bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficiencies of and Motivations for Contracting Out in the Public Sector: The Case of Social Services in Spain
Authors: Chow Danny , Garrido‐Rodríguez Juan Carlos , Zafra‐Gómez José Luis 
Published: November 2024

ABSTRACTDebates on contracting out to the private sector is primarily focused on the cost efficiency of its provision, drawing on experiences with hard or technical services such as waste and water management. This paper focuses on a growing interest in the role and impact of sourcing decisions in softer or more human‐centered services, such as social services, where sourcing decisions are more complex or multifaceted. Using actual cost data obtained from open access government sources on social services in Spain, the first objective was to compare the cost efficiencies of different sourcing decisions using estimations of Technology Gap Ratios of different municipalities through Order‐M Panel Data. The second objective analyzed motivations for contracting out through a survey of municipal managers in Andalusia using principal components analysis combined with multinominal logit regressions. Our findings suggest that while contracting out to the private sector is, relatively speaking, the most cost efficient, most municipalities have decided to keep service provision in‐house. Decisions to contract out social services are not based only on cost but also incorporate a range of other considerations such as the municipalities' population size, its stakeholder expectations, and other complexities associated with service provision.
Novel Variants in Medium and Low Penetrance Predisposing Genes in a Hungarian Malignant Melanoma Cohort With Increased Risk
Authors: Bokor Barbara Anna , Abdolreza Aliasgari , Kaptás Flóra , Pál Margit , Battyani Zita , Széll Márta , Nagy Nikoletta 
Published: November 2024

ABSTRACTBoth germline and somatic variants contribute to the genetic background and pathogenesis of melanoma. Germline variants include the presence of rare pathogenic or likely pathogenic variants of high, medium, and low penetrance melanoma‐predisposing genes. Rare variants of high penetrance melanoma‐predisposing genes are associated with melanoma development, whereas the medium and low penetrance predisposing genes can significantly increase melanoma risk. In this study, we clarified the germline genetic background of a Hungarian melanoma cohort (n = 17). Using a gene panel of 30 melanoma‐predisposing genes, germline genetic variants were identified in 10 of the 17 patients (58.82%). A novel, likely pathogenic, missense variant (p.Y143C) in a medium penetrance melanoma‐predisposing gene, melanocortin 1 receptor gene (MC1R), and two novel, likely pathogenic nonsense variants in low penetrance genes, p.Q218Ter in caspase 8 (CASP8) and p.Q40Ter in the fat mass‐ and obesity‐associated (FTO) gene were detected. This study highlights the importance of elucidating the germline genetic background of melanoma, which may improve prediction of individual risk and the risk of family members and to optimize preventive, screening, and therapeutic measures for each patient and melanoma‐prone families.
Whole‐genome sequencing analysis of Japanese autism spectrum disorder trios
Authors: Furukawa Sawako , Kushima Itaru , Kato Hidekazu , Kimura Hiroki , Nawa Yoshihiro , Aleksic Branko , Banno Masahiro , Yamamoto Maeri , Uematsu Mariko , Nagasaki Yukako , Ogi Tomoo , Ozaki Norio , Ikeda Masashi 
Published: November 2024

AimAutism spectrum disorder (ASD) is a genetically and phenotypically heterogeneous neurodevelopmental disorder with a strong genetic basis. Conducting the first comprehensive whole‐genome sequencing (WGS) analysis of Japanese ASD trios, this study aimed to elucidate the clinical significance of pathogenic variants and enhance the understanding of ASD pathogenesis.MethodsWGS was performed on 57 Japanese patients with ASD and their parents, investigating variants ranging from single‐nucleotide variants to structural variants (SVs), short tandem repeats (STRs), mitochondrial variants, and polygenic risk score (PRS).ResultsPotentially pathogenic variants that could explain observed phenotypes were identified in 18 patients (31.6%) overall and in 10 of 23 patients (43.5%) with comorbid intellectual developmental disorder (IDD). De novo variants in PTEN, CHD7, and HNRNPH2 were identified in patients referred for genetic counseling who exhibited previously reported phenotypes, including one patient with ASD who had profound IDD and macrocephaly with PTEN L320S. Analysis of the AlphaFold3 protein structure indicated potential inhibition of intramolecular interactions within PTEN. SV analysis identified deletions in ARHGAP11B and TMLHE. A pathogenic de novo mitochondrial variant was identified in a patient with ASD who had a history of encephalitis and cognitive decline. GO enrichment analysis of genes with nonsense variants and missense variants (Missense badness, PolyPhen‐2, and Constraint >1) showed associations with regulation of growth and ATP‐dependent chromatin remodeler activity. No reportable results were obtained in the analysis of STR and PRS.ConclusionCharacterizing the comprehensive genetic architecture and phenotypes of ASD is a fundamental step towards unraveling its complex biology.
Negative Affect and Planning Ability in Preschool Children: A Mediation Model of Working Memory, Inhibition, and Cognitive Flexibility
Authors: Filipiak Sara , Hawrot Anna 
Published: November 2024

