bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved land monitoring to assess large-scale tree plantation expansion and trajectories in Northern Mozambique
Authors: Bey Adia , Meyfroidt Patrick 
Published: September 2021

Abstract
Tree planting has the potential to address a wide range of environmental and economic challenges. However, planting initiatives can also do more harm than good. Characteristics such as land tenure and land use before conversion to tree plantation are key to assessing the potential risks and benefits of tree planting initiatives. Here, we present a new remote sensing technique to distinguish tree plantations from natural forests, measure plantation expansion, and specify pre-conversion land use. Focusing on Northern Mozambique, we found that 70% of large-scale tree plantation expansion between 2001–2017 occurred on cropland, while the remainder occurred on natural forest and grasslands. We also compare our remote sensing-derived plantation data with government cadastral records. Over 40% of plantation expansion occurred on lands not legally designated for this land use. Where tree plantation expansion is intended to mitigate climate change mitigation and boost rural economies, improved land monitoring techniques are needed to support assessment of the climate- and socio-economic impacts of expansion. The remote sensing technique presented here can support such assessments, increase transparency and facilitate adaptive management.
Immigration, Passing, and the Racial Other in Neo-Victorian Imperialist Fiction: The Case of Carnival Row (2019–)
Authors: Pedro Dina 
Published: September 2021

Abstract
In this article, I provide a close reading of Season 1 of the neo-Victorian TV series Carnival Row as both an ambivalent postcolonial and neo-passing narrative. I first draw on previous criticism on postcolonial neo-Victorianism and turn-of-the-century American passing novels in order to analyze Carnival Row’s contradictory revision of imperial London through its re-imagining in a fictional city named The Burgue. I then explore the conflicting ways in which the series tackles (neo-)imperialism and colonialization, as it simultaneously criticizes and reproduces imperial ideologies and stereotypes of the racial Other. Finally, I argue that Carnival Row seems to offer a new take on American passing novels by allowing Philo, the mixed-race male protagonist, to embrace his biracial nature without meeting a tragic fate at the end of Season 1. Nonetheless, by choosing a White actor (Orlando Bloom) to play the role of the passer, the series culturally appropriates a form of Black oppression for the entertainment of a White audience. Thus, despite the series’ well-intentioned attempts to criticize (neo-)imperial, racist, and xenophobic practices, it ultimately perpetuates—rather than subverts—those very same ideologies.
Utility of white matter disease and atrophy on routinely acquired brain imaging for prediction of long-term delirium risk: population-based cohort study
Authors: Pendlebury Sarah T , Thomson Ross J , Welch Sarah J V , Kuker Wilhelm , Rothwell Peter M ,   for the Oxford Vascular Study
Published: September 2021

Abstract

Background
brain imaging done as part of standard care may have clinical utility beyond its immediate indication. Using delirium as an exemplar, we determined the predictive value of baseline brain imaging variables [white matter changes (WMC) and atrophy] for delirium risk on long-term follow-up after transient ischemic attack (TIA)/stroke in a population-based cohort study.

Methods
surviving TIA/stroke participants in the Oxford Vascular Study (OXVASC) were assessed prospectively for delirium during all hospitalisations over 6 months (2013–14). Using logistic regression, independent associations were determined between baseline OXVASC computed tomography or magnetic resonance brain imaging measures of WMC and cerebral atrophy (none/mild versus moderate/severe) and delirium adjusted for age, sex, baseline stroke severity, depression, illness severity and pre-admission cognition.

Results
among 1,565 TIA/stroke survivors with 194 hospital admissions (158 patients, mean/standard deviation age at admission = 79.2/11.5 years), delirium occurred in 59 (37%). WMC and atrophy on baseline imaging were associated with delirium [odds ratio (OR) = 3.41, 1.21–5.85, P = 0.001 and OR = 2.50, 1.23–5.08, P = 0.01 (unadjusted) and OR = 2.67, 1.21–5.85, P = 0.02 and OR = 2.18, 1.00–4.73, P = 0.05 (adjusted age and sex)]. Associations were strengthened when analyses were restricted to patients hospitalised within 5 years of baseline brain imaging [OR = 6.04, 2.39–15.24, P &lt; 0.0001 and OR = 4.64, 1.46–14.82, P = 0.009 (unadjusted)] but only WMC remained significant after adjustment for all covariates including pre-admission cognition (OR = 4.83, 1.29–18.13, P = 0.02 for Mini-Mental State Examination and OR = 5.15, 1.26–21.09, P = 0.02 for Montreal Cognitive Assessment).

