Variability in the analysis of a single neuroimaging dataset by many teams.

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2-5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.

No detection of methane on Mars from early ExoMars Trace Gas Orbiter observations.

The detection of methane on Mars has been interpreted as indicating that geochemical or biotic activities could persist on Mars today1. A number of different measurements of methane show evidence of transient, locally elevated methane concentrations and seasonal variations in background methane concentrations2-5. These measurements, however, are difficult to reconcile with our current understanding of the chemistry and physics of the Martian atmosphere6,7, which-given methane's lifetime of several centuries-predicts an even, well mixed distribution of methane1,6,8. Here we report highly sensitive measurements of the atmosphere of Mars in an attempt to detect methane, using the ACS and NOMAD instruments onboard the ESA-Roscosmos ExoMars Trace Gas Orbiter from April to August 2018. We did not detect any methane over a range of latitudes in both hemispheres, obtaining an upper limit for methane of about 0.05 parts per billion by volume, which is 10 to 100 times lower than previously reported positive detections2,4. We suggest that reconciliation between the present findings and the background methane concentrations found in the Gale crater4 would require an unknown process that can rapidly remove or sequester methane from the lower atmosphere before it spreads globally.

Publisher Correction: No detection of methane on Mars from early ExoMars Trace Gas Orbiter observations.

The surname of author Cathy Quantin-Nataf was misspelled 'Quantin-Nata', authors Ehouarn Millour and Roland Young were missing from the ACS and NOMAD Science Teams list, and minor changes have been made to the author and affiliation lists; see accompanying Amendment. These errors have been corrected online.

Early Convalescent Plasma for High-Risk Outpatients with Covid-19.

BACKGROUND: Early administration of convalescent plasma obtained from blood donors who have recovered from coronavirus disease 2019 (Covid-19) may prevent disease progression in acutely ill, high-risk patients with Covid-19. METHODS: In this randomized, multicenter, single-blind trial, we assigned patients who were being treated in an emergency department for Covid-19 symptoms to receive either one unit of convalescent plasma with a high titer of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or placebo. All the patients were either 50 years of age or older or had one or more risk factors for disease progression. In addition, all the patients presented to the emergency department within 7 days after symptom onset and were in stable condition for outpatient management. The primary outcome was disease progression within 15 days after randomization, which was a composite of hospital admission for any reason, seeking emergency or urgent care, or death without hospitalization. Secondary outcomes included the worst severity of illness on an 8-category ordinal scale, hospital-free days within 30 days after randomization, and death from any cause. RESULTS: A total of 511 patients were enrolled in the trial (257 in the convalescent-plasma group and 254 in the placebo group). The median age of the patients was 54 years; the median symptom duration was 4 days. In the donor plasma samples, the median titer of SARS-CoV-2 neutralizing antibodies was 1:641. Disease progression occurred in 77 patients (30.0%) in the convalescent-plasma group and in 81 patients (31.9%) in the placebo group (risk difference, 1.9 percentage points; 95% credible interval, -6.0 to 9.8; posterior probability of superiority of convalescent plasma, 0.68). Five patients in the plasma group and 1 patient in the placebo group died. Outcomes regarding worst illness severity and hospital-free days were similar in the two groups. CONCLUSIONS: The administration of Covid-19 convalescent plasma to high-risk outpatients within 1 week after the onset of symptoms of Covid-19 did not prevent disease progression. (SIREN-C3PO ClinicalTrials.gov number, NCT04355767.).

The golden age of social science.

Social science is entering a golden age, marked by the confluence of explosive growth in new data and analytic methods, interdisciplinary approaches, and a recognition that these ingredients are necessary to solve the more challenging problems facing our world. We discuss how developing a "lingua franca" can encourage more interdisciplinary research, providing two case studies (social networks and behavioral economics) to illustrate this theme. Several exemplar studies from the past 12 y are also provided. We conclude by addressing the challenges that accompany these positive trends, such as career incentives and the search for unifying frameworks, and associated best practices that can be employed in response.

Understanding the potential causes of gastrointestinal dysfunctions in multiple system atrophy.

