bluuebunny/crossref_metadata_2025 huggingface dataset:
Reference points in sequential bargaining: theory and experiment
Authors: Brekke Kjell Arne , Ciccone Alice , Heggedal Tom‐Reiel , Helland Leif
Published: October 2023

We introduce loss aversion in an infinite‐horizon, alternating‐offers model. When outside options serve as reference points, the equilibrium of our model follows that of the standard Rubinstein bargaining model (i.e., outside options do not affect the equilibrium unless they are binding). However, when reference points are given by the resources that players contribute to the pie, the bargaining outcome changes such that a player's share increases in her contribution. We test our model's predictions in the laboratory. As predicted, only binding outside options affect the division of the pie. Data also show that contributions matter for bargaining outcomes when they are activated as reference points, but not quite as predicted by our theory. Proposers gain a higher share of the pie only when they have contributed a higher share than the opponent has.
Comparison of the effectiveness of three different rhinoplasty techniques to correct stenotic nostrils using silicone models: A case study
Authors: Franklin Phil H. , Riggs Julia , Liu Nai‐Chieh
Published: October 2023

Objective

To compare the effects of three different rhinoplasty techniques on the postoperative cross‐sectional areas (CSAs) of the nares and nasal vestibuli.

Study design

Experimental study.

Sample population

Ninety‐nine 3D‐printed, remolded silicone models of a single French bulldog's rostral nose.

Methods

Models were fabricated based on a computed tomographic (CT) scan of the nose of a French bulldog with moderately stenotic nares. Each model underwent either vertical wedge resection (VW), modified horizontal wedge resection (MHW), or ala‐vestibuloplasty (AVP) performed by a single surgeon (n = 33 per group). Preoperative and postoperative CT scans of the models were performed, and CSAs of the airway from the nares to the caudal end of the nasal vestibules were calculated.

Results

All three rhinoplasty techniques increased CSAs (adjusted p values <.001) but to different levels caudally within the nasal vestibule. Vertical wedge resection achieved this up to the start of the alar fold, MHW up to halfway between the nares and the alar fold and AVP up to the caudal nasal vestibule. Average percentage increases in CSA were 26%, 15% and 74%, respectively. Ala‐vestibuloplasty led to larger CSAs than VW and MHW from the nares to the caudal nasal vestibule (adjusted p values <.05). The proportional difference within each technique was <7%.

Conclusion

Ala‐vestibuloplasty resulted in a larger increase in the airway CSA of silicone modeled nares and nasal vestibules of a single French bulldog in comparison with VW and MHW.

Clinical significance

Ala‐vestibuloplasty can be considered for French bulldogs with moderately stenotic nares and evidence of nasal vestibular stenosis.
Degenerations of negative Kähler–Einstein surfaces
Authors: Mandel Holly
Published: October 2023

Every compact Kähler manifold with negative first Chern class admits a unique metric such that . Understanding how families of these metrics degenerate gives insight into their geometry and is important for understanding the compactification of the moduli space of negative Kähler–Einstein metrics. I study a special class of such families in complex dimension two. Following the work of Sun and Zhang in the Calabi–Yau case [2019, arXiv:1906.03368], I construct a Kähler–Einstein neck region interpolating between canonical metrics on components of the central fiber. This provides a model for the limiting geometry of metrics in the family.
Semiautomatic Mapping of Center Pivot Irrigated Areas Using Sentinel-2 Images and GEOBIA Approach
Authors: Maranha Leandro Guimarães , Antunes Alzir Felippe Buffara
Published: October 2023

Image analysis and feature extraction of remoted sensing data are significant for mapping irrigated agriculture areas as a source of information to improve water management and agricultural planning. This paper presents an image segmented base approach GEOBIA (Geographic Object-Based Image Analysis) to extract irrigated areas by Center Pivot Irrigation System (CPIS). This study suggests a semi-automated recognition of circular patterns for the mapping of irrigated regions by center pivots, using Sentinel -2 MSI images, 10 meters spatial resolution. A set of images from different seasons, humid and dry are used to maximize de CPIS’s occurrence. A multiresolution segmentation method was applied, and a large number of segment-based shape features was extracted and used as input to a feature selection procedure (shape descriptors: Area; Compactness; Circularity Factor; Length/Width; Radius of smallest enclosing ellipse; and Roundness). In addition, another shape descriptor “Circularity Factor” was developed in this research and played an important role during preliminaries classification processes. The accuracy assessment of preliminaries classifications has validated used the Circularity Factor together with the other chosen shape descriptors to reach better results to CPIS’s detection. Furthermore, 86.23% of the CPIS mapped in the classification process is in accordance with the ground truth map. This methodology can be used to map large areas in a relatively short time and provides a tool for monitoring irrigated areas.
X-ray multi-scale microfabrication system and x-ray imaging evaluation system all in one beamline
Authors: Yamamoto Kanta , Utsumi Yuichi , Sakurai Ikuya , Okada Ikuo , Hanada Kenji , Ishizawa Hidehiro , Takeo Masahiro , Watanabe Taki , Amano Sho , Suzuki Satoru , Sumitomo Koji , Yamaguchi Akinobu
Published: October 2023

