iDirac: a field-portable instrument for long-term autonomous measurements of isoprene and selected VOCs

The iDirac is a new instrument to measure selected hydrocarbons in the remote atmosphere. A robust design is central to its specifications, with portability, power efficiency, low gas consumption and autonomy as the other driving factors in the instrument development. The iDirac is a dual-column isothermal oven gas chromatograph with photoionisation detection (GC-PID). The instrument is designed and built in-house. It features a modular design, with the novel use of open-source technology for accurate instrument control. Currently configured to measure biogenic isoprene, the system is suitable for a range of compounds. For isoprene measurements in the field, the instrument precision (relative standard deviation) is ±10 %, with a limit of detection down to 38 pmol mol−1 (or ppt). The instrument was first tested in the field in 2015 during a ground-based campaign, and has since shown itself suitable for deployment in a variety of environments and platforms. This paper describes the instrument design, operation and performance based on laboratory tests in a controlled environment as well as during deployments in forests in Malaysian Borneo and central England

10 Years of Pressurized Intraperitoneal Aerosol Chemotherapy (PIPAC): A Systematic Review and Meta-Analysis

Background: Pressurized intraperitoneal aerosol chemotherapy (PIPAC) is a novel intraperitoneal drug delivery method of low-dose chemotherapy as a pressurized aerosol in patients affected by peritoneal cancer of primary or secondary origin. We performed a systematic review and meta-analysis with the aim of assessing the feasibility, safety, and efficacy of PIPAC. Methods: A systematic literature search was performed using Medline and Web of Science databases from 1 January 2011, to inception, to 31 December 2021. Data were independently extracted by two authors. The Newcastle-Ottawa Scale was used to assess the quality and risk of bias of studies. Meta-analysis was performed for pathological response, radiological response, PCI variation along treatment, and for patients undergoing three or more PIPAC. Pooled analyses were performed using the Freeman–Tukey double arcsine transformation, and 95% CIs were calculated using Clopper–Pearson exact CIs in all instances. Results: A total of 414 papers on PIPAC were identified, and 53 studies considering 4719 PIPAC procedure in 1990 patients were included for analysis. The non-access rate or inability to perform PIPAC pooled rate was 4% of the procedures performed. The overall proportion of patients who completed 3 or more cycles of PIPAC was 39%. Severe toxicities considering CTCAE 3–4 were 4% (0% to 38.5%). In total, 50 studies evaluated deaths within the first 30 postoperative days. In the included 1936 patients were registered 26 deaths (1.3%). The pooled analysis of all the studies reporting a pathological response was 68% (95% CI 0.61–0.73), with an acceptable heterogeneity (I2 28.41%, p = 0.09). In total, 10 papers reported data regarding the radiological response, with high heterogeneity and a weighted means of 15% (0% to 77.8%). PCI variation along PIPAC cycles were reported in 14 studies. PCI diminished, increased, or remained stable in eight, one and five studies, respectively, with high heterogeneity at pooled analysis. Regarding survival, there was high heterogeneity. The 12-month estimated survival from first PIPAC for colorectal cancer, gastric cancer, gynecological cancer and hepatobiliary/pancreatic cancer were, respectively, 53%, 25%, 59% and 37%. Conclusions: PIPAC may be a useful treatment option for selected patients with PM, with acceptable grade 3 and 4 toxicity and promising survival benefit. Meta-analysis showed high heterogeneity of data among up-to-date available studies. In a subset analysis per primary tumor origin, pathological tumor regression was documented in 68% of the studies with acceptable heterogeneity. Pathological regression seems, therefore, a reliable outcome for PIPAC activity and a potential surrogate endpoint of treatment response. We recommend uniform selection criteria for patients entering a PIPAC program and highlight the urgent need to standardize items for PIPAC reports and datasets

Genetic and epigenetic alterations of cdh1 regulatory regions in hereditary and sporadic gastric cancer

E-cadherin is a key player in gastric cancer (GC) and germline alterations of CDH1, its encoding gene, are responsible for Hereditary Diffuse Gastric Cancer (HDGC) syndrome. This study aimed at elucidating the role of genetic variants and DNA methylation of CDH1 promoter and enhancers in the regulation of gene expression. For this purpose, we analyzed genetic variants of the CDH1 gene through Next-Generation Sequencing (NGS) in a series of GC cell lines (NCI-N87, KATO-III, SNU-1, SNU-5, GK2, AKG, KKP) and the corresponding CDH1 expression levels. By bisulfite genomic sequencing, we analyzed the methylation status of CDH1 regulatory regions in 8 GC cell lines, in a series of 13 sporadic GC tissues and in a group of 20 HDGC CDH1-negative patients and 6 healthy controls. The NGS analysis on CDH1 coding and regulatory regions detected genetic alterations in 3 out of 5 GC cell lines lacking functional E-cadherin. CDH1 regulatory regions showed different methylation patterns in patients and controls, GC cell lines and GC tissues, expressing different E-cadherin levels. Our results showed that alterations in terms of genetic variants and DNA methylation patterns of both promoter and enhancers are associated with CDH1 expression levels and have a role in its regulation.This research and its authors were funded by IRCCS IRST (G.T., C.M., R.D. V.A., M.R., F.R., M.C., S.P., G.M., D.C., P.U.) and by FEDER-Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020–Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT–Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274) (C.S.J., R.B.-M., A.A., C.O.). This work was also financed by the project NORTE-01-0145-FEDER-000029 (CANCER)-supported by Norte Portugal Regional Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)–project POCI-01-0145-FEDER-016390 (CancelStem) and PTDC/BTM-TEC/30164/2017 (3DChroMe), funded by ERDF, POCI and FCT

