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PICOTEES:a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts

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Journal of Genetics and Genomics 2024年第2期51卷 243-251页

作者： Xinran Dong Yulan Lu Lanting Guo Chuan Li Qi ni Bingbing Wu Huijun Wang Lin Yang Songyang Wu Qi Sun Hao Zheng Wenhao zhou Shuang Wang Center for Molecular Medicine Children's Hospital of Fudan UniversityShanghai 201102China Key Laboratory of Birth Defects Children's Hospital of Fudan UniversityShanghai 201102China Department of Bioinformatics Hangzhou Nuowei Information Technology Co.LtdHangzhouZhejiang 310000China The Third Research Institute of the Ministry of Public Security Shanghai 200031China Xiamen Campus of Children's Hospital of Fudan University XiamenFujian 361006China Institutes for Systems Genetics West China HospitalChengduSichuan 610041China Shanghai Putuo People's Hospital Tongji UniversityShanghai 200060China

The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://***:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.

关键词： Privacy protecti on Rare diseases in children Genetic testing Web system Trusted executi on envir onment

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Plant regeneration in the new era:from molecular mechanisms to biotechnology applications

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Science China(Life Sciences) 2024年第7期67卷 1338-1367页

作者： Chunli Chen Yuxin Hu Momoko Ikeuchi Yuling jiao Kalika Prasad Ying Hua Su Jun Xiao Lin Xu Weibing Yang Zhong Zhao Wenkun zhou Yun zhou jian Gao jia-Wei Wang National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of Sciences(CAS)China National Botanical GardenBeijing 100093China Division of Biological Sciences Graduate School of Science and TechnologyNara Institute of Science and TechnologyNara 630-0192Japan State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Indian Institute of Science Education and Research Pune 411008IndiaThiruvananthapuram 695551India State Key Laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTai’an 271018China Sino-German Joint Research Center on Agricultural Biology Shandong Agricultural UniversityTai’an 271018China Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology(IGDB)CASBeijing 100101China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) IGDBCASBeijing 100101China National Key Laboratory of Plant Molecular Genetics CEMPSInstitute of Plant Physiology and Ecology(SIPPE)CASShanghai 200032China CEPAMS SIPPECASShanghai 200032China Hefei National Laboratory for Physical Sciences at the Microscale CEMPSSchool of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China State Key Laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of Botany and Plant Pathology and Center for Plant Biology Purdue UniversityWest Lafayette 47907USA School of Life Science and Technology Shang

Plants or tissues can be regenerated through various *** animal regeneration,cell totipotency and pluripotency are the molecular basis of plant *** systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant ***,plant hormones,cell division,epigenetic remodeling,and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic *** research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species,with various plant species using distinct mechanisms and displaying significant differences in regenerative *** multi-omics studies at the single-cell level,tracking plant regeneration processes in real-time,and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration,improve crop regeneration efficiency,and contribute to future crop design.

关键词： apical meristem model species regeneration phytohormone plant cell reprogramming somatic embryogenesis

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Stem Cell-Based Hair Cell Regeneration and Therapy in the Inner Ear

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Neuroscience Bulletin 2024年第1期40卷 113-126页

作者： Jieyu Qi Wenjuan Huang Yicheng Lu Xuehan Yang Yinyi zhou Tian Chen Xiaohan Wang Yafeng Yu jia-Qiang Sun Renjie Chai State Key Laboratory of Digital Medical Engineering Department of Otolaryngology Head and Neck SurgeryZhongda HospitalSchool of Life Sciences and TechnologyAdvanced Institute for Life and HealthJiangsu Province High-Tech Key Laboratory for Bio-Medical ResearchSoutheast UniversityNanjing 210096China Hospital of Southeast University Nanjing 210096China First Affiliated Hospital of Soochow University Suzhou 215006China Department of Otolaryngology-Head and Neck Surgery The First Affliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230001China Department of Otolaryngology Head and Neck Surgery Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610072China Co-Innovation Center of Neuroregeneration Nantong UniversityNantong 226001China Institute for Stem Cell and Regeneration Chinese Academy of ScienceBeijing 100101China

Hearing loss has become increasingly prevalent and causes considerable disability,thus gravely burdening the global *** loss of hair cells is a main cause of sensorineural hearing loss,and currently,the only relatively effective clinical treatments are limited to digital hearing equipment like cochlear implants and hearing aids,but these are of limited benefit in *** is therefore urgent to understand the mechanisms of damage repair in order to develop new neuroprotective *** present,how to promote the regeneration of functional hair cells is a key scientific question in the field of hearing ***-ple signaling pathways and transcriptional factors trigger the activation of hair cell progenitors and ensure the maturation of newborn hair cells,and in this article,we first review the principal mechanisms underlying hair cell *** then further discuss therapeutic strategies involving the co-regulation of multiple signaling pathways in order to induce effective functional hair cell regeneration after degeneration,and we summarize current achievements in hair cell ***,we discuss potential future approaches,such as small molecule drugs and gene therapy,which might be applied for regenerating functional hair cells in the clinic.

