Article
Ecology
Kelly A. Speer, Melissa T. R. Hawkins, Mary Faith C. Flores, Michael R. McGowen, Robert C. Fleischer, Jesus E. Maldonado, Michael G. Campana, Carly R. Muletz-Wolz
Summary: Animal specimens in natural history collections are valuable resources for studying the historical context of pathogen dynamics and spillovers. However, RNA viruses are difficult to study in historical specimens due to the lack of optimized protocols for RNA extraction. This study optimized the recovery of RNA from formalin-fixed ethanol-preserved museum specimens, expanding the usability of these specimens for zoonotic disease surveys. The extracted RNA from historical museum specimens is highly fragmented but suitable for short-read sequencing and targeted amplification.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Otorhinolaryngology
Jared A. Shenson, George S. Liu, Joyce Farrell, Nikolas H. Blevins
Summary: This study demonstrates the feasibility of using multispectral imaging and deep learning to enhance surgical vision for automated identification of normal human head and neck tissues. By developing and testing a novel multispectral imaging system and utilizing convolutional neural network machine learning models, the accuracy of tissue classification was significantly improved, outperforming traditional white-light imaging and surgical residents in tissue identification.
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2021)
Article
Medical Laboratory Technology
Feng-Ming Hsu, Yih-Leong Chang, Chung-Yung Chen, Shu-Rung Lin, Jason Chia-Hsien Cheng
Summary: HPR is an alternative RNA profiling approach with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
CLINICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Pascal Steffen, Jun Li, Jason Chandra, Mahsa S. Ahadi, Anthony J. Gill, Alexander F. Engel, Mark P. Molloy
Summary: Histological risk factors for lymph node metastasis in early-stage colorectal cancers have been described, with molecular features such as effector proteins of epithelial-mesenchymal transition (EMT) showing potential for enhancing metastatic risk assessment. Proteomic and gene expression profiling were used to identify these features, suggesting a link between EMT effectors and locoregional metastasis in T1/T2 CRC. Further development is needed for routine implementation of these findings.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Oncology
Amin Talebi, Jean Paul Thiery, Mohammad Amin Kerachian
Summary: Chimeric transcripts are important for diagnosis and prognosis, but their identification from FFPE tissues is limited due to the reduced quality and quantity of RNA. Strategies need to be developed to overcome these limitations and maximize the potential of FFPE tissues as a source for fusion transcript identification.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Infectious Diseases
Shawn T. Clark, Yvonne C. W. Yau, Aaron Campigotto, Farhad Gharabaghi, Susan E. Richardson, Manal Tadros
Summary: In this study, we evaluated the performance of a DNA-based test for detecting fungal DNA in archived human biopsy tissues. Our results indicate that the best performance can be achieved when fungi are observed under a microscope before testing, suggesting that this test should only be used under these conditions.
Article
Pathology
Georgia Karpathiou, Maureen Vincent, Jean Marc Dumollard, Mousa Mobarki, Michel Peoc'h
Summary: The study compared the PD-L1 expression in HNSCC tissues upon arrival and after storage, revealing a significant decrease in tumor proportional score and immune cells expression. Immediate assay of PD-L1 expression is preferable in routine practice to avoid decreased expression levels.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Biochemistry & Molecular Biology
Charlotte Vernisse, Aurelie Petit, Veronique Pantesco, Pascal Chanez, Delphine Gras, Edouard Tuaillon, Christophe Duperray, Isabelle Vachier, Said Assou, Arnaud Bourdin
Summary: This paper presents an optimized protocol for microarray analysis of intracellular target-sorted human bronchial club cells. The protocol includes fixation and permeabilization steps and the addition of RNase inhibitors to ensure the preservation of high-quality RNA. The results show successful cell sorting and the generation of a transcriptomic signature for club cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Pitchasak Chankuson, Paramee Chumsri
Summary: The aim of this research is to use dielectric barrier discharge to produce ozone in order to extend the shelf life and preserve the quality of mangosteen. The optimal conditions for the system included a minimum breakdown voltage of about 6 kV(p-p), a resonance frequency of 224 kHz, and an oxygen flow rate of 2 L/min. The study found that treating fruit with ozone at an oxygen flow rate lower than 2 L/min resulted in an approximately 11-fold increase in the maximal ethylene concentration compared to untreated fruit.
APPLIED SCIENCES-BASEL
(2023)
Article
Oncology
Alessandra Borgognone, Garazi Serna, Marc Noguera-Julian, Lidia Alonso, Mariona Parera, Francesc Catala-Moll, Lidia Sanchez, Roberta Fasani, Roger Paredes, Paolo Nuciforo
Summary: The comparison of fresh-frozen (FF) and FFPE colorectal cancer (CRC) tissues revealed differences in microbial diversity and composition, with FF samples enriched in representative CRC-associated bacteria and FFPE samples mainly enriched in typical contaminants. An internal quality index showed a correlation between the similarity within sample pairs and the dominance of contaminant taxa. These findings may provide useful indications for accurate and reproducible metagenomics analyses, especially in larger studies in human cancer genomics using FFPE specimens.
