bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal gene expression during asexual development of the apicomplexan
Sarcocystis neurona
Authors: Dangoudoubiyam Sriveny , Norris Jamie K. , Namasivayam Sivaranjani , de Paula Baptista Rodrigo , Cannes do Nascimento Naila , Camp Joseph , Schardl Christopher L. , Kissinger Jessica C. , Howe Daniel K. 
Published: May 2024

ABSTRACT

Asexual replication in the apicomplexan
Sarcocystis neurona
involves two main developmental stages: the motile extracellular merozoite and the sessile intracellular schizont. Merozoites invade host cells and transform into schizonts that undergo replication via endopolygeny to form multiple (64) daughter merozoites that are invasive to new host cells. Given that the capabilities of the merozoite vary significantly from the schizont, the patterns of transcript levels throughout the asexual lifecycle were determined and compared in this study. RNA-Seq data were generated from extracellular merozoites and four intracellular schizont development time points. Of the 6,938 genes annotated in the
S. neurona
genome, 6,784 were identified in the transcriptome. Of these, 4,111 genes exhibited significant differential expression between the merozoite and at least one schizont development time point. Transcript levels were significantly higher for 2,338 genes in the merozoite and 1,773 genes in the schizont stages. Included in this list were genes encoding the secretory pathogenesis determinants (SPDs), which encompass the surface antigen and SAG-related sequence (SAG/SRS) and the secretory organelle proteins of the invasive zoite stage (micronemes, rhoptries, and dense granules). As anticipated, many of the
S. neurona
SPD gene transcripts were abundant in merozoites. However, several SPD transcripts were elevated in intracellular schizonts, suggesting roles unrelated to host cell invasion and the initial establishment of the intracellular niche. The hypothetical genes that are potentially unique to the genus
Sarcocystis
are of particular interest. Their conserved expression patterns are instructive for future investigations into the possible functions of these putative
Sarcocystis
-unique genes.

IMPORTANCE

The genus
Sarcocystis
is an expansive clade within the Apicomplexa, with the species
S. neurona
being an important cause of neurological disease in horses. Research to decipher the biology of
S. neurona
and its host-pathogen interactions can be enhanced by gene expression data. This study has identified conserved apicomplexan orthologs in
S. neurona
, putative
Sarcocystis
-unique genes, and gene transcripts abundant in the merozoite and schizont stages. Importantly, we have identified distinct clusters of genes with transcript levels peaking during different intracellular schizont development time points, reflecting active gene expression changes across endopolygeny. Each cluster also has subsets of transcripts with unknown functions, and investigation of these seemingly
Sarcocystis
-unique transcripts will provide insights into the interesting biology of this parasite genus.
Different sampling strategies for optimal detection of the overall genetic diversity of methicillin-resistant
Staphylococcus aureus
Authors: Zohar Cretnik Tjasa , Maric Leon , Rupnik Maja , Janezic Sandra 
Published: May 2024

ABSTRACT

Surveillance schemes for methicillin-resistant
Staphylococcus aureus
(MRSA) are widely established at the national and international levels. Due to the simple standardization of the protocol, mainly isolates from bloodstream infections are used. However, the limitations of this simple surveillance system are well described. We conducted a comprehensive analysis of MRSA isolates in a large Slovenian region over 5 years to identify the optimal sample group for assessing the overall MRSA diversity. At the same time, this study provides to date non-available molecular characterization of Slovenian MRSA isolates. A total of 306 MRSA isolates from various sources were sequenced and phenotypically tested for resistance. The isolates exhibited significant molecular diversity, encompassing 30 multi locus sequence type (MLST) sequence types (STs), 39 ST-SCC
mec
genetic lineages, 49
spa
types, and 29 antibiotic resistance profiles. Furthermore, the isolate pool comprised 57 resistance genes, representing 22 resistance mechanisms, and 96 virulence genes. While bloodstream isolates, commonly used in surveillance, provided insights into frequently detected clones, they overlooked majority of clones and important virulence and resistance genes. Blood culture isolates detected 21.3%
spa
types, 24.1% resistance phenotypes, and 28.2% MLST-SCC
mec
profiles. In contrast, strains from soft tissues demonstrated superior genomic diversity capture, with 65.3%
spa
types, 58.6% resistance phenotypes, and 71.8% MLST-SCC
mec
profiles. These strains also encompassed 100.0% of virulence and 82.5% of resistance genes, making them better candidates for inclusion in surveillance programs. This study highlights the limitations of relying solely on bloodstream isolates in MRSA surveillance and suggests incorporating strains from soft tissues to obtain a more comprehensive understanding of the epidemiology of MRSA.

