bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental and Computational Investigation of Flow Boiling in a 52 μm Hydraulic Diameter Microchannel Evaporator With Inlet Restrictions and Heat Spreading
Authors: Anderson Caleb , Gao Zhaosheng , Hanchak Michael , Bandhauer Todd 
Published: February 2024

Abstract
Microchannel flow boiling presents an effective thermal management strategy for high heat flux (&gt;1 kW/cm2) devices. Fundamental mechanisms of microchannel flow boiling behaviors are difficult to determine due to macroscopic limitations of experimental hardware. In addition, flow stabilizing features of microchannel evaporators such as inlet restrictions and heat spreading further complicate fluid flow and heat transfer dynamics. Computational models, when utilized with experiments, can provide a more detailed understanding of behaviors which cannot be determined experimentally. The present study developed a computational model for flow boiling heat transfer in a 52 μm silicon microchannel evaporator designed to cool a laser diode bar, with inlet restrictions and a nonuniform heating profile at the channel level. A conjugate heat transfer model along with a coupled level set and volume of fluid (CLSVOF) model was created in ansysfluent and compared with experimental flow boiling data to gain further insights into the performance of a realistic microdevice. Heat spreading in the channel outside of the heater footprint was observed due to the high thermal conductivity of the silicon substrate. The inlet orifices impacted local flow patterns by creating a large pressure drop and forming a recirculation zone immediately downstream. This behavior resulted in pressure recovery zones and regions of separated flow boiling behavior. Bubbly, slug, and churn flows were seen to be dominant flow regimes. The heat transfer coefficient was found to be dependent on heat flux and flow regime, and more weakly on mass flux and outlet vapor quality.
Foraminifera as a model of eukaryotic genome dynamism
Authors: Timmons Caitlin , Le Kristine , Rappaport H. B. , Sterner Elinor G. , Maurer-Alcalá Xyrus X. , Goldstein Susan T. , Katz Laura A. 
Published: February 2024

ABSTRACT

In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual’s life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of
Allogromia laticollaris
strain Cold Spring Harbor (CSH), one of few cultivable foraminifera species. We show that haploidy and diploidy are brief moments in the
A. laticollaris
life cycle and that
A. laticollaris
nuclei endoreplicate up to 12,000 times the haploid genome size. We find that
A. laticollaris
reorganizes a highly endoreplicated nucleus into thousands of haploid genomes through a non-canonical mechanism called
Zerfall
, in which the nuclear envelope degrades and extrudes chromatin into the cytoplasm. Based on these findings, along with changes in nuclear architecture across the life cycle, we believe that
A. laticollaris
uses spatio-temporal mechanisms to delineate germline and somatic DNA within a single nucleus. The analyses here extend our understanding of the genome dynamics across the eukaryotic tree of life.

IMPORTANCE

In traditional depictions of eukaryotes (i.e., cells with nuclei), life cycles alternate only between haploid and diploid phases, overlooking studies of diverse microeukaryotic lineages (e.g., amoebae, ciliates, and flagellates) that show dramatic variation in DNA content throughout their life cycles. Endoreplication of genomes enables cells to grow to large sizes and perhaps to also respond to changes in their environments. Few microeukaryotic life cycles have been studied in detail, which limits our understanding of how eukaryotes regulate and transmit their DNA across generations. Here, we use microscopy to study the life cycle of
Allogromia laticollaris
strain CSH, an early-diverging lineage within the Foraminifera (an ancient clade of predominantly marine amoebae). We show that DNA content changes significantly throughout their life cycle and further describe an unusual process called
Zerfall
, by which this species reorganizes a large nucleus with up to 12,000 genome copies into hundreds of small gametic nuclei, each with a single haploid genome. Our results are consistent with the idea that all eukaryotes demarcate germline DNA to pass on to offspring amidst more flexible somatic DNA and extend the known diversity of eukaryotic life cycles.
Surface colonization by
Flavobacterium johnsoniae
promotes its survival in a model microbial community
Authors: Magesh Shruthi , Hurley Amanda I. , Nepper Julia F. , Chevrette Marc G. , Schrope Jonathan H. , Li Chao , Beebe David J. , Handelsman Jo 
Published: February 2024

ABSTRACT

Flavobacterium johnsoniae
is a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community,
T
he
H
itchhikers
o
f the
R
hizosphere (THOR), we determined the effects of colonization on the fitness of
F. johnsoniae
in the community. Insertion sequencing, a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that the deletion of colonization genes in
F. johnsoniae
affected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization by
F. johnsoniae
and form the basis for further understanding its ecology in the rhizosphere.

