bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthetic data for the study of the CUORE detector response function
Authors: Gianvecchio’ Alberto
Published: February 2022

CUORE (Cryogenic Underground Observatory for Rare Events) is a ton-scale experiment located at LNGS (Laboratori Nazionali del Gran Sasso) in Italy whose goal is to search for neutrino-less double beta decay (0υββ) in 130Te.

CUORE exploits an array of 988 TeO2 crystals operated as Low-Temperature Detectors (LTDs) at 10 mK. These detectors show an excellent energy resolution, making the experiment one of the most competitive 0υββ searches in the world. In this scenario, the proposed research deals with the generation of synthetic (mock) data for the study of the CUORE detector response function. The production of synthetic data is a new tool we designed to consider all the missing information from a Montecarlo simulation: the detector non-idealities, as well as noise and pulse shape. The mock data are processed with the CUORE official analysis software, allowing us the evaluation of its impact on the final results.
Non-unitarity and sterile neutrinos at the DUNE near detector
Authors: Urrea Salvador
Published: February 2022

We study the capabilities of the DUNE near detector to probe the 3+1 sterile formalism and the non-unitarity of the leptonic sector. We add to the current analyses in the literature, the use of the charged current events for the υτ appearance channel and the consideration of the energy spectral uncertainty (shape uncertainty) for the different channels which plays an important role, especially at the near detector, and has been usually overlooked in the literature. We find that even with this more conservative and realistic approach, we still obtain an improvement in the sensitivity with respect to the current bounds.
Exploring the Violation of Lorentz Invariance using Atmospheric Neutrinos at INO-ICAL
Authors: Sahoo Sadashiv , Kumar Anil , Agarwalla Sanjib Kumar
Published: February 2022

We explore the signature of Lorentz Invariance Violation (LIV) in the Standard Model Extension framework by observing the atmospheric neutrinos and antineutrinos separately with the help of magnetized Iron Calorimeter (ICAL) detector at the proposed India-based Neutrino Observatory (INO). Using 500 kt-yr exposure of ICAL, we place stringent bounds on the CPT-violating LIV parameters α

μτ
, α

ॉμ
, and aeT
(one-at-a-time) at 95% C.L. (1 d.o.f). We demonstrate the advantages of charge identification capability and hadron energy information at ICAL while constraining these LIV parameters. We also explore interesting correlations among various LIV parameters.
Spin and spin-flavor oscillations due to neutrino charge radii interaction with an external environment
Authors: Shakhov Vadim , Stankevich Konstantin , Studenikin Alexander
Published: February 2022

We derive the effective neutrino evolution Hamiltonian and corresponding expressions for the neutrino flavour and spin-flavour oscillation probabilities accounting for the neutrino interactions with an external electric current though the neutrino charge radius and anapole moment. The obtained results are of interest for neutrino astrophysical applications.
Guidelines for optimal design of radio-frequency in-vacuum coaxial transmission line for mirror cleaning service in ITER diagnostics
Authors: Danisi A. , Vayakis G. , Walsh M.
Published: February 2022

Several optical diagnostics in the ITER fusion reactor make use of big mirrors which are placed within the ITER vacuum vessel (VV), and therefore cannot have high accessibility. Plasma deposits developing on these mirrors may hinder the reflectivity of the mirror themselves, requiring a remote cleaning operation. The radio-frequency (RF) discharge mirror cleaning service operates a plasma discharge in the vicinity of the mirror, eroding the deposit layer and therefore cleaning the mirror remotely. In order to achieve this, RF power needs to be sent from outside the VV to the mirror, using a transmission line. Very stringent design requirements are applicable to the design of this RF line, such as vacuum compatibility, high power handling, low losses, overall matching, no cable over-heating, etc. This paper analytically addresses the design optimization of the RF mirror cleaning transmission line, taking into account ITER requirements, in order to give robust guidelines for the possible ad-hoc cable design adaptation that is to be undertaken case-by-case. The design guidelines are based on underlying transmission line theory, from which a set of design equations are drawn. The optimal design is achieved using design optimization considerations in the available design space. These guidelines are considered to be a useful design tool for optical diagnostics requiring mirror cleaning operation, and are aimed at harmonising the transmission line design procedures across the different cases.
Increasing spatiotemporal proximity of heat and precipitation extremes in a warming world quantified by a large model ensemble
Authors: Raymond Colin , Suarez-Gutierrez Laura , Kornhuber Kai , Pascolini-Campbell Madeleine , Sillmann Jana , Waliser Duane E
Published: February 2022

Increases in climate hazards and their impacts mark one of the major challenges of climate change. Situations in which hazards occur close enough to one another to result in amplified impacts, because systems are insufficiently resilient or because hazards themselves are made more severe, are of special concern. We consider projected changes in such compounding hazards using the Max Planck Institute Grand Ensemble under a moderate (RCP4.5) emissions scenario, which produces warming of about 2.25 °C between pre-industrial (1851–1880) and 2100. We find that extreme heat events occurring on three or more consecutive days increase in frequency by 100%–300%, and consecutive extreme precipitation events increase in most regions, nearly doubling for some. The chance of concurrent heat and drought leading to simultaneous maize failures in three or more breadbasket regions approximately doubles, while interannual wet-dry oscillations become at least 20% more likely across much of the subtropics. Our results highlight the importance of taking compounding climate extremes into account when looking at possible tipping points of socio-environmental systems.
‘Bog here, marshland there’: tensions in co-producing scientific knowledge on solar geoengineering in the Arctic
Authors: Mettiäinen Ilona , Buck Holly Jean , MacMartin Douglas G , Ricke Katharine L
Published: February 2022

