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JOURNAL ARTICLE
Zekun Li, Nadia Benabdallah, Diane S Abou, Brian C Baumann, Farrokh Dehdashti, David H Ballard, Jonathan Liu, Uday Jammalamadaka, Richard Laforest, Richard L Wahl, Daniel L J Thorek, Abhinav K Jha
Single-photon emission-computed tomography (SPECT) provides a mechanism to estimate regional isotope uptake in lesions and at-risk organs after administration of α -particle-emitting radiopharmaceutical therapies ( α -RPTs). However, this estimation task is challenging due to the complex emission spectra, the very low number of detected counts (~20 times lower than in conventional SPECT), the impact of stray-radiation-related noise at these low counts, and the multiple image-degrading processes in SPECT...
January 2023: IEEE Transactions on Radiation and Plasma Medical Sciences
#2
MULTICENTER STUDY
Katina Robison, Kyle Wohlrab, Chanelle J Howe, Holly E Richter, Vivian Sung, Kerri S Bevis, Christine Luis, Carolyn McCourt, Jerry Lowder, John Occhino, Gretchen Glaser, Elizabeth Lokich, Gena Dunivan, Amy Brown, Elena Tunitsky-Bitton, Stephanie Wethington, Chi Chiung Grace Chen, David Rahn, Matthew Carlson, Robin Cram, Christina Raker, Melissa A Clark
OBJECTIVE: To compare quality of life (QOL) among patients with endometrial intraepithelial neoplasia or early-stage endometrial cancer and stress urinary incontinence (SUI) who chose to have concomitant surgery with cancer surgery alone. METHODS: A multicenter, prospective cohort study was conducted across eight U.S. sites. Potentially eligible patients were screened for SUI symptoms. Those who screened positive were offered referral to urogynecology and incontinence treatment, including concomitant surgery...
April 1, 2023: Obstetrics and Gynecology
#3
JOURNAL ARTICLE
Panlai Shi, Hongbin Liang, Yaqin Hou, Duo Chen, Huanan Ren, Conghui Wang, Yanjie Xia, Da Zhang, Don Leigh, David S Cram, Xiangdong Kong
BACKGROUND: Next-generation sequencing for copy number variants is often used as a follow-up investigation of unusual fetal ultrasound results and is capable of detecting copy number variations with a resolution of ∼0.1 Mb. In a prenatal setting, observation and subsequent management of pregnancies with a fetal variant of uncertain significance remains problematic for counseling. OBJECTIVE: This study aimed to follow the decision-making processes in pregnancies with a fetal variant of uncertain significance and prospectively assess copy number variation interpretations and implications under the newer 2020 American College of Medical Genetics and Genomics guidelines...
January 27, 2023: American Journal of Obstetrics and Gynecology
#4
REVIEW
Jessica E M van der Wal, Claire N Spottiswoode, Natalie T Uomini, Mauricio Cantor, Fábio G Daura-Jorge, Anap I Afan, Mairenn C Attwood, Jenny Amphaeris, Fatima Balasani, Colleen M Begg, Cameron J Blair, Judith L Bronstein, Iahaia O Buanachique, Rion R T Cuthill, Jewel Das, Apurba Deb, Tanmay Dixit, Gcina S Dlamini, Edmond Dounias, Isa I Gedi, Martin Gruber, Lilian S Hoffmann, Tobias Holzlehner, Hussein A Isack, Eliupendo A Laltaika, David J Lloyd-Jones, Jess Lund, Alexandre M S Machado, L Mahadevan, Ignacio B Moreno, Chima J Nwaogu, Valdomiro L Pereira, Raymond Pierotti, Seliano A Rucunua, Wilson F Dos Santos, Nathalia Serpa, Brian D Smith, Irina Tolkova, Tint Tun, João V S Valle-Pereira, Brian M Wood, Richard W Wrangham, Dominic L Cram
Human-wildlife cooperation occurs when humans and free-living wild animals actively coordinate their behavior to achieve a mutually beneficial outcome. These interactions provide important benefits to both the human and wildlife communities involved, have wider impacts on the local ecosystem, and represent a unique intersection of human and animal cultures. The remaining active forms are human-honeyguide and human-dolphin cooperation, but these are at risk of joining several inactive forms (including human-wolf and human-orca cooperation)...
