bluuebunny/crossref_metadata_2025 huggingface dataset:
Commentary: Epistemological Positionalities
Authors: Singh Jaspal Naveel
Published: September 2021

Understanding how people resist European colonial modernity by collaboratively constructing southern epistemological positionalities is crucial for plotting plans about what applied linguists can do to promote social justice in the third decade of the 21st century. Epistemological positionalities describe how speakers metapragmatically theorize the knowledge they make or do not make relevant in communication. From the articles collected in this volume we learn how previously colonized people find new ways to re-envision what kinds of knowledges are important to them, which knowledges oppress them and how they can know differently and collaboratively to advance social justice and imagine hopeful and liveable decolonial futures. In this commentary I emphasize that instead of simply giving previously colonised people bits of European modern knowledge (such as access to inner-circle Englishes), applied linguists must encourage the people who we research to theorize their own knowledge, i.e. to assume epistemological positionalities, that are meaningful to themselves and to the communities from which they come.
MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys
Authors: Liu Tiantian , Xu Peirong , Du Yueyao , Lu Hui , Zhao Hongyu , Wang Tao
Published: September 2021

As our understanding of the microbiome has expanded, so has the recognition of its critical role in human health and disease, thereby emphasizing the importance of testing whether microbes are associated with environmental factors or clinical outcomes. However, many of the fundamental challenges that concern microbiome surveys arise from statistical and experimental design issues, such as the sparse and overdispersed nature of microbiome count data and the complex correlation structure among samples. For example, in the human microbiome project (HMP) dataset, the repeated observations across time points (level 1) are nested within body sites (level 2), which are further nested within subjects (level 3). Therefore, there is a great need for the development of specialized and sophisticated statistical tests. In this paper, we propose multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys. We develop a variational approximation method for maximum likelihood estimation and inference. It uses optimization, rather than sampling, to approximate the log-likelihood and compute parameter estimates, provides a robust estimate of the covariance of parameter estimates and constructs a Wald-type test statistic for association testing. We evaluate and demonstrate the performance of our method using extensive simulation studies and an application to the HMP dataset. We have developed an R package MZINBVA to implement the proposed method, which is available from the GitHub repository https://github.com/liudoubletian/MZINBVA.
miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms
Authors: Rawal Hukam Chand , Ali Shakir , Mondal Tapan Kumar
Published: September 2021

In recent years, microRNAs (miRNAs) and tRNA-derived RNA fragments (tRFs) have been reported extensively following different approaches of identification and analysis. Comprehensively analyzing the present approaches to overcome the existing variations, we developed a benchmarking methodology each for the identification of miRNAs and tRFs, termed as miRNA Prediction Methodology (miRPreM) and tRNA-induced small non-coding RNA Prediction Methodology (tiRPreM), respectively. We emphasized the use of respective genome of organism under study for mapping reads, sample data with at least two biological replicates, normalized read count support and novel miRNA prediction by two standard tools with multiple runs. The performance of these methodologies was evaluated by using Oryza coarctata, a wild rice species as a case study for model and non-model organisms. With organism-specific reference genome approach, 98 miRNAs and 60 tRFs were exclusively found. We observed high accuracy (13 out of 15) when tested these genome-specific miRNAs in support of analyzing the data with respective organism. Such a strong impact of miRPreM, we have predicted more than double number of miRNAs (186) as compared with the traditional approaches (79) and with tiRPreM, we have predicted all known classes of tRFs within the same small RNA data. Moreover, the methodologies presented here are in standard form in order to extend its applicability to different organisms rather than restricting to plants. Hence, miRPreM and tiRPreM can fulfill the need of a comprehensive methodology for miRNA prediction and tRF identification, respectively, for model and non-model organisms.
Efficient change-points detection for genomic sequences via cumulative segmented regression
Authors: Jia Shengji , Shi Lei
Published: September 2021

Motivation

Knowing the number and the exact locations of multiple change points in genomic sequences serves several biological needs. The cumulative-segmented algorithm (cumSeg) has been recently proposed as a computationally efficient approach for multiple change-points detection, which is based on a simple transformation of data and provides results quite robust to model mis-specifications. However, the errors are also accumulated in the transformed model so that heteroscedasticity and serial correlation will show up, and thus the variations of the estimated change points will be quite different, while the locations of the change points should be of the same importance in the original genomic sequences.

Results

In this study, we develop two new change-points detection procedures in the framework of cumulative segmented regression. Simulations reveal that the proposed methods not only improve the efficiency of each change point estimator substantially but also provide the estimators with similar variations for all the change points. By applying these proposed algorithms to Coriel and SNP genotyping data, we illustrate their performance on detecting copy number variations.

