keyword
https://read.qxmd.com/read/38535561/total-infectome-characterization-of-respiratory-infections-during-the-2022-23-covid-19-outbreak-in-china-revealed-extensive-coinfections-with-links-to-sars-cov-2-status-age-and-disease-severity
#1
JOURNAL ARTICLE
Zhongzhou Yang, Kanru Cai, Yuqi Liao, Wei-Chen Wu, Li Xing, Minxuan Hu, Jiali Ren, Jieyun Zhang, Xiuyun Zhu, Ke Yuan, Shunyao Wang, Hui Huang, Chunhui Yang, Mingxia Zhang, Mang Shi, Hongzhou Lu
Between 7 December 2022 and 28 February 2023, China experienced a new wave of COVID-19 that swept across the entire country and resulted in an increasing amount of respiratory infections and hospitalizations. The purpose of this study is to reveal the intensity and composition of coinfecting microbial agents. In total, 196 inpatients were recruited from The Third People's Hospital of Shenzhen, and 169 respiratory and 73 blood samples were collected for metagenomic next-generation sequencing. The total "Infectome" was characterized and compared across different groups defined by the SARS-CoV-2 detection status, age groups, and severity of disease...
February 29, 2024: Pathogens
https://read.qxmd.com/read/38535545/resurgence-of-dengue-virus-serotype-3-in-minas-gerais-brazil-a-case-report
#2
Talita Adelino, Maurício Lima, Natália R Guimarães, Joilson Xavier, Vagner Fonseca, Luiz Marcelo R Tomé, Maira Alves Pereira, Vanessa Ferreira Machado, Luiz Carlos Junior Alcantara, Felipe C de Melo Iani, Marta Giovanetti
This report provides a detailed overview of the resurgence of DENV-3 in the state of Minas Gerais, Brazil, which is a concerning scenario in the context of dengue, a mosquito-borne viral disease. Historically, Brazil has grappled with dengue epidemics caused primarily by the DENV-1 and DENV-2 serotypes. However, in 2023, a significant shift in this pattern was observed as DENV-3 made a notable resurgence. This resurgence was characterized by the increase in DENV-3 cases within the country and the region of the Americas...
February 24, 2024: Pathogens
https://read.qxmd.com/read/38535349/microbiome-of-invasive-tick-species-haemaphysalis-longicornis-in-north-carolina-usa
#3
JOURNAL ARTICLE
Loganathan Ponnusamy, Nicholas V Travanty, D Wes Watson, Steven W Seagle, Ross M Boyce, Michael H Reiskind
Ticks are one of the most important vectors of human and animal disease worldwide. In addition to pathogens, ticks carry a diverse microbiota of symbiotic and commensal microorganisms. In this study, we used next-generation sequencing (NGS) to survey the microbiomes of Haemaphysalis longicornis (Acari: Ixodidae) at different life stages collected from field populations in North Carolina (NC), USA. Sequence analyses were performed using QIIME2 with the DADA2 plugin and taxonomic assignments using the Greengenes database...
February 24, 2024: Insects
https://read.qxmd.com/read/38535124/future-of-dutch-ngs-based-newborn-screening-exploring-the-technical-possibilities-and-assessment-of-a-variant-classification-strategy
#4
JOURNAL ARTICLE
Gea Kiewiet, Dineke Westra, Eddy N de Boer, Emma van Berkel, Tom G J Hofste, Martine van Zweeden, Ronny C Derks, Nico F A Leijsten, Martina H A Ruiterkamp-Versteeg, Bart Charbon, Lennart Johansson, Janneke Bos-Kruizinga, Inge J Veenstra, Monique G M de Sain-van der Velden, Els Voorhoeve, M Rebecca Heiner-Fokkema, Francjan van Spronsen, Birgit Sikkema-Raddatz, Marcel Nelen
In this study, we compare next-generation sequencing (NGS) approaches (targeted panel (tNGS), whole exome sequencing (WES), and whole genome sequencing (WGS)) for application in newborn screening (NBS). DNA was extracted from dried blood spots (DBS) from 50 patients with genetically confirmed inherited metabolic disorders (IMDs) and 50 control samples. One hundred IMD-related genes were analyzed. Two data-filtering strategies were applied: one to detect only (likely) pathogenic ((L)P) variants, and one to detect (L)P variants in combination with variants of unknown significance (VUS)...
