bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multispecies emergence of dual
bla
KPC/NDM
carbapenemase-producing Enterobacterales recovered from invasive infections in Chile
Authors: Quesille-Villalobos Ana M. , Solar Camila , Martínez Jose R. W. , Rivas Lina , Quiroz Valeria , González Ana M. , Riquelme-Neira Roberto , Ugalde Juan A. , Peters Anne , Ortega-Recalde Oscar , Araos Rafael , García Patricia , Lebreton Francois , Munita Jose M. , Diaz Lorena 
Published: December 2024

ABSTRACT

Carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) represent a significant global threat. The emergence of dual CP-CRE is particularly alarming, as they can potentially compromise the efficacy of newer antibiotics, further decreasing therapeutic alternatives. Herein, we report the emergence of multiple species of CP-CRE recovered from invasive infections in Chile that simultaneously harbor
bla
KPC
and
bla
NDM
and provide an in-depth genomic characterization of these worrisome pathogens. We collected carbapenem-resistant Enterobacterales (CRE) isolates from invasive infections over a 4-year period, across 11 healthcare centers in Chile. Bacterial species and the presence of carbapenemase genes were confirmed using MALDI-TOF and PCR assays, respectively. Antimicrobial susceptibility testing was conducted through disk diffusion and broth microdilution methods. Dual CP-CRE isolates were subjected to short- and long-read whole genome sequencing to perform a detailed genomic characterization of the isolates and of the mobile genetic elements harboring the enzymes. From a total of 1,335 CRE isolates, we observed an increase in the prevalence of CP-CRE, from 11% in 2019 to 38% in 2022. A total of 11 dual CP-CRE isolates were recovered, all of them harboring
bla
KPC
and
bla
NDM
. Species corresponded to
Escherichia coli
(
n
= 6),
Klebsiella pneumoniae
(
n
= 2),
Klebsiella oxytoca
(
n
= 2), and
Citrobacter freundii
(
n
= 1). Dual CP-CRE isolates exhibited resistance to all tested β-lactams except for cefiderocol. The
bla
KPC
and
bla
NDM
encoding genes were located on independent plasmids. Platforms harboring
bla
KPC
were diverse and included IncN, IncF, and IncFIB plasmids. In contrast,
bla
NDM-7
was only found on fairly conserved IncX3 plasmids. We report that a rapid increase of CP-CRE in Chile, alongside with the emergence of multiple bacterial species of CP-CRE co-harboring
bla
KPC-2/3
and
bla
NDM-7
, underscores a critical public health challenge. Our data suggest that the dissemination of
bla
NDM-7
was predominantly facilitated by IncX3 plasmids, whereas the spread of
bla
KPC
involved multiple plasmid backbones. Active surveillance and genomic monitoring are critical to inform public policy and curtail the spread of these highly resistant pathogens.
Transcriptional delineation of polysaccharide utilization loci in the human gut commensal
Segatella copri
DSM18205 and co-culture with exemplar
Bacteroides
species on dietary plant glycans
Authors: Panwar Deepesh , Briggs Jonathon , Fraser Alexander S. C. , Stewart William A. , Brumer Harry 
Published: December 2024

ABSTRACT

There is growing interest in members of the genus
Segatella
(family
Prevotellaceae
) as members of a well-balanced human gut microbiota (HGM).
Segatella
are particularly associated with the consumption of a diet rich in plant polysaccharides comprising dietary fiber. However, understanding of the molecular basis of complex carbohydrate utilization in
Segatella
species is currently incomplete. Here, we used RNA sequencing (RNA-seq) of the type strain
Segatella copri
DSM 18205 (previously
Prevotella copri
CB7) to define precisely individual polysaccharide utilization loci (PULs) and associated carbohydrate-active enzymes (CAZymes) that are implicated in the catabolism of common fruit, vegetable, and grain polysaccharides (
viz
. mixed-linkage β-glucans, xyloglucans, xylans, pectins, and inulin). Although many commonalities were observed, several of these systems exhibited significant compositional and organizational differences
vis-à-vis
homologs in the better-studied
Bacteroides
(sister family
Bacteroidaceae
), which predominate in post-industrial HGM. Growth on β-mannans, β(1, 3)-galactans, and microbial β(1, 3)-glucans was not observed, due to an apparent lack of cognate PULs. Most notably,
S. copri
is unable to grow on starch, due to an incomplete starch utilization system (Sus). Subsequent transcriptional profiling of bellwether Ton-B-dependent transporter-encoding genes revealed that PUL upregulation is rapid and general upon transfer from glucose to plant polysaccharides, reflective of de-repression enabling substrate sensing. Distinct from previous observations of
Bacteroides
species, we were unable to observe clearly delineated substrate prioritization on a polysaccharide mixture designed to mimic
in vitro
diverse plant cell wall digesta. Finally, co-culture experiments generally indicated stable co-existence and lack of exclusive competition between
S. copri
and representative HGM
Bacteroides
species (
Bacteroides thetaiotaomicron
and
Bacteroides ovatus
) on individual polysaccharides, except in cases where corresponding PULs were obviously lacking.