关键词： Hearing loss Cochlea-Stem cell Hair cell regeneration

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Temporal and spatial regulation of biomimetic vascularization in 3D-printed skeletal muscles

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Bio-Design and Manufacturing 2024年第5期7卷 597-610页

作者： Minxuan jia Tingting Fan Tan jia Xin Liu Heng Liu Qi Gu Key Laboratory of Organ Regeneration and Reconstruction State Key Laboratory of Membrane BiologyInstitute of ZoologyChinese Academy of SciencesBeijing 100101China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Orthopaedics Beijing Jishuitan HospitalCapital Medical UniversityBeijing 100035China

In the intricate skeletal muscle tissue,the symbiotic relationship between myotubes and their supporting vasculature is pivotal in delivering essential oxygen and *** study explored the complex interplay between skeletal muscle and endothelial cells in the vascularization ofmuscle *** harnessing the capabilities of three-dimensional(3D)bioprinting and modeling,we developed a novel approach involving the co-construction of endothelial and muscle cells,followed by their subsequent *** findings highlight the importance of the interaction dynamics between these two cell ***,introducing endothelial cells during the advanced phases of muscle differentiation enhanced myotube ***,it stimulated the development of the vascular network,paving the way for the early stages of vascularized skeletal muscle *** methodology proposed in this study indicates the potential for constructing large-scale,physiologically aligned skeletal ***,it highlights the need for exploring the delicate equilibrium and mutual interactions between muscle and endothelial *** on the multicell-type interaction model,we can predict promising pathways for constructing even more intricate tissues or organs.

关键词： Skeletal muscle Vascularization 3D bioprinting Cell interaction

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Application of Cone-beam Computed Tomography in Interventional Therapies for Liver Malignancy:A Consensus Statement by the Chinese College of Interventionalists

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Journal of Clinical and Translational Hepatology 2024年第10期12卷 886-891页

作者： Bin-Yan Zhong Zhong-Zhi jia Wen Zhang Chang Liu Shi-Hong Ying Zhi-Ping Yan Cai-Fang ni Clinical Guidelines Committee of Chinese College of Interventionalists Department of Interventional Radiology The First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina Department of Interventional and Vascular Surgery The Affiliated Changzhou Second People’s Hospital of Nanjing Medical UniversityChangzhouJiangsuChina Department of Interventional Radiology Zhongshan HospitalFudan University Shanghai Institution of Medical ImagingFudan UniversityShanghaiChina Division of Liver Department of General SurgeryWest China HospitalSichuan UniversityChengduSichuanChina Department of Minimal Invasive Surgery Shangjin Nanfu HospitalChengduSichuanChina Department of Radiology First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina 不详

Despite its crucial role in interventional therapies for liver malignancy,cone-beam computed tomography(CBCT)has not yet been fully integrated into clinical practice due to several complicating factors,including nonstandardized operations and limited recognition of CBCT among interventional *** response,the Chinese College of Interventionalists has released a consensus statement aimed at standardizing and promoting the application of CBCT in the interventional therapies for liver *** statement summarizes CBCT scanning techniques,and operational standards,and highlights its potential applications in clinical practice.

关键词： Cone-beam computed tomography Interventional radiology Liver malignancy Consensus statement Chemoembolization Ablation

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Chiral quantum heating and cooling with an optically controlled ion

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Light(Science & Applications) 2024年第7期13卷 1393-1400页

作者： Jin-Tao Bu jian-Qi Zhang Ge-Yi Ding jia-Chong Li jia-Wei Zhang Bin Wang Wen-Qiang Ding Wen-Fei Yuan Liang Chen Qi Zhong Ali Keçebaş Şahin KÖzdemir Fei zhou Hui Jing Mang Feng State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and MathematicsInnovation Academy of Precision Measurement Science and TechnologyChinese Academy of Sciences430071 WuhanChina. University of the Chinese Academy of Sciences 100049 BeijingChina. Research Center for Quantum Precision Measurement Guangzhou Institute of Industry Technology511458 GuangzhouChina. Department of Engineering Science and Mechanics and Materials Research InstitutePennsylvania State UniversityUniversity ParkState CollegePA 16802USA. Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control of Ministry of Education Department of Physics and Synergetic Innovation Center for Quantum Effects and ApplicationsHunan Normal University410081 ChangshaChina. Department of Physics Zhejiang Normal University321004 JinhuaChina

