Sequence stratigraphy, basin morphology and sea-level history for the Permian Kapp Starostin Formation of Svalbard, Norway

Based on seven measured sections from Svalbard, the marine strata of the Permian Kapp Starostin Formation are arranged into seven transgressive–regressive sequences (TR1–TR7) of c. 4–5 Ma average duration, each bound by a maximum regressive surface. Facies, including heterozoan-dominated limestones, spiculitic cherts, sandstones, siltstones and shales, record deposition within inner, middle and outer shelf areas. The lowermost sequence, TR1, comprises most of the basal Vøringen Member, which records a transgression across the Gipshuken Formation following a hiatus of unknown duration. Temperate to cold, storm-dominated facies established in inner to middle shelf areas between the latest Artinskian and Kungurian. Prolonged deepening during sequences TR2 and TR3 was succeeded by a long-term shallowing-upward trend that lasted until the latest Permian (TR4–TR7). A major depocentre existed in central and western Spitsbergen while to the north, Dickson Land remained a shallow platform, leading to a shallow homoclinal ramp in NE Spitsbergen and Nordaustlandet. The Middle Permian extinction (late Capitanian) is recorded near the base of TR6 in deeper parts of the basin only; elsewhere this sequence is not recorded. Likewise the youngest sequence, TR7, extending to the upper formational contact of latest Permian age, is found only in the basin depocentre. Comparison with age-equivalent strata in the Sverdrup Basin of Canada reveals a remarkably similar depositional history, with, for example, two (third-order) sea-level cycles recorded in the Late Permian of both regions, in keeping with the global record. Sequence stratigraphy may therefore be a powerful correlative tool for onshore and offshore Permian deposits across NW Pangaea

Reward processing in autism: a thematic series

This thematic series presents theoretical and empirical papers focused on understanding autism from the perspective of reward processing deficits. Although the core symptoms of autism have not traditionally been conceptualized with respect to altered reward-based processes, it is clear that brain reward circuitry plays a critical role in guiding social and nonsocial learning and behavior throughout development. Additionally, brain reward circuitry may respond to social sources of information in ways that are similar to responses to primary rewards, and recent clinical data consistently suggest abnormal behavioral and neurobiologic responses to rewards in autism. This thematic series presents empirical data and review papers that highlight the utility of considering autism from the perspective of reward processing deficits. Our hope is that this novel framework may further elucidate autism pathophysiology, with the ultimate goal of yielding novel insights with potential therapeutic implications

Validation and characterisation of a novel peptide that binds monomeric and aggregated beta-amyloid and inhibits the formation of neurotoxic oligomers

Although the formation of β-amyloid (Aβ) deposits in the brain is a hallmark of Alzheimer disease (AD), the soluble oligomers rather than the mature amyloid fibrils most likely contribute to Aβ toxicity and neurodegeneration. Thus, the discovery of agents targeting soluble Aβ oligomers is highly desirable for early diagnosis prior to the manifestation of a clinical AD phenotype and also more effective therapies. We have previously reported that a novel 15-amino acid peptide (15-mer), isolated via phage display screening, targeted Aβ and attenuated its neurotoxicity (Taddei, K., Laws, S. M., Verdile, G., Munns, S., D'Costa, K., Harvey, A. R., Martins, I. J., Hill, F., Levy, E., Shaw, J. E., and Martins, R. N. (2010) Neurobiol. Aging 31, 203–214). The aim of the current study was to generate and biochemically characterize analogues of this peptide with improved stability and therapeutic potential. We demonstrated that a stable analogue of the 15-amino acid peptide (15M S.A.) retained the activity and potency of the parent peptide and demonstrated improved proteolytic resistance in vitro (stable to t = 300 min, c.f. t = 30 min for the parent peptide). This candidate reduced the formation of soluble Aβ42 oligomers, with the concurrent generation of non-toxic, insoluble aggregates measuring up to 25–30 nm diameter as determined by atomic force microscopy. The 15M S.A. candidate directly interacted with oligomeric Aβ42, as shown by coimmunoprecipitation and surface plasmon resonance/Biacore analysis, with an affinity in the low micromolar range. Furthermore, this peptide bound fibrillar Aβ42 and also stained plaques ex vivo in brain tissue from AD model mice. Given its multifaceted ability to target monomeric and aggregated Aβ42 species, this candidate holds promise for novel preclinical AD imaging and therapeutic strategies

