An initial benchmark of the quality of the diagnosis and surgical treatment of breast cancer in South Africa by S Nietz, H Cubasch, I Buccimazza, S Čačala, B Phakathi, M Joffe, W C C Chen, S Norris, P Ruff

“…Rates of positive margins (5.7%), overall axillary surgery (95.8%) and appropriate treatment sequencing in locally advanced breast cancer patients (98.4%) consistently reached minimum international standards. …”
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Fine mapping of qRC10-2, a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages. by Ning Xiao, Wei-Nan Huang, Xiao-Xiang Zhang, Yong Gao, Ai-Hong Li, Yi Dai, Ling Yu, Guang-Qing Liu, Cun-Hong Pan, Yu-Hong Li, Zheng-Yuan Dai, Jian-Min Chen

“…A total of 113 codominant simple-sequence repeat (SSR) markers were developed, with a parental polymorphism of 17.3%. …”
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Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity by Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad, Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar, Ann Caplin, Daniel Muliaditan, Aditi Gnanasekar, Ceyda Coruh, Qiushi Jin, Kristen Turner, Shu Xian Teo, Andy Wing Chun Pang, Ludmil B. Alexandrov, Christelle En Lin Chua, Frank B. Furnari, John Maciejowski, Thomas G. Paulson, Julie A. Law, Howard Y. Chang, Feng Yue, Ramanuj DasGupta, Jean Zhao, Paul S. Mischel, Vineet Bafna

“…We identify 371 BFB events through whole genome sequencing of 2557 primary tumors and cancer cell lines. …”
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A Two-Way Mendelian Randomization Analysis on the Link between Thyroid Activity Function and Coronary Atherosclerosis by Le-tai Li, Jia-jie Leng, Yu-xiang Luo, Rong-jia Liu, Zhuo-xuan Song, Meng Ye, Zhen-han Li, Zhen-rui Cao, Ying-jiu Jiang, Hong-tao Tie

“…Following the application of strict criteria to eliminate linkage disequilibrium, palindromic sequences, and heterozygous alleles, a bidirectional Mendelian Randomization (MR) analysis was conducted between the thyroid gland and coronary atherosclerosis using inverse variance weighting (IVW), weighted median (WM), and MR-Egger techniques. …”
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Association between oral microbiome and sleep disorders in U.S. adults: analysis of NHANES database 2009–2012 by Guihua Hao, Yiwen Wu, Xiaoqiao Mo, Xiaomei Zhao, Lili Hou, Tian Xie

“…The oral microbiome was characterized by 16 S ribosomal RNA gene sequencing. Logistic regression models were conducted to quantify the association of α-diversity with different sleep status controlling for potential confounding variables, and principal coordinate analysis along with permutational multivariate analysis of variance for β-diversity. …”
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Fecal microbiome analysis in patients with metabolic syndrome and type 2 diabetes by Laura Isabel Sinisterra Loaiza, Diego Fernández-Edreira, Jose Liñares-Blanco, Alberto Cepeda, Alejandra Cardelle-Cobas, Carlos Fernandez-Lozano

“…To analyze the microbiota composition, amplicon sequencing of 16S rRNA genes was performed on stool samples. …”
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High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot... by Dongliang Wu, Chuanzhi Zhao, Walid Korani, Ethan A. Thompson, Hui Wang, Gaurav Agarwal, Jake C. Fountain, Albert Culbreath, C. Corley Holbrook, Xingjun Wang, Josh P. Clevenger, Baozhu Guo

“…QTL analyses identified two major QTLs, explaining 41.43% and 43.69% of the phenotypic variance within 3.6 cM and 0.28 cM intervals using the peanut Axiom_Arachis-v1 and Axiom_Arachis-v2 SNP arrays, respectively, on chromosome A01. …”
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Genetic Associations of <i>ACOX2</i> Gene with Milk Yield and Composition Traits in Chinese Holstein Cows by Hui Cao, Zhe Wang, Lingna Xu, Bo Han, Dongxiao Sun

