bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of MALDI-TOF MS, real-time PCR, antigen detection, and automated biochemical testing for the identification of
Burkholderia pseudomallei
Authors: Campbell Stuart , Taylor Brooke , Menouhos Dimitrios , Hennessy Jann , Mayo Mark , Baird Robert , Currie Bart J. , Meumann Ella M. 
Published: September 2024

ABSTRACT

Burkholderia pseudomallei
is the causative agent of melioidosis, a disease highly endemic to Southeast Asia and northern Australia, though the area of endemicity is expanding. Cases may occur in returning travelers or, rarely, from imported contaminated products. Identification of
B. pseudomallei
is challenging for laboratories that do not see this organism frequently, and misidentifications by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and automated biochemical testing have been reported. The
in vitro
diagnostic database for use with the Vitek MS has recently been updated to include
B. pseudomallei
and we aimed to validate the performance for identification in comparison to automated biochemical testing with the Vitek 2 GN card, quantitative real-time polymerase chain reaction (qPCR) targeting the type III secretion system, and capsular polysaccharide antigen detection using a lateral flow immunoassay (LFA). We tested a “derivation” cohort including geographically diverse
B. pseudomallei
and a range of closely related
Burkholderia
species, and a prospective “validation” cohort of
B. pseudomallei
and
B. cepacia
complex clinical isolates. MALDI-TOF MS had a sensitivity of 1.0 and specificity of 1.0 for the identification and differentiation of
B. pseudomallei
from related
Burkholderia
species when a certainty cutoff of 99.9% was used. In contrast, automated biochemical testing for
B. pseudomallei
identification had a sensitivity of 0.83 and specificity of 0.88. Both qPCR and LFA correctly identified all
B. pseudomallei
isolates with no false positives. Due to the high level of accuracy, we have now incorporated MALDI-TOF MS into our laboratory’s
B. pseudomallei
identification workflow.

IMPORTANCE

Burkholderia pseudomallei
causes melioidosis, a disease associated with high morbidity and mortality that disproportionately affects rural areas in Southeast Asia and northern Australia. The known area of endemicity is expanding and now includes the continental United States. Laboratory identification can be challenging which may result in missed or delayed diagnoses and poor patient outcomes. In this study, we compared mass spectrometry using an updated spectral database with multiple other methods for
B. pseudomallei
identification and found mass spectrometry highly accurate. We have therefore incorporated this fast and cost-effective method into our laboratory’s workflow for
B. pseudomallei
identification.
Breast cancer colonization by
Malassezia globosa
accelerates tumor growth
Authors: Liu Miao-Miao , Zhu Hui-Hui , Bai Jie , Tian Zi-Ye , Zhao Yu-Jing , Boekhout Teun , Wang Qi-Ming 
Published: September 2024

ABSTRACT

Malassezia globosa
is a lipophilic
basidiomycetous
yeast that occurs abundantly in breast tumors and that may contribute to a shortened overall survival of breast cancer (BRAC) patients, suggesting that the yeast may participate in the carcinogenesis of BRAC. However, the mechanisms involved in the
M. globosa
-based acceleration of BRAC are unknown. Here, we show that
M. globosa
can colonize mammary tissue in 7,12-dimethylbenz[a] anthracene-induced mice. The abundance of
M. globosa
shortened the overall survival and increased the tumor incidence. Transcriptome data illustrated that IL-17A plays a key role in tumor growth due to
M. globosa
colonization, and tumor-associated macrophage infiltration was elevated during
M. globosa
colonization which triggers M2 polarization of macrophages via toll-like receptors 4/nuclear factor kappa-B (Nf-κB) signaling. Our results show that the expression of sphingosine kinase 1 (Sphk1) is increased in breast tumors after inoculation with
M. globosa
. Moreover, we discovered that Sphk1-specific small interfering RNA blocked the formation of lipid droplets, which can effectively alleviate the expression of the signal transducer and activator of the transcription 3 (STAT3)/Nf-κB pathway. Taken together, our results demonstrate that
M. globosa
could be a possible factor for the progression of BRAC. The mechanisms by which
M. globosa
promotes BRAC development involve the IL-17A/macrophage axis. Meanwhile, Sphk1 overexpression was induced by
M. globosa
infection, which also promoted the proliferation of MCF-7 cells.

