bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons and Insights From the Implementation of the Cohort Model for a PICU: A Case Study Research
Authors: Ninemire Margaret R. , Petrescu Matei , Musick Matthew A. , Shekerdemian Lara S. , Kumar Shelley , Dinh Julie , Thammasitboon Satid 
Published: June 2022

Objectives:
The subspecialty cohort model allows for creation of smaller diagnosis pools, enabling concentration of expertise and collaboration. Given unknown effects of this model on team dynamics in a PICU, we examined how the cohort-model implementation was perceived by our providers and how this organizational change affected the work environment.

Design:
Case study research approach consisting of surveys, operational observations, and semistructured interviews. A descriptive survey was derived from an integrated conceptual framework (i.e., teamwork and psychologic safety). Sensitized by the framework and quantitative survey data, we conducted a thematic analysis from field notes and interview data.

Setting:
A quaternary-care, children’s hospital with a 31-bed PICU.

Subjects:
PICU providers and nurses and subspecialists.

Intervention:
Implementation of the subspecialty cohort model.

Measurements and Main Results:
A total of 308 and 269 responses from pre- and postcohort surveys, respectively, were analyzed. Overall, 76% of physicians and 74% of nurses viewed the cohort model favorably. Three themes emerged: community-from disruption to redistribution, transforming identity-expert or generalist, and expansive learning from focused practice. The findings provided insights, informed by a theory of “Community of Practice,” as lessons learned and ways to enhance the cohort model.

Conclusions:
Our transition to a cohort PICU model offers lessons on impacts of PICU model changes on communities and teams. These theory-informed insights and implications can guide others undergoing similar transitions.
Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence
Authors: Sakamoto Tomoaki , Ikematsu Shuka , Nakayama Hokuto , Mandáková Terezie , Gohari Gholamreza , Sakamoto Takuya , Li Gaojie , Hou Hongwei , Matsunaga Sachihiro , Lysak Martin A. , Kimura Seisuke 
Published: June 2022

AbstractThe ability to respond to environmental variability is essential for living systems, especially to sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a drastic type of phenotypic plasticity known as heterophylly, a phenomenon where leaf form is altered in response to the surrounding environment. Although heterophylly has been studied in various plant species, its molecular mechanism has not been fully elucidated. To establish the genetic basis and analyze the evolutionary processes responsible for heterophylly, we assembled the chromosome-level genome of R. aquatica by combining data from Illumina short-read sequencing, PacBio long-read sequencing, and High-throughput Chromosome Conformation Capture (Hi-C) sequencing technologies. Fine-scale comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during R. aquatica speciation. The genomic information above was the basis for the transcriptome analyses to examine the mechanisms involved in heterophylly, especially in response to the submerged condition, which uncovered that the ethylene and blue light signaling pathways participate in regulating heterophylly under submerged conditions. The assembled R. aquatica reference genome provides novel insights into the molecular mechanisms and evolution of heterophylly.
Colour vision is aligned with natural scene statistics at 4 months of age
Authors: Skelton Alice E. , Franklin Anna , Bosten Jenny M. 
Published: June 2022

AbstractVisual perception in adult humans is thought to be optimised to represent the statistical regularities of natural scenes (Parraga et al., 2000; Simoncelli, 2003). For example, in adults, visual sensitivity to different hues shows an asymmetry which coincides with the statistical regularities of colour in the natural world (Bosten et al., 2015). Infants are sensitive to statistical regularities in social and linguistic stimuli, but whether or not infants’ visual systems are tuned to natural scene statistics is currently unclear. We measured colour discrimination in infants to investigate whether or not the visual system can represent chromatic scene statistics in very early life. Our results reveal the earliest association between vision and natural scene statistics that has yet been found: even as young as four months of age, colour vision is aligned with the distributions of colours in natural scenes.Research HighlightsWe find infants’ hue sensitivity is aligned with the distribution of colours in the natural world, as it is in adultsAt just 4 months, infants’ visual systems are tailored to extract and represent the statistical regularities of the natural worldThis points to a drive for the human brain to represent statistical regularities even at a young age.
Trends and determinants of unmet need for modern contraception among adolescent girls and young women in Tanzania, 2004-2016
Authors: Kagoye Sophia Adam , Jahanpour Ola , Obure Joseph , Mahande Michael Johnson , Renju Jenny 
Published: June 2022

