FiPhA: an open-source platform for fiber photometry analysis

Significance

Fiber photometry (FP) is a widely used technique in modern behavioral neuroscience, employing genetically encoded fluorescent sensors to monitor neural activity and neurotransmitter release in awake-behaving animals. However, analyzing photometry data can be both laborious and time-consuming.

Aim

We propose the fiber photometry analysis (FiPhA) app, which is a general-purpose FP analysis application. The goal is to develop a pipeline suitable for a wide range of photometry approaches, including spectrally resolved, camera-based, and lock-in demodulation.

Approach

FiPhA was developed using the R Shiny framework and offers interactive visualization, quality control, and batch processing functionalities in a user-friendly interface.

Results

This application simplifies and streamlines the analysis process, thereby reducing labor and time requirements. It offers interactive visualizations, event-triggered average processing, powerful tools for filtering behavioral events, and quality control features.

Conclusions

FiPhA is a valuable tool for behavioral neuroscientists working with discrete, event-based FP data. It addresses the challenges associated with analyzing and investigating such data, offering a robust and user-friendly solution without the complexity of having to hand-design custom analysis pipelines. This application thus helps standardize an approach to FP analysis.

FiPhA: An Open-Source Platform for Fiber Photometry Analysis

Significance

Fiber photometry is a widely used technique in modern behavioral neuroscience, employing genetically encoded fluorescent sensors to monitor neural activity and neurotransmitter release in awake-behaving animals, However, analyzing photometry data can be both laborious and time-consuming.

Aim

We propose the FiPhA (Fiber Photometry Analysis) app, which is a general-purpose fiber photometry analysis application. The goal is to develop a pipeline suitable for a wide range of photometry approaches, including spectrally resolved, camera-based, and lock-in demodulation.

Approach

FiPhA was developed using the R Shiny framework and offers interactive visualization, quality control, and batch processing functionalities in a user-friendly interface.

Results

This application simplifies and streamlines the analysis process, thereby reducing labor and time requirements. It offers interactive visualizations, event-triggered average processing, powerful tools for filtering behavioral events and quality control features.

Conclusions

FiPhA is a valuable tool for behavioral neuroscientists working with discrete, event-based fiber photometry data. It addresses the challenges associated with analyzing and investigating such data, offering a robust and user-friendly solution without the complexity of having to hand-design custom analysis pipelines. This application thus helps standardize an approach to fiber photometry analysis.

Nicotine exposure decreases likelihood of SARS-CoV-2 RNA expression and neuropathology in the hACE2 mouse brain but not moribundity

Individuals infected by SARS-CoV-2 are at risk of developing neurological-related post-acute disorders. Disputed epidemiological data indicated nicotine may reduce the severity of infection. Here we find exposure to nicotine in drinking water does not alter the moribundity of hACE2 mice. However, pre-exposure to nicotine decreased the likelihood of SARS-CoV-2 RNA expression and pathology in the brain. These results suggest mechanisms involving targets of nicotine could be leveraged to prevent the neurovirulence of SARS-CoV-2.

Editor's Highlight: Comparative Toxicity of Organophosphate Flame Retardants and Polybrominated Diphenyl Ethers to Caenorhabditis elegans

With the phasing-out of the polybrominated diphenyl ether (PBDE) flame retardants due to concerns regarding their potential developmental toxicity, the use of replacement compounds such as organophosphate flame retardants (OPFRs) has increased. Limited toxicity data are currently available to estimate the potential adverse health effects of the OPFRs. The toxicological effects of 4 brominated flame retardants, including 3 PBDEs and 3,3',5,5'-tetrabromobisphenol A, were compared with 6 aromatic OPFRs and 2 aliphatic OPFRs. The effects of these chemicals were determined using 3 biological endpoints in the nematode Caenorhabditis elegans (feeding, larval development, and reproduction). Because C. elegans development was previously reported to be sensitive to mitochondrial function, results were compared with those from an in vitro mitochondrial membrane permeabilization (MMP) assay. Overall 11 of the 12 flame retardants were active in 1 or more C. elegans biological endpoints, with only tris(2-chloroethyl) phosphate inactive across all endpoints including the in vitro MMP assay. For 2 of the C. elegans endpoints, at least 1 OPFR had similar toxicity to the PBDEs: triphenyl phosphate (TPHP) inhibited larval development at levels comparable to the 3 PBDEs; whereas TPHP and isopropylated phenol phosphate (IPP) affected C. elegans reproduction at levels similar to the PBDE commercial mixture, DE-71. The PBDEs reduced C. elegans feeding at lower concentrations than any OPFR. In addition, 9 of the 11 chemicals that inhibited C. elegans larval development also caused significant mitochondrial toxicity. These results suggest that some of the replacement aromatic OPFRs may have levels of toxicity comparable to PBDEs.