Multiple system atrophy (MSA) is a rare, progressive neurodegenerative disorder characterised by autonomic, pyramidal, parkinsonian and/or cerebellar dysfunction. Autonomic symptoms of MSA include deficits associated with the gastrointestinal (GI) system, such as difficulty swallowing, abdominal pain and bloating, nausea, delayed gastric emptying, and constipation. To date, studies assessing GI dysfunctions in MSA have primarily focused on alterations of the gut microbiome, however growing evidence indicates other structural components of the GI tract, such as the enteric nervous system, the intestinal barrier, GI hormones, and the GI-driven immune response may contribute to MSA-related GI symptoms. Here, we provide an in-depth exploration of the physiological, structural, and immunological changes theorised to underpin GI dysfunction in MSA patients and highlight areas for future research in order to identify more suitable pharmaceutical treatments for GI symptoms in patients with MSA.

Prediction of in-hospital deterioration in normotensive pulmonary embolism remains elusive: external validation of the calgary acute pulmonary embolism score.

Acute pulmonary embolism (PE) is a frequently diagnosed condition. Prediction of in-hospital deterioration is challenging with current risk models. The Calgary Acute Pulmonary Embolism (CAPE) score was recently derived to predict in-hospital adverse PE outcomes but has not yet been externally validated. Retrospective cohort study of normotensive acute pulmonary embolism cases diagnosed in our emergency department between 2017 and 2019. An external validation of the CAPE score was performed in this population for prediction of in-hospital adverse outcomes and a secondary outcome of 30-day all-cause mortality. Performance of the simplified Pulmonary Embolism Severity Index (sPESI) and Bova score was also evaluated. 712 patients met inclusion and exclusion criteria, with 536 patients having a sPESI score of 1 or more. Among this population, the CAPE score had a weak discriminative power to predict in-hospital adverse outcomes, with a calculated c-statistic of 0.57. In this study population, an external validation study found weak discriminative power of the CAPE score to predict in-hospital adverse outcomes among normotensive PE patients. Further efforts are needed to define risk assessment models that can identify normotensive PE patients at risk for in hospital deterioration. Identification of such patients will better guide intensive care utilization and invasive procedural management of PE.

Sample preparation for planar chromatography.

High-performance thin-layer chromatography has favorable properties for high-throughput separations with a high matrix tolerance. Sample preparation, however, is sometimes required to control specific matrix interferences and to enhance the detectability of target compounds. Trends in contemporary applications have shifted from absorbance and fluorescence detection to methods employing bioassays and mass spectrometry. Traditional methods (shake-flask, heat at reflux, Soxhlet, and hydrodistillation) are being challenged by automated instrumental approaches (ultrasound-assisted and microwave-assisted solvent extraction, pressurized liquid extraction, and supercritical fluid extraction) and the quick, easy cheap, efficient, rugged, and safe extraction method for faster and streamlined sample processing. Liquid-liquid extraction remains the most widely used approach for sample clean-up with increasing competition from solid-phase extraction. On-layer sample, clean-up by planar solid-phase extraction is increasingly used for complex samples and in combination with heart-cut multimodal systems. The automated spray-on sample applicator, the elution head interface, biological detection of target and non-target compounds, and straightforward mass spectrometric detection are highlighted as the main factors directing current interest toward faster and simpler sample workflows, analysis of more complex samples, and the determination of minor contaminants requiring high concentration factors.

Identifying risk factors for poor multidimensional recovery after major surgery: A systematic review.

Traditional risk factors used for predicting poor postoperative recovery have focused on postoperative complications, adverse symptoms (nausea, pain), length of hospital stay, and patient quality of life. Despite these being traditional performance indicators of patient postoperative "status," they may not fully define the multidimensional nature of patient recovery. The definition of postoperative recovery is thus evolving to include patient-reported outcomes that are important to the patient. Previous reviews have focused on risk factors for the above traditional outcomes after major surgery. Yet, there remains a need for further study of risk factors predicting multidimensional patient-focused recovery, and investigation beyond the immediate postoperative period after patients are discharged from the hospital. This review aimed to appraise the current literature identifying risk factors for multidimensional patient recovery. METHODS: A systematic review without meta-analysis was performed to qualitatively summarize preoperative risk factors for multidimensional recovery 4-6 weeks after major surgery (PROSPERO, CRD42022321626). We reviewed three electronic databases between January 2012 and April 2022. The primary outcome was risk factors for multidimensional recovery at 4-6 weeks. A GRADE quality appraisal and a risk of bias assessment were completed. RESULTS: In total, 5150 studies were identified, after which 1506 duplicates were removed. After the primary and secondary screening, nine articles were included in the final review. Interrater agreements between the two assessors for the primary and secondary screening process were 86% (k = 0.47) and 94% (k = 0.70), respectively. Factors associated with poor recovery were found to include ASA grade, recovery tool baseline score, physical function, number of co-morbidities, previous surgery, and psychological well-being. Mixed results were reported for age, BMI, and preoperative pain. Due to the observational nature, heterogeneity, multiple definitions of recovery, and moderate risk of bias of the primary studies, the quality of evidence was rated from very low to low. CONCLUSION: Our review found that there were few studies assessing preoperative risk factors as predictors for poor postoperative multidimensional recovery. This confirms the need for higher quality studies assessing risk for poor recovery, ideally with a consistent and multi-dimensional definition of recovery.