Solar geoengineering has been suggested as a means to cool the planet and ameliorate climate impacts in the Arctic. However, few studies approach this idea from the viewpoint of Arctic communities. We explore the substantive rationale for public engagement with solar geoengineering research, including the premises that: (a) evaluation of local impacts by communities can generate better knowledge about what modeling results mean; and (b) ideas and questions surfaced in public discussions can contribute to and shape scientific research. We convened focus groups in Finnish Lapland, conducted scientific analysis of climate model output on albedo modification based upon the discussions, and returned a year later to discuss the results. The increased granularity of scientific information highlighted the limited scientific basis for decisions, which turned the discussions back towards questions of ethics and justice. We conclude that while there are serious limitations to global public decision-making on climate intervention, in the absence of formal governance, co-producing research could act as one de facto form of governance.
Disentangling the separate and confounding effects of temperature and precipitation on global maize yield using machine learning, statistical and process crop models
Authors: Yin Xiaomeng , Leng Guoyong , Yu Linfei
Published: February 2022

Temperature impacts on crop yield are known to be dependent on concurrent precipitation conditions and vice versa. To date, their confounding effects, as well as the associated uncertainties, are not well quantified at the global scale. Here, we disentangle the separate and confounding effects of temperature and precipitation on global maize yield under 25 climate scenarios. Instead of relying on a single type of crop model, as pursued in most previous impact assessments, we utilize machine learning, statistical and process-based crop models in a novel approach that allows for reasonable inter-method comparisons and uncertainty quantifications. Through controlling precipitation, an increase in warming of 1 °C could cause a global yield loss of 6.88%, 4.86% or 5.61% according to polynomial regression, long short-term memory (LSTM) and process-based crop models, respectively. With a 10% increase in precipitation, such negative temperature effects could be mitigated by 3.98%, 1.05% or 3.10%, respectively. When temperature is fixed at the baseline level, a 10% increase in precipitation alone could lead to a global yield growth of 0.23%, 1.43% or 3.09% according to polynomial regression, LSTM and process-based crop models, respectively. Further analysis demonstrates substantial uncertainties in impact assessment across crop models, which show a larger discrepancy in predicting temperature impacts than precipitation effects. Overall, global-scale assessment is more uncertain under drier conditions than under wet conditions, while a diverse uncertainty pattern is found for the top ten maize producing countries. This study highlights the important role of climate interactions in regulating yield response to changes in a specific climate factor and emphasizes the value of using both machine learning, statistical and process crop models in a consistent manner for a more realistic estimate of uncertainty than would be provided by a single type of model.
Farming analysis of intercropping of long bean on palm oil plantations (case study)
Authors: Adri  , Yardha
Published: February 2022

The research was carried out in the oil palm plantation of farmers in Naga Sari Village, Mestong District, Muaro Jambi Regency, Jambi Province. The age of oil palm was 2 years with a spacing of 8 x 9 m. This research was started from October 2019 to February 2020. The research method was a case study on long bean intercropping on smallholder oil palm plantations was covering an area of 3,600 m2. Input and output datas were obtained by recording all farming activities, included of payment of wages and purchases of materials and yield. The purpose of this study was to analyze the long bean intercropping system farming on immature oil palm plantations. The results showed that the long bean intercropping system on immature oil palm plantations was feasible and profitable to cultivate. The amount of revenue is IRD 14,700,000, - with operating profits of IRD 8,260,000, R/C 2.28 and B/C 1,283. The break-even point of production is 1,840 kg and the price break even point is IRD 1,533/kg. The balance of payment of wages with the purchase of materials is 68.5% : 31.5%.
HLA3D: an integrated structure-based computational toolkit for immunotherapy
Authors: Li Xingyu , Lin Xue , Mei Xueyin , Chen Pin , Liu Anna , Liang Weicheng , Chang Shan , Li Jian
Published: February 2022

Motivation

The human major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA), plays an important role in the adaptive immune system by presenting non-self-peptides to T cell receptors. The MHC region has been shown to be associated with a variety of diseases, including autoimmune diseases, organ transplantation and tumours. However, structural analytic tools of HLA are still sparse compared to the number of identified HLA alleles, which hinders the disclosure of its pathogenic mechanism.

Result

To provide an integrative analysis of HLA, we first collected 1296 amino acid sequences, 256 protein data bank structures, 120 000 frequency data of HLA alleles in different populations, 73 000 publications and 39 000 disease-associated single nucleotide polymorphism sites, as well as 212 modelled HLA heterodimer structures. Then, we put forward two new strategies for building up a toolkit for transplantation and tumour immunotherapy, designing risk alignment pipeline and antigenic peptide prediction pipeline by integrating different resources and bioinformatic tools. By integrating 100 000 calculated HLA conformation difference and online tools, risk alignment pipeline provides users with the functions of structural alignment, sequence alignment, residue visualization and risk report generation of mismatched HLA molecules. For tumour antigen prediction, we first predicted 370 000 immunogenic peptides based on the affinity between peptides and MHC to generate the neoantigen catalogue for 11 common tumours. We then designed an antigenic peptide prediction pipeline to provide the functions of mutation prediction, peptide prediction, immunogenicity assessment and docking simulation. We also present a case study of hepatitis B virus mutations associated with liver cancer that demonstrates the high legitimacy of our antigenic peptide prediction process. HLA3D, including different HLA analytic tools and the prediction pipelines, is available at http://www.hla3d.cn/.
Construct a variable-length fragment library for de novo protein structure prediction
Authors: Feng Qiongqiong , Hou Minghua , Liu Jun , Zhao Kailong , Zhang Guijun
Published: February 2022