Conclusions
WMC and atrophy on brain imaging done up to 5 years earlier predicted delirium and may have clinical utility in risk stratification. Associations with WMC but not atrophy were independent of pre-admission cognitive impairment.
Is Medication Adherence Predictive of Cardiovascular Outcomes and Blood Pressure Control? The Systolic Blood Pressure Intervention Trial (SPRINT)
Authors: Glasser Stephen P , Vitolins Mara , Rocco Michael V , Still Carolyn Harmon , Cofield Stacey S , Haley William E , Goff David 
Published: September 2021

Abstract

BACKGROUND
Adherence to study medications is crucial to evaluating treatment effects in clinical trials. To assess whether in the SPRINT trial, adherence and cardiovascular outcomes are associated regardless of intervention assignment.

METHODS
This study included 9,361 participants aged ≥50 years, recruited from 102 clinics. Participants were randomized to a Standard Treatment Group (targeted systolic blood pressure [SBP] &lt;140 mm Hg) or an Intensive Treatment Group (targeted SBP &lt;120 mm Hg) and followed for incident cardiovascular events until the study was halted early for benefit. The 8-item Morisky Medication Adherence Scale (MMAS-8) was administered at baseline, and at the 12- and 48-month (or close out) visit.

RESULTS
Adjusting for covariates, there was no association between the baseline 8-item MMAS-8 and the likelihood of the primary composite endpoint, any of the secondary endpoints, or blood pressure (BP) control. Low adherence was associated with a higher body mass index, SBP, diastolic BP, and Patient Health Questionnaire, and high adherence was associated with a higher Montreal Cognitive Assessment. There was no difference in the MMAS-8 over time by treatment arm assignment. For the primary outcome (a composite of myocardial infarction, other acute coronary syndromes, stroke, heart failure, or death from cardiovascular causes), baseline odds ratios (95% confidence intervals) for the Low vs. Medium and vs. High; and, for Medium vs. High MMAS-8 were 1.02 (0.82–1.28), 1.07 (0.85–1.34), and 1.05 (0.88–1.250).

CONCLUSIONS
In SPRINT, medication adherence as measured using the MMAS-8 was not associated with outcomes or BP control.
Locus-specific expression analysis of transposable elements
Authors: Schwarz Robert , Koch Philipp , Wilbrandt Jeanne , Hoffmann Steve 
Published: September 2021

Abstract
Transposable elements (TEs) have been associated with many, frequently detrimental, biological roles. Consequently, the regulations of TEs, e.g. via DNA-methylation and histone modifications, are considered critical for maintaining genomic integrity and other functions. Still, the high-throughput study of TEs is usually limited to the family or consensus-sequence level because of alignment problems prompted by high-sequence similarities and short read lengths. To entirely comprehend the effects and reasons of TE expression, however, it is necessary to assess the TE expression at the level of individual instances. Our simulation study demonstrates that sequence similarities and short read lengths do not rule out the accurate assessment of (differential) expression of TEs at the instance-level. With only slight modifications to existing methods, TE expression analysis works surprisingly well for conventional paired-end sequencing data. We find that SalmonTE and Telescope can accurately tally a considerable amount of TE instances, allowing for differential expression recovery in model and non-model organisms.
Viola: a structural variant signature extractor with user-defined classifications
Authors: Sugita Itsuki , Matsuyama Shohei , Dobashi Hiroki , Komura Daisuke , Ishikawa Shumpei 
Published: September 2021

Abstract

Summary
Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g. cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data.

Availability and implementation
Viola is available on pip (https://pypi.org/project/Viola-SV/) and the source code is on GitHub (https://github.com/dermasugita/Viola-SV).