We have completed a system that can achieve both deep x-ray lithography and submicron x-ray lithography with a single beamline by introducing the combination of x-ray plane and cylindrical mirrors. This x-ray lithography system can provide a large-scale microfabrication processing with 210 × 300 mm2 (A4 size). To exploit multiscale lithography, the beamline has a beam transport vacuum duct with a two-stage stacked structure and a 5-axis stage. This two-stage stacked structure allows us to fabricate both micron scale structures with high aspect ratios and submicron scale structures using the same beamline. In addition, x-ray imaging and computer tomography (CT) system are connected to the x-ray lithography system for nondestructive inspection and evaluation of the fabricated microstructures. The x-ray imaging system constructed this study has a relatively low energy range of x-ray energy in the beamline, which is in the range of 2–15 keV or less. Therefore, relatively good absorption contrast can be obtained for plastic materials, biomaterials, and the like. Since nondestructive imaging of the processed shape by x-ray lithography is possible, it is a very useful system in processing and evaluation can be performed simultaneously. This system also enables us to obtain the live images with keeping the creature alive in liquid using an indirect x-ray imaging system which converts x-ray images to visible light images through the fluorescent plate.
Mapping SARS-CoV-2 antigenic relationships and serological responses
Authors: Wilks Samuel H. , Mühlemann Barbara , Shen Xiaoying , Türeli Sina , LeGresley Eric B. , Netzl Antonia , Caniza Miguela A. , Chacaltana-Huarcaya Jesus N. , Corman Victor M. , Daniell Xiaoju , Datto Michael B. , Dawood Fatimah S. , Denny Thomas N. , Drosten Christian , Fouchier Ron A. M. , Garcia Patricia J. , Halfmann Peter J. , Jassem Agatha , Jeworowski Lara M. , Jones Terry C. , Kawaoka Yoshihiro , Krammer Florian , McDanal Charlene , Pajon Rolando , Simon Viviana , Stockwell Melissa S. , Tang Haili , van Bakel Harm , Veguilla Vic , Webby Richard , Montefiori David C. , Smith Derek J.
Published: October 2023

During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)–1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.
Complete genome sequence of
Lactiplantibacillus plantarum
BBC32B isolated from human feces sample
Authors: Kumar Vikram , Taneja Neetu Kumra , Kumar Shakti , Vashist Atul , Ahire Jayesh J. , Mishra Vijendra
Published: October 2023

We report complete genome sequence of
Lactiplantibacillus plantarum
BBC32B, which was isolated from human feces sample and submitted to Microbial-Type Culture Collection (MTCC), India with deposition number MTCC 25432. The bacteria from Lactobacillaceae family contained 3,411,152 bp; 3,425 protein coding genes, sharing 69.67% average nucleotide identity with closest species of
Lactobacillus brevis
ATCC367.
Elevated temperature alters microbial communities, but not decomposition rates, during 3 years of
in situ
peat decomposition
Authors: Roth Spencer W. , Griffiths Natalie A. , Kolka Randall K. , Oleheiser Keith C. , Carrell Alyssa A. , Klingeman Dawn M. , Seibert Angela , Chanton Jeffrey P. , Hanson Paul J. , Schadt Christopher W.
Published: October 2023

Peatlands are large carbon sinks with primary production outpacing decomposition of organic matter. Results from the
S
pruce and
P
eatland
R
esponses
U
nder
C
hanging
E
nvironments (SPRUCE) study show net losses of organic matter and increased greenhouse gas production from peatlands in response to whole-ecosystem warming. Here, we investigated how warming and elevated CO
2
impact peat microbial communities and peat soil decomposition rates and characterized microbial communities through amplicon sequencing and compositional changes across four depth increments. Microbial diversity and community composition were significantly impacted by soil depth, temperature, and CO
2
treatment. Bacterial/archaeal α-diversity increased significantly with increasing temperature, and fungal α-diversity was lower under elevated CO
2
treatments.
Trans
domain microbial networks showed higher complexity of microbial communities in decomposition ladder depths from the warmed enclosures, and the number of highly connected hub taxa within the networks was positively correlated with temperature. Methanogenic hubs were identified in the networks constructed from the warmest enclosures, indicating increased importance of methanogenesis in response to warming. Microbial community responses were not however reflected in measures of peat soil decomposition, as warming and elevated CO
2
had no significant short-term effects on soil mass loss or composition. Regardless of treatment, on average only 4.5% of the original soil mass was lost after 3 years and variation between replicates was high, potentially masking treatment effects. Previous results at the SPRUCE experiment have shown warming is accelerating organic-matter decomposition and CO
2
and CH
4
production, and our results suggest these changes may be driven by warming-induced shifts in microbial communities.