Feasibility and safety of PIPAC combined with additional surgical procedures: PLUS study.

PIPAC (Pressurized IntraPeritoneal Aerosol Chemotherapy) is a minimally invasive approach relying on physical principles for improving intraperitoneal drug delivery, including optimizing the homogeneity of drug distribution through an aerosol. Feasibility and safety of the new approach are now consolidated and data on its effectiveness are continuously increasing. Although any surgical procedure associated with PIPAC had always been discouraged due to the high risk of complications, surgical practice is constantly changing: with growing expertise, more and more surgical teams associate PIPAC with surgery. PLUS study is part of the retrospective international cohort studies including 10 centers around the world (India, Italy, France, Germany, Belgium, Russia, Saudi Arabia, Switzerland) and 96 cases of combined approaches evaluated through a propensity score analysis. the procedures most frequently associated with PIPAC were not only adhesiolysis, omentectomy, adnexectomy, umbilical/inguinal hernia repairs, but also more demanding procedures such as intestinal resections, gastrectomy, splenectomy, bowel repair/stoma creation. Although the evidence is currently limited, PLUS study demonstrated that PIPAC associated with additional surgical procedures is linked to an increase of surgical time (p < 0.001), length of stay (p < 0.001) and medical complication rate (p < 0.001); the most frequently reported medical complications were mild or moderate in severity, such as abdominal pain, nausea, ileus and hyperthermia. No difference in terms of surgical complications was registered; neither reoperation or postoperative deaths were reported. these results suggest that PIPAC can be safely combined in expert centers with additional surgeries. Widespread change of practice should be discouraged before the results of ongoing prospective studies are available

Encephalopathy associated with autoimmune thyroid disease in patients with Graves' disease: clinical manifestations, follow-up, and outcomes

<p>Abstract</p> <p>Background</p> <p>The encephalopathy associated with autoimmune thyroid disease (EAATD) is characterized by neurological/psychiatric symptoms, high levels of anti-thyroid antibodies, increased cerebrospinal fluid protein concentration, non-specific electroencephalogram abnormalities, and responsiveness to the corticosteroid treatment in patients with an autoimmune thyroid disease. Almost all EAATD patients are affected by Hashimoto's thyroiditis (HT), although fourteen EAATD patients with Graves' disease (GD) have been also reported.</p> <p>Methods</p> <p>We have recorded and analyzed the clinical, biological, radiological, and electrophysiological findings and the data on the therapeutic management of all GD patients with EAATD reported so far as well as the clinical outcomes in those followed-up in the long term.</p> <p>Results</p> <p>Twelve of the fourteen patients with EAATD and GD were women. The majority of GD patients with EAATD presented with mild hyperthyroidism at EAATD onset or shortly before it. Active anti-thyroid autoimmunity was detected in all cases. Most of the patients dramatically responded to corticosteroids. The long term clinical outcome was benign but EAATD can relapse, especially at the time of corticosteroid dose tapering or withdrawal. GD and HT patients with EAATD present with a similar clinical, biological, radiological, and electrophysiological picture and require an unaffected EAATD management.</p> <p>Conclusions</p> <p>GD and HT equally represent the possible background condition for the development of EAATD, which should be considered in the differential diagnosis of all patients with encephalopathy of unknown origin and an autoimmune thyroid disease, regardless of the nature of the underlying autoimmune thyroid disease.</p

Atmospheric isoprene measurements reveal larger-than-expected Southern Ocean emissions

Isoprene is a key trace component of the atmosphere emitted by vegetation and other organisms. It is highly reactive and can impact atmospheric composition and climate by affecting the greenhouse gases ozone and methane and secondary organic aerosol formation. Marine fluxes are poorly constrained due to the paucity of long-term measurements; this in turn limits our understanding of isoprene cycling in the ocean. Here we present the analysis of isoprene concentrations in the atmosphere measured across the Southern Ocean over 4 months in the summertime. Some of the highest concentrations ( >500 ppt) originated from the marginal ice zone in the Ross and Amundsen seas, indicating the marginal ice zone is a significant source of isoprene at high latitudes. Using the United Kingdom Earth System Model we show that current estimates of sea-to-air isoprene fluxes underestimate observed isoprene by a factor >20. A daytime source of isoprene is required to reconcile models with observations. The model presented here suggests such an increase in isoprene emissions would lead to >8% decrease in the hydroxyl radical in regions of the Southern Ocean, with implications for our understanding of atmospheric oxidation and composition in remote environments, often used as proxies for the pre-industrial atmosphere.V.F. and N.R.P.H. were supported in the analysis of the data by UKRI NERC project Southern Ocean Clouds (NE/T006366/1)