“…Herein, we evaluated its genetic effects on milk production traits in 922 Chinese Holstein cows. By sequencing the entire coding region and 2000 bp of the 5′ and 3′ flanking sequences of the <i>ACOX2</i> gene, we identified a total of five SNPs, including one SNP in the 5′ UTR, one in intron 5, and three in the 3′ flanking region. …”
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Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study. by Eugene Duff, Fernando Zelaya, Fidel Alfaro Almagro, Karla L Miller, Naomi Martin, Thomas E Nichols, Bernd Taschler, Ludovica Griffanti, Christoph Arthofer, Gwenaëlle Douaud, Chaoyue Wang, Thomas W Okell, Richard A I Bethlehem, Klaus Eickel, Matthias Günther, David K Menon, Guy Williams, Bethany Facer, David J Lythgoe, Flavio Dell'Acqua, Greta K Wood, Steven C R Williams, Gavin Houston, Simon S Keller, Catherine Holden, Monika Hartmann, Lily George, Gerome Breen, Benedict D Michael, Peter Jezzard, Stephen M Smith, Edward T Bullmore, COVID-CNS Consortium

“…A multi-modal brain MRI protocol comprising sequences for T1-weighted MRI, T2-FLAIR, diffusion MRI (dMRI), resting-state functional MRI (fMRI), susceptibility-weighted imaging (swMRI), and arterial spin labelling (ASL), was defined in close approximation to prior UK Biobank (UKB) and C-MORE protocols for Siemens 3T systems. …”
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Investigating the Role of Intravoxel Incoherent Motion Diffusion-Weighted Imaging in Evaluating Multiple Sclerosis Lesions by Othman I. Alomair, Sami A. Alghamdi, Abdullah H. Abujamea, Ahmed Y. AlfIfi, Yazeed I. Alashban, Nyoman D. Kurniawan

“…The field strength was 1.5 Tesla. The imaging sequences included three-dimensional (3D) T₁, 3D fluid-attenuated inversion recovery, two-dimensional (2D) T₁, T₂-weighted imaging, and 2D diffusion-weighted imaging (DWI) sequences. …”
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Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses. by William H Palmer, Nathan C Medd, Philippa M Beard, Darren J Obbard

“…Using full transcriptome sequencing of infected males and females, we examine the transcriptional response of flies to Kallithea virus infection and describe differential regulation of virus-responsive genes. …”
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Uncovering pyrethroid resistance mechanisms in Anopheles punctulatus group mosquitoes: A novel insight from Keerom, Papua, Indonesia by Lepa Syahrani, Puji B. S. Asih, Ismail E. Rozi, Astari Dwiranti, Dendi H. Permana, Irdayanti Irdayanti, Anom Bowolaksono, Din Syafruddin

“…Molecular identification and detection of kdr mutations (L1014F/S) were performed using species-specific polymerase chain reaction and sequencing protocols. Allele frequencies were analyzed using Hardy–Weinberg equilibrium models, and statistical comparisons were made using one-way analysis of variance. …”
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Immunoinformatic-driven design and evaluation of multi-epitope mRNA vaccine targeting HIV-1 gp120 by Muhammad Zeeshan Ahmed, Muhammad Zeeshan Ahmed, Tazeen Rao, Zeeshan Mutahir, Sarfraz Ahmed, Najeeb Ullah, Suvash Chandra Ojha

“…The endeavor to devise an HIV vaccine capable of eliciting robust and broadly cross-reactive humoral and cellular immune responses is a formidable undertaking, primarily due to the pronounced genetic heterogeneity of HIV-1, the variances observed in virus subtypes (clades) across distinct geographic regions, and the polymorphic nature of human leukocyte antigens (HLA). …”
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Comprehensive Analysis of Phenotypic Traits in Chinese Cabbage Using 3D Point Cloud Technology by Chongchong Yang, Lei Sun, Jun Zhang, Xiaofei Fan, Dongfang Zhang, Tianyi Ren, Minggeng Liu, Zhiming Zhang, Wei Ma