Supplementary information
Supplementary data are available at Bioinformatics online.
Sustaining Transmission in Different Host Species: The Emblematic Case ofSarcoptes scabiei
Authors: Browne Elizabeth , Driessen Michael M , Cross Paul C , Escobar Luis E , Foley Janet , López-Olvera Jorge R , Niedringhaus Kevin D , Rossi Luca , Carver Scott 
Published: September 2021

AbstractSome pathogens sustain transmission in multiple different host species, but how this epidemiologically important feat is achieved remains enigmatic. Sarcoptes scabiei is among the most host generalist and successful of mammalian parasites. We synthesize pathogen and host traits that mediate sustained transmission and present cases illustrating three transmission mechanisms (direct, indirect, and combined). The pathogen traits that explain the success of S. scabiei include immune response modulation, on-host movement capacity, off-host seeking behaviors, and environmental persistence. Sociality and host density appear to be key for hosts in which direct transmission dominates, whereas in solitary hosts, the use of shared environments is important for indirect transmission. In social den-using species, combined direct and indirect transmission appears likely. Empirical research rarely considers the mechanisms enabling S. scabiei to become endemic in host species—more often focusing on outbreaks. Our review may illuminate parasites’ adaptation strategies to sustain transmission through varied mechanisms across host species.
Changes in the language system as amyloid-β accumulates
Authors: Reinartz Mariska , Gabel Silvy , Schaeverbeke Jolien , Meersmans Karen , Adamczuk Katarzyna , Luckett Emma Susanne , De Meyer Steffi , Van Laere Koen , Sunaert Stefan , Dupont Patrick , Vandenberghe Rik 
Published: September 2021

Abstract
Language dysfunction is common in Alzheimer’s disease. There is increasing interest in the preclinical or asymptomatic phase of Alzheimer’s disease.
Here we examined in 35 cognitively intact older adults (age range 52–78 years at baseline, 17 male) in a longitudinal study design the association between accumulation of amyloid over a 5–6-year period, measured using PET, and functional changes in the language network measured over the same time period using task-related functional MRI. In the same participants, we also determined the association between the longitudinal functional MRI changes and a cross-sectional measure of tau load as measured with 18F-AV1451 PET.
As predicted, the principal change occurred in posterior temporal cortex. In the cortex surrounding the right superior temporal sulcus, the response amplitude during the associative-semantic versus visuo-perceptual task increased over time as amyloid load accumulated (Pcorrected = 0.008). In a whole-brain voxel-wise analysis, amyloid accumulation was also associated with a decrease in response amplitude in the left inferior frontal sulcus (Pcorrected = 0.009) and the right dorsomedial prefrontal cortex (Pcorrected = 0.005). In cognitively intact older adults, cross-sectional tau load was not associated with longitudinal changes in functional MRI response amplitude.
Our findings confirm the central role of the neocortex surrounding the posterior superior temporal sulcus as the area of predilection within the language network in the earliest stages of Alzheimer’s disease. Amyloid accumulation has an impact on cognitive brain circuitry in the asymptomatic phase of Alzheimer’s disease.
Genetic Architecture Underlying Differential Resting-state Functional Connectivity of Subregions Within the Human Visual Cortex
Authors: Zhang Cun , Cai Huanhuan , Xu Xiaotao , Li Qian , Li Xueying , Zhao Wenming , Qian Yinfeng , Zhu Jiajia , Yu Yongqiang 
Published: September 2021

Abstract
The human visual cortex is a heterogeneous entity that has multiple subregions showing substantial variability in their functions and connections. We aimed to identify genes associated with resting-state functional connectivity (rsFC) of visual subregions using transcriptome-neuroimaging spatial correlations in discovery and validation datasets. Results showed that rsFC of eight visual subregions were associated with expression measures of eight gene sets, which were specifically expressed in brain tissue and showed the strongest correlations with visual behavioral processes. Moreover, there was a significant divergence in these gene sets and their functional features between medial and lateral visual subregions. Relative to those associated with lateral subregions, more genes associated with medial subregions were found to be enriched for neuropsychiatric diseases and more diverse biological functions and pathways, and to be specifically expressed in multiple types of neurons and immune cells and during the middle and late stages of cortical development. In addition to shared behavioral processes, lateral subregion associated genes were uniquely correlated with high-order cognition. These findings of commonalities and differences in the identified rsFC-related genes and their functional features across visual subregions may improve our understanding of the functional heterogeneity of the visual cortex from the perspective of underlying genetic architecture.
Modulating Gamma Oscillations Promotes Brain Connectivity to Improve Cognitive Impairment
Authors: Liu Chunyan , Han Tao , Xu Zhexue , Liu Jianghong , Zhang Mo , Du Jialin , Zhou Qilin , Duan Yiran , Li Yuanyuan , Wang Jiaojian , Cui Dehua , Wang Yuping 
Published: September 2021

