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Bacterial genomes are chimeras of DNA of different ancestries. Deconstructing chimeric genomes is central to understanding the evolutionary trajectories of their disparate components and thus the organisms as a whole in the light of their evolutionary contexts. Of specific interest is to delineate and quantify native (vertically inherited) and alien (horizontally acquired) components of bacterial genomes and also specify genomic fractions that represent different donor sources. An agglomerative clustering procedure that prioritizes grouping of proximal similar genomic segments has previously been invoked for this purpose in conjunction with a recursive segmentation procedure. Surprisingly, however, the relative strengths and weaknesses of different clustering approaches to deciphering bacterial chimerism have not yet been investigated, despite the need to robustly interpret tens of thousands of completely sequenced bacterial genomes and nearly complete genome assemblies available in the public databases. To bridge this knowledge gap and develop more robust approaches, we assessed different clustering methods, including segment order based (proximal) clustering, hierarchical clustering, affinity propagation clustering, and a novel network clustering approach on chimeric genomes modeled after bacterial genomes representing a broad spectrum of compositional complexity. Although segment order-based clustering and network clustering compared favorably with the other approaches in discriminating between native and alien DNA at genome optimized settings, network clustering did consistently better than other methods at parametric settings optimized on all test genomes together. Segment order-based clustering and hierarchical clustering outperformed other methods in alien DNA identification while preserving donor identity in the genomes. Our study highlights the strengths and weaknesses of different approaches and suggests how this can be leveraged to achieve a more robust deconstruction of bacterial chimerism.

INTRODUCTION/BACKGROUND: The USPSTF (United States Preventive Service Task Force) guidelines suggest criteria centering on smoking status and age to select patients for lung cancer screening. Despite the significant advances in screening with low-dose computed tomography (LDCT), cancer detection rate is low (1.1%), highlighting the need to investigate possible ways to refine the current lung cancer screening strategy. Our aim was to determine clinical risk factors predictive of lung cancer in an urban safety-net hospital. MATERIALS AND METHODS: We performed a retrospective chart review of 2847 patients who received LDCT screening for lung cancer between 3/1/2015 and 12/31/2019. Patient demographics and medical history were collected. A bivariate logistic regression was used to evaluate predictors of lung cancer. RESULTS: Compared to the National Lung Cancer Screening Trial (NLST) population, our screening cohort had significantly more African Americans (38.2% vs 4.5%, p

Biorepositories provide a critical resource for gaining knowledge of emerging infectious diseases and offer a mechanism to rapidly respond to outbreaks; the emergence of the novel coronavirus, SARS-CoV-2, has proved their importance. During the COVID-19 pandemic, the absence of centralized, national biorepository efforts meant that the onus fell on individual institutions to establish sample repositories. As a safety-net hospital, Boston Medical Center (BMC) recognized the importance of creating a COVID-19 biorepository to both support critical science at BMC and ensure representation in research for its urban patient population, most of whom are from underserved communities. This article offers a realistic overview of the authors' experience in establishing this biorepository at the onset of the COVID-19 pandemic during the height of the first surge of cases in Boston, Massachusetts, with the hope that the challenges and solutions described are useful to other institutions. Going forward, funders, policymakers, and infectious disease and public health communities must support biorepository implementation as an essential element of future pandemic preparedness.

