bluuebunny/crossref_metadata_2025_split huggingface dataset:
Commentary: Epistemological Positionalities
Authors: Singh Jaspal Naveel 
Published: September 2021

Abstract
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

AbstractAs 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

Abstract
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

Abstract

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.
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

Abstract

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

Abstract
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.
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

Abstract

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

AbstractUnmanned 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

AbstractThe 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.