bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways
Authors: Banerjee Shefali , Smith Cathy , Geballe Adam P , Rothenburg Stefan , Kitzman Jacob O , Brennan Greg 
Published: November 2022

Abstract
Cross-species spillover events are responsible for many of the pandemics in human history including COVID-19; however, the evolutionary mechanisms that enable these events are poorly understood. We have previously modeled this process using a chimeric vaccinia virus expressing the rhesus cytomegalovirus–derived protein kinase R (PKR) antagonist RhTRS1 in place of its native PKR antagonists: E3L and K3L (VACVΔEΔK + RhTRS1). Using this virus, we demonstrated that gene amplification of rhtrs1 occurred early during experimental evolution and was sufficient to fully rescue virus replication in partially resistant African green monkey (AGM) fibroblasts. Notably, this rapid gene amplification also allowed limited virus replication in otherwise completely non-permissive human fibroblasts, suggesting that gene amplification may act as a ‘molecular foothold’ to facilitate viral adaptation to multiple species. In this study, we demonstrate that there are multiple barriers to VACVΔEΔK + RhTRS1 replication in human cells, mediated by both PKR and ribonuclease L (RNase L). We experimentally evolved three AGM-adapted virus populations in human fibroblasts. Each population adapted to human cells bimodally, via an initial 10-fold increase in replication after only two passages followed by a second 10-fold increase in replication by passage 9. Using our Illumina-based pipeline, we found that some single nucleotide polymorphisms (SNPs) which had evolved during the prior AGM adaptation were rapidly lost, while thirteen single-base substitutions and short indels increased over time, including two SNPs unique to human foreskin fibroblast (HFF)–adapted populations. Many of these changes were associated with components of the viral RNA polymerase, although no variant was shared between all three populations. Taken together, our results demonstrate that rhtrs1 amplification was sufficient to increase viral tropism after passage in an ‘intermediate species’ and subsequently enabled the virus to adopt different, species-specific adaptive mechanisms to overcome distinct barriers to viral replication in AGM and human cells.
Changes in Etiology of Invasive Bacterial Infections in Infants Under 3 Months of Age in Korea, 2006–2020
Authors: Song Seung Ha , Lee Hoan Jong , Song Eun Song , Ahn Jong Gyun , Park Su Eun , Lee Taekjin , Cho Hye-Kyung , Lee Jina , Kim Yae-Jean , Jo Dae Sun , Kim Jong-Hyun , Kang Hyun Mi , Lee Joon Kee , Kim Chun Soo , Kim Dong Hyun , Kim Hwang Min , Choi Jae Hong , Eun Byung Wook , Kim Nam Hee , Cho Eun Young , Kim Yun-Kyung , Oh Chi Eun , Kim Kyung-Hyo , Ma Sang Hyuk , Jung Hyun Joo , Lee Kun Song , Kim Kwang Nam , Lee Hyunju , Choi Eun Hwa 
Published: November 2022

Objectives:
Invasive bacterial infection (IBI) causes a significant burden in infants. In this study, we analyzed changes in epidemiology of IBI among infants in Korea.

Methods:
A retrospective multicenter-based surveillance for IBIs in infants <3 months of age was performed during 2006–2020. Cases were classified as an early-onset disease (EOD) (0–6 days) or late-onset disease (LOD) (7–89 days). The temporal trend change in proportion of pathogens was analyzed.

Results:
Among 1545 cases, the median age was 28 days (IQR: 12, 53) and EOD accounted for 17.7%. Among pathogens, S. agalactiae (40.4%), E. coli (38.5%), and S. aureus (17.8%) were the most common and attributed for 96.7%. Among EOD (n = 274), S. agalactiae (45.6%), S. aureus (31.4%), E. coli (17.2%) and L. monocytogenes (2.9%) were most common. Among LOD (n = 1274), E. coli (43.1%), S. agalactiae (39.3%), S. aureus (14.9%) and S. pneumoniae (1.3%) were most common. In the trend analysis, the proportion of S. aureus (r s = −0.850, P < 0.01) decreased significantly, while that of S. agalactiae increased (r s = 0.781, P < 0.01).

Conclusion:
During 2006–2020, among IBI in infants <3 months of age, S. agalactiae, E. coli, and S. aureus were most common and an increasing trend of S. agalactiae was observed.
Enhancing bladder management for intrapartum/postpartum women at a maternity hospital in Taiwan: a best practice implementation project
Authors: Pan Wan-Lin , Chen Li-Li , Wang Chia-Hui , Mu Pei-Fan , Tsay Shwu-Feng , Gau Meei-Ling 
Published: November 2022

ABSTRACT

Introduction and aims:
Voiding dysfunction is a common perinatal condition. Appropriate bladder management and monitoring during labor and postpartum improves bladder function and reduces the incidence of infections and complications. This project aimed to promote evidence-based bladder management strategies for perinatal women at a maternity hospital in Taiwan.