Quantum heat engines and refrigerators are open quantum systems,whose dynamics can be well understood using a non-Hermitian formalism.A prominent feature of non-Hermiticity is the existence of exceptional points(EPs),which has no counterpart in closed quantum *** has been shown in classical systems that dynamical encirclement in the vicinity of an EP,whether the loop includes the EP or not,could lead to chiral mode ***,we show that this is valid also for quantum systems when dynamical encircling is performed in the vicinity of their Liouvillian EPs(LEPs),which include the effects of quantum jumps and associated noise—an important quantum feature not present in previous *** demonstrate,using a Paul-trapped ultracold ion,the first chiral quantum heating and refrigeration by dynamically encircling a closed loop in the vicinity of an *** witness the cycling direction to be associated with the chirality and heat release(absorption)of the quantum heat engine(quantum refrigerator).Our experiments have revealed that not only the adiabaticity breakdown but also the Landau–Zener–Stückelberg process play an essential role during dynamic encircling,resulting in chiral thermodynamic *** observations contribute to further understanding of chiral and topological features in non-Hermitian systems and pave a way to exploring the relation between chirality and quantum thermodynamics.

关键词： quantum chiral dynamical

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Ecological Network Resilience of Shiyang River Basin: An Arid Inland Watershed of Northwest China

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Chinese Geographical Science 2024年第5期34卷 951-966页

作者： HE Yangxi LIU Chunfang ni Bowen LIAN Hugang School of Management Northwest Normal UniversityLanzhou 730070China Research Center of Land Use and Comprehensive Improvement Engineering of Gansu Province Lanzhou 730070China

Due to the uncertainties posed by climate change,resilience has become an increasingly important variable for evaluating regional ecosystem *** assessment of Ecological Network Resilience(ENR)is crucial for establishing mitigation strategies and sustainable socioeconomic development in arid *** River Basin is an arid watershed in Northwest China with complex characteristics,its ENR and spatial differentiation characteristics in 2020 were investigated in this work based on the Complex Adaptive System(CAS)*** results indicated that the mean Ecological Network Resilience Index(ENRI)value for the Shiyang River Basin was 0.390 in 2020,and the mean values in the southern mountainous,middle oasis,and northern desert regions of the basin were 0.598,0.461,and 0.237,respectively,demonstrating evident spatial ***,the ENR of the basin exhibited distinct distribution characteristics across different dimension,whereas the trend of the integrated ENR of the basin was consistent with that of elemental,structural,and functional resilience,indicating the constructed three-region ENR model based on the logical relationship of element-structure-function was suitable for evaluation of the ENR in arid inland river ***,strategies for enhancing regional ENR were proposed from the perspective of adapting to climate change.

关键词： Ecological Network Resilience(ENR) Complex Adaptive System(CAS) element-structure-function Shiyang River Basin Northwest China

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Establishment and validation of a predictive model for peripherally inserted central catheter-related thrombosis in patients with liver cancer

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World Journal of Gastrointestinal Surgery 2024年第7期16卷 2221-2231页

作者： Xiao-Fei Chen Hao-Jun Wu Tang Li jia-Bin Liu Wen-Jie zhou Qiang Guo Department of Thyroid Surgery West China Hospital of Sichuan UniversityChengdu 610041Sichuan ProvinceChina The Second Department of General Surgery Chengdu Shangjinnanfu HospitalWest China Hospital of Sichuan UniversityChengdu 611730Sichuan ProvinceChina Department of Biliary Surgery West China Hospital of Sichuan UniversityChengdu 610041Sichuan ProvinceChina Department of Hepatobiliary and Pancreatic Surgery Chengdu Shangjinnanfu HospitalWest China Hospital of Sichuan UniversityChengdu 611730Sichuan ProvinceChina Department of Vascular Surgery West China Hospital of Sichuan UniversityChengdu 610041Sichuan ProvinceChina

BACKGROUND Peripherally inserted central catheters(PICCs)are commonly used in hospitalized patients with liver cancer for the administration of chemotherapy,nutrition,and other ***,PICC-related thrombosis is a serious complication that can lead to morbidity and mortality in this patient *** risk factors have been identified for the development of PICC-related thrombosis,including cancer type,stage,comorbidities,and catheter *** these risk factors and developing a predictive model can help healthcare providers identify high-risk patients and implement preventive measures to reduce the incidence of *** To analyze the influencing factors of PICC-related thrombosis in hospitalized patients with liver cancer,construct a predictive model,and validate *** Clinical data of hospitalized patients with liver cancer admitted from January 2020 to December 2023 were ***-five cases of PICC-related thrombosis in hospitalized patients with liver cancer were collected,and 220 patients who underwent PICC placement during the same period but did not develop PICC-related thrombosis were randomly selected as controls.A total of 255 samples were collected and used as the training set,and 77 cases were collected as the validation set in a 7:3 *** patient information,case data,catheterization data,coagulation indicators,and Autar Thrombosis Risk Assessment Scale scores were *** and multivariate unconditional logistic regression analyses were performed on relevant factors,and the value of combined indicators in predicting PICC-related thrombosis in hospitalized patients with liver cancer was evaluated using receiver operating characteristic(ROC)curve *** Univariate analysis showed statistically significant differences(P<0.05)in age,sex,Karnofsky performance status score(KPS),bedridden time,activities of daily living impairment,parenteral nutrition,catheter duration,d