IMPORTANCE

Literature has suggested that
Malassezia globosa
is associated with breast tumors; however, this association has not been confirmed. Here, we found that
M. globosa
colonizes in breast fat pads leading to tumor growth. As a lipophilic yeast, the expression of sphingosine kinase 1 (Sphk1) was upregulated to promote tumor growth after
M. globosa
colonization. Moreover, the IL-17A/macrophages axis plays a key role in mechanisms involved in the
M. globosa
-induced breast cancer acceleration from the tumor immune microenvironment perspective.
Complete genome of
Streptococcus agalactiae
strain XM_1
Authors: Guo Yingzhu , Zhu Yao , Lin Xinzhu , Wang Dai 
Published: September 2024

ABSTRACT

Streptococcus agalactiae
can cause a variety of human diseases, posing a deadly threat especially in the case of infections in newborns. A strain of
Streptococcus agalactiae
, designated as XM_1, was isolated from a newborn with severe clinical symptoms. Here, the genome sequence of
Streptococcus agalactiae
strain XM_1 is presented.
Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome
Authors: Liu Luyao , Ma Lin , Liu Huan , Zhao Fan , Li Pu , Zhang Junhua , Lü Xin , Zhao Xin , Yi Yanglei 
Published: September 2024

ABSTRACT

Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death. Modulating the gut microbiome is a promising therapeutic approach for managing SIRS. This study assesses the therapeutic potential of the Xuanfei Baidu (XFBD) formula in treating SIRS. The results showed that XFBD administration effectively reduced mortality rates and inflammation in SIRS mice. Using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we substantiated that the therapeutic effects of XFBD are partly attributed to gut microbiota modulation. We conducted
in vitro
experiments to accurately assess the gut microbiome remodeling effects of 51 compounds isolated from XFBD. These compounds exhibited varying abilities to induce a microbial structure that closely resembles that of the healthy control group. By quantifying their impact on microbial structure and clustering their regulatory patterns, we devised multiple gut microbiome remodeling compound (GMRC) cocktails. GMRC cocktail C, comprising aucubin, gentiopicroside, syringic acid, gallic acid, p-hydroxybenzaldehyde, para-hydroxybenzoic acid, and isoimperatorin, demonstrated superior efficacy in treating SIRS compared to a single compound or to other cocktails. Finally,
in vitro
experiments showcased that GMRC cocktail C effectively rebalanced bacteria composition in SIRS patients. This study underscores XFBD’s therapeutic potential in SIRS and highlights the importance of innovative treatment approaches for this disease by targeting the gut microbiota.

IMPORTANCE
Developing effective treatment strategies for systemic inflammatory response syndrome (SIRS) is crucial due to its severe and often life-threatening nature. While traditional treatments like dexamethasone have shown efficacy, they also come with significant side effects and limitations. This study makes significant strides by demonstrating that the Xuanfei Baidu (XFBD) formula can substantially reduce mortality rates and inflammation in SIRS mice through effective modulation of the gut microbiota. By quantitatively assessing the impact of 51 compounds derived from XFBD on the gut microbiome, we developed a potent gut microbiome remodeling compound cocktail. This cocktail outperformed individual compounds and other mixtures in efficacy against SIRS. These findings highlight the potential of XFBD as a therapeutic solution for SIRS and underscore the critical role of innovative strategies targeting the gut microbiota in addressing this severe inflammatory condition.
TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs
Authors: Sweet Philip , Burroughs Matthew , Jang Sungyeon , Contreras Lydia 
Published: September 2024

ABSTRACT

The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined
D
10
values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (
D
10
< 200 Gy) and radiation-tolerant (
D
10
> 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (
D
10
< 200 Gy) in the training data set had been confined to the phylum
Proteobacterium
, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a
Bacteroidota
species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.