Although remarkable achievements, such as AlphaFold2, have been made in end-to-end structure prediction, fragment libraries remain essential for de novo protein structure prediction, which can help explore and understand the protein-folding mechanism. In this work, we developed a variable-length fragment library (VFlib). In VFlib, a master structure database was first constructed from the Protein Data Bank through sequence clustering. The hidden Markov model (HMM) profile of each protein in the master structure database was generated by HHsuite, and the secondary structure of each protein was calculated by DSSP. For the query sequence, the HMM-profile was first constructed. Then, variable-length fragments were retrieved from the master structure database through dynamically variable-length profile–profile comparison. A complete method for chopping the query HMM-profile during this process was proposed to obtain fragments with increased diversity. Finally, secondary structure information was used to further screen the retrieved fragments to generate the final fragment library of specific query sequence. The experimental results obtained with a set of 120 nonredundant proteins show that the global precision and coverage of the fragment library generated by VFlib were 55.04% and 94.95% at the RMSD cutoff of 1.5 Å, respectively. Compared with the benchmark method of NNMake, the global precision of our fragment library had increased by 62.89% with equivalent coverage. Furthermore, the fragments generated by VFlib and NNMake were used to predict structure models through fragment assembly. Controlled experimental results demonstrate that the average TM-score of VFlib was 16.00% higher than that of NNMake.
Blood–brain barrier permeable β-blockers linked to lower risk of Alzheimer’s disease in hypertension
Authors: Beaman Emily Eufaula , Bonde Anders Nissen , Larsen Sara Marie Ulv , Ozenne Brice , Lohela Terhi Johanna , Nedergaard Maiken , Gíslason Gunnar Hilmar , Knudsen Gitte Moos , Holst Sebastian Camillo
Published: February 2022

Alzheimer's disease is a neurodegenerative disorder in which the pathological accumulation of amyloid-β and tau begins years before symptom onset. Emerging evidence suggests that β-blockers (β-adrenergic antagonists) increase brain clearance of these metabolites by enhancing CSF flow. Our objective was to determine whether β-blocker treatments that easily cross the blood–brain barrier reduce the risk of Alzheimer's disease compared to less permeable β-blockers.

Data from the Danish national registers were used to identify a retrospective cohort of individuals with hypertension, and those treated with β-blockers were included in the analysis. People with indications for β-blocker use other than hypertension (e.g. heart failure) were only retained in a sensitivity analysis. β-blockers were divided into three permeability groups: low, moderate and high. We used multivariable cause-specific Cox regression to model the effect of β-blocker blood–brain barrier permeability on time to dementia outcomes, adjusting for baseline comorbidities, demographics and socioeconomic variables. Death was modelled as a competing risk. The 10-year standardized absolute risk was estimated as the averaged person-specific risks per treatment.

In a cohort of 69 081 (median age = 64.4 years, 64.8% female) people treated with β-blockers for hypertension, highly blood–brain barrier-permeable β-blockers were associated with reduced risk of Alzheimer's disease versus low permeability β-blockers (−0.45%, P < 0.036). This effect was specific to Alzheimer's diagnoses and did not extend to dementia in general. Propensity score analysis matching high and low blood–brain barrier-permeable patients also detected a decreased Alzheimer's risk (−0.92%, P < 0.001) in the high permeability group compared to the low, as did a 1-year landmark analysis (−0.57%, P < 0.029) in which events within the first year of follow-up were ignored as likely unrelated to treatment.

Our results suggest that amongst people taking β-blockers for hypertension, treatment with highly blood–brain barrier permeable β-blockers reduces the risk of Alzheimer's disease compared to low permeability drugs. Our findings support the hypothesis that highly permeable β-blockers protect against Alzheimer's disease by promoting waste brain metabolite clearance.
Renin, aldosterone, the aldosterone-to-renin ratio, and incident hypertension among normotensive subjects from the general population
Authors: Arnold Natalie , Hermanns Iris M , Schulz Andreas , Hahad Omar , Schmitt Volker H , Panova-Noeva Marina , Prochaska Jürgen H , Binder Harald , Pfeiffer Norbert , Beutel Manfred , Lackner Karl J , Münzel Thomas , Wild Philipp S
Published: February 2022

Aims

To investigate the predictive ability of direct plasma renin and aldosterone concentrations as well as their ratio [aldosterone-to-renin (ARR)] for incident hypertension in the general population.