AbstractBackgroundUnintended pregnancy at a young age can lead to poor reproductive health, social and economic outcomes. The high rate of unintended teenage pregnancies in Tanzania is indicative of inadequate availability and uptake of modern contraception. Determining trends and determinants of unmet need for modern contraception among adolescent girls and young women (AGYW) in Tanzania will help address the burden of unintended pregnancies.MethodologyAn analytical cross-sectional study design was conducted using secondary data from three consecutive Tanzania Demographic and Health Surveys (TDHS) 2004/05, 2010 and 2015/6. Data analysis was performed using Stata version 15.0. Data analysis considered the complex survey design. Categorical and continuous variables were summarized using descriptive statistics. Poisson regression model was used to determine factors associated with unmet need for modern contraception.ResultsA steady decline in unmet need for modern contraception was observed from 31.8% in 2004/05 to 27.5% in 2015/16 survey. In the multivariable analysis, higher prevalence of unmet need for modern contraception was observed among adolescents, participants with at least one live birth, from poor wealth tertile, and those sexually active during the past four weeks.ConclusionDespite declining levels, the unmet need for modern contraception among young women in Tanzania remains high. AGYW under 19 years, those from poor households, and those who are postpartum are most at risk. Greater efforts are required to meet the reproductive health needs and rights of these sub-groups of AGYW in order to facilitate uptake of modern contraceptives and therefore reducing the risk of unintended pregnancies and unmet need for modern contraception.
Proteomics for the discovery of clinical delirium biomarkers: A systematic review of Major Studies
Authors: Wiredu Kwame , Aduse-Poku Edmund , Shaefi Shahzad , Gerber Scott A 
Published: June 2022

AbstractDelirium represents a significant healthcare burden, diagnosed in over two million elderly Americans each year. In the surgical population, delirium remains the most common complication among elderly patients and is associated with longer hospital stays, higher costs of care, increased mortality and functional impairment. The pathomechanism of disease is poorly understood, with current diagnostic approaches somewhat subjective and arbitrary, and definitive diagnostic biomarkers are currently lacking. Despite the recent interest in delirium research, biomarker discovery for it remains new. Most attempts to discover biomarkers are targeted studies that seek to assess the involvement of one or more members of a focused panel of candidates in delirium. For a more unbiased, systems-biology view, we searched literature from MEDLINE, Cochrane Central, Web of Science, SCOPUS, and Dimensions between 2016 and 2021 for untargeted proteomic discovery studies for biomarkers of delirium conducted on human geriatric subjects. Two reviewers conducted independent review of all search results, and resolved discordance by concensus. From an overall search of 1172 publications, eight peer-reviewed studies met our defined inclusion criteria. The 370 unique peri-operative biomarkers identified in these reports are enriched in pathways involving the activation of the immune system, inflammatory response, and the coagulation cascade. IL-6 was the most commonly identified biomarker. By reviewing the distribution of protein biomarker candidates from these studies, we conclude that a panel of proteins, rather than a single biomarker, would allow for discriminating delirium cases from non-cases. The paucity of hypothesis-generating studies in the peer-reviewed literature also suggests that a systems-biology view of delirium pathomechanisms has yet to fully emerge.
Bidirectional changes in excitability upon loss of both CAMK2A and CAMK2B
Authors: Kool Martijn J. , Bodde Hanna E. , Elgersma Ype , van Woerden Geeske M. 
Published: June 2022