IMPORTANCE

In this study, we investigated the diversity of methicillin-resistant
Staphylococcus aureus
(MRSA), a bacterium that can cause infections that are difficult to treat due to its resistance to antimicrobial agents. Currently, surveillance programs for MRSA mainly rely on isolates from bloodstream infections, employing a standardized protocol. However, this study highlights the limitations of this approach and introduces a more comprehensive method. The main goal was to determine which group of samples is best suited to understand the overall diversity of MRSA and to provide, for the first time, molecular characterization of Slovenian MRSA isolates. Our results suggest that including MRSA strains from soft tissue infections rather than just blood infections provides a more accurate and comprehensive view of bacterial diversity and characteristics. This insight is valuable for improving the effectiveness of surveillance programs and for developing strategies to better manage MRSA infections.
Extended-spectrum beta-lactamase-producing
Escherichia coli
and
Klebsiella pneumoniae
: insights from a tertiary hospital in Southern Thailand
Authors: Romyasamit Chonticha , Sornsenee Phoomjai , Kawila Soontara , Saengsuwan Phanvasri 
Published: May 2024

ABSTRACT

Broad-spectrum ampicillin-resistant and third-generation cephalosporin-resistant Enterobacteriaceae, particularly
Escherichia coli
and
Klebsiella pneumoniae
that have pathological features in humans, have become a global concern. This study aimed to investigate the prevalence, antimicrobial susceptibility, and molecular genetic features of extended-spectrum beta-lactamase (ESBL)-producing
E. coli
and
K. pneumoniae
isolates in Southern Thailand. Between January and August 2021, samples (
n
= 199) were collected from a tertiary care hospital in Southern Thailand. ESBL and AmpC-lactamase genes were identified using multiplex polymerase chain reaction (PCR). The genetic relationship between ESBL-producing
E. coli
and
K. pneumoniae
was determined using the enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction. ESBL-producing
E. coli
and
K. pneumoniae
isolates were mostly collected from catheter urine samples of infected female patients. The ESBL production prevalence was highest in the medical wards (
n
= 75, 37.7%), followed by that in surgical wards (
n
= 64, 32.2%) and operating rooms (
n
= 19, 9.5%). Antimicrobial susceptibility analysis revealed that all isolates were resistant to ampicillin, cefotaxime, ceftazidime, ceftriaxone, and cefuroxime; 79.4% were resistant to ciprofloxacin; and 64.3% were resistant to trimethoprim-sulfamethoxazole. In ESBL-producing
K. pneumoniae
and
E. coli
,
bla
TEM
(
n
= 57, 72.2%) and
bla
CTX-M
(
n
= 61, 50.8%) genes were prominent; however, no
bla
VEB
,
bla
GES
, or
bla
PER
were found in any of these isolates. Furthermore, only ESBL-producing
K. pneumoniae
had co-harbored
bla
TEM
and
bla
SHV
genes at 11.6%. The ERIC-PCR pattern of multidrug-resistant ESBL-producing strains demonstrated that the isolates were clonally related (95%). Notably, the presence of multidrug-resistant and extremely resistant ESBL producers was 83.4% and 16.6%, respectively. This study highlights the presence of
bla
TEM
,
bla
CTX-M
, and co-harbored genes in ESBL-producing bacterial isolates from hospitalized patients, which are associated with considerable resistance to beta-lactamase and third-generation cephalosporins.

