Assessment of different pre-treatment methods for the removal of limonene in citrus waste and their effect on methane potential and methane production rate

The objective of this study was to assess the limonene removal efficiency of three pre-treatment methods when applied to citrus waste and to evaluate their effects on the biochemical methane potential (BMP) and the methane production rate (MPR) using batch anaerobic testsPostprint (published version

A Brief Measure for the Assessment of Competence in Coping With Death: The Coping With Death Scale Short Version.

Context. The coping with death competence is of great importance for palliative care professionals, who face daily exposure to death. It can keep them from suffering compassion fatigue and burnout, thus enhancing the quality of the care provided. Despite its relevance, there are only two measures of professionals’ ability to cope with death. Specifically, the Coping with Death Scale (CDS) has repeatedly shown psychometric problems with some of its items. Objective. The aim of this study was to develop and validate a short version of the CDS. Methods. Nine items from the original CDS were chosen for the short version. Two cross-sectional surveys were conducted in Spanish (N ¼ 385) and Argentinian (N ¼ 273) palliative care professionals. The CDS and the Professional Quality of Life Scale were used in this study. Statistical analyses included two confirmatory factor analyses (CFAs), followed by a standard measurement invariance routine. Reliability estimates and evidence of validity based on relations with other measures were also gathered. Results. CFA models had excellent fit in both the Spanish (c2(27) ¼ 107.043, P < 0.001; Comparative Fit Index [CFI] ¼ 0.978; Tucker-Lewis Index [TLI] ¼ 0.970; Root Mean Square Error of Approximation [RMSEA] ¼ 0.093 [0.075, 0.112]; Standardized Root Mean Square Residual ¼ 0.030) and Argentinian (c2(27) ¼ 102.982, P < 0.001; CFI ¼ 0.963; TLI ¼ 0.950; RMSEA ¼ 0.106 [0.085, 0.128]) samples. A standard measurement invariance routine was carried out. The most parsimonious model (c2(117) ¼ 191.738, P < 0.001; CFI ¼ 0.987; TLI ¼ 0.992; RMSEA ¼ 0.046 [0.034, 0.058]; Standardized Root Mean Square Residual ¼ 0.043) offered evidence of invariance across countries, with no latent mean differences. Evidence of reliability and evidence of validity based on relations with other measures were also appropriate. Conclusion. Results indicated the psychometric boundaries of the short version of the CDS.post-print172 K

Pulmonary vascular proliferation in patients with severe COVID-19: an autopsy study

3 p.Diffuse alveolar damage and thrombi are the most common lung histopathological lesions reported in patients with severe COVID-19. Although some studies have suggested increased pulmonary angiogenesis, the presence of vascular proliferation in COVID-19 lungs has not been well characterised. Glomeruloid-like microscopic foci and/or coalescent vascular proliferations measuring up to 2 cm were present in the lung of 14 out of 16 autopsied patients. These lesions expressed CD31, CD34 and vascular endothelial cadherin. Platelet-derived growth factor receptor-? immunohistochemistry and dual immunostaining for CD34/smooth muscle actin demonstrated the presence of pericytes. These vascular alterations may contribute to the severe and refractory hypoxaemia that is common in patients with severe COVID-19.Instituto de Salud Carlos IIICIBERONCInstituto Ramón y Cajal de Investigación Sanitaria Intramural COVID1

Accurate Identification of ALK Positive Lung Carcinoma Patients: Novel FDA-Cleared Automated Fluorescence In Situ Hybridization Scanning System and Ultrasensitive Immunohistochemistry

Background: Based on the excellent results of the clinical trials with ALK-inhibitors, the importance of accurately identifying ALK positive lung cancer has never been greater. However, there are increasing number of recent publications addressing discordances between FISH and IHC. The controversy is further fuelled by the different regulatory approvals. This situation prompted us to investigate two ALK IHC antibodies (using a novel ultrasensitive detection-amplification kit) and an automated ALK FISH scanning system (FDA-cleared) in a series of non-small cell lung cancer tumor samples. Methods: Forty-seven ALK FISH-positive and 56 ALK FISH-negative NSCLC samples were studied. All specimens were screened for ALK expression by two IHC antibodies (clone 5A4 from Novocastra and clone D5F3 from Ventana) and for ALK rearrangement by FISH (Vysis ALK FISH break-apart kit), which was automatically captured and scored by using Bioview's automated scanning system. Results: All positive cases with the IHC antibodies were FISH-positive. There was only one IHC-negative case with both antibodies which showed a FISH-positive result. The overall sensitivity and specificity of the IHC in comparison with FISH were 98% and 100%, respectively. Conclusions: The specificity of these ultrasensitive IHC assays may obviate the need for FISH confirmation in positive IHC cases. However, the likelihood of false negative IHC results strengthens the case for FISH testing, at least in some situation

