Project description:Invasive group A streptococcal (iGAS) disease cases increased in the first half of 2022 in the Netherlands, with a remarkably high proportion of emm4 isolates. Whole-genome sequence analysis of 66 emm4 isolates, 40 isolates from the pre-coronavirus disease 2019 (COVID-19) pandemic period 2009-2019 and 26 contemporary isolates from 2022, identified a novel Streptococcus pyogenes lineage (M4NL22), which accounted for 85 % of emm4 iGAS cases in 2022. Surprisingly, we detected few isolates of the emm4 hypervirulent clone, which has replaced nearly all other emm4 in the USA and the UK. M4NL22 displayed genetic differences compared to other emm4 strains, although these were of unclear biological significance. In publicly available data, we identified a single Norwegian isolate belonging to M4NL22, which was sampled after the isolates from this study, possibly suggesting export of M4NL22 to Norway. In conclusion, our study identified a novel S. pyogenes emm4 lineage underlying an increase of iGAS disease in early 2022 in the Netherlands and the results have been promptly communicated to public health officials.
Project description:The lifestyle medicine core competencies were developed by a committee of physicians from several medical specialties to provide guidance on the knowledge and skills needed for physicians to provide high quality lifestyle interventions that optimize chronic disease outcomes. These competencies were published in the Journal of the American Medical Association (JAMA) in 2010 and used as the foundation for the first lifestyle medicine course and for the lifestyle medicine board certification examination. In the ensuing years, interest in the field and application has expanded to a variety of health professionals. With evolution of the lifestyle medicine evidence-base, the competencies have been updated. This article sums up the changes in their organization and content. Regular updates are anticipated to align with the ongoing scientific studies and evolution of the field.
Project description:Unlabelled: The integrative analysis of multiple high-throughput data sources that are available for a common sample set is an increasingly common goal in biomedical research. Joint and individual variation explained (JIVE) is a tool for exploratory dimension reduction that decomposes a multi-source dataset into three terms: a low-rank approximation capturing joint variation across sources, low-rank approximations for structured variation individual to each source and residual noise. JIVE has been used to explore multi-source data for a variety of application areas but its accessibility was previously limited. We introduce R.JIVE, an intuitive R package to perform JIVE and visualize the results. We discuss several improvements and extensions of the JIVE methodology that are included. We illustrate the package with an application to multi-source breast tumor data from The Cancer Genome Atlas.Availability and implementationR.JIVE is available via the Comprehensive R Archive Network (CRAN) under the GPLv3 license: https://cran.r-project.org/web/packages/r.jive/Contactelock@umn.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Project description:Rapeseed is a critical cash crop globally, and understanding its distribution can assist in refined agricultural management, ensuring a sustainable vegetable oil supply, and informing government decisions. China is the leading consumer and third-largest producer of rapeseed. However, there is a lack of widely available, long-term, and large-scale remotely sensed maps on rapeseed cultivation in China. Here this study utilizes multi-source data such as satellite images, GLDAS environmental variables, land cover maps, and terrain data to create the China annual rapeseed maps at 30 m spatial resolution from 2000 to 2022 (CARM30). Our product was validated using independent samples and showed average F1 scores of 0.869 and 0.971 for winter and spring rapeseed. The CARM30 has high spatial consistency with existing 10 m and 20 m rapeseed maps. Additionally, the CARM30-derived rapeseed planted area was significantly correlated with agricultural statistics (R2 = 0.65-0.86; p < 0.001). The obtained rapeseed distribution information can serve as a reference for stakeholders such as farmers, scientific communities, and decision-makers.
Project description:E-JOURNAL LINKED ABSTRACT URL http://www.current-oncology.com/index.php/oncology/article/view/840/ Pseudocirrhosis is a rare form of liver disease that causes clinical symptoms and shows radiographic signs of cirrhosis, but that has histologic features suggesting a distinct pathologic process. In the setting of cancer, hepatic metastases and systemic chemotherapy are suspected causes of pseudocirrhosis. We present the case of a 49-year-old woman with medullary thyroid carcinoma metastatic to the liver who developed pseudocirrhosis. The patient was initially enrolled in a phase i clinical trial of 5-fluorouracil, leucovorin, and oxaliplatin (folfox) in combination with sunitinib (NCT00599924). After this patient’s liver metastases regressed measurably, she was switched to sunitinib maintenance. After 4 months of combination therapy with folfox–sunitinib and 15 months of sunitinib maintenance, she developed abdominal bloating, early satiety, and right upper quadrant pain that increased with inspiration. Computed tomography of the abdomen revealed cirrhotic morphology changes in the liver, including the appearance of a nodular surface and capsular retraction. The patient had no risk factors for cirrhosis and laboratory testing for causes of liver disease were normal or negative. Core-needle liver biopsy demonstrated sheets and nests of epithelioid and spindle cells resembling the primary tumor; septal fibrosis and regenerative nodules typical of cirrhosis were not observed. The background hepatic plate architecture was intact. Laboratory studies showed increased aminotransferases, alkaline phosphatase, and international normalized ratio, and decreased albumin. Portal hypertension, esophageal varices, portal hypertensive gastropathy, and hepatic hydrothorax developed as a result of advanced liver disease. Because of disease progression, sunitinib was discontinued, and the patient was managed with sorafenib. Pseudocirrhosis has often been attributed to chemotherapeutic agents, particularly in the context of metastatic breast cancer. The toxicity profiles of folfox and sunitinib include hepatic steatosis and other forms of hepatotoxicity, but cirrhotic-like disease has not been reported. Considering the transformation of discrete hepatic metastases into a diffuse carcinomatous infiltrate and the unrelated toxicities of folfox and sunitinib, we diagnosed this patient with carcinomatous pseudocirrhosis secondary to metastatic medullary thyroid carcinoma. We discuss the diagnosis of pseudocirrhosis in this case and review the literature regarding pseudocirrhosis in cancer.