AbstractThe mammalian Ca2+/calmodulin-dependent protein kinase II (CAMK2) family consists of 4 different CAMK2 genes, encoding CAMK2A, CAMK2B, CAMK2D and CAMK2G, which have high structural homology. CAMK2A and CAMK2B are abundantly expressed in the brain; they play a unique role in proper neuronal functioning, since both CAMK2A and CAMK2B knockout mice show several behavioural and cellular phenotypes. However, our recent finding that deletion of both CAMK2A and CAMK2B is lethal indicates that they show redundancy and that the full spectrum of CAMK2 function in neurons remains to be uncovered. For example, it still remains unclear which overlapping functions are present at a single cell level in neuronal transmission and excitability.In order to get more insight into the full spectrum of CAMK2 functions in neurons, we performed whole-cell patch clamp experiments in inducible Camk2a/Camk2b double knockout mice, as well as the CAMK2A and CAMK2B knockout mice. We found that whereas deletion of only CAMK2A or CAMK2B did not change excitability, simultaneous deletion of CAMK2A and CAMK2B resulted in a decrease in excitability 10 days after deletion in CA1 pyramidal neurons, which reversed to increased excitability 21 days after deletion. Additionally, loss of both CAMK2A and CAMK2B resulted in a decreased frequency of both miniature excitatory and inhibitory postsynaptic currents (mEPSC and mIPSC) 21 days after deletion, but not 10 days after deletion, an effect not seen in the single mutants. Our results indicate that CAMK2 is critically important to maintain normal excitability of hippocampal CA1 pyramidal cells, as well as normal inhibitory and excitatory synaptic transmission. Together, these results lead to new insights in how CAMK2 regulates normal neuronal function and highlight the importance of having both CAMK2A and CAMK2B expressed in high levels in the brain.
A mechanistic understanding of biofilm morphogenesis: Coexistence of mobile and sessile aggregates and phase-separated patterns
Authors: Bera Palash , Wasim Abdul , Ghosh Pushpita 
Published: June 2022

AbstractMost bacteria in the natural environment self-organize into collective phases such as cell clusters, swarms, patterned colonies, or biofilms. The occurrence of different phases and their coexistence is governed by several intrinsic and extrinsic factors such as the growth, motion, and physicochemical interactions. Hence, it is crucial to predict the conditions under which a collective phase emerges due to the individual-level interactions. Here we develop a particle-based biophyiscal model of bacterial cells and self-secreted extracellular polymeric substances (EPS) to decipher the interplay of growth, motility-mediated dispersal, and mechanical interactions during microcolony morphogenesis. We show that depending upon the heterogeneous production and physicochemical properties of EPS, whether sticky or nonadsorbing in nature, the microcolony dynamics and architecture significantly varies. In particular, in sticky EPS, microcolony shows the coexistence of both motile and sessile aggregates rendering a transition towards biofilm formation. Wherein for the nonad-sorbing EPS, which behaves as depletant in the media, a variety of phase-segregated patterned colonies either localizing the matrix component or cells at the colony periphery may emerge. We identified that the interplay of differential dispersion and the mechanical interactions among the components of the colony determines the fate of the colony morphology. Our results provide a significant understanding of the mechano-self-regulation during biofilm morphogenesis and open up possibilities of designing experiments to test the predictions.
Planktonic functional diversity changes in synchrony with lake ecosystem state
Authors: O’Brien Duncan A. , Gal Gideon , Thackeray Stephen J. , Matsuzaki Shin-ichiro S. , Blanchard Julia L. , Clements Christopher F. 
Published: June 2022

AbstractManaging ecosystems to effectively preserve function and services requires reliable tools that can infer changes in the stability and dynamics of a system. Conceptually, functional diversity (FD) appears a viable monitoring metric due to its mechanistic influence on ecological processes, but it is unclear whether changes in FD occur prior to state responses or vice versa. We examine the lagged relationship between planktonic FD and abundance-based metrics of system state (e.g. biomass) across five highly monitored lake communities using both correlation and non-linear causality approaches. Overall, phytoplankton and zooplankton FD display synchrony with lake state but each lake is idiosyncratic in the strength of relationship. It is therefore unlikely that changes in plankton FD are identifiable before changes in more easily collected abundance metrics. This suggests that FD is unlikely to be a viable early indicator, but has value as an alternative state measure if considered at the lake level.Graphical AbstractData accessibility statement:Lake Kinneret and Lake Kasumigaura data are available on request, with all other data publicly available and referenced throughout. All code for analysis is available in the Zenodo record (to be released) and the associated GitHub repository (https://github.com/duncanobrien/plankton-FD).
Quantitative trait locus mapping of osmotic stress response in the fungal wheat pathogenZymoseptoria tritici
Authors: Stapley Jessica , McDonald Bruce A. 
Published: June 2022

