bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-level variation influences Methanothermococcus fitness in marine hydrothermal systems
Authors: Hoffert Michael , Anderson Rika , Reveillaud Julie , Murphy Leslie , Stepanauskas Ramunas , Huber Julie A. 
Published: May 2021

AbstractHydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus strains and their transcripts were more abundant than others in individual vent sites, and among the genes differentiating the Methanothermococcus SAGs were those related to nitrogen fixation and the CRISPR/Cas immune system. SAGs possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
Genome assemblies across the diverse evolutionary spectrum of Leishmania protozoan parasites
Authors: Warren Wesley C. , Akopyants Natalia S. , Dobson Deborah E. , Hertz-Fowler Christiane , Lye Lon-Fye , Myler Peter J. , Ramasamy Gowthaman , Shanmugasundram Achchuthan , Silva-Franco Fatima , Steinbiss Sascha , Tomlinson Chad , Wilson Richard K. , Beverley Stephen M. 
Published: May 2021

AbstractWe report high-quality draft assemblies and gene annotation for 13 species and/or strains of the protozoan parasite genera Leishmania, Endotrypanum and Crithidia, which span the phylogenetic diversity of the Leishmaniinae sub-family within the kinetoplastid order of the phylum Euglenazoa. These resources will support studies on the origins of parasitism.
Three-dimensional tracking of tethered particles for probing nanometer-scale single-molecule dynamics using plasmonic microscope
Authors: Ma Guangzhong , Wan Zijian , Yang Yunze , Jing Wenwen , Wang Shaopeng 
Published: May 2021

AbstractThree-dimensional (3D) tracking of surface-tethered single-particle reveals the dynamics of the molecular tether. However, most 3D tracking techniques lack precision, especially in axial direction, for measuring the dynamics of biomolecules with spatial scale of several nanometers. Here we present a plasmonic imaging technique that can track the motion of ∼100 tethered particles in 3D simultaneously with sub-nanometer axial precision at millisecond time resolution. By tracking the 3D coordinates of tethered particle with high spatial resolution, we are able to determine the dynamics of single short DNA and study its interaction with enzyme. We further show that the particle motion pattern can be used to identify specific and non-specific interactions in immunoassays. We anticipate that our 3D tracking technique can contribute to the understanding of molecular dynamics and interactions at the single-molecule level.
Apical Actin-myosin Network Regulates the Tight Junction of Polarized Madin-Darby Canine Kidney Cells
Authors: Lu Chia-hsuan , Wen Fu-Lai , Hsueh Shawn Ching-Chung , Wu Wen-hsiu , Lin Yu-Fang , Prouveur Mathieu , Boudier Thomas , Lin Keng-hui 
Published: May 2021

AbstractThe tight junction outlines the apicolateral border of epithelial cells like a belt, sealing the paracellular space when cells form contacts with each other. The permeability and morphology of tight junction are regulated by actomyosin contractility, which has been conventionally thought from the purse-string-like circumferential actomyosin belt along tight junction. Spatially, the tight junction is close to the apical actin network, which exerts inward contractions orthogonal to the tight junction. To test the contributions from apical actin network, we laser-ablated spots on the apical surface of polarized Madin-Darby Canine Kidney (MDCK) epithelial cells. Laser ablation severed the apical cytoskeleton network, decreased in-plane tension, increased the apical surface area, and rendered the tight junction less tortuous in shape. Consistent with these observations, changes in MDCK cell sheet morphology due to cell proliferation, or perturbation with the ROCK inhibitor Y27632 increased the density of the apical actin network and decreased tight junction tortuosity. The morphological analysis revealed scutoids in flat MDCK cell sheets, contrary to predictions from a previous model that only considered cell-cell interactions as line tension. Additional cell-cell interactions from apical in-plane tension provides probable cause for the occurrence of scutoids on flat geometry. Taken together, our findings identify the importance of the apical actin network exerting in-plane apical tension to regulate tight-junction mechanobiology and epithelial cell shape.Significance StatementThe tight junction is located at the apicolateral cell border and regulates paracellular diffusion. Adjacent to the tight junction, the actin cytoskeleton forms a dense network beneath the apical surface and an actomyosin belt that circumscribes the lateral surface of the cell. Tight junctions are connected to the actin cytoskeleton which regulates paracellular transport, but the role of tension-mediated regulation of the tight junction by various actin structures is poorly understood. Here, we provide evidence that tension on the tight junction is mediated by the apical actin network. Our results provide a reinterpretion of past reports and broaden our understanding the mechanobiology of tight junctions.
A fast and objective hidden Markov modeling for accurate analysis of biophysical data with numerous states
Authors: Liu Hanjin , Shima Tomohiro 
Published: May 2021