IMPORTANCE

There is currently a great level of interest in improving the composition and function of the human gut microbiota (HGM) to improve health. The bacterium
Segatella copri
is prevalent in people who eat plant-rich diets and is therefore associated with a healthy lifestyle. On one hand, our study reveals the specific molecular systems that enable
S. copri
to proliferate on individual plant polysaccharides. On the other, a growing body of data suggests that the inability of
S. copri
to grow on starch and animal glycans, which dominate in post-industrial diets, as well as host mucin, contributes strongly to its displacement from the HGM by
Bacteroides
species, in the absence of direct antagonism.
Tethered release of the pseudorabies virus deubiquitinase from the capsid promotes enzymatic activity
Authors: Antinone Sarah E. , Miller John S. , Huffmaster Nicholas J. , Pickard Gary E. , Smith Gregory A. 
Published: December 2024

ABSTRACT

Herpesviruses carry an assortment of proteins in the interstitial space between the capsid and membrane envelope, collectively referred to as the tegument. Upon virion fusion with a cell, envelope integrity is disrupted, and many tegument constituents disperse into the cytosol to carry out individual effector functions, while others direct transport of the capsid to the nucleus. To gain insight into the tegument dynamics that occur with disruption of envelope integrity, we used a combination of single-particle fluorescence and biochemical approaches that leveraged the previously established use of n-ethylmaleimide to inhibit virion dynamics. We document that the large tegument protein (pUL36), which is stably bound to the capsid surface at its C-terminus, is also conditionally bound to the capsid via its N-terminal deubiquitinase (DUB) domain. The DUB is released, while remaining tethered to the capsid by the pUL36 C-terminus, by a mechanism dependent on reactive cysteines. Mutation of these cysteines locks the DUB in a capsid bound state and suppresses enzymatic activity.

IMPORTANCE
Neuroinvasive alphaherpesviruses, such as herpes simplex virus and pseudorabies virus, cause a broad range of diseases in humans and other animals. Novel strategies to interfere with the virion structural rearrangements required for infectivity could prove valuable to treat infections, yet critical aspects of the virion architecture and its metastability remain poorly defined. In this study, we document that the pUL36 tegument protein exhibits conditional capsid binding in its N-terminal deubiquitinase domain that regulates enzymatic activity during infection.
Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model
Authors: Lv Huibin , Teo Qi Wen , Lee Chang-Chun D. , Liang Weiwen , Choi Danbi , Mao Kevin J. , Ardagh Madison R. , Gopal Akshita B. , Mehta Arjun , Szlembarski Matt , Bruzzone Roberto , Wilson Ian A. , Wu Nicholas C. , Mok Chris K. P. 
Published: December 2024

ABSTRACT

Understanding how immune history influences influenza immunity is essential for developing effective vaccines and therapeutic strategies. This study examines the antigenic imprinting of influenza hemagglutinin (HA) and neuraminidase (NA) using a mouse model with sequential infections by H1N1 virus strains exhibiting substantial antigenic differences in HA. In our pre-2009 influenza infection model, we observed that mice with more extensive infection histories produced higher levels of functional NA-inhibiting antibodies (NAI). However, following further infection with the 2009 pandemic H1N1 strain, these mice demonstrated a reduced NAI to the challenged virus. Interestingly, prior exposure to older strains resulted in a lower HA antibody response (neutralization and HAI) to the challenged virus in both pre- and post-2009 scenarios, potentially due to faster viral clearance facilitated by immune memory recall. Overall, our findings reveal distinct trajectories in HA and NA immune responses, suggesting that immune imprinting can differentially impact these proteins based on the extent of antigenic variation in influenza viruses.