关键词： Liver cancer Peripherally inserted central catheters Thrombosis Model Verify

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Enhance the Performance of Directional Feature-based Palmprint Recognition by Directional Response Stability Measurement

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Machine Intelligence Research 2024年第3期21卷 597-614页

作者： Haitao Wang Wei jia School of Computer Science and Information Engineering Hefei University of TechnologyHefei230009China

Palmprint recognition is an emerging biometrics technology that has attracted increasing attention in recent years. Many palmprint recognition methods have been proposed, including traditional methods and deep learning-based methods. Among the traditional methods, the methods based on directional features are mainstream because they have high recognition rates and are robust to illumination changes and small noises. However, to date, in these methods, the stability of the palmprint directional response has not been deeply studied. In this paper, we analyse the problem of directional response instability in palmprint recognition methods based on directional feature. We then propose a novel palmprint directional response stability measurement (DRSM) to judge the stability of the directional feature of each pixel. After filtering the palmprint image with the filter bank, we design DRSM according to the relationship between the maximum response value and other response values for each pixel. Using DRSM, we can judge those pixels with unstable directional response and use a specially designed encoding mode related to a specific method. We insert the DRSM mechanism into seven classical methods based on directional feature, and conduct many experiments on six public palmprint databases. The experimental results show that the DRSM mechanism can effectively improve the performance of these methods. In the field of palmprint recognition, this work is the first in-depth study on the stability of the palmprint directional response, so this paper has strong reference value for research on palmprint recognition methods based on directional features.

关键词： Biometrics palmprint recognition directional response stability directional coding-based methods directional feature

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Imaging, pathology, and diagnosis of solitary fibrous tumor of the pancreas: A case report and review of literature

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World Journal of Clinical Cases 2024年第5期12卷 995-1003页

作者： Wen-Wen Wang Shu-Ping zhou Xiang Wu Luo-Luo Wang Yi Ruan Jun Lu Hai-Li Li Xu-Ling ni Li-Li Qiu Xin-Hua zhou Department of Hepatobiliary and Pancreatic Surgery The Affiliated Li Huili HospitalNingbo University School of MedicineNingbo 315000Zhejiang ProvinceChina ningbo College of Health Sciences Ningbo College of Health SciencesNingbo 315000Zhejiang ProvinceChina Health Science Center Ningbo UniversityNingbo 315000Zhejiang ProvinceChina Department of Hepatobiliary and Pancreatic Surgery The Affiliated Hangzhou First People’s HospitalZhejiang University School of MedicineHangzhou310006Zhejiang ProvinceChina Department of Diagnosis Ningbo Diagnostic Pathology CenterNingbo 315000Zhejiang ProvinceChina

BACKGROUND A solitary fibrous tumor(SFT)is often located in the pleura,while SFT of the pancreas is extremely ***,we report a case of SFT of the pancreas and discuss imaging,histopathology,and immunohistochemistry for accurate diagnosis and *** SUMMARY A 54-year-old man presented to our hospital with pancreatic occupancy for over a *** were no previous complaints of *** blood pressure was *** glucose,tumor markers,and enhanced computed tomography(CT)suggested a malignant *** the CT appearance of pancreatic cancer varies,we could not confirm the diagnosis;therefore,we performed endoscopic ultrasound-guided fine-needle biopsy(EUS-FNB).Pathology and immunohistochemistry were consistent with SFT of the *** posto-perative pathology and immunohistochemistry were consistent with the puncture *** patient presented for a follow-up examination one month after discharge with no adverse *** Other diseases must be excluded in patients with a pancreatic mass that cannot be *** and pathological histology have diagnostic value for pancreatic *** puncture biopsy under ultrasound can help diagnose pancreatic masses that cannot be diagnosed *** is an effective treatment for SFT of the pancreas;however,long-term follow-up is strongly recommended because of the possibility of malignant transformation of the tumor.

关键词： Pancreas Neoplasm fibrous tumor Endoscopic ultrasound-guided fine-needle biopsy Treatment Case report

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