AbstractThe hidden Markov model (HMM) is widely used to analyze biophysical chronological data with discrete states, such as binding/detachment of biomolecules, protein/nucleotide conformational changes and step-like movement of single proteins. Despite its usefulness, classical HMM fitting has practical drawbacks that it requires the determination of the number of hidden states and fine initialization of many parameters before fitting. To overcome these drawbacks, several HMM pre-analyses have been reported, but do not provide enough accuracy when data have unknown kinetics and/or low signal-to-noise ratio. Therefore, in many cases, HMM fitting needs trial-and-error manual process that can impair the objectivity of the analysis. Moreover, for data composed of numerous hidden states, such as stepping data of cytoskeletal motors, there has been difficulty in HMM analysis because the large number of parameters were hardly properly initialized. Here, by combining a statistical step-finding method and the Gaussian mixture model clustering, we developed a new algorithm for more objective HMM analysis. Our algorithm can execute accurate state number estimation and parameter optimization with fully automated way. Simulation analysis demonstrated that our algorithm accurately fit both fast- and slow-transition trajectories. Compared with the previous method, the speed of our algorithm was 10–20 times faster for standard size data. Our algorithm also showed the accurate fit of the simulated motor-stepping data with more than 10 transition states, suggesting the applicability of the method to the data with numerous states. Furthermore, the algorithm is flexible enough to cope with cases where some kinetics are known in advance. Some available prior information, such as the dwell time of each state, can be integrated into the algorithm via two user-tunable parameters. In summary, our method enables fast, accurate and objective HMM analysis, and broadens the application range of HMM fitting that can provide more accurate interpretation of a wide variety of biophysical data.
Uterine artery embolisation or myomectomy for women with uterine fibroids wishing to avoid hysterectomy: a cost–utility analysis of the FEMME trial
Authors: Rana D , Wu O , Cheed V , Middleton LJ , Moss J , Lumsden M‐A , McKinnon W , Daniels J , Sirkeci F , Manyonda I , Belli A‐M , McPherson K ,   the FEMME Trial Collaborative Group
Published: May 2021

ObjectivesTo assess the cost‐effectiveness of uterine artery embolisation (UAE) and myomectomy for women with symptomatic uterine fibroids wishing to avoid hysterectomy.DesignEconomic evaluation alongside the FEMME randomised controlled trial.Setting29 UK hospitals.PopulationPremenopausal women who had symptomatic uterine fibroids amenable to UAE or myomectomy wishing to avoid hysterectomy. 254 women were randomised to UAE (127) and myomectomy (127).MethodsA within‐trial cost–utility analysis was conducted from the perspective of the UK NHS.Main outcome measuresQuality‐adjusted life years (QALYs) measured using the EuroQoL EQ‐5D‐3L, combined with costs to estimate cost‐effectiveness over 2 and 4 years of follow‐up.ResultsOver a 2‐year time horizon, UAE was associated with higher mean costs (difference £645; 95% CI −1381 to 2580) and lower QALYs (difference −0.09; 95% CI −0.11 to −0.04) when compared with myomectomy. Similar results were observed over the 4‐year time horizon. Thus, UAE was dominated by myomectomy. Results of the sensitivity analyses were consistent with the base case results for both years. Over 2 years, UAE was associated with higher costs (difference £456; 95% CI −1823 to 3164) and lower QALYs (difference −0.06; 95% CI −0.11 to −0.02).ConclusionsMyomectomy is a cost‐effective option for the treatment of uterine fibroids. The differences in costs and QALYs are small. Women should be fully informed and have the option to choose between the two procedures.Tweetable abstractFully informed women with uterine fibroids should have a choice between uterine artery embolisation or myomectomy.
Fermentation and the microbial community of Japanese koji and miso: A review
Authors: Allwood Joanne G. , Wakeling Lara T. , Bean David C. 
Published: May 2021