Availability and implementation

The proposed algorithms are implemented in R program and the codes are provided in the online supplementary material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Preferences for active surveillance or standard oesophagectomy: discrete-choice experiment
Authors: van der Wilk Berend J. , Spronk Inge , Noordman Bo J. , Eyck Ben M. , Haagsma Juanita A. , Coene Peter-Paul L. O. , van der Harst Erwin , Heisterkamp Joos , Lagarde Sjoerd M. , Wijnhoven Bas P. L. , van Lanschot J. Jan B.
Published: September 2021

Over one-quarter of patients would choose not to undergo standard oesophagectomy again, at least 1 year after they underwent neoadjuvant chemoradiotherapy and standard oesophagectomy. These patients had worse short- and long-term health-related quality of life (HRQoL) than patients who chose standard oesophagectomy. Considering both treatments, 5-year survival and long-term HRQoL were considered most important factors by individual patients.
Liver transplant outcomes after ex vivo machine perfusion: a meta-analysis
Authors: Liew Belle , Nasralla David , Iype Satheesh , Pollok Joerg-Matthias , Davidson Brian , Raptis Dimitri A
Published: September 2021

Background

The pressure on liver-transplant programmes has expanded the usage of extended-criteria allografts. Machine perfusion may be better than conventional static cold storage (SCS) in alleviating ischaemia–reperfusion injury in this setting. Recipient outcomes with hypothermic or normothermic machine perfusion were assessed against SCS here.

Methods

A search in MEDLINE, EMBASE and Scopus was conducted in February 2021. Primary studies investigating ex vivo machine perfusion were assessed for the following outcomes: morbidity, ICU and hospital stay, graft and patient survival rates and relative costs. Meta-analysis was performed to obtain pooled summary measures.

Results

Thirty-four articles involving 1742 patients were included, of which 20 were used for quantitative synthesis. Odds ratios favoured hypothermic machine perfusion (over SCS) with less early allograft dysfunction, ischaemic cholangiopathy, non-anastomotic strictures and graft loss. Hypothermic machine perfusion was associated with a shorter hospital stay and normothermic machine perfusion with reduced graft injury. Two randomized clinical trials found normothermic machine perfusion reduced major complication risks.

Conclusion

Machine perfusion assists some outcomes with potential cost savings.
Soft Cops or Social Justice Activists: Social Work’s Relationship to the state in the context of BLM and Neoliberalism
Authors: Baines Donna
Published: September 2021

In the current dual context of Black Lives Matter/defund the police and calls for accountability to those whom social work has harmed as part of the state machinery, this article returns to the debate on state theory. The article explores three state-linked forms of care, coercion and control: stealth coercion/control (in aged-care); population-linked coercion/control, and police and carceral-linked coercion/control. The article analyses what is missing in state theory in a neoliberal world and argues that social work needs models of practice and theory that are themselves a form of resistance and relative autonomy from the state in that they challenge the oppressive state machinery while making demands on the state for equity and fairness. This model permits social work to be humble in the face of lived experience and grounded in the priorities of the community, rather than uncritically legitimising state-linked oppression and securing the ground for profit and accumulation. The article concludes that while this social justice-engaged model will be essential for those moving into the new practice contexts resulting from defunding the police, it is also a model that will serve to strengthen the relevance and integrity of all social work practice.
Functional neurological disorder: lighting the way to a new paradigm for medicine
Authors: Edwards Mark J
Published: September 2021

In this Essay, Mark Edwards argues that the plight of people with functional neurological disorder within healthcare highlights a general problem with a broken paradigm of modern medicine. He argues that the passivity of the traditional sick role needs replacing with a participatory, rehabilitative medical practice.
The role of astrocytes in prion-like mechanisms of neurodegeneration
Authors: Smethurst Phillip , Franklin Hannah , Clarke Benjamin E , Sidle Katie , Patani Rickie
Published: September 2021

Accumulating evidence suggests that neurodegenerative diseases are not merely neuronal in nature but comprise multicellular involvement, with astrocytes emerging as key players. The pathomechanisms of several neurodegenerative diseases involve the deposition of misfolded protein aggregates in neurons that have characteristic prion-like behaviours such as template-directed seeding, intercellular propagation, distinct conformational strains and protein-mediated toxicity. The role of astrocytes in dealing with these pathological prion-like protein aggregates and whether their responses either protect from or conspire with the disease process is currently unclear. Here we review the existing literature implicating astrocytes in multiple neurodegenerative proteinopathies with a focus on prion-like behaviour in this context.
Impaired Hearing and Altered Subplate Circuits During the First and Second Postnatal Weeks of Otoferlin-Deficient Mice
Authors: Mukherjee Didhiti , Meng Xiangying , Kao Joseph P Y , Kanold Patrick O
Published: September 2021

Sensory deprivation from the periphery impacts cortical development. Otoferlin deficiency leads to impaired cochlear synaptic transmission and is associated with progressive hearing loss in adults. However, it remains elusive how sensory deprivation due to otoferlin deficiency impacts the early development of the auditory cortex (ACX) especially before the onset of low threshold hearing. To test that, we performed in vivo imaging of the ACX in awake mice lacking otoferlin (Otof−/−) during the first and second postnatal weeks and found that spontaneous and sound-driven cortical activity were progressively impaired. We then characterized the effects on developing auditory cortical circuits by performing in vitro recordings from subplate neurons (SPN), the first primary targets of thalamocortical inputs. We found that in Otof−/− pups, SPNs received exuberant connections from excitatory and inhibitory neurons. Moreover, as a population, SPNs showed higher similarity with respect to their circuit topology in the absence of otoferlin. Together, our results show that otoferlin deficiency results in impaired hearing and has a powerful influence on cortical connections and spontaneous activity in early development even before complete deafness. Therefore, peripheral activity has the potential to sculpt cortical structures from the earliest ages, even before hearing impairment is diagnosed.
Implementation of the ICCPR in Macao since 1999: The Position of Aliens as an Illustration
Authors: Wang Chao
Published: September 2021