IMPORTANCE

Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO
2
concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.
Metabolite diversity among representatives of divergent
Prochlorococcus
ecotypes
Authors: Kujawinski Elizabeth B. , Braakman Rogier , Longnecker Krista , Becker Jamie W. , Chisholm Sallie W. , Dooley Keven , Kido Soule Melissa C. , Swarr Gretchen J. , Halloran Kathryn
Published: October 2023

The euphotic zone of the surface ocean contains distinct physical-chemical regimes that vary in light and nutrient concentrations as an inverse function of depth. The most numerous phytoplankter of the mid- and low-latitude ocean is the picocyanobacterium
Prochlorococcus
, which consists of ecologically distinct subpopulations (i.e., “ecotypes”). Ecotypes have different temperature, light, and nutrient optima and display distinct relative abundances along gradients of these niche dimensions. As a primary producer,
Prochlorococcus
fixes and releases organic carbon to neighboring microbes as part of the microbial loop. However, little is known about the specific molecules
Prochlorococcus
accumulates and releases or how these processes vary among its ecotypes. Here, we characterize the metabolite diversity of
Prochlorococcus
by profiling three ecologically distinct cultured strains: MIT9301, representing a high-light-adapted ecotype dominating shallow tropical and sub-tropical waters; MIT0801, representing a low-light-adapted ecotype found throughout the euphotic zone; and MIT9313, representing a low-light-adapted ecotype relatively most abundant at the base of the euphotic zone. In both intracellular and extracellular metabolite profiles, we observe striking differences across strains in the accumulation and release of molecules, such as the DNA methylating agent S-adenosyl-methionine (intracellular) and the branched-chain amino acids (intracellular) and their precursors (extracellular). While some differences reflect variable genome content across the strains, others likely reflect variable regulation of conserved pathways. In the extracellular profiles, we identify molecules such as pantothenic acid and aromatic amino acids that may serve as currencies in
Prochlorococcus
’ interactions with neighboring microbes and, therefore, merit further investigation.

IMPORTANCE

Approximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacterium
Prochlorococcus
. Ecologically distinct subpopulations (or ecotypes) of
Prochlorococcus
are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. We measured the chemical profile of three cultured ecotype strains, observing striking differences among them that have implications for the likely chemical impact of
Prochlorococcus
subpopulations on their surroundings in the wild. Subpopulations differ in abundance along gradients of temperature, light, and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models of
Prochlorococcus
physiology and marine carbon dynamics.
Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance
Authors: McCracken Gregory R. , Gaston Daniel , Pettipas Janice , Loder Allana , Majer Anna , Grudeski Elsie , Labbé Geneviève , Joy Bryn K. , Patriquin Glenn , LeBlanc Jason J.
Published: October 2023

During the COVID-19 pandemic, SARS-CoV-2 detection using nucleic acid amplification tests (NAATs) played a key role in clinical management and public health interventions. However, mutations could jeopardize NAAT-based detection if they occur in the NAAT target site, potentially resulting in false negative results. However, mutation monitoring is challenged as the exact location of commercial NAAT target sites is not divulged by manufacturers. This study sequenced commercial SARS-CoV-2 NAAT target sites to assess the impact of mutations occurring in these regions. The resulting sequences for the Xpert, Cobas, and ID NOW SARS-CoV-2 assays were queried against SARS-CoV-2 genome databases to identify mutations in circulating strains. Synthetic DNAs and clinical specimens harboring NAAT target site mutations were used to assess mutation impact. Of 17,600 NAAT target site mutation occurrences in a genome database, 269 compromised target detection. These represented 24 unique mutations that reduced NAAT target sensitivity and nine led to target detection failure. Only seven of these mutations were previously recognized. Overall, this reactive strategy along with passive surveillance identified 29 novel mutations that compromised detection with Xpert and Cobas targets. Knowledge of commercial NAAT target sites, paired with a strategy for mutation impact assessment and ongoing genetic surveillance, provided a robust framework for commercial NAAT target site quality assurance. The question remains of who should be responsible for NAAT target site quality assurance, but collaborative efforts between methods users, industry, and regulatory agencies would be ideal.

IMPORTANCE

Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.
Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium
Authors: Khot Varada , Strous Marc , Dong Xiaoli , Kiesser Alyse K.
Published: October 2023

In many industries, from food to biofuels, contamination of production systems with predators is a costly problem and requires the maintenance of sterile operating conditions. In this study, we look at the robustness of one such alkaliphilic consortium, comprised largely of a cyanobacterium
Candidatus
Phormidium alkaliphilum, to viral predation. This consortium has existed without a community crash for several years in laboratory and pilot-scale environments. We look at clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems and viral dynamics in this consortium at four conditions using metagenomic analyses. Results show that while there are active viral members in this community, viral predation of the cyanobacteria is low and does not affect the community dynamics. The multiple CRISPR arrays within the Phormidium were found to be static following the initial lab establishment of consortium. Multiple cryptic CRISPR-Cas systems were detected with uncertain viral protection capacity. Our results suggest that the dynamics of potential viruses and CRISPR-Cas-mediated immunity likely play an important role in the initial establishment of consortia and may continue to support the functional robustness of engineered microbial communities throughout biotechnology applications.