Continuous isoprene measurements in a UK temperate forest for a whole growing season: effects of drought stress during the 2018 heatwave

Isoprene concentrations were measured at four heights below, within and above the forest canopy in Wytham Woods (UK) throughout the summer of 2018 using custom-built gas chromatographs (the iDirac). These observations were complemented with selected ancillary variables, including air temperature, photosynthetically active radiation (PAR), occasional leaf gas exchange measurements and satellite retrievals of normalized difference vegetation and water indices (NDVI and NDWI). The campaign overlapped with a long and uninterrupted heatwave accompanied by moderate drought. Peak isoprene concentrations during the heatwave-drought were up to a factor of 4 higher than those before or after. Higher temperatures during the heatwave could not account for all the observed isoprene; the enhanced abundances correlated with drought stress. Leaf-level emissions confirmed this and also included compounds associated with ecosystem stress. This work highlights that a more in-depth understanding of the effects of drought stress is required to better characterize isoprene emissions

Timing is everything: the regulation of type III secretion

Type Three Secretion Systems (T3SSs) are essential virulence determinants of many Gram-negative bacteria. The T3SS is an injection device that can transfer bacterial virulence proteins directly into host cells. The apparatus is made up of a basal body that spans both bacterial membranes and an extracellular needle that possesses a channel that is thought to act as a conduit for protein secretion. Contact with a host-cell membrane triggers the insertion of a pore into the target membrane, and effectors are translocated through this pore into the host cell. To assemble a functional T3SS, specific substrates must be targeted to the apparatus in the correct order. Recently, there have been many developments in our structural and functional understanding of the proteins involved in the regulation of secretion. Here we review the current understanding of protein components of the system thought to be involved in switching between different stages of secretion

Exploring the coupled ocean and atmosphere system with a data science approach applied to observations from the Antarctic Circumnavigation Expedition

The Southern Ocean is a critical component of Earth’s climate system, but its remoteness makes it challenging to develop a holistic understanding of its processes from the small scale to the large scale. As a result, our knowledge of this vast region remains largely incomplete. The Antarctic Circumnavigation Expedi�tion (ACE, austral summer 2016/2017) surveyed a large number of variables describing the state of the ocean and the atmosphere, the freshwater cycle, atmospheric chemistry, and ocean biogeochemistry and microbiology. This circumpolar cruise included visits to 12 remote islands, the marginal ice zone, and the Antarctic coast. Here, we use 111 of the observed variables to study the latitudinal gradients, seasonality, shorter-term variations, geographic setting of environmental processes, and interactions between them over the duration of 90 d. To re�duce the dimensionality and complexity of the dataset and make the relations between variables interpretable we applied an unsupervised machine learning method, the sparse principal component analysis (sPCA), which describes environmental processes through 14 latent variables. To derive a robust statistical perspective on these processes and to estimate the uncertainty in the sPCA decomposition, we have developed a bootstrap approach. Our results provide a proof of concept that sPCA with uncertainty analysis is able to identify temporal patterns from diurnal to seasonal cycles, as well as geographical gradients and “hotspots” of interaction between envi�ronmental compartments. While confirming many well known processes, our analysis provides novel insights into the Southern Ocean water cycle (freshwater fluxes), trace gases (interplay between seasonality, sources, and sinks), and microbial communities (nutrient limitation and island mass effects at the largest scale ever reported). More specifically, we identify the important role of the oceanic circulations, frontal zones, and islands in shap�ing the nutrient availability that controls biological community composition and productivity; the fact that sea ice controls sea water salinity, dampens the wave field, and is associated with increased phytoplankton growth and net community productivity possibly due to iron fertilisation and reduced light limitation; and the clear regional patterns of aerosol characteristics that have emerged, stressing the role of the sea state, atmospheric chemical processing, and source processes near hotspots for the availability of cloud condensation nuclei and hence cloud formation. A set of key variables and their combinations, such as the difference between the air and sea surface temperature, atmospheric pressure, sea surface height, geostrophic currents, upper-ocean layer light intensity, surface wind speed and relative humidity played an important role in our analysis, highlighting the necessity for Earth system models to represent them adequately. In conclusion, our study highlights the use of sPCA to identify key ocean–atmosphere interactions across physical, chemical, and biological processes and their associated spatio-temporal scales. It thereby fills an important gap between simple correlation analyses and complex Earth system models. The sPCA processing code is available as open-access from the following link: https://renkulab.io/gitlab/ACE-ASAID/spca-decomposition (last access: 29 March 2021). As we show here, it can be used for an exploration of environmental data that is less prone to cognitive biases (and confirmation biases in particular) compared to traditional regression analysis that might be affected by the underlying research question