IMPORTANCE

Microbial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step toward unraveling these interactions, we explored the role of surface colonization in microbial community interactions using
T
he
H
itchhikers
O
f the
R
hizosphere (THOR), a genetically tractable model community of three bacterial species,
Flavobacterium johnsoniae
,
Pseudomonas koreensis
, and
Bacillus cereus
. We identified
F. johnsoniae
genes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote the success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.
Complete genome sequence of
Opitutales
bacterium strain ASA1, isolated from soil
Authors: Islam Md. Samiul , Yamamoto Kyosuke , Morita Naoki , Yumoto Isao , Kato Souichiro , Nakai Ryosuke , Igarashi Kensuke 
Published: February 2024

ABSTRACT

We present the complete genome of
Opitutales
bacterium ASA1, isolated from soil. The genome is 5,821,695 bp with 4,638 protein-coding sequences. The genome data suggest that this strain belongs to the class
Opitutae
of the phylum
Verrucomicrobiota
, and its genome has six unique biosynthetic gene clusters associated with secondary metabolites.
Natural compounds from freshwater mussels disrupt fungal virulence determinants and influence fluconazole susceptibility in the presence of macrophages in
Cryptococcus neoformans
Authors: Gutierrez-Gongora Davier , Woods Michael , Prosser Ryan S. , Geddes-McAlister Jennifer 
Published: February 2024

ABSTRACT

Cryptococcus neoformans
is a human fungal pathogen responsible for fatal infections, especially in patients with a depressed immune system. Overexposure to antifungal drugs due to prolonged treatment regimens and structure-similar applications in agriculture have weakened the efficacy of current antifungals in the clinic. The rapid evolution of antifungal resistance urges the discovery of new compounds that inhibit fungal virulence determinants, rather than directly killing the pathogen, as alternative strategies to overcome disease and reduce selective pressure toward resistance. Here, we evaluated the efficacy of freshwater mussel extracts (crude and clarified) against the production of well-defined virulence determinants (i.e., thermotolerance, melanin, capsule, and biofilm) and fluconazole resistance in
C. neoformans
. We demonstrated the extracts’ influence on fungal thermotolerance, capsule production, and biofilm formation, as well as susceptibility to fluconazole in the presence of macrophages. Additionally, we measured the inhibitory activity of extracts against commercial peptidases (family representatives of cryptococcal orthologs) related to fungal virulence determinants and fluconazole resistance, and integrated these phenotypic findings with quantitative proteomics profiling. Our approach defined distinct signatures of each treatment and validated a new mechanism of anti-virulence action toward the polysaccharide capsule from a selected extract following fractionation. By understanding the mechanisms driving the antifungal activity of mussels, we may develop innovative treatment options to overcome fungal infections and promote susceptibility to fluconazole in resistant strains.

IMPORTANCE
As the prevalence and severity of global fungal infections rise, along with an increasing incidence of antifungal resistance, new strategies to combat fungal pathogens and overcome resistance are urgently needed. Critically, our current methods to overcome fungal infections are limited and drive the evolution of resistance forward; however, an anti-virulence approach to disarm virulence factors of the pathogen and promote host cell clearance is promising. Here, we explore the efficacy of natural compounds derived from freshwater mussels against classical fungal virulence determinants, including thermotolerance, capsule production, stress response, and biofilm formation. We integrate our phenotypic discoveries with state-of-the-art mass spectrometry-based proteomics to identify mechanistic drivers of these antifungal properties and propose innovative avenues to reduce infection and support the treatment of resistant strains.
Duration of cardiopulmonary resuscitation and outcomes for adults with in-hospital cardiac arrest: retrospective cohort study
Authors: Okubo Masashi , Komukai Sho , Andersen Lars W , Berg Robert A , Kurz Michael C , Morrison Laurie J , Callaway Clifton W 
Published: February 2024

Abstract

Objective
To quantify time dependent probabilities of outcomes in patients after in-hospital cardiac arrest as a function of duration of cardiopulmonary resuscitation, defined as the interval between start of chest compression and the first return of spontaneous circulation or termination of resuscitation.

Design
Retrospective cohort study.

Setting
Multicenter prospective in-hospital cardiac arrest registry in the United States.

Participants
348 996 adult patients (≥18 years) with an index in-hospital cardiac arrest who received cardiopulmonary resuscitation from 2000 through 2021.