IMPORTANCE

Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.
Characterization of biofilm formation by
Exiguobacterium
strains in response to arsenic exposure
Authors: Pavez Valentina B. , Pacheco Nicolás , Castro-Severyn Juan , Pardo-Esté Coral , Álvarez Javiera , Zepeda Phillippi , Krüger Gabriel , Gallardo Karem , Melo Francisco , Vernal Rolando , Aranda Carlos , Remonsellez Francisco , Saavedra Claudia P.
Published: October 2023

The Salar de Huasco (SH) salt lake in northern Chile is an extreme environment characterized by high atmospheric pressure, UV radiation, salinity, variable temperatures, and the presence of heavy metals, including arsenic.
Exiguobacterium
bacteria have adapted to thrive in these challenging conditions and possess various resistance mechanisms, including biofilm formation, redox reactions, methylation, and altered respiration. In this study,
Exiguobacterium
strains isolated from the SH were assessed for their capacity to form biofilms in the presence of arsenic, a metalloid that exists in different oxidation states, in order to understand their resistance mechanisms to this heavy metal. The minimum inhibitory concentration (MIC) of each strain against different concentrations of arsenic [III] and [V], biofilm formation using crystal violet staining, and the expression of genes related to biofilm formation were evaluated. The structure of the biofilms was characterized using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Furthermore, the extracellular polymeric substances (EPS) produced during biofilm formation were purified, quantified, and their composition determined. The results showed that the tested
Exiguobacterium
strains exhibit a significant ability to form biofilms when exposed to arsenic. This biofilm contributes to their arsenic resistance, shedding light on the underlying mechanisms. These findings enhanced our understanding of the biofilm formation process, its role in arsenic resistance, and the adaptive strategies employed by bacteria in extreme environments. This study also contributes to the field of microbial resistance mechanisms that have implications for environmental and biotechnological applications.

IMPORTANCE

In this work, we characterized the composition, structure, and functional potential for biofilm formation of
Exiguobacterium
strains isolated from the Salar de Huasco in Chile in the presence of arsenic, an abundant metalloid in the Salar that exists in different oxidation states. Our results showed that the
Exiguobacterium
strains tested exhibit a significant capacity to form biofilms when exposed to arsenic, which would contribute to their resistance to the metalloid. The results highlight the importance of biofilm formation and the presence of specific resistance mechanisms in the ability of microorganisms to survive and thrive under adverse conditions.
Autophagy facilitates intracellular survival of pathogenic rickettsiae in macrophages via evasion of autophagosomal maturation and reduction of microbicidal pro-inflammatory IL-1 cytokine responses
Authors: Voss Oliver H. , Gaytan Hodalis , Ullah Saif , Sadik Mohammad , Moin Imran , Rahman M. Sayeedur , Azad Abdu F.
Published: October 2023

The genus
Rickettsia
is comprised of obligate intracellular bacterial parasites of a wide range of arthropod and vertebrate hosts. Some
Rickettsia
species (spp.) are responsible for serious human diseases globally. One interesting feature of these stealthy group of pathogens is their ability to exploit host cytosolic defense responses to their benefits. However, the precise mechanism by which pathogenic
Rickettsia
spp. elude host immune defense responses remains to be determined. Here, we observed that pathogenic
Rickettsia typhi
and
Rickettsia rickettsii
(Sheila Smith [SS]), but not non-pathogenic
Rickettsia montanensis
, become ubiquitinated and induce autophagy upon entry into bone marrow-derived macrophages. Moreover, unlike
R. montanensis
, both
R. typhi
and
R. rickettsii
(SS) colocalized with LC3B and not with Lamp2 upon host cell entry. Finally, we observed that both
R. typhi
and
R. rickettsii
, but not
R. montanensis
, reduce pro-inflammatory interleukin-1 (IL-1) cytokine responses, likely via an autophagy-mediated mechanism. In summary, we identified a previously unappreciated pathway by which both pathogenic
R. typhi
and
R. rickettsii
(SS), but not the non-pathogenic
R. montanensis,
become ubiquitinated, induce autophagy, avoid autolysosomal destruction, and reduce microbicidal IL-1 cytokine responses to establish an intracytosolic niche in macrophages.