AbstractOsmotic stress is a ubiquitous and potent stress for all living organisms, but few studies have investigated the genetic basis of salt tolerance in filamentous fungi. The main aim of this study was to identify regions of the genome associated with tolerance to potassium chloride in the wheat pathogenZymoseptoria tritici.A secondary aim was to identify candidate genes affecting salt tolerance within the most promising chromosomal regions. We achieved these aims with a quantitative trait locus (QTL) mapping study using offspring from two crosses grown in vitro in the presence or absence of osmotic stress imposed by 0.75M KCl. We identified significant QTL for most of the traits in both crosses. Several QTL overlapped with QTL identified in earlier studies for other traits and some QTL explained trait variation in both the control and salt stress environments. A significant QTL on chromosome 3 explained variation in colony radius at 8 days post inoculation (dpi) in the KCl environment as well as colony radius KCl tolerance at 8 dpi. The QTL peak had a high LOD and encompassed an interval containing only 36 genes. Six of these genes present promising candidates for functional analyses. A GO enrichment analysis of QTL unique to the KCl environment found evidence for enrichment of functions involved in osmotic stress responses.
The Arabidopsis D27-like1 is a cis/cis/trans-β-carotene Isomerase that Contributes to Strigolactone Biosynthesis and Negatively Impacts Abscisic Acid Level
Authors: Yang Yu , Abuauf Haneen , Song Shanshan , Wang Jian You , Alagoz Yagiz , Moreno Juan C. , Mi Jianing , Ablazov Abdugaffor , Jamil Muhammad , Ali Shawkat , Zheng Xiongjie , Balakrishna Aparna , Blilou Ikram , Al-Babili Salim 
Published: June 2022

ABSTRACTThe enzyme DWARF27 (D27) catalyzes the reversible isomerization of all-trans- into 9-cis-β-carotene, initiating strigolactone (SL) biosynthesis. Genomes of higher plants encode two D27-homologs, D27-like1 and -like2, with unknown functions. Here, we investigated the enzymatic activity and biological function of the Arabidopsis D27-like1. In vitro enzymatic assays and Expression in Synechocystis sp. PCC6803 revealed a yet not reported 13-cis/15-cis/9-cis- and a 9-cis/all-trans-β-carotene isomerization. Although disruption of AtD27-like1 did not cause SL deficiency phenotypes, overexpression of AtD27-like1 in the Atd27 mutant restored the more-branching phenotype, indicating a contribution of AtD27-like1 to SL biosynthesis. Accordingly, generated Atd27 Atd27like1 double mutants showed more pronounced branching phenotype, compared to Atd27. The contribution of AtD27-like1 to SL biosynthesis is likely due to its formation of 9-cis-β-carotene that was present at higher levels in AtD27-like1 overexpressing lines. In contrast, AtD27-like1 expression correlated negatively with the content of 9-cis-violaxanthin, a precursor of abscisic acid (ABA), in shoots. Consistently, ABA levels were higher in shoots and also in dry seeds of the Atd27like1 and Atd27 Atd27like1 mutants. Transgenic lines expressing β-glucuronidase (GUS) driven by the AtD27LIKE1 promoter and transcript analysis performed with hormone-treated Arabidopsis seedlings unraveled that AtD27LIKE1 is expressed in different tissues and regulated ABA and auxin. Taken together, our work revealed a cis/cis-β-carotene isomerase activity that affects the content of both cis-carotenoid derived plant hormones ABA and SLs.
Excessive Mechanotransduction in Sensory Neurons Causes Joint Contractures in a Mouse Model of Arthrogryposis
Authors: Ma Shang , Dubin Adrienne E. , Romero Luis O. , Loud Meaghan , Salazar Alexandra , Wang Yu , Chesler Alex T. , Wilkinson Katherine , Vásquez Valeria , Marshall Kara L. , Patapoutian Ardem 
Published: June 2022