Main outcome measures
Survival to hospital discharge and favorable functional outcome at hospital discharge, defined as a cerebral performance category score of 1 (good cerebral performance) or 2 (moderate cerebral disability). Time dependent probabilities of subsequently surviving to hospital discharge or having favorable functional outcome if patients pending the first return of spontaneous circulation at each minute received further cardiopulmonary resuscitation beyond the time point were estimated, assuming that all decisions on termination of resuscitation were accurate (that is, all patients with termination of resuscitation would have invariably failed to survive if cardiopulmonary resuscitation had continued for a longer period of time).

Results
Among 348 996 included patients, 233 551 (66.9%) achieved return of spontaneous circulation with a median interval of 7 (interquartile range 3-13) minutes between start of chest compressions and first return of spontaneous circulation, whereas 115 445 (33.1%) patients did not achieve return of spontaneous circulation with a median interval of 20 (14-30) minutes between start of chest compressions and termination of resuscitation. 78 799 (22.6%) patients survived to hospital discharge. The time dependent probabilities of survival and favorable functional outcome among patients pending return of spontaneous circulation at one minute’s duration of cardiopulmonary resuscitation were 22.0% (75 645/343 866) and 15.1% (49 769/328 771), respectively. The probabilities decreased over time and were <1% for survival at 39 minutes and <1% for favorable functional outcome at 32 minutes’ duration of cardiopulmonary resuscitation.

Conclusions
This analysis of a large multicenter registry of in-hospital cardiac arrest quantified the time dependent probabilities of patients’ outcomes in each minute of duration of cardiopulmonary resuscitation. The findings provide resuscitation teams, patients, and their surrogates with insights into the likelihood of favorable outcomes if patients pending the first return of spontaneous circulation continue to receive further cardiopulmonary resuscitation.
VersKiK qualitative study design: actual follow-up needs of paediatric cancer survivors, their informal caregivers and follow-up stakeholder perceptions in Germany
Authors: Aleshchenko Ekaterina , Swart Enno , Voigt Mathias , Langer Thorsten , Calaminus Gabriele , Glogner Juliane , Baust Katja 
Published: February 2024

IntroductionThis article presents the study design of the qualitative part of the VersKiK study (Long-term care, care needs and wellbeing of individuals after cancer in childhood or adolescence: study protocol of a large scale multi-methods non-interventional study) aiming to explore actual follow-up needs of childhood and adolescence cancer survivors and their informal caregivers, gaps in current follow-up care provision and trajectories of cancer survivors’ transition from paediatric to adult healthcare.Methods and analysisWe will conduct up to 30 interviews with survivors of childhood and adolescence cancer and their informal caregivers with up to 20 participant observations of follow-up appointments. The results of these will be discussed in up to four focus groups with healthcare professionals and representatives of self-help groups. The study design aims to evaluate follow-up care after childhood cancer considering perspectives from survivors, their informal caregivers as well as healthcare providers. The combination of different data sources will allow us to get an in-depth understanding of the current state of follow-up care after paediatric cancer in Germany and to suggest recommendations for care improvement.Ethics and disseminationThe VersKiK study was approved by the Ethics Committee Otto von Guericke University on 2 July 2021 (103/21), by the Ethics Committee of Johannes Gutenberg University Mainz on 16 June 2021 (2021-16035), by the Ethics Committee University of Lübeck on 10 November 2021 (21-451), by the Ethics Committee University of Hospital Bonn on 28 February 2022 (05/22). For each part of the qualitative study, a separate written informed consent is prepared and approved accordingly by the ethics committees named above.Trial registration numberRegistered at German Clinical Trial Register, ID: DRKS00026092.
Left atrial appendage occlusion for patients with valvular diseases without atrial fibrillation (the OPINION Study): study protocol for a multicentre, randomised controlled trial
Authors: Ju Fan , Yuan Xin , Sun Hansong 
Published: February 2024