Key Points Hemolysis releases 5.8S rRNA and activates blood coagulation in human and zebrafish via FXII and Hgfac, respectively.Only the 3'-end 26 nucleotides of 5.8S rRNA were necessary and sufficient for this activation., Visual Abstract, Hemolytic disorders are characterized by hemolysis and are prone to thrombosis. It has previously been shown that the RNA released from damaged blood cells activates clotting. However, the nature of the RNA released from hemolysis is still elusive. We found that after hemolysis, red blood cells from both zebrafish and humans released RNA that contained mostly 5.8S ribosomal RNA (5.8S rRNA), This RNA activated coagulation in zebrafish and human plasmas. By using both natural and synthetic 5.8S rRNA and its truncated fragments, we found that the 3'-end 26-nucleotide-long RNA (3'-26 RNA) and its stem-loop secondary structure were necessary and sufficient for clotting activity. Corn trypsin inhibitor (CTI), a coagulation factor XII (FXII) inhibitor, blocked 3'-26 RNA–mediated coagulation activation in the plasma of both zebrafish and humans. CTI also inhibited zebrafish coagulation in vivo. 5.8S rRNA monoclonal antibody inhibited both 5.8S rRNA– and 3'-26 RNA–mediated zebrafish coagulation activity. Both 5.8S rRNA and 3'-26 RNA activated normal human plasma but did not activate FXII-deficient human plasma. Taken together, these results suggested that the activation of zebrafish plasma is via an FXII-like protein. Because zebrafish have no FXII and because hepatocyte growth factor activator (Hgfac) has sequence similarities to FXII, we knocked down the hgfac in adult zebrafish. We found that plasma from this knockdown fish does not respond to 3'-26 RNA. To summarize, we identified that an rRNA released in hemolysis activates clotting in human and zebrafish plasma. Furthermore, we showed that fish Hgfac plays a role in rRNA-mediated activation of coagulation.

Pulmonary sclerosing pneumocytoma (PSP) is a benign tumor originating from primitive respiratory epithelium which tends to present as an asymptomatic solitary lesion in the periphery of the lung. It primarily occurs in women, with a 5:1 ratio of female to male, and in East Asian populations. We describe a rare case of a gallium-68 (68Ga)-DOTATATE avid PSP in a middle-aged man of North African ancestry. Contrast-enhanced computed tomography (CT) revealed an enhancing ovoid 2-cm solid lesion within the periphery of the left upper lobe abutting the superior portion of the lateral left ventricular wall. A fluorine-18-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) demonstrated low-level FDG uptake, but a 68Ga-DOTATATE PET/CT showed avid tracer uptake, concerning for a carcinoid tumor. The lesion was surgically excised, and the histopathologic analysis revealed the typical morphologic and histochemical markers of a PSP. We conclude that, although rare, PSP can be a differential consideration when evaluating a 68Ga-DOTATATE-avid solitary lung nodule concerning for carcinoid tumor, in all genders and in ethnicities other than East Asian.

The amyloidogenic transthyretin (TTR) variant, V122I, occurs in 4% of the African American population and frequently presents as a restricted cardiomyopathy. While heterozygosity for TTR V122I predominates, several compound heterozygous cases have been previously described. Herein, we detail features of ATTRv amyloidosis associated with novel compound heterozygous TTR mutation, T60I/V122I and provide evidence supporting the amyloidogenecity of T60I.A 63-year-old African American female presented with atrial fibrillation, congestive heart failure, autonomic and peripheral neuropathy.Congophilic deposits in a rectal biopsy were immunohistochemically positive for TTR. Serum screening by isoelectric focussing revealed two TTR variants in the absence of wild-type protein. DNA sequencing identified compound heterozygousThis report provides clinical and experimental results supporting the amyloidogenic nature of a novel TTR T60I variant.

Background: As the housekeeping genes generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, multiple studies indicate that not all housekeeping genes display stable expression across cells and tissues and under various healthy and diseased conditions, which can introduce systematic errors into experimental results. The selection and validation of housekeeping genes as controls for each studied condition represent crucial steps in ensuring the validity of obtained results; however, up till now, sex has not been typically considered as a biological variable.Methods: In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the stabile expression of genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to describe any sexual dimorphisms in mRNA expression stability.Results: Just above half of the considered studies informed properly about the sex of the samples. Found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. The extensively used 18S gene displays sex-based variability in adipose tissue, although PPIA and RPL19 do not, and hence, represent robust housekeeping genes. All results generated during this study are readily available by accessing an open web resource (https://bioinfo.cipf.es/metafun-HKG) for consultation and reuse in further studies.Conclusions: This sex-based analysis proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB.

