bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progress towards a targeted biorefinery of Chromochloris zofingiensis: a review
Authors: Wood Eleanor E. , Ross Michael E. , Jubeau Sébastien , Montalescot Valéria , Stanley Michele S. 
Published: June 2022

AbstractBiorefinery approaches offer the potential to improve the economics of the microalgae industry by producing multiple products from a single source of biomass. Chromochloris zofingiensis shows great promise for biorefinery due to high biomass productivity and a diverse range of products including secondary carotenoids, predominantly astaxanthin; lipids such as TAGs; carbohydrates including starch; and proteins and essential amino acids. Whilst this species has been demonstrated to accumulate multiple products, the development of an integrated downstream process to obtain these is lacking. The objective of this review paper is to assess the research that has taken place and to identify the steps that must be taken to establish a biorefinery approach for C. zofingiensis. In particular, the reasons why C. zofingiensis is a promising species to target for biorefinery are discussed in terms of cellular structure, potential products, and means to accumulate desirable components via the alteration of culture conditions. Future advances and the challenges that lie ahead for successful biorefinery of this species are also reviewed along with potential solutions to address them.
Invariance properties of the natural gradient in overparametrised systems
Authors: van Oostrum Jesse , Müller Johannes , Ay Nihat 
Published: June 2022

AbstractThe natural gradient field is a vector field that lives on a model equipped with a distinguished Riemannian metric, e.g. the Fisher–Rao metric, and represents the direction of steepest ascent of an objective function on the model with respect to this metric. In practice, one tries to obtain the corresponding direction on the parameter space by multiplying the ordinary gradient by the inverse of the Gram matrix associated with the metric. We refer to this vector on the parameter space as the natural parameter gradient. In this paper we study when the pushforward of the natural parameter gradient is equal to the natural gradient. Furthermore we investigate the invariance properties of the natural parameter gradient. Both questions are addressed in an overparametrised setting.
The concentration effects on structural and magnetic properties of Fe2V1-xMnxGe Heusler alloys
Authors: Boyraz C. , Guler A. , Aksu P. , Arda L. 
Published: June 2022

AbstractThis study presents the concentration-dependent structural, morphological, and magnetic properties of Fe2V1-xMnxGe Heusler alloys (x = 0.0, 0.25, and 0.50) have not been studied previously in the literature, and are investigated by using X-ray Diffractometer, Scanning Electron Microscope (SEM), and Physical Properties Measurement System (PPMS). We observed from the X-ray diffraction measurements that (except x = 0) Fe2V1-xMnxGe samples have had L21-type crystal structure, matching well with the literature. In all SEM images, some holes and crack-type formations are observed. Increasing Mn content in Fe2V1-xMnxGe Heusler alloys can effectively inhibit grain boundary migration. Except for Fe2VGe, the other alloys in the series are investigated to be soft ferromagnets at 5 K with saturation magnetic moment. The (M-H) graphs especially for Fe2V0.75Mn0.25Ge and Fe2V0.5Mn0.5Ge measured at 5 K reveal almost no coercive fields and easy magnetization. Namely, the system easily saturates without needing any high fields. The obtained results show that these new samples may be suitable candidates for technological applications.
Predictors of mental health symptomatology among Kurdish patients who recovered from COVID-19 in Iraq
Authors: Ibrahim Hawkar , Goessmann Katharina , Ahmad Araz Ramazan , Saeed Ayoub Kareem , Neuner Frank 
Published: June 2022

AbstractWhile a growing body of research has documented severe psychosocial consequences of the new Coronavirus disease (COVID-19) for the affected people, research mainly focused either on health care workers or the general population. There is a dearth of scientific research on the mental health status of recovered patients, especially in low- and middle-income countries. The purpose of the current study was to determine the mental health symptomatology and its associated factors among Iraqis who recovered from COVID-19. Participants were Iraqi Kurdish individuals who had previously been diagnosed with COVID-19 during the first wave of COVID-19, and they were recruited based on lists of recovered patients provided by from public health institutions. Using standardized demographic and mental health questionnaires, structured telephone interviews with 57 recovered patients were contacted. It was found that 31.6% of the participating recovered patients with COVID-19 met the diagnostic criteria for post-traumatic stress disorder (PTSD), and 21.05% were classified with probable depression. Hospitalized survivors had higher PTSD and depression symptoms than those not hospitalized. We also found that higher levels of PTSD and depression symptoms were predicted by younger age, hospitalization due to COVID-19, and having a family member who died from COVID-19. In the context of the global COVID-19 pandemic, psychological and psychiatric treatment may be particularly relevant for younger adult patients and those with more severe COVID-19 symptoms who experienced hospitalized care.
Prompt control of a Serratia marcescens outbreak in a neonatal intensive care unit informed by whole-genome sequencing and comprehensive infection control intervention package
Authors: Howard-Jones Annaleise R. , Janto Catherine , Jennings Zoe , Branley James , Wang Qinning , Sintchenko Vitali , Samarasekara Harsha 
Published: June 2022