AbstractDementia causes a substantial global economic burden, but effective treatment is lacking. Recently, studies have revealed that gamma-band waves of electrical brain activity, particularly 40 Hz oscillations, are closely associated with high-order cognitive functions and can activate microglia to clear amyloid-β deposition. Here, we found that compared with sham stimulation, applying 40-Hz high-frequency repetitive transcranial magnetic stimulation (rTMS) over the bilateral angular gyrus in patients with probable Alzheimer’s disease (AD; n = 37) resulted in up to 8 weeks of significantly improved cognitive function. Power spectral density analysis of the resting-state electroencephalography (EEG) demonstrated that 40-Hz rTMS modulated gamma-band oscillations in the left posterior temporoparietal region. Further testing with magnetic resonance imaging and TMS-EEG revealed the following: 40-Hz rTMS 1) prevented gray matter volume loss, 2) enhanced local functional integration within bilateral angular gyrus, as well as global functional integration in bilateral angular gyrus and the left middle frontal gyrus, 3) strengthened information flow from the left posterior temporoparietal region to the frontal areas and strengthened the dynamic connectivity between anterior and posterior brain regions. These findings demonstrate that modulating gamma-band oscillations effectively improves cognitive function in patients with probable AD by promoting local, long-range, and dynamic connectivity within the brain.
An Evaluation of Hepatitis E Virus Molecular Typing Methods
Authors: Baylis Sally A , Adlhoch Cornelia , Childs Liam ,   and the HEV Sequencing Study Group, Stühler Anett , Karlsson Marie , Molier Michel , Suin Vanessa , Lamoral Sophie , Nasheri Neda , Harlow Jennifer , Rešetnjak Irina , Abravanel Florence , Lhomme Sebastien , Izopet Jacques , Pavio Nicole , Pellerin Marie , Eiden Martin , Boettcher Birke , Kaiser Marco , Schilling-Loeffler Katja , Johne Reimar , Schwarz Tatjana , Corman Victor M , Wenzel Jürgen J , Klein Jasmin , Bennett Charlene , DeGascun Cillian , Dean Jonathan , Ciccaglione Anna Rita , Villano Umbertina , Bruni Roberto , Di Bartolo Ilaria , De Sabato Luca , La Rosa Giuseppina , Ferraro Giusy Bonanno , Mancini Pamela , Suffredini Elisabetta , Garbuglia Anna Rosa , Boxman Ingeborg , Dirks René , Zwartkruis-Nahuis Ans , Hogema Boris , de Sousa Rita , Velebit Branko , Avellón Ana , Sánchez Gloria , Cuevas-Ferrando Enric , Norder Heléne , Bachofen Claudia , Vonlanthen Isabelle , Kubacki Jakub , Lacher David , Mammel Mark , Kulka Michael 
Published: September 2021

Abstract

Background
Hepatitis E virus (HEV) is a major cause of acute viral hepatitis. Better understanding of HEV subtypes involved in hepatitis E infections is essential. Investigation of sources and routes of transmission and the identification of potential clusters/outbreaks rely upon molecular typing of viral strains. A study was carried out to evaluate the ability of laboratories to undertake molecular typing with genotype and subtype determination.

Methods
A blinded panel of 11 different Orthohepevirus A strains was distributed to 28 laboratories performing HEV sequence analysis. Laboratories used their routine HEV sequencing and genotyping methods.

Results
Results were returned by 25 laboratories. Overall, 93% samples were assigned to the correct genotype and 81% were assigned to the correct subtype. Fragments amplified for typing ranged in size and the sequencing assays targeted both the structural and non-structural protein-coding regions. There was good agreement between the reported sequences where methods targeted overlapping fragments. In some cases, incorrect genotypes/subtypes were reported, including those not contained in the panel, and in one case, a genotype was reported for a blinded control sample containing Zika virus; collectively these data indicate contamination problems.