Methods:
The project was implemented using the JBI framework and the JBI Practical Application of Clinical Evidence System. Implementation audits were conducted by examining nurses and intrapartum and postpartum women. Ten criteria were applied in the baseline audit, and two follow-up audits were conducted to assess actual compliance with best-practice recommendations. Through a Getting Research into Practice analysis, we identified three barriers to changing practice.

Results:
A comparison of the audit outcomes revealed that all criteria had improved by the second follow-up audit cycle. Specifically, the compliance rate increased from 37% and 50% to 100% for criteria 1 and 2, respectively; from 0% to 100% for criteria 3, 5, and 10; and from 7%, 28%, 50%, and 17% to 100%, 100%, 97%, and 100% for criteria 4, 6, 8, and 9, respectively. Following implementation, the frequency of intrapartum intermittent catheterization (53.44–38.30%) and the postpartum incidence of urinary retention (9.09–8.51%) decreased. The time to first voiding after vaginal delivery and between the first and the second voiding decreased from 5.51 and 4.01 h to 2.32 and 2.29 h, respectively.

Conclusions:
This evidence-based implementation project achieved substantial improvements in bladder management. Relational leadership theory, which integrates empowerment, purposefulness, ethical behaviors, and process orientation, underpinned the project.
Soil resistance and recovery during neotropical forest succession
Authors: van der Sande Masha T. , Powers Jennifer S. , Kuyper Thom W. , Norden Natalia , Salgado-Negret Beatriz , Silva de Almeida Jarcilene , Bongers Frans , Delgado Diego , Dent Daisy H. , Derroire Géraldine , do Espirito Santo Mario Marcos , Dupuy Juan Manuel , Fernandes Geraldo Wilson , Finegan Bryan , Gavito Mayra E. , Hernández-Stefanoni José Luis , Jakovac Catarina C. , Jones Isabel L. , das Dores Magalhães Veloso Maria , Meave Jorge A. , Mora Francisco , Muñoz Rodrigo , Pérez-Cárdenas Nathalia , Piotto Daniel , Álvarez-Dávila Esteban , Caceres-Siani Yasmani , Dalban-Pilon Coralie , Dourdain Aurélie , Du Dan V. , García Villalobos Daniel , Nunes Yule Roberta Ferreira , Sanchez-Azofeifa Arturo , Poorter Lourens 
Published: November 2022

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.
This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
Animal seed dispersal recovery during passive restoration in a forested landscape
Authors: Estrada-Villegas Sergio , Stevenson Pablo R. , López Omar , DeWalt Saara J. , Comita Liza S. , Dent Daisy H. 
Published: November 2022

Seed dispersal by animals is key for restoration of tropical forests because it maintains plant diversity and accelerates community turnover. Therefore, changes in seed dispersal during forest restoration can indicate the recovery of species interactions, and yet these changes are rarely considered in forest restoration planning. In this study, we examined shifts in the importance of different seed dispersal modes during passive restoration in a tropical chronosequence spanning more than 100 years, by modelling the proportion of trees dispersed by bats, small birds, large birds, flightless mammals and abiotic means as a function of forest age. Contrary to expectations, tree species dispersed by flightless mammals dominated after 20 years of regeneration, and tree richness and abundance dispersed by each mode mostly recovered to old growth levels between 40 and 70 years post-abandonment. Seed dispersal by small birds declined over time during regeneration, while bat dispersal played a minor role throughout all stages of succession. Results suggest that proximity to old growth forests, coupled with low hunting, explained the prevalence of seed dispersal by animals, especially by flightless mammals at this site. We suggest that aspects of seed dispersal should be monitored when restoring forest ecosystems to evaluate the reestablishment of species interactions.
This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
Restoration interventions mediate tropical tree recruitment dynamics over time
Authors: Kulikowski Andy J. , Zahawi Rakan A. , Werden Leland K. , Zhu Kai , Holl Karen D. 
Published: November 2022

Forest restoration is increasingly heralded as a global strategy to conserve biodiversity and mitigate climate change, yet long-term studies that compare the effects of different restoration strategies on tree recruit demographics are lacking. We measured tree recruit survival and growth annually in three restoration treatments—natural regeneration, applied nucleation and tree plantations—replicated at 13 sites in southern Costa Rica—and evaluated the changes over a decade. Early-successional seedlings had 14% higher survival probability in the applied nucleation than natural regeneration treatments. Early-successional sapling growth rates were initially 227% faster in natural regeneration and 127% faster in applied nucleation than plantation plots but converged across restoration treatments over time. Later-successional seedling and sapling survival were similar across treatments but later-successional sapling growth rates were 39% faster in applied nucleation than in plantation treatments. Results indicate that applied nucleation was equally or more effective in enhancing survival and growth of naturally recruited trees than the more resource-intensive plantation treatment, highlighting its promise as a restoration strategy. Finally, tree recruit dynamics changed quickly over the 10-year period, underscoring the importance of multi-year studies to compare restoration interventions and guide ambitious forest restoration efforts planned for the coming decades.
This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
The community capacity curve applied to reforestation: a framework to support success
Authors: Herbohn John , Ota Liz , Gregorio Nestor , Chazdon Robin , Fisher Robert , Baynes Jack , Applegate Grahame , Page Tony , Carias Dora , Romero Claudia , Putz Francis E. , Firn Jennifer 
Published: November 2022