Abstract

Objective:
This report describes a cluster of patients infected by Serratia marcescens in a metropolitan neonatal intensive care unit (NICU) and a package of infection control interventions that enabled rapid, effective termination of the outbreak.

Design:
Cross-sectional analytical study using whole-genome sequencing (WGS) for phylogenetic cluster analysis and identification of virulence and resistance genes.

Setting:
NICU in a metropolitan tertiary-care hospital in Sydney, Australia.

Patients:
All neonates admitted to the level 2 and level 3 neonatal unit.

Interventions:
Active inpatient and environmental screening for Serratia marcescens isolates with WGS analysis for identification of resistance genes as well as cluster relatedness between isolates. Planning and implementation of a targeted, multifaceted infection control intervention.

Results:
The cluster of 10 neonates colonized or infected with Serratia marcescens was identified in a metropolitan NICU. Two initial cases involved devastating intracranial infections with brain abscesses, highlighting the virulence of this organism. A targeted and comprehensive infection control intervention guided by WGS findings enabled termination of this outbreak within 15 days of onset. WGS examination demonstrated phylogenetic linkage across the cluster, and genomic unrelatedness of later strains identified in the neonatal unit and elsewhere.

Conclusions:
A comprehensive, multipronged, infection control package incorporating close stakeholder engagement, frequent microbiological patient screening, environmental screening, enhanced cleaning, optimization of hand hygiene and healthcare worker education was paramount to the prompt control of Serratia marcescens transmission in this neonatal outbreak. WGS was instrumental in establishing relatedness between isolates and identification of possible transmission pathways in an outbreak setting.
Discounted optimal stopping problems in first-passage time models with random thresholds
Authors: Gapeev Pavel V. , Al Motairi Hessah 
Published: June 2022

AbstractWe derive closed-form solutions to some discounted optimal stopping problems related to the perpetual American cancellable dividend-paying put and call option pricing problems in an extension of the Black–Merton–Scholes model. The cancellation times are assumed to occur when the underlying risky asset price process hits some unobservable random thresholds. The optimal stopping times are shown to be the first times at which the asset price reaches stochastic boundaries depending on the current values of its running maximum and minimum processes. The proof is based on the reduction of the original optimal stopping problems to the associated free-boundary problems and the solution of the latter problems by means of the smooth-fit and modified normal-reflection conditions. We show that the optimal stopping boundaries are characterised as the maximal and minimal solutions of certain first-order nonlinear ordinary differential equations.
On a class of critical N-Laplacian problems
Authors: Ho Tsz Chung , Perera Kanishka 
Published: June 2022

AbstractWe establish some existence results for a class of critical $N$-Laplacian problems in a bounded domain in $\mathbb {R}^{N}$. In the absence of a suitable direct sum decomposition of the underlying Sobolev space to which the classical linking theorem can be applied, we use an abstract linking theorem based on the $\mathbb {Z}_2$-cohomological index to obtain a non-trivial critical point.
Liver function tests in primary care provide a key opportunity to diagnose and engage patients with hepatitis C
Authors: McLeod A. , Hutchinson S. J. , Weir A. , Barclay S. , Schofield J. , Frew C. Gillespie , Goldberg D. J. , Heydtmann M. , Wilson-Davies E. 
Published: June 2022

