Manuscript in preparation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens (human)
SUBMITTER:
PROVIDER: S-BSST1091 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description:IntroductionWith the rising complexity of modern multimarker analytical techniques and notable scientific publication retractions required for erroneous statistical analysis, there is increasing awareness of the importance of research transparency and reproducibility. The development of mature open-source tools for literate programming in multiple langauge paradigms has made fully-reproducible authorship possible.ObjectivesWe describe the procedure for manuscript preparation using RMarkdown and the R statistical programming language with application to JMSACL or any other Elsevier journal.MethodsAn instructional manuscript has been prepared in the RMarkdown markup language with stepwise directions on preparing sections, subsections, lists, tables, figures and reference management in an entirely reproducible format.ResultsFrom RMarkdown code, a submission-ready PDF is generated and JMSACL-compatible LaTeX code is generated. These can be uploaded to the Editorial Manager.ConclusionA completely reproducible manuscript preparation pipeline using the R and RMarkdown is described.
| S-EPMC8662334 | biostudies-literature
Project description:The rapid advances in Generative AI tools have produced both excitement and worry about how AI will impact academic writing. However, little is known about what norms are emerging around AI use in manuscript preparation or how these norms might be enforced. We address both gaps in the literature by conducting a survey of 271 academics about whether it is necessary to report ChatGPT use in manuscript preparation and by running GPT-modified abstracts from 2,716 published papers through a leading AI detection software to see if these detectors can detect different AI uses in manuscript preparation. We find that most academics do not think that using ChatGPT to fix grammar needs to be reported, but detection software did not always draw this distinction, as abstracts for which GPT was used to fix grammar were often flagged as having a high chance of being written by AI. We also find disagreements among academics on whether more substantial use of ChatGPT to rewrite text needs to be reported, and these differences were related to perceptions of ethics, academic role, and English language background. Finally, we found little difference in their perceptions about reporting ChatGPT and research assistant help, but significant differences in reporting perceptions between these sources of assistance and paid proofreading and other AI assistant tools (Grammarly and Word). Our results suggest that there might be challenges in getting authors to report AI use in manuscript preparation because (i) there is not uniform agreement about what uses of AI should be reported and (ii) journals might have trouble enforcing nuanced reporting requirements using AI detection tools.
| S-EPMC11244834 | biostudies-literature
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.
| S-EPMC3267587 | biostudies-literature
Project description:ObjectivesTo enhance reproducible research by creating a broadly accessible, free, open-source software tool for connecting Microsoft Word to statistical programs (R/R Markdown, Python, SAS, Stata) so that results may be automatically updated in a manuscript.Materials and methodsWe developed StatTag for Windows as a Microsoft Word plug-in using C# and for macOS as a native application using Objective-C. Source code is available under the MIT license at https://github.com/stattag.ResultsStatTag links analysis file(s) (R/R Markdown, SAS, Stata, or Python) and a Word document, invokes the statistical program(s) to obtain results, and embeds selected output in the document. StatTag can accommodate multiple statistical programs with a single document and features an interface to view, edit, and rerun statistical code directly from Word.Discussion and conclusionStatTag may facilitate reproducibility within increasingly multidisciplinary research teams, improve research transparency through review and publication, and complement data-sharing initiatives.
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Project description:Manuscript symbols can be stored, recognized and retrieved from an entropic digital memory that is associative and distributed but yet declarative; memory retrieval is a constructive operation, memory cues to objects not contained in the memory are rejected directly without search, and memory operations can be performed through parallel computations. Manuscript symbols, both letters and numerals, are represented in Associative Memory Registers that have an associated entropy. The memory recognition operation obeys an entropy trade-off between precision and recall, and the entropy level impacts on the quality of the objects recovered through the memory retrieval operation. The present proposal is contrasted in several dimensions with neural networks models of associative memory. We discuss the operational characteristics of the entropic associative memory for retrieving objects with both complete and incomplete information, such as severe occlusions. The experiments reported in this paper add evidence on the potential of this framework for developing practical applications and computational models of natural memory.
| S-EPMC9352019 | biostudies-literature
Project description:In this article, we employ simple descriptive methods in order to explore the peculiar behavior of the symbols in the Voynich Manuscript. Such an analysis reveals a group of symbols which are further analyzed for the possibility of being compounds (or ligatures), using a specifically developed method. The results suggest the possibility that the alphabet of the manuscript is a lot smaller, and steganographic type of encoding is proposed to explain the newly revealed properties.
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Project description:Molecular characterization of Group B strep in South Africa
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Project description:Most palm leaf manuscripts are generally accessible in deteriorated condition, including cracks, discoloration, moisture and humidity, and insects bite. Such a manuscript is considered challenging in the research field. We captured deteriorated Tamil palm leaves around 262 dataset samples are 'Naladiyar(27)',' Tholkappiyam(221)', and' Thirikadugam(14)' which are genned up mortal health, discipline, authoritative text on Tamil grammar. We contribute the high-quality raw dataset with the aid of a Nikon camera, pre-enhance samples by editing software tool, and applied the Otsu threshold to deliver the ground images through binarization as readily accessible content presenting a highly time-consuming task to play a vital role in Machine/Deep/ Transfer learning, AI, and ANN.
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Project description: Not available
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