IMPORTANCE

Rickettsia
spp. are intracellular bacterial parasites of a wide range of arthropod and vertebrate hosts. Some rickettsiae are responsible for several severe human diseases globally. One interesting feature of these pathogens is their ability to exploit host cytosolic defense responses to their benefits. However, the precise mechanism by which pathogenic
Rickettsia
spp. elude host defense responses remains unclear. Here, we observed that pathogenic
Rickettsia typhi
and
Rickettsia rickettsii
(Sheila Smith [SS]), but not non-pathogenic
Rickettsia montanensis
, become ubiquitinated and induce autophagy upon entry into macrophages. Moreover, unlike
R. montanensis
,
R. typhi
and
R. rickettsii
(SS) colocalized with LC3B but not with Lamp2 upon host cell entry. Finally, we observed that both
R. typhi
and
R. rickettsii
(SS), but not
R. montanensis
, reduce pro-inflammatory interleukin-1 (IL-1) responses, likely via an autophagy-mediated mechanism. In summary, we identified a previously unappreciated pathway by which both pathogenic
R. typhi
and
R. rickettsii
(SS) become ubiquitinated, induce autophagy, avoid autolysosomal destruction, and reduce microbicidal IL-1 cytokine responses to establish an intracytosolic niche in macrophages.
Clinical and molecular epidemiology of carbapenem-resistant Enterobacteriaceae in pediatric inpatients in South China
Authors: Xiong Zhile , Zhang Chao , Sarbandi Kurosh , Liang Zhuwei , Mai Jialiang , Liang Bingshao , Cai Hao , Chen Xiantang , Gao Fei , Lan Fangjun , Liu Xiaochun , Liu Shuyan , Zhou Zhenwen
Published: October 2023

Carbapenem-resistant Enterobacteriaceae (CRE) are a substantial health burden. Existing management guidelines are primarily based on clonal evidence. Therefore, epidemiological data are required. We evaluated the risk factors for CRE colonization and described the molecular and clinical characteristics of CRE colonization in pediatric inpatients in Guangzhou, China. Pediatric inpatients from three hospitals in Guangzhou, China, between July 2019 and January 2021 were included. Fecal samples were collected and screened for CRE. Microbiological cultures were grown on MacConkey agar plates, and bacteria were identified with a mass spectrometry microbial identification system. Antimicrobial susceptibility was tested with a VITEK2 system, and carbapenemase genes were amplified. A case-control study was conducted to evaluate the risk factors for fecal CRE colonization in pediatric inpatients. Of 4,033 patients screened, 158 (3.92%) were positive for CRE, including
Escherichia coli
(51.27%),
Klebsiella pneumoniae
(37.97%), and
Enterobacter cloacae
(6.96%). The most common carbapenemase genes were blaNDM-5 (51.89%), blaNDM-1 (15.19%), and blaIMP-4 (7.60%) and blaKPC-2 (3.80%). Hematological malignancies, respiratory diseases, otolaryngological diseases, nervous system diseases, oral administration of third-generation cephalosporins, and the combined use of two or more antibiotics were independently associated with CRE colonization. The most prevalent carbapenem-resistant
K. pneumoniae
sequence types (STs) were ST11 (8.06%), ST37 (8.06%), and ST76 (8.06%), and the most prevalent carbapenem-resistant
E. coli
STs were ST10 (9.88%), ST48 (13.58%), and ST58 (8.64%). Pediatric inpatients were colonized by a diversity of CRE strains. Infection control and prevention measures should be implemented to reduce CRE colonization.

IMPORTANCE

This study assessed the clinical and molecular epidemiology of carbapenem-resistant Enterobacteriaceae in pediatric inpatients at three hospitals in South China by means of screening stool samples for carbapenem-resistant genes and a nested case-control study to determine risk factors for carriage of carbapenem-resistant Enterobacteriaceae. Of 4,033 fecal samples screened, 158 (3.92%) were positive for CRE, including
Escherichia coli
(51.27 %),
Klebsiella pneumoniae
(37.97%), and
Enterobacter cloacae
(6.96%). The most common carbapenemase genes harbored by gastrointestinal CRE strains were blaNDM-5, blaNDM-1, and blaIMP-4. Hematological malignancies, respiratory diseases, otolaryngological diseases, nervous system diseases, oral administration of third-generation cephalosporins, and the combined use of two or more antibiotics were independently associated with CRE colonization.
Supplemental Material: Germanium-rich nanoparticles in Cu-poor sphalerite: A new mechanism for Ge enrichment
Authors: Sun Guotao , Zhou Jia-xi , al. et
Published: October 2023

LA-ICP-MS trace-element data of sphalerite from the Banbianjie deposit.
Supplemental Material: Integrated Re-Os, Ar/Ar, and U-Pb geochronology directly dates the timing of mineralization at the Mina Justa and Marcona deposits, Peru
Authors: Rodríguez-Mustafa María A. , et al.
Published: October 2023

Tables containing sample details and isotope ratios used to calculate the U-Pb and Ar/Ar dates. Extra sample pictures, cross sections showing sample locations, and age spectrum plots and isochron diagrams of the samples analyzed for Ar/Ar geochronology.
Measurement scales of mental health related to climate change: a scoping review protocol using artificial intelligence
Authors: Dominguez-Rodriguez Alejandro , Villarreal-Zegarra David , Malaquias-Obregon Sofía , Herdoiza-Arroyo Paulina Erika , González-Cantero Joel Omar , Chávez-Valdez Sarah Margarita , Cruz-Martínez Roberto Rafael
Published: October 2023

Introduction

Human actions have influenced climate changes around the globe, causing extreme weather phenomena and impacting communities worldwide. Climate change has caused, directly or indirectly, health effects such as injury and physical injuries, which impact morbidity and mortality. Similarly, there is evidence that exposure to climatic catastrophes has serious repercussions on psychological well-being, and rising temperatures and drought have detrimental effects on mental health.