July 2022: Conservation Letters
#5
JOURNAL ARTICLE
Li Wang, Xiaohong Wang, Min Li, Yun Liu, Xianghong Ou, Lei Chen, Xiaoguang Shao, Song Quan, Jinliang Duan, Wei He, Huan Shen, Ling Sun, Yuexin Yu, David S Cram, Donald Leigh, Yuanqing Yao
OBJECTIVE: Preimplantation Genetic Testing - Aneuploidy (PGT-A) for embryo selection has undergone significant advancements in the last 2 decades and yet many studies still fail to demonstrate any clinical benefits over traditional embryo morphology selection (Mo-S). To understand this conundrum, we performed a multi-center clinical study of PGT-A patients, where Mo-S and euploid selection (Eu-S) outcomes were directly compared. METHOD: All suitable blastocysts were biopsied and analyzed for chromosome copy number...
August 2022: Prenatal Diagnosis
#6
JOURNAL ARTICLE
Hong-Lei Duan, Jie Li, Wan-Jun Wang, David S Cram, Wei Liu, Pei-Xuan Cao, Xiang-Yu Zhu, Ya-Li Hu
OBJECTIVE: To evaluate the detection rate (DR) by prenatal cell-free DNA test for pathogenic copy number variations (CNVs)＞2 Mb among pregnancies with fetal ultrasound abnormalities. MATERIALS AND METHODS: This was a retrospective study on 29 pregnant women with fetuses diagnosed as microdeletion/microduplication syndromes by prenatal chromosome microarray analysis (CMA). Cell-free DNA from the maternal plasma was sequenced on the NextSeq CN500 sequencer...
November 2021: Taiwanese Journal of Obstetrics & Gynecology
#7
MULTICENTER STUDY
Li Wang, Xiaohong Wang, Yun Liu, Xianghong Ou, Min Li, Lei Chen, Xiaoguang Shao, Song Quan, Jinliang Duan, Wei He, Huan Shen, Ling Sun, Yuexin Yu, David S Cram, Donald Leigh, Yuanqing Yao
OBJECTIVE: Investigate the chromosome status and transfer outcomes of embryos selected using routine "best morphology" IVF practices. METHOD: A prospective multi-center, non-selection cohort study involving patients undertaking IVF treatment. Study entry conditions were blastocyst biopsy, >1 embryo with chromosome analysis and frozen transfer of the best morphology embryo. Primary analyses were βhCG positive, implantation, ongoing pregnancy and birth rates and pregnancy-stage progression failures...
December 2021: Prenatal Diagnosis
#8
JOURNAL ARTICLE
Qiaowei Liang, Wanqian Gu, Ping Chen, Yuezhen Li, Yanqiu Liu, Mao Tian, Qiaomiao Zhou, Hongbo Qi, Yuhong Zhang, Jun He, Qing Li, Lingfang Tang, Juan Tang, Yanling Teng, Yulin Zhou, Shengwen Huang, Zongjie Lu, Mengnan Xu, Wei Hou, Ting Huang, Youqiong Li, Rong Li, Lanping Hu, Shaoying Li, Qiwei Guo, Zhaozhen Zhuo, Yan Mou, David S Cram, Lingqian Wu
The aim of the study was to assess the clinical utility of a third-generation sequencing (TGS) approach termed comprehensive analysis of thalassemia alleles (CATSA) for identifying both α and β thalassemia genetic carrier status. Prospective blood samples (n = 1759) with abnormal hemoglobin parameters were screened for pathogenic thalassemia variants by CATSA on the PacBio TGS platform. In 1159 individuals, a total of 1317 pathogenic thalassemia variants were identified and confirmed by independent PCR-based tests...
September 2021: Journal of Molecular Diagnostics: JMD
#9
JOURNAL ARTICLE
Panlai Shi, Yuan Wang, Hongbin Liang, Yaqin Hou, Duo Chen, Ganye Zhao, Peng Dai, Yanjie Xia, Yin Feng, David S Cram, Xiangdong Kong
OBJECTIVES: To evaluate the clinical potential of a higher resolution noninvasive prenatal screening (NIPS-Plus) test for detection of microdeletion/microduplication syndromes (MMS) in addition to common aneuploidies. METHODS: In a multicenter prospective study, 37,002 pregnant women with unremarkable first-trimester ultrasound scans had a NIPS-Plus test. Ultrasound screen positive women were not included in this study. RESULTS: Of 36,970 ultrasound negative women there were 291 NIPS-Plus screen positive results indicating 237 aneuploidies and 54 MMS...
September 2021: Prenatal Diagnosis
#10
JOURNAL ARTICLE
Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S Cram, Yu Zhang
BACKGROUND: Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretation of identified variants a challenge in terms of precision and efficiency. In addition, the non-standardized phenotypic description of human diseases also makes it difficult to establish an integrated analysis pathway for variant annotation and interpretation. Solutions to these bottlenecks are urgently needed...