AbstractMiso is a well‐known traditional Japanese fermented food, with a characteristic savory flavor and aroma, known predominately as the seasoning in miso soup. Miso production involves a two‐stage fermentation, where first a mold, such as Aspergillus oryzae, is inoculated onto a substrate to make koji. A subsequent fermentation, this time by bacteria and yeast, occurs when the koji is added to a salt and soybean mash, with the miso left to ferment for up to 2 years. The microbial community of miso is considered essential to the development of the unique taste, texture, and nutritional profile of miso. Despite the importance of microorganisms in the production of miso, very little research has been undertaken to characterize and describe the microbial process. In this review, we provide an overview of the two‐stage fermentation process, describe what is currently known about the microbial communities involved and consider any potential health benefits associated with the consumption of miso, along with food safety concerns. As the popularity of miso continues to expand globally and is produced under new environmental conditions, understanding the microbiological processes involved will assist to ensure that global production of miso is safe as well as delicious.
Utility of positron emission tomography imaging in the diagnosis of chronic Q fever: A Systematic Review
Authors: Sivabalan Pirathaban , Visvalingam Rozanne , Grey Victoria , Blazak John , Henderson Andrew , Norton Robert 
Published: May 2021

AbstractChronic Q fever is a diagnostic challenge. Diagnosis relies on serology and/or the detection of DNA from blood or tissue samples. PET‐CT identifies tissues with increased glucose metabolism, thus identifying foci of inflammation. Our aim was to review the existing literature on the use of PET‐CT to help diagnose chronic Q fever. A literature search was conducted in PubMed and Google Scholar to ascertain publications that included the terms ‘Positron Emission Tomography’ and ‘PET CT’ in combination with subheadings ‘chronic Q fever’ and ‘Coxiella burnetii’ within the search. To broaden our search retrieval, we used the terms ‘chronic Q fever’ and ‘PET‐CT’. Published literature up to 16th April 2020 was included. 274 articles were initially identified. Post‐exclusion criteria, 46 articles were included. Amongst case reports and series, the most frequent focus of infection was vascular, followed by musculoskeletal then cardiac. 79.5% of patients had a focus detected with 55.3% of these having proven infected prosthetic devices. Amongst the retrospective and prospective studies, a total of 394 positive sites of foci were identified with 186 negative cases. Some had follow‐up scans (53), with 75.5% showing improvement or resolution. Average timeframe for documented radiological resolution post‐initiating treatment was 8.86 months. PET‐CT is a useful tool in the management of chronic Q fever. Knowledge of a precise focus enables for directed surgical management helping reduce microbial burden, preventing future complications. Radiological resolution of infection can give clinicians reassurance on whether antimicrobial therapy can be ceased earlier, potentially limiting side effects.
Slipping rib syndrome
Authors: Bong Jonathan , Healey David 
Published: May 2021