Selective targeting of nanomedicine to inflamed cerebral vasculature to enhance the blood-brain barrier.

Drug targeting to inflammatory brain pathologies such as stroke and traumatic brain injury remains an elusive goal. Using a mouse model of acute brain inflammation induced by local tumor necrosis factor alpha (TNFα), we found that uptake of intravenously injected antibody to vascular cell adhesion molecule 1 (anti-VCAM) in the inflamed brain is >10-fold greater than antibodies to transferrin receptor-1 and intercellular adhesion molecule 1 (TfR-1 and ICAM-1). Furthermore, uptake of anti-VCAM/liposomes exceeded that of anti-TfR and anti-ICAM counterparts by ∼27- and ∼8-fold, respectively, achieving brain/blood ratio >300-fold higher than that of immunoglobulin G/liposomes. Single-photon emission computed tomography imaging affirmed specific anti-VCAM/liposome targeting to inflamed brain in mice. Intravital microscopy via cranial window and flow cytometry showed that in the inflamed brain anti-VCAM/liposomes bind to endothelium, not to leukocytes. Anti-VCAM/LNP selectively accumulated in the inflamed brain, providing de novo expression of proteins encoded by cargo messenger RNA (mRNA). Anti-VCAM/LNP-mRNA mediated expression of thrombomodulin (a natural endothelial inhibitor of thrombosis, inflammation, and vascular leakage) and alleviated TNFα-induced brain edema. Thus VCAM-directed nanocarriers provide a platform for cerebrovascular targeting to inflamed brain, with the goal of normalizing the integrity of the blood-brain barrier, thus benefiting numerous brain pathologies.

Three Zone Scanning Protocol For Lung Ultrasound: An Anatomical Basis.

Lung ultrasound is rapidly gaining popularity based on point of care ease of use, diagnostic fidelity and lack of ionising radiation. This was particularly notable at the beginning of the COVID-19 pandemic, where concerns of contamination of the x-ray department led to a reluctance to order frequent chest x-rays. Early COVID-19 lung involvement is of a bronchopneumonia, and patches of consolidation adjacent to the chest wall were easily detectable by ultrasound. A large number of proposed scanning protocols were advocated and are often complex and largely based on traditional stethoscope examination or access points on the chest wall rather than the underlying lung anatomy. A surgical understanding of lung anatomy and related surface anatomy has led us to develop a simplified three zone scanning protocol in 2013. The anterior zone corresponds to the upper lobe, and the posterior zone is divided between upper lobe and lower lobe. The relationship between lung lobes and the surface of the chest wall provides the anatomical basis for a simple three scanning zone lung ultrasound protocol.

Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

BACKGROUND: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. RESULTS: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. CONCLUSION: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende .

Dynamic neural reconfiguration for distinct strategies during competitive social interactions.

Information exchange between brain regions is key to understanding information processing for social decision-making, but most analyses ignore its dynamic nature. New insights on this dynamic might help us to uncover the neural correlates of social cognition in the healthy population and also to understand the malfunctioning neural computations underlying dysfunctional social behavior in patients with mental disorders. In this work, we used a multi-round bargaining game to detect switches between distinct bargaining strategies in a cohort of 76 healthy participants. These switches were uncovered by dynamic behavioral modeling using the hidden Markov model. Proposing a novel model of dynamic effective connectivity to estimate the information flow between key brain regions, we found a stronger interaction between the right temporoparietal junction (rTPJ) and the right dorsolateral prefrontal cortex (rDLPFC) for the strategic deception compared with the social heuristic strategies. The level of deception was associated with the information flow from the Brodmann area 10 to the rTPJ, and this association was modulated by the rTPJ-to-rDLPFC information flow. These findings suggest that dynamic bargaining strategy is supported by dynamic reconfiguration of the rDLPFC-and-rTPJ interaction during competitive social interactions.

