This work presents a novel dc-dc bidirectional buck–boost converter between a battery pack and the inverter to regulate the dc-bus in an electric vehicle (EV) powertrain. The converter is based on the versatile buck–boost converter, which has shown an excellent performance in different fuel cell systems operating in low-voltage and hard-switching applications. Therefore, extending this converter to higher voltage applications such as the EV is a challenging task reported in this work. A high-efficiency step-up/step-down versatile converter can improve the EV powertrain efficiency for an extended range of electric motor (EM) speeds, comprising urban and highway driving cycles while allowing the operation under motoring and regeneration (regenerative brake) conditions. DC-bus voltage regulation is implemented using a digital two-loop control strategy. The inner feedback loop is based on the discrete-time sliding-mode current control (DSMCC) strategy, and for the outer feedback loop, a proportional-integral (PI) control is employed. Both digital control loops and the necessary transition mode strategy are implemented using a digital signal controller TMS320F28377S. The theoretical analysis has been validated on a 400 V  Electric vehicles (EVs) are an essential part of meeting global goals on reducing the carbon footprint of vehicle emissions that contribute to climate change ,2. All tIn EVs, the battery is generally sized by the energy requirements to allow a specific range to be reached. Still, there is not a linear relationship between car range and battery capacity because adding the weight of the battery reduces the efficiency on the road ,3. The bThe induction machine (IM) and the permanent magnet synchronous machine (PMSM) are the most used ,8,9 elecConnecting a DC-DC converter between the battery and the inverter allows optimizing the inverter’s DC input voltage, improving power capability, and maximizing the electric motor efficiency . A bidirIn , the autAn interleaved zero voltage switching (ZVS) version, included in multifunctional power electronic interface and operating at 60 kHz, is presented in , achieviThe noninverting buck–boost converter with coupled inductors known as the versatile buck–boost converter and shown in A novel bidirectional version of the versatile buck–boost converter is presented to extend its use in electric vehicle applications. This new converter shares some similarities with their previous ones see  to preseA novel high-voltage high-switching bidirectional converter is presented. This new converter has step-up and step-down characteristics in both current directions to extend the EV traction inverter efficiency under a wide range of speeds. This converter guarantees a high power conversion efficiency for EV powertrain applications due to silicon carbide (SiC) devices and the design with a low winding-to-winding parasitic capacitance of the coupled inductor. It can operate in boost or buck mode.A two-loop digital control design with a current (inner loop) controller and a voltage (outer loop) controller regulate the DC-bus voltage during traction and regenerative modes. The proposed controller ensures zero steady-state voltage error and fast transient responses to the voltage reference and power variations.A DSMCC control is proposed for the inner loop of the voltage feedback outer loop. The proposed controller ensures fast-tracking of the control set-points and low steady-state error under demanding tests that include system start-up and dc bus voltage reference with small and large variations. It is the first time that the DSMCC control strategy is used for the versatile buck–boost converter.This work presents a novel high-voltage bidirectional buck–boost converter with digital control that allows the regulation of the high-voltage DC-bus for EV applications. This voltage regulation and the energy flow between the battery and the motor drive are managed by means of a two-loop digital current control strategy, which facilitates the hysteresis transition between voltage step-up and step-down modes. The resulting control provides output voltage regulation in the presence of variations in output voltage and load power. The whole system is tested experimentally in a 1.6 kW prototype applied to a resistive load and an EV hardware emulation platform. Based on This paper is organized as follows: C, a constant input voltage M and equal values for the primary (The converter scheme depicted in quations :(1)dig for the output current n-th time sample period that ensures the control surface  is reacThe Euler approximation leads to the following discrete-time output current expression, assuming the averaged model that the converter’s current output slope x in Equation , and Hence, the resulting expression of the duty cycle isdx[n]=1 can be Equation . In steaIn order to guarantee dc bus voltage regulation, it is necessary to add a slower outer voltage control loop. With this new loop, the switching converter can be operated as a controlled current source due to the control DSMCC ensures the load current will follow the current reference. Therefore, the current-controlled buck–boost converter is operated as a current source that allows driving the energy consumption of the load. From the point of view of the dc voltage control loop, voltage variations with power constant should be compensated charging or discharging the dc bus capacitor . Hence, The output current reference to output voltage transfer function is obtained from Equation (13)HvoiThe loop-gain of the external closed loop voltage can be written as:Equation ) can be quations  and 14)(14)G(s)=quations  is placeu and the hysteresis buck–boost transition method introduced in [Validation of the proposed current control strategy is performed on a 1.6 kW versatile buck–boost converter. A Texas Instruments TMS320F28377S Digital Signal Processor (DSP) is used to implement the proposed control algorithm to calculate the variable control duced in , which wduced in .The simulated and experimental results for the system startup in closed-loop are given in ost mode , the outi is the instantaneous current through the capacitor Energy management system in auxiliary supply in EV topologies and the use of dc-dc converter as an interface between the primary energy source and high-voltage powertrain are some of the applications for EVs. This application can be studied using a powertrain emulation system or simulation . Some ex 3U) see  in resisThis paper proposed the bidirectional versatile buck–boost converter modified to operate at high voltage. This converter is an alternative to conventional topologies based on the boost converter in electric vehicle applications. The versatile converter has been located between the battery and traction inverter to regulate the dc bus in electric vehicle powertrains. The use of a high-efficiency step-up/step-down converter can improve the performance efficiency of the EV powertrain. This improvement includes an extensive range of electric motor speeds, which comprises urban and highway driving cycles. The proposed dc-dc bidirectional buck–boost converter is responsible for the dc bus voltage regulation through an outer voltage feedback loop and an inner current programmed controller. A Texas Instruments TMS320F28377S DSC is used to implement the digital control loops. The digital implementation of this current controller has allowed to include a dead-zone avoidance technique that effectively has suppressed very effectively undesirable nonlinear phenomena in the buck–boost mode transitions such as sub-harmonics or other undesirable nonlinear phenomena. The theoretical analyses have been validated using simulations and experimental tests performed on a 400-V


This process involves the transport of proteins from the endoplasmic reticulum to the Golgi complex, concentration within condensing vacuoles and zymogen granules, and release into the extra-acinar lumen at the apical plasma membrane. Subsequent studies showed that supramaximal secretagogue stimulation resulted in blockade of apical exocytosis and release of intracellular granules from the baso-lateral plasma membrane into the intercellular space. This was shown to be a key pathogenic mechanism in the early evolutionary stages of acute pancreatitis. Normal exocytosis is governed by local cytosolic Ca2+ spikes in the granular apical region. The Ca2+ is released from intracellular stores in the endoplasmic reticulum via inositol trisphosphate and ryanodine receptors, and acid stores via the two-pore channel and ryanodine receptors. Apical cytosol Ca2+ spiking also causes increased mitochondrial ATP production, to provide the energy source driving the mechanism of exocytosis.1Since the early 1970’s Ole Peterson has been at the forefront of many of the major scientific discoveries that have moulded our understanding of pancreatic acinar cell physiology and of the pathophysiology leading to acinar cell necrosis and acute pancreatitis.2+ overloading. The consequences are direct trypsinogen activation within the zymogen granules with intra-cytosolic release of trypsin, as well as release into the intercellular space. There is also mitochondrial Ca2+ overload with reduced ATP formation. These processes combine to produce acinar cell necrosis and an ever-expanding surrounding focus of tissue destruction. This is amplified by activation of both pancreatic stellate cells  generating toxic nitric oxide levels, and activation of resident macrophages (by released ADP and ATP acting on purinergic receptors) generating a series of cytokines including tumour necrosis factor-α. These processes result in further recruitment of circulating inflammatory cells into the foci of developing pancreatic necrosis. In clinically severe acute pancreatitis, the excessive inflammatory cell activation triggers an uncontrolled systemic anti-inflammatory response leading to multi-organ failure, especially affecting the lungs and kidneys.Pathogenic signals including fatty acids, alcohol, bile acids, and physical pressure result in sustained cytosolic Ca2 The link between SARS-CoV-2 and pancreatitis was identified very early on in the COVID-19 pandemic but it's true significance remains unclear.3 The nature of the link remains contentious, with some groups suggesting that the viral infection was not directly linked to the pancreatitis and even that many cases of pancreatitis were spurious since the raised amylase seen in patients with COVID-19 was mostly the result of a non-specific manifestation of shock in a critical illness. It has been open to debate whether this is direct viral damage of pancreatic cells or whether the damage is an indirect consequence resulting from the immune response.4 This is of considerably more than academic interest, as it has been proposed that although diagnosis of acute pancreatitis is relatively rare in COVID-19, pancreatic inflammation may be a critical factor in COVID-19 associated deaths. In the context of a critically severe illness represented by COVID-19 the revised 2012 Atlanta Criteria for defining the diagnosis and level of severity may be misinterpreted and/or overinterpreted. This is illustrated by the COVID PAN collaborative study in which the results of serum amylase and/or lipase levels were not reported, and there was also no mention of the characteristic diagnostic findings of acute pancreatitis on contrast-enhanced