SummarySlipping rib syndrome (SRS) is an underdiagnosed condition that can lead to debilitating lower chest and upper abdominal pain (Am J Med Sci 2019; 357: 168). It is caused by hypermobility of the anterior ends of the costal cartilages of false ribs, allowing the eighth to tenth ribs to slip under the rib above, giving its name (Semin Pediatr Surg 2018; 27: 183). Failure to recognize this syndrome can expose patients to extensive and unnecessary investigations for unclear symptoms. Although more commonly reported in adults, SRS is a relatively uncommon but recognized cause of lower chest or upper abdomen pain in adolescence (Pediatr Anesth 2001; 11: 740). It is important for clinicians to familiarize themselves with and consider the diagnosis of SRS when assessing and managing adolescents with persistent thoracic pain. We present a case of a 14‐year‐old girl with unresolved thoracic pain for more than 4 years and was ultimately diagnosed with SRS.
Development of a questionnaire to assess clinician perspectives of the usefulness of the Functional Independence Measure (FIM) and cognitive screening tests
Authors: Fox Sarah Therese , Thompson Leah Elizabeth , Rowland Jeffrey T. J. 
Published: June 2021

AbstractObjectiveA pilot questionnaire was developed to investigate the cognitive tests that clinicians employ in their clinical practice and whether they perceive the Functional Independence Measure (FIM) to add clinical value.MethodsA 10‐item pilot questionnaire was created and distributed to 43 health professionals of a single health service in Australia. A snowballing approach to sampling was used.ResultsThere were 39 respondents. Less than half of respondents thought the FIM added clinical value, and 15% stated that they would use the FIM to assess cognition on subacute wards. Ninety‐seven per cent (97%) of respondents stated that they would rely more heavily on cognitive screening tests than the FIM.ConclusionParticipant responses to this survey of a single health service raise interesting questions about how useful clinicians perceive the FIM to be, beyond a costing and benchmarking role. Clinicians may prefer cognitive screening tests to the FIM, in clinical practice.
Systematic review shows the benefits of involving the fathers of preterm infants in early interventions in neonatal intensive care units
Authors: Filippa Manuela , Saliba Sahar , Esseily Rana , Gratier Maya , Grandjean Didier , Kuhn Pierre 
Published: May 2021

AbstractAimThis review identifies interventions involving the fathers of preterm infants that have been tested in neonatal intensive care units (NICU). It examines their effects on the fathers and infants and highlights any differences between fathers and mothers who took part in the same interventions.MethodsA systematic search was performed in English from 1995 to 1 September 2020, using the CINAHL, Cochrane Central Register of Controlled Trials, Embase, PubMed and PsycINFO databases. We examined 14 peer‐reviewed studies that investigated NICU interventions involving 478 fathers, whose 511 infants were born before 37 weeks of gestation. These included empirical studies with clinical outcomes.ResultsStudies on fathers' interventions in NICUs were limited and mainly restricted to basic skin‐to‐skin contact or tactile interventions. The interventions had similar general positive effects on mothers and fathers when it came to infant physiological and behavioural reactions. There was also evidence of a positive effect on the fathers, including their mental health.ConclusionIncluding fathers as active partners in the care of their preterm newborn infants produced good outcomes for both of them. Further research is needed to develop new, multimodal and interactive interventions that provide fathers with positive contact with their preterm infants.
COVID‐19 in children and the effect of schools reopening on potential transmission to household members
Authors: Shapiro Ben David Shirley , Rahamim‐Cohen Daniella , Tasher Diana , Geva Adi , Azuri Joseph , Ash Nachman 
Published: May 2021

