epidemic显示文摘 | Vatche G. Agopian Fady M. Kaldas Johnny C. Hong Meredith Whittaker Curtis Holt Abbas Rana Ali Zarrinpar Henrik Petrowsky Douglas Farmer Hasan Yersiz Victor Xia Jonathan R. Hiatt Ronald W. Busuttil | 2012 | Annals of Surgery2012，，4： | 2 |
| 18 | A CMOS based analog standard cell product family 显示文摘 | Smith L D Farmer H R Kunesh M | 1989 | IEEE Journal of Solid-State Circuits1989，24，4： | 2 |
| 19 | Pretransplant Model to Predict Posttransplant Survival in Liver Transplant Patients显示文摘 | Rafik M. Ghobrial Jeffery Gornbein Randy Steadman Natale Danino James F. Markmann Curtis Holt Dean Anselmo Farin Amersi Pauline Chen Douglas G. Farmer Steve Han Francisco Derazo Sammy Saab Leonard I. Goldstein Sue V. McDiarmid Ronald W. Busuttil | 2002 | Annals of Surgery2002，，3： | 2 |
| 20 | Hepatocellular carcinoma screening in patients waiting for liver transplantation: A decision analytic model显示文摘 | Sammy Saab David Ly Jose Nieto Fasiha Kanwal David Lu Steven Raman Rafael Amado Barbara Nuesse Francisco Durazo Steven Han Douglas G. Farmer Rafik M. Ghobrial Hasan Yersiz Pauline Chen Kathy Schwegel Leonard I. Goldstein Myron Tong Ronald W. Busuttil | 2003 | Liver Transplantation2003，，7： | 2 |
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