This article provides an overview of the local adaptation of the International Covenant on Civil and Political Rights (ICCPR) in Macao since 1999 and a comparative analysis of the different models of protection of the rights and freedoms of non-residents in Macao and Hong Kong as an illustration of selective adaptation of international human rights law in China’s special administrative regions. The article argues that the theory of selective adaptation of international human rights law helps us to understand the local interpretation and adaptation of international human rights law by identifying the resonance between international human rights laws and the normative discourse underlying locally transformed legislation. Given the similarity in wording of certain provisions of the ICCPR and of the Basic Law, the varying interpretation of these provisions and varying treatment of aliens in the implementation of the ICCPR illustrates the paradigm of selective adaptation of international norms as a coping strategy to balance local needs against the requirement for compliance with external rules. The article suggests the importance of a normative consensus in the local implementation of international human rights standards in that the sharing of international human rights rules does not necessarily indicate consensus on the normative order underlying those rules.
Association of Pneumococcal Serotype With Susceptibility to Antimicrobial Drugs: A Systematic Review and Meta-analysis
Authors: Andrejko Kristin , Ratnasiri Buddhika , Lewnard Joseph A
Published: September 2021

Background

Pneumococcal serotypes differ in antimicrobial susceptibility. However, patterns and causes of this variation are not comprehensively understood.

Methods

We undertook a systematic review of epidemiologic studies of pneumococci isolated from carriage or invasive disease among children globally from 2000–2019. We evaluated associations of each serotype with nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole. We evaluated differences in the prevalence of nonsusceptibility to major antibiotic classes across serotypes using random-effects meta-regression models and assessed changes in prevalence of nonsusceptibility after implementation of pneumococcal conjugate vaccines (PCVs). We also evaluated associations between biological characteristics of serotypes and their likelihood of nonsusceptibility to each drug.

Results

We included data from 129 studies representing 32 187 isolates across 52 countries. Within serotypes, the proportion of nonsusceptible isolates varied geographically and over time, in settings using and those not using PCVs. Factors predicting enhanced fitness of serotypes in colonization as well as enhanced pathogenicity were each associated with higher likelihood of nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole. Increases in prevalence of nonsusceptibility following PCV implementation were evident among non-PCV serotypes, including 6A, 6C, 15A, 15B/C, 19A, and 35B; however, this pattern was not universally evident among non-PCV serotypes. Postvaccination increases in nonsusceptibility for serotypes 6A and 19A were attenuated in settings that implemented PCV13.

Conclusions

In pneumococci, nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole is associated with more frequent opportunities for antibiotic exposure during both prolonged carriage episodes and when serotypes cause disease. These findings suggest multiple pathways leading to resistance selection in pneumococci.
Nocardia Infections in Hematopoietic Cell Transplant Recipients: A Multicenter International Retrospective Study of the Infectious Diseases Working Party of the European Society for Blood and Marrow Transplantation
Authors: Averbuch Diana , De Greef Julien , Duréault Amelie , Wendel Lotus , Tridello Gloria , Lebeaux David , Mikulska Malgorzata , Gil Lidia , Knelange Nina , Zuckerman Tsila , Roussel Xavier , Robin Christine , Xhaard Alienor , Aljurf Mahmoud , Beguin Yves , Le Bourgeois Amandine , Botella-Garcia Carmen , Khanna Nina , Van Praet Jens , Kröger Nicolaus , Blijlevens Nicole , Ducastelle Leprêtre Sophie , Ho Aloysius , Roos-Weil Damien , Yeshurun Moshe , Lortholary Olivier , Fontanet Arnaud , de la Camara Rafael , Coussement Julien , Maertens Johan , Styczynski Jan ,   European Study Group for Nocardia in Hematopoietic Cell Transplantation, Arat M , Blau I W , Bron D , Carlson K , Collin M , Cordonnier C , Ganser A , Gruhn B , Junghanss C , Marchand T , Martin S , Milone G A , Nagler A , Pagliuca S , Ram R , Ribera J M , de la Serna J , Stamouli M , Villate A
Published: September 2021

Background

Nocardiosis is rare after hematopoietic cell transplantation (HCT). Little is known regarding its presentation, management, and outcome in this population.

Methods

This retrospective international study reviewed nocardiosis episodes in HCT recipients (1/1/2000–31/12/2018; 135 transplant centers; 33 countries) and described their clinical, microbiological, radiological, and outcome characteristics.