Methods and results

Concentration of renin and aldosterone were measured by a chemiluminescence immunoassay using the fully automated LIAISON® platform (DiaSorin) among 5362 participants of the population-based Gutenberg Health Study, who were normotensive and had no clinically overt cardiovascular disease at baseline. During a follow-up period of 5 years, 18.6% (n = 996) developed a new-onset hypertension. Comparing extreme quartiles of biomarker distribution, the relative risk (RR) for incident arterial hypertension was found to be 1.58 [95% confidence interval (CI) 1.25–2.00; P = 0.00015; Q1 vs. Q4ref] for renin; 1.29 (95% CI 1.05–1.59, P = 0.018; Q4 vs. Q1ref) for aldosterone and 1.70 (95% CI 1.33–2.12; P < 0.0001; Q4 vs. Q1ref) for ARR after multivariable adjustment in men. In females, only high ARR was independently predictive for incident hypertension over 5 years [RR 1.29 (95% CI 1.04–1.62); P = 0.024]. Even in the subgroup of individuals having biomarker concentrations within the reference range, high ARR was predictive for new-onset hypertension in men [RR 1.44 (95% CI 1.13–1.83); P = 0.003]. Finally, synergistic effects of co-prevalent obesity and ARR on incident hypertension were also demonstrated, resulting in markedly higher risk estimates as seen for biomarker alone [RR of 2.70 (95% CI 2.05–3.6) for Q4 of ARR and having body mass index ≥ 30 kg/m2 vs. low ARR (Q1ref) and normal weight; P < 0.0001].

Conclusion

Among normotensives from the general population ARR possesses a stronger predictive value for incident hypertension than renin or aldosterone alone. The prediction of arterial hypertension by ARR was even stronger in obese subjects.
Delayed administration of epinephrine is associated with worse neurological outcomes in patients with out-of-hospital cardiac arrest and initial pulseless electrical activity: insight from the nationwide multicentre observational JAAM-OHCA (Japan Association for Acute Medicine) registry
Authors: Enzan Nobuyuki , Hiasa Ken ichi , Ichimura Kenzo , Nishihara Masaaki , Iyonaga Takeshi , Shono Yuji , Tohyama Takeshi , Funakoshi Kouta , Kitazono Takanari , Tsutsui Hiroyuki
Published: February 2022

Aims

The delayed administration of epinephrine has been proven to worsen the neurological outcomes of patients with out-of-hospital cardiac arrest (OHCA) and shockable rhythm or asystole. We aimed to investigate whether the delayed administration of epinephrine might also worsen the neurological outcomes of patients with witnessed OHCA and initial pulseless electrical activity (PEA).

Methods and results

The JAAM-OHCA Registry is a multicentre registry including OHCA patients between 2014 and 2017. Patients with emergency medical services (EMS)-treated OHCA and initial PEA rhythm were included. The primary exposure was the time from the EMS call to the administration of epinephrine. The secondary exposure was the time to epinephrine dichotomized as early (≤15 min) or delayed (>15 min). The primary outcome was the achievement of a favourable neurological outcome, defined as Cerebral Performance Categories Scale 1–2 at 30 days after OHCA. Out of 34 754 patients with OHCA, 3050 patients were included in the present study. After adjusting for potential confounders, the delayed administration of the epinephrine was associated with a lower likelihood of achieving a favourable neurological outcome [adjusted odds ratio (OR) 0.96; 95% confidence interval (CI) 0.93–0.99; P = 0.016]. The percentage of patients who achieved a favourable neurological outcome in the delayed epinephrine group was lower than that in the early epinephrine group (1.3% vs. 4.7%; adjusted OR 0.33; 95% CI 0.15–0.72; P = 0.005). A restricted cubic spline analysis demonstrated that delayed epinephrine administration could decrease the likelihood of achieving a favourable neurological outcome; this was significant within the first 10 min.

Conclusions

The delayed administration of epinephrine was associated with worse neurological outcomes in patients with witnessed OHCA patients with initial PEA.
Pre-admission antiplatelet therapy and treatment effect of ticagrelor vs. prasugrel in patients with acute coronary syndromes—a subgroup analysis of the ISAR-REACT 5 trial
Authors: Lahu Shqipdona , Ndrepepa Gjin , Neumann Franz-Josef , Menichelli Maurizio , Bernlochner Isabell , Richardt Gert , Wöhrle Jochen , Witzenbichler Bernhard , Hemetsberger Rayyan , Mayer Katharina , Akin Ibrahim , Cassese Salvatore , Gewalt Senta , Xhepa Erion , Kufner Sebastian , Valina Christian , Sager Hendrik B , Joner Michael , Ibrahim Tareq , Laugwitz Karl-Ludwig , Schunkert Heribert , Schüpke Stefanie , Kastrati Adnan
Published: February 2022

Aims

To assess whether the efficacy and safety of ticagrelor vs. prasugrel in patients with acute coronary syndromes (ACSs) are influenced by pre-admission treatment with aspirin and/or clopidogrel.

Methods and results

Patients (n = 4018) were categorized into two groups: pre-admission aspirin and/or clopidogrel group (n = 1455) and no pre-admission aspirin or clopidogrel group (n = 2563). The primary endpoint was the composite of all-cause death, myocardial infarction, or stroke; the secondary safety endpoint was Bleeding Academic Research Consortium (BARC) type 3–5 bleeding, both at 1 year. Patients in the pre-admission aspirin and/or clopidogrel group had a higher risk of ischaemic events, but a similar risk of bleeding to patients in the no pre-admission aspirin or clopidogrel group (cumulative incidences 10.5% vs. 6.7%, and 5.7% vs. 5.7%, respectively). The primary endpoint occurred in 81/717 patients assigned to ticagrelor and 69/738 patients assigned to prasugrel in the pre-admission aspirin and/or clopidogrel group [11.5% vs. 9.5%; hazard ratio (HR) = 1.23; 95% confidence interval (CI) 0.89–1.69], and in 103/1295 patients assigned to ticagrelor and 68/1268 patients assigned to prasugrel in the no pre-admission aspirin or clopidogrel group [8.0% vs. 5.4%; HR = 1.50 (1.10–2.03); Pint = 0.38]. BARC type 3–5 bleeding events did not differ between ticagrelor and prasugrel in patients in the pre-admission aspirin and/or clopidogrel (6.2% vs. 4.5%) or no pre-admission aspirin or clopidogrel (5.3% vs. 5.1%) group (Pint = 0.54).