IntroductionAtrial fibrillation (AF) is a significant cause of perioperative stroke in aortic and mitral valve surgeries. Although several large studies have evaluated surgical left atrial appendage occlusion (SLAAO) during cardiac surgeries, their retrospective nature and an uncontrolled broad spectrum of conditions leave them subject to potential residual confounding. This trial aims to test the hypothesis that opportunistic SLAAO can prevent long-term stroke after cardiac surgery in patients receiving mitral or aortic valve surgeries without a history of AF and with a CHA2DS2-VASc score of 2 or higher.Methods and designThis study is a single-blinded, multicentre, randomised controlled trial. A total of 2118 patients planning to undergo aortic or mitral surgery without AF will be recruited and equally randomised into intervention or control arms at a 1:1 ratio. In the intervention arm, suture excision of the left atrial appendage (LAA) will be performed during the operation in addition to the original surgery plan. In the control arm, the operation will be performed according to the surgery plan without any intervention on the LAA. The primary outcome is a composite of newly occurred ischaemic stroke or transient ischaemic attack and cardiovascular mortality during a 1-year follow-up. Secondary outcomes include postoperative AF, cardiovascular mortality, newly occurred ischaemic stroke, newly occurred transient ischaemic attack, newly occurred haemorrhagic stroke, bleeding events, and AF-associated health utilisation.Ethics and disseminationThe Ethics Committee in Fuwai Hospital approved this study. Patients will give informed consent to the study. An information leaflet will be provided to participating patients to introduce the SLAAO procedure. Patients and the public will not get involved in developing the research hypothesis, study design or any other part of this protocol. We plan to publish several papers in peer-reviewed journals about the current research and these will include a description of the study’s development and the main findings of the study.Trial registration numberChiCTR2100042238.
Measurement properties of the incremental step test for people with chronic obstructive pulmonary disease: a cross-sectional study
Authors: Gonçalves Tânia , Carlos Winck João , Silva Fátima , Caneiras Cátia , Montes António Mesquita , Vilarinho Rui 
Published: February 2024

ObjectivesThe new incremental step test (IST) is a field test that was developed for people with chronic obstructive pulmonary disease (COPD), based on the characteristics of the incremental shuttle walk test (ISWT); however, its measurement properties still need to be determined. We aimed, first, to assess the construct validity (through the comparison with the ISWT), within-day reliability and measurement error of the IST in people with COPD; and, second, to identify whether the participants have a learning effect in the IST.DesignCross-sectional study, conducted according to COnsensus-based Standards for the selection of health status Measurement INstruments guidelines.SettingA family health unit in Portugal, April 2022 to June 2023.Participants and analysis63 participants (67.5±10.5 years) attended two sessions to perform two IST and two ISWT, separately. Spearman’s correlations were used to compare the best performances between the IST and the ISWT. Intraclass correlation coefficient (ICC2,1) was used for reliability, and the SE of measurement (SEM), minimal detectable change at 95% CI (MDC95) and Bland and Altman 95% limits of agreement (LoA) were used for measurement error. The learning effect was explored with the Wilcoxon signed-rank test.ResultsThe IST was significant and strongly correlated with the ISWT (0.72<ρ<0.74, p<0.001), presented an ICC2,1of 0.95 (95% CI 0.92 to 0.97), SEM=11.7 (18.9%), MDC95=32.4 (52.2%) and the LoA were −33.61 to 31.48 for the number of steps. No difference was observed between the number of steps of the two attempts of the IST (p>0.05).ConclusionsThe IST can be suggested as a valid and reliable test to assess exercise capacity in people with COPD, with no learning effect when two IST are performed on the same day. The measurement error of the IST is considered indeterminate.Trial registration numberNCT04715659.
Bundle of care to drive improvements in palliative and end-of-life care (PEOLC) in an acute tertiary hospital
Authors: Bell Liam , Sebastian Amanda , Palazzi Kerrin , Farquhar Saxon , Attia John , Lacey Jeanette 
Published: February 2024

ObjectivesThere is little evidence to suggest the best model of palliative and end-of-life care (PEOLC) in an acute care hospital. We introduced a bundle of care to drive improvements in PEOLC; this bundle included three full-time nursing positions providing a palliative care clinical consult service with physician backup, as well as educating staff, using the NSW Resuscitation Plan and the Last-Days-of-Life Toolkit.MethodsTwo audits were performed at John Hunter Hospital, a tertiary hospital in Newcastle, Australia, each sampling from all deaths in a 12-month period, one prior to and one after the bundle of care was introduced. Sampling was stratified into deaths that occurred within 4–48 hours of admission and after 48 hours. Key outcomes/data points were recorded and compared across the two time periods.ResultsStatistically significant improvements noted included: lower mortality on the wards after 48 hours of admission, better recognition of the dying patient, increased referral to palliative care nurses and physicians, reduction in the number of medical emergency team calls and increase in the use of comfort care and resuscitation plans. Currently, 73% of patients have their end-of-life wishes observed as per their advance care directive.ConclusionA bundle of care involving dedicated nurses with physician backup providing a consult service and education is an effective method for driving improvements in PEOLC.
Diversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle
Authors: Wynn Emily L. , Browne A. Springer , Clawson Michael L. 
Published: February 2024

Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle ( n = 202) and bison ( n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.