Results

We identified 81 nocardiosis episodes in 74 allo- and 7 auto-HCT recipients. Nocardiosis occurred a median of 8 (IQR: 4–18) months post-HCT. The most frequently involved organs were lungs (70/81; 86%) and brain (30/81; 37%); 29 (36%) patients were afebrile; 46/81 (57%) had disseminated infections. The most common lung imaging findings were consolidations (33/68; 49%) or nodules (32/68; 47%); brain imaging findings were multiple brain abscesses (19/30; 63%). Ten of 30 (33%) patients with brain involvement lacked neurological symptoms. Fourteen of 48 (29%) patients were bacteremic. Nocardia farcinica was the most common among molecularly identified species (27%; 12/44). Highest susceptibility rates were reported to linezolid (45/45; 100%), amikacin (56/57; 98%), trimethoprim-sulfamethoxazole (57/63; 90%), and imipenem (49/57; 86%). One-year and last follow-up (IQR: 4–42.5 months) all-cause mortality were 40% (32/81) and 52% (42/81), respectively. In the multivariable analysis, underlying disease not in complete remission (HR: 2.81; 95% CI: 1.32–5.95) and prior bacterial infection (HR: 3.42; 95% CI: 1.62–7.22) were associated with higher 1-year all-cause mortality.

Conclusions

Nocardiosis is a late post-HCT infection usually manifesting as a pulmonary disease with frequent dissemination, brain infection, and bacteremia. Brain imaging should be performed in HCT recipients with nocardiosis regardless of neurological symptoms. Overall mortality is high.
SARS-CoV-2 Nucleocapsid Plasma Antigen for Diagnosis and Monitoring of COVID-19
Authors: Wang Hannah , Hogan Catherine A , Verghese Michelle , Solis Daniel , Sibai Mamdouh , Huang ChunHong , Röltgen Katharina , Stevens Bryan A , Yamamoto Fumiko , Sahoo Malaya K , Zehnder James , Boyd Scott D , Pinsky Benjamin A
Published: September 2021

Background

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen in blood has been described, but the diagnostic and prognostic role of antigenemia is not well understood. This study aimed to determine the frequency, duration, and concentration of nucleocapsid antigen in plasma and its association with coronavirus disease 2019 (COVID-19) severity.

Methods

We utilized an ultrasensitive electrochemiluminescence immunoassay targeting SARS-CoV-2 nucleocapsid antigen to evaluate 777 plasma samples from 104 individuals with COVID-19. We compared plasma antigen to respiratory nucleic acid amplification testing (NAAT) in 74 individuals with COVID-19 from samples collected ±1 day of diagnostic respiratory NAAT and in 52 SARS-CoV-2–negative individuals. We used Kruskal–Wallis tests, multivariable logistic regression, and mixed-effects modeling to evaluate whether plasma antigen concentration was associated with disease severity.

Results

Plasma antigen had 91.9% (95% CI 83.2%–97.0%) clinical sensitivity and 94.2% (84.1%–98.8%) clinical specificity. Antigen-negative plasma samples belonged to patients with later respiratory cycle thresholds (Ct) when compared with antigen-positive plasma samples. Median plasma antigen concentration (log10 fg/mL) was 5.4 (interquartile range 3.9–6.0) in outpatients, 6.0 (5.4–6.5) in inpatients, and 6.6 (6.1–7.2) in intensive care unit (ICU) patients. In models adjusted for age, sex, diabetes, and hypertension, plasma antigen concentration at diagnosis was associated with ICU admission [odds ratio 2.8 (95% CI 1.2–6.2), P=.01] but not with non-ICU hospitalization. Rate of antigen decrease was not associated with disease severity.

Conclusions

SARS-CoV-2 plasma nucleocapsid antigen exhibited comparable diagnostic performance to upper respiratory NAAT, especially among those with late respiratory Ct. In addition to currently available tools, antigenemia may facilitate patient triage to optimize intensive care utilization.
Co-simulation and Formal Verification of Co-operative Drone Control With Logic-Based Specifications
Authors: Bernardeschi Cinzia , Domenici Andrea , Fagiolini Adriano , Palmieri Maurizio
Published: September 2021

Unmanned aerial vehicle (UAV) co-operative systems are complex cyber-physical systems that integrate a high-level control algorithm with pre-existing closed implementations of lower-level vehicle kinematics. In model-driven development, simulation is one of the techniques that are usually applied, together with testing, in the analysis of system behaviours. This work proposes a method and tools to validate the design of UAV co-operative systems based on co-simulation and formal verification. The method uses the Prototype Verification System, an interactive theorem prover based on a higher-order logic language, and the Functional Mock-up Interface, a widely accepted standard for co-simulation. In this paper, results on the co-simulation and proofs of safety requirements of a representative co-ordination algorithm are shown and discussed in a scenario where quadcopters are deployed and perform space-coverage operations.
Density-Based Dynamically Self-Parameterized Clustering for Material Inspection
Authors: Radha P , Selvakumar N , Raja Sekar J , Johnsonselva J V
Published: September 2021

The ultrasonic based nondestructive testing (NDT) is the common technique used to perform material testing using ultrasonic signals. These signals are difficult to interpret and the examiner has to focus on every sampling signal to observe the changes in characteristics of signals. The core target points of the proposed work are used to identify the size and position of the defects as fast as possible. For that, an unsupervised machine learning approach is proposed to analyze defects such as shrinkage, porosity, crack, discontinuity, lack of fusion, lack of penetration and overlap. This would be helpful in the domain of material science and knowledge mining to study the structural integrity of metals during the manufacturing process and can be applied in automobile industries to increase the quality of manufactured parts. The proposed work incorporates a novel Density-Based Dynamically Self-Parameterized Clustering for Material Inspection (DBDSPCMI) method to effectively predict and identify the defect size and its position. The proposed method proves to be effective with an accuracy of 97.04% in measuring defect size and 95% in identifying defect position.
Reliability Evaluation of Clustered Faults for Regular Networks Under the Probabilistic Diagnosis Model
Authors: Li Xiao-Yan , Zhang Yufang , Liu Ximeng , Wang Xiangke , Cheng Hongju
Published: September 2021