Adenomatous and carcinomatous changes in hamartomatous polyps of the small intestine (Peutz-Jeghers syndrome): report of a case and review of the literature

The authors report the unique case of a patient with the Peutz-Jeghers (P-J) syndrome who had multiple small bowel hamartomatous polyps, some of which also showed adenomatous and carcinomatous changes. Over the course of 30 years, over 100 small bowel and colonic polyps were resected; all histologically demonstrated the typical features seen in hamartomatous polyps. Several jejunoileal polyps excised during the last few months of the patient's life showed not only hamartomatous features but also adenomatous epithelium. As far as the authors can determine, this is the first documented case of adenomatous changes found within a small bowel hamartomatous polyp. In addition, at least one duodenal polyp demonstrated areas of hamartoma, adenoma, and in situ carcinoma. The literature on the occurrence of gastrointestinal adenomas and carcinomas in patients with the P-J syndrome is reviewed, and the relationship of hamartomas, adenomas, and carcinomas of the gastrointestinal tract is discussed.

Adenomatous and carcinomatous changes in hamartomatous polyps of the small intestine (Peutz-Jeghers syndrome): report of a case and review of the literature

The authors report the unique case of a patient with the Peutz-Jeghers (P-J) syndrome who had multiple small bowel hamartomatous polyps, some of which also showed adenomatous and carcinomatous changes. Over the course of 30 years, over 100 small bowel and colonic polyps were resected; all histologically demonstrated the typical features seen in hamartomatous polyps. Several jejunoileal polyps excised during the last few months of the patient's life showed not only hamartomatous features but also adenomatous epithelium. As far as the authors can determine, this is the first documented case of adenomatous changes found within a small bowel hamartomatous polyp. In addition, at least one duodenal polyp demonstrated areas of hamartoma, adenoma, and in situ carcinoma. The literature on the occurrence of gastrointestinal adenomas and carcinomas in patients with the P-J syndrome is reviewed, and the relationship of hamartomas, adenomas, and carcinomas of the gastrointestinal tract is discussed.

Adenomatous and carcinomatous changes in hamartomatous polyps of the small intestine (Peutz-Jeghers syndrome): report of a case and review of the literature

The authors report the unique case of a patient with the Peutz-Jeghers (P-J) syndrome who had multiple small bowel hamartomatous polyps, some of which also showed adenomatous and carcinomatous changes. Over the course of 30 years, over 100 small bowel and colonic polyps were resected; all histologically demonstrated the typical features seen in hamartomatous polyps. Several jejunoileal polyps excised during the last few months of the patient's life showed not only hamartomatous features but also adenomatous epithelium. As far as the authors can determine, this is the first documented case of adenomatous changes found within a small bowel hamartomatous polyp. In addition, at least one duodenal polyp demonstrated areas of hamartoma, adenoma, and in situ carcinoma. The literature on the occurrence of gastrointestinal adenomas and carcinomas in patients with the P-J syndrome is reviewed, and the relationship of hamartomas, adenomas, and carcinomas of the gastrointestinal tract is discussed.

Adenomas of the small intestine: a clinicopathologic review of 51 cases and a study of their relationship to carcinoma

The authors studied 51 patients who had small bowel tumors that contained adenomatous epithelium. These rare lesions were identified among 392,000 surgical pathology cases seen during a 62-year period. Grossly and histologically, adenomas arising in the mucosa of the small intestine are similar to the adenomas found in the colon. Of the 51 patients, 18 had adenomas, and 33 had tumors that contained both adenoma and carcinoma in the same lesion, including five intramucosal and 28 invasive carcinomas. The location of the tumor usually determined which clinical problems were produced. The data indicate that adenomas originating in the small bowel mucosa probably are premalignant lesions and that many primary adenocarcinomas of the small intestine arise in adenomas. Of the authors' 130 apparently primary small bowel carcinomas (including the papilla of Vater), 33 (25%) histologically demonstrated adenomatous epithelium in the same lesion. Factors associated with an increased chance of finding carcinoma in an adenoma include adenoma type, size of lesion, location, and multicentricity. Carcinomas appear to develop more frequently in papillary (villous) adenomas than in ordinary adenomas. The larger the lesion is, the more likely carcinoma will be identified. Adenomas involving the ampulla contain carcinoma more often than do lesions found elsewhere in the duodenum and small intestine. Three patients had multiple adenomatous polyps of the small bowel; two of these individuals also had duodenal carcinomas. Various problems in pathologic diagnosis and clinical management are discussed.