Community involvement is critical for the success of many interventions designed to promote reforestation. To secure this involvement, it helps to recognize that communities are heterogenous both within and among themselves and possess diverse mixes of livelihood assets required to implement reforestation. We explore the relationship between livelihood assets and reforestation success and outline a conceptual model that we call the community capacity curve (CCC) applied to reforestation. We argue that the shape of the CCC is sigmoidal. Importantly, communities at the lower end of the CCC have limited capacity to implement reforestation projects without substantial and ongoing capacity building and other sorts of support, including through livelihood projects that improve food security and provide cash benefits. Communities at the higher part of the CCC have greater capacity to implement reforestation projects, especially projects focused on biodiversity and environmental services. The CCC can help design, implement, monitor and assess reforestation projects, select appropriate livelihood activities and types of reforestation, select communities suited to a reforestation project, guide implementation and understand projects' successes and failure. The CCC also provides a framework to engage with policy makers and funding bodies to explore the types of support for communities to reforest successfully.This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
Placenta-associated adverse pregnancy outcomes in women experiencing mild or severe hyperemesis gravidarum – a systematic review and meta-analysis
Authors: Moberg Tilda , Van der Veeken Lennart , Persad Emma , Hansson Stefan R. , Bruschettini Matteo 
Published: November 2022

AbstractBackgroundNausea and vomiting in pregnancy (NVP) affects 50-80% of pregnant women and is correlated to the level of human chorionic gonadotropin (hCG). Hyperemesis gravidarum (HG) is a severe condition, with an incidence of 0.2-1.5%, characterized by consistent nausea, vomiting, weight loss and dehydration continuing after the second trimester.AimThe aim of this systematic review was to investigate a potential correlation between NVP or HG with adverse pregnancy outcomes and hCG levels.MethodA systematic search in PubMed, Embase and CINAHL Complete was conducted. Studies on pregnant women with nausea in the first or second trimester, reporting either pregnancy outcomes or levels of hCG were included. The primary outcomes were preterm delivery (PTD), preeclampsia, miscarriage, and fetal growth restriction. Risk of bias was assessed using ROBINS-I. The overall certainty of evidence was assessed using GRADE.ResultsThe search resulted in 2023 potentially relevant studies; 23 were included. The evidence was uncertain for all outcomes, however women with HG had a tendency to have an increased risk for preeclampsia [odds ratio (OR) 1.18, 95% confidence of interval (CI) 1.03 to 1.35], PTD [OR 1.35, 95% CI 1.13 to 1.61], small for gestational age (SGA) [OR 1.24, 95% CI 1.13 to 1.35], and low birth weight (LBW) [OR 1.35, 95% CI 1.26 to 1.44]. Further, a higher foetal female/male ratio was observed [OR 1.36, 95% CI 1.15 to 1.60]. Meta-analyses were not performed for women with NVP; however, most of these studies indicated that women with NVP have a lower risk for PTD and LBW and a higher risk for SGA, and a higher fetal female/male ratio.ConclusionThere may be an increased risk in women with HG and a decreased risk in women with NVP for adverse placenta-associated pregnancy outcomes, however the evidence is very uncertain.PROSPERO:CRD42021281218
Association between maternal breastmilk microbiota composition and rotavirus vaccine response in African, Asian, and European infants: a prospective cohort study
Authors: Mandolo Jonathan , Parker Edward P. K. , Bronowski Christina , Sindhu Kulandaipalayam Natarajan C. , Darby Alistair C. , Cunliffe Nigel A. , Kang Gagandeep , Iturriza-Gómara Miren , Kamng’ona Arox W. , Jere Khuzwayo C. 
Published: November 2022