[18F]FDG PET/CT-based response assessment of stage IV non-small cell lung cancer treated with paclitaxel-carboplatin-bevacizumab with or without nitroglycerin patches

Purpose Nitroglycerin (NTG) is a vasodilating drug, which increases tumor blood flow and consequently decreases hypoxia. Therefore, changes in [18F] fluorodeoxyglucose positron emission tomography ([18F] FDG PET) uptake pattern may occur. In this analysis, we investigated the feasibility of [18F] FDG PET for response assessment to paclitaxel-carboplatin-bevacizumab (PCB) treatment with and without NTG patches. And we compared the [18F] FDG PET response assessment to RECIST response assessment and survival. Methods A total of 223 stage IV non-small cell lung cancer (NSCLC) patients were included in a phase II study (NCT01171170) randomizing between PCB treatment with or without NTG patches. For 60 participating patients, a baseline and a second [18F] FDG PET/computed tomography (CT) scan, performed between day 22 and 24 after the start of treatment, were available. Tumor response was defined as a 30 % decrease in CT and PET parameters, and was compared to RECIST response at week 6. The predictive value of these assessments for progression free survival (PFS) and overall survival (OS) was assessed with and without NTG. Results A 30 % decrease in SUVpeak assessment identified more patients as responders compared to a 30 % decrease in CT diameter assessment (73 % vs. 18 %), however, this was not correlated to OS (SUVpeak30 p = 0.833; CTdiameter30 p = 0.557). Changes in PET parameters between the baseline and the second scan were not significantly different for the NTG group compared to the control group (p value range 0.159-0.634). The CT-based (part of the [18F] FDG PET/CT) parameters showed a significant difference between the baseline and the second scan for the NTG group compared to the control group (CT diameter decrease of 7 +/- 23 % vs. 19 +/- 14 %, p = 0.016, respectively). Conclusions The decrease in tumoral FDG uptake in advanced NSCLC patients treated with chemotherapy with and without NTG did not differ between both treatment arms. Early PET-based response assessment showed more tumor responders than CT-based response assessment (part of the [18F] FDG PET/CT); this was not correlated to survival. This might be due to timing of the [18F] FDG PET shortly after the bevacizumab infusion

Multi-source data approach for personalized outcome prediction in lung cancer screening: update from the NELSON trial

Trials show that low-dose computed tomography (CT) lung cancer screening in long-term (ex-)smokers reduces lung cancer mortality. However, many individuals were exposed to unnecessary diagnostic procedures. This project aims to improve the efficiency of lung cancer screening by identifying high-risk participants, and improving risk discrimination for nodules. This study is an extension of the Dutch-Belgian Randomized Lung Cancer Screening Trial, with a focus on personalized outcome prediction (NELSON-POP). New data will be added on genetics, air pollution, malignancy risk for lung nodules, and CT biomarkers beyond lung nodules (emphysema, coronary calcification, bone density, vertebral height and body composition). The roles of polygenic risk scores and air pollution in screen-detected lung cancer diagnosis and survival will be established. The association between the AI-based nodule malignancy score and lung cancer will be evaluated at baseline and incident screening rounds. The association of chest CT imaging biomarkers with outcomes will be established. Based on these results, multisource prediction models for pre-screening and post-baseline-screening participant selection and nodule management will be developed. The new models will be externally validated. We hypothesize that we can identify 15-20% participants with low-risk of lung cancer or short life expectancy and thus prevent ~140,000 Dutch individuals from being screened unnecessarily. We hypothesize that our models will improve the specificity of nodule management by 10% without loss of sensitivity as compared to assessment of nodule size/growth alone, and reduce unnecessary work-up by 40-50%