Abstract
Since the advent of direct-acting antiviral therapy, the elimination of hepatitis c virus (HCV) as a public health concern is now possible. However, identification of those who remain undiagnosed, and re-engagement of those who are diagnosed but remain untreated, will be essential to achieve this. We examined the extent of HCV infection among individuals undergoing liver function tests (LFT) in primary care. Residual biochemistry samples for 6007 patients, who had venous blood collected in primary care for LFT between July 2016 and January 2017, were tested for HCV antibody. Through data linkage to national and sentinel HCV surveillance databases, we also examined the extent of diagnosed infection, attendance at specialist service and HCV treatment for those found to be HCV positive. Overall HCV antibody prevalence was 4.0% and highest for males (5.0%), those aged 37–50 years (6.2%), and with an ALT result of 70 or greater (7.1%). Of those testing positive, 68.9% had been diagnosed with HCV in the past, 84.9% before the study period. Most (92.5%) of those diagnosed with chronic infection had attended specialist liver services and while 67.7% had ever been treated only 38% had successfully cleared infection. More than half of HCV-positive people required assessment, and potentially treatment, for their HCV infection but were not engaged with services during the study period. LFT in primary care are a key opportunity to diagnose, re-diagnose and re-engage patients with HCV infection and highlight the importance of GPs in efforts to eliminate HCV as a public health concern.
Making ProB Compatible with SWI-Prolog
Authors: GELEßUS DAVID , LEUSCHEL MICHAEL 
Published: June 2022

AbstractEven though the core of the Prolog programming language has been standardized by ISO since 1995, it remains difficult to write complex Prolog programs that can run unmodified on multiple Prolog implementations. Indeed, implementations sometimes deviate from the ISO standard and the standard itself fails to cover many features that are essential in practice. Most Prolog applications thus have to rely on nonstandard features, often making them dependent on one particular Prolog implementation and incompatible with others. We examine one such Prolog application: ProB, which has been developed for over 20 years in SICStus Prolog. The article describes how we managed to refactor the codebase of ProB to also support SWI-Prolog, with the goal of verifying ProB’s results using two independent toolchains. This required a multitude of adjustments, ranging from extending the SICStus emulation in SWI-Prolog on to better modularizing the monolithic ProB codebase. We also describe notable compatibility issues and other differences that we encountered in the process, and how we were able to deal with them with few major code changes.
Indo‐Pacific Sector Dominates Southern Ocean Carbon Outgassing
Authors: Prend Channing J. , Gray Alison R. , Talley Lynne D. , Gille Sarah T. , Haumann F. Alexander , Johnson Kenneth S. , Riser Stephen C. , Rosso Isabella , Sauvé Jade , Sarmiento Jorge L. 
Published: June 2022

AbstractThe Southern Ocean modulates the climate system by exchanging heat and carbon dioxide (CO2) between the atmosphere and deep ocean. While this region plays an outsized role in the global oceanic anthropogenic carbon uptake, CO2 is also released to the atmosphere across large swaths of the Antarctic Circumpolar Current (ACC). Southern Ocean outgassing has long been attributed to remineralized carbon from upwelled deep water, but the precise mechanisms by which this water reaches the surface are not well constrained from observations. Using data from a novel array of autonomous biogeochemical profiling floats, we examine Southern Ocean air‐sea CO2 fluxes and the pathways that transfer carbon from the ocean interior into the mixed layer where air‐sea exchange occurs. These float‐based flux estimates of unprecedented spatial resolution indicate that carbon outgassing occurs predominantly in the Indo‐Pacific sector of the ACC due to variations in the mean surface ocean partial pressure of CO2 (pCO2). We show that this zonal asymmetry in surface pCO2, and consequently air‐sea carbon fluxes, stems primarily from regional variability in the mixed‐layer entrainment of upwelled carbon‐rich deep water. These results suggest that a sustained circumpolar observing system is crucial to monitor future changes in oceanic carbon release and uptake.
The Curiosity Rover's Exploration of Glen Torridon, Gale Crater, Mars: An Overview of the Campaign and Scientific Results
Authors: Bennett Kristen A. , Fox Valerie K. , Bryk Alex , Dietrich William , Fedo Christopher , Edgar Lauren , Thorpe Michael T. , Williams Amy J. , Wong Gregory M. , Dehouck Erwin , McAdam Amy , Sutter Brad , Millan Maëva , Banham Steven G. , Bedford Candice C. , Bristow Thomas , Fraeman Abigail , Vasavada Ashwin R. , Grotzinger John , Thompson Lucy , O’Connell‐Cooper Catherine , Gasda Patrick , Rudolph Amanda , Sullivan Robert , Arvidson Ray , Cousin Agnes , Horgan Briony , Stack Kathryn M. , Treiman Allan , Eigenbrode Jennifer , Caravaca Gwénaël 
Published: June 2022