June 3, 2021: BMC Genomics
#11
COMPARATIVE STUDY
Yanfei Cheng M M, Qian Yu, Minyue Ma, Hui Wang, Shuang Tian, Wenling Zhang, Jinning Zhang M M, Yifan Liu, Qi Yang, Xiao Pan, Hongbin Liang, Li Wang, Don Leigh, David S Cram, Yuanqing Yao
OBJECTIVE: To apply long-read, third-generation sequencing as a part of a general workup strategy for performing structural rearrangement (PGT-SR) and monogenic disease (PGT-M) embryo testing. DESIGN: Prospective study. SETTING: In vitro fertilization unit. PATIENT(S): Couples presenting for PGT-SR (n = 15) and PGT-M (n = 2). INTERVENTION(S): Blastocyst biopsy with molecular testing for translocation breakpoints or mutations (targets)...
September 2021: Fertility and Sterility
#12
JOURNAL ARTICLE
Chuanfeng Zhang, Mengjiao Cao, Tangshan Lv, Hongyan Wang, Xiaoxiao Liu, Yong Xie, Nonghua Lv, Hongtan Chen, David S Cram, Jing Zhong, Linfu Zhou
In China, there is a high prevalence of antibiotic-resistant Helicobacter pylori infections in the population. The aim of the study was to assess a new ARMS-PCR test for detection of H. pylori clarithromycin resistance (CR) and quinolone resistance (QR) mutations and evaluate the spectrum of antibiotic resistance in patients from three Chinese provinces. Sanger sequencing and multiplex ARMS-PCR were used to detect H. pylori CR and QR bacteria in gastric biopsy samples. Among the 1,182 patients enrolled with gastritis, 643 (54...
March 1, 2021: European Journal of Clinical Microbiology & Infectious Diseases
#13
JOURNAL ARTICLE
Xiya Zhou, Xiangbin Chen, Yulin Jiang, Qingwei Qi, Na Hao, Chengkun Liu, Mengnan Xu, David S Cram, Juntao Liu
Next-generation sequencing (NGS) is emerging as a new method for the detection of clinically significant copy number variants (CNVs). In this study, we developed and validated rapid CNV-sequencing (rCNV-seq) for clinical application in prenatal diagnosis. Low-pass whole-genome sequencing was performed on PCR libraries prepared from amniocyte genomic DNA. From 10-40 ng of input DNA, PCR-free libraries consistently produced sequencing data with high unique read mapping ratios, low read redundancy, low coefficient of variation for all chromosomes and high genomic coverage...
January 28, 2021: Life
#14
JOURNAL ARTICLE
Sai Liu, Hui Wang, Don Leigh, David S Cram, Li Wang, Yuanqing Yao
PURPOSE: To investigate use of the third-generation sequencing (TGS) Oxford Nanopore system as a new approach for preimplantation genetic testing (PGT). METHODS: Embryos with known structural variations underwent multiple displacement amplification to create fragments of DNA (average ~ 5 kb) suitable for sequencing on a nanopore. RESULTS: High-depth sequencing identified the deletion interval for the relatively large HBA1/2--SEA alpha thalassemia deletion...
February 2021: Journal of Assisted Reproduction and Genetics
#15
JOURNAL ARTICLE
Mengmeng Liu, Yunshan Zhong, Hongqian Liu, Desheng Liang, Erhong Liu, Yu Zhang, Feng Tian, Qiaowei Liang, David S Cram, Hua Wang, Lingqian Wu, Fuli Yu
BACKGROUND: Current copy number variation (CNV) identification methods have rapidly become mature. However, the postdetection processes such as variant interpretation or reporting are inefficient. To overcome this situation, we developed REDBot as an automated software package for accurate and direct generation of clinical diagnostic reports for prenatal and products of conception (POC) samples. METHODS: We applied natural language process (NLP) methods for analyzing 30,235 in-house historical clinical reports through active learning, and then, developed clinical knowledge bases, evidence-based interpretation methods and reporting criteria to support the whole postdetection pipeline...
November 2020: Molecular Genetics & Genomic Medicine
#16
JOURNAL ARTICLE
Long Huang, Xiao-Liu Jiang, Hong-Bin Liang, Jian-Cheng Li, Li-Han Chin, Jian-Ping Wei, Rui-Ru Wang, Jing Cai, Qiang Xiong, Lien-Tu Wang, David S Cram, An-Wen Liu
BACKGROUND: Patients newly diagnosed with lung adenocarcinoma with bone metastases (LABM) have poor survival rates after treatment with conventional therapies. To improve outcomes, we retrospectively investigated whether the application of a more comprehensive genetic test of tumor biopsies samples from LABM patients could provide the basis for treatment with more effective tyrosine kinase inhibitors (TKIs) regimens. METHODS: Fine needle biopsies were taken from the primary tumor (PT) and a secondary bone metastasis (BM) of 17 LABM patients before treatment...