computed tomography and magnetic resonance imaging.5 Which leaves us with a pressing need to identify and characterise the specific mechanisms associated with the initiation of pancreatitis by SARS-CoV2 and how the severity is determined.In this latest work produced by Ole Petersen along with his longstanding co-workers Julia and Oleg Gerasimenko we are shown new insights into the pathogenic effects of the SARS-CoV-2 on pancreatic lobular cells.6 The transmembrane serine protease 2 (TMPRSS2) is also required for cleavage of sites S1 and S2 for membrane fusion and receptor mediated endocytosis.6 ACE2 and TMPRSS2 have both been identified in pancreatic endothelial pericytes and also in pancreatic ductal cells.8 Expression of ACE2 and TMPRSS2 in human acini have also been found but this seems to be at low levels and patchy in distribution.8 Genetic variants of TMPRSS2 may account for differential susceptibility to SARS-CoV-2 infection and COVID-19 disease severity.9SARS-CoV-2 tropism towards distinct tissues is governed by cellular factors expressed on target cells. Viral entry requires attachment of the spike protein to angiotensin-converting enzyme 2 (ACE2).10 Nevertheless ischaemia can cause oedema of the pancreas along with raised circulating enzyme levels without necessarily causing pancreatitis, which requires acinar cell necrosis as a defining characteristic. Post-mortem examinations have detected SARS-CoV-2 nucleocapsid protein in pancreatic exocrine cells, raising the question whether infection of pancreatic ducts and acinar cells is associated not just with elevated amylase and lipase levels elevations in patients with SARS-CoV-2-associated pneumonia, but also acute oedematous pancreatitis.8 None of the post-mortem studies on the four patients who died from COVID-19 however with pancreatic exocrine 2 nucleocapsid protein expression had any gross pathological or histological features of pancreatitis.8SARS- CoV-2 is also able to cause diffuse severe endothelial inflammation, and microvascular thrombosis in several anatomical sites, leading to diffuse microischaemia, an established cause of acute pancreatitis.2 Whether this is sufficient to initiate pancreatic acinar cell necrosis of itself is unclear at the present time, but may be contributory along with the aforementioned hypothetical mechanisms. Even so pancreatic IL-18 activated macrophages could promote clinical deterioration in otherwise critically ill patients. It is also significant that in the Gerasimenko model spike protein, or even just part of the spike protein, could cause pancreatitis in a susceptible individual, perhaps giving a mechanism to explain reports of acute pancreatitis following vaccination.Nevertheless, we can hypothesize three routes by which SARS-CoV-2 might cause acute pancreatitis: (i) direct infection of pancreatic acinar cells, (ii) infection of pancreatic ductal cells with subsequent lobular disruption, and (iii) microischaemia leading to pancreatic acinar necrosis. The paper by Gerasimenko and colleagues is a breakthrough in demonstrating that there is a direct action of SARS-CoV2 on the pancreatic parenchymal stellate cells leading to the production of IL-18 and activation of resident pancreatic macrophages.


The COVID-19 pandemic has led to over 100 million cases worldwide. The UK has had over 4 million cases, 400 000 hospital admissions and 100 000 deaths. Many patients with COVID-19 suffer long-term symptoms, predominantly breathlessness and fatigue whether hospitalised or not. Early data suggest potentially severe long-term consequence of COVID-19 is development of long COVID-19-related interstitial lung disease (LC-ILD).The UK Interstitial Lung Disease Consortium (UKILD) will undertake longitudinal observational studies of patients with suspected ILD following COVID-19. The primary objective is to determine ILD prevalence at 12 months following infection and whether clinically severe infection correlates with severity of ILD. Secondary objectives will determine the clinical, genetic, epigenetic and biochemical factors that determine the trajectory of recovery or progression of ILD. Data will be obtained through linkage to the Post-Hospitalisation COVID platform study and community studies. Additional substudies will conduct deep phenotyping. The Xenon MRI investigation of Alveolar dysfunction Substudy will conduct longitudinal xenon alveolar gas transfer and proton perfusion MRI. The POST COVID-19 interstitial lung DiseasE substudy will conduct clinically indicated bronchoalveolar lavage with matched whole blood sampling. Assessments include exploratory single cell RNA and lung microbiomics analysis, gene expression and epigenetic assessment.All contributing studies have been granted appropriate ethical approvals. Results from this study will be disseminated through peer-reviewed journals.This study will ensure the extent and consequences of LC-ILD are established and enable strategies to mitigate progression of LC-ILD. The COVID-19 pandemic has led to over 100 million cases worldwide. In the UK alone, there have been over 4 million cases, over 400 000 hospital admissions and over 100 000 deaths. A large number of people diagnosed with COVID-19 suffer from long-term symptoms, predominantly breathlessness and fatigue whether or not they were admitted to hospital. However, long-term symptoms following COVID-19 are more common in people who suffered more severe acute disease.5–7SARS-CoV-2 leads to pronounced inflammation within the lung and leads to the development of acute respiratory distress syndrome in a substantial proportion of those infected. While data demonstrate that a short course of corticosteroids can improve survival in patients with hypoxia, there is considerable evidence of long-term inflammation even following short-term corticosteroid therapy.10–12129Xe and 1H MRI are sensitive to gas transfer limitation, microstructural airway changes and alveolar perfusion deficit in patients with both acute and long COVID-19. These methods also have some ability to dissect both inflammatory and fibrotic pathophysiology and are highly sensitive to disease progression in established ILDs.14–18Pilot data from our consortiumGiven the large number of patients infected with SARS-CoV-2, it is vital that the extent of LC-ILD is determined; its natural history defined particularly whether it is time-limited inflammation and reversible, or develops into persistent, or even progressive, fibrosis. Determining the natural history of LC-ILD, and risk factors as well as biomarkers related to outcome such as disease progression, will enable a precise approach to possible treatments such as immunomodulation or antifibrotic therapy,To address the development of ILD following SARS-COV-2 infection, we will determine the prevalence and natural history of LC-ILD in the 12 months following COVID-19 through linkage to the Post-Hospitalisation COVID (PHOSP-COVID) platform study, the REACT community study and unique collections such as the Xenon MRI investigation of Alveolar dysfunction Substudy (XMAS) and POST COVID-19 interstitial lung DiseasE (POSTCODE) substudies. The UK Interstitial Lung Disease Consortium (UKILD) will undertake a longitudinal observational study of patients with suspected ILD following COVID-19, to determine the clinical, genetic, epigenetic and biochemical factors that determine the trajectory of recovery or progression.The UKILD-Long COVID study is a prospective multicentre observational cohort study that will be managed through the Imperial College National Heart and Lung Institute and funded by the UKRI Medical Research Council and an NIHR professorship (RGJ). The primary study aims to define the prevalence and risk factors for LC-ILD using data from 10 000 stratified patients, collected from the UK’s national PHOSP for COVID platform study, together with 2000 non-hospitalised patients referred for assessment up to 3 months for investigation of persistent respiratory symptoms post-COVID-19, such as breathlessness and cough . These pUp to 80 participants will undergo detailed longitudinal xenon and proton MRI coupled with measures of flow-mediated endothelial function in the microvasculature measured by EndoPat.Up to 50 participants will undergo bronchoscopy with bronchoalveolar lavage (BAL) for single cell and/or bulk RNA sequencing (RNA-seq), with matched flow cytometry analysis, as well as microbiome analysis.The primary objective of the study is to determine the prevalence of ILD at 12 months following SARS-CoV-2 infection and whether clinical severity correlates with severity of ILD in survivors.To further define the LC-ILD population, in particular, to describe the emerging phenotypes and risk factors of LC-ILD.To determine the natural history of LC-ILD phenotypes longitudinally.To explore pathomechanisms of LC-ILD for candidate prognostic and theranostic biomarkers.The primary end point of the study is as radiologically confirmed diagnosis of fibrotic or non-fibrotic ILD in the 12 months following COVID-19. Substudies will have a co-primary end point of change in the radiological extent of LC-ILD.Progressive lung function impairment between 3 and 12 months, defined as ≥10% relative decline in Forced Vital Capacity (FVC), or ≥10% relative decline in Diffusion Capacity in Lung of Carbon Monoxide (DLco), or increasing radiological extent of LC-ILD using image analysis.20Resolution of ILD, as defined by ≥10% relative improvement in FVC, DLco or reduction of radiological extent.Persistence of ILD in those not meeting definition of progression or resolution.Presence of interstitial lung abnormalities on radiological images that do not meet definition of ILD.A comprehensive series of clinical, molecular, MRI and biochemical parameters will be assessed as biomarkers.The PHOSP-COVID study (ISRCTN10980107) is a national consortium that provides a platform to study the long-term consequences of COVID hospitalisations.Patients aged ≥18 years with (a) evidence of SARS-CoV-2 infection earlier confirmed by microbiology or serology and (b) clinical suspicion of Long COVID ILD warranting CT or consideration for proton MRI.Up to 50 participants from various severity strata including hospitalised and non-hospitalised patients will undergo clinically indicated BAL with matched whole blood sampling up to 6 months and then again between 12 months±3 months following infection with a minimum of 6 months between bronchoscopy and whole blood sampling for deep phenotyping. Assessments will include exploratory analysis such as single cell and bulk RNAseq, flow cytometry analysis, lung microbiomics and epigenetic assessment. Participants eligible for secondary analyses will be recorded and monitored on a real-time study dashboard to support balanced recruitment of gender, age and severity of acute infection. Participants in secondary analyses will be largely recruited from specialist centres for radiological imaging and bronchoscopy procedures, with other centres referring.Patients aged ≥18 years with (a) evidence of SARS-CoV-2 infection confirmed by microbiology or serology and (b) clinical suspicion of Long COVID ILD warranting CT or consideration for proton MRI, with architectural distortion of the lung defined by abnormal displacement of bronchi, vessels, fissures or septa caused by diffuse or localised lung disease, particularly interstitial fibrosis.Confirmed ILD diagnosis prior to the diagnosis