ABSTRACTPast research in developmental psychology has revealed close links between affect and planning ability over the life‐span. However, such links have rarely been studied in children from non‐clinical samples. To address this gap, the present study investigates whether negative affect, understood as a temperamental trait, affects planning ability in 5‐year‐old children. Moreover, it examines whether selected cognitive processes, that is inhibition, verbal working memory, and cognitive flexibility, mediate this relationship. A total of 103 children aged M = 5 years 4 months, SD = 2.7 months, and their parents participated in the study. The analyses, which employed a path mediation model, revealed that negative affect's influence on planning was entirely mediated by flexibility. Moreover, flexibility partially mediated the relationship between inhibition and planning, and verbal working memory had a direct effect on planning. The results provide a new insight into the relationship between negative affect and planning ability in non‐clinical preschool children.
Fertilizer addition effect of novel recycling fertilizers from human excreta in a pot experiment with maize (Zea mays L.)
Authors: Boness Jan‐Ole , Kautz Timo , Hoffmann‐Bahnsen Roland 
Published: November 2024

AbstractRecycling nutrients from human faeces is a practicable and effective process in terms of the circular economy. To test this, we carried out a pot experiment with a hygienized human faeces compost (HHFC) and a nitrified urine fertilizer (NUF) made from contents of dry toilets to determine the short‐term fertilizer addition effect. HHFC variants were created in increments equivalent to 10, 20, and 30 t ha−1 dry matter weight (DM) and as joint fertilizer application of HHFC and NUF. For the classification of the fertilizer addition effect, soluble concentrations of nitrogen, phosphorus, and potassium in the soil as well as contents in the plant (Zea mays L.) were analysed after a trial period of 8 weeks. Above‐ground biomass, plant height, and chlorophyll content of the leaves were also assessed. The sole compost variants showed no to slightly higher DM yields than the control, whereas the combined compost urine fertilizer variant achieved around 80% of the DM yield of the mineral‐fertilizer applied reference treatment. The soil's total nitrogen storage is significantly increased in our experiment by the addition of HHFC. The concentration of soluble phosphorus in the soil increases significantly with increased compost applications. However, in the combined compost urine fertilizer variant, sufficient nitrogen supply results in a low level of soluble phosphorus because of high plant biomass production. This trend is reflected in the phosphorus content of plant material. HHFC is considered a good phosphorus fertilizer, which is also confirmed in this experiment. A similar picture emerges for the supply of potassium from HHFC. Although the liquid urine fertilizer (combined with HHFC) does not achieve the DM yield of the mineral reference variant in the early phase of plant growth, it has clear advantages in supplying the crop with nitrogen. This study shows that the recycling of nutrients from human faeces is a potential strategy for conserving finite resources and promoting energy‐efficient agricultural practices in line with the circular economy.
GV and GW invariants via the enhanced movable cone
Authors: Nabijou Navid , Wemyss Michael 
Published: November 2024