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Facies arrangement and cyclostratigraphic architecture of the templet member and the kapp starostin formation (Permian) on Spitsbergen, Svalbard

Because of outstanding outcrops, Spitsbergen (Svalbard archipelago) provides unique opportunities to investigate the whole Upper Palaeozoic succession in great detail. This study can help to interpret the stratigraphic history and depositional evolution at other locations exposing coeval shelf strata along the northern margin of Pangea, e.g., the southern Barents Sea and Arctic Canada. Bed-scale outcrop observations are combined with microfacies studies to interpret the sedimentary settings and depositional environment of the Upper Palaeozoic strata. A sequencestratigraphic analysis has been carried out to evaluate the relative timing of sediment facies deposition in response to sea-level changes. The Early Artinskian to Kazanian successions of the Templet Member and the Kapp Starostin Formation were divided into five parasequences that are superimposed on a long-term, second-order, sea-level fall. These parasequences record a fundamental change of the sedimentary setting, from a restricted-marine, warm-water carbonate platform to an open-marine, cold-water, biosiliceous-carbonate ramp system. A cross-section across Svalbard comprising nine onshore sections shows that during deposition of the Kapp Starostin Formation a major depocentre marked by thick parasequences and a higher proportion of deep-water facies (bedded cherts) is located in the southwest of Spitsbergen (at Akseløya), whereas northeastern Svalbard records shallow-water microfacies. Svalbard was tectonically passive during the Permian; the local differences in accommodation space and facies were most likely linked to the rejuvenation of pre-existing structural elements, inherited from the Carboniferous. A deepening of the depositional environment combined with cold-water climatic conditions as recorded in our study area has also been documented in other Upper Palaeozoic successions around the Arctic, such as the Finnmark Platform (Norwegian Barents Sea) and the Sverdrup Basin (Arctic Canada). This transition in the depositional environment along the northern margin of Pangea is the result of large-scale changes in oceanic circulation patterns and local palaeogeographic changes during the northward movement of Pangea

A new variant in the ZCCHC8 gene:diverse clinical phenotypes and expression in the lung

Introduction:Pulmonary fibrosis is a severe disease which can be familial. A genetic cause can only be found in ∼40% of families. Searching for shared novel genetic variants may aid the discovery of new genetic causes of disease. Methods:Whole-exome sequencing was performed in 152 unrelated patients with a suspected genetic cause of pulmonary fibrosis from the St Antonius interstitial lung disease biobank. Variants of interest were selected by filtering for novel, potentially deleterious variants that were present in at least three unrelated pulmonary fibrosis patients. Results:The novel c.586G&gt;A p.(E196K) variant in the ZCCHC8 gene was observed in three unrelated patients: two familial patients and one sporadic patient, who was later genealogically linked to one of the families. The variant was identified in nine additional relatives with pulmonary fibrosis and other telomererelated phenotypes, such as pulmonary arterial venous malformations, emphysema, myelodysplastic syndrome, acute myeloid leukaemia and dyskeratosis congenita. One family showed incomplete segregation, with absence of the variant in one pulmonary fibrosis patient who carried a PARN variant. The majority of ZCCHC8 variant carriers showed short telomeres in blood. ZCCHC8 protein was located in different lung cell types, including alveolar type 2 (AT2) pneumocytes, the culprit cells in pulmonary fibrosis. AT2 cells showed telomere shortening and increased DNA damage, which was comparable to patients with sporadic pulmonary fibrosis and those with pulmonary fibrosis carrying a telomere-related gene variant, respectively. Discussion:The ZCCHC8 c.586G&gt;A variant confirms the involvement of ZCCHC8 in pulmonary fibrosis and short-telomere syndromes and underlines the importance of including the ZCCHC8 gene in diagnostic gene panels for these diseases.</p