bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infectious complications and optimising infection prevention for children with cochlear implants
Authors: Davidson Lucy , Foley David A , Clifford Patricia , Blyth Christopher C , Bowen Asha C , Hazelton Briony , Kuthubutheen Jafri , McLeod Charlie , Rodrigues Stephen , Tay Siu Min , Campbell Anita J 
Published: February 2022

AimTo describe the clinical epidemiology of children receiving cochlear implants, as well as the management and outcomes of cochlear implant infections and adherence to infection prevention measures.MethodsA retrospective observational study was conducted in children ≤18 years who received cochlear implants in Western Australia's tertiary paediatric hospital. Information was obtained from medical and laboratory records regarding demographics, indication for implant, implant infection and preoperative Staphylococcus aureus screening/decolonisation. Immunisation history was examined using the Australian Immunisation Register.ResultsOverall, 118 children received cochlear implants, with 158 devices inserted (599 cochlear implant insertion‐years). An implant infection rate of 3.8% (6/158) was identified during the study period (four pneumococcal and two community‐acquired methicillin resistant S. aureus infections). All required surgical management, with an overall median duration of antibiotic therapy of 37 days (interquartile range (IQR) 29–48) and median length of stay of 8 days (IQR 8–9.5). All devices were retained and there were no relapses or deaths. Half of the children who developed cochlear implant infections (50%, 3/6) were up‐to‐date with additional pneumococcal vaccinations and no children (0%, 0/118) received S. aureus screening/decolonisation before implant insertion.ConclusionsFavourable outcomes were achieved with cochlear implant retention; however, the treatment was burdensome for families. We demonstrate significant scope to improve adherence to existing infection prevention strategies and provide direction for optimising preventative measures in the future. These include ensuring parental education, additional pneumococcal vaccinations and S. aureus decolonisation which are delivered as an infection prevention bundle to the growing population of infants receiving cochlear implants.
Tax competition and phantom FDI
Authors: Pulina Giuseppe , Zanaj Skerdilajda 
Published: February 2022

AbstractOffshore financial centers are almost never the final destination of the foreign direct investments (FDI) they receive. A large portion of these investments are phantom FDI, which ultimately flow to third countries or return back to the source country in a process called round‐tripping. This paper develops a model in which onshore countries compete internationally with tax instruments to attract capital from abroad, in the presence of an offshore financial center that encourages phantom FDI. We show that the presence of offshore financial centers is beneficial to technologically advanced countries, whereas it is detrimental to others. Finally, we use this framework to analyze the effectiveness of Controlled Foreign Company (CFC) rules against profit shifting recently implemented in Europe and the associated loss of tax base.
Cytolysin A-mediated protein exportation efficiency and its role in enhancing the fitness of live recombinant Salmonella Typhi vaccine strain
Authors: Loh F.-K. , Nathan S. , Chow S.-C. , Fang C.-M. 
Published: February 2022

Abstract
The genetic fusion of cytolysin A (clyA) to heterologous antigen expressed in live Salmonella vector demonstrated efficient translocation into periplasmic space and extracellular medium. Accumulating evidence has shown that clyA-mediated antigen delivery improved growth fitness and enhanced immunogenicity of live vector vaccine, but the factors influencing this protein exportation has not been investigated. In this study, Toxoplasma gondii antigen fused at C-terminal of clyA protein was expressed in live S. Typhi vector via both plasmid and chromosomal-based expressions. The bivalent strains showed comparable growth rates as monovalent strains, but in varies antigen exportation efficiency. ClyA-fusion antigen with positive charges was translocated to the extracellular spaces, whereas those with negative charges were retained in the cytoplasm. Furthermore, excessive cellular resources expenditure on antigen expression, especially antigen with larger size, could limit the clyA-fusion antigen exportation, resulting in undesirable metabolic burden that eventually affects the growth fitness. Altogether, the present work indicates potential linkage of factors mainly on antigen properties and expression platforms that may affect clyA-mediated antigen delivery to enhance the growth fitness of live vector strain.
Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli
Authors: Saraiva M. M. S. , Silva N. M. V. , Ferreira V. A. , Moreira Filho A. L. B. , Givisiez P. E. N. , Freitas Neto O. C. , Berchieri Júnior A. , Gebreyes W. A. , de Oliveira C. J. B. 
Published: February 2022