Conclusion

In patients with ACS, pre-admission therapy with aspirin and/or clopidogrel has no influence on the relative efficacy and safety of ticagrelor and prasugrel.
Cost-effectiveness of a programme to address sedentary behaviour in older adults: results from the SITLESS RCT
Authors: Deidda Manuela , Coll-Planas Laura , Tully Mark A , Giné-Garriga Maria , Kee Frank , Roqué i Figuls Marta , Blackburn Nicole E , Guerra-Balic Míriam , Rothenbacher Dietrich , Dallmeier Dhayana , Caserotti Paolo , Skjødt Mathias , McIntosh Emma ,   the SITLESS Consortium
Published: February 2022

Background

This study details the within-trial economic evaluation and long-term economic model of SITLESS, a multi-country, three-armed randomized controlled trial comparing a combined intervention of exercise referral schemes (ERS) enhanced by self-management strategies (SMS) against ERS alone and usual care (UC).

Methods

A cost-utility analysis, conducted from the base-case perspective of the National Health Service and personal and social services, estimated the incremental cost per incremental quality-adjusted life year (QALY) and years in full capability (YFC). A secondary analysis combined the costs with a broad set of outcomes within a cost-consequence framework, from a societal perspective. A Markov-type decision-analytic model was developed to project short-term changes in physical activity to long-term outcomes and costs, over a 5- and 15-year time horizon.

Results

The results of the within-trial analysis show that SMS+ERS is highly likely to be cost-effective compared to ERS alone (ICER €4270/QALY), but not compared to UC. Participants allocated to the SMS+ERS group also showed an improvement in YFC compared to ERS alone and UC. The long-term analysis revealed that SMS+ERS is likely to be a cost-effective option compared to ERS and UC over a 5-year, but not with a 15-year horizon, being then dominated by ERS alone.

Conclusion

This research provides new evidence that SMS is a cost-effective add-on to ERS strategies. This economic evaluation informs the case for further, cost-effective, refinement of lifestyle change programmes targeted to older adults, with the aim of ultimately reducing the impact of non-communicable diseases in this population.
Effective treatment for massive neonatal catheter-related right atrial thrombosis
Authors: Gong Shuji , Yang Yifeng , Tan Mingliang , Chen Jinlan
Published: February 2022

Catheter-related thrombosis is a common complication caused by central venous catheters. Although right atrial thrombosis is uncommon, it may lead to life-threatening situations. Here, we report 2 cases of neonates with massive catheter-related right atrial thrombosis after congenital heart disease surgery. During therapeutic management, we attempted different treatments but failed to clear the mass. Finally, we found thrombectomy to be the most effective method for treating massive catheter-related right atrial thrombosis with favourable results.
A Systematic Review of European Clinical Practice Guidelines for Respiratory Syncytial Virus Prophylaxis
Authors: Reeves Rachel M , van Wijhe Maarten , Lehtonen Toni , Stona Luca , Teirlinck Anne C , Vazquez Fernandez Liliana , Li You , Osei-Yeboah Richard , Fischer Thea K , Heikkinen Terho , van Boven Michiel , Bøås Håkon , Donà Daniele , Barbieri Elisa , Campbell Harry ,   RESCEU Investigators, Nair Harish , Campbell Harry , Shi Ting , Zhang Shanshan , Li You , Openshaw Peter , Wedzicha Jadwicha , Falsey Ann , Miller Mark , Beutels Philippe , Bont Louis , Pollard Andrew , Molero Eva , Martinon-Torres Federico , Lehtonen Toni , Heikkinen Terho , Meijer Adam , Fischer Thea Kølsen , van den Berge Maarten , Giaquinto Carlo , Mikolajczyk Rafael , Abram Michael , Hackett Judy , Tafesse Eskinder , Cai Bing , Knirsch Charles , Myint Tin Tin , Lopez Antonio Gonzalez , Dieussaert Ilse , Dermateau Nadia , Stoszek Sonia , Gallichan Scott , Kieffer Alexia , Demont Clarisse , Cheret Arnaud , Gavart Sandra , Aerssens Jeroen , Wyffels Veronique , Cleenewerck Matthias , Fuentes Robert , Kumar Veena
Published: February 2022

Background

Since the widespread adoption of palivizumab prophylaxis in Europe, there have been a number of clinical practice guidelines (CPGs) published for the prevention of respiratory syncytial virus (RSV) infection in children. The aim of this systematic review was to identify CPGs for the prevention of RSV infection across Europe.

Methods

We performed a systematic literature search and contacted European influenza and respiratory virus networks and public health institutions, to identify national CPGs for the prevention of RSV infection. The Reporting Items for practice Guidelines in Healthcare (RIGHT) Statement checklist was applied to extract data and review the quality of reporting.