ABSTRACTBackgroundMaternal breastmilk is a source of pre- and pro-biotics that impact neonatal gut microbiota colonisation. Since oral rotavirus vaccines (ORVs) are administered at a time when infants are often breastfed, breastmilk microbiota composition may have a direct or indirect influence on vaccine take and immunogenicity.MethodsUsing standardised methods across sites, we compared breastmilk microbiota composition in relation to geographic location and ORV response in cohorts prospectively followed up from birth to 18 weeks of age in India (n= 307), Malawi (n= 119), and the UK (n= 60).ResultsBreastmilk microbiota diversity was higher in India and Malawi than the UK across three longitudinal samples spanning weeks of life 1 to 13. Dominant taxa such asStreptococcusandStaphylococcuswere consistent across cohorts; however, significant geographic differences were observed in the prevalence and abundance of common and rare genera throughout follow-up. No significant associations were identified between breastmilk microbiota composition and ORV outcomes including seroconversion, post-dose 1 vaccine shedding, and/or post-vaccination rotavirus-specific IgA level.ConclusionsOur findings suggest that breastmilk microbiota composition may not be a key factor in shaping trends in ORV response within or between countries.
Association of diagnosis delay and disease activity with burden on Daily life in 4150 European patients with Systemic Lupus Erythematosus
Authors: Cornet Alain , Andersen Jeanette , Marchiori Francesca , Rubio Blanca , Mertz Philippe , Arnaud Laurent ,   the patient association Lupus Europe
Published: November 2022

ABSTRACTObjectiveDespite significant improvements in diagnosis delay and treatment strategies, the burden of Systemic Lupus Erythematosus (SLE) remains high. The objective of the study was to assess the association between diagnosis delay, disease activity and burden on daily life (BoDL) in a large sample of European patients with SLE.MethodsIn May 2020, Lupus Europe, the European umbrella patient association for SLE, conducted a multilingual anonymous online cross-sectional study to individuals with a self-reported physician’s diagnosis of SLE living in Europe. The BoDL score was computed using 1 to 5 Likert scales on 5 domains (mobility, anxiety/depression, self-care, daily activities and pain/discomfort) and the sum was rescaled on a 0 (minimum Burden on daily life) to 100 (maximum BoDL) scale. Comparisons between independent groups were made using the Mann-Whitney test for continuous outcomes and the Chi-2 test (or Fisher’s exact test) for quantitative data.ResultsData of 4,150 SLE patients from 35 European countries were analysed. Those with a diagnosis of SLE within 2 years of first symptoms had significantly lower mean BoDL scores than those diagnosed after 5 years (33.6 versus 44.0, p<0.001). The BoDL score was better in SLE patients feeling that their lupus had been under control during the last 3 months versus the others (34.0% versus 47.6%, p<0.001).ConclusionThis large international study highlights the association between diagnosis delay and self-perceived disease activity with the burden of the disease on the daily life of people living with SLE. Healthcare pathways, which may accelerate diagnosis and optimize therapeutic management, are necessary to improve patients’ outcomes in SLE.
Exploration of wastewater surveillance for Monkeypox virus
Authors: Mejia Edgard M , Hizon Nikho A , Dueck Codey E , Lidder Ravinder , Daigle Jade , Wonitowy Quinn , Medina Nestor G , Mohammed Umar P , Cox Graham W , Safronetz David , Hagan Mable , Strong Jim , Nichani Anil , Mulvey Michael R , Mangat Chand S 
Published: November 2022

AbstractThe sudden emergence and spread of Monkeypox in non-endemic parts of the world is currently not well understood. Infections are often mis-diagnosed and surveillance strategies are scarce. Wastewater-based surveillance (WBS) of human Monkeypox virus (MPXV) can help supplement our current clinical surveillance and mitigation efforts. WBS has shown to be an effective tool in monitoring the spread of other infectious pathogens, such as SARS-CoV-2 and its variants, and has helped guide public health actions. In this study, we describe how WBS can be used to detect MPXV in wastewater. We conducted WBS for MPXV in 22 wastewater treatment plants (WWTPs) over a period of 14 weeks. Nucleic acids were extracted using the MagAttract PowerMicrobiome DNA/RNA extraction kit. Three real-time qPCR assays were assessed for the detection of MPXV in wastewater. These included the G2R assays (G2R_WA and G2R_G) developed by the Centers for Disease Control and Prevention (CDC) in 2010, as well as an in-house-developed assay (G2R_NML). The G2R_G (generic) assay was designed to detect both the Congo and West African clades (re-named to Clades one and two, respectively) of viruses while the G2R_WA assay was designed to detect the West African clade (Clade one). The G2R_NML assay was designed using reference genomes of the 2022 MPXV outbreak. Our results show that all three assays have similar limits of detection and are all able to detect the presence of MPXV in wastewater. Following detection through real time qPCR, Sanger sequencing was performed on the resulting amplicon products, with the assembled contigs then undergoing analysis using nucleotide Basic Local Alignment Search Tool (BLAST). Due in part to the longer amplicon size of the G2R_NML assay, a significantly greater number of positive detections were identified as originating from MPXV compared to the CDC G2R assays. The ability to detect trace amounts of MPXV in wastewater as well as obtain Sanger sequence confirmation, has allowed for the successful surveillance of this virus in wastewater.