Article
Biochemistry & Molecular Biology
Martyna Bednarczyk, Malgorzata Muc-Wierzgon, Sylwia Dziegielewska-Gesiak, Dariusz Waniczek
Summary: This study analyzed the changes in the transcriptional activity of autophagy-related genes and the ubiquitination process in colorectal cancer tissue. The results showed dysregulation of ubiquitination and autophagy processes, especially in the early stages of cancer, which may contribute to tumor progression and poor prognosis.
Article
Cell Biology
Rong Tang, Ling Zhu, Ping Zhu, Ru Yin, Chunxia Zheng
Summary: PAXgene Blood RNA tubes are commonly used for preserving RNA stability, but the presence of blood clots can affect the quality of RNA. This study analyzed 15 pairs of clot and nonclot samples and found that large blood clots significantly reduce RNA integrity.
BIOPRESERVATION AND BIOBANKING
(2023)
Article
Oncology
Tomohiro Fujiwara, Vaiyapuri Sumathi, Michael Parry, Jonathan Stevenson, Yusuke Tsuda, Yoichi Kaneuchi, Lee Jeys
Summary: The study aimed to investigate the effect of margin quantity and quality on local control for myxofibrosarcoma and undifferentiated pleomorphic sarcoma. The results showed that margin quality and quantity have an impact on local recurrence rate, especially in patients with 0.1-9.9 mm margins, where better margin quality was associated with lower recurrence risk.
Article
Microbiology
Suk Yee Lam, Athanasia Ioannou, Prokopis Konstanti, Thijmen Visseren, Michail Doukas, Maikel Petrus Peppelenbosch, Clara Belzer, Gwenny Manel Fuhler
Summary: This study aimed to investigate microbial associations in human disease using FFPE tissues, but found that bacterial contaminants and human DNA co-extraction can affect analysis. While bacterial DNA amplification was improved for specific markers using qPCR, amplicon sequencing remained challenging. Despite some separation at genus level, there was considerable overlap of bacterial genera within tissues and controls, with no diversity differences following decontamination.
Article
Chemistry, Analytical
Markus Karjalainen, Anton Kontunen, Anna Anttalainen, Meri Makela, Soma Varga, Maiju Lepomaki, Osmo Anttalainen, Pekka Kumpulainen, Niku Oksala, Antti Roine, Antti Vehkaoja
Summary: Effective surgical margin assessment is crucial for good oncological outcomes, and new methods are being actively developed. One such method is the analysis of the chemical composition of surgical smoke to evaluate margins. In a simulated experiment using porcine tissues, we analyzed the delay in smoke transportation and evaluated its impact on tissue classification. The results showed that with a typical smoke evacuator setting, it takes about 1 second for the smoke to reach the sensor from the surgical plume.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Editorial Material
Oncology
Takeshi Yamada, Akihisa Matsuda, Goro Takahashi, Hiroshi Yoshida
ANNALS OF SURGICAL ONCOLOGY
(2022)
Article
Oncology
Koji Ueda, Takeshi Yamada, Ryo Ohta, Akihisa Matsuda, Hiromichi Sonoda, Sho Kuriyama, Goro Takahashi, Takuma Iwai, Kohki Takeda, Toshimitsu Miyasaka, Seiichi Shinji, Noriyasu Chika, Hideyuki Ishida, Hiroshi Yoshida
Summary: This study evaluated BRAF(V600E) mutations in Japanese right-side colon cancer patients and found that these mutations occur at a high frequency, especially in the cecum. Liquid biopsy can detect BRAF(V600E) mutations in plasma and has a high detection rate in patients with advanced cancer. Additionally, spatial heterogeneity of BRAF(V600E) mutations was observed.
Review
Surgery
Shintaro Kanaka, Akihisa Matsuda, Takeshi Yamada, Ryo Ohta, Hiromichi Sonoda, Seiichi Shinji, Goro Takahashi, Takuma Iwai, Kohki Takeda, Koji Ueda, Sho Kuriyama, Toshimitsu Miyasaka, Hiroshi Yoshida
Summary: This systematic review and meta-analysis compares the postoperative short-term outcomes between preoperative colonic stenting (BTS) and emergency resection (ER) for right-sided malignant large bowel obstruction (MLBO). The analysis indicates that BTS results in a reduction in postoperative complications and mortality rates compared to ER for right-sided MLBO.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2022)
Article
Medicine, General & Internal
Kotaro Nanno, Seiichi Shinji, Takeshi Yamada, Akihisa Matsuda, Ryo Ohta, Hiromichi Sonoda, Takuma Iwai, Kohki Takeda, Kazuhide Yonaga, Koji Ueda, Sho Kuriyama, Toshimitsu Miyasaka, Hiromasa Komori, Yoshinobu Shioda, Hiroshi Yoshida
Summary: A peritoneal loose body (PLB) is a tissue completely separated from other intraperitoneal organs, typically found incidentally during surgery, examination, or autopsy. We report a case of a giant PLB located outside the peritoneal cavity, adjacent to the rectovesical excavation. Although it was fixed and preoperative diagnosis was uncertain, laparoscopic removal of the mass was feasible.