Results

A total of 20 national CPGs were identified, all published between 2000 and 2018. The greatest discrepancy between guidelines was the recommendations for palivizumab prophylaxis for premature infants, with recommendations varying by gestational age. All guidelines recommended or considered the use of palivizumab in infants with bronchopulmonary dysplasia, 85% (n = 17) in children with congenital heart disease (CHD), and 60% (n = 12) in children with severe combined immunodeficiency.

Conclusions

We recommend that agencies publishing RSV prevention guidelines adopt the RIGHT reporting requirements when updating these guidelines to improve the presentation of the evidence-base for decisions.
Fragment-Based Drug Discovery forTrypanosoma bruceiGlycosylphosphatidylinositol-Specific Phospholipase C through Biochemical and WaterLOGSY-NMR Methods
Authors: Ibrahim Mohammed Auwal , Yamasaki Tomoko , Furukawa Koji , Yamasaki Kazuhiko
Published: February 2022

Glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC) of Trypanosoma brucei, the causative protozoan parasite of African trypanosomiasis, is a membrane-bound enzyme essential for antigenic variation, because it catalyses the release of the membrane-bound form of variable surface glycoproteins. Here, we performed a fragment-based drug discovery of TbGPI-PLC inhibitors using a combination of enzymatic inhibition assay and water ligand observed via gradient spectroscopy (WaterLOGSY) NMR experiment. The TbGPI-PLC was cloned and overexpressed using an Escherichia coli expression system followed by purification using three-phase partitioning and gel filtration. Subsequently, the inhibitory activity of 873 fragment compounds against the recombinant TbGPI-PLC led to the identification of 66 primary hits. These primary hits were subjected to the WaterLOGSY NMR experiment where 10 fragment hits were confirmed to directly bind to the TbGPI-PLC. These included benzothiazole, chlorobenzene, imidazole, indole, pyrazol and quinolinone derivatives. Molecular docking simulation indicated that six of them share a common binding site, which corresponds to the catalytic pocket. The present study identified chemically diverse fragment hits that could directly bind and inhibit the TbGPI-PLC activity, which constructed a framework for fragment optimization or linking towards the design of novel drugs for African trypanosomiasis.
A1 USING HUMAN NEONATAL ORGANOIDS TO EXPLORE GUT-IMMUNE SYSTEM INTERACTIONS OF THE NEONATAL INTESTINE
Authors: Allaire J M , Sharafianardakani Z , Poon B , Piper H , Jacobson K , Lavoie P , Vallance B
Published: February 2022

Background

Necrotizing Enterocolitis (NEC) affects around 10% of preterm babies and is one of the leading causes of death for newborns. NEC is characterized by exaggerated inflammation of the intestinal mucosa, possibly triggered by aberrant exposure to gut microbes, leading to hypoxic conditions and the death of intestinal tissues. It has been hypothesized that NEC develops when the immature intestine (epithelium and immune system) is unable to properly balance these new microbial interactions. To date, NEC is poorly understood and due to the difficulty of modeling the human neonatal intestine, few therapeutic options are available.

Intestinal epithelial cells (IEC) are important players in promoting beneficial host-microbe interactions in the gut, being the primary barrier that separates the host’s mucosal immune system from luminal microbiota, as well as key players in mediating signaling between microbes and the host. Based on their location, IEC are also subject to injury associated with maladaptive immune responses against gut microbes. Many studies have shown that immune cells (such as T helper 17 cells) interact with IEC to promote gut health and function. These interactions include educating IEC on how to respond to, and fight pathogenic microbes, yet also remain tolerant to commensal microbes.

Aims

This project seeks to develop an in vitro human neonatal intestinal organoid model to study developmental changes in IEC and their functional interactions with neonatal Th17 cells.

Methods

3D organoids were established from human neonatal intestinal biopsies and then co-cultured with the supernatant of differentiated Th17 cells or with recombinant cytokines, IL-17 and IL-22. Changes in barrier function, cell proliferation, production of mucins and anti-microbial peptides (AMP) were analyzed by qPCR and immunostaining.

Results

Using 3D neonatal organoids we observed that the supernatants from neonatal Th17 cells (containing IL-17, IL-22 etc.) promoted the proliferation, differentiation and barrier function of the neonatal epithelium. By using specific recombinant cytokine (IL22, IL17) and neutralizing IL-22 antibodies in parallel, we demonstrated that the high levels of IL-22 produced by neonatal Th17 cells specifically induced proliferation of IEC, AMP and mucus production as compared to control media treated organoids, as shown by increases in Ki67, Reg3γ and Muc2 markers.

Conclusions

This experimental model mimicking the neonatal intestinal environment can be used to study interactions between neonatal IEC and immune cells. Our findings can provide clinically relevant information and clues to how developmental changes in the newborn intestine can influence susceptibility to NEC while demonstrating our development of a simple, yet accurate and clinically applicable model of the neonatal gut.

Funding Agencies

CAG, CIHRBCCHRI, CCC, C.H.I.L.D. Fdn
A2 MUCUS DEFICIENCY IMPACTS INTESTINAL EPITHELIAL CELL PROLIFERATION INDEPENDENT OF THE MICROBIOTA
Authors: Han X , Tsai K , Allaire J M , Crowley S M , Lorentzian A , Maxwell C , Vallance B
Published: February 2022

Background

Intestinal homeostasis is highly dependent on the proliferation and differentiation of intestinal epithelial cells (IEC). IEC arise from intestinal stem cells (ISCs) that reside at the bottom of intestinal crypts. Following proliferation, the IEC migrate up as transient amplifying (TA) cells, and differentiate into mature IEC subtypes. When this process is disrupted, it can lead to aberrant IEC proliferation and differentiation. Mucus production by secretory goblet cells is also crucial for intestinal homeostasis, as mucus separates the IEC from luminal microbiota. Surprisingly, mice lacking Muc2, the main protein component of mucus, display increased distal colonic IEC proliferation and crypt hyperplasia at baseline, suggesting a relationship between Muc2 production and IEC proliferation.