Systemic acquired acclimation (SAA) is a key biological process essential for plant survival under conditions of abiotic stress. SAA was recently shown to be controlled by a rapid systemic signaling mechanism termed the reactive oxygen species (ROS) wave in Arabidopsis (Arabidopsis thaliana). MYB30 is a key transcriptional regulator mediating many different biological processes. MYB30 was found to act downstream of the ROS wave in systemic tissues of Arabidopsis in response to local high light (HL) stress treatment. However, the function of MYB30 in systemic signaling and SAA is unknown. To determine the relationship among MYB30, the ROS wave, and systemic acclimation in Arabidopsis, the SAA response to HL stress of myb30 mutants and wild-type plants was determined. Although myb30 plants were found to display enhanced rates of ROS wave propagation and their local tissues acclimated to the HL stress, they were deficient in SAA to HL stress. Compared to wild type, the systemic transcriptomic response of myb30 plants was also deficient, lacking in the expression of over 3,500 transcripts. A putative set of 150 core transcripts directly associated with MYB30 function during HL stress was determined. Our study identifies MYB30 as a key regulator that links systemic ROS signaling with systemic transcriptomic responses, SAA, and plant acclimation to HL stress. In addition, it demonstrates that plant acclimation and systemic ROS signaling are interlinked and that the lack of systemic acclimation drives systemic ROS signaling to occur at faster rates, suggesting a feedback mechanism (potentially involving MYB30) between these two processes.

Inflammatory myofibroblastic tumors (IMT) of the uterus may be underrecognized as their morphology and immunophenotype may overlap with myxoid variants of uterine smooth muscle tumors and endometrial stromal tumors. Although ALK is a helpful biomarker, not all uterine IMTs are ALK-rearranged, and a small subset of myxoid leiomyosarcomas is ALK-positive. Herein, we evaluated a series of 23 IMTs for the novel endometrial stromal markers interferon-inducible transmembrane protein-1 (IFITM1) and BCOR, the novel myoid marker transgelin, and possible predictive markers p16 and p53 by immunohistochemistry to determine their expression profile and potential prognostic value. Patients' ages ranged from 8 to 59 (mean 39) years and tumors from 2 to 20 (mean 8.2) cm. Follow-up was available for 12/23 (52%) patients; 9/12 (75%) without evidence of disease, 2/12 (17%) alive with disease, and 1/12 (8%) dead from disease. Four IMTs were classified as malignant due to extrauterine disease at diagnosis and/or recurrence. IFITM1 was positive (combined score>2) in 19/23 (83%), BCOR in 8/20 (40%), and transgelin in 22/23 (96%) of tumors. IFITM1 and BCOR were more often expressed in the myxoid component, and transgelin in the compact areas. p16 expression was absent in 5/23 (22%) of IMTs, while p53 was wildtype in all tumors. p16-negative IMTs included all 4 classified as malignant and one where the patient was lost to follow-up. Molecular data were available in 2 malignant IMTs, both of which harbored CDKN2A deletions. We conclude that caution is advised when using IFITM1, BCOR, and transgelin as markers for endometrial and smooth muscle tumors, as these are commonly expressed in IMTs. However, we did identify an association among lack of p16 staining, CKDN2A deletions, and aggressive behavior that merits corroboration by other studies. As a result of this finding, we recommend the use of p16 in the diagnostic work-up of uterine IMTs due to its potential prognostic significance.

Despite achieving a hematologic complete response after treatment, many patients with AL amyloidosis do not attain recovery of organ function and/or experience hematologic relapse. A persistent plasma cell clone producing amyloidogenic light chains at levels below the detection threshold of traditional serologic methods is hypothesized to impede organ response in some patients. Assessment of minimal residual disease (MRD) may therefore have clinical importance as a more stringent treatment response tool for patients in a hematologic complete response. We used 2-tube, 10-color combination multiparametric flow cytometry to assess for MRD at a minimum sensitivity of 1 in 105 nucleated cells. Of 65 patients in hematologic complete response, 36 (55%) were found to have a residual clonal plasma cell population in the bone marrow. Comparing the MRD-negative and MRD-positive groups, renal response was observed in 88% vs 64% (P = .06), cardiac response in 75% vs 59% (P = .45), and any organ response in 90% vs 75% (P = .20) of patients. Depth of organ response as measured by the percent decrease in 24-hour proteinuria and brain natriuretic peptide was 96% vs 91% (P = .16) and 55% vs 46% (P = .66), respectively. These data suggest a possible correlation between MRD negativity and higher probability of organ response after treatment in AL amyloidosis. Future prospective studies with a larger cohort are needed to determine the clinical relevance of these improvements. This trial was registered at www.clinicaltrials.gov as #NCT00898235.

