False positive diagnosis of malignancy in a case of cryptogenic organising pneumonia presenting as a pulmonary mass with mediastinal nodes detected on fluorodeoxyglucose-positron emission tomography: a case report

<p>Abstract</p> <p>Introduction</p> <p>We report the case of a patient with positive findings on a lung emission tomography/computed tomography (PET/CT) scan, with possible contra lateral mediastinal involvement, which strongly suggested an inoperable lung carcinoma. The lung mass proved to be a cryptogenic organising pneumonia. While the latter has previously been shown to be PET/CT positive, mediastinal involvement simulating malignant spread has not been previously reported.</p> <p>Case presentation</p> <p>A 50-year-old Caucasian woman presented with a history of unproductive cough and was found to have a mass in the right upper lobe as shown on chest X-ray and a computed tomography scan. A subsequent PET/CT scan showed strong uptake in the right upper lobe (maximum standard uptake values (SUVmax) 9.6) with increased uptake in the adjacent mediastinum and contralateral mediastinal nodes. Surgical resection and mediastinoscopy revealed cryptogenic organising pneumonia, with enlarged reactive mediastinal lymph nodes.</p> <p>Conclusion</p> <p>The case illustrates the limits of PET/CT scanning as a diagnostic tool, and emphasizes the importance of obtaining histological confirmation of malignant diseases whenever possible.</p

Asthma and COPD as co-morbidities in patients hospitalised with Covid-19 disease: a global systematic review and meta-analysis

Background: Factors predisposing to increased mortality with COVID-19 infection have been identified as male sex, hypertension, obesity, and increasing age. Early studies looking at airway diseases gave some contradictory results. The purpose of our study was to determine global variation in studies in patients hospitalized with COVID-19 in the prevalence of COPD and asthma; and to determine whether the presence of asthma or COPD affected mortality in the same hospital population. Methods: A systematic review and meta-analysis of the published literature of COPD and asthma as co-morbidities in patients hospitalized with COVID-19 was performed, looking firstly at the prevalence of these diseases in patients hospitalized with COVID-19, and secondly at the relative risk of death from any cause for patients with asthma or COPD. Results: Prevalence of both airway diseases varied markedly by region, making meaningful pooled global estimates of prevalence invalid and not of clinical utility. For individual studies, the interquartile range for asthma prevalence was 4.21 to 12.39%, and for COPD, 3.82 to 11.85%. The relative risk of death with COPD for patients hospitalized with COVID-19 was 1.863 (95% CI 1.640–2.115), while the risk with asthma was 0.918 (95% CI 0.767 to 1.098) with no evidence of increased mortality. Conclusions: For asthma and COPD, prevalence in patients hospitalized with COVID-19 varies markedly by region. We found no evidence that asthma predisposed to increased mortality in COVID-19 disease. For COPD, there was clear evidence of an association with increased mortality. Trial registration: The trial was registered with PROSPERO: registration number CRD42021289886

Data extraction methods for systematic review (semi)automation: Update of a living systematic review [version 2; peer review: 3 approved]

Background: The reliable and usable (semi)automation of data extraction can support the field of systematic review by reducing the workload required to gather information about the conduct and results of the included studies. This living systematic review examines published approaches for data extraction from reports of clinical studies. Methods: We systematically and continually search PubMed, ACL Anthology, arXiv, OpenAlex via EPPI-Reviewer, and the dblp computer science bibliography. Full text screening and data extraction are conducted within an open-source living systematic review application created for the purpose of this review. This living review update includes publications up to December 2022 and OpenAlex content up to March 2023. Results: 76 publications are included in this review. Of these, 64 (84%) of the publications addressed extraction of data from abstracts, while 19 (25%) used full texts. A total of 71 (93%) publications developed classifiers for randomised controlled trials. Over 30 entities were extracted, with PICOs (population, intervention, comparator, outcome) being the most frequently extracted. Data are available from 25 (33%), and code from 30 (39%) publications. Six (8%) implemented publicly available tools Conclusions: This living systematic review presents an overview of (semi)automated data-extraction literature of interest to different types of literature review. We identified a broad evidence base of publications describing data extraction for interventional reviews and a small number of publications extracting epidemiological or diagnostic accuracy data. Between review updates, trends for sharing data and code increased strongly: in the base-review, data and code were available for 13 and 19% respectively, these numbers increased to 78 and 87% within the 23 new publications. Compared with the base-review, we observed another research trend, away from straightforward data extraction and towards additionally extracting relations between entities or automatic text summarisation. With this living review we aim to review the literature continually

Rare, Threatened and Endangered Plants and Animals of Oregon

Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within the next 100 years. The major cause of this phenomenon is large-scale destruction of native habitats, which has increased since European settlement began in the mid 1800\u27s - in Oregon and throughout the New World. Once lost, a species can never be recovered, and there is no way of knowing how useful it may have been. We do know that human beings and many of their industries depend on plant and animal products. About 50% of all pharmaceuticals have a natural component as an active ingredient, yet less than one percent of the world\u27s species have been chemically analyzed and tested. Many invertebrates and plants contain undescribed and highly functional compounds. Limnanthes floccosa subsp. grandiflora, or wooly meadow-foam, a rare plant that grows in southwest Oregon, has been recently found to produce a hybrid with the more common member of the genus, Limnanthes alba. This hybrid grows well in the poorly drained soils of the Willamette Valley and produces a valuable oil used for soaps, plastic and rubber production. In addition, the new hybrid meadow-foam does not require the field burning necessary for other crops. This species, and many other Oregon natives, will be lost without intervention. The purpose of this book is to provide land managers, owners and interested parties with a list of those species in Oregon which are in greatest jeopardy