of COVID-19.No CT chest evidence of architectural distortion.Life-limiting illness within 12 months.Further exclusion criteria have been selected to support distinction of cases and controls during follow-up. Cases will have evidence of a radiological abnormality at baseline scan (up to 6 months) post-COVID-19, with architectural distortion of the lung defined by abnormal displacement of bronchi, vessels, fissures or septa caused by diffuse or localised lung disease, particularly interstitial fibrosis,Individuals meeting the inclusion criteria for UKILD-Long COVID will be followed up using the PHOSP-COVID platform, or using specific substudy consent. Clinical, molecular, biochemical and patient-reported outcome measure (PROM) data will be captured in the PHOSP platform using predefined case report forms with linkage to retrospective and prospective social and healthcare records. Up to 40% of individuals enrolled in PHOSP will undergo research-specific biosampling and linkages to enhanced clinical records. PHOSP case report forms will be completed during the acute COVID admission and at 3, 6 and 12 months posthospitalisation. Eligible non-hospitalised individuals presenting at Long COVID clinics will have physiological tests and biosampling  performed alongside a full clinical history with clinical evaluation and testing. Longitudinal follow-up will be performed at least 6 months following initial assessment up to 15 months postinfection and will be guided by clinical need. The primary analysis will focus on the prevalence of MDT-confirmed ILD at any time point up to date of censorship within the wider cohort, as well as prevalence of genetic risk factors and radiological patterns, assessed overall and according to severity strata.Participants and controls will also be eligible for enrolment into two specific predefined substudies.129Xe and 1H MRI are sensitive to gas transfer limitation, microstructural airway changes and alveolar perfusion deficit in patients with both acute and long COVID-19. These methods also have some ability to dissect both inflammatory and fibrotic pathophysiology and are highly sensitive to disease progression in established ILDs.An anticipated 80 participants representing hospitalised patients from various severity strata including non-hospitalised patients will undergo longitudinal xenon alveolar gas transfer and proton perfusion MRI up to 6 months and then again between 12 months±3 months following infection with a minimum of 6 months between MRI scans. Pilot data from our consortium indicate that novel functional imaging methods using In a subset of patients, MRI will be coupled with Endopat measurements, a Food and Drug Administration-approved non-invasive tool which measures changes in flow-mediated endothelial function in the microvasculature and is sensitive to changes in systemic vascular function patients with chronic lung disease,The prevalence of MDT-confirmed LC-ILD at both early (up to 6 months) and then again at late (12 months±3 months) time points will be assessed within the total study population. The prevalence of broader radiological abnormalities and phenotypic patterns will also be assessed in a descriptive analysis, together with demographics, haematological and biochemical profiles, physiological performance and PROM. Analyses will be performed overall and stratified according to hospitalised and non-hospitalised, as well as severity of infection in hospitalised patients defined above.All posthospitalised study participants that are part of the PHOSP-COVID study will be linked to the centralised National COVID-19 Chest Imaging Database (NCCID). Imaging data for the relevant NCCID patients will be accessible to UKILD-Long COVID study research groups after completion and approval of NCCID Data Access Requests. Similarly, imaging data from the PHOSP-COVID study will be accessible to UKILD-Long COVID study research groups after completion and approval of PHOSP-COVID Data Access Requests. NCCID will provide pre-COVID-19 and acute COVID-19 (inpatient chest X-ray (CXR) and CT) imaging, while PHOSP-COVID will provide posthospital discharge (CXR and CT) imaging for hospitalised patients only. Imaging data-flows vary slightly for NCCID and PHOSP-COVID.For non-hospitalised patients, the imaging data transfer process will replicate that being performed in NCCID and PHOSP-COVID. Data will be sent via Image Exchange Portal (IEP) from each hospital site to Royal Surrey University Hospital NHS Foundation Trust, and then to the National Consortium of Intelligent Medical Imaging (NCIMI) for storage and distribution.Putative genetic risk factors for lung fibrosis or severe COVID-19 outcomes, as defined by genome-wide association screens,Baseline and longitudinal changes in biomarkers reflecting LC-ILD evolution, including circulating factors and cell-types from detailed serological and cellular analysis, will be assessed in multilevel models for repeated measures to test associations according to the presence or absence of LC-ILD at late time points (12 months±3 months), and according to progression, resolution or persistence of radiological patterns over follow-up time points.A restricted sample of participants with presence of architectural distortion confirmed by HRCT will undergo deep phenotyping in the two separate substudies XMAS and POSTCODE.129hyperpolarised xenon MRI (Xe-MR) coupled with measures of endothelial dysfunction (EndoPAT) between early and late time points. Paired analyses will be performed to test the hypothesis that the red blood cell to tissue plasma ratio (RBC/TP), or diffusion-weighted mean diffusive length scale (LmD), measured by Xe-MR, reduces over time in people with LC-ILD; alveolar-interstitial-capillary gas transfer (RBC/TP), acinar microstructure (LmD) and Dynamic Contrast Enhanced (DCE) lung perfusion (mean capillary transit time (MTT), pulmonary blood volume (PBV)) have been observed to be sensitive to progression in IPF.1H and CT structural imaging and calliper. Image analysis from data acquired at the three-129XE MRI sites will be performed centrally in Sheffield with input from UCL on the quantitative CT, Oxford and Nottingham (free breathing 1H MRI).XMAS will capture radiological changes in longitudinal 129Xe RBC/TP in paired analysis. Secondary analyses will assess changes in 129Xe LmD, and 1H DCE MTT, PBV, as well as differences between severity strata with longitudinal modelling data.The primary analysis will be the change in radiological extent between early and late time points as measured by POSTCODE will perform multi-omic phenotyping at early time points (up to 6 months) and assess potential changes later time points (12 months±3 months). Single cell RNA-seq and lung microbiomeIn addition, this cohort will undergo bulk whole blood RNAseq and analysis of epigenetic modifications at both the early and late time points to identify longitudinal biological signatures reflecting distinct resolving phenotypes, compared with persisting or progressive. Defining epigenetic signatures will test the hypothesis that COVID-19 promotes epigenetic changes that can predispose people to lung fibrosis.The primary aim is to characterise the genetic and epigenetic signal from the airways and the microbiome in patients with pulmonary fibrosis post-SARS-Cov-2 infection, while secondary aims will be to elucidate changes in the host and microbiome over time following SARS-Cov-2 infection, as well as differences in the microbiome, genetic and epigenetic signatures between patients with progressive and non-progressive disease.Primary analyses will assess the change in the multi-omic signals between early and late time points in paired analysis according to the separate platforms. Secondary analyses will determine biological signatures of resolving LC-ILD phenotypes compared with non-resolving in baseline and longitudinal models.Up to 10 000 participants are expected to be recruited through the PHOSP-COVID consortium, with a further 2000 non-hospitalised participants recruited. Post-COVID-related breathlessness has been reported to affect approximately 40% of people hospitalised with severe disease and 10%–20% of people who suffered mild COVID. Preliminary analysis from UK and international studies have described up to 80% of hospitalised patients with COVID-19 have the presence of symptoms, radiology and lung function changes concordant with ILD, depending on the severity of the underlying illness. We anticipate approximately 20% (2400/12 000) of people recruited into UKILD-Long COVID study will have features consistent with ILD for characterisation, which will provide sufficient sample size for descriptive analysis, evaluation of incidence and prevalence and assessment of risk factors.Genome-wide genotype data are funded through GenOMICC and will be available for >4000 participants enrolled in PHOSP-COVID; we will conduct genome-wide array genotyping in an additional 2000 non-hospitalised participants. A common MUC5B polymorphism associated with (non-COVID) idiopathic pulmonary fibrosis has an OR for disease >2. Anticipating approximately 20% of non-hospitalised participants will have features consistent with ILD (400/2000), there will be sufficient power to detect associations with ORs >1.65  at p<0.0025 with correction for multiple testing of a restricted set of 20 independent variants.An anticipated 1000 LC-ILD participants representing balanced strata of initial severity and a minimum 200 controls will be assessed in longitudinal analysis to identify biomarkers that describe the natural history. Data from prior biomarker studies in IPF estimate a sample size of 1000 achieves 90% power to detect a 13 ng/mL difference in mean MMP7 levels, with a combined SD of 0.18 ng/mL in an unbalanced analysis assuming 85% resolving disease, providing a standardised effect of 0.72.The Xe-MR substudy will be staged. Stage 1 will include an interim analysis of the effect and variability between 12-month (first wave) and 3-month (second wave) unpaired scans after recruitment of 20 participants to each arm. Only hospitalised participants with radiological evidence of architectural distortion will be enrolled at stage 1. Stage 2 will use the findings from stage 1 to guide strata representation and required sample size for a longitudinal analysis of Xe-MR, with an anticipated maximum of 80 cases imaged at both early and late time points. A sample size of 80 repeat scans will provide 90% power to observe effect sizes above 0.40 at alpha 0.05, assuming more variability in LC-ILD than observed in IPF.The BAL substudy will be performed in up to 50 cases representing balanced numbers of hospitalised and non-hospitalised participants, and 10 controls. Participants will be invited to support the strength of these data through a follow-up bronchoscopy at 12 (12 months±3 months) months and repeat measures. Participants who undergo bronchoscopy will be consented for whole blood sampling to perform longitudinal whole blood RNA-seq and epigenetic analyses. Assuming 50 cases, medium-sized effects in exploratory biological signatures (Cohen’s d=0.5) will be powered at >90% in paired analysis with no correction for familywise error, or 70% when controlling for 15 independent comparisons. Large effects (Cohen’s d=0.8) will be powered at a similar rate when controlling for 10 000 comparisons.As management of Long COVID and post-COVID-19 pathologies must be adaptive