bluuebunny/crossref_metadata_2025_split huggingface dataset:
A numerical investigation of changes in lens shape during accommodation
Authors: Cabeza-Gil I. , Grasa J. , Calvo B. 
Published: May 2021

AbstractThe purpose of this study was to investigate how the mechanical properties and geometry of the lens influence the changes in lens shape during accommodation. To do so, ex vivo stretching tests of the isolated lens were simulated via finite element analysis. In these tests, the lens is stretched from the accommodated state to the non-accommodated state. Several key characteristics of the lens were studied: the stiffness gradient of the lens material, the distribution of the capsule thickness, the mechanical properties of the capsule and the material comprising the lens, nucleus and cortex, and the influence of two different age-related lens geometries (17 and 29 y/o subjects). To determine the effects on the changes in lens shape during accommodation, changes in the anterior and posterior radius, the lens and nucleus thicknesses and the equatorial lens diameter were analysed. The results suggest that multiple factors exert statistically significant influences on how the lens changes its shape, but two factors predominate over the rest: the stiffness ratio between the nucleus and cortex and the stiffness of the capsule, specifically the posterior surface.
Promotion effects of microwave heating on coalbed methane desorption compared with conductive heating
Authors: Wang Zhijun , Wang Xiaojuan 
Published: May 2021

AbstractAs a clean energy resource, coalbed methane (CBM) has drawn worldwide attention. However, the CBM reservoir has strong adsorption capacity and low permeability and thus requires stimulation. As a means to stimulate coalbed methane recovery, thermal injection faces geological and economic challenges because it uses conventional conductive heating (CH) to transfer heat. Realized by the conversion of the electromagnetic energy into the thermal energy, microwave heating (MH) may be a sound stimulation method. Although previous research suggested that MH had potential as a stimulation method for coalbed methane recovery, it is not clear if MH is superior to CH for enhancing coalbed methane recovery. This paper compares the effect of MH and CH on methane desorption from coal using purpose-built experimental equipment. To compare the MH and CH experimental results, the desorption temperature for each CH desorption test was set to the maximum temperature reached in the correlative MH desorption test. The results show that although the cumulative desorbed volume (CDV) of methane under MH was less than that desorbed by CH in the initial desorption stage, the final total CDV under MH for the three different power settings was ~ 12% to ~ 21% more than that desorbed by CH at the same temperatures. CH and MH both change the sample’s microstructure but MH enlarges the pores, decreases methane adsorption, promotes methane diffusion, and improves permeability more effectively than CH. Rapid temperature rise and the changes in the coal’s microstructure caused by MH were the main reasons for its superior performance. These findings may provide reference for selecting the most appropriate type of heating for thermal injection assisted coalbed methane recovery.
Uvulopalatopharyngoplasty may decrease the incidence of Parkinson’s disease associated with obstructive sleep apnea
Authors: Lee Heung Man , Han Kyung-Do , Suh Jeffrey D. , Cho Jae Hoon 
Published: May 2021

AbstractThe purpose of this study was to investigate whether the incidence of Parkinson’s disease (PD) is increased among patients with obstructive sleep apnea (OSA) and whether surgical treatment can prevent such an increase. This was a retrospective cohort study. We analysed the claims data from the Korea National Health Insurance Service. A total of 202,726 patients who were newly diagnosed with OSA between 2007 and 2014 were included. The patients were divided into two groups: patients who underwent uvulopalatopharyngoplasty (surgery group, n = 22,742) and those who did not (conservative group, n = 179,984). The control group (n = 1,013,630) was selected by propensity score matching. They were tracked until 31st December 2015. The hazard ratio of PD diagnosis (95% confidence interval) in the OSA group with respect to the control group was calculated using the Cox proportional hazard model. In the conservative group, the incidence of PD (hazard ratio 2.57 [2.32–2.85]) was significantly higher than that in the control group, while the incidence of PD in the surgery group was similar to that in the control group (hazard ratio 1.45 [0.89–2.22]). Patients with OSA are at an increased risk of developing PD, and uvulopalatopharyngoplasty may mitigate this risk.
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Authors: Melkonian Chrats , Fillinger Lucas , Atashgahi Siavash , da Rocha Ulisses Nunes , Kuiper Esther , Olivier Brett , Braster Martin , Gottstein Willi , Helmus Rick , Parsons John R. , Smidt Hauke , van der Waals Marcelle , Gerritse Jan , Brandt Bernd W. , Röling Wilfred F. M. , Molenaar Douwe , van Spanning Rob J. M. 
Published: May 2021