Aims

We investigated how mucus production impacts IEC proliferation and differentiation in the intestinal crypt.

Methods

We used wildtype (Muc2+/+) and Muc2 deficient (Muc2-/-) littermates to measure distal colon crypt length and IEC proliferation pattern via microscopy. Organoids were also derived from distal colons of Muc2+/+ and Muc2-/- mice, and quantified for size, density and proliferation for 7 days to test whether the hyper-proliferation phenotype was also seen in vitro, thus epithelial-intrinsic. Crypts and organoids were collected for RNA sequencing to examine changes in IEC proliferation pathways. Proliferation assessments were repeated in germ-free (GF) Muc2+/+ and Muc2-/- mice. Muc2-/- mice were also cross-bred with Lgr5-EGFP-IRES-CreERT2 mice to investigate the contribution of ISCs to IEC hyperproliferation resulting from Muc2 deficiency.

Results

Significant crypt hyperplasia was observed in the distal colons of Muc2-/- mice in concert with a > twofold increase in Ki67+ TA cells as compared to Muc2+/+ mice. Similarly, Muc2-/- organoids also displayed significantly greater size, density and an increased number of Ki67+ cells than Muc2+/+ organoids. Hyperproliferation was also seen in GF mice and organoids, suggesting that mucus impacts IEC proliferation independent of the microbiome. Muc2-/- Lgr5-EGFP+ mice showed no significant increase in numbers of Lgr5+ cells, indicating that Muc2 deficiency does not directly impact ISC number, but rather their proliferation and differentiation reflected in increased numbers of TA cells. RNA-sequencing results suggested that changes in lipid metabolism may underlie the increased IEC proliferation seen in Muc2-/- mice.

Conclusions

Mucus not only promotes IEC homeostasis by separating luminal bacteria from the intestinal epithelium, but also intrinsically modifies IEC proliferation independent of the microbiota. Taken together, our results emphasize the importance of mucus in controlling gut health through mechanisms independent of its role in barrier function.

Funding Agencies

CCC, CIHRC.H.I.L.D Foundation
A8 REPEATED SUBMERGENCE OF AIR-LIQUID INTERFACE COLONOID CULTURES IMPAIRS INFLAMMATORY AND REGENERATIVE RESPONSES
Authors: Rees W D , Telkar N , Lin D , Wong M , Poloni C , Fathi A , Kobor M , Zachos N , Ted S
Published: February 2022

Background

Damage in the intestinal epithelium is repaired via de-differentiation of mature intestinal epithelial cells to a stem-like state. Indeed, literature has primarily focused on acute forms of intestinal damage, but there is a lack of models to study how intestinal stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). A previous report found that growth of mouse intestinal organoids in air-liquid interface (ALI) follows by submergence caused differentiation and reversible injury, but this has not been demonstrated in human cells or with repeated cycles of injury. Understanding how chronic damage alters human intestinal stem cell fate and function is imperative to developing novel therapies that repair the epithelium in people with IBD

Aims

To develop a robust in vitro model to differentiate and damage human intestinal epithelial cells, with or without the addition of bacterial flagellin to mimic pathogen exposure.

Methods

Human colonoid monolayers were seeded on Transwell inserts for 10 days until fully confluent and then differentiated by removing the apical media to create ALI growth conditions for 7 days. To induce damage, media was added to the apical side of the Transwell, with or without the addition of flagellin in the basolateral compartment. Following submergence induced damage, the apical media was removed and collected for chemokine analysis, and the cells were grown back in ALI for 3 days to recover them from injury. This cycle was repeated 5 times to induce chronic damage. Cells were collected for qPCR analysis, immunofluorescence imaging, RNA sequencing and DNA methylation analysis

Results

Repeated rounds of damage impaired the ability of intestinal epithelial cells (IECs) to respond to TLR stimulation (a decrease in basolateral IL-8 with each round), likely due to a decrease in TLR signaling pathways, as demonstrated by GSEA and qPCR. Chronic submergence damage led to an increase in differentiation of cells expressing MUC2, SLC26a3 and CHGA, and a decrease in stemness as shown by qPCR for BMI1, HOPX, and LGR5. After several rounds of damage, colonoid monolayers were unable to regrow as monolayers after passaging, likely due to a decrease in YAP signaling. We also identified mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer.

Conclusions

We have developed a novel chronic damage model of recurrent IEC injury, which possibly mimics pathologies seen in people with inflammatory bowel disease. This model can be used to understand how chronic damage alters the ability of IECs to respond to pathogens and regenerate to repair and protect the epithelium from further damage.

Funding Agencies

CCC
A12 STEPWISE COORDINATION OF COLONIC NEUTROPHILS AND INNATE LYMPHOID CELLS IN THE ONSET AND RESOLUTION OF CLOSTRIDIOIDES DIFFICILE TOXIN-INDUCED INJURY
Authors: Flannigan K L , Serra A , Hirota S A
Published: February 2022

Background

While our understanding and use of treatments for Clostridioides difficile infection (CDI) has improved, initial CDI still carries significant morbidity and mortality owing to heterogeneity in host immune responses. Further, host immunity is a critical modulator of fecal microbiota transplantation (FMT) success in CDI. Thus, understanding the host immune response during CDI is essential.