JOURNAL OF NIPPON MEDICAL SCHOOL
(2023)
Article
Gastroenterology & Hepatology
Shintaro Kanaka, Takeshi Yamada, Akihisa Matsuda, Goro Takahashi, Masatoku Arai, Toru Takiguchi, Hideki Tayama, Hiroshi Yoshida
Summary: Vascular Ehlers-Danlos syndrome is a rare connective tissue disease with a high risk of severe complications, leading to a shorter life expectancy for patients. The optimal management of the complications associated with this syndrome remains unclear, but specific life-saving measures may be necessary for patients experiencing certain severe complications.
CLINICAL JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Gastroenterology & Hepatology
Akihisa Matsuda, Takeshi Yamada, Takao Takahashi, Keiji Hirata, Takeshi Nagasaka, Kei Ishimaru, Kazuhiro Sakamoto, Keiji Koda, Toshiaki Ishikawa, Hideyuki Ishida, Kenji Matsuda, Hidekazu Kuramochi, Yoichiro Yoshida, Hiromichi Sonode, Hiroshi Yoshida
Summary: This study aims to evaluate the predictive value of genomic mutations in ctDNA for primary and acquired resistance to anti-EGFR therapy, as well as the association of these mutations with secondary resistance to anti-EGFR therapy in first-line treatment of wild-type tissue RAS mCRC patients.
JOURNAL OF THE ANUS RECTUM AND COLON
(2022)
Article
Oncology
Shun Ishiyama, Takeshi Yamada, Masato Nakamura, Masanobu Enomoto, Kiichi Sugimoto, Hajime Yokomizo, Chihiro Kosugi, Ryo Ohta, Kei Ishimaru, Hiromichi Sonoda, Keiichiro Ishibashi, Hidekazu Kuramochi, Yoichiro Yoshida, Daisuke Ichikawa, Keiji Hirata, Hiroshi Yoshida, Yojiro Hashiguchi, Hideyuki Ishida, Keiji Koda, Kenji Katsumata, Kazuhiro Sakamoto
Summary: The study demonstrated that dose-escalation therapy of regorafenib is well tolerated for Japanese patients, with improved survival rates and low incidence of adverse events.
INTERNATIONAL JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yohei Ikeno, Maya Inomata, Yuka Tsukimura, Yuta Suzuki, Hiroto Takeuchi, Yui Harada, Risako Kon, Nobutomo Ikarashi, Yoshihiko Chiba, Takeshi Yamada, Junzo Kamei, Hiroyasu Sakai
Summary: Cisplatin-induced muscle atrophy can be attenuated by EPA through down-regulation of up-regulated Ub gene expression.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Medicine, General & Internal
Maki Nakai, Takeshi Yamada, Kenta Sekiya, Ai Sato, Meishi Hankyo, Sho Kuriyama, Goro Takahashi, Tomoko Kurita, Keiko Yanagihara, Hiroshi Yoshida, Ryuji Ohashi, Hiroyuki Takei
Summary: Liquid biopsy was used to detect PIK3CA mutations in patients with breast cancer. The study found that PIK3CA mutations can be detected even in patients with no mutations in their primary tumors. Combining tissue and liquid biopsies can provide clinically useful information for patients with breast cancer.
JOURNAL OF NIPPON MEDICAL SCHOOL
(2022)
Article
Medicine, General & Internal
Katsuyoshi Ankoh, Seiichi Shinji, Takeshi Yamada, Akihisa Matsuda, Ryo Ohta, Hiromichi Sonoda, Masahiro Hotta, Goro Takahashi, Yohei Kaneya, Takuma Iwai, Kohki Takeda, Koji Ueda, Sho Kuriyama, Toshimitsu Miyasaka, Kazuhide Yonaga, Yoshinobu Shioda, Hiroshi Yoshida, Ryuji Ohashi
Summary: Metastasis of lung cancer to the small intestine is an oncological emergency that can lead to intestinal obstruction and bleeding. Analysis of data from patients with small-intestinal metastases showed rapid growth in tumor volume, which may be influenced by the degree of primary tumor atypia and intratumoral hemorrhage.
JOURNAL OF NIPPON MEDICAL SCHOOL
(2022)
Article
Medicine, General & Internal
Kohki Takeda, Akihisa Matsuda, Takeshi Yamada, Seiichi Shinji, Ryo Ohta, Hiromichi Sonoda, Takuma Iwai, Koji Ueda, Sho Kuriyama, Toshimitsu Miyasaka, Hiroshi Yoshida
Summary: This report presents a case of successful laparoscopic surgery in a patient with kyphosis who had rectal cancer. Detailed preoperative simulation and discussions were conducted to ensure a successful outcome.
JOURNAL OF NIPPON MEDICAL SCHOOL
(2022)