Two Alleles of NF-κB in the Sea Anemone Nematostella vectensis Are Widely Dispersed in Nature and Encode Proteins with Distinct Activities

BACKGROUND. NF-κB is an evolutionarily conserved transcription factor that controls the expression of genes involved in many key organismal processes, including innate immunity, development, and stress responses. NF-κB proteins contain a highly conserved DNA-binding/dimerization domain called the Rel homology domain. METHODS/PRINCIPAL FINDINGS. We characterized two NF-κB alleles in the sea anemone Nematostella vectensis that differ at nineteen single-nucleotide polymorphisms (SNPs). Ten of these SNPs result in amino acid substitutions, including six within the Rel homology domain. Both alleles are found in natural populations of Nematostella. The relative abundance of the two NF-κB alleles differs between populations, and departures from Hardy-Weinberg equilibrium within populations indicate that the locus may be under selection. The proteins encoded by the two Nv-NF-κB alleles have different molecular properties, in part due to a Cys/Ser polymorphism at residue 67, which resides within the DNA recognition loop. In nearly all previously characterized NF-κB proteins, the analogous residue is fixed for Cys, and conversion of human RHD proteins from Cys to Ser at this site has been shown to increase DNA-binding ability and increase resistance to inhibition by thiol-reactive compounds. However, the naturally-occurring Nematostella variant with Cys at position 67 binds DNA with a higher affinity than the Ser variant. On the other hand, the Ser variant activates transcription in reporter gene assays more effectively, and it is more resistant to inhibition by a thiol-reactive compound. Reciprocal Cys<->Ser mutations at residue 67 of the native Nv-NF-κB proteins affect DNA binding as in human NF-κB proteins, e.g., a Cys->Ser mutation increases DNA binding of the native Cys variant. CONCLUSIONS/SIGNIFICANCE. These results are the first demonstration of a naturally occurring and functionally significant polymorphism in NF-κB in any species. The functional differences between these alleles and their uneven distribution in the wild suggest that different genotypes could be favored in different environments, perhaps environments that vary in their levels of peroxides or thiol-reactive compounds.National Institutes of Health (CA047763); National Science Foundation (FP-91656101-0); Environmental Protection Agency (F5E11155); Conservation International Marine Management Area Science Program; Boston University (SPRInG grant); Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution; The Beacon Institute for Rivers and Estuaries; the J Seward Johnson Fund; Boston University (5 P42 ES07381

Validation of elemental and isotopic abundances in late-M spectral types with the benchmark HIP 55507 AB system

M dwarfs are common host stars to exoplanets but often lack atmospheric abundance measurements. Late-M dwarfs are also good analogs to the youngest substellar companions, which share similar $T_{\rm eff}\sim2300-2800~K$. We present atmospheric analyses for the M7.5 companion HIP 55507 B and its K6V primary star with Keck/KPIC high-resolution ($R\sim35,000$) $K$ band spectroscopy. First, by including KPIC relative radial velocities between the primary and secondary in the orbit fit, we improve the dynamical mass precision by 60% and find $M_B=88.0_{-3.2}^{+3.4}$ $M_{\rm Jup}$, putting HIP 55507 B above the stellar-substellar boundary. We also find that HIP 55507 B orbits its K6V primary star with $a=38^{+4}_{-3}$ AU and $e=0.40\pm0.04$. From atmospheric retrievals of HIP 55507 B, we measure $\rm [C/H]=0.24\pm0.13$, $\rm [O/H]=0.15\pm0.13$, and $\rm C/O=0.67\pm0.04$. Moreover, we strongly detect $\rm ^{13}CO$ ($7.8\sigma$ significance) and tentatively detect $\rm H_2^{18}O$ ($3.7\sigma$ significance) in companion's atmosphere, and measure $\rm ^{12}CO/^{13}CO=98_{-22}^{+28}$ and $\rm H_2^{16}O/H_2^{18}O=240_{-80}^{+145}$ after accounting for systematic errors. From a simplified retrieval analysis of HIP 55507 A, we measure $\rm ^{12}CO/^{13}CO=79_{-16}^{+21}$ and $\rm C^{16}O/C^{18}O=288_{-70}^{+125}$ for the primary star. These results demonstrate that HIP 55507 A and B have consistent $\rm ^{12} C/^{13}C$ and $\rm ^{16}O/^{18}O$ to the $<1\sigma$ level, as expected for a chemically homogeneous binary system. Given the similar flux ratios and separations between HIP 55507 AB and systems with young, substellar companions, our results open the door to systematically measuring $\rm ^{13}CO$ and $\rm H_2^{18}O$ abundances in the atmospheres of substellar or even planetary-mass companions with similar spectral types.Comment: Accepted to ApJ, 28 pages, 14 figure

Representation of behaviour change interventions and their evaluation : Development of the Upper Level of the Behaviour Change Intervention Ontology [version 2; peer review: 2 approved]

Funding Information: Grant information: This work is supported by Wellcome through a collaborative award to The Human Behaviour-Change Project [201524]. MMM is funded by a Marie-Sklodowska-Curie fellowship [EU H2020 EDGE program grant agreement No. 713567].Peer reviewedPublisher PD