March 7, 2024: International Journal of Neonatal Screening
https://read.qxmd.com/read/38535123/harnessing-next-generation-sequencing-as-a-timely-and-accurate-second-tier-screening-test-for-newborn-screening-of-inborn-errors-of-metabolism
#5
JOURNAL ARTICLE
Toby Chun Hei Chan, Chloe Miu Mak, Matthew Chun Wing Yeung, Eric Chun-Yiu Law, Jana Cheung, Tsz Ki Wong, Vincent Wing-Sang Cheng, Jacky Kwan Ho Lee, Jimmy Chi Lap Wong, Cheuk Wing Fung, Kiran Moti Belaramani, Anne Mei Kwun Kwok, Kwok Yeung Tsang
In this study, we evaluated the implementation of a second-tier genetic screening test using an amplicon-based next-generation sequencing (NGS) panel in our laboratory during the period of 1 September 2021 to 31 August 2022 for the newborn screening (NBS) of six conditions for inborn errors of metabolism: citrullinemia type II (MIM #605814), systemic primary carnitine deficiency (MIM #212140), glutaric acidemia type I (MIM #231670), beta-ketothiolase deficiency (#203750), holocarboxylase synthetase deficiency (MIM #253270) and 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (MIM # 246450)...
March 5, 2024: International Journal of Neonatal Screening
https://read.qxmd.com/read/38535092/performance-of-a-novel-eight-color-flow-cytometry-panel-for-measurable-residual-disease-assessment-of-chronic-lymphocytic-leukemia
#6
JOURNAL ARTICLE
Xiao Chen, Xia Chen, Sishu Zhao, Yu Shi, Ninghan Zhang, Zhen Guo, Chun Qiao, Huimin Jin, Liying Zhu, Huayuan Zhu, Jianyong Li, Yujie Wu
BACKGROUND: Measurable residual disease (MRD) is an important prognostic indicator of chronic lymphocytic leukemia (CLL). Different flow cytometric panels have been developed for the MRD assessment of CLL in Western countries; however, the application of these panels in China remains largely unexplored. METHODS: Owing to the requirements for high accuracy, reproducibility, and comparability of MRD assessment in China, we investigated the performance of a flow cytometric approach (CD45-ROR1 panel) to assess MRD in patients with CLL...
March 27, 2024: Cytometry. Part B, Clinical Cytometry
https://read.qxmd.com/read/38534951/ductal-adenocarcinoma-of-the-prostate-with-novel-genetic-alterations-characterized-by-next-generation-sequencing
#7
Alexandra Zara Rozalen, Jose Manuel Martin, Rithika Rajendran, Maneesh Jain, Victor E Nava
Ductal adenocarcinoma of the prostate (DAP) is an uncommon variant of prostate cancer associated with aggressive disease and poor outcome. It presents most frequently as a mixed tumor combined with acinar adenocarcinoma. Although the histopathological features of DAP are well known, its genomic characteristics are still evolving, prompting the suggestion that all DAP would benefit from molecular analysis with the purpose of improving tumor recognition, genetic classification, and, ultimately, personalized therapy...
March 19, 2024: Current Oncology
https://read.qxmd.com/read/38534936/barriers-and-unequal-access-to-timely-molecular-testing-results-addressing-the-inequities-in-cancer-care-delays-across-canada
#8
Stephanie Snow, Christine Brezden-Masley, Michael D Carter, Neesha Dhani, Cassandra Macaulay, Ravi Ramjeesingh, Michael J Raphael, Monika Slovinec D'Angelo, Filomena Servidio-Italiano
Genomic medicine is a powerful tool to improve diagnosis and outcomes for cancer patients by facilitating the delivery of the right drug at the right dose at the right time for the right patient. In 2023, a Canadian conference brought together leaders with expertise in different tumor types. The objective was to identify challenges and opportunities for change in terms of equitable and timely access to biomarker testing and reporting at the education, delivery, laboratory, patient, and health-system levels in Canada...
March 6, 2024: Current Oncology
https://read.qxmd.com/read/38534697/post-covid-19-pandemic-rebound-of-macrolide-resistant-mycoplasma-pneumoniae-infection-a-descriptive-study
#9
JOURNAL ARTICLE
Fan-Fan Xing, Kelvin Hei-Yeung Chiu, Chao-Wen Deng, Hai-Yan Ye, Lin-Lin Sun, Yong-Xian Su, Hui-Jun Cai, Simon Kam-Fai Lo, Lei Rong, Jian-Liang Chen, Vincent Chi-Chung Cheng, David Christopher Lung, Siddharth Sridhar, Jasper Fuk-Woo Chan, Ivan Fan-Ngai Hung, Kwok-Yung Yuen
The rebound characteristics of respiratory infections after lifting pandemic control measures were uncertain. From January to November 2023, patients presenting at a teaching hospital were tested for common respiratory viruses and Mycoplasma pneumoniae using a combination of antigen, nucleic acid amplification, and targeted next-generation sequencing (tNGS) tests. The number and rate of positive tests per month, clinical and microbiological characteristics were analyzed. A rapid rebound of SARS-CoV-2 was followed by a slower rebound of M...