AbstractThe Mars Science Laboratory rover, Curiosity, explored the clay mineral‐bearing Glen Torridon region for 1 Martian year between January 2019 and January 2021, including a short campaign onto the Greenheugh pediment. The Glen Torridon campaign sought to characterize the geology of the area, seek evidence of habitable environments, and document the onset of a potentially global climatic transition during the Hesperian era. Curiosity roved 5 km in total throughout Glen Torridon, from the Vera Rubin ridge to the northern margin of the Greenheugh pediment. Curiosity acquired samples from 11 drill holes during this campaign and conducted the first Martian thermochemolytic‐based organics detection experiment with the Sample Analysis at Mars instrument suite. The lowest elevations within Glen Torridon represent a continuation of lacustrine Murray formation deposits, but overlying widespread cross bedded sandstones indicate an interval of more energetic fluvial environments and prompted the definition of a new stratigraphic formation in the Mount Sharp group called the Carolyn Shoemaker formation. Glen Torridon hosts abundant phyllosilicates yet remains compositionally and mineralogically comparable to the rest of the Mount Sharp group. Glen Torridon samples have a great diversity and abundance of sulfur‐bearing organic molecules, which are consistent with the presence of ancient refractory organic matter. The Glen Torridon region experienced heterogeneous diagenesis, with the most striking alteration occurring just below the Siccar Point unconformity at the Greenheugh pediment. Results from the pediment campaign show that the capping sandstone formed within the Stimson Hesperian aeolian sand sea that experienced seasonal variations in wind direction.
The extracellular matrix and perineuronal nets in memory
Authors: Fawcett James W. , Fyhn Marianne , Jendelova Pavla , Kwok Jessica C. F. , Ruzicka Jiri , Sorg Barbara A. 
Published: June 2022

AbstractAll components of the CNS are surrounded by a diffuse extracellular matrix (ECM) containing chondroitin sulphate proteoglycans (CSPGs), heparan sulphate proteoglycans (HSPGs), hyaluronan, various glycoproteins including tenascins and thrombospondin, and many other molecules that are secreted into the ECM and bind to ECM components. In addition, some neurons, particularly inhibitory GABAergic parvalbumin-positive (PV) interneurons, are surrounded by a more condensed cartilage-like ECM called perineuronal nets (PNNs). PNNs surround the soma and proximal dendrites as net-like structures that surround the synapses. Attention has focused on the role of PNNs in the control of plasticity, but it is now clear that PNNs also play an important part in the modulation of memory. In this review we summarize the role of the ECM, particularly the PNNs, in the control of various types of memory and their participation in memory pathology. PNNs are now being considered as a target for the treatment of impaired memory. There are many potential treatment targets in PNNs, mainly through modulation of the sulphation, binding, and production of the various CSPGs that they contain or through digestion of their sulphated glycosaminoglycans.
Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion
Authors: Sikder Md Maniruzzaman , Vestergård Mette , Kyndt Tina , Topalović Olivera , Kudjordjie Enoch Narh , Nicolaisen Mogens 
Published: June 2022

Abstract
In-depth understanding of metabolite-mediated plant-nematode interactions can guide us towards novel nematode management strategies. To improve our understanding of the effects of secondary metabolites on soil nematode communities, we grew Arabidopsis thaliana genetically altered in glucosinolate, camalexin, or flavonoid synthesis pathways, and analyzed their root-associated nematode communities using metabarcoding. To test for any modulating effects of the associated microbiota on the nematode responses, we characterized the bacterial and fungal communities. Finally, as a proxy of microbiome-modulating effects on nematode invasion, we isolated the root-associated microbiomes from the mutants and tested their effect on the ability of the plant parasitic nematode Meloidogyne incognita to penetrate tomato roots. Most mutants had altered relative abundances of several nematode taxa with stronger effects on the plant parasitic Meloidogyne hapla than on other root feeding taxa. This probably reflects that M. hapla invades and remains embedded within root tissues and is thus intimately associated with the host. When transferred to tomato, microbiomes from the flavonoid over-producing pap1-D enhanced M. incognita root-invasion, whereas microbiomes from flavonoid-deficient mutants reduced invasion. This suggests microbiome-mediated effect of flavonoids on Meloidogyne infectivity plausibly mediated by the alteration of the abundances of specific microbial taxa in the transferred microbiomes, although we could not conclusively pinpoint such causative microbial taxa.
Associations between fear of COVID-19, dental anxiety, and psychological distress among Iranian adolescents
Authors: Tofangchiha Maryam , Lin Chung-Ying , Scheerman Janneke F. M. , Broström Anders , Ahonen Hanna , Griffiths Mark D. , Tadakamadla Santosh Kumar , Pakpour Amir H. 
Published: June 2022