Despite the recent effort of researchers to develop specific instruments to assess the effects of climate change on mental health, the evidence on measures of its impact is still scarce, and the constructs are heterogeneous. The aim of this scoping review is to describe the instruments developed and validated to assess the impact of mental health related to climate change.

Methods and analysis

This review is registered at Open Science Framework (https://osf.io/zdmbk). This scoping review will follow the reporting elements chosen for systematic review and meta-analysis (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). We proposed a PO question, as it places no restrictions on the participants (P), and the outcome (O) are measurement instruments on mental health related to climate change. A search will be conducted in different databases (PubMed, Scopus, Web of Science, PsycINFO). We will use an open-source artificial intelligence screening tool (ASReview LAB) for the title and abstract review. The full-text review will be performed by three researchers. If there is a disagreement between two independent reviewers, a third reviewer will take the final decision. We will use the COnsensus-based Standards for the selection of health Measurement INstruments tool to assess the risk of bias for each included study. The review will be conducted starting in September 2023.

Ethics and dissemination

The planned scoping review does not require ethical approval since it will not involve an ethical risk to the participants. The results obtained from this study will be presented at conferences, congresses and scientific publications.
EMPOWERED trial: protocol for a randomised control trial of digitally supported, highly personalised and measurement-based care to improve functional outcomes in young people with mood disorders
Authors: Hickie Ian B , Iorfino Frank , Rohleder Cathrin , Song Yun Ju Christine , Nichles Alissa , Zmicerevska Natalia , Capon William , Guastella Adam J , Leweke F Markus , Scott Jan , McGorry Patrick , Mihalopoulos Cathrine , Killackey Eoin , Chong Min K , McKenna Sarah , Aji Melissa , Gorban Carla , Crouse Jacob J , Koethe Dagmar , Battisti Robert , Hamilton Blake , Lo Alice , Hackett Maree L , Hermens Daniel F ,   Mind Plasticity Consortia,   headspace Camperdown Consortia, Scott Elizabeth M
Published: October 2023

Objectives

Many adolescents and young adults with emerging mood disorders do not achieve substantial improvements in education, employment, or social function after receiving standard youth mental health care. We have developed a new model of care referred to as ‘highly personalised and measurement-based care’ (HP&MBC). HP&MBC involves repeated assessment of multidimensional domains of morbidity to enable continuous and personalised clinical decision-making. Although measurement-based care is common in medical disease management, it is not a standard practice in mental health. This clinical effectiveness trial tests whether HP&MBC, supported by continuous digital feedback, delivers better functional improvements than standard care and digital support.

Method and analysis

This controlled implementation trial is a PROBE study (Prospective, Randomised, Open, Blinded End-point) that comprises a multisite 24-month, assessor-blinded, follow-up study of 1500 individuals aged 15–25 years who present for mental health treatment. Eligible participants will be individually randomised (1:1) to 12 months of HP&MBC or standardised clinical care. The primary outcome measure is social and occupational functioning 12 months after trial entry, assessed by the Social and Occupational Functioning Assessment Scale. Clinical and social outcomes for all participants will be monitored for a further 12 months after cessation of active care.

Ethics and dissemination

This clinical trial has been reviewed and approved by the Human Research Ethics Committee of the Sydney Local Health District (HREC Approval Number: X22-0042 & 2022/ETH00725, Protocol ID: BMC-YMH-003-2018, protocol version: V.3, 03/08/2022). Research findings will be disseminated through peer-reviewed journals, presentations at scientific conferences, and to user and advocacy groups. Participant data will be deidentified.

Trial registration number

ACTRN12622000882729.
Community intervention to improve defibrillation before ambulance arrival in residential neighbourhoods with a high risk of out-of-hospital cardiac arrest: study protocol of a cluster-randomised trial (the CARAMBA trial)
Authors: Juul Grabmayr Anne , Malta Hansen Carolina , Bo Nanna , Sheikh Annam Pervez , Hassager Christian , Ersbøll Annette , Kjaergaard Jesper , Lippert Freddy , Tjørnhøj-Thomsen Tine , Gislason Gunnar , Torp-Pedersen Christian , Folke Fredrik
Published: October 2023

Introduction

In Denmark, multiple national initiatives have been associated with improved bystander defibrillation and survival following out-of-hospital cardiac arrest (OHCA) in public places. However, OHCAs in residential neighbourhoods continue to have poor outcomes. The Cardiac Arrest in Residential Areas with MoBile volunteer responder Activation trial aims to improve bystander defibrillation and survival following OHCA in residential neighbourhoods with a high risk of OHCA. The intervention consists of: (1) strategically deployed automated external defibrillators accessible at all hours, (2) cardiopulmonary resuscitation (CPR) training of residents and (3) recruitment of residents for a volunteer responder programme.