IMPORTANCE
Influenza viruses continue to pose a significant threat to human health, with vaccine effectiveness remaining a persistent challenge. Individual immune history is a crucial factor that can influence antibody responses to subsequent influenza exposures. While many studies have explored how pre-existing antibodies shape the induction of anti-HA antibodies following influenza virus infections or vaccinations, the impact on anti-NA antibodies has been less extensively studied. Using a mouse model, our study demonstrates that within pre-2009 H1N1 strains, an extensive immune history negatively impacted anti-HA antibody responses but enhanced anti-NA antibody responses. However, in response to the 2009 pandemic H1N1 strain, which experienced an antigenic shift, both anti-HA and anti-NA antibody responses were hindered by antibodies from prior pre-2009 H1N1 virus infections. These findings provide important insights into how antigenic imprinting affects both anti-HA and anti-NA antibody responses and underscore the need to consider immune history in developing more effective influenza vaccination strategies.
Serine/threonine protein kinase mediates rifampicin resistance in
Brucella melitensis
through interacting with ribosomal protein RpsD and affecting antioxidant capacity
Authors: Yuan Yaqin , Ning Wenqing , Chen Junjie , Li Jiquan , Xue Tianqi , An Cuihong , Mao Lingling , Zhang Guangzhi , Zhou Shizhong , Ding Jiabo , Yang Xiaowen , Ye Jianqiang 
Published: December 2024

ABSTRACT

Brucellosis, a zoonotic disease, has re-emerged in both humans and animals, causing significant economic losses globally. Recently, an increasing number of rifampicin-resistant
Brucella
strains have been isolated worldwide without detectable mutations in known antibiotic resistance genes. Here, this study identified the deletion of serine/threonine protein kinase (STPK) gene in
B. melitensis
as an efficient trigger for rifampicin resistance using bioinformatics predictions, a transposon mutant library, and gene mutation strains. Notably, the absence of the STPK could increase the expression of ribosomal proteins and genes involved in sulfur metabolism and reduced glutathione, and decrease NADPH oxidase activity and NADP
+
/NADPH ratio, which is associated with the antioxidant capacity of
B. melitensis
. Moreover, co-immunoprecipitation revealed that STPK could efficiently interact with the ribosomal protein RpsD, possibly altering protein translation and riboswitch expression. These findings demonstrate that the STPK gene mediates resistance by regulating sulfur metabolism to counteract the reactive oxygen species induced by rifampicin. Furthermore, the approaches developed in this study provide a platform for screening new resistance genes in
Brucella
spp., and the identified STPK or its pathway can serve as a potential target for new drug development against rifampicin-resistant
Brucella
spp.

IMPORTANCE

New rifampicin resistance gene in
Brucella melitensis
is identified via bioinformatics predictions and a whole-genome transposon mutant library, new mechanisms of rifampicin resistance in
B. melitensis
, and new function of serine/threonine protein kinase gene and its interaction proteins.
Study of Parameters and Characteristics of Turbulent Flow in the Working Zone of a Wind Tunnel
Authors: Poddaeva O. I. , Zubkov A. F. 
Published: December 2024

Abstract
This study presents an experimental investigation of turbulent flow characteristics within a wind-tunnel environment. A methodology was developed to analyze the parameters and characteristics of the turbulent flow in the wind tunnel’s test section. This methodology encompasses the determination of the reproducible range of air velocity, airflow velocity instability, nonuniformity of the airflow velocity field. The findings from the velocity field analysis demonstrate the feasibility of conducting aerodynamic tests on models subjected to a uniform flow within the wind tunnel.
Low-temperature Stepper Motor Operating in High Magnetic Field
Authors: Iafarova A. F. , Kholin D. I. , Sosin S. S. 
Published: December 2024

Abstract—
A stepper electric motor has been designed to rotate a sample in an experimental cell inside a cryostat with 3He pumping. The device based on a rotor with crossed electrical windings, operates in an external magnetic field generated by a superconducting magnet. A prototype of the motor was mounted on a microwave spectrometer with a rectangular resonator. Test angular dependence of the magnetic resonance spectrum was obtained in a well-studied weak ferromagnet $${\text{MnC}}{{{\text{O}}}_{3}}$$ at temperatures 0.5–7.5 K in the range of angles ±100° from the initial position. Overheating of the cell and cryostat was studied and the heat release during operation of the mechanism was estimated.
Primary thymic mucosa-associated lymphoid tissue (MALT) lymphoma with Sjogren’s syndrome and diffuse cystic lung disease: a complex respiratory presentation of a multifaceted autoimmune disease
Authors: Fu Michele Y , O'Neill Robert , Silverstone Elizabeth J , Yates Deborah H 
Published: December 2024