Approximately 15% of stage I lung adenocarcinomas will recur despite adequate surgical therapy. Adjuvant therapy may benefit specific high-risk subsets; however, it is unclear which patients are sufficiently predisposed to recurrence to warrant intensified therapy.517 AJCC 8th edition stage I/0 lung adenocarcinomas ≤ 4 cm total size were graded (WHO-2015 and WHO-2021) and compared to stage subgroupings using 7-year recurrence free (RFS), disease specific (DSS), and overall survival (OS). Low malignant potential (LMP) adenocarcinoma was assigned as previously defined. Univariate/multivariate analysis was performed to assess risk factors associated with aggressive behavior.Vascular invasion was the most significant histologic feature on multivariate analysis for both RFS (HR = 4.68, p 0.001) and DSS (HR = 3.67, p = 0.001) and nearly reached significance for OS (HR = 1.47, p = 0.060). Angioinvasive adenocarcinomas comprised 26 % of the cohort and exhibited a 7-year 64 % RFS, 73 % DSS, and 50 % OS; in contrast to 20 % WHO-2015-G3 (7-year 71 % RFS, 79 % DSS,54 % OS), 44 % WHO-2021-G3 (7-year 79 % RFS, 85 % DSS,56 % OS), and 21 % stage IB (7-year 72 % RFS, 79 % DSS, and 50 % OS) adenocarcinomas. The majority (50 %) of overall mortality was disease specific for angioinvasive adenocarcinoma whereas ≤25 % of overall mortality was disease specific for the remaining tumors. Angioinvasive adenocarcinomas were proportionally more common among those still smoking at diagnosis (49 %), male sex (49 %), and black race (16 %) than other subtypes.Patients with AJCC 8th ed. stage I angioinvasive lung adenocarcinomas are at high-risk of cancer-specific mortality and should be considered for clinical trials evaluating benefit of adjuvant therapy.

β2-microglobulin amyloidosis was first described in the 1980s as a protein deposition disease associated with long-term haemodialysis. More recently, two inherited forms resulting from separate point mutations in the β2-microglobulin gene have been identified. In this report, we detail a novel β2M variant, P32L, caused by a unique dinucleotide mutation that is linked to systemic hereditary β2-microglobulin amyloidosis. Three family members from a Portuguese kinship featured cardiomyopathy, requiring organ transplantation in one case, along with soft tissue involvement; other involvements included gastrointestinal, neuropathic and sicca syndrome. In vitro studies with recombinant P32L, P32G, D76N and wild-type β2-microglobulin were undertaken to compare the biophysical properties of the proteins. The P32L variant was caused by the unique heterozygous dinucleotide mutation c.154_155delinsTT. Amyloid disease featured lowered serum β2-microglobulin levels with near equal amounts of circulating P32L and wild-type proteins; amyloid deposits were composed exclusively of P32L variant protein. In vitro studies of P32L demonstrated thermodynamic and chemical instability and enhanced susceptibility to proteolysis with rapid formation of pre-fibrillar oligomeric structures by N- and C-terminally truncated species under physiological conditions. This work provides both clinical and experimental evidence supporting the critical role of P32 residue replacement in β2M amyloid fibrillogenesis.

In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and ending with an output of differentially expressed genes and their functional characterization. The first section covers de novo transcriptome assembly for organisms lacking reference genomes or for those interested in probing against the background of organism-specific transcriptomes assembled from RNA-Seq data. Section 2 covers both gene- and transcript-level quantifications, leading to the third and final section on differential expression analysis between two or more conditions. The pipeline starts with raw sequence reads, followed by quality assessment and preprocessing of the input data to ensure a robust estimate of the transcripts and their differential regulation. The preprocessed data can be inputted into the de novo transcriptome flow to assemble transcripts, functionally annotated using tools such as InterProScan or Blast2Go and then forwarded to differential expression analysis flow, or directly inputted into the differential expression analysis flow if a reference genome is available. An online repository containing sample data has also been made available, as well as custom Python scripts to modify the output of the programs within the pipeline for various downstream analyses.