Adenomas of the small intestine: a clinicopathologic review of 51 cases and a study of their relationship to carcinoma

The authors studied 51 patients who had small bowel tumors that contained adenomatous epithelium. These rare lesions were identified among 392,000 surgical pathology cases seen during a 62-year period. Grossly and histologically, adenomas arising in the mucosa of the small intestine are similar to the adenomas found in the colon. Of the 51 patients, 18 had adenomas, and 33 had tumors that contained both adenoma and carcinoma in the same lesion, including five intramucosal and 28 invasive carcinomas. The location of the tumor usually determined which clinical problems were produced. The data indicate that adenomas originating in the small bowel mucosa probably are premalignant lesions and that many primary adenocarcinomas of the small intestine arise in adenomas. Of the authors' 130 apparently primary small bowel carcinomas (including the papilla of Vater), 33 (25%) histologically demonstrated adenomatous epithelium in the same lesion. Factors associated with an increased chance of finding carcinoma in an adenoma include adenoma type, size of lesion, location, and multicentricity. Carcinomas appear to develop more frequently in papillary (villous) adenomas than in ordinary adenomas. The larger the lesion is, the more likely carcinoma will be identified. Adenomas involving the ampulla contain carcinoma more often than do lesions found elsewhere in the duodenum and small intestine. Three patients had multiple adenomatous polyps of the small bowel; two of these individuals also had duodenal carcinomas. Various problems in pathologic diagnosis and clinical management are discussed.

Adenomas of the small intestine: a clinicopathologic review of 51 cases and a study of their relationship to carcinoma

The authors studied 51 patients who had small bowel tumors that contained adenomatous epithelium. These rare lesions were identified among 392,000 surgical pathology cases seen during a 62-year period. Grossly and histologically, adenomas arising in the mucosa of the small intestine are similar to the adenomas found in the colon. Of the 51 patients, 18 had adenomas, and 33 had tumors that contained both adenoma and carcinoma in the same lesion, including five intramucosal and 28 invasive carcinomas. The location of the tumor usually determined which clinical problems were produced. The data indicate that adenomas originating in the small bowel mucosa probably are premalignant lesions and that many primary adenocarcinomas of the small intestine arise in adenomas. Of the authors' 130 apparently primary small bowel carcinomas (including the papilla of Vater), 33 (25%) histologically demonstrated adenomatous epithelium in the same lesion. Factors associated with an increased chance of finding carcinoma in an adenoma include adenoma type, size of lesion, location, and multicentricity. Carcinomas appear to develop more frequently in papillary (villous) adenomas than in ordinary adenomas. The larger the lesion is, the more likely carcinoma will be identified. Adenomas involving the ampulla contain carcinoma more often than do lesions found elsewhere in the duodenum and small intestine. Three patients had multiple adenomatous polyps of the small bowel; two of these individuals also had duodenal carcinomas. Various problems in pathologic diagnosis and clinical management are discussed.

Primary adenocarcinoma of the jejunum and ileum. A clinicopathologic study

The clinical and pathologic features of 43 primary adenacarcinomas of the small intestine (32 jejunal and 11 ileal) are reported. Seventy-four percent of the patients presented with partial or complete small bowel obstruction, 56% complained of abdominal pain, 37% had symptoms of anemia (weakness, easy fatigability), and 35% had lost weight. Anemic hemoglobin levels occurred in 69%, and a palpable abdominal mass in 25%. Treatment consisted of a "curative" or "palliative" resection, or a bypass procedure. Seventy-nine percent of the tumors showed an annular, constricting pattern, while the remaining 21% had a predominantly fungating or polypoid appearance. Three individuals currently free of clinical recurrence have been followed less than 5 years. Of the remaining 40 patients, a 5-year cure was achieved in 11 (28%), including 6 (15%) who at present have no recurrence and 5 (13%) who subsequently died of other causes. Within 5 years, 28 of these 40 patients (70%) were known or presumed dead tumor, and 1 had succumbed to other causes (2%). Various pathologic features were correlated with the clinical course. Documented lymph node metastasis proved to be the most valuable prognostic finding, 88% of these individuals dying of tumor, as contrasted to 45% of those with tumor-free nodes. A few cases of superficially invasive carcinoma found in an otherwise benign adenomatous lesion had a good prognosis when symptoms were produced mainly by the adenoma, the carcinoma being a relatively minor component.