Conclusions
In general, identification of genotypes was good; however, in a small number of cases, there was a failure to generate sequences from some of the samples. There was generally broad agreement between the use of online typing tools such as the one provided by HEVnet and curated lists of published HEV reference sequences; however, going forward harmonization between these resources is essential.
An Event-B-Based Approach to Model and Verify Behaviors for Component-Based Applications
Authors: Mammar Amel , Hamel Lazhar , Graiet Mohamed 
Published: September 2021

Abstract
Many disciplines have adopted component-based principles to avail themselves of the many advantages they bring, especially component reusability. In a short time, the component-based architecture became a renown branch in the IT world and the center of interest of many researchers. Much work has been conducted in this context for the verification of component-based applications (CBAs). However, the main focus has been on the structural aspect of such compositions, while the behavioral aspect has seldom been dealt with. In this paper, our goal is to close this gap and propose a formal approach to verify the behavioral correctness of CBAs. We first define a set of requirements to be satisfied by the structure and the behavior of a CBA, represented by a set of interactions that may occur between their components. Then, we build a formal Event-B model to represent these requirements in a rigorous and non-ambiguous way. The use of the Event-B refinement technique allows us to master the complexity of CBAs by introducing their elements in an incremental manner. The correctness of the development is ensured by establishing a set of proof obligations, under the Rodin platform, and also by animating it with the ProB animator/model checker. The approach is illustrated by a running example.
A model of indirect contagion based on a news similarity network
Authors: Cajueiro Daniel O , Bastos Saulo B , Pereira Camila C , Andrade Roberto F S 
Published: September 2021

AbstractOur objective is to model indirect contagion among companies. We use pieces of news about companies to measure the similarities between them. We assume that two companies are similar if we may associate a story about one company with the story about another company and vice-versa. First, after statistically eliminating arbitrary similarities between companies, we introduce a network based on the news similarities. Second, we evaluate a vector of stationary probabilities associated with the process of contagion that takes place in the network and we use these pieces of information to define the notion of centrality. Third, we use this vector of stationary probabilities to build an associated graph that reveals the most important paths of information contagion. Finally, we build a model of indirect contagion and evaluate the size of the information avalanches that take place in the similarity network.
Populations size estimations using SS-PSE among MSM in four European cities: how many MSM are living with HIV?
Authors: Johnston Lisa Grazina , McLaughlin Katherine R , Gios Lorenzo , Cordioli Maddalena , Staneková Danica Valkovičová , Blondeel Karel , Toskin Igor , Mirandola Massimo ,   for The SIALON II Network*
Published: September 2021

Abstract

Background
Although men who have sex with men (MSM) are considered at high risk for transmission of sexually transmitted infections, including HIV, there are few studies estimating the population size of MSM in Europe. We used network data from a survey of MSM in four cities to perform successive sampling–population size estimations (SS-PSE) to estimate MSM population sizes.

Methods
Data were collected in 2013–14 in Bratislava, Bucharest, Verona and Vilnius using respondent-driven sampling (RDS). SS-PSE uses a Bayesian framework to approximate the RDS sampling structure via a successive sampling model and uses the selection order of the sample to provide information about the distribution of network sizes over the population members of MSM.

Results
We estimate roughly 4600 MSM in Bratislava, 25 300 MSM in Bucharest, 7200 in Verona and 2900 in Vilnius. This represents 2.9% of the estimated adult male population in Bratislava, 2.3% in Bucharest, 2.7% in Verona and 1.5% in Vilnius. The number of MSM living with HIV would roughly be 200 in Bratislava, 4554 in Bucharest, 690 in Verona and 100 in Vilnius.

Conclusions
Benefits of this method are that no additional information from an RDS survey needs to be collected, that the sizes can be calculated ex post facto a survey and that there is a software programme that can run the SS-PSE models. However, this method relies on having reliable priors. Although many countries are estimating the sizes of their vulnerable populations, European countries have yet to incorporate similar and novel methods.