In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and ending with an output of differentially expressed genes and their functional characterization. The first section covers de novo transcriptome assembly for organisms lacking reference genomes or for those interested in probing against the background of organism-specific transcriptomes assembled from RNA-Seq data. Section 2 covers both gene- and transcript-level quantifications, leading to the third and final section on differential expression analysis between two or more conditions. The pipeline starts with raw sequence reads, followed by quality assessment and preprocessing of the input data to ensure a robust estimate of the transcripts and their differential regulation. The preprocessed data can be inputted into the de novo transcriptome flow to assemble transcripts, functionally annotated using tools such as InterProScan or Blast2Go and then forwarded to differential expression analysis flow, or directly inputted into the differential expression analysis flow if a reference genome is available. An online repository containing sample data has also been made available, as well as custom Python scripts to modify the output of the programs within the pipeline for various downstream analyses.

Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant

INTRODUCTION AND OBJECTIVE:Identifying non-invasive biomarkers that distinguish Lichen Sclerosus (LS) induced from non-LS induced urethral strictures would have broad implications for the diagnosis...

INTRODUCTION AND OBJECTIVE:Lichen sclerosus (LS) is a chronic inflammatory condition that can affect both the penile skin and urethral epithelium in men. Over time, severe impairment of sexual and ...

Aging of the population emphasizes the need for research on aging-related problems, among which frailty is a key element because of its clinical as well as social implications. After a review of empirical research of frailty in old adults, the objective of this research is fourfold: (1) assess the adequacy of a comprehensive index of frailty; (2) test for the effects of different socioeconomic and anthropometric variables of an index of frailty; (3) study the effect of frailty on quality of life and general health; and (4) prove grounds for potential gender differences in all these concepts surrounding frailty as well as in frailty itself. This study relies on data from the SHARE project at wave 6, with a total of 4498 Spain-dwelling people aged 60 or older (M = 73.56, SD = 8.89), of which 46.1% were male and 53.9% were female. Statistical analyses included Confirmatory Factor Analysis and Full Structural Equation Models with multi-group comparison based upon gender. Results provide evidence of adequacy for this measure of frailty. Evidence shows how different variables have an impact on frailty, which further affects quality of life and health. Finally, gender differences are studied and discussed with previous literature. We conclude that results are consistent with previous literature on frailty in old people. Limitations and future research needs are also presented.

Aims/hypothesis Non-alcoholic fatty liver disease (NAFLD) is frequently associated with type 2 diabetes mellitus. Progression of NAFLD is mediated, among other things, by activation of inflammatory pathways. In the present study, the role of the proinflammatory cytokine LIGHT (TNFSF14) was explored in NAFLD and type 2 diabetes mellitus in mice deficient for the cytokine. Methods Light-deficient (Light-/-) mice and WT controls were fed a regular chow diet (RCD) or a high-fat high-cholesterol diet (HFHCD) for 16 weeks. The expression of LIGHT and its receptors, herpes virus entry mediator (HVEM) and lymphotoxin β receptor (LTβR), was investigated in both dietary regimens. Glucose tolerance, insulin sensitivity, non-alcoholic fatty liver (NAFL), systemic and tissue inflammation, and metabolic gene expression were explored in Light-/- and WT mice fed an RCD and an HFHCD. The effect of Light deficiency was also evaluated in hepatic tissue and in inflammation in HFHCD-fed Irs2+/- mice with impaired insulin signalling. Results Light deficiency did not have an effect on metabolism, in NAFL or in tissue and systemic inflammation, in RCD-fed WT mice. HVEM and LTβR were markedly increased in livers of HFHCD-fed WT mice compared with RCD-fed WT controls. In WT mice under HFHCD, Light deficiency improved glucose tolerance and insulin sensitivity. Non-alcoholic fatty liver disease activity (NAS) score, hepatic CD3+ T lymphocytes and F4/80+ macrophages were decreased in HFHCD-fed Light-/- mice compared with HFHCD-fed WT controls. Consistent with a potential role of adipose tissue in hepatic homeostasis, Light-/- mice exhibited augmented anti-inflammatory F4/80+CD206+ adipose tissue macrophages and reduced proinflammatory F4/80+CD11c+ adipose tissue macrophages. Moreover, adipose tissue explants from Light-/- mice showed diminished secretion of monocyte chemoattractant protein 1 (MCP1), TNF-α and IL-17 cytokines. Circulating Light-/- leucocytes consistently displayed augmented levels of the patrolling Ly6Clow monocytes, decreased Th9 T cell subset and diminished plasma TNF-α and IL-6 levels. Similarly, Light deficiency in Irs2+/- mice, which display impaired insulin signalling, also reduced NAFL as well as systemic and adipose tissue inflammation. Analysis of hepatic gene expression in Light-/- mouse livers showed reduced levels of Zbtb16, the transcription factor essential for natural killer T (NKT) cell function, and two genes related to NAFLD and fibrosis, Klf6 and Tlr4. Conclusions/interpretation These results indicate that Light deficiency in HFHCD improves hepatic glucose tolerance, and reduces hepatic inflammation and NAFL. This is accompanied by decreased systemic inflammation and adipose tissue cytokine secretion and by changes in the expression of key genes such as Klf6 and Tlr4 involved in NAFLD. These results suggest that therapies to block LIGHT-dependent signalling might be useful to restore hepatic homeostasis and to restrain NAFLD.