Mucosa-associated lymphoid tissue (MALT) lymphoma is a rare form of B-cell lymphoma which can potentially affect the stomach, spleen, salivary glands, skin, lungs, orbit, and, rarely, the thymus. Patients with Sjögren’s syndrome (SjS) are at a 15–20 times increased risk of developing lymphoma compared to the general population.Here, we present a case of primary thymic MALT lymphoma and associated diffuse cystic lung disease, incidentally identified on routine chest imaging. Thymic MALT lymphoma has to date been reported primarily in women of Chinese origin, mainly without cystic lung disease. Diffuse cystic lung disease is well documented in women with SjS and the differential diagnoses also include lymphangioleiomyomatosis, which occurs almost exclusively in women.In the case presented, CT and positron emission tomography-CT showed a large hypermetabolic anterior mediastinal mass, as well as multiple thin-walled bilateral pulmonary cysts of widely varying sizes, without abnormal uptake. The patient was largely asymptomatic. Lung function testing, however, revealed restriction rather than obstruction, which is unusual in diffuse cystic lung disease. Biopsy of the mediastinal mass confirmed thymic MALT lymphoma which was treated medically with resultant improved lung function. This case highlights the association between SjS and MALT lymphoma, illustrates features which enable distinction between different causes of cystic lung disease in SjS, and comments on the multiplicity of SjS-related lung manifestations.
Chocolate intake and risk of type 2 diabetes: prospective cohort studies
Authors: Liu Binkai , Zong Geng , Zhu Lu , Hu Yang , Manson JoAnn E , Wang Molin , Rimm Eric B , Hu Frank B , Sun Qi 
Published: December 2024

Abstract

Objective
To prospectively investigate the associations between dark, milk, and total chocolate consumption and risk of type 2 diabetes (T2D) in three US cohorts.

Design
Prospective cohort studies.

Setting
Nurses’ Health Study (NHS; 1986-2018), Nurses’ Health Study II (NHSII; 1991-2021), and Health Professionals Follow-Up Study (HPFS; 1986-2020).

Participants
At study baseline for total chocolate analyses (1986 for NHS and HPFS; 1991 for NHSII), 192 208 participants without T2D, cardiovascular disease, or cancer were included. 111 654 participants were included in the analysis for risk of T2D by intake of chocolate subtypes, assessed from 2006 in NHS and HPFS and from 2007 in NHSII.

Main outcome measure
Self-reported incident T2D, with patients identified by follow-up questionnaires and confirmed through a validated supplementary questionnaire. Cox proportional hazards regression was used to estimate hazard ratios and 95% confidence intervals (CIs) for T2D according to chocolate consumption.

Results
In the primary analyses for total chocolate, 18 862 people with incident T2D were identified during 4 829 175 person years of follow-up. After adjusting for personal, lifestyle, and dietary risk factors, participants consuming ≥5 servings/week of any chocolate showed a significant 10% (95% CI 2% to 17%; P trend=0.07) lower rate of T2D compared with those who never or rarely consumed chocolate. In analyses by chocolate subtypes, 4771 people with incident T2D were identified. Participants who consumed ≥5 servings/week of dark chocolate showed a significant 21% (5% to 34%; P trend=0.006) lower risk of T2D. No significant associations were found for milk chocolate intake. Spline regression showed a linear dose-response association between dark chocolate intake and risk of T2D (P for linearity=0.003), with a significant risk reduction of 3% (1% to 5%) observed for each serving/week of dark chocolate consumption. Intake of milk, but not dark, chocolate was positively associated with weight gain.