and responsive to novel research findings, two planned interim analyses are to be conducted to inform the likely number of outcome events and the expected power in substudies. The first planned interim will be performed after 3-month follow-up of the first 1000 participants through PHOSP (10%) to provide initial insights into expected radiological patterns and to preliminarily describe the potential LC-ILD burden for the support of clinical management. The second planned interim will be performed following completion of 20 12-month Xe-MR from the primary wave of infection and 20 3-month Xe-MR from secondary waves. An unpaired analysis will assess the difference, variability and standardised effect to inform recruitment to the longitudinal Xe-MR cohort.Data verification, case report forms (CRFs), study co-ordinator.This study will be conducted in accordance with the International Conference on Harmonisation of Good Clinical Practice (ICH GCP), the research governance framework for health and social care and according to the principles as outlined in the Declaration of Helsinki.All conduct within the study will comply with the principles outlined in the Declaration of Helsinki and GCP. A study coordinator will ensure compliance with good clinical practice, support collaborative working with independent partners , oversee central recruitment targets for substudies and support public dissemination.Electronic CRFs will be used to collect data. Data will be submitted electronically to a protected online database. Anonymised data may be entered by study staff in order to minimise workload on site clinical staff. Patient identities will be protected and all information held securely. Sharing of data with industrial partners will comply with General Data Protection Regulations.Data entered on CRFs and the online database will be subject to quality checks to reference source data on a regular basis by the study co-ordinator or nominated deputy to ensure standardisation and validity of the data collected. The study may be monitored by the sponsor or other regulatory bodies. For the purposes of audit and compliance monitoring, clinical study data will be available to delegated members of the local study teams, as well as to representatives of the sponsor and the study co-ordinating team. All trial data, data monitoring and audit will be available for inspection as necessitated by research ethics committee inspection. Participants will be consented to their study data being released for this purpose.All of the investigations we are performing as part of this research are safe and happen in the hospital on a daily basis. However, as with all procedures there are risks of complications. Patients are at risk of a small amount of discomfort from the blood tests required as part of the study. Venepuncture will be performed by qualified personnel according to best practice techniques to minimise any adverse events (AEs) and where possible, taken at the same time as clinically indicated blood samples to avoid repeated sampling.For patients undergoing bronchoscopy, the possible risks are detailed in the POSTCODE patient information sheet. Common side effects are a transient sore throat and hoarse voice and fever like influenza symptoms can occur and last for 24–48 hours and usually settle spontaneously or with simple analgesia. A rare complication is a chest infection, this occurs in <1% of cases.35For patients undergoing Xenon or proton MRI, the possible risks are detailed in the respective patient information sheets. Ethics for the XMAS substudy are in place at the respective sites of Sheffield, Nottingham and Oxford—see accompanying protocols .All AEs will be recorded and monitored until resolution or until it has determined that intervention as part of the study was not the cause. All AEs, whether expected or not, will be recorded. All serious adverse events (SAEs) will be reported to the Chief Investigator within 24 hours. However, hospitalisations for elective treatment of a pre-existing condition do not need reporting as SAEs.The trial will be overseen by the UKILD consortium steering committee. The first planned interim analysis will be performed after 3-month follow-up of the first 1000 hospitalised participants, recruited through PHOSP-COVID, to provide initial insights into expected radiological patterns and the potential LC-ILD burden. The second planned interim will be performed following completion of 20 independent 12-month Xe-MR scans from the primary wave of infection and 20 independent 3-month Xe-MR scans from secondary waves.Action for pulmonary fibrosis charity and patient partners have been involved from the conception of this study to inform study design and conduct. They will also form part of the ongoing steering committee appraising patient facing material and facilitating the dissemination of findings to IPF patients and their families.The results from this study will be disseminated via regional and national conference platforms, as well as being submitted for publication in open access peer-reviewed journals in accordance with UK Research Council policies. Any publication will include a list of investigators, with authors being determined in line with the International Committee of Medical Journal Editors guidelines, as well as an acknowledgement of roles of the study sponsor and funder(s).This longitudinal observational study was designed by the UKILD consortium in response to the global SARS-CoV-2 pandemic to proactively characterise viral-induced lung changes. UKILD represents a network of national ILD centres with integrated academic groups working in collaboration with large platforms for COVID-19 research, including the Coronavirus Clinical Characterisation Consortium (ISARIC-4C), PHOSP-COVID platform and REACT Long COVID studies. The study will inform the prevalence and burden of LC-ILD to improve local referral pathways and guide follow-up where fibrosis is suspected, while findings regarding the natural history and mechanisms of LC-ILD will support discovery of diagnostic, prognostic and theranostic biomarkers to improve patient management. Collectively, the objectives of this study will ensure that the extent and consequences of LC-ILD are established using existing and novel diagnostic approaches, informing the design of future clinical trials and strategies to mitigate disease progression.


The clinical response to anakinra observed by this patient concurrently treated with antibiotics indirectly confirms the potentially pathogenic role of IL-1 in maintaining the pericardial disease and shows how IL-1 blockade might allow avoiding the pericardiocentesis procedure. The report supports the hypothesis that anakinra is an effective and safe tool in the early treatment of acute pericarditis of presumed bacterial origin nonresponding to targeted antibiotic therapy. Dear Editor,Interleukin-1 (IL-1) is known to be a pleiotropic cytokine with a master role in the genesis of pericarditis . The effStaphylococcus aureus, also found on his nose and skin swabs, a targeted antibiotic treatment with oxacillin was prescribed. He also complained of chest pain suggestive of acute pericarditis, and echocardiography revealed a moderately severe circumferential pericardial effusion  with signs of systolic collapse of the right atrium and mild diastolic collapse of the free wall of the right ventricle . This patient had a long-lasting severe eczematous dermatitis sparing only the face and came to our Emergency Department due to high-spiking fevers and shivering. Lab works showed increased inflammatory markers and neutrophil leukocytosis. Given the positivity of his blood cultures for a methicillin-sensitive Staphylococcus aureus are a major clinical problem owing to their high incidence and widespread emergence of antibiotic-resistant bacterial strains. The identification of specific immune impairments in humans that predispose to Staphylococcus aureus infections, for instance a breakage in the epidermal barrier for subjects with chronic inflammatory dermatoses, has provided new insights into the key immune responses that are involved in invasive infections. Pericarditis caused by Staphylococcus aureus is a rare event [Complications arising from life-threatening invasive infections caused by re event . As withre event . The usere event . Early ure event . Conversre event , and indre event . Therefore event , 10. In re event . Neverthre event . This prStaphylococcus aureus can induce both biosynthesis and release of IL-1, which has a pivotal role in the serosal inflammation and T cell polarization. Ikejima et al. revealed that certain strains of Staphylococcus aureus associated with toxic shock syndrome induce human blood monocytes to secrete IL-1 in vitro, and IL-1 was detected both by its ability to cause fever in rabbits using the leukocytic pyrogen assay and by its mitogenic activity towards thymocytes in the so-called lymphocyte-activating factor assay. Moreover, the stimulation of monocyte IL-1 production was easily quantified, providing a simple method of assaying the toxic shock syndrome toxin. The authors argued that both sudden fever and other components of the acute phase response may be attributed to a massive release of IL-1 in the case of an infection caused by toxic shock syndrome toxin-producing Staphylococcus aureus [It is established that s aureus .2 and PGI2), platelet-activating factor and nitric oxide combined with tissue neutrophil infiltration and subsequent increased vascular smooth muscle relaxation, vascular leak, development of hypotension, shock and multi-organ failure [IL-1 is also one of several proinflammatory cytokines produced during most infections and mostly during sepsis, and the systemic inflammatory response syndrome that serves to initiate the host response and integrate nonspecific immunity may be beneficial to the host, with promotion of neutrophil recruitment and anti-microbial peptide release: however, if produced for extended periods of time or in excessive quantity, IL-1 might contribute to morbidity and mortality. Indeed, during sepsis, dysregulation of the finely tuned balance between IL-1 production and its inhibition may result in severe inflammation, tissue damage and organ dysfunction. In fact, uncontrolled IL-1 production has been directly linked to increased release of prostaglandins  in patients with comorbidity factors. Thus, anakinra administration in daily practice should require careful monitoring, especially in patients with comorbidities and concomitant treatments, such as glucocorticoids .The clinical response to anakinra observed by our patient concurrently treated with antibiotics indirectly confirms the potentially pathogenic role of IL-1 in maintaining the pericardial disease and shows how IL-1 blockade might allow avoiding the pericardiocentesis procedure. Our report supports the hypothesis that anakinra is an effective and safe tool in the early treatment of acute pericarditis of presumed bacterial origin nonresponding to targeted antibiotic therapy. On the other hand, our positive experience should not encourage overlooking caution when administering anakinra to patients with a history of any infections or with underlying conditions which may predispose to infections. Interesting will be to investigate whether early IL-1 blockade could play a role in the risk of relapses after a first episode of acute pericarditis.