Background Type 1 diabetes mellitus (T1DM) patients display increased risk of cardiovascular disease (CVD) and are characterized by a diminished regulatory T (Treg) cell content or function. Previous studies have shown an association between decreased CDKN2A/2B/2BAS gene expression and enhanced CVD. In the present study the potential relationship between CDKN2A/2B/2BAS gene expression, immune cell dysfunction and increased cardiovascular risk in T1DM patients was explored. Methods A cross-sectional study was performed in 90 subjects divided into controls and T1DM patients. Circulating leukocyte subpopulations analysis by flow cytometry, expression studies on peripheral blood mononuclear cell by qPCR and western blot and correlation studies were performed in both groups of subjects. Results Analysis indicated that, consistent with the described T cell dysfunction, T1DM subjects showed decreased circulating CD4+CD25+CD127− Treg cells. In addition, T1DM subjects had lower mRNA levels of the transcription factors FOXP3 and RORC and lower levels of IL2 and IL6 which are involved in Treg and Th17 cell differentiation, respectively. T1DM patients also exhibited decreased mRNA levels of CDKN2A (variant 1 p16Ink4a), CDKN2A (p14Arf, variant 4), CDKN2B (p15Ink4b) and CDKN2BAS compared with controls. Notably, T1DM patients had augmented pro-atherogenic CD14++CD16+-monocytes, which predict cardiovascular acute events and enhanced common carotid intima-media thickness (CC-IMT). Conclusions Decreased expression of CDKN2A/2B/2BAS in leukocytes associates with increased CC-IMT atherosclerosis surrogate marker and proatherogenic CD14++CD16+ monocytes in T1DM patients. These results suggest a potential role of CDKN2A/2B/2BAS genes in CVD risk in T1DM. Electronic supplementary material The online version of this article (10.1186/s12967-019-1977-1) contains supplementary material, which is available to authorized users.