Abstract
Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2 × 5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), AGPs monensin (MON), lincomycin (LCM) and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively. The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared with sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.
Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia and the Pacific Islands
Authors: Kozhar Olga , Kim Mee‐Sook , Ibarra Caballero Jorge , Klopfenstein Ned B. , Cannon Phil G. , Stewart Jane E. 
Published: February 2022

AbstractEmerging plant pathogens have been increasing exponentially over the last century. To address this issue, it is critical to determine whether these pathogens are native to ecosystems or have been recently introduced. Understanding the ecological and evolutionary processes fostering emergence can help to manage their spread and predict epidemics/epiphytotics. Using restriction site‐associated DNA sequencing data, we studied genetic relationships, pathways of spread and the evolutionary history of Phellinus noxius, an emerging root‐rotting fungus of unknown origin, in eastern Asia, Australia and the Pacific Islands. We analysed patterns of genetic variation using Bayesian inference, maximum‐likelihood phylogeny, population splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent‐based theory using Approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from an unsampled population to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate P. noxius spread occurred thousands of generations ago, contradicting previous assumptions that this pathogen was recently introduced to multiple geographical regions. Our results suggest that recent emergence of P. noxius in eastern Asia, Australia and the Pacific Islands has probably been driven by anthropogenic and natural disturbances, such as deforestation, land‐use change, severe weather events and/or introduction of exotic plants. This study provides a novel example of applying genome‐wide allele frequency data to unravel the dynamics of pathogen emergence under changing ecosystem conditions.
Opportunities for studying propagule pressure using gene flow reveal its role in accelerating biological invasions
Authors: Greve Michelle , Pertierra Luis R. 
Published: February 2022

When an alien species establishes at a new location, it must spread to become an invader. The extent to which propagule pressure promotes the spread of invaders, especially at local scales, is often difficult to quantify because it requires a reliable measure of, and variation in, rate of spread, and of propagule pressure across similar areas. In this issue of Molecular Ecology, Mairal et al. (2022) make use an unique system of paired sub‐Antarctic islands, one with very infrequent human activities, and another inhabited by scientists, to assess the role of propagule pressure and anthropogenic disturbance in the introduction and spread of a major global invader, Poa annua L., to and on the islands. Genetic admixture between different genetic clusters is virtually absent from the little‐visited island, while the inhabited island experienced more introduction events, but also significant admixture between genetic clusters. Detailed distribution maps of P. annua spanning more than 50 years allowed the authors to link genetic diversity to residence time. The nature of the system, and the multifaceted approach used by the authors, allows for new insights into the mechanism by which propagule pressure results in the spread of invasive species.
Incidence of white matter lesions in hospitalized COVID‐19 patients: A meta‐analysis
Authors: Rastogi Aarushi , Bhaskar Sonu Menachem Maimonides 
Published: February 2022

AbstractObjectiveNovel coronavirus disease 2019 (COVID‐19) has been found to be associated with encephalopathy and brain imaging abnormalities. The identification of incident white matter lesions, known to be associated with cerebral microcirculatory failure and cerebrovascular disease, in COVID‐19 patients is of clinical and scientific interest. We performed a meta‐analysis to investigate the incidence of white matter lesions (WMLs) in hospitalized COVID‐19 patients.MethodsPubMed, EMBASE, and the Cochrane Library were searched for studies on brain imaging abnormalities in hospitalized COVID‐19 patients. The terms used included “white matter lesions,” “white matter hyperintensity,” “COVID‐19,” “coronavirus,” and “SARS‐CoV‐2.” A random‐effects meta‐analysis was conducted to obtain a pooled estimate of WML prevalence in hospitalized COVID‐19 patients.ResultsA total of 4 eligible studies involving 362 patients (144 with WMLs and 218 without) were included in the meta‐analysis. We found the pooled estimate of WML prevalence to be 20% (ES 0.20; 95% CI 0.00–0.54; p = .03).ConclusionsThe estimated pooled prevalence rate of WMLs was approximately 20% in hospitalized COVID‐19 patients, albeit lower than the crude prevalence rate (39.8%).
EQUAL Candida score, an effective tool for predicting the outcomes of Candida tropicalis candidaemia: A retrospective cohort study
Authors: Leepattarakit Teera , Tulyaprawat Orawan , Vongseenin Chyanis , Rujirachun Pongprueth , Wattanachayakul Phuuwadith , Phichinitikorn Prawut , Phoompoung Pakpoom , Ngamskulrungroj Popchai 
Published: February 2022