IMPORTANCE
We advocate for evidence-based guidelines and antimicrobial stewardship programs to encourage rational and appropriate antibiotic use, ultimately reducing the selection pressure for drug-resistant bacteria and lowering the likelihood of ESBL-producing bacterial infections.
Mutation of
hmgA
, encoding homogentisate 1,2-dioxygenase, is responsible for pyomelanin production but does not impact the virulence of
Burkholderia cenocepacia
in a chronic granulomatous disease mouse lung infection
Authors: Moustafa Dina A. , Wu Linda , Ivey Melissa , Fankhauser Sarah C. , Goldberg Joanna B. 
Published: May 2024

ABSTRACT

The
Burkholderia cepacia
complex (Bcc) is a group of Gram-negative opportunistic bacteria often associated with fatal pulmonary infections in patients with impaired immunity, particularly those with cystic fibrosis (CF) and chronic granulomatous disease (CGD). Some Bcc strains are known to naturally produce pyomelanin, a brown melanin-like pigment known for scavenging free radicals; pigment production has been reported to enable Bcc strains to overcome the host cell oxidative burst. In this work, we investigated the role of pyomelanin in resistance to oxidative stress and virulence in strains J2315 and K56-2, two epidemic CF isolates belonging to the
Burkholderia cenocepacia
ET-12 lineage. We previously reported that a single amino acid change from glycine to arginine at residue 378 in homogentisate 1,2-dioxygenase (HmgA) affects the pigment production phenotype: pigmented J2315 has an arginine at position 378, while non-pigmented K56-2 has a glycine at this position. Herein, we performed allelic exchange to generate isogenic non-pigmented and pigmented strains of J2315 and K56-2, respectively, and tested these to determine whether pyomelanin contributes to the protection against oxidative stress
in vitro
as well as in a respiratory infection in CGD mice
in vivo
. Our results indicate that the altered pigment phenotype does not significantly impact these strains’ ability to resist oxidative stress with H
2
O
2
and NO
in vitro
and did not change the virulence and infection outcome in CGD mice
in vivo
suggesting that other factors besides pyomelanin are contributing to the pathophysiology of these strains.

IMPORTANCE

The
Burkholderia cepacia
complex (Bcc) is a group of Gram-negative opportunistic bacteria that are often associated with fatal pulmonary infections in patients with impaired immunity, particularly those with cystic fibrosis and chronic granulomatous disease (CGD). Some Bcc strains are known to naturally produce pyomelanin, a brown melanin-like pigment known for scavenging free radicals and overcoming the host cell oxidative burst. We investigated the role of pyomelanin in
Burkholderia cenocepacia
strains J2315 (pigmented) and K56-2 (non-pigmented) and performed allelic exchange to generate isogenic non-pigmented and pigmented strains, respectively. Our results indicate that the altered pigment phenotype does not significantly impact these strains’ ability to resist H
2
O
2
or NO
in vitro
and did not alter the outcome of a respiratory infection in CGD mice
in vivo
. These results suggest that pyomelanin may not always constitute a virulence factor and suggest that other features are contributing to the pathophysiology of these strains.
Provenance history of the eastern Pearl River Mouth Basin: Implications for the evolution of the South China margin
Authors: Li Yichao , Gong Chenglin , Qiu Xinwei , Breitfeld H. Tim , Barbarand Jocelyn , Colin Christophe 
Published: May 2024

Abstract
The provenance history of the Pearl River Mouth Basin is of great significance for understanding how the South China margin evolved from a Mesozoic Andean-type subduction margin into the present-day rifted passive margin. However, the long-term provenance history of continental margin basins in the northern South China Sea is poorly understood. Newly identified Mesozoic–Cenozoic successions from the Lufeng Sag in the eastern Pearl River Mouth Basin provide valuable records of the provenance history and related evolution of the South China margin. Here, we trace the provenance of the eastern Pearl River Mouth Basin using U-Pb ages of zircon and ZTR values (proportions of zircon, tourmaline, and rutile in all transparent heavy minerals) of heavy minerals, and determine the tectonic setting and crustal thickness using trace element ratios and Eu anomalies in zircon. The results show that from the middle Eocene strata—which have a U-Pb age spectrum similar to strata of the Upper Cretaceous—to the Miocene strata, the proportion of Mesozoic age populations gradually increases, while the proportion of Paleozoic age populations decreases. In addition, following the middle Eocene high values, the ZTR values decreased during the late Eocene and then increased during the early Oligocene. Based on the variations in zircon age populations and ZTR values, the middle Eocene sediment is interpreted to have been recycled from Upper Cretaceous to middle Eocene successions, followed by an early Oligocene provenance change from intrabasinal to extrabasinal sources. Moreover, the zircon trace element ratios and Eu anomalies indicate that a widespread Mesozoic continental magmatic arc formed before ca. 90 Ma along the South China margin, and the crust simultaneously thickened during this time. In accordance with the provenance history, the evolution of the South China margin is divided into three tectonic phases: the Paleo-Pacific, Proto-South China Sea, and South China Sea. During the transition from the Paleo-Pacific to the Proto-South China Sea tectonic phase, sediment was recycled from Upper Cretaceous to middle Eocene successions in the eastern Pearl River Mouth Basin. During the transition from the Proto-South China Sea to the South China Sea tectonic phases, the provenance changed from intrabasinal to extrabasinal sources.
Structural, Electromagnetic and Thermodynamic Analysis of Ion Pollutants Adsorption in Water by Gallium Nitride Nanomaterial: a Green Chemistry Application
Authors: Mollaamin F. , Monajjemi M. 
Published: May 2024