The complete hydrogenation and partial sulfonation to the susceptible carbon double bonds of the PI segment led to the preparation of [polystyrene-b-poly] as well as [polystyrene-b-poly(sulfonated isoprene-co-isoprene)], respectively. The hydrogenation of the polyisoprene block results in enhanced segmental immiscibility, whereas the relative sulfonation induces an amphiphilic character in the final modified material. The successful synthesis of the pristine diblock copolymer through anionic polymerization and the relative chemical modification reactions were verified using several molecular and structural characterization techniques. The thin film structure–properties relationship was investigated using atomic force microscopy under various conditions such as different solvents and annealing temperatures. Small-angle X-ray scattering was employed to identify the different observed nanostructures and their evolution upon thermal annealing.An approach to obtaining various nanostructures utilizing a well-studied polystyrene- The modification reaction scheme is illustrated in In this study, after synthesizing the diblock copolymer of the PS-χ parameter due to the diminished side-groups (hydrogenation) or the existence of heteroatoms (sulfonation) in the PI blocks. Finally, small-angle X-ray scattering (SAXS) was carried out in order to investigate the morphology of the specific copolymer sequences in bulk, further verifying the temperature effect on the adopted structures.The polystyrene block remained intact due to the selective reagent attack towards the double bonds of the PI segments, eventually leading to three different chemical structures capable of adopting various morphologies based on the spin casting solution  and annealing conditions used. Specifically, after the successful verification of the chemical modifications through size exclusion chromatography (SEC), nuclear magnetic resonance (NMR) and infrared spectroscopy (IR), all copolymer sequences were morphologically characterized in terms of atomic force microscopy (AFM) in the thin film state. AFM studies were performed for all the copolymer sequences under various parameters such as casting solvent  and different annealing temperatures (room temperature (R.T.), 80 °C, 100 °C and 120 °C). The manipulation of the enthalpic parameters of each sequence holds a significant role on the final adopted morphology, which is strongly affected by the use of selective/non-selective solvents, as well as the enhanced b-polyisoprene (SI), being the precursor for the post-synthetic chemical modification reactions, was synthesized by sequential anionic polymerization under high vacuum techniques. The purification of all reagents involved in the polymerization has already been described in the literature  (SEP) after complete hydrogenation or to polystyrene-b-poly(sulfonated isoprene-co-isoprene) (SI/sulf) after partial sulfonation. The initial SI copolymer was subjected to two different chemical modifications in order to alter, completely or partially, the chemical structure of the PI segment leading either to  copolymer or polystyrene-b-poly(sulfonated isoprene-co-isoprene). The chemical modification of SI block copolymer was achieved i) through almost 100% hydrogenation of the PI block in order to obtain a SEP copolymer and ii) through the sulfonation reaction of the PI obtaining a partially sulfonated PI block (43% yield). We report the synthesis of the polystyrene-1H-NMR and 13C-NMR techniques were used. A fully hydrogenated material was obtained since the characteristic chemical shifts attributed to the PI1,4 and PI3,4 were completely eliminated while the degree of sulfonation was calculated at approximately 43% through 1H-NMR. This led to a block copolymer containing PS and coexistent PI sulfonated and non-sulfonated monomeric units. All copolymers were molecularly characterized through various techniques in order to verify the successful synthesis and post-polymerization modifications. The chemically modified copolymers were characterized via SEC in order to justify the absence of any undesired side reactions. For the verification of the synthesized SEP and SI/sulf samples, FT-IR, The structural characterization on the thin film self-assembly of both the copolymer precursor and the final modified materials is reported for the first time to the best of our knowledge. By adopting the spin casting method under specific conditions and varying significant parameters such as solvent  and annealing temperature  different topologies were justified when studied with atomic force microscopy. It is evident that the pristine copolymer had less well-ordered structures probably due to the fast evaporation rate of the solvents used during the spin casting and the fact that the samples were only annealed for short periods. The highest repulsion among PS and PEP chains led to the formation of long-range morphologies using different solvents and annealing temperatures. For the SI/sulf system, morphologies ranging from disordered to spherical micelles, and even to cylindrical structures, were observed deriving from the process treatment along with the amphiphilic character of the specific material. d-spacing were justified. The results obtained from AFM were further supported by small-angle X-ray scattering experiments, as could be clearly observed on the 2D power spectral density data. The different adopted nanostructures in bulk were determined using SAXS and the effect of thermal annealing on the obtained morphologies as well as on


Changes in brain resting-state functional connectivity (rsFC) were investigated using a longitudinal design by following a 2-month focused attention meditation (FAM) practice and analyzing their association with FAM practice time. Ten novice meditators were recruited from a university meditation course. Participants were scanned with a resting-state fMRI sequence with multi-echo EPI acquisition at baseline and at the 2-month follow-up. Total FAM practice time was calculated from the daily log of the participants. We observed significantly increased rsFC between the posterior cingulate cortex (PCC) and dorsal attention network (DAN), the right middle temporal (RMT) region and default mode network (DMN), the left and right superior parietal lobules (LSPL/RSPL) and DMN, and the LSPL/RSPL and DAN. Furthermore, the rsFC between the LSPL and medial prefrontal cortex was significantly associated with the FAM practice time. These results demonstrate increased connectivity within the DAN, between the DMN and DAN, and between the DMN and visual cortex. These findings demonstrate that FAM can enhance the brain connection among and within brain networks, especially DMN and DAN, indicating potential effect of FAM on fast switching between mind wandering and focused attention and maintaining attention once in the attentive state. Most examinations are task related, especially those that include meditation or engage trained skills, and are susceptible to expectancy and knowledge-based biases that can change neural signals. Brain activations observed during meditation provide evidence for increases of neural activity while practicing meditation; however, the findings may have been influenced by the individual variance of performing the required meditation during the fMRI scanning. Only when the state of neural activity has increased through repeated meditation practice, when meditation is not being practiced such as during rest, and has become a trait of the brain, will it provide a neural basis for enhanced attentional control and emotional regulation that can translate to daily life. To address how meditation training alters trait-level neural reorganization, we conducted a longitudinal examination of how 8 weeks of Focused Attention Meditation (FAM) training alters task-independent resting-state functional connectivity using multi-echo functional magnetic resonance imaging.The Practice of meditation has been associated with altered neural activity and reorganization /ventral attention network (VAN)10, respectively.Meditation comes in many forms, such as focused attention or open monitoring or non-dual awareness. Here we examined FAM training, which involves reorienting attention onto an internal or external object and inhibiting distraction of mind wandering or random thoughts. Mind wandering and reorienting attention were associated with neural activity in the default mode network (DMN)14, although they are not completely consistent. Experienced meditators exhibited increased activation during meditation in the anterior cingulate and medial prefrontal cortex  compared to controls11. Long-term meditators showed significantly more activation in the majority of attention regions of interest  than novice meditators during meditation12. This study also reported that long-term meditators had more activation in the left superior frontal gyrus and middle frontal gyrus  when compared to incentive novice meditators . Similar findings extend to individuals randomized to an 8-week course in mindfulness meditation training, which was associated with decreased cortical midline recruitment associated with internal self-referential process (DMN areas)13 and increased activity in brain regions implicated in external visual attention, including inferior and superior parietal lobes (DAN areas) and middle occipital gyrus 14.FAM has been reported with generally increased task-related neural activation in brain regions that have been reported involved in brain attention processing17 and cortical thickness21 in brain regions involving self-referential and attention processing, such as superior parietal gyri (posterior regions in DAN), precuneus (a posterior region in DMN), anterior cingulate, superior and middle frontal gyri, and orbitofrontal  regions in meditators. Longitudinal sMRI studies demonstrated the increases in gray matter density after an 8-week meditation training, which provide more direct evidence of the effects of meditation on brain structural changes in posterior cingulate cortex and temporoparietal junction (posterior regions in DMN)23. One of the longitudinal sMRI studies found that reductions in perceived stress were correlated with changes in gray matter density, demonstrating that neuroplastic changes induced by meditation are associated with improvements in mental states.Structural magnetic resonance imaging (sMRI) has associated FAM with trait changes of the brain structure. A number of sMRI studies found increased gray matter density26 and the meditation-state functional connectivity (msFC) between meditators and controls27. Other studies compared the same subjects at different conditions: rsFC and msFC in experienced meditators28. These cross-sectional resting-state and state-related meditation studies generally involved the changes of functional connectivity in two brain networks: the DMN and DAN, although the directions of changes may not agree well. Longitudinal studies have been performed but mainly focused on the potential benefits of meditation on specific medical groups, such as cognition of