Conclusions
Increased consumption of dark, but not milk, chocolate was associated with lower risk of T2D. Increased consumption of milk, but not dark, chocolate was associated with long term weight gain. Further randomized controlled trials are needed to replicate these findings and further explore the mechanisms.
Treatment options for chronic hypotony: a scoping review protocol
Authors: Khalil Rana , Dias Karla Orsine Murta , Sutaria Aman , Shah Diya , Bokre Desta , Petrushkin Harry 
Published: December 2024

IntroductionChronic ocular hypotony (low intraocular pressure (IOP)) is a potentially sight-threatening condition. Although there is some controversy as to what constitutes non-physiological IOP, generally it is accepted as an IOP of 6.5 mm Hg or less, measured on three separate occasions and lasting for at least 3 months. There is a paucity of data in the literature describing the management of this potentially blinding condition. As such, there is no standardised treatment regime available and no consensus on expected visual prognosis.Methods and analysisThe protocol for this scoping review will follow best practice as outlined by the JBI Scoping Review Methodology Group. This review will employ the population, concept, and context model for synthesis of the review questions. Databases searched will be Ovid Medline, Ovid Embase, The Cochrane Central Register of Controlled Trials, Web of Science and Scopus databases, as well as reference lists of relevant articles and the grey literature. Key concepts identified for conducting the literature search will be ‘Ocular hypotony’, ‘medication’ and ‘surgery’. Eligibility criteria include all adults undergoing medical or surgical treatment for chronic ocular hypotony. In order to validate this search strategy, we performed a sample search on Ovid Medline from 1946 to February 2024. Following the selection process, a custom form was developed in Microsoft Excel for data charting. We intend to summarise the data using a narrative model, with the study findings grouped based on similarities in the type of treatment and outcomes assessed.Ethics and disseminationEthical approval was not required, as our review will only include published data. We will publish the review in an open-access, peer-reviewed journal and publicise our findings at international meetings.
Patient experience of opioid use disorder treatment medications: a systematic review of contemporary qualitative research
Authors: Lowry Natalie , Najia Carina , Kelleher Mike , Mitcheson Luke , Marsden John 
Published: December 2024

ObjectivesOpioid agonist, partial agonist and antagonist medications are used to treat opioid use disorder (OUD). This was the first omnibus narrative systematic review of the contemporary qualitative literature on patient experiences of receiving these medications.DesignNarrative systematic review using the sample, phenomenon of interest, design, evaluation and research framework.Data sourcesPubMed, Embase and APA PsycINFO were searched between 1 January 2000 and 14 June 2023, with the addition of hand searches.Eligibility criteria for selecting studiesQualitative and mixed methods studies among adults with experience of receiving OUD treatment medication in community and criminal justice settings.Data extraction and synthesisOne reviewer conducted searches using the pre-registered strategy. Two independent reviewers screened studies and assessed quality using the Consolidation Criteria for Reporting Qualitative tool. Identified reports were first categorised using domains from the addiction dimensions for assessment and personalised treatment (an instrument developed to guide OUD treatment planning), then by narrative synthesis.ResultsFrom 1129 studies, 47 reports (published between 2005 and 2023) were included. Five major themes (and nine subthemes) were identified: (1) expectations about initiating treatment (barriers to access; motivations to receive medication); (2) responses to medication induction and stabilisation; (3) experience of the dispensing pharmacy (attending; medication dispensing); (4) experiences of maintenance treatment (services; dose adjustment; personal and social functioning); and (5) social factors (integration and stigma) and experiences of discontinuing treatment. Together these themes reflected and endorsed the importance of patient-centred care and clinically integrated services. Further qualitative research in real-world settings is needed on extended-release buprenorphine given the relative novelty of this medication option.ConclusionsA narrative systematic review of the qualitative studies of medications for OUD endorsed the importance of patient-centred care and clinically integrated services.PROSPERO registration numberCRD42019139365.
How a growing dendritic crystal reaches its stationary crystallization velocity
Authors: Alexandrov Dmitri V. , Titova Ekaterina A. , Toropova Liubov V. 
Published: December 2024

AbstractMotivated by important applications in materials science, geo- and biophysics, we develop a theory answering the question of how a growing dendritic crystal reaches its stationary crystallization velocity. To do this, we compare existing theoretical approaches, computational simulations and experimental data for crystal growth laws at certain time intervals. Taking these laws into account, we stitch together all known asymptotics and derive two generalized expressions for the crystal growth velocity as a function of time. We analyze a behaviour of these generalized laws and compare them with experiments. Both expressions have similar behaviour and well describe the experimental data. Therefore, the choice between these expressions is more a matter of taste.