Neuroinflammation as an etiological trigger for depression comorbid with inflammatory bowel disease.

Patients with inflammatory bowel disease (IBD) suffer from depression at higher rates than the general population. An etiological trigger of depressive symptoms is theorised to be inflammation within the central nervous system. It is believed that heightened intestinal inflammation and dysfunction of the enteric nervous system (ENS) contribute to impaired intestinal permeability, which facilitates the translocation of intestinal enterotoxins into the blood circulation. Consequently, these may compromise the immunological and physiological functioning of distant non-intestinal tissues such as the brain. In vivo models of colitis provide evidence of increased blood-brain barrier permeability and enhanced central nervous system (CNS) immune activity triggered by intestinal enterotoxins and blood-borne inflammatory mediators. Understanding the immunological, physiological, and structural changes associated with IBD and neuroinflammation may aid in the development of more tailored and suitable pharmaceutical treatment for IBD-associated depression.

Targeted In Vivo Loading of Red Blood Cells Markedly Prolongs Nanocarrier Circulation.

Engineering drug delivery systems for prolonged pharmacokinetics (PK) has been an ongoing pursuit for nearly 50 years. The gold standard for PK enhancement is the coating of nanoparticles with polymers, namely polyethylene glycol (PEGylation), which has been applied in several clinically used products. In the present work, we utilize the longest circulating and most abundant component of blood─the erythrocyte─to improve the PK behavior of liposomes. Antibody-mediated coupling of liposomes to erythrocytes was tested in vitro to identify a loading dose that did not adversely impact the carrier cells. Injection of erythrocyte targeting liposomes into mice resulted in a ∼2-fold improvement in the area under the blood concentration versus time profile versus PEGylated liposomes and a redistribution from the plasma into the cellular fraction of blood. These results suggest that in vivo targeting of erythrocytes is a viable strategy to improve liposome PK relative to current, clinically viable strategies.

Physiological Responses to a Haunted-House Threat Experience: Distinct Tonic and Phasic Effects.

Threats elicit physiological responses, the frequency and intensity of which have implications for survival. Ethical and practical limitations on human laboratory manipulations present barriers to studying immersive threat. Furthermore, few investigations have examined group effects and concordance with subjective emotional experiences to threat. The current preregistered study measured electrodermal activity in 156 adults while they participated in small groups in a 30-min haunted-house experience involving various immersive threats. Results revealed positive associations between (a) friends and tonic arousal, (b) unexpected attacks and phasic activity (frequency and amplitude), (c) subjective fear and phasic frequency, and (d) dissociable sensitization effects linked to baseline orienting response. Findings demonstrate the relevance of (a) social dynamics (friends vs. strangers) for tonic arousal and (b) subjective fear and threat predictability for phasic arousal.

Enhanced Training Benefits of Video Recording Surgery With Automated Hand Motion Analysis.

BACKGROUND: Hand motion analysis by video recording during surgery has potential for evaluation of surgical performance. The aim was to identify how technical skill during open surgery can be measured unobtrusively by video recording during a surgical procedure. We hypothesized that procedural-step timing, hand movements, instrument use and Shannon entropy differ with expertise and training and are concordant with a performance-based validated individual procedure score. METHODS: Surgeon and non-surgeon participants with varying training and levels of expertise were video recorded performing axillary artery exposure and control (AA) on un-preserved cadavers. Color-coded gloves permitted motion-tracking and automated extraction of entropy data from recordings. Timing and instrument-use metrics were obtained through observational video reviews. Shannon entropy measured speed, acceleration and direction by computer-vision algorithms. Findings were compared with individual procedure score for AA performance RESULTS: Experts had lowest entropy values, idle time, active time and shorter time to divide pectoralis minor, using fewer instruments. Residents improved with training, without reaching expert levels, and showed deterioration 12-18 months later. Individual procedure scores mirrored these results. Non-surgeons differed substantially. CONCLUSIONS: Hand motion entropy and timing metrics discriminate levels of surgical skill and training, and these findings are congruent with individual procedure score evaluations. These measures can be collected using consumer-level cameras and analyzed automatically with free software. Hand motion with video timing data may have widespread application to evaluate resident performance and can contribute to the range of evaluation and testing modalities available to educators, training course designers and surgical quality assurance programs.