Methods and analysis

This is a prospective, pair-matched, cluster-randomised, superiority trial with clusters of 26 residential neighbourhoods, testing the effectiveness of the intervention in a real-world setting. The areas are randomised for intervention or control. Intervention and control areas will receive the standard OHCA emergency response, including volunteer responder activation. However, targeted automated external defibrillator deployment, CPR training and volunteer responder recruitment will only be provided in the intervention areas. The primary outcome is bystander defibrillation, and the secondary outcome is 30-day survival. Data on patients who had an OHCA will be collected through the Danish Cardiac Arrest Registry.

Ethics and dissemination

Approval to store OHCA data has been granted from the Legal Office, Capital Region of Denmark (j.nr: 2012-58-0004, VD-2018-28, I-Suite no: 6222, and P-2021-670). In Denmark, formal approval from the ethics committee is only obtainable when the study regards testing medicine or medical equipment on humans or using genome or diagnostic imagine as data source. The Ethics Committee of the Capital Region of Denmark has evaluated the trial and waived formal approval unnecessary (H-19037170). Results will be published in peer-reviewed papers and shared with funders, stakeholders, and housing organisations through summaries and presentations.

Trial registration number

ClinicalTrials.gov Registry (NCT04446585).
Potassium canrenoate in brain-dead organ donors: a randomised controlled clinical trial protocol (CANREO-PMO)
Authors: Belarif Lilia , Girerd Sophie , Jaisser Frédéric , Lepage Xavier , Merckle Ludovic , Duarte Kevin , Girerd Nicolas , Guerci Philippe
Published: October 2023

Introduction

Ischaemia/reperfusion injuries (IRIs) are associated with poorer survival of kidney grafts from expanded criteria donors. Preclinical studies have shown that mineralocorticoid receptor antagonists (MRAs) prevent acute and chronic post-ischaemic renal dysfunction by limiting IRI. However, data concerning the safety of MRAs in brain-dead donor patients are scarce. We seek to investigate the tolerance of MRAs on the haemodynamics in this population.

Methods and analysis

CANREO-PMO is a randomised, controlled, single-centre, double-blind study. Brain-dead organ donors hospitalised in intensive care are randomised 1:1 after consent to receive 200 mg potassium canrenoate or its matching placebo every 6 hours until organ procurement. The primary outcome is a hierarchical composite endpoint that includes: (1) cardiocirculatory arrest, (2) the impossibility of kidney procurement, (3) the average hourly dose of norepinephrine/epinephrine between randomisation and departure to the operating room, and (4) the average hourly volume of crystalloids and/or colloids received. Thirty-six patients will be included. The secondary endpoints evaluated among the graft recipients are the: (1) vital status of the kidney graft recipients and serum creatinine level with estimated glomerular filtration rate (GFR) according to Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) at 3 months after renal transplantation, (2) percentage of patients dependent on dialysis and/or with an estimated GFR <20 mL/min/1.73 m2at 3 months, (3) vital status of the kidney graft recipients at 3 months, and (4) vital status of the kidney graft recipients and creatinine levels (in μmol/L), with the estimated GFR according to CKD-EPI (in mL/min/1.73 m2), at 1 year, 3 years and 10 years after transplantation.

Ethics and dissemination

This trial has full ethical approval (Comité de Protection des Personnes: CPP Ouest II-ANGERS, France), and the written consent of relatives will be obtained. Results will be reported at conferences, peer-reviewed publications and using social media channels.

Trial registration number

NCT04714710.
Impact of the COVID-19 pandemic on the conduct of non-COVID-19 clinical trials: protocol for a scoping review
Authors: Shang Wenru , Wei Lili , Liu Yujia , Pu Haosheng , Li Xiuxia , Niu Junqiang , Ge Long , Lu Cuncun , Yang Kehu
Published: October 2023

Introduction

The COVID-19 pandemic posed a detrimental impact on the conduct of non-COVID-19 related clinical trials, raising concerns about the completeness of these studies and waste of resources. While several measures and strategies have been suggested to address these issues, a thorough and timely summarisation is still lacking. Therefore, our aim is to conduct a scoping review to summarise the negative effects of COVID-19 on non-COVID-19 clinical trials, outline the effective measures for mitigating these impacts, and provide insights for future pandemics.