AbstractA key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from familiesRhodocyclaceaeandPeptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
Cryo-EM structure of ABCG5/G8 in complex with modulating antibodies
Authors: Zhang Hanzhi , Huang Ching-Shin , Yu Xinchao , Lee Jonas , Vaish Amit , Chen Qing , Zhou Mingyue , Wang Zhulun , Min Xiaoshan 
Published: May 2021

AbstractThe heterodimer of ATP-binding cassette transporter ABCG5 and ABCG8 mediates the excretion of sterols from liver and intestine, playing a critical role in cholesterol homeostasis. Here, we present the cryo-EM structure of ABCG5/G8 in complex with the Fab fragments from two monoclonal antibodies at 3.3Å resolution. The high-resolution structure reveals a unique dimer interface between the nucleotide-binding domains (NBD) of opposing transporters, consisting of an ordered network of salt bridges between the conserved NPXDFXXD motif and serving as a pivot point that may be important for the transport cycle. While mAb 11F4 increases the ATPase activity potentially by stabilization of the NBD dimer formation, mAb 2E10 inhibits ATP hydrolysis, likely by restricting the relative movement between the RecA and helical domain of ABCG8 NBD. Our study not only provides insights into the structural elements important for the transport cycle but also reveals novel epitopes for potential therapeutic interventions.
Cooperative root graft networks benefit mangrove trees under stress
Authors: Vovides Alejandra G. , Wimmler Marie-Christin , Schrewe Falk , Balke Thorsten , Zwanzig Martin , Piou Cyril , Delay Etienne , López-Portillo Jorge , Berger Uta 
Published: May 2021

AbstractThe occurrence of natural root grafts, the union of roots of the same or different trees, is common and shared across tree species. However, their significance for forest ecology remains little understood. While early research suggested negative effects of root grafting with the risk of pathogen transmission, recent evidence supports the hypothesis that it is an adaptive strategy that reduces stress by facilitating resource exchange. Here, by analysing mangrove root graft networks in a non-destructive way at stand level, we show further evidence of cooperation-associated benefits of root grafting. Grafted trees were found to dominate the upper canopy of the forest, and as the probability of grafting and the frequency of grafted groups increased with a higher environmental stress, the mean number of trees within grafted groups decreased. While trees do not actively ‘choose’ neighbours to graft to, our findings point to the existence of underlying mechanisms that regulate ‘optimal group size’ selection related to resource use within cooperating networks. This work calls for further studies to better understand tree interactions (i.e. network hydraulic redistribution) and their consequences for individual tree and forest stand resilience.
The highly dynamic nature of bacterial heteroresistance impairs its clinical detection
Authors: Pereira Cátia , Larsson Jimmy , Hjort Karin , Elf Johan , Andersson Dan I. 
Published: May 2021

AbstractMany bacterial species and antibiotic classes exhibit heteroresistance, a phenomenon in which a susceptible bacterial isolate harbors a resistant subpopulation that can grow in the presence of an antibiotic and cause treatment failure. The resistant phenotype is often unstable and without antibiotic selection it reverts back to susceptibility. Here we studied the dynamics by which these resistant subpopulations are enriched in the presence of antibiotic and recede back to their baseline frequency in the absence of selection. An increasing understanding of this instability will allow more effective diagnostics and treatment of infections caused by heteroresistant bacteria. We show for clinical isolates of Escherichia coli and Salmonella enterica that different antibiotics at levels below the MIC of the susceptible main population can cause rapid enrichment of resistant subpopulations with increased copy number of genes that cause resistance. Modelling and growth rate measurements of bacteria with increased gene copy number in cultures and by microscopy of single-cells in a microfluidic chip show that the fitness cost of gene amplifications and their intrinsic instability drives their rapid loss in the absence of selection. Using a common antibiotic susceptibility test, we demonstrate that this test strongly underestimates the occurrence of heteroresistance in clinical isolates.
The ribosome