As the scale of the system expands, processor failures are inevitable. Fault diagnosis has great significance in analyzing the reliability of multiprocessing systems. Probabilistic fault diagnosis is a method that attempts to diagnose nodes correctly with high probability. In this paper, we extend the threshold $t \leq 2$ to threshold $t=3$ for regular networks based on probabilistic diagnosis algorithm and determine the status of a cluster of nodes by analyzing the local performance. Moreover, we evaluate the global performance based on the Poisson distribution and the Binomial distribution and show that the achievement in terms of correctness demonstrates a good performance. Finally, we employ the probabilistic diagnosis scheme to explore some well-known networks, including complete cubic networks, dual cubes and hierarchical hypercubes as well.
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market
Authors: Deckers Marie , Van Braeckel Julien , Vanneste Kevin , Deforce Dieter , Fraiture Marie-Alice , Roosens Nancy h.c
Published: September 2021

Following the European Commission No. 1332/2008 regulation and the consequent necessity of a scientific evaluation of food enzymes (FEs) for their approval for sale on the European Union market, many FE dossiers have been submitted to the European Commission and various documents currently co-exist. In order to centralize all relevant information in one structured location that is easily accessible to support enforcement laboratories and the competent authorities, we developed a web application, called Food Enzyme Database (FEDA). FEDA allows searching and collection of information originating from many different sources in one centralized portal. Queries can be performed using key information types, which include information on the producing company, production source (strain type, genetically modified microorganism status), type of enzyme protein and evaluation status with employed evaluation criteria. The database contains all current publicly available information. Centralizing all information coupled with intuitive searching functionality also allows the generation of general statistics regarding the current market situation. FEDA is open access and is freely available at the following location: https://feda.sciensano.be.

Database URL : https://feda.sciensano.be
Fibrosis and MAGNIFI-CD Activity Index at Magnetic Resonance Imaging to Predict Treatment Outcome in Perianal Fistulizing Crohn’s Disease Patients
Authors: van Rijn Kyra L , Meima-van Praag Elise M , Bossuyt Patrick M , D’Haens Geert R , Gecse Krisztina B , Horsthuis Karin , Snijder Harmanna J , Tielbeek Jeroen A W , Buskens Christianne J , Stoker Jaap
Published: September 2021

Background and Aims

Characteristic magnetic resonance imaging [MRI] features associated with long-term perianal fistula closure are still being discussed. This study evaluated the predictive value of degree of fibrosis and disease activity (MAGNIFI-CD index) at MRI for long-term clinical closure of Crohn’s perianal fistulas.

Methods

Crohn’s disease [CD] patients treated with surgical closure following anti-tumour necrosis factor [anti-TNF] induction or anti-TNF alone for high perianal fistulas as part of a patient preference randomized controlled trial [PISA-II] between 2013 and 2020 with a post-treatment MRI and long-term clinical follow-up data were retrospectively included. Two radiologists scored the degree of fibrosis and MAGNIFI-CD index at pre- and post-treatment MRI. The accuracy of post-treatment MRI findings in predicting long-term clinical closure [12 months after the MRI] was evaluated using receiver operating characteristics [ROC] analysis.

Results

Fifty patients were included: 31 female, median age 33 years (interquartile range [IQR] 26–45). Fourteen patients showed a 100% fibrotic fistula at post-treatment MRI, all of which had long-term clinical closure. Median MAGNIFI-CD index at post-treatment MRI was 0 [IQR 0–5] in 25 patients with long-term clinical closure and 16 [IQR 10-20] in 25 patients without. ROC analysis showed an area under the curve of 0.90 (95% confidence interval [CI] 0.82–0.99) for degree of fibrosis and 0.95 [95% CI 0.89–1.00] for the MAGNIFI-CD index, with a Youden cut-off point of 6 [91% specificity, 87% sensitivity].

Conclusions

Degree of fibrosis and MAGNIFI-CD index at post-treatment MRI are accurate in predicting long-term clinical closure and seem valuable in follow-up of perianal CD. A completely fibrotic tract at MRI is a robust indicator for long-term fistula closure.

EudraCT

2013-002932-25 and 2018-002064-15
Defining Transabdominal Intestinal Ultrasound Treatment Response and Remission in Inflammatory Bowel Disease: Systematic Review and Expert Consensus Statement
Authors: Ilvemark Johan F K F , Hansen Tawnya , Goodsall Thomas M , Seidelin Jakob B , Al- Farhan Heba , Allocca Mariangela , Begun Jakob , Bryant Robert V , Carter Dan , Christensen Britt , Dubinsky Marla C , Gecse Krisztina B , Kucharzik Torsten , Lu Cathy , Maaser Christian , Maconi Giovanni , Nylund Kim , Palmela Carolina , Wilson Stephanie R , Novak Kerri , Wilkens Rune
Published: September 2021

Background and Aims

No consensus exists on defining intestinal ultrasound response, transmural healing, or transmural remission in inflammatory bowel disease, nor clear guidance for optimal timing of assessment during treatment. This systematic review and expert consensus study aimed to define such recommendations, along with key parameters included in response reporting.