RET Fusion Testing in Patients With NSCLC: The RETING Study

Introduction: RET inhibitors with impressive overall response rates are now available for patients with NSCLC, yet the identi fication of RET fusions remains a dif ficult challenge. Most guidelines encourage the upfront use of next -generation sequencing (NGS), or alternatively, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) when NGS is not possible or available. Taken together, the suboptimal performance of single-analyte assays to detect RET fusions, although consistent with the notion of encouraging universal NGS, is currently widening some of the clinical practice gaps in the implementation of predictive biomarkers in patients with advanced NSCLC. Methods: This situation prompted us to evaluate several RET assays in a large multicenter cohort of RET fusion -positive NSCLC (n 1 / 4 38) to obtain real -world data. In addition to RNA -based NGS (the criterion standard method), all positive specimens underwent break -apart RET FISH with two different assays and were also tested by an RT-PCR assay. Results: The most common RET partners were KIF5B (78.9%), followed by CCDC6 (15.8%). The two RET NGSpositive but FISH -negative samples contained a KIF5B(15)RET(12) fusion. The three RET fusions not identi fied with RT-PCR were AKAP13(35)-RET(12) , KIF5B(24)-RET(9) and KIF5B(24)-RET(11) . All three false -negative RT-PCR cases were FISH -positive, exhibited a typical break -apart pattern, and contained a very high number of positive tumor cells with both FISH assays. Signet ring cells, psammoma bodies, and pleomorphic features were frequently observed (in 34.2%, 39.5%, and 39.5% of tumors, respectively). Conclusions: In-depth knowledge of the advantages and disadvantages of the different RET testing methodologies could help clinical and molecular tumor boards implement and maintain sensible algorithms for the rapid and effective detection of RET fusions in patients with NSCLC. The likelihood of RET false -negative results with both FISH and RT-PCR reinforces the need for upfront NGS in patients with NSCLC. (c) 2024 The Authors. Published by Elsevier Inc. on behalf of the International Association for the Study of Lung Cancer. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

How the microbiome can help detect precancerous lesions and prevent anal cancer

This is a summary of: Serrano-Villar, S. et al. Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer. Nat. Med. https://doi.org/10.1038/s41591-023-02407-3 (2023).[EN] This study reveals that the production of cobalamin and succinyl-CoA is increased in the anal microbiome of patients with precancerous anal lesions. Testing for these two metabolites significantly improves diagnostic accuracy over standard cytology screening, which suggests potential for enhanced screening strategies for anal cancer.Peer reviewe

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer

Human papillomavirus can cause preinvasive, high-grade squamous intraepithelial lesions (HSILs) as precursors to cancer in the anogenital area, and the microbiome is suggested to be a contributing factor. Men who have sex with men (MSM) living with human immunodeficiency virus (HIV) have a high risk of anal cancer, but current screening strategies for HSIL detection lack specificity. Here, we investigated the anal microbiome to improve HSIL screening. We enrolled participants living with HIV, divided into a discovery (n = 167) and validation cohort (n = 46), and who were predominantly (93.9%) cisgender MSM undergoing HSIL screening with high-resolution anoscopy and anal biopsies. We identified no microbiome composition signatures associated with HSILs, but elevated levels of microbiome-encoded proteins producing succinyl coenzyme A and cobalamin were significantly associated with HSILs in both cohorts. Measurement of these candidate biomarkers alone in anal cytobrushes outperformed anal cytology as a diagnostic indicator for HSILs, increasing the sensitivity from 91.2% to 96.6%, the specificity from 34.1% to 81.8%, and reclassifying 82% of false-positive results as true negatives. We propose that these two microbiome-derived biomarkers may improve the current strategy of anal cancer screening. © 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.This work was supported by the ERANET TRANSCAN-2 program, JTC 2016 (SCRAtCH project, grant agreement no. 643638), funded by Instituto de Salud Carlos III (project AC17/00019), AECC (grant TRNSC17002SER), Lombardy Foundation for Biomedical Research, Italy (SCRAtCH project, grant agreement no. 643638); Federal Ministry of Education and Research, Germany (SCRAtCH project, grant agreement no. 643638); and the Research Council of Norway and Norwegian Cancer Society, Norway (SCRAtCH project, grant agreement no. 643638). The work was also supported by grants PI18/00154, ICI20/00058 and PI21/00141, funded by Instituto de Salud Carlos III and cofounded by the European Union, and grants PID2020-112758RB-I00 and PDC2021-121534-I00 funded by the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI) (https://doi.org/10.13039/501100011033) and the European Union (‘NextGenerationEU’). The authors thank all of the study participants and their families and the staff involved in this study for their commitment to clinical research.The data used for these analyses are available as supporting material at https://github.com/sajanraju/SCRAtCH-Codes. All of the sequences are publicly available in the European Nucleotide Archive database under accession number PRJEB58898. The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium via the PRIDE partner repository70 with the dataset identifier PXD037268.Peer reviewe

Epigenetic prediction of response to anti-PD-1 treatment in non-small-cell lung cancer: a multicenter, retrospective analysis