Abstract
Gallium nitride (Ga–N) nanocage can effectively remove alkali and alkaline earth metal ions from water. Therefore, it has been found a selective competition for metal cations in the Ga–N. The electronic, magnetic and thermodynamic properties of alkali-alkaline earth metal ion-adsorbed Ga–N have been investigated using density functional theory. The results denote that alkali/alkaline earth-metal ion-adsorbed Ga–N systems are stable compounds, with the most stable adsorption site being the center of the cage ring. In addition, because of charge transfer from Ga–N to the alkali/alkaline earth-metal cations show clear n-type adsorbing behavior. The absorption of alkali metal atoms on alkali/alkaline earth-metal cations occur via chemisorption. In this article, the behavior of trapping of main group cations of Li+, Na+, K+, Be2+, Mg+ and Ca2+ by gallium nitride nanocone was observed for sensing the water metal cations. The essence of covalent traits for these clusters has displayed the similar energy value and image of the PDOS for the p states of N, the d states of Ga and s orbitals of metal cations including Li+, Na+, K+/Be2+, Mg2+ and Ca2+ through water treatment. The partial density of states (PDOS) can also estimate a certain charge assembly between Li+, Na+, K+/Be2+, Mg2+ and Ca2+ and Ga–N which indicate the complex dominant of metallic features and an exact degree of covalent traits between alkali/alkaline earth-metal cations and gallium nitride nanocage. Furthermore, the NMR spectroscopy has indicated the remarkable peaks around metal elements of Li+, Na+, K+, Be2+, Mg+ and Ca2+ through the trapping in the Ga–N during ion detection and removal from water; however, there are some fluctuations in the chemical shielding behaviors of isotropic and anisotropy attributes. In addition, all accounted $$\Delta G_{R}^{o}$$ amounts are very close, which demonstrate the agreement of the measured specifications by all methodologies and the reliability of the computing values.
Correlations between ambient air pollution and the prevalence of hospitalisations and emergency room visits for respiratory diseases in children: a systematic review
Authors: de Souza Aline Priscila , Souza Gomez Carla Cristina , Gonçalves de Oliveira Ribeiro Maria Angela , Dornhofer Paro Costa Paula , Ribeiro José Dirceu 
Published: May 2024

Objective
It is known that exposure to air pollution is associated with an increased risk for cardiovascular and respiratory diseases. This review aimed to summarise observational studies on the impact of short and long-term exposure to ambient air pollution on prevalence of hospitalisations and/or emergency department visits caused by respiratory diseases in children and adolescents.

Sources
Pubmed, Scopus, Embase and Cochrane Library databases were searched for the years 2018 to December 2022, including studies in any language.

Summary of the findings

A total of 15 studies published between 2018 and 15 January 2022 were included in this review. PM
2.5
was the most type of particulate matter studied. Short-term exposure to PM
2,5
, PM
10
, NO
2
, SO
2
and O
3
, even at concentrations less than the current health-based guidelines, was significantly correlated with increased risk of outpatient/hospital visits and hospitalisations for respiratory diseases by children.