Methods

Electronic databases were searched from inception to July 26, 2021, using pre-defined terms. Studies were eligible if at least two intestinal ultrasound [IUS] assessments at different time points during treatment were reported, along with an appropriate reference standard. The QUADAS-2 tool was used to examine study-level risk of bias. An international panel of experts [n = 18] rated an initial 196 statements [RAND/UCLA process, scale 1–9]. Two videoconferences were conducted, resulting in additional ratings of 149 and 13 statements, respectively.

Results

Out of 5826 records, 31 full-text articles, 16 abstracts, and one research letter were included; 83% [40/48] of included studies showed a low concern of applicability, and 96% [46/48] had a high risk of bias. A consensus was reached on 41 statements, with clear definitions of IUS treatment response, transmural healing, transmural remission, timing of assessment, and general considerations when using intestinal ultrasound in inflammatory bowel disease.

Conclusions

Response criteria and time points of response assessment varied between studies, complicating direct comparison of parameter changes and their relation to treatment outcomes. To ensure a unified approach in routine care and clinical trials, we provide recommendations and definitions for key parameters for intestinal ultrasound response, to incorporate into future prospective studies.
Safety of very high-power short-duration radiofrequency ablation for pulmonary vein isolation: a two-centre report with emphasis on silent oesophageal injury
Authors: Halbfass Philipp , Wielandts Jean-Yves , Knecht Sébastien , Le Polain de Waroux Jean-Benoît , Tavernier René , De Wilde Vincent , Sonne Kai , Nentwich Karin , Ene Elena , Berkovitz Artur , Mueller Julian , Lehmkuhl Lukas , Reichart Amelie , Lüsebrink Ulrich , Duytschaever Mattias , Deneke Thomas
Published: September 2021

Aims

Very high-power short-duration (vHPSD) via temperature-controlled ablation (TCA) is a new modality to perform radiofrequency pulmonary vein isolation (PVI), conceivably at the cost of a narrower safety margin towards the oesophagus. In this two-centre trial, we aimed to determine the safety of vHPSD-based PVI with specific emphasis on silent oesophageal injury.

Methods and results

Ninety consecutive patients with atrial fibrillation (AF) underwent vHPSD-PVI (90 W, 3–4 s, TCA) using the QDOT MICRO catheter, in conjunction with the nGEN (Bad Neustadt, n = 45) or nMARQ generator (Bruges, n = 45). All patients underwent post-ablation oesophageal endoscopy. Procedural parameters and complications were recorded. A subgroup of 21 patients from Bad Neustadt underwent cerebral magnetic resonance imaging (cMRI) to detect silent cerebral events (SCEs). Mean age was 67 ± 9 years, 59% patients were male, and 66% patients had paroxysmal AF. Pulmonary vein isolation was obtained in all cases after 96 ± 29 min. No steam pop, cardiac tamponade, stroke, or fistula was reported. None of the 90 patients demonstrated oesophageal ulceration (0%). Charring was not observed in the nMARQ cohort (0% vs. 11% in the nGEN group). In 5 out of 21 patients (24%), cMRI demonstrated SCE (exclusively nGEN cohort).

Conclusion

Temperature-controlled vHPSD catheter ablation allows straightforward PVI without evidence of oesophageal ulcerations or symptomatic complications. Catheter tip charring and silent cerebral lesions when using the nGEN generator have led to further modification.
The nutrient-improvement bacteria selected byAgave lechuguillaT. and their role in the rhizosphere community
Authors: Medina-de la Rosa Guadalupe , García-Oliva Felipe , Alpuche-Solís Ángel G , Ovando-Vázquez Cesaré , López-Lozano Nguyen E
Published: September 2021

Agave lechuguilla has one of the widest distributions among other agave species in the Chihuahuan Desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to their association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus-mineralizing bacteria in two subregions of the Chihuahuan Desert. We found that mature plants of lechuguilla stimulated the activity and abundance of nutrient-improvement rhizobacteria, and these soil samples had a higher content of total organic carbon, ammonium (NH4) and nitrite + nitrate (NO2+NO3). Nutrient availability seems to be an essential driver of the bacterial community's structure since the genera with more connections (hubs) were those with known mechanisms related to the availability of nutrients, such as env. OPS17 (Bacteroidetes), Gemmatimonadaceae uncultured, S0134terrestrial group, BD211terrestrial group (Gemmatimonadetes), Chthoniobacteracea and Candidatus Udaeobacter (Verrucomicrobia). This work shows that the late growth stages of lechuguilla recruit beneficial bacteria that favor its establishment and tolerance to harsh conditions of the arid lands.
Plant–microbe–microbe interactions influence the faba bean nodule colonization by diverse endophytic bacteria
Authors: Youseif Sameh H , Abd El-Megeed Fayrouz H , Abdelaal Ali S , Ageez Amr , Martínez-Romero Esperanza
Published: September 2021