March 15, 2024: Antibiotics
https://read.qxmd.com/read/38534459/the-effects-of-salinity-and-genotype-on-the-rhizospheric-mycobiomes-in-date-palm-seedlings
#10
JOURNAL ARTICLE
Mahmoud W Yaish, Aya Al-Busaidi, Bernard R Glick, Talaat Ahmed, Juha M Alatalo
Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool...
March 15, 2024: Biology
https://read.qxmd.com/read/38534348/implementing-whole-genome-sequencing-wgs-in-clinical-practice-advantages-challenges-and-future-perspectives
#11
REVIEW
Petar Brlek, Luka Bulić, Matea Bračić, Petar Projić, Vedrana Škaro, Nidhi Shah, Parth Shah, Dragan Primorac
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations...
March 13, 2024: Cells
https://read.qxmd.com/read/38533931/low-cycle-number-multiplex-pcr-a-novel-strategy-for-the-construction-of-amplicon-libraries-for-next-generation-sequencing
#12
JOURNAL ARTICLE
Meng Lu, Xiuxiu Sun, Yuxin Zhao, Linlin Zheng, Junjie Lin, Chen Tang, Kaiyue Chao, Ye Chen, Kai Li, Yuxun Zhou, Junhua Xiao
Multiplex PCR is a critical step when preparing amplicon library for next-generation sequencing. However, there are several challenges related to multiplex PCR including poor uniformity, nonspecific amplification, and primer-dimers. To address these issues, we propose a novel solution strategy that involves using a low cycle number (<10 cycles) in multiplex PCR and then employing carrier DNAs and magnetic beads for the selection of targeted products. This technique improves the amplicon uniformity while also reducing primer-dimers and PCR artifacts...
March 27, 2024: Electrophoresis
https://read.qxmd.com/read/38533679/the-utility-of-electrodiagnostic-testing-in-unprovoked-rhabdomyolysis-in-the-era-of-next-generation-sequencing
#13
JOURNAL ARTICLE
Michael P Skolka, Margherita Milone, William J Litchy, Ruple S Laughlin, Devon I Rubin, Teerin Liewluck
INTRODUCTION/AIMS: Rhabdomyolysis is an etiologically heterogeneous, acute necrosis of myofibers characterized by transient marked creatine kinase (CK) elevation associated with myalgia, muscle edema, and/or weakness. The study aimed to determine the role of electrodiagnostic (EDX) testing relative to genetic testing and muscle biopsy in patients with unprovoked rhabdomyolysis in identifying an underlying myopathy. METHODS: EDX database was reviewed to identify unprovoked rhabdomyolysis patients who underwent EDX testing between January 2012 and January 2022...
March 27, 2024: Muscle & Nerve
https://read.qxmd.com/read/38533516/the-challenge-of-managing-ischemic-stroke-in-brucellosis-a-case-report
#14
Linfa Chen, Xiaolong Lin, Xiuqu Cai, Shiting Zeng, Yanquan Yuan, Zhiyong Huang, Jinjin Yan, You Li
A 64-year-old woman was admitted to the hospital for sudden weakness in one of her left limbs. The patient was diagnosed with acute ischemic stroke (IS) of undetermined cause and received intravenous thrombolysis. Following thrombolysis, the patient's left limb weakness improved, but she subsequently developed recurrent high fever and delirium. Further diagnostic tests revealed that she had been infected with Brucella melitensis . The patient showed significant improvement during anti-infection treatment for Brucellosis and secondary prevention treatment for IS...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38533514/single-cell-transcriptome-sequencing-provides-insight-into-multiple-chemotherapy-resistance-in-a-patient-with-refractory-dlbcl-a-case-report
#15
Kewei Zhao, Qiuhui Li, Pengye Li, Tao Liu, Xinxiu Liu, Fang Zhu, Liling Zhang
Relapsed and refractory diffuse large B-cell lymphoma (DLBCL) is associated with poor prognosis. As such, a comprehensive analysis of intratumoral components, intratumoral heterogeneity, and the immune microenvironment is essential to elucidate the mechanisms driving the progression of DLBCL and to develop new therapeutics. Here, we used single-cell transcriptome sequencing and conventional bulk next-generation sequencing (NGS) to understand the composite tumor landscape of a single patient who had experienced multiple tumor recurrences following several chemotherapy treatments...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38533204/corrigendum-extension-of-mitogenome-enrichment-based-on-single-long-range-pcr-mtdnas-and-putative-mitochondrial-derived-peptides-of-five-rodent-hibernators
#16
Sarah V Emser, Helmut Schaschl, Eva Millesi, Ralf Steinborn
[This corrects the article DOI: 10.3389/fgene.2021.685806.].