Abstract
Given any smooth germ of a 3-fold flopping contraction, we first give a combinatorial characterisation of which Gopakumar–Vafa (GV) invariants are non-zero, by prescribing multiplicities to the walls in the movable cone. On the Gromov–Witten (GW) side, this allows us to describe, and even draw, the critical locus of the associated quantum potential. We prove that the critical locus is the infinite hyperplane arrangement of Iyama and the second author and, moreover, that the quantum potential can be reconstructed from a finite fundamental domain. We then iterate, obtaining a combinatorial description of the matrix that controls the transformation of the non-zero GV invariants under a flop. There are three main ingredients and applications: (1) a construction of flops from simultaneous resolution via cosets, which describes how the dual graph changes; (2) a closed formula, which describes the change in dimension of the contraction algebra under flop; and (3) a direct and explicit isomorphism between quantum cohomologies of different crepant resolutions, giving a Coxeter-style, visual proof of the Crepant Transformation Conjecture for isolated cDV singularities.
The ability of
sarA
to limit protease production plays a key role in the pathogenesis of
Staphylococcus aureus
osteomyelitis irrespective of the functional status of
agr
Authors: Beenken Karen E. , Campbell Mara J. , Smeltzer Mark S. 
Published: November 2024

ABSTRACT

We demonstrate that mutation of the staphylococcal accessory regulator A (
sarA
) in the USA300 strain LAC limits virulence in a murine osteomyelitis model to a greater extent than mutation of the accessory gene regulator (
agr
) and that it does so irrespective of the functional status of
agr
. Protease production was decreased in the
agr
mutant but increased in
sarA
and
sarA/agr
mutants to a degree that limited biofilm formation. Extracellular protein A (eSpa) and full-length extracellular nuclease (Nuc1) were absent in the conditioned medium (CM) from
sarA
and
sarA
/
agr
mutants, and their abundance was restored in both mutants by eliminating protease production. Cytotoxicity of CM for osteoblasts and osteoclasts was also reduced in both mutants. Cytotoxicity was restored in a protease-deficient
sarA
mutant but not in the protease-deficient
sarA
/
agr
mutant. Reduced cytotoxicity was correlated with the reduced abundance of full-length α-toxin, LukF, and LukS in
sarA
and
sarA
/
agr
mutants. The abundance of these toxins in their full-length form was increased in the protease-deficient
sarA
mutant by comparison to LAC, demonstrating that mutation of
sarA
increases the production of these toxins but increased protease production limits their abundance in full-length and presumably functional forms. Most importantly, eliminating protease production enhanced the virulence of
sarA
and
sarA/agr
mutants, but had no impact in the
agr
mutant. We conclude that a key factor in the attenuation of LAC
sarA
and
sarA
/
agr
mutants in osteomyelitis is the increased production of extracellular proteases and its impact on virulence factors that contribute to biofilm formation and cytotoxicity.

IMPORTANCE

The persistent emergence of antibiotic-resistant strains has rekindled interest in anti-virulence strategies to combat
S. aureus
infections. Numerous reports describe anti-virulence strategies focusing on key regulatory elements that globally influence virulence factor production, the two most commonly targeted being the accessory gene regulator (
agr
) and the staphylococcal accessory regulator A (
sarA
). We demonstrate that mutation of
sarA
limits virulence to a greater extent than mutation of
agr
and that this can be attributed to increased protease production in both
sarA
and
sarA
/
agr
mutants. This illustrates the critical role of
sarA
in protease-mediated post-translational regulation in
S. aureus
. It also suggests that an inhibitor of
sarA
would be more effective than an inhibitor of
agr
in overcoming the therapeutic recalcitrance of osteomyelitis and that such an inhibitor would remain effective even in the context of
agr
mutants known to arise
in vivo
during the transition from acute to chronic infection.
The complete genome sequence of the stolbur pathogen “
Candidatus
Phytoplasma solani” from
Pentastiridius leporinus
Authors: Toth Rafael , Huettel Bruno , Eini Omid , Varrelmann Mark , Kube Michael 
Published: November 2024

ABSTRACT

The complete genome of “
Candidatus
Phytoplasma solani” GOE was obtained from the infected vector
Pentastiridius leporinus
by single-molecule real-time sequencing. This 16SrXII-P phytoplasma is associated with the economically important sugar beet disease “syndrome basses richesses.” The genome sequence is an essential resource for diagnosis and understanding pathogen–host interaction.
Draft genome of a human gut-derived
Blautia
sp. that ameliorates colitis and colitis-associated sociability deficits in mice
Authors: Murphy Michaela A. , Brown D. Garrett , Bell Rickesha S. , Weis Allison M. , Barrios Logan A. , Stephens W. Zac , Round June L. 
Published: November 2024