September 17, 2020: Molecular Medicine
#17
JOURNAL ARTICLE
Zheng Wang, Lin Zhang, Lei He, Di Cui, Chenglong Liu, Liangyu Yin, Min Zhang, Lei Jiang, Yuyan Gong, Wang Wu, Bi Liu, Xiaoyu Li, David S Cram, Dongge Liu
Objective: Histology grade, subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival. The aim of the study was to investigate the relationship between chromosomal instability, morphological subtypes and the grading system used in lung non-mucinous adenocarcinoma (LNMA). Methods: We developed a whole genome copy number variation (WGCNV) scoring system and applied next generation sequencing to evaluate CNVs present in 91 LNMA tumor samples...
June 2020: Chinese Journal of Cancer Research
#18
JOURNAL ARTICLE
Yangxia Li, Tangshan Lv, Chaochao He, Hongyan Wang, David S Cram, Linfu Zhou, Jun Zhang, Weiqin Jiang
Background: Helicobacter pylori bacterium is a major cause of gastritis. With increasing use of antibiotics to treat infections, mutation resistant strains have emerged in most human populations. To effectively treat patients to help resolve infections, the clinician needs information on the antibiotic susceptibility profile of the infection. Therefore, a rapid and accurate test is required to provide this information. To address this issue, we designed and validated a real time multiplex ARMS-PCR assay for rapid detection of highly prevalent H...
2020: Gut Pathogens
#19
JOURNAL ARTICLE
C Alina Cansler, Sharon M Hood, J Morgan Varner, Phillip J van Mantgem, Michelle C Agne, Robert A Andrus, Matthew P Ayres, Bruce D Ayres, Jonathan D Bakker, Michael A Battaglia, Barbara J Bentz, Carolyn R Breece, James K Brown, Daniel R Cluck, Tom W Coleman, R Gregory Corace, W Wallace Covington, Douglas S Cram, James B Cronan, Joseph E Crouse, Adrian J Das, Ryan S Davis, Darci M Dickinson, Stephen A Fitzgerald, Peter Z Fulé, Lisa M Ganio, Lindsay M Grayson, Charles B Halpern, Jim L Hanula, Brian J Harvey, J Kevin Hiers, David W Huffman, MaryBeth Keifer, Tara L Keyser, Leda N Kobziar, Thomas E Kolb, Crystal A Kolden, Karen E Kopper, Jason R Kreitler, Jesse K Kreye, Andrew M Latimer, Andrew P Lerch, Maria J Lombardero, Virginia L McDaniel, Charles W McHugh, Joel D McMillin, Jason J Moghaddas, Joseph J O'Brien, Daniel D B Perrakis, David W Peterson, Susan J Prichard, Robert A Progar, Kenneth F Raffa, Elizabeth D Reinhardt, Joseph C Restaino, John P Roccaforte, Brendan M Rogers, Kevin C Ryan, Hugh D Safford, Alyson E Santoro, Timothy M Shearman, Alice M Shumate, Carolyn H Sieg, Sheri L Smith, Rebecca J Smith, Nathan L Stephenson, Mary Stuever, Jens T Stevens, Michael T Stoddard, Walter G Thies, Nicole M Vaillant, Shelby A Weiss, Douglas J Westlind, Travis J Woolley, Micah C Wright
Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire...
June 22, 2020: Scientific Data
#20
JOURNAL ARTICLE
Liangpu Xu, Aiping Mao, Hui Liu, Baoheng Gui, Kwong W Choy, Hailong Huang, Qian Yu, Xiaojie Zhang, Meihuan Chen, Na Lin, Lingji Chen, Jin Han, Yan Wang, Min Zhang, Xiaoyu Li, Deqin He, Yuan Lin, Jianguang Zhang, David S Cram, Hua Cao
Multiple molecular tests are currently needed for accurate carrier testing for thalassemia. Therefore, long-molecule sequencing (LMS) was evaluated as an alternate on the PacBio Sequel platform for genotyping carriers of α-thalassemia or β-thalassemia. Multiplex long PCR was used to generate representative amplicons for the α (HBA1/2) and β (HBB) gene loci. Following LMS, circular consensus sequencing reads were aligned to the hg19 reference genome and variants called using FreeBayes software version 1...
August 2020: Journal of Molecular Diagnostics: JMD
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