Nevin Manimala

Eur J Neurosci. 2022 Nov 12. doi: 10.1111/ejn.15861. Online ahead of print.

ABSTRACT

In the present study, we examined neural circuit formation in the forebrain of the Olig2 knockout (Olig2-KO) mouse model and found disruption of the anterior commissure at the late fetal stage. Axon bundles of the anterior commissure encountered the wall of the third ventricle and ceased axonal extension. L1-CAM immunohistochemistry showed that Olig2-KO mice lose decussation formation in the basal forebrain. DiI tracing revealed that the thin bundles of the anterior commissure axons crossed the midline but ceased further extension into the deep part of the contralateral side. Furthermore, some fractions of DiI-labeled axons were oriented dorsolaterally, which was not observed in the control mouse forebrain. The rostral part of the third ventricle was much wider in the Olig2-KO mice than in wild-type mice, which likely resulted in the delay of midline fusion and subsequent delay and malformation of the anterior commissure. We analyzed gene expression alterations in the Olig2-KO mice using a public database and found multiple genes, which are related to axon guidance and epithelial-mesenchymal transition, showing subtle expression changes. These results suggest that Olig2 is essential for anterior commissure formation, likely by regulating multiple biological processes.

PMID:36370145 | DOI:10.1111/ejn.15861

Am J Clin Pathol. 2022 Nov 12:aqac132. doi: 10.1093/ajcp/aqac132. Online ahead of print.

ABSTRACT

OBJECTIVES: To perform the first meta-analysis regarding the pooled risk of malignancy (ROM) of each category of the Yokohama system for reporting breast fine-needle aspiration, as well as assess the latter’s diagnostic accuracy using this new system.

METHODS: Two databases were searched, followed by data extraction, study quality assessment, and statistical analysis.

RESULTS: The “Insufficient,” “Benign,” “Atypical,” “Suspicious,” and “Malignant” Yokohama system categories were associated with a pooled ROM of 17% (95% CI, 10%-28%), 1% (95% CI, 1%-3%), 20% (95% CI, 17%-23%), 86% (95% CI, 79%-92%), and 100% (95% CI, 99%-100%), respectively. When both “Suspicious” and “Malignant” interpretations were regarded as cytologically positive, sensitivity (SN) was 91% (95% CI, 87.6%-93.5%) and false-positive rate (FPR) was 2.33% (95% CI, 1.30-4.14%). A summary receiver operating characteristic curve was constructed and the pooled area under the curve was 97.3%, while the pooled diagnostic odds ratio was 564 (95% CI, 264-1,206), indicating a high level of diagnostic accuracy. When only “Malignant” interpretations were regarded as cytologically positive, the pooled FPR was lower (0.75%; 95% CI, .39%-1.42%) but at the expense of SN (76.61%; 95% CI, 70.05%-82.10%).

CONCLUSIONS: Despite Yokohama’s system early success, more data would be needed to unravel the system’s value in clinical practice.

PMID:36370120 | DOI:10.1093/ajcp/aqac132

Nucleic Acids Res. 2022 Nov 12:gkac1040. doi: 10.1093/nar/gkac1040. Online ahead of print.

ABSTRACT

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.

PMID:36370099 | DOI:10.1093/nar/gkac1040

Addiction. 2022 Nov 12. doi: 10.1111/add.16086. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Impulse Control Disorders (ICDs) are iatrogenic and idiopathic conditions with psychosocial and economic consequences for the affected individuals and their families (e.g., bankruptcy and divorce). However, the definition of ICDs has changed over time and ICDs are not consistently included within existing taxonomies. We discuss the origins of the ICD diagnostic construct and its unsolved tensions.

METHODS: To contextualize the ICD diagnostic construct we provided an overview of its origins in past centuries and followed its development across multiple editions of the Diagnostic and Statistical Manual and the International Classification of Diseases, as well as its definition within emerging ontologies.

RESULTS: Two independent roots of the ICD construct emerged: a) the interest in behavioral excess as expressed in encyclopedic compilations (XVIII century); b) the juridical debate on disruptive conduct and responsibility (XIX-XX century). These roots underlie the repeated taxonomical remodeling observed across the XX and XXI centuries and three critical issues persisting in both clinical practice and research. First, the number of ICDs keeps increasing across the spectrum of human behaviors, disregarding common pathogenetic and phenomenological grounds. Second, ICDs substantially overlap with other mental conditions. Impulsivity is often neglected as minor inconvenience or side effect when co-occurring with major diagnoses (e.g., depression), and therefore inadequately managed. Finally, ICDs definitions display an unsolved tension between being conceived as hobby, moral fault, or pathological drive, which may be responsible for stigma and delayed intervention.