the elderly29, anxiety of the stressed community30, and symptoms of posttraumatic stress disorder (PTSD) subjects31. Therefore, the causal effect of meditation on the trait rsFC measure of novice meditators has not been systematically studied.Brain resting-state functional connectivity (rsFC) can provide the trait measure for coherent neural activity between different regions of the brain during the resting state. Therefore, rsFC can provide a less biased account of neural network changes with meditation practice compared to task-based fMRI. Meditation studies in functional connectivity have conducted cross-sectional studies to compare the rsFC between meditators and controls23 and resting-state rsFC26 changes, our first hypothesis was that FAM would result in stronger connection within the DAN and/or between the DAN and the visual cortex, for maintaining attentive status over a long period of time. In addition, there would be a stronger connection between DMN and DAN/visual cortex for switching between mind wandering and focused attention. We further hypothesized that rsFC would vary among participants according to the practice time of meditation. While amount of adherence to a meditation practice may reflect an expectancy bias during a task or meditative state during scanning, changes in task-free resting connectivity are less susceptible to these biases and would better reflect baseline changes in brain dynamics associated with and potentially caused by greater practice. We tested the hypotheses by using a longitudinal study design and multi-echo (ME) BOLD fMRI to assess the changes in brain rsFC after practicing FAM over a 2-month period. ME BOLD fMRI, instead of frequently used single-echo BOLD fMRI, has been adopted in the study because of its effectiveness in mitigating imaging artifacts due to subject motion and various sources on physiological noises and thereby increasing SNR33. This noise is particularly relevant to the meditation studies as there are often peripheral physiological changes in respiration and heart rate and their variability with meditation practice34, which can differentially influence detection of BOLD signal and estimates of functional connectivity at baseline and the 2-month follow-up. We expect that the ME fMRI technique will largely increase the reliability of our longitudinal mediation results.Consistent with the FAM training process and meditation results from morphologicalThe demographic characteristics of all the participants, including age, gender, handedness and meditation practice time are shown in Table After meditation training, we observed longitudinally increased functional connectivity between the posterior cingulate cortex (PCC) seed and the bilateral inferior parietal regions Fig. a, the riUsing the raw BOLD time series without denoising, no longitudinal change of rsFC with any seed regions of interest (ROI) was observed after meditation practice. Using the BOLD signal time series with conventional denoising, generally less extents of the rsFC changes Fig.  was obseWe observed that the longitudinal changes of rsFC between the LSPL seed and medial prefrontal region (mPFC)  was significantly associated with individual practice time Fig. , using tThe z-scores of rsFC at baseline and follow-up are shown in Fig. After meditation training, longitudinal changes in GM density were not significant at any regions of the brain at both voxel-levels of p < 0.005 and p < 0.01. In addition, longitudinal changes in GM density were not associated with practice time at both voxel-levels of p < 0.005 and p < 0.01.The results of our study showed that 2-month meditation training increased brain functional connectivity, even when participants were not in meditative state, within the DAN, between the DMN and DAN, and between the DMN and VC, as compared to the functional connectivity at baseline. The longitudinal changes of functional connectivity between the LSPL and medial prefrontal cortex were associated with the amount of meditation practice time over a 2-month period. These findings demonstrate that FAM, regardless of each individual’s chosen object of attention, increases functional connectivity within attentional networks as well as increases connectivity across distributed brain regions serving attention, self-referential, and visual processes. The findings also demonstrate that 2-month meditation training has a significant impact on the brain functional connectivity but not on the brain structure. Therefore the observed changes in functional connectivity are solely functional changes and not related to structural changes.36. Further analysis from finger-tip pulse oximeters (monitored during the ME-BOLD acquisitions) showed a trend of reduced heart rate (p = 0.093) after 2-month meditation training. The changes of heart rate may further underscore the importance of quality denoising in physiological noises because the changes may influence detection of BOLD signal and thereby estimates of functional connectivity differently at baseline and follow-up. The enhancement of ME-BOLD in the meditation study is consistent with the benefits of ME-BOLD demonstrated in signal-to-noise ratio32, specifically in high susceptibility regions in orbitofrontal and inferior temporal cortex36, and in brain development35.The more regional extents were generally observed for the changes of rsFC using the BOLD signal time series with ME-ICA denoising than with the conventional denoising. We postulate that more extents of the rsFC changes reflect a highly effective ME-ICA processing pipeline in mitigating imaging artifacts due to subject motion and physiological noises such as cardiac and respiratory pulsations24. The finding is also in line with increased connectivity between certain regions of the DMN and certain regions of the attentional networks27. For instance, Brewer et al. found the increased connectivity between the PCC and dorsal anterior cingulate cortex (dACC) during meditative state in experienced meditators  and the auditory/salience region27 in 8-week meditators (8 weekly 150-min group lessons) relative to controls. Several other studies, however, found decreased connectivity or stronger anticorrelation between the DMN and attentional networks 29. We speculate that the discrepancies may be attributed to the analytical approach , specific regions examined, meditation type , meditation state , and meditation practice time (either novice meditators or experienced meditators). For example, Josipovic et al. studied experienced meditators  and regressed out global signal fluctuations. They reported stronger anticorrelation between the DMN and extrinsic network  during focused-attention meditation but weaker correlation during non-dual awareness meditation28. The reported anticorrelation may be caused by their regressing out the global signal fluctuations. The anticorrelation (change of polarity) between brain networks after regressing out the global signals has been reported in both resting-state BOLD and ASL studies37.The longitudinal increase in rsFC between the DMN and DAN after meditation practice extends the current literature that reports the stronger rsFC during meditation between the DMN and DAN for experienced meditators  to self-relevant feeling, thoughts, and memory, releasing the distraction, and reorienting attention back to the intended meditation object. The process of meditation involves attentional regulation and self-monitoring. Therefore, meditation practice may require functional coupling of the DAN and the DMN to coordinate this complex process. These brain networks were shown to be more functionally coupled during the meditative state27. Our results suggest that the increased coupling during the meditative state may carry over to the rest state with repetitive meditation practice .The increased rsFC between the DMN and DAN and between the DMN and VC were generally observed. Please note that the LSPL seed (part of DAN) was shown with consistently increased rsFC with anterior mPFC . Only at follow-up, the rsFC between the LSPL seed and mPFC was positively associated with practice time with voxel-level p of 0.005 but not significant after multiple correction. Therefore, the rsFC association with practice time at follow-up can be attributed to the change of rsFC from baseline rather than its baseline rsFC. we have extended the literature by using the longitudinal design to investigate the functional connectivity change and drawing a direct inference for the causal relationship between practice time and functional connectivity change. The rsFC change in the mPFC is also in good agreement with the previous reports for the association of structural and functional changes in the mPFC with meditation21. Experienced meditators demonstrated heightened rsFC with mPFC within DMN compared to controls25. Taking it together with our results that indicate meditation practice can heighten the rsFC between the mPFC with a region in DAN, we can further confirm the role of the mPFC in integrating information gathered from internal and external environments. The stronger connectivity of mPFC with the DMN and DAN from meditation practice may effectively resolve the conflicts between the two networks and therefore achieve fast switching of brain networks. These results suggest that a 2-month meditation training can lead to changes in brain functional connectivity, which may reflect cortical remodeling between brain regions.The practice time was significantly correlated with the rsFC change between the LSPL seed of the DAN and the mPFC of the DMN. This positive association is supported by the association between the number of years of meditation experience and rsFC between the DAN and DMNThe study is not without limitations. First, we included a relatively small sample size and different variations of FAM practice. However, the sample size was shown with sufficient power in detecting the longitudinal rsFC changes, and we were able to observe significant changes of rsFC after a 2-month meditation training, further supporting the larger effect size from the applied multi-echo fMRI method. Second, we did not include a control group. However, the longitudinal change of rsFC was observed correlating with meditation practice time. Hence, it is unlikely that the results were due to expectancy bias but rather reflected the efforts participants put into their meditation practice. Third, a short follow-up period and only one follow-up time were used in the study. As such, the results may not be generalized to long-term meditation. A study with a larger sample size, matched control group and longer follow-up is warranted to confirm the association of the changes in functional connectivity with meditation.We demonstrated increased functional connectivity within the attention network, between the default mode network and attention network, and between the default mode network and visual cortex after novice meditators practiced 2-month meditation. The findings indicate the potential effects of meditation on enhancing the brain capability of fast switching