We gain unique insights into materiality judgments about accounting errors by examining SEC comment letter correspondence. We document that managers typically use multiple quantitative benchmarks in their materiality analyses, with earnings being the most common benchmark. In most of the cases we review, managers deem the error immaterial despite its exceeding the traditional “5 percent of earnings” rule of thumb, often in multiple periods and by a large degree. Instead of attempting to conceal these overages, managers tend to forthrightly acknowledge them, often asserting that the benchmark is abnormally low during the violation period. We find that 17–26 percent of these “low benchmark” assertions are suspect (although none of these “low benchmark” assertions are challenged by the SEC). We also document substantial variation in the extent to which qualitative factors are mentioned as considerations. The SEC generally is deferential toward managers' arguments and judgments but is more likely to challenge immateriality claims when managers admit there are qualitative factors that indicate errors are material. L'importance relative des erreurs comptables : donnees provenant des lettres de commentaires de la SEC Les auteurs recueillent de precieux renseignements au sujet des jugements portes sur l'importance relative des erreurs comptables en analysant les lettres de commentaires de la SEC. Les gestionnaires, constatent‐ils, utilisent habituellement de multiples indices de reference quantitatifs dans leurs analyses de l'importance relative, l'indice des resultats etant le plus frequemment employe. Dans la plupart des cas etudies par les auteurs, les gestionnaires jugent l'erreur negligeable en depit du fait qu'elle excede la regle empirique des « 5 pour cent des benefices », souvent de beaucoup et a plusieurs reprises. Plutot que de tenter de dissimuler ces depassements, les gestionnaires tendent a les reconnaitre sans ambages, affirmant dans bien des cas que l'indice de reference est anormalement bas pour la periode de transgression. Les auteurs constatent que 17 a 26 pour cent de ces affirmations quant au niveau faible des indices sont suspectes (bien qu'aucune desdites affirmations ne soit mise en doute par la SEC). Ils notent aussi une variation appreciable de la mesure dans laquelle les facteurs qualitatifs sont allegues. La SEC respecte generalement les arguments invoques et les jugements portes par les gestionnaires, mais elle est davantage susceptible de remettre en question leurs affirmations quant au caractere negligeable des ecarts lorsque les gestionnaires admettent que certains facteurs qualitatifs indiquent que les erreurs sont importantes.

Primary pulmonary extra‐nodal marginal zone lymphoma of mucosa‐associated lymphoid tissue (MALT lymphoma), also known as bronchus‐associated lymphoid tissue (BALT lymphoma), is the most common primary pulmonary lymphoma but is rare (, A middle‐aged male presents with dyspnoea and multifocal consolidations. Biopsy shows pulmonary MALT lymphoma, a rare lung tumour.

Objectives Severe COVID-19 results in a glucocorticoid responsive form of acute respiratory distress (ARDS)/diffuse alveolar damage (DAD). Herein we compare the immunopathology of lung tissue procured at autopsy in patients dying of SARS-CoV-2 with those dying of DAD prior to the COVID-19 pandemic. Methods Autopsy gross and microscopic features stratified by duration of illness in twelve patients who tested positive for SARS-CoV-2 viral RNA as well as seven patients dying of DAD prior to the COVID-19 pandemic were evaluated with multiplex (5-plex: CD4, CD8, CD68, CD20, AE1/AE3) and SARS-CoV immunohistochemistry to characterize the immunopathologic stages of DAD. Results We observed a distinctive pseudopalisaded histiocytic hyperplasia interposed between the exudative and proliferative phase of COVID-19 associated DAD which was most pronounced at the fourth week from symptom onset. Pulmonary macrothrombi were seen predominantly in cases with pseudopalisaded histiocytic hyperplasia and/or proliferative phase DAD. Neither pseudopalisaded histiocytic hyperplasia nor pulmonary macrothrombi were seen in non-COVID-19 DAD cases, whereas microthrombi were common in DAD regardless of etiology. Conclusion The inflammatory pattern of pseudopalisaded histiocytic hyperplasia may represent the distinctive immunopathology associated with the dexamethasone responsive form of DAD seen in severe COVID-19.

Background: Pulmonary actinomycosis is a rare and slowly progressive bacterial infection that is often mistaken for lung cancer. Multiple case reports caution against premature diagnosis of malignancy without proper consideration of potential Actinomyces infection. However, no cases in the English literature have been reported that demonstrate the possible coexistence of Actinomyces and lung cancer. Case Description: We present two cases of patients with culture-positive Actinomyces who were later found to have concomitant biopsy-proven lung adenocarcinoma. Conclusions: In the workup of a newly identified lung mass, positive culture for Actinomyces does not rule out an underlying malignancy.