AbstractBackgroundCandida tropicalis is the most common non‐albicans Candida species found in Asia‐Pacific countries, including Thailand. The pathogen is known for its great virulence, which causes a high case‐fatality rate. Associations between case fatality and patient characteristics, infectious disease unit consultation and EQUAL Candida score were investigated.MethodsThis retrospective cohort study was conducted with 160 cases of C. tropicalis bloodstream infection between 2015 and 2019 at a single, large, tertiary centre in Thailand. Clinical characteristics, clinical presentations, patient outcomes (30‐day case‐fatality rate) and independent predictive factors were analysed.ResultsThe 30‐day case‐fatality rate was 68.1%. The median of the EQUAL Candida score was 8. Independent factors for the prediction of case fatality were septic shock (hazard ratio, 1.84), the use of mechanical ventilation (hazard ratio, 2.03) and the EQUAL Candida score (hazard ratio, 0.75).ConclusionsThe predictive factors for 30‐day case fatality were septic shock, mechanical ventilation use and the EQUAL Candida score. It is recommended that the EQUAL score be considered for patients infected with C. tropicalis candidaemia to reduce the case‐fatality rate.
The effect of oil prices on headline and core inflation in Jordan
Authors: Hijazine Rami , Al‐Assaf Ghazi 
Published: February 2022

AbstractThis paper examined the effect of oil prices on headline and core inflation in Jordan over the period 2002Q1–2019Q4. Using the Johansen cointegration test and the vector error correction model, the empirical findings show that, in the short‐run, oil prices have a positive significant effect on headline inflation, and a unidirectional Granger causality relationship from oil prices only to headline inflation is found, while core inflation is not affected by oil prices movements. In the long run, oil prices—that appear to be transitory—have no substantial positive effect on headline or core inflation, while both inflation indices are affected by the GDP growth, interest rate, and the import prices for the core inflation model. The study suggests that policymakers should be concerned about targeting core inflation movements when implementing monetary policies.
Dementia care in Nepalese old age homes: Critical challenges as perceived by healthcare professionals
Authors: Shrestha Soni , Tranvåg Oscar 
Published: February 2022

AbstractAimTo explore and describe critical challenges in current dementia care practice as perceived by healthcare professionals (HCPs) in old age homes (OAHs) in Kathmandu, Nepal.BackgroundIn Nepal, the number of older people with dementia is rapidly rising, and there is a need for knowledge of how to provide quality dementia care in OAHs.MethodsAn exploratory hermeneutic design, employing qualitative interviews with eleven HCPs caring for residents with dementia in a total of five OAHs.FindingsThe analysis showed that HCPs found limited educational training in dementia‐specific care to be a critical challenge leading to reduced quality in caregiving practice. Insufficient HCP competence in dementia‐specific care undermined adequate coping with residents’ cognitive disturbances and the behavioural and psychological symptoms in dementia (BPSD). Poor HCP/medical doctor (MD)‐to‐patient ratio was perceived as a critical challenge preventing proper diagnostic examination, treatment and dementia‐specific care practice.ConclusionsLimited educational training, sparse competence in mastering residents’ cognitive disturbances and BPSD, and insufficient resources to ensure sufficient numbers of HCPs and MDs for proper diagnostic examination, treatment and dementia‐specific care were identified as critical challenges restricting quality dementia care in these Nepalese OAHs.Implications for practiceThe study findings indicate a need for a clear Nepalese policy and a national plan for dementia care in OAHs that includes strategies for HCP educational training and how to provide resources to ensure a sufficient workforce of HCPs and MDs for proper diagnostic examination, treatment and dementia‐specific care.
The psychological journey of weight gain in psychosis
Authors: Waite Felicity , Langman Amy , Mulhall Sophie , Glogowska Margaret , Hartmann‐Boyce Jamie , Aveyard Paul , Lennox Belinda ,   Oxford Cognitive Approaches to Psychosis Patient Advisory Group, Kabir Thomas , Freeman Daniel 
Published: February 2022