CONCLUSION: The reasons that made ICDs difficult to define from their first conceptualization are the same ones that now complicate taxonomic efforts and diagnosis. Tracing back ICDs’ roots and criticalities can help define a common and less ambiguous theoretical framework, which may also result in the demise of the ICD construct and a move towards better defined and more useful ontologies.

PMID:36370093 | DOI:10.1111/add.16086

Laryngoscope. 2022 Dec;132(12):2301-2306. doi: 10.1002/lary.29983. Epub 2021 Dec 11.

ABSTRACT

OBJECTIVES/HYPOTHESIS: Reconstruction of mucosal defects using free mucosal grafts has become a common procedure during endoscopic sinus surgery. Epithelialization of mucosal grafts affects postoperative complications and outcomes, which could be influenced by different recipient tissue. However, morphological changes occurring in the grafts transplanted over different tissues remain unexplored.

STUDY DESIGN: An animal study.

METHODS: Free mucoperichondrial grafts were prepared from the nasal septum of rabbits; the cartilage group had reconstruction on the nasal septal cartilage, and the perichondrium group had reconstruction on the contralateral perichondrium. The nasal septum was removed after 1 and 4 weeks of reconstruction, and the graft was histologically evaluated.

RESULTS: After 1 week of reconstruction, the mucosal epithelium of grafts in the cartilage group disappeared, whereas the columnar epithelium of grafts was preserved in the perichondrium group. After 4 weeks of reconstruction, the mucosal defect site was covered with mucosal epithelium in both groups. However, while squamous epithelium was mostly observed in the cartilage group, columnar epithelium containing the healthy ciliary and goblet cells was observed in the perichondrium group. Statistically significant differences were detected in the parameters of epithelial morphology between the two groups, which were higher in the perichondrium group.

CONCLUSIONS: In the reconstruction of mucosal defects using free mucosal grafts, difference in recipient tissue affects the graft epithelial morphology.

LEVEL OF EVIDENCE: NA Laryngoscope, 132:2301-2306, 2022.

PMID:36370085 | DOI:10.1002/lary.29983

Bioinformatics. 2022 Nov 12:btac732. doi: 10.1093/bioinformatics/btac732. Online ahead of print.

ABSTRACT

SUMMARY: The development of new vaccines and antibody therapeutics typically takes several years and requires over $1bn in investment. Accurate knowledge of the paratope (antibody binding site) can speed up and reduce the cost of this process by improving our understanding of antibody-antigen binding. We present Paragraph, a structure-based paratope prediction tool that outperforms current state-of-the-art tools using simpler feature vectors and no antigen information.

AVAILABILITY: Source code is freely available at www.github.com/oxpig/Paragraph.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:36370083 | DOI:10.1093/bioinformatics/btac732

Ann Med. 2022 Dec;54(1):2785-2795. doi: 10.1080/07853890.2022.2131328.

ABSTRACT

BACKGROUND: Improvements in screening and imaging technologies and treatment of liver disease have influenced the trend in diagnosis for stage I liver cancer. In this article, recent trends in age, incidence, tumour size, and survival of different stages of liver cancer are analysed.

METHODS: Surveillance, Epidemiology, and end results data from the National Cancer Institute were used to analyse trends in age-adjusted incidence rate, mean tumour size at diagnosis, age at diagnosis, and 5-year survival probability for stage I liver cancer.

RESULTS: Stage I cases of liver cancer increased most tremendously over the study period, with a greater increase from 2004 to 2012 following a smaller increase from 2012 to 2015. Moreover, the mean age of stage I liver cancer increased by 1.72 years from 2004 to 2015. The 5-year-overall survival for stage I liver cases worsened from 97.9% to 83.7% from 2004 to 2011, whereas the 10-year survival probability for stage I cases worsened from 97.3% in 2004 to 79.6% in 2006. Comparing with higher stage cases, stage I liver cancer were more likely to be females, be married, live in metro areas, receive chemotherapy, and carry medical insurance.