Background Lung CT Screening Reporting and Data System (LungRADS) Category 4 represents lung nodules with the highest likelihood of cancer. For LungRADS-4 lesions, if positron emission tomography (PET) is negative, there currently exists no uniform guideline on subsequent follow-up, particularly whether the surveillance interval can be extended. We sought to investigate the incidence of cancer, our surveillance practice and any clinical factors associated with cancer in this patient subset. Methods We retrospectively stratified LungRADS-4 patients screened at our institution from March 2015 to February 2019 into subgroups: PET-positive, PET-negative, and no PET performed. PET negativity was defined as the absence of a radiologist’s suspicion, or a maximum standardized uptake value at or below the mediastinal value. Results Of the 191 LungRADS-4 patients identified, 67 (35.1%) met criteria for PET negativity. Cancer was diagnosed in 28.8% (55/191) of the entire cohort, 77.8% (35/45) of the PET-positive subgroup, 22.4% (15/67) of the PET-negative subgroup, and 6.3% (5/79) of the no PET subgroup. The most common follow-up modality after a negative PET scan was a CT scan (47/67, 70.1%), with a median interval of 3.1 months. Clinical variables including nodule location/size, chronic obstructive pulmonary disease, family history of lung cancer, pack-years, and number of years quit in former smokers were not significantly associated with greater cancer risk among PET-negatives. Conclusion For LungRADS-4/PET-negative lesions, the cancer risk remained high despite lack of activity on PET. As such, we believe the current surveillance practice of continuing to follow LungRADS-4/PET-negative patients as LungRADS-4 patients is appropriate.

Introduction: Despite FDA approval of pembrolizumab in microsatellite instability-high (MSI-H)/mismatch repair deficient solid tumors, approximately half of patients with MSI-H endometrial cancer are treatment-refractory. We sought to evaluate pre-treatment MSI-H endometrial tumor samples to examine cell subpopulation differences in the tumor microenvironment (TME) associated with resistance to pembrolizumab. Methods: Archival tumor samples from MSI-H endometrial cancer patients treated with pembrolizumab at MD Anderson Cancer Center were obtained under an IRB-approved protocol. Twenty-one patients were identified, and pre-treatment archival tumor samples were collected and submitted for RNA-seq and imaging mass cytometry (IMC) with an optimized 38-antibody panel to identify predictive immuno-genomic signatures and cell subpopulations associated with treatment response. Results: Among the 21 patients treated with pembrolizumab, there were 14 responders and 7 non-responders. Based on transcriptomic signatures, TME heterogeneity was observed. The 14 responders consisted of samples with immunologically “hot” (5/5; 100%), “cold” (6/8; 75%), and “warm” TMEs (3/8; 37.5%) while the 7 non-responders consisted of only “cold” (2/8; 25%) and “warm” (5/8; 62.5%) TME samples. There was an enrichment of fibroblasts and endothelial cell transcriptomic signatures in the samples of the non-responders compared to responders (p=0.018) with a trend of increasing enrichment in those signatures as response strength decreased. IMC performed on archival tissue from 20 patients demonstrated similar trend of higher population of activated fibroblasts (SMA+, MFAP5+) and endothelial cells (CD31+) in non-responders. Furthermore, non-responders had significantly higher total regulatory T cells (CD4+FOXP3+) in the tumor (p=0.027) and stroma (p=0.0282) compared to responders. Additionally, significantly higher activated regulatory T cells (CD4+FOXP3+CD25+) were observed in the tumor (p=0.016) and stroma (p=0.008) of non-responders compared to responders. Similar abundance of total and subpopulations of CD8+ T cells were observed between responders and non-responders. Conclusion: The MSI-H endometrial TME is heterogeneous. Increased presence of fibroblasts, endothelial cells, and regulatory T-cells in the TME correlate with innate resistance to pembrolizumab. Treatment aimed toward the reduction of these cellular subpopulations may improve sensitivity to PD-1 inhibitors. Future studies are needed to validate these findings. Citation Format: Jeffrey A. How, Minghao Dang, Sammy Ferri-Borgogno, Elizabeth Euscher, Melinda S. Yates, Weiyi Peng, Shrina D. Patel, Jared J. Burks, Ivo Vletic, Javier Gomez, Karen Lu, Samuel C. Mok, Linghua Wang, Amir A. Jazaeri. Predictors of innate resistance to pembrolizumab in patients with microsatellite instability-high endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1248.