AbstractAimThe effect of reopening schools on children's contribution to SARS‐CoV‐2 transmission, especially within households, remains controversial. This study describes the clinical presentation of a large ambulatory COVID‐19 paediatric cohort and evaluates the role of children in household transmission prior to and following school reopening.MethodsA retrospective database cohort study was conducted in a large Health Maintenance Organization in Israel. Data of all paediatric, laboratory‐confirmed Coronavirus cases between 28/2/2020 and 20/6/2020 were extracted. All cases were analysed for household contacts and primary cases within each family cluster.ResultsA total of 1,032 cases under 18 years old (median age 12 years) were included. Of these cases, 432 (41.9%) were asymptomatic; 122 (11.8%) cases acquired the infection at school, and 45 of them were part of two school clusters; 846 children had at least one positive household contact, in 498 family clusters, and among them, 293 primary cases were identified. Only 27 (9.2%) primary cases were under 18 years of age and six (2%) were below 10. The proportion of primary cases did not change after the re‐opening of educational facilities.ConclusionChildren, particularly under 10 years of age, are less likely to be the vector for SARS‐CoV‐2 infection within household settings. Opening educational facilities did not change transmission dynamics.
Provenance study of the glazed tiles body in the Mingzhongdu site
Authors: Yang Guimei , Wang Zhi , Yao Zhengquan , Yang Yuzhang , Wei Guofeng 
Published: June 2021

AbstractIn order to define the provenance of the raw material of the glazed tile bodies excavated at the site of Mingzhongdu (Fengyang, China), X‐ray fluorescence spectrometry (XRF), X‐ray powder diffraction (XRD) and inductively coupled plasma‐mass spectrometer (ICP‐MS) were used. A comparative analysis was performed using glazed tiles excavated from the Qiaojianzi kiln in Fengyang (FQY), a kiln in Dangtu (DY), Nanjing Ming Palace (NMGG) and Dabaoensi in Nanjing (DEBS). The data suggest that the clay of the glazed tiles in Mingzhongdu came from the local area, while the others were from Dangtu and unknown areas. Clays are usually more or less refined, and minerals such as quartz, feldspar and mullite are often added. This study provides a direct basis for the material source of the glazed tile body in Mingzhongdu, and offers some useful data for further study of the firing system of glazed tiles in Mingzhongdu.
Transition to independent living: Signs of self‐determination in the discussions of Mexican students with intellectual disability
Authors: Rubio‐Jimenez Ana Luisa , Kershner Ruth 
Published: May 2021

Accessible summary

Self‐determination means that people decide for themselves about their future. Self‐determination is very important in people's transition to adulthood and independent living.

Six young adults talked with peers and facilitators about their transition to living in an independent‐living flat in Mexico.

We wanted to learn what it was like for these young adults to transition to independent living.

The young adults shared that: (a) It is their decision whether to move to an independent‐living flat; (b) They feel that living independently is challenging; (c) Learning new things at independent‐living contexts makes them feel good about themselves as young adults.

Talking with young people about their independent‐living experiences is important for planning transitions according to their own strengths and interests.

Talking to others can help people decide where and with whom to live.

AbstractBackgroundYoung people with intellectual disability experience important transitions as they move towards independent adult living. Transition is supported by self‐determination, comprising volition (making conscious choices) and agency (acting with intention). Dialogic interactions that legitimise students’ voices potentially promote self‐determination. Consequently, this project aimed to involve young people actively in talking together about their futures.MethodsThe research project took place in a university‐based transition programme in Mexico: Building Bridges. Six Mexican young adults with intellectual disability participated. The research project focused on their experiences of self‐determination in personal, social, and educational contexts. Data collection incorporated discussion sessions and participant observations. In discussions, students shared their experiences of transition to Building Bridges, and an independent‐living flat. A thematic analysis was conducted.FindingsThe students’ transition to Building Bridges was difficult, but they believed that they were learning and growing with support. Regarding their transition to the independent‐living context, the students perceive that whether to move or not is their decision, that independent living is challenging, and that the things they are learning make them feel good about themselves.ConclusionsListening to students’ views prompts consideration of how transition programmes could enhance their self‐determination. For instance, by reflecting and negotiating rules with them; or giving them options, such as sleeping at the flat one day per week initially. Self‐determination is exercised within the context of relationships. Creating spaces for dialogues that allows educators and/or researchers to learn and reflect with students might be a way to know and legitimise students’ experiences, and plan transitions based on their strengths and interests.