bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short‐term professional bereavement reactions and their links with the meaning of patient death: Evidence from network analyses
Authors: Chen Chuqian , Zhang Robert Jiqi 
Published: October 2023

AbstractObjectivesTaking a dimensional view, this study aims to understand, among professional caregivers after patient deaths, the symptom distribution and development of the short‐term bereavement reaction (SBR) network and the node‐level links between the meaning of patient death (MPD) and the SBR network.MethodsA cross‐sectional secondary analysis was conducted with existing data from 220 Chinese urban hospital nurses and physicians who experienced the most recent patient death within a month. MPD was measured by the 10 formative items of the meaning of patient death model, and SBR was measured by the Short‐term Bereavement Reactions Subscale of the Professional Bereavement Scale. Both Gaussian graphical network analysis and Bayesian network analysis were applied to the SBR network, and Gaussian graphical network analysis was used to estimate the MPD‐SBR network.ResultsFrustrated and guilty are central nodes in the regularized partial correlation SBR network. Meanwhile, a traumatic event and failure at work are important bridge nodes between the MPD network and the SBR network. In the Bayesian SBR network, moved by the family's understanding, moved by the family's gratitude and sad mainly drive other nodes.ConclusionAfter a patient death, nurses' and physicians' SBR networks feature professional‐dimension symptoms at their core, while they follow ‘personal to professional’ and ‘concrete to abstract’ symptom development patterns. The personal meaning of a traumatic event and the professional meaning of a failure at work play key roles in bridging the MPD and SBR networks, and meanings of both the personal and the professional dimensions can link to professional‐dimension reactions.Reporting MethodThe manuscript followed the STROBE checklist for reporting cross‐sectional studies.Patient or Public ContributionNo patient or public contribution.
The thickness variability of fluvial cross‐strata as a record of dune disequilibrium and palaeohydrology proxy: A test against channel deposits
Authors: Colombera Luca , Reesink Arnold J. H. , Duller Robert A. , Jeavons Victoria A. , Mountney Nigel P. 
Published: October 2023

ABSTRACTStrata produced by fluvial dunes can provide insight into the hydrological regime of ancient rivers. Recent experiments indicate that conditions of disequilibrium between bedforms and formative flows may be inferred from the coefficient of variation of preserved dune cross‐set thickness, suggesting that this quantity may act as a proxy for the flashiness of river floods relative to the time required for full bedform translation. To assess whether this idea is applicable to interpretations of the stratigraphic record, this study examines published data relating to more than 2600 cross‐sets from 53 sedimentary units of 19 river systems. The presented analyses must not be over‐interpreted, because the considered rivers span different environmental settings, the data sources are heterogeneous in terms of type and dimensionality, and some variables were established by applying empirical relationships. Yet, significant findings are revealed. Larger rivers exhibit discharge and bedform characteristics that are more conducive to disequilibrium; however, a modest increase in the coefficient of variation of cross‐set thickness, CV(Dst), as opposed to the expected decrease, is seen as a function of river size. Crucially, smaller CV(Dst) values are not systematically associated with conditions that should favour dune disequilibrium. Meanwhile, only ca 25% of the studied examples demonstrate cross‐set thickness statistics compatible with quantitative formulations of the autogenic control by variable dune topography – the notion of ‘variability‐dominated’ preservation. These findings indicate that the variability in cross‐set thickness may be a poor predictor of discharge variability, perhaps because of the multiplicity of factors controlling dune preservation, such as bedform hierarchy, transport stage and depth‐dependent variations in dune disequilibrium. To improve interpretations of cross‐stratified deposits, further research is needed: (i) to establish the value of process‐to‐product models for reverse product‐to‐process interpretations; and (ii) to define representative samples for preserved dune deposits accounting for temporal and spatial variability in preservation potential.
Reference points in sequential bargaining: theory and experiment
Authors: Brekke Kjell Arne , Ciccone Alice , Heggedal Tom‐Reiel , Helland Leif 
Published: October 2023

AbstractWe 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

AbstractObjectiveTo compare the effects of three different rhinoplasty techniques on the postoperative cross‐sectional areas (CSAs) of the nares and nasal vestibuli.Study designExperimental study.Sample populationNinety‐nine 3D‐printed, remolded silicone models of a single French bulldog's rostral nose.MethodsModels 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.ResultsAll 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%.ConclusionAla‐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 significanceAla‐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

AbstractEvery 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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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.