2024: Frontiers in Genetics
https://read.qxmd.com/read/38532782/identification-of-a-novel-non-v600e-braf-mutation-in-papillary-thyroid-cancer
#17
Marco Capezzone, Maja Rossi, Elisabetta Macerola, Silvia Cantara, Francesco Pepe, Eugenia Maria Morabito, Gilda Dalmazio, Sara Bardi, Agostino Ognibene, Massimo Alessandri, Gabriele Materazzi, Luigi De Napoli, Michele Cirianni, Liborio Torregrossa
Papillary thyroid cancer (PTC) is a common endocrine malignancy, and its incidence is reported to be constantly increasing. BRAF mutation is detected in approximately 44% of PTCs, and the most common BRAF mutation is thymine (T) to adenine (A) missense mutation in nucleotide 1796 (T1796A, V600E). Although BRAFV600E represents 95% of all BRAF mutations, uncommon BRAF mutations have been reported in thyroid carcinomas and represent an alternative mechanism of BRAF activation with unclear clinical significance...
2024: Case Reports in Endocrinology
https://read.qxmd.com/read/38532566/analyses-of-tertiary-lymphoid-structures-observed-in-cases-of-merkel-cell-carcinoma-showing-spontaneous-regression
#18
JOURNAL ARTICLE
Motoki Nakamura, Maki Yoshimitsu, Tetsuya Magara, Shinji Kano, Hiroshi Kato, Akimichi Morita
Merkel cell carcinoma (MCC) is a high-grade skin cancer, but spontaneous regression is observed at a markedly higher frequency than in other carcinomas. Although spontaneous regression is a phenomenon that greatly impacts treatment planning, we still cannot predict it. We previously reported on the prognostic impact of the presence or absence of tertiary lymphoid structures (TLS) and of Merkel cell polyomavirus (MCPyV) infection. To learn more about the spontaneous regression of MCC, detailed analyses were performed focusing on spontaneous regression cases...
March 2024: Experimental Dermatology
https://read.qxmd.com/read/38532509/when-rare-meets-common-treatable-genetic-diseases-are-enriched-in-the-general-psychiatric-population
#19
JOURNAL ARTICLE
Venuja Sriretnakumar, Ricardo Harripaul, James L Kennedy, Joyce So
Mental illnesses are one of the biggest contributors to the global disease burden. Despite the increased recognition, diagnosis and ongoing research of mental health disorders, the etiology and underlying molecular mechanisms of these disorders are yet to be fully elucidated. Moreover, despite many treatment options available, a large subset of the psychiatric patient population is nonresponsive to standard medications and therapies. There has not been a comprehensive study to date examining the burden and impact of treatable genetic disorders (TGDs) that can present with neuropsychiatric features in psychiatric patient populations...
March 26, 2024: American Journal of Medical Genetics. Part A
https://read.qxmd.com/read/38532348/comparison-of-metagenomic-next-generation-sequencing-and-conventional-culture-for-the-diagnostic-performance-in-febrile-patients-with-suspected-infections
#20
JOURNAL ARTICLE
Hui Yang, Nannan Xu, Meichen Yan, Lulu Yang, Sai Wen, Shanshan Wang, Chunmei Qu, Ke Xu, Xuying Yang, Gang Wang
BACKGROUND: Timely and accurate identification of pathogens is crucial for appropriate treatment and prognosis of infectious diseases. As an increasingly popular pathogen detection method, the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in febrile patients with suspected infection requires further exploration. METHODS: This study included 368 febrile patients with suspected infections who were admitted to the Infectious Disease Department of Qilu Hospital, Shandong University between January 5, 2021 and April 14, 2023...
March 26, 2024: BMC Infectious Diseases
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