ABSTRACT

Blautia
is a genus of anaerobic, gram-positive bacteria commonly found in mammalian gastrointestinal tracts. Yet, how variations among different
Blautia
strains can impact host health is poorly understood. We present a
Blautia
sp. genome isolated from human feces whose supplementation to mice can ameliorate colitis severity and associated sociability deficits.
The Cwr1 protein kinase localizes to the plasma membrane and mediates resistance to cell wall stress in
Candida albicans
Authors: Naseem Shamoon , Zahumenský Jakub , Lanze Carla E. , Douglas Lois M. , Malínský Jan , Konopka James B. 
Published: November 2024

ABSTRACT

The plasma membrane is critical for the virulence of the human fungal pathogen
Candida albicans
. In addition to functioning as a protective barrier, the plasma membrane plays dynamic roles in a wide range of functions needed for virulence including nutrient uptake, cell wall synthesis, morphogenesis, resistance to stress, and invasive hyphal growth. Screening a collection of
C. albicans
mutants identified an understudied gene that is important for invasive hyphal growth, which we have termed
CWR1
(Cell Wall Regulatory kinase). A mutant strain lacking
CWR1
displayed defects in resisting stressful conditions that exacerbate cell wall defects. The Cwr1 protein shows strong similarity to protein kinases, suggesting it plays a regulatory role in coordinating plasma membrane and cell wall functions. A Cwr1–green fluorescent protein (GFP) fusion protein localized to punctate patches associated with the plasma membrane that partially overlapped Membrane Compartment of Can1 (MCC)/eisosome domains. In contrast to the static MCC/eisosome domains, the Cwr1–GFP patches were very dynamic. Truncation mutants lacking C-terminal sequences distal to the protein kinase domain failed to show detectable localization at the plasma membrane. Surprisingly, these mutant strains did not show the defects of a
cwr1Δ
mutant, suggesting that localization to punctate patches associated with the plasma membrane is not essential for Cwr1 function. Altogether, these data indicate that Cwr1 contributes to the regulation of plasma membrane functions that promote proper morphogenesis and resistance to cell wall stress, both of which are important for
C. albicans
virulence.

IMPORTANCE

The ability of
Candida albicans
to grow invasively in the host and resist stress is critical for it to be an effective human pathogen. Identifying the genes that promote these processes is important for developing new strategies to block infection. Therefore, genetic methods were used in this study to identify a novel gene that is needed for invasive growth and stress resistance (Cell Wall Regulatory kinase [
CWR1
]). Interestingly, the Cwr1 protein localized to punctate patches in the plasma membrane, some of which co-localized with specialized subdomains of the plasma membrane known as eisosomes that are known to promote stress resistance and invasive growth in the host. Thus, these studies identified a novel regulator of traits that are critical for
C. albicans
pathogenesis.
Genomic epidemiology of invasive Group A Streptococcus infections in Argentina, 2023: high prevalence of
emm
1-global and detection of
emm
1 hypervirulent lineages
Authors: Cipolla Lucía , Gianecini Ariel , Poklepovich Tomas , Etcheverry Paula , Rocca Florencia , Prieto Mónica 
Published: November 2024

ABSTRACT

The aim of this study is to describe the genomic epidemiology of invasive Group A Streptococcus (iGAS) in Argentina during 2023. A total of 476 invasive GAS isolates were subtyped and analyzed by whole-genome sequencing. A high prevalence of the
emm
1-type strain was observed. Among the
emm
1 strains, two highly virulent international variants,
emm
1-UK and
emm
1-DK, were identified. Additionally, a local variant, called
emm
1-ST1319, was detected. This seminal study provides initial insights into the genomic landscape of iGAS, contributing to active surveillance to monitor emerging virulent
emm
1 lineages and cross-border transmission in South America.