IMPORTANCE

Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses
de novo
-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.
Where are we with gastric cancer screening in Europe in 2024?
Authors: Leja Mārcis 
Published: September 2024

The absolute number of annual cases of gastric cancer in Europe is rising. The Council of the European Union has recommended implementation of gastric cancer screening for countries or regions with a high gastric cancer incidence and death rates. However, as of 2024 no organised gastric cancer screening programme has been launched in Europe.There are several ways to decrease gastric cancer burden, but thescreen and treat strategyforHelicobacter pylori (H. pylori) seems to be the most appropriate for Europe. It has to be noted that increased use of antibiotics would be associated with this strategy.Only organised population-based cancer screening is recommended in the European Union, therefore gastric cancer screening also is expected to fulfil the criteria of an organised screening programme. In this respect, several aspects of screening organisation need to be considered before full implementation of gastric cancer prevention in Europe; the age range of the target group, test types,H. pylorieradication regimens and surveillance strategies are among them. Currently, ongoing projects (GISTAR, EUROHELICAN, TOGAS and EUCanScreen) are expected to provide the missing evidence. Feedback from the decision-makers and the potential target groups, including vulnerable populations, will be important to planning the programme.This paper provides an overview of the recent decisions of the European authorities, the progress towards gastric cancer implementation in Europe and expected challenges. Finally, a potential algorithm for gastric cancer screening in Europe is proposed.
Agreement between patient-reported flares and clinically significant flare status in patients with rheumatoid arthritis in sustained remission: data from the ARCTIC REWIND trials
Authors: Holten Karen , Paulshus Sundlisæter Nina , Sexton Joseph , Kjørholt Kaja E , Nordberg Lena Bugge , Moholt Ellen , Uhlig Till , van der Heijde Désirée , Solomon Daniel H , Haavardsholm Espen A , Lillegraven Siri , Aga Anna-Birgitte 
Published: September 2024

ObjectivesTo explore the agreement between patient-reported flare status and clinically significant flare status in patients with rheumatoid arthritis (RA) in sustained remission.MethodPatients with RA in remission for ≥12 months on stable treatment were included in the ARCTIC REWIND tapering trials and pooled 12-month data used in current analyses. Patient-reported flare status was assessed according to the Outcome Measures in Rheumatology flare questionnaire; ‘Are you having a flare of your RA at this time?’ (yes/no). A clinically significant flare was defined as a combination of Disease Activity Score (DAS) >1.6, increase in DAS of ≥0.6 and 2 swollen joints, or the rheumatologist and patient agreed that a clinically significant flare had occurred. Agreement coefficient, sensitivity, specificity and predictive values of patient-reported flare status with regard to clinically significant flare status were determined.ResultsOf 248 patients, 64% were women, age 56.1 (11.8) years, disease duration 4.1 (2.8–7.4) years, DAS 0.8 (0.3). 35% of patients reported a flare at least once, clinically significant flares were recorded in 21%. 48/53 clinically significant flares (91%) led to an intensification of disease-modifying antirheumatic drugss. In 621/682 (91%) visits, patient-reported and clinically significant flare status were in agreement, agreement coefficient 0.89. Sensitivity and specificity were both 91%, positive predictive value of patient-reported flare status 46% and negative predictive value 99%.ConclusionAmong patients in sustained remission, patient-reported flare status was accurate in ruling out a clinically significant flare. About half of the patient-reported flares were assessed to be clinically significant. These findings support a potential for using patient-reported flare status in remote monitoring of patients with RA in sustained remission.
Use of a five-category partner-type classification within a chlamydia and gonorrhoea service evaluation highlights opportunities for targeted partner notification to improve STI control
Authors: McMahon Beth Louise , Buitendam Erna , Symonds Merle , Estcourt Claudia S , Saunders John 
Published: September 2024

ObjectivesPartner notification (PN) is a key component of sexually transmitted infection control. British Association for Sexual Health and HIV guidelines now recommend partner-centred PN outcomes using a five-category partner classification (established, new, occasional, one-off, sex worker). We evaluated the reporting of partner-centred PN outcomes in two contrasting UK sexual health services.MethodsUsing the electronic patient records of 40 patients with a positive gonorrhoea test and 180 patients with a positive chlamydia test, we extracted PN outcomes for the five most recent sexual contacts within the appropriate lookback period.Results180 patients with chlamydia reported 262 partners: 220 were contactable (103 established, 9 new, 43 occasional, 52 one-off, 13 unknown/unrecorded). 40 patients with gonorrhoea reported 88 partners: 53 were contactable (7 established, 1 new, 14 occasional, 10 one-off and 21 unknown/not recorded). No sex worker partners were reported. Most established partners of people with chlamydia (96/103) or gonorrhoea (7/7) were notified but fewer (60/103 and 6/7, respectively) attended for testing. Of those, 39 had a positive chlamydia test and two had a positive gonorrhoea test. For both chlamydia and gonorrhoea, most occasional and new partners were reported to be notified but there was a sharper decline in those tested. For both infections, one-off partners had the lowest rates of accessing services and testing. For chlamydia, 81% were notified (42/52), 23% accessed services (12/52) and 21% tested (11/52). However, 91% of those tested were positive (10/11). The number of contactable one-off gonorrhoea contacts was small and few attended.ConclusionsMeasuring partner-centred PN outcomes was feasible. There were differences in partner engagement with PN between the different infections and partner types. If these findings are replicated in larger samples, it suggests that interventions to target one-off partners who have low rates of PN engagement yet high levels of positivity could play a key role in reducing infection at population level.
Specific amino acid changes correlate with pathogenic flavobacteria
Authors: Gélinas Vincent , Paquet Valérie E. , Paquet Maude F. , Charette Steve J. , Vincent Antony T. 
Published: September 2024

Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.
Structure and astrophysical role of the neutron-rich $$55 \le Z \le 92$$ isotopes: status and perspectives
Authors: Kiss Gábor Gyula , Podolyák Zsolt 
Published: September 2024

AbstractHeavy neutron-rich nuclei are of great interest. Phenomena like shell evolution ($$N\sim 126$$

N
∼
126

, $$Z\sim 82$$

Z
∼
82

), prolate–triaxial–oblate–spherical shape evolution ($$Z=$$

Z
=

70–80), possible deformed shell closures or structure change in the rare-earth region are under intense scrutiny. This latter is closely linked to the rare-earth r-process peak, while the $$N \sim 126$$

N
∼
126

nuclei are connected to the third r-process peak at $$A \sim 195$$

A
∼
195

. Recent technical developments (e.g. increasing beam intensities at fragmentation facilities, new detection systems) provided huge amount of new experimental data, published in the last decade, allowing to probe structure and astrophysical models. Experimental methods and recent results are reviewed and future opportunities discussed.
2d (0, 2) gauge theories from branes: Recent progress in brane brick models
Authors: Franco Sebastián 
Published: September 2024

We discuss the realization of [Formula: see text] [Formula: see text] gauge theories in terms of branes focusing on Brane Brick Models, which are T-dual to D1-branes probing toric Calabi–Yau 4-folds. These brane setups fully encode the infinite class of [Formula: see text] [Formula: see text] quiver gauge theories on the worldvolume of the D1-branes and substantially streamline their connection to the probed geometries. We review various methods for efficiently generating Brane Brick Models. These algorithms are then used to construct [Formula: see text] [Formula: see text] gauge theories for the cones over all the smooth Fano 3-folds and two infinite families of Sasaki–Einstein 7-manifolds with known metrics.
Effectiveness of External Precooling and Vibration Induced by BUZZY on Pain and Anxiety During Inferior Alveolar Nerve Block Injection in Children
Authors: Narimany Reyhane , Faghihian Reyhaneh , Jafarzadeh Samani Mehdi 
Published: September 2024

Purpose: Children’s fear of the injection of local anesthetic agents affects their cooperation in pediatric dentistry. Different techniques are available to decrease the injection pain, including the use of precooling agents or vibrators. The present study investigated the effectiveness of Buzzy (Buzzy MMJ Labs, Atlanta, GA, USA). This device transfers cold and external vibration to the injection site during the inferior alveolar nerve block (IANB) injection.Materials and Methods: The present self‐control, randomized, and double‐blind clinical trial evaluated 30 children aged 6–12, who had bilateral mandibular permanent or primary carious molar teeth. On one side, the BUZZY was applied before and during the IANB injection, and the other side was considered as control. On both sides, a topical anesthetic gel was applied before injection. The pain severity and children’s anxiety were determined using Wong–Baker, face, leg, activity, cry, consolability (FLACC) scales, and the heart rate.Results: The mean age of the participants was 7.18 ± 1.5 years, with 12 girls and 18 boys. The Wong–Baker scale and FLACC scale did not show any statistically significant difference between BUZZY and control (p value = 0.9 and 0.15, respectively). In addition, BUZZY tool did not significantly decrease pain and anxiety during injection, assessed through the heart rate difference (p = 0.38).Conclusion: Under the limitations of the present study, a combination of precooling and vibration using the BUZZY device did not decrease pain and anxiety in children during the IANB injection.