between mind wandering and focused attention and maintaining attention once in attentive state.31. This p value is equivalent to a t value of 3.01 and an effect size of 0.81. Another meditation training study demonstrated the increased CEN-DAN rsFC  after 3-day meditation experience with a t value of at least 3.7430. This t value is equivalent to an effect size of 0.88 for their sample size of 18 subjects. Our adopted ME BOLD fMRI method increased the effect size at least 24% for the DMN connectivity (using the PCC seed) with the medium-to-high motion subjects32. Compared to conventional BOLD, ME BOLD reduced the standard deviation of PCC rsFC  with a p value of at most 0.005Eleven participants  were recruited from a Binghamton University meditation course, which is called “Meditation—Calm, Focus, and Reason”. Two of the participants reported to have had a brief meditation period in their prior yoga classes in which no specific guidance for meditation was given. The rest of the participants had never had meditation experience before. As such, all participants were novice meditators who had an interest in practicing meditation.The meditation course reviewed several types of meditation across multiple culture regions, explored the methods of general meditative techniques, and investigated the impact of meditation upon physical, mental, and emotional fitness via literature reviews. The instructor also provided guided meditation for 15 min once or twice per week during class in order to expose students to a range of meditation styles. Participants were allowed to choose their own object of attention during the meditation practice, for example, their breath, a point on the wall, a phrase, or anything else as they saw fit. Participants were instructed during class to sit comfortably, relax shoulders, close/open eyes, concentrate on a selected point focus , and repeatedly bring the attention back to the selected focus if they noticed their attention had drifted. Homework exercise was assigned to practice FAM for a minimum of 10 min per session and at least 5 sessions per week and each session on a different day, and to write a weekly journal by describing their practice experiences.All eleven participants attended the baseline MRI scans, which occurred prior to any homework assignments but after 4 sessions of instructor-guided in-class practice. Ten subjects completed follow-up scans after 2 months, with one female subject unable to attend. During the practice period, participants recorded their practice time for each session in a separate log. To ensure accuracy, the logs were released to the principal investigator after the course instructor released their final grades. The total practice time was calculated as the sum of all meditation practice time  between the baseline and follow-up scans.0, field of view (FOV): 25 cm, receiver bandwidth (rBW): 25 kHz. Next, the resting-state BOLD fMRI was performed. The acquisition was implemented with ME echo planar imaging (EPI) readout: FOV: 24 cm, matrix size: 64 All participants (11 participants at baseline and 10 participants at the 2-month follow-up) were scanned on the same 3 T GE MR750 scanner  at Cornell University MRI Facility using a 32-channel receive-only phased-array head coil. The study was approved by the Institutional Review Board of Cornell University, and all participants gave written informed consent. All methods described in this manuscript were carried out in accordance with the approved guidelines. The scan began with a three-plane localizer to define the anatomy of interest. Sagittal T1-weighted magnetization prepared rapid gradient echo (MPRAGE) images covering the whole brain were acquired in 5 min 30 s with parameters: 176 slices with matrix size: 40; T1-weighted images were normalized to the MNI anatomical template using nonlinear registration using FSL FNIRT41. The ME BOLD data was processed following the ME-ICA pipeline, detailed elsewhere32. ME-ICA started with a multi-echo principal component analysis (ME-PCA) on ME BOLD data to remove thermal noise, proceeded with FastICA to decompose the dimensionally reduced PCA results into independent components (ICs), classified the ICs into BOLD components and non-BOLD artifacts according to the assessments of component-level TE-dependence, and finally combined the BOLD components to form optimally combined time series. The images from the first four TRs were discarded for increased stability. Motion artifacts were regressed out from the remaining optimally combined BOLD time series with linear regression models using six rigid-body parameters of translation and rotation (by referencing to the first BOLD volume). The BOLD signal time series with ME-ICA denoising were obtained for further analysis.For each subject, ME BOLD signal time series were transformed to the standard brain space using the T1-weighted images as an intermediate. Specifically, BOLD time series and T1-weighted images were registered using 12-parameter affine registrationTo test the effectiveness of the ME-ICA denoising pipeline, for comparison purpose, we also calculated the raw BOLD signal time series without denoising and the BOLD signal time series with conventional denoising. The raw BOLD signal time series was generated by averaging ME BOLD images with TE-dependent weights. The BOLD signal time series with conventional denoising preprocessed the raw BOLD time series by regressing out the white matter and CSF signal fluctuations and motion effects (6-parameter rigid body motion) and applying a band-pass filter  Hz.42: the PCC  for the DMN, the LMT  and RMT  for the VC, the LSPL  and RSPL  for the DAN. All seed ROIs were defined as a sphere with a volume of ~ 2 cm3 centered at each seed voxel. These regions were then used as seed regions to create functional correlation maps in the datasets. The rsFC map for each volunteer and each seed ROI were calculated using Pearson correlation coefficients between time series from the seed ROI and those from the voxels throughout the entire brain. The time series from each seed ROI was calculated as the mean time series across all the voxels within the seed ROI.The three BOLD signal time series was used separately to calculate rsFC maps. Based on our hypotheses, five ROIs were chosen from the DMN, DAN, and VC. The locations of the seeds were selected from the previous workFor each of BOLD signal time series, the five functional connectivity maps from each participant were then transformed into z-score maps by using a Fisher z-transformation in order to achieve a normal distribution of z-scores at each voxel over the population for group-level statistics. The z-score maps were further smoothed with a 6 × 6 × 6 mm Gaussian kernel.To assess whether the changes of rsFC reflect the underlying structural changes, we performed a voxel-based morphometry (VBM) analysis to evaluate the brain structural changes from meditation. The Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) method has been used to achieve more accurate inter-subject registration of brain structural images. We adopted the DARTEL-based VBM analysis using SPM12. First, T1-weighted images were segmented into GM and WM probability maps and transformed into the MNI space, which were initial import in DARTEL. Second, the procedure of Run DARTEL (create Templates) was performed to estimate the deformations that best align the GM and WM images together. Specifically, an initial template was created from the imported GM and WM images. The first iteration of registration warped each image to the initial template using the DARTEL approach, following by generating a new template by the average of the registered images. The registered images were iteratively updated using the template created in the previous run. The step resulted in six templates and a flow field map that parameterized the deformation for every image. Third, the procedure of Normalized to MNI Space and smoothing was performed. The flow field map  was applied to the GM images to create spatially normalized GM images in the MNI space. A Gaussian smoothing kernel of 6 mm was applied to the normalized GM images.In order to assess the changes of rsFC between baseline and follow-up at the group level, the z-score maps were compared using SPM12 via a paired t-test with gender as a covariate on a voxel-by-voxel basis. Age of the participants was not considered as a covariate because the maximum difference among their ages is only 1 year. After the initial models, handedness was included as an additional covariate to evaluate its effect on the changes of rsFC. The statistical maps were thresholded at a voxel-level p-value of 0.005. A cluster-level p-value of 0.05 was used to correct for multiple comparisons. The automated anatomical labeling (AAL) atlas binary mask was used to include only the significant clusters within the gray matter area. A more liberal voxel-level threshold of p < 0.01 was used to view the trends for extended significant regions, although a corrected cluster-level threshold of p < 0.05 was still used for comparisons. Similar to the analyses in the rsFC images, the GM density images were compared between baseline and follow-up via a paired t-test with gender as a covariate; the association of the longitudinal changes in GM density with practice time was modeled via a multiple linear regression with gender and meditation practice time as covariates.To investigate the association of the longitudinal rsFC changes with total meditation practice time, the difference of the z-score maps between baseline and follow-up was modeled using SPM12 on a voxel basis via multiple linear regression with gender and meditation practice time as covariates. The voxel-level p-value and corrected cluster-level p-value thresholds were set in the same way as those in the aforementioned group comparison of rsFC maps between baseline and follow-up. Because the BOLD signal time series with ME-ICA denoising were demonstrated more effective in detecting the longitudinal rsFC changes, the association analyses and later post-hoc regional analyses were investigated using only the BOLD signal time series with ME-ICA denoising.Post-hoc regional analyses were performed to visualize the longitudinal rsFC changes. The significant clusters obtained from the voxel-based longitudinal rsFC changes were separated into different ROIs. According to locations of brain resting-state networks, several regions were combined into ROIs for the network analyses, and the ROIs were named with seed-network conventions. For instance, PCC-DAN stands for the within-the-DAN clusters, which exhibited significant changes with PCC rsFC. Post-hoc regional analyses were also performed to visualize the relationship between the longitudinal rsFC changes and meditation practice time. The longitudinal rsFC changes in the ROIs  were analyzed using multiple linear regression analysis with gender and meditation practice time as covariates. Pearson partial correlation was calculated between the longitudinal rsFC changes and meditation practice time while adjusting the effect of gender.