Aims

To assess the cellular immune responses that trigger the onset and resolution of injury and inflammation in CDI.

Methods

Colonic injury and inflammation triggered by CDI was modelled in mice using intrarectal installation of C. difficile toxins A and B (TcdA/B). Colonic tissue was collected at various timepoints following TcdA/B exposure to assess gene expression (qPCR), cytokine production (ELISA) and immune cell responses (flow cytometry). Knockout mice and neutralizing antibodies were used to deplete cytokines or cells.

Results

Examinion of colonic gene expression at different times following TcdA/B exposure found a dominant transcriptional signature related to neutrophil adhesion and diapedesis. In addition to the typical neutrophil chemokines Cxcl1 and Cxcl2, TcdA/B exposure also increased expression of neutrophil effector genes including Elane (neutrophil elastase). Neutrophil influx in response to TcdA/B was a critical driver of intestinal injury as antibody-mediated depletion of neutrophils lead to significantly less damage in the colon following TcdA/B exposure. Along with neutrophil influx, there were high levels of antimicrobial gene expression in the colon after TcdA/B exposure including RegIIIγ, S100a8, and Socs3, all genes regulated by IL-22. Upon further investigation, IL-22 was a significant mediator in the host response to TcdA/B exposure as it was upregulated >150-fold in the colon and originated from type 3 innate lymphoid cells (ILC3). Further, TcdA/B exposure in IL-22-/- mice lead to significantly more colonic damage compared to wildtype (WT) mice. Subsequent screening of previously published RNAseq data from IL-22-treated mouse colonic organoids identified various upregulated proteins involved in immune regulation, including the gene Slpi that encodes a protein (secretory leukocyte peptidase inhibitor) that inhibits leukocyte proteases, including neutrophil elastase. While TcdA/B challenge robustly induced the expression of Slpi in the colon of WT mice, IL-22-/- mice failed to express increased levels of Slpi and had greater levels of neutrophil elastase activity in the colon.

Conclusions

Together these data suggest a stepwise immune response to TcdA/B where ILC3 produce IL-22 to induce epithelial release of SLPI that attenuates the damaging effects of early neutrophil responses. Strategies to upregulate IL-22 may help control damage triggered by CDI and promote resolution of injury.

Funding Agencies

Lloyd Sutherland Chair in GI Research, Canadian Research Chair
A15 GIARDIA DUODENALIS INDUCES REGIOSPECIFIC ALTERATIONS TO INTESTINAL MUCOSAL GLYCOSYLATION PATTERNS
Authors: Fekete E , Allain T , Buret A
Published: February 2022

Background

Disruption of intestinal barrier function is important in the pathogenesis of numerous intestinal diseases and can lead to increased intestinal permeability. During infection with the protozoan parasite Giardia duodenalis, intestinal permeability is increased in part due to disruption of the intestinal mucus barrier. Intestinal mucus is composed primarily of the heavily glycosylated MUC2 mucin. Glycosylation of mucins is important for maintaining the structure of the mucus gel, and glycans are key mediators of host-microbe interactions, as they provide binding sites to microbes and can be degraded as a nutrient source. Changes to mucin glycosylation patterns have been noted during intestinal inflammation and bacterial infection, and may contribute to altered intestinal permeability and dysbiosis. We hypothesized that intestinal mucosal glycosylation patterns may be disrupted during Giardia infection, and that this may contribute to Giardia-induced barrier dysfunction.

Aims

Characterize changes to mucosal glycosylation patterns in the small and large intestines during in vivo Giardia infection.

Methods

3–4 week old C57BL/6 mice were infected with Giardia duodenalis strain GS/M for 7 days. Tissue sections from the jejunum and colon were collected and stained with various fluorescein-coupled lectins (CONA, DBA, PNA, WGA, SNA, UEA-1) and fluorescence was quantified and normalized to tissue area. Quantitative PCR (qPCR) was performed for glycosyltransferase genes in the jejunum and colon.

Results

In the jejunum, abundance of N-acetylglucosamine increased upon infection, while sialic acid and fucose abundance were significantly decreased in infected mice compared to controls. Conversely, in the distal colon, mannose and sialic acid abundance increased significantly upon infection.

Expression of mucin-associated glycosyltransferase genes was also altered in the small and large intestines of Giardia infected mice. In the jejunums of infected mice, expression of the sulfotransferase Chst4 decreased, while the fucosyltransferase Fut2 and the sialyltransferase St6GalNAc1 increased in comparison to controls. In both the jejunum and distal colon, expression of the core 2 synthase C2GnT1 increased, while expression of the core 1 synthase C1GalT1 was similar between control and infected mice.

Conclusions

Glycosylation patterns and the expression of glycosyltransferase genes are altered in both the small and large intestines of Giardia-infected mice. Disruptions to mucin glycans appear to be regiospecific, suggesting that unique mechanisms are involved in the regulation of mucosal glycosylation during parasitic infection throughout different regions of the gut. These findings uncover a novel mechanism in the pathogenesis of Giardia infection, and may be important in understanding intestinal barrier dysfunction in a variety of different gastrointestinal diseases.

Funding Agencies

CCC