Legume root nodules harbor rhizobia and other non-nodulating endophytes known as nodule-associated bacteria (NAB) whose role in the legume symbiosis is still unknown. We analysed the genetic diversity of 34 NAB isolates obtained from the root nodules of faba bean grown under various soil conditions in Egypt using 16S rRNA and concatenated sequences of three housekeeping genes. All isolates were identified as members of the family Enterobacteriaceae belonging to the genera Klebsiella, Enterobacter and Raoultella. We identified nine enterobacterial genospecies, most of which have not been previously reported as NAB. All isolated strains harbored nifH gene sequences and most of them possessed plant growth-promoting (PGP) traits. Upon co-inoculation with an N2 fixing rhizobium (Rlv NGB-FR128), two strains (Enterobacter sichanensis NGB-FR97 and Klebsiella variicola NGB-FR116) significantly increased nodulation, growth and N-uptake of faba bean plants over the single treatments or the uninoculated control. The presence of these enterobacteria in nodules was significantly affected by the host plant genotype, symbiotic rhizobium genotype and endophyte genotype, indicating that the nodule colonization process is regulated by plant–microbe–microbe interactions. This study emphasizes the importance of nodule-associated enterobacteria and suggests their potential role in improving the effectiveness of rhizobial inoculants.
Comparative Genomics Reveals Recent Adaptive Evolution in Himalayan Giant Honeybee Apis laboriosa
Authors: Lin Dan , Lan Lan , Zheng Tingting , Shi Peng , Xu Jinshan , Li Jun
Published: September 2021

The Himalayan giant honeybee, Apis laboriosa, is the largest individual honeybee with major ecological and economic importance in high-latitude environments. However, our understanding of its environmental adaptations is circumscribed by the paucity of genomic data for this species. Here, we provide a draft genome of wild A. laboriosa, along with a comparison to its closely related species, Apis dorsata. The draft genome of A. laboriosa based on the de novo assembly is 226.1 Mbp in length with a scaffold N50 size of 3.34 Mbp, a GC content of 32.2%, a repeat content of 6.86%, and a gene family number of 8,404. Comparative genomics analysis revealed that the genes in A. laboriosa genome have undergone stronger positive selection (2.5 times more genes) and more recent duplication/loss events (6.1 times more events) than those in the A. dorsata genome. Our study implies the potential molecular mechanisms underlying the high-altitude adaptation of A. laboriosa and will catalyze future comparative studies to understand the environmental adaptation of modern honeybees.
Regional lithospheric deformation beneath the East Qinling-Dabie orogenic belt based on ambient noise tomography
Authors: Wei Yu , Zhang Shuangxi , Li Mengkui , Wu Tengfei , Hua Yujin , Zhang Yu , Cai Jianfeng
Published: September 2021

The Qinling–Dabie orogenic belt, which contain the arc-shaped Dabbashan orocline and is the world's largest belt of HP/UHP metamorphic rocks, formed by a long-term complex amalgamation process between the North China Block and the Yangtze Block. To understand the collision processes and tectonic evolution, we constructed a 3-D S-wave velocity model from the surface to a depth of ∼120 km in the eastern Qinling-Dabie orogenic belt and its adjacent region by inverting 5–70 s phase velocity dispersion data of Rayleigh waves extracted from ambient noise data. Our 3-D model reveals low velocities in the middle–lower crust and high velocities in the upper mantle beneath the orogenic belt, suggesting the delamination of the lower crust. Our results support a two-stage exhumation model for the HP/UHP rocks in the study area. First-stage exhumation was caused by the slab breaking away from the subducted Yangtze Block during the Early–Middle Triassic. Partial melting of the lithospheric mantle caused by slab breakoff-related asthenospheric upwelling weakened the lithospheric mantle beneath the orogenic belt, and continued convergence of the two continental blocks led to further thickening of the lower crust. Such processes promoted lower-crust delamination, which triggered the second-stage exhumation of the HP/UHP rocks. In the Dabbashan orocline, two deep-rooted high-velocity domes, that is, Hannan–Micang and Shennong–Huangling domes, acted as a pair of indenters during the formation stage. High-velocity lower crust was observed beneath the Dabbashan orocline. In addition, our 3-D model reveals that high-velocity lithospheric mantle extends from the Sichuan Basin to the Dabbashan orocline, with a subhorizontal distribution, providing strong support for the high-velocity lower crust. We also observed the destruction of lithospheric mantle beneath the Yangtze Block; the destruction area is bounded by the North–South Gravity Lineament, suggesting that the destruction mechanism of the Yangtze Block may be similar to the North China Block.
Rayleigh-wave ellipticity in weakly heterogeneous layered media
Authors: Haney Matthew M , Tsai Victor C
Published: September 2021