CONCLUSIONS: The incidence of stage I liver cancer has increased over the study period, with an increase in age of diagnosis, decrease in tumour size, and generally stable overall survival rate with slight decrease. These trends emphasized the importance of early detection of liver cancer and regular screening and better treatment for high-risk populations.RESEARCH HIGHLIGHTSImprovements in screening and imaging technologies and treatment of liver disease have influenced the trend in diagnosis for liver cancer.Stage I cases of liver cancer increased most tremendously over the study period, with a greater increase from 2004 to 2012 following a smaller increase from 2012 to 2015.These trends emphasized the importance of early detection of liver cancer and regular screening and better treatment for high-risk populations.

PMID:36370068 | DOI:10.1080/07853890.2022.2131328

Indian Pediatr. 2022 Nov 15;59(11):863-866.

ABSTRACT

OBJECTIVE: The study was conducted to evaluate the ocular toxicity of ethambutol given in both intensive and continuation phases of treatment in children with drug-sensitive tuberculosis.

METHODS: A prospective study of 94 eyes from 47 patients receiving an ethambutol-containing regimen was conducted between 1 December, 2018 and 31 August, 2020. Visual acuity, visual field, visual evoked response (VER), contrast sensitivity, colour perception, and retinal nerve fiber layer (RNFL) thickness [using optical coherence tomography (OCT)] were tested for each patient before, during, and after the treatment.

RESULTS: On follow-up, visual acuity, color vision, contrast sensitivity, fundus, and visual fields were not affected in any of the patients. There was no statistically significant increase in the mean latency of the P(100) wave at any point in time. On OCT, no significant loss of mean RNFL thickness was detected.

CONCLUSIONS: Ethambutol is safe to use up to a dose of 20 mg/kg/day throughout the entire course of anti-tubercular therapy in children with drug-sensitive tuberculosis.

PMID:36370014

Res Synth Methods. 2022 Nov 12. doi: 10.1002/jrsm.1610. Online ahead of print.

ABSTRACT

An overview of reviews aims to collect, assess, and synthesize evidence from multiple systematic reviews (SRs) on a specific topic using rigorous and reproducible methods. An important methodological challenge in conducting an overview of reviews is the management of overlapping data due to the inclusion of the same primary studies in SRs. We present a free, open-source R package called ccaR (https://github.com/thdiakon/ccaR) that provides easy-to-use functions for assessing the degree of overlap of primary studies in an overview of reviews with the use of the corrected cover area (CCA) index. A worked example with and without consideration of chronological structural missingness is outlined, illustrating the steps involved in, calculating the CCA index and creating a publication-ready heatmap. We expect ccaR to be useful for overview authors, methodologists, and reviewers who are familiar with the basics of R and contribute to the discussion on different methodological approaches for implementing the CCA index. Future research and applications could further investigate the functionality or potential limitations of our package and other potential uses. This article is protected by copyright. All rights reserved.

PMID:36369993 | DOI:10.1002/jrsm.1610

Vet Q. 2022 Nov 12:1-18. doi: 10.1080/01652176.2022.2145619. Online ahead of print.

ABSTRACT

BACKGROUND: The complex etiopathology of retained placenta (RP) and hazards associated with it has made it crucial for researchers and clinical veterinarians to study pathogenesis, early-warning diagnosis, and treatment.

OBJECTIVES: This study aimed to screen the potential prognostic markers of RP in dairy cows using plasma metabolomics coupled with clinical laboratory indicators.

METHODS: Blood samples were collected from 260 dairy cows at 21, 14, 7, and 0 days before parturition and 7, 14, and 21 days after parturition. Consequently, 10 healthy cows and 10 cows with RP with similar parity, body condition score, and age were included in the study. The changes in clinical laboratory indicators of the enrolled cows from 21 before parturition to 21 days after parturition were assessed. After initial overview of the multivariate statistical data using PCA analysis, the data were subjected to orthogonal partial least-squares discriminant analysis.

RESULTS: Compared with cows with RP at 7 days before parturition, the levels of endothelin and 6-keto-prostaglandin F1α were increased in healthy cows while the level of estradiol and progesterone decreased. Adenine dinucleotide phosphate, hypoxanthine, guanine dinucleotide phosphate, inosine monophosphate, and L-arginine were revealed as potential prognostic markers of cows with RP at 7 days before parturition involved in the regulation of taste transduction, purine and glutathione metabolism, and autophagy.

CONCLUSIONS: The best period for the early-warning diagnosis of RP in dairy cows is 7 days before parturition, and purine metabolism and autophagy may play a vital role in the occurrence and development of RP in dairy cows.

PMID:36369933 | DOI:10.1080/01652176.2022.2145619