Conclusions
Our findings emphasise the importance and urgency of long-term control of air pollution and pollution-related diseases, especially among children and adolescents. There is a need for further research employing more homogeneous methodologies for assessing exposure and outcome measurements, in order to enable systematic reviews with meta-analysis.
Comparison of parent or caregiver-completed development screening tools with Bayley Scales of Infant Development: a systematic review and meta-analysis
Authors: Balasubramanian Haribalakrishna , Ahmed Javed , Ananthan Anitha , Srinivasan Lakshmi , Mohan Diwakar 
Published: May 2024

BackgroundParent/caregiver-completed developmental testing (PCDT) is integral to developmental care in children; however, there is limited information on its accuracy. In this systematic review, we compared the diagnostic accuracy of PCDT with concurrently administered Bayley Scales of Infant Development for detection of developmental delay (DD) in children below 4 years of age.MethodsWe searched databases PubMed, Embase, CINAHL, PsycINFO and Google Scholar until November 2023. Bivariate and multiple thresholds summary receiver operating characteristics were used to obtain the summary sensitivity and specificity with 95% CIs. The Quality Assessment of Diagnostic Accuracy Studies-2 tool was used for risk of bias assessment.ResultsA total of 38 studies (31 in the meta-analysis) were included. Ages and Stages Questionnaire (ASQ) and Parent Report of Children’s Abilities-Revised (PARCA-R) were the most commonly evaluated PCDTs. ASQ score >2 SD below the mean had an overall sensitivity of 0.72 (0.6, 0.82) and 0.63 (0.50, 0.75) at a median specificity of 0.89 (0.82, 0.94) and 0.81 (0.76, 0.86) for diagnosing moderate to severe DD and severe DD, respectively. PARCA- R had an overall sensitivity of 0.69 (0.51, 0.83) at median specificity of 0.75 (0.64, 0.83) for predicting severe DD. Participant selection bias and partial verification bias were found in over 50% of the studies. The certainty of evidence was low for the studied outcomes.ConclusionsThe most commonly studied parental tools, ASQ and PARCA-R, have moderate to low sensitivity and moderate specificity for detecting DD in young children. High risk of bias and heterogeneity in the available data can potentially impact the interpretation of our results.PROSPERO registration numberCRD42021268629.
18F-FDG PET/MR for diagnosis of primary central nervous system lymphoma: protocol for a systematic review and meta-analysis
Authors: Qiu Xiaowei , Zheng Hong , Zhong Fangming , Shen Bin 
Published: May 2024

BackgroundPrimary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin’s lymphoma with poor prognosis. 18F-flourodeoxyglucose positron emission tomography (PET)/magnetic resonance (MR) combines the advantages of PET and MR. The aim of this study is to evaluate the validity of PET/MR for the diagnosis of PCNSL by means of a meta-analysis.Methods and analysisWanfang Database, SinoMed, China National Knowledge Infrastructure, the Cochrane Library, PubMed and Embase will be searched for candidate studies about PET/MRI in PCNSL diagnosis from database inception to October 2024. The following keywords will be applied: “Primary central nervous system lymphoma”, “Primary intracerebral lymphoma”, “Positron Emission Tomography Magnetic Resonance” and “PET-MR”. Studies meeting the inclusion criteria will be included. Studies without full true positive, false positive, false negative and true negative values; studies reported in languages other than English and Chinese; conference abstracts not available in full text and case reports will be excluded. Quality Assessment of Diagnostic Accuracy Studies will be used to evaluate the study quality. The STATA software (V.15.0) and Meta-Disc software (V.1.4) will be used to carry out meta-analysis. When heterogeneity is evident, subgroup analysis will be used to investigate the origin of heterogeneity. The robustness of the analysis will be checked with sensitivity analysis.Ethics and disseminationThis research is based on public databases and does not require ethical approval. The results will seek publication in a peer-reviewed journal after the completion of this systematic review and meta-analysis.PROSPERO registration numberCRD42023472570.
Some remarks on the subrack lattice of finite racks
Authors: Kayacan Selçuk 
Published: May 2024

The set of all subracks [Formula: see text] of a finite rack [Formula: see text] forms a lattice under inclusion. We prove that if a rack [Formula: see text] satisfies a certain condition then the homotopy type of the order complex of [Formula: see text] is a [Formula: see text]-sphere, where [Formula: see text] is the number of maximal subracks of [Formula: see text]. The rack [Formula: see text] satisfying the condition of this general result is necessarily decomposable. Two particular instances occur when [Formula: see text] is a group rack, and when [Formula: see text] is a conjugacy class rack of a nilpotent group. We also studied the subrack lattices of indecomposable racks by focusing on the conjugacy class racks of symmetric or alternating groups and determined the homotopy types of the corresponding order complexes in some cases.