AbstractDistal arthrogryposis (DA) is a collection of rare disorders characterized by congenital joint contractures. Most DA mutations are in muscle- and joint-related genes, and the anatomical defects originate cell-autonomously within the musculoskeletal system. However, gain-of-function (GOF) mutations in PIEZO2, a principal mechanosensor in somatosensation, cause DA subtype 5 via unknown mechanisms. We show that expression of a GOF PIEZO2 mutation in proprioceptive sensory neurons mainly innervating muscle spindles and tendons is sufficient to induce DA5-like phenotypes in mice. Overactive PIEZO2 causes anatomical defects via increased activity within the peripheral nervous system during postnatal development. Remarkably, Botox and a dietary fatty acid that modulates PIEZO2 activity markedly reduce DA5-like deficits. This reveals an unexpected role for somatosensory neurons: excessive mechanosensation within these neurons disrupts musculoskeletal development.
Mouse tissue harvest-induced hypoxia rapidly alters the in vivo metabolome, between-genotype metabolite level differences, and 13C-tracing enrichments
Authors: Rauckhorst Adam J. , Borcherding Nicholas , Pape Daniel J. , Kraus Alora S. , Scerbo Diego A. , Taylor Eric B. 
Published: June 2022

SummaryMetabolism is potently regulated by oxygen as the terminal acceptor of the electron transport chain. Thus, a challenge for capturing the in vivo metabolome of animal tissues is to achieve rapid freezing after dissection-induced loss of perfusion before the onset of hypoxia-driven metabolomic remodeling. However, the timing of the metabolomic changes elicited by post-dissection freezing delays are not well described. We addressed this problem by carefully and systematically assessing broad, genotype-specific, and 13C isotopologue metabolomic change resulting from post-dissection, ex vivo mouse tissue metabolism. Based on experiments with mouse liver, heart muscle, and skeletal muscle, we show that broad metabolomic change is rapid, that both false negative and false positive between genotype differences are induced, and that 13C-isotopologue abundances and enrichment percentages change with post-dissection hypoxia. These findings provide a previously absent, systematic illustration of the extensive and confounding metabolomic changes occurring within the early minutes of delayed tissue freezing.
Serotype specific sugars impact structure but not functions of the trimeric autotransporter adhesin EmaA of Aggregatibacter actinomycetemcomitans
Authors: Tang-Siegel Gaoyan G. , Radermacher Michael , Mintz Keith P. , Ruiz Teresa 
Published: June 2022

ABSTRACTThe human oral pathobiont Aggregatibacter actinomycetemcomitans expresses multiple virulence factors including the trimeric, extracellular matrix protein adhesin A (EmaA). The posttranslational modification of EmaA is proposed to be dependent on the sugars and enzymes associated with O-polysaccharide (O-PS) synthesis of the lipopolysaccharide (LPS). This modification is important for the structure and function of this adhesin. To determine if the composition of the sugars alters structure and/or function, the prototypic 202 kDa protein was expressed in a non-serotype b, emaA mutant strain. The transformed strain displayed EmaA adhesins similar in appearance to the prototypic adhesin as observed by 2D electron microscopy of whole-mount negatively stained bacterial preparations. Biochemical analysis indicated that the protein monomers were post-translationally modified. 3D electron tomographic reconstruction and structure analyses of the functional domain revealed three well-defined subdomains (SI, SII and SIII) with a linker region between SII and SIII. Structural changes were observed in all three subdomains and the linker region of the adhesins synthesized compared with the known structure. These changes however did not affect the ability of the strain to bind collagen or form biofilms. The data suggest that changes in the composition of the glycan moiety alter the 3D structure of the molecule without negatively affecting the function(s) associated with this adhesin.IMPORTANCEThe human oral pathogen A. actinomycetemcomitans is a causative agent of periodontal and several systemic diseases. EmaA is a trimeric autotransporter protein adhesin important for the colonization of this pathobiont in vivo. This adhesin is modified with sugars associated with the O-polysaccharide (O-PS) and the modification is mediated using the same enzymes involved in lipopolysaccharide (LPS) biosynthesis. The interaction with collagen is not mediated by the specific binding between the glycans and collagen but is attributed to changes in the final quaternary structure necessary to maintain an active adhesin. In this study, we have determined that the composition of the sugars utilized in the post-translational modification of this adhesin is exchangeable without compromising functional activities.