AbstractBackgroundRapid weight gain is common with antipsychotic medication. Lost confidence, low mood and medication non‐adherence often follow. Yet, the dynamic interactions between the physical and psychological consequences of weight gain, and implications for intervention, are unknown.ObjectivesWe examined first‐person accounts of weight gain to identify preferences for weight change interventions.DesignA qualitative design was used to explore patients’ experiences of weight change in the context of psychosis.MethodSemi‐structured interviews, analysed using grounded theory, were conducted with 10 patients with psychosis. Sample validation was conducted with peer researchers with lived experience of psychosis.ResultsPatients described that initially the extent and speed of weight gain was overshadowed by psychotic experiences and their treatment. This led to a shocking realisation of weight gain. The psychological impact of weight gain, most strikingly on the self‐concept, was profound. Loss of self‐worth and changed appearance amplified a sense of vulnerability. There were further consequences on mood, activity and psychotic experiences, such as voices commenting on appearance, that were additional obstacles in the challenging process of weight loss. Sedative effects of medication also contributed. Unsuccessful weight loss left little hope and few preferences for interventions. Early information about common weight gain trajectories and working with experts‐by‐experience were valued. Rebuilding self‐confidence, efficacy and worth may be a necessary first step.ConclusionsThe journey of weight gain in patients with psychosis is characterised by loss of self‐worth, agency and hope. There are multiple stages in the journey, each with different psychological reactions, that may need different treatment responses.
Holocene evolution and depositional model of a bayhead delta, Lake Illawarra, Australia
Authors: Hopley Carl A. , Jones Brian G. 
Published: February 2022

AbstractExtensive research into the evolution of wave‐dominated estuaries has been documented since the 1960s. However, there has only been limited research on the prograding bay‐head deltas that are the primary drivers for the rate and stage of estuary evolution. This paper presents the findings of a high‐resolution spatial study into the evolution of the Macquarie Rivulet bayhead delta in the Lake Illawarra barrier estuary. The delta’s evolution has been established based on sedimentological analysis of 74 cores, two14C ages and 45 amino acid racemization ages. This study intersected two Pleistocene and 10 Holocene sedimentary facies associations representing both the retrogradational and progradational phases of delta development. The distribution of bayhead delta facies associations in shallow barrier estuaries is initially controlled by the antecedent morphology, but, in contrast to deeper estuaries, this influence decreases as sedimentation proceeds. Changing relative sea level also has a major control on facies distribution with transgressive facies deposited as relative sea‐level rises being replaced by prograding deltaic facies during the highstand and subsequent minor relative sea‐level fall. Fluvial sediment supply and river flood events affect the rate of delta progradation, and produce low and high flow sediment deposits within the overall deltaic sequence. The low tidal flux in barrier estuaries, the muddy cohesive nature of the sediments and the prevalence of bioturbation means that primary sedimentary structures are rarely preserved in these bayhead delta facies. The depositional model of bayhead delta evolution shown by the Macquarie Rivulet delta would be widely applicable to other similar barrier estuary settings.
A deep trajectory clustering method based on sequence‐to‐sequence autoencoder model
Authors: Wang Chao , Lyu Fangzheng , Wu Sensen , Wang Yuanyuan , Xu Liuchang , Zhang Feng , Wang Shaowen , Wang Yongheng , Du Zhenhong 
Published: February 2022

AbstractMost existing trajectory clustering methods use point matching similarity measurement strategies to compare trajectory objects; however, such methods have poor similarity measurement accuracy, which reduces clustering quality. To address this research gap, this article considers a combination of trajectory‐feature learning and clustering. A deep trajectory clustering (DTC) method toward clustering‐friendly spaces is proposed to simultaneously learn trajectory representations (i.e., low‐dimensional vectors are used to represent trajectories) and cluster centroids, and further acquire the cluster assignments end to end. We first use a sequence‐to‐sequence autoencoder network for pretraining to obtain preliminary trajectory vectors, and then jointly optimize the learned representations and cluster centroids under the same framework. The effectiveness of DTC is demonstrated in synthetic datasets, and the learned representations in the real world can be used to identify hot routes in cities.
Temporal changes in transcripts of miniature inverted‐repeat transposable elements during rice endosperm development
Authors: Nagata Hiroki , Ono Akemi , Tonosaki Kaoru , Kawakatsu Taiji , Sato Yutaka , Yano Kentaro , Kishima Yuji , Kinoshita Tetsu 
Published: February 2022

SUMMARYThe repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs may escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. Genome‐wide DNA demethylation is also observed in the endosperm after fertilization. In the present study, we used a custom microarray to survey the transcripts generated from TEs during rice endosperm development and at selected time points in the embryo as a control. The expression patterns of TE transcripts are dynamically up‐ and downregulated during endosperm development, especially those of miniature inverted‐repeat TEs (MITEs). Some TE transcripts were directionally controlled, whereas the other DNA transposons and retrotransposons were not. We also discovered the NUCLEAR FACTOR Y binding motif, CCAAT, in the region near the 5′ terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.