IMPORTANCE

Amid the increase in invasive
Streptococcus pyogenes
infections in Argentina in 2023, the implementation of genomic analysis of isolates allowed us to detect at the national level the prevalence of the
emm
1 type and within the M1 type, emerging national and international hypervirulent lineages. These findings from our report shed light on the distribution of invasive Group A Streptococcus, laying the foundation for genomic surveillance of this pathogen.
Improved Zika virus plaque assay using Vero/TMPRSS2 cell line
Authors: Oluwasemowo Olukunle O. , Graham Monica E. , Murugesh Deepa K. , Borucki Monica K. 
Published: November 2024

ABSTRACT

Plaque assay is the gold standard for the quantification of viable cytopathic viruses like Zika virus (ZIKV). Some strains of ZIKV produce plaques that are very difficult to accurately visualize and count on the commonly used Vero cell line. From data generated in our lab, we became curious if Vero/TMPRSS2 cells may be a better alternative; therefore, we compared the plaque forming units of two strains of ZIKV on Vero/TMPRSS2 cells to those produced by Vero cells. We also compared the virus stock titer generated on Vero/TMPRSS2 cells to that generated by the Vero cell line. Although the Vero cells generated higher quantity of ZIKV stocks, the Vero/TMPRSS2 cells produced plaques with significantly improved morphology and visibility and may, therefore, be a better alternative to use for performing plaque assays for strains of ZIKV that are more difficult to titer on regular Vero cells.

IMPORTANCE
While there are several methods of viral quantification, the plaque assay remains the gold standard for accurate quantification of replication-competent, cytopathic viruses including Zika virus (ZIKV). Vero cells are commonly used to titer ZIKV stock via the plaque assay. Prior to the initiation of this study, we observed that ZIKV-PRV strain plaque assays using Vero cells often yielded plaques that were very small, overly diffuse, and hard to count. We also observed that the ZIKV-CAM strain often did not produce plaques at all on Vero cells. This study shows that Vero cells expressing TMPRSS2 improve the morphology and visibility of plaques produced by ZIKV-PRV and ZIKV-CAM compared to regular Vero cells and may, therefore, be a better alternative to use for performing plaque assays for these strains and perhaps for other strains of ZIKV that are difficult to titer. However, Vero cells proved to be superior for generating high titer stock.
Exploration of urease-aided calcium carbonate mineralization by enzyme analyses of
Neobacillus mesonae
strain NS-6
Authors: Ma Zhiwei , Chen Mengyao , Lu Juncheng , Liu Shichuang , Ma Yanling 
Published: November 2024

ABSTRACT

Urease containing nickel cofactor is crucial for urea-hydrolytic induced calcium carbonate (CaCO
3
) precipitation (UICP). However, limited information exists regarding the influence of amino acid residues interacting with nickel ions in its structure on induced CaCO
3
mineralization. Herein, RT-qPCR was used to demonstrate that the addition of NiCl
2
dramatically upregulated the expression of urease structural gene
ureC
that was correlated with nickel binding in
Neobacillus mesonae
strain NS-6. Homology modeling and molecular docking were employed to construct the three-dimensional structure of urease and seek the key residues involved in nickel binding process, and virtual mutation technology was adopted to inform three key residues coordinated with nickel ions and urea, His249, His275, and Asp363. Four metrics, including root mean square deviation values for mutations of those key residues in urease-urea complexes severally and wild-type, were calculated by molecular dynamics simulations when they were mutated into alanine, respectively. Subsequently, the mutations of H249A, H275A, and D363A were characterized using western blotting to reveal a decrease in the relative expression and activity of urease, along with a corresponding reduction in CaCO
3
precipitation. Ultimately, the mutations also exhibited that they had lower substrate affinity and catalytic efficiency for urea through enzymatic properties analysis. The findings suggested that those residues played a pivotal role in UICP of strain NS-6, which would expand the theoretical basis for modulating urease activity.

IMPORTANCE

Urease-producing bacterium is of great importance in diverse application fields, such as environmental remediation, due to its key driving characteristics in catalyzing urea hydrolysis via urea-hydrolytic induced CaCO
3
precipitation (UICP). As essential cofactors of urease, nickel ions play a crucial role in regulating urease catalysis and maintaining structural stability. Numerous investigations have emphasized the impact of nickel ions on urease activity in recent years, to our best knowledge, only a few literatures have studied the molecular-level regulation of nickel-ligand residues. This study focused on the highly urease-producing bacterial
Neobacillus mesonae
NS-6 to explore the effects of specific nickel-ligand residues on the urease-aided CaCO
3
mineralization process using molecular simulation predictions and targeted mutation experiments. The aim was to provide a molecular-level understanding of the interactive effects between urea and critical residues associated with the urease active center, as well as propose an effective modification strategy to enhance the application of UICP in future environmental areas.