Background: Anti-programmed death-1 (PD-1) treatment for advanced non-small-cell lung cancer (NSCLC) has improved the survival of patients. However, a substantial percentage of patients do not respond to this treatment. We examined the use of DNA methylation profiles to determine the efficacy of anti-PD-1 treatment in patients recruited with current stage IV NSCLC. Methods: In this multicentre study, we recruited adult patients from 15 hospitals in France, Spain, and Italy who had histologically proven stage IV NSCLC and had been exposed to PD-1 blockade during the course of the disease. The study structure comprised a discovery cohort to assess the correlation between epigenetic features and clinical benefit with PD-1 blockade and two validation cohorts to assess the validity of our assumptions. We first established an epigenomic profile based on a microarray DNA methylation signature (EPIMMUNE) in a discovery set of tumour samples from patients treated with nivolumab or pembrolizumab. The EPIMMUNE signature was validated in an independent set of patients. A derived DNA methylation marker was validated by a single-methylation assay in a validation cohort of patients. The main study outcomes were progression-free survival and overall survival. We used the Kaplan-Meier method to estimate progression-free and overall survival, and calculated the differences between the groups with the log-rank test. We constructed a multivariate Cox model to identify the variables independently associated with progression-free and overall survival. Findings: Between June 23, 2014, and May 18, 2017, we obtained samples from 142 patients: 34 in the discovery cohort, 47 in the EPIMMUNE validation cohort, and 61 in the derived methylation marker cohort (the T-cell differentiation factor forkhead box P1 [FOXP1]). The EPIMMUNE signature in patients with stage IV NSCLC treated with anti-PD-1 agents was associated with improved progression-free survival (hazard ratio [HR] 0·010, 95% CI 3·29 × 10 −4–0·0282; p=0·0067) and overall survival (0·080, 0·017–0·373; p=0·0012). The EPIMMUNE-positive signature was not associated with PD-L1 expression, the presence of CD8+ cells, or mutational load. EPIMMUNE-negative tumours were enriched in tumour-associated macrophages and neutrophils, cancer-associated fibroblasts, and senescent endothelial cells. The EPIMMUNE-positive signature was associated with improved progression-free survival in the EPIMMUNE validation cohort (0·330, 0·149–0·727; p=0·0064). The unmethylated status of FOXP1 was associated with improved progression-free survival (0·415, 0·209–0·802; p=0·0063) and overall survival (0·409, 0·220–0·780; p=0·0094) in the FOXP1 validation cohort. The EPIMMUNE signature and unmethylated FOXP1 were not associated with clinical benefit in lung tumours that did not receive immunotherapy. Interpretation: Our study shows that the epigenetic milieu of NSCLC tumours indicates which patients are most likely to benefit from nivolumab or pembrolizumab treatments. The methylation status of FOXP1 could be associated with validated predictive biomarkers such as PD-L1 staining and mutational load to better select patients who will experience clinical benefit with PD-1 blockade, and its predictive value should be evaluated in prospective studies

Incidence and clearance of anal high-risk human papillomavirus in HIV-positive men who have sex with men: Estimates and risk factors

Background: To estimate incidence and clearance of high-risk human papillomavirus (HR-HPV), and their risk factors, in men who have sex with men (MSM) recently infected by HIV in Spain; 2007-2013. Methods: Multicenter cohort. HR-HPV infection was determined and genotyped with linear array. Two-state Markov models and Poisson regression were used. Results: We analysed 1570 HR-HPV measurements of 612 MSM over 13 608 person-months (p-m) of follow-up. Median (mean) number of measurements was 2 (2.6), median time interval between measurements was 1.1 years (interquartile range: 0.89-1.4). Incidence ranged from 9.0 [95% confidence interval (CI) 6.8-11.8] per 1000 p-m for HPV59 to 15.9 (11.7-21.8) per 1000 p-m for HPV51. HPV16 and HPV18 had slightly above average incidence: 11.9/1000 p-m and 12.8/1000 p-m. HPV16 showed the lowest clearance for both 'prevalent positive' (15.7/1000 p-m; 95% CI 12.0-20.5) and 'incident positive' infections (22.1/1000 p-m; 95% CI 11.8-41.1). More sexual partners increased HR-HPV incidence, although it was not statistically significant. Age had a strong effect on clearance (P-value < 0.001) due to the elevated rate in MSM under age 25; the effect of HIV-RNA viral load was more gradual, with clearance rate decreasing at higher HIV-RNA viral load (P-value 0.008). Conclusion: No large variation in incidence by HR-HPV type was seen. The most common incident types were HPV51, HPV52, HPV31, HPV18 and HPV16. No major variation in clearance by type was observed, with the exception of HPV16 which had the highest persistence and potentially, the strongest oncogenic capacity. Those aged below 25 or with low HIV-RNA- viral load had the highest clearanceThis work was supported by grants from the Fondo de Investigacio´n Sanitaria [PI06/0372, PS09/2181], Red de Investigacio´n en SIDA (RIS) [RD06/006/0026 and RD12/0017/0018 to C.G.] and CIBERESP [group 54A-CB06/02/1009