The rapid development of modern computational chemistry has led to a growing need to understand the microscopic mechanisms determining the properties of molecular and solid materials at an atomic level. The interactions between atoms and electrons are governed by the laws of quantum mechanics; hence, accurate and efficient computational methods for solving the quantum-mechanical equations are needed. The Kohn-Sham density functional theory (DFT) ab initio accuracy, and has been applied to a variety of applications Computational chemistry methods have become increasingly important in recent years, as manifested by their rapidly extending applications in a large number of diverse fields, such as computations of molecular structures and properties, the design of pharmaceutical drugs and novel materials, etc. In part as a result of this general trend, the size of the systems which can be computationally studied has also increased, generating even further needs for large-scale applications. This is because larger molecular systems show interesting phenomena and have important implications in modern biochemistry, biotechnology, and nanotechnology. Thus, it is of great importance to apply and further develop computational methods which provide physically sound models for large molecules at a reasonable computational cost. A representative approach is the linear scaling technique A deep understanding of the excitations in molecules and solids are of fundamentally importance in many technological applications. There is already a rich set of theoretical and simulation methods for excited-state calculations, such as the GW plus Bethe-Salpeter equation The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods on high performance computing (HPC) This editorial sums up the contents of our Research Topic “Advances in Density Functional Theory and Beyond for Computational Chemistry” and a total of nine original research contributions have been included in this article collection, involving linear-scaling density functional theory, multiple scattering theory, ab initio molecular dynamics, deep potential model, hybrid and double-hybrid functional theory, second-order Møller–Plesset perturbation theory, coupled cluster theory and high performance computing.Luo et al. described an efficient parallel implementation of linear-scaling density matrix trace correcting purification algorithm Linear-scaling DFT Cao et al. investigated a reduced scaling full-potential DFT method based on the multiple scattering theory code MuST The Korringa–Kohn–Rostoker Green’s function method ab initio molecular dynamics) has been extensively employed to explore the dynamical information of electronic systems. However, it remains extremely challenging to reliably predict electronic properties of systems with a radical nature using first-principles DFT calculations due to the presence of the static correlation. To address this challenge, Li and Chai proposed TAO-DFT  with AIMD to explore the dynamical properties of nanosystems with a radical nature at finite temperatures. A variety properties of n-acenes (n = 2–8) at 300 K are presented including the instantaneous/average radical nature and infrared spectra of n-acenes containing n linearly fused benzene rings (n = 2–8).AIMD  Yang et al. presented a Newton Krylov method The coupled cluster (CC) theory Williams-Young et al. proposed a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple graphics processing units (GPU) per compute node. They demonstrated that the performance and scalability of the implementation of the purposed method in the NWChemEx The above article collection demonstrates that the DFT methods have broad impacts on a variety of subjects in computational chemistry and related disciplines. In conjunction with high-performance computation and machine-learning techniques, the DFT framework undergoes another round of fast developments. It can be expected that more accurate DFT approaches with more efficient algorithms will be available in the near future.


Negative regulatory elements (NREs) down-regulate gene expression by inhibiting the activities of promoters or enhancers. The repressing activity of NREs can be measured globally by massively parallel reporter assays (MPRAs). However, most existing algorithms are designed for the statistical detection of positively enriched signals in MPRA datasets. To identify reduced signals in MPRA experiments, we designed a NRE identification program, fast-NR, by integrating the count and graphic features of sequenced reads to detect NREs using datasets generated by experiments of self-transcribing active regulatory region sequencing (STARR-seq). Fast-NR identified hundreds of silencers in human K562 cells that can be validated by independent methods. We calculate p values using cumulative density function (CDF) of negative binomial distribution (NBD). Next, we use the single nucleotides that pass the initial screen as anchors and extend the genomic window to upstream and downstream to a total of 601 bp. We further examine the p values of each nucleotide in each 601bp window and keep only windows in which 3/4 of all nucleotides are with a p value below 10−5. If two windows overlap, we keep the one in the shared region with smaller p values. Then, we compare the similarity between the curves of reporter cDNA and the input insert DNA reads, and discard any window with a curve similarity score higher than the arbitrary threshold. Finally, we correct p values for each window of identified NRE by Benjamini–Hochberg (BH) test and keep only these with a corrected p value smaller than 10−5.DNA fragments of NRE activity reduce their own expression levels in the STARR-seq reporter cDNA library. To identify NREs, we first calculate  Fast-NR , and tesp values by cumulative density function (CDF) of the negative binomial distribution for the sequenced reporter cDNA reads. The probability mass function of the number of We calculate We compare the shape of the curves of the reporter cDNA and the input insert DNA reads. Cosine, Pearson, Euclidean, and an in-house method gradient (linear slope correlation) are used to calculate the curve similarity in this research.The method of cosine computes the cosine distance between the 1-D arrays of Euclidean method computes the Euclidean distance between the 1-D arrays of Pearson computes the Pearson correlation coefficient between the 1-D arrays of This algorithm computes the Pearson correlation coefficients between the gradients of the curves of the reporter cDNA and the input insert DNA reads. The coverage and genomic location values of each silencer form a 2-D array, represented by p values in our program.Bonferroni and Benjamini–Hochberg (BH) adjustments are applied to correct To test the performance of Fast-NR, we downloaded STARR-seq datasets for silencer identification in human K562 (GSE142207)  and for We simulated a pair of STARR-seq datasets to test the NRE identification powers of Fast-NR and other methods including csaw , MEDIPS Program csaw detects differentially enriched regions in ChIP-seq dataset by using a sliding window strategy. MEDIPS identifies differentially methylated sites in the dataset generated by methylated DNA immunoprecipitation sequencing (MeDIP-seq). MEDIPS fails to detect any silencer at all from libraries in which 30, 50, and 70% reads are retained for the simulated silencers, while csaw identifies less than 100 silencers independent of what percentages of reads are retained . These rProgram PePr is similar to csaw in their differential signal detection power for ChIP-seq datasets. PePr identifies most simulated silencers when reads are retained at three different levels  , suggestp value thresholds are applied. Indeed, all these three methods detect fewer silencers as the p value threshold becomes more stringent  of these identified at p < 0.01. These results provoked us to examine the overlapping rates of silencers identified by Fast-NR and CRADLE in K562. In fact, decent amounts of silencers identified by these two methods overlapped in K562 but not in A549  for the NREs identified in A549 and found that the cosine distances between cDNA and plasmid curves are much higher than the random chosen genomic control regions   and thoup values sequentially, which may also, theoretically, reduce false positive rate. However, the thresholds applied could be too strict and exclude some true silencers. We recommend the users to test the threshold effects and choose appropriate thresholds for their own analysis.Another issue we would like to point out is the promoter used in the reporter plasmids. In STARR-seq and related methods, promoter choice could affect the outcome because the promoter used may be irresponsive to some CREs. We speculate that using promoters of house-keeping genes and cell type-specific genes may allow the identification of more CREs that may prefer to regulate different types of promoters. To save the computation time, we filtered potential NREs by applying thresholds on both read counts and Though STARR-seq measures regulatory activity of tested DNA fragment in episomal environment, it provides a catalogue of CREs that can be further tested at their endogenous loci by alternative methods. We did not take sequencing bias into consideration because experimental data that can be used to determine to what extent biases may affect NRE identification were not available. In summary, by combining read count-based negative binomial test and shape similarity comparison, we have shown that Fast-NR is potentially usable for silencer identification, thus providing a powerful and robust computational method for NRE identification.Silencers are negative regulatory elements that control the precise gene expression during cell proliferation and differentiation. The increasing needs for global silencer characterization require a reliable and user-friendly computational method. Our method Fast-NR integrates single nucleotide read count information and graphic information to detect silencers genome widely. Fast-NR identifies NREs at single base resolution. The wide application of Fast-NR will accelerate the genetic and epigenetic studies of the intriguing functional mechanisms of silencers.