Identification of a queen and king recognition pheromone in the subterranean termite Reticulitermes flavipes.

Chemical communication is fundamental to success in social insect colonies. Species-, colony-, and caste-specific blends of cuticular hydrocarbons (CHCs) and other chemicals have been well documented as pheromones, mediating important behavioral and physiological aspects of social insects. More specifically, royal pheromones used by queens (and kings in termites) enable workers to recognize and care for these vital individuals and maintain the reproductive division of labor. In termites, however, no royal-recognition pheromones have been identified to date. In the current study, solvent extracts of the subterranean termite Reticulitermes flavipes were analyzed to assess differences in cuticular compounds among castes. We identified a royal-specific hydrocarbon-heneicosane-and several previously unreported and highly royal enriched long-chain alkanes. When applied to glass dummies, heneicosane elicited worker behavioral responses identical to those elicited by live termite queens, including increased vibratory shaking and antennation. Further, the behavioral effects of heneicosane were amplified when presented with nestmate termite workers' cuticular extracts, underscoring the importance of chemical context in termite royal recognition. Thus, heneicosane is a royal-recognition pheromone that is active in both queens and kings of R. flavipes The use of heneicosane as a queen and king recognition pheromone by termites suggests that CHCs evolved as royal pheromones ∼150 million years ago, ∼50 million years before their first use as queen-recognition pheromones in social Hymenoptera. We therefore infer that termites and social Hymenoptera convergently evolved the use of these ubiquitous compounds in royal recognition.

Genome-Wide Methylation Mapping Using Nanopore Sequencing Technology Identifies Novel Tumor Suppressor Genes in Hepatocellular Carcinoma.

Downregulation of multiple tumor suppressor genes (TSGs) plays an important role in cancer formation. Recent evidence has accumulated that cancer progression involves genome-wide alteration of epigenetic modifications, which may cause downregulation of the tumor suppressor gene. Using hepatocellular carcinoma (HCC) as a system, we mapped 5-methylcytosine signal at a genome-wide scale using nanopore sequencing technology to identify novel TSGs. Integration of methylation data with gene transcription profile of regenerated liver and primary HCCs allowed us to identify 10 potential tumor suppressor gene candidates. Subsequent validation led us to focus on functionally characterizing one candidate-glucokinase (GCK). We show here that overexpression of GCK inhibits the proliferation of HCC cells via induction of intracellular lactate accumulation and subsequently causes energy crisis due to NAD+ depletion. This suggests GCK functions as a tumor suppressor gene and may be involved in HCC development. In conclusion, these data provide valuable clues for further investigations of the process of tumorigenesis in human cancer.

Early markers of cystic fibrosis structural lung disease: follow-up of the ACFBAL cohort.

Little is known about early predictors of later cystic fibrosis (CF) structural lung disease. This study examined early predictors of progressive structural lung abnormalities in children who completed the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial at age 5-years and participated in an observational follow-up study (CF-FAB).Eight Australian and New Zealand CF centres participated in CF-FAB and provided follow-up chest computed-tomography (CT) scans for children who had completed the ACFBAL study with baseline scans at age 5-years. CT scans were annotated using PRAGMA-CF scoring. Ordinal regression analysis and linear regression were used to investigate associations between PRAGMA-CF (Perth-Rotterdam Annotated Grid Morphometric Analysis for CF) outcomes at follow-up and variables measured during the ACFBAL study.99 out of 157 ACFBAL children (mean±sd age 13±1.5 years) participated in the CF-FAB study. The probability of bronchiectasis at follow-up increased with airway disease severity on the baseline CT scan. In multiple regression (retaining factors at p<0.05) the extent of bronchiectasis at follow-up was associated with baseline atelectasis (OR 7.2, 95% CI 2.4-22; p≤ 0.001), bronchoalveolar lavage (BAL) log2 interleukin (IL)-8 (OR 1.2, 95% CI 1.05-1.5; p=0.010) and body mass index z-score (OR 0.49, 95% CI 0.24-1.00; p=0.05) at age 5 years. Percentage trapped air at follow-up was associated with BAL log2 IL-8 (coefficient 1.3, 95% CI 0.57-2.1; p<0.001) at age 5 years.The extent of airway disease, atelectasis, airway inflammation and poor nutritional status in early childhood are risk factors for progressive structural lung disease in adolescence.