Abstract
Objectives
The present study evaluated the association of fear of COVID-19 with dental anxiety, oral health-related quality of life (OHRQoL), and psychological distress (depression, anxiety and stress), as well as exploring the mediating role of dental anxiety in the association of fear of COVID-19 with OHRQoL and psychological distress.

Methods
A cross-sectional study was conducted among adolescents in high schools of Qazvin city (Iran) from March-June 2021, recruited through a two-stage cluster sampling method. All the adolescents completed a self-administered survey assessing (i) fear of COVID-19, (ii) depression, anxiety and stress, (iii) OHRQoL, and (iv) dental anxiety. Structural equation modelling was used to evaluate all the hypothesised associations, and the model fit was estimated.

Results
A total of 2429 adolescents participated in the study. The conceptual model fitted the data well. Fear of COVID-19 had a direct effect on dental anxiety (B = 0.316; bias-corrected bootstrapping 95% CI = 0.282, 0.349), depression (B = 0.302; bias-corrected bootstrapping 95% CI = 0.259, 0.347), anxiety (B = 0.289; bias-corrected bootstrapping 95% CI = 0.246, 0.334), stress (B = 0.282; bias-corrected bootstrapping 95% CI = 0.237, 0.328), and OHRQoL (B = −0.354; bias-corrected bootstrapping 95% CI = −0.530, −0.183). Also, dental anxiety mediated the association of fear of COVID-19 with depression, anxiety stress, and OHRQoL.

Conclusions
High levels of fear of COVID-19 were associated with high levels of dental anxiety and poorer OHRQoL. Moreover, fear of COVID-19 was positively associated with anxiety, depression and stress. Increased levels of dental anxiety were also associated with increased anxiety, stress, depression, and poorer OHRQoL.
Incidence of Duchenne muscular dystrophy in the modern era; an Australian study
Authors: Kariyawasam Didu , D’Silva Arlene , Mowat David , Russell Jacqui , Sampaio Hugo , Jones Kristi , Taylor Peter , Farrar Michelle 
Published: June 2022

AbstractDuchenne muscular dystrophy (DMD), an X-linked recessive condition is maternally inherited in two-thirds of affected boys. It is important to establish carrier status of female relatives to restore reproductive confidence for non-carriers and facilitate reproductive options and cardiac surveillance for carriers. This study investigates disease incidence within an Australian model of cascade screening and evolving genetic diagnostic technologies. A retrospective population-based cohort study of all genetically and/or histopathologically confirmed males with DMD, born in New South Wales and the Australian Capital Territory was undertaken from 2002–2012. Cases were identified using state-wide molecular laboratory and clinical databases. The annual disease incidence and “theoretically” preventable cases were extrapolated over the study period. Proband genotype/phenotype, pedigree analysis, carrier-risk and extent of cascade screening were also determined. The cumulative incidence of disease was 19.7 per 100,000 male live births and 1 in 5076 live born males were diagnosed with DMD. Differences in disease incidence were not statistically different when compared between 2002–2007 and 2008–2012 (incidence rate ratio = 1.13, 95% CI 0.76–1.69, p = 0.52). The incidence rate ratio of theoretically preventable cases did not significantly change between 2002–2007 and 2008–2012 (incidence rate ratio = 2.07, 95% CI 0.58–9.21, p = 0.23). Current diagnostic and cascade screening models have limitations in their impact on disease incidence, due to a spectrum of logistical, patient and condition related factors. Innovative approaches to reduce DMD incidence may be better achieved by preconception or early pregnancy carrier screening, prenatal exome sequencing and newborn screening.