Methods and analysis

This scoping review will be conducted in line with the Joanna Briggs Institute’s scoping review methodological framework, and the results will be reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Relevant articles will be searched in PubMed, Embase and the Cochrane Library from 1 December 2019 to 1 July 2023. We will also screen the reference lists of the included studies manually to identify more potentially relevant articles. Articles focusing on the adverse impacts of COVID-19 on non-COVID-19 clinical trials and effective measures for mitigating them will be included. Two investigators will perform study selection and data extraction independently. A narrative summary as well as a descriptive analysis of the basic characteristics and key results of the included studies will be performed.

Ethics and dissemination

Ethical approval is not required, as this scoping review will be completed based only on published literature. The findings of this scoping review will be disseminated through a peer-reviewed publication and/or conference presentations.
Epidemiology of tuberculosis in Kazakhstan: data from the Unified National Electronic Healthcare System 2014–2019
Authors: Sakko Yesbolat , Madikenova Meruyert , Kim Alexey , Syssoyev Dmitriy , Mussina Kamilla , Gusmanov Arnur , Zhakhina Gulnur , Yerdessov Sauran , Semenova Yuliya , Crape Byron Lawrence , Sarria-Santamera Antonio , Gaipov Abduzhappar
Published: October 2023

Objectives

This study aims to estimate tuberculosis (TB) incidence, mortality rates and survival HRs in Kazakhstan, using large-scale administrative health data records during 2014–2019.

Design

A retrospective cohort study.

Settings

Data for patients with TB in Kazakhstan during 2014–2019, reported in the Unified National Electronic Healthcare System.

Participants

Patients with TB in Kazakhstan (ICD-10 (The International Classification of Diseases, 10th revision) codes: A15–A19).

Outcome measures

Demographic factors, diagnoses and comorbidities were analysed using descriptive, bivariate and multivariable statistical analyses. TB incidence and mortality rates were calculated, and Cox regression and Kaplan-Meier survival analysis were performed to assess risk factors for survival rates.

Results

Of the 149 122 patients with TB, 91 437 (61%) were males, and 139 931 (94%) had respiratory TB. From 2014 to 2019, TB incidence declined from 227 to 15.2 per 100 000 individuals, while all-cause mortality increased from 8.4 to 15.2 per 100 000. Age-specific TB incidence was lowest for 0–10 years of age and highest for 20 years of age. Being older, man, urban residence versus rural, retired versus employed, having HIV and having diabetes versus no comorbidities were associated with lower survival rates.

Conclusion

To date, this is the largest TB published study for Kazakhstan, characterising TB incidence and mortality trends by demographic factors, and risk factors for survival rates. The findings highlight the need for targeted interventions to address the growing burden of TB, particularly among older adults, men, urban residents and those with HIV and diabetes. The study underscores the importance of using administrative health data to inform policy and health system responses to TB in Kazakhstan.
Barriers and coping responses towards infant and young child feeding practices in rural Ethiopia: a descriptive qualitative study
Authors: Gizaw Abraham Tamirat , Sopory Pradeep , Sudhakar Morankar
Published: October 2023

Objective

To explore barriers and coping responses toward infant and young child practices (IYCFP) in rural Ethiopia.

Methods

A descriptive qualitative study using semi-structured in-depth interviews and focus group discussions was conducted with 98 mothers having infants and young children aged 0–24 months in rural Ethiopia. The mothers were selected purposively by stratifying into four age groups of infants and young children in months: 0–5, 6–8, 9–12 and 13–24. Thematic analysis was performed to elucidate the main ideas regarding the barriers and coping responses to IYCFP across the participant stratum using ATLAS.ti analytical software (V.7.5.18).

Results

Two main themes emerged from the data. First, there was a discourse on optimal IYCFP that reflects the knowledge and efforts to adhere to recommendations for early breastfeeding initiation, exclusive breast feeding for the first 6 months and introduction of complementary foods at 6 months. Second, in a discourse on struggling with everyday realities, barriers against optimal feeding practices and coping responses were presented. Mothers’ responses in the four age strata as barriers to IYCFP were inadequate knowledge towards breast milk, perceived insufficiency of breast milk, beliefs, mothers’ excessive workload, limited partner support, food price inflation and shortage, gender roles, dowry demand and cultural understanding of marriage. Relying on cheaper food items and backyard garden was used to cope with the barriers.

Conclusions

Barriers towards IYCFP are numerous which extend from intrapersonal to sociocultural factors. Therefore, reducing mothers’ work burden to enable appropriate IYCFP by empowering women economically and addressing gender inequalities through collective societal approaches for promoting appropriate feeding is vital in rural communities.
British Society of Gastroenterology guidelines on the management of functional dyspepsia
Authors: Narendren Ahthavan , Boddupalli Srikar , Segal Jonathan P
Published: October 2023

In 2022, the British Society of Gastroenterology released guidelines on the management of functional dyspepsia (FD), providing a long-anticipated evidence-based approach to the diagnosis, classification and management of patients with FD. This review summarises the key recommendations of the recent guidelines on the management of FD.