“…By using multi-view image sequences and structure-from-motion algorithms, 3D point clouds of 50 plants from each of the 17 Chinese cabbage varieties were reconstructed. …”
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Integrated functional genomic analysis identifies regulatory variants underlying a major QTL for disease resistance in European sea bass by Robert Mukiibi, Serena Ferraresso, Rafaella Franch, Luca Peruzza, Giulia Dalla Rovere, Massimiliano Babbucci, Daniela Bertotto, Anna Toffan, Francesco Pascoli, Sara Faggion, Carolina Peñaloza, Costas S. Tsigenopoulos, Ross D. Houston, Luca Bargelloni, Diego Robledo

“…Results The estimated heritability of VNN resistance was high (h 2 ~ 0.40), and a major QTL explaining up to 38% of the genetic variance of the trait was confirmed on chromosome 3, with individuals with the resistant QTL genotype showing a 90% survivability against a VNN outbreak. …”
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Changes in Soil Microbial Community Structure and Assembly Process Under Different Forest Restoration Strategies in Cold Temperate Forests of Northeastern China by Rongze Luo, Mingyu Wang, Youjia Zhang, Hong Wang, Xiangyu Meng, Xin Gao, Yuhe Zhang, Xin Sui, Maihe Li

“…Furthermore, analysis of variance for differences between groups shows that <i>Incoybe</i> plays a crucial role in artificial restoration. …”
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Dissection of the genetic basis and molecular mechanism of ovule number per ovary in oilseed rape (Brassica napus L.) by Muslim Qadir, Muslim Qadir, Muslim Qadir, Xinyi Lin, Farhan Nabi, Kishore Kumar Ashok, Xue-Rong Zhou, Qingbin Sun, Peiman Shi, Xinfa Wang, Jiaqin Shi, Hanzhong Wang

“…Integration of linkage QTL mapping, transcriptome sequencing and BLAST analysis identified 15 homologues of reported ovule number genes and 327 DEGs in the QTL regions, which were considered as direct and potential candidate genes. …”
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The fungal gut microbiota in pediatric-onset multiple sclerosis by Nelson Mok, Natalie C. Knox, Natalie C. Knox, Feng Zhu, Douglas L. Arnold, Amit Bar-Or, Charles Noah Bernstein, Christine Bonner, Jessica D. Forbes, Morag Graham, Morag Graham, Ruth Ann Marrie, Julia O’Mahony, E. Ann Yeh, Yinshan Zhao, Gary Van Domselaar, Gary Van Domselaar, Brenda Banwell, Emmanuelle Waubant, Helen L. Tremlett

“…Using metataxonomic sequencing of the fungal internal transcribed spacer region 2, the fungal profiles were compared between participants using visualizations, statistical tests, and predictive analysis. …”
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Immunophenotype-guided interpretable radiomics model for predicting neoadjuvant anti-PD-1 response in stage III–IV d-MMR/MSI-H colorectal cancer by Xuan Zhang, Zhenhui Li, Yiwen Zhang, Yanli Li, Xi Zhong, Wenjing Jiang, Xiaobo Chen, Zaiyi Liu, Liebin Huang, Caixia Zhang, Lizhu Liu, Ruimin You, Xiaoping Yi

“…SHAP analysis identified higher large dependence emphasis and lower variance as potential predictors of pCR, which quantified the homogeneity of the tumors.Conclusion Two immunophenotypes were constructed and identified at both bulk RNA level and IHC level. …”
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Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring by J. Iwan Jones, Amanda Arnold, Dominik Buchner, John F. Murphy, Jasmine N. Childress, Pedro Beja, Florian Altermatt, Kristian Meissner, Ian Adams, Meri Anderson, Yaisel J. Borrell, Andrew G. Briscoe, Kat Bruce, Cátia Chaves, Chris Conyers, Kristy Deiner, Vasco Elbrecht, Álvaro Fueyo, Tim Goodall, Javier Granero‐Castro, Cristina Hartmann‐Fatu, Eleanor Jones, Elvira Mächler, Filipa M. S. Martins, Sam McGreig, Lyndall Pereira‐da‐Conceicoa, James L. Pretty, Daniel S. Read, Ben Price, Florian Leese, Rosetta C. Blackman

“…The strongest methodological influences on variance in metrics derived from DNA‐based methods were attributed to sequencing (read count per sample) and laboratory (strong variation within samples). …”
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