We derive approximate expressions for the ellipticity (i.e. horizontal-to-vertical or vertical-to-horizontal ratio) of Rayleigh waves propagating in a layered medium. The approximation is based on the generalized energy equation for Rayleigh waves, which has been used previously to obtain perturbational results for ellipticity. For a medium with weakly heterogeneous layers, we obtain an approximation from the perturbational result by taking the background medium to be homogeneous. The generalized energy equation also requires an auxiliary function and we discuss how the various possible functions are related to the homogeneous Rayleigh-wave eigenfunction. The analysis reveals that, within the weak approximation, the product of ellipticity and squared phase velocity is linearly related to squared shear wave velocity in the subsurface. We show the accuracy of the approximation with a simple layer-over-half-space model and then demonstrate its utility in a linear inversion scheme for shear wave velocity.
Effect of cyclic loading at elevated temperatures on the magnetic susceptibility of a magnetite-bearing ore
Authors: Dudzisz Katarzyna , Walter Mario , Krumholz Ralf , Reznik Boris , Kontny Agnes
Published: September 2021

Cyclic loading at elevated temperatures occurs either naturally during tectonic or volcanic-induced earthquakes or can be human-induced due to various geological engineering activities. The aim of this study is to test if mechanical fatigue in rocks can be monitored by magnetic methods. For this purpose, the effect of cyclic-mechanical loading (150 ± 30 MPa) on the magnetic susceptibility and its anisotropy of a magnetite-bearing ore with varying temperatures (400 and 500 °C) and environment (air and vacuum) was investigated. Our study shows that magnetic susceptibility decreases significantly (up to 23 per cent) under air conditions and in vacuum (up to 4 per cent) within the first ca. 1000 cycles. Further loading does not significantly affect the magnetic susceptibility which then remains more or less constant. The decrease of susceptibility parameters is stronger at 500 °C compared to 400 °C under both experimental conditions. Magnetic susceptibility was always measured after decompression of the loaded sample at room temperature so that magnetostriction can be excluded as a reason for these changes. The higher the temperature at which samples were loaded the more pronounced is the oxidation of magnetite to haematite. The transformation of magnetite into haematite under ambient conditions is the most important mechanism influencing bulk magnetic properties. The weak changes in magnetic susceptibility after vacuum loadings are probably caused by intragranular microcracks formed on the surface of magnetite grains. These surface deformation structures are accompanied by the refinement of magnetic domains, which is observed by magnetic force microscopy. Bulk magnetic grain size modifications are also confirmed by hysteresis parameters as well as by the increasing Hopkinson peak ratios determined from magnetic susceptibility measurements over Curie point. The degree of magnetic anisotropy and shape factor only change for the air-treated samples and are therefore related to the haematite formation and not to irreversible ductile deformation in magnetite. Our experimental study shows that cyclic loading can change significantly the magnetic properties of a rock due to mineral transformation below < 1000 cycles and that the first stages of mechanical fatigue, which are a precursor of the failure of rock, are closely associated with these transformations.
Building health literacy system capacity: a framework for health literate systems
Authors: Sørensen Kristine , Levin-Zamir Diane , Duong Tuyen V , Okan Orkan , Brasil Virginia Visconde , Nutbeam Don
Published: September 2021

The human and social implications of poor health literacy are substantial and wide-ranging. Health literacy represents the personal competencies and organizational structures, resources and commitment that enable people to access, understand, appraise and use information and services in ways that promote and maintain good health. A large-scale societal improvement of health literacy will require political buy-in and a systematic approach to the development of health literacy capacity at all levels. This article builds the case for enhancing health literacy system capacity and presents a framework with eight action areas to accommodate the structural transformation needed at micro, meso and macro levels, including a health literate workforce, health literate organization, health literacy data governance, people-centred services and environments based on user engagement, health literacy leadership, health literacy investments and financial resources, health literacy-informed technology and innovation, and partnerships and inter-sectoral collaboration. Investment in the health literacy system capacity ensures an imperative and systemic effort and transformation which can be multiplied and sustained over time and is resilient towards external trends and events, rather than relying on organizational and individual behavioural change alone. Nevertheless, challenges still remain, e.g. to specify the economic benefits more in detail, develop and integrate data governance systems and go beyond healthcare to engage in health literacy system capacity within a wider societal context.
Coproduction to improve preventive health services—experiences from Germany
Authors: Abu-Omar Karim , Weissenfels Anja , Mino Eriselda , Naber Inga , Klamroth Sarah , Geidl Wolfgang , Pfeifer Klaus
Published: September 2021

Due to the beneficial impact of regular physical activity (PA) on non-communicable diseases, the number of countries integrating exercise referral schemes (ERSs) into their healthcare systems is growing. Owing to the limitations of existing PA promotion concepts in Germany’s healthcare system, efforts are currently being made towards developing a nationwide referral pathway. A research group at the Friedrich-Alexander-University Erlangen-Nürnberg is coordinating these efforts within a project funded by the Federal Ministry of Health. The aim is to develop, implement and evaluate a regional-level ERS that has the potential to be scaled up across Germany in the event of its demonstrated effectiveness. The project is based on an adapted Cooperative Planning approach requiring interaction between the academic sector and different actors of the healthcare sector. The present commentary reflects on challenges faced in the early stages of the co-production process. Besides the development of an adequate co-production methodology, it critically discusses stakeholder participation, knowledge gaps and actors’ willingness to take responsibility. In addition, although patients are represented by dedicated organizations, their perspective cannot be adequately captured using a co-production approach. Despite the joint development of an ERS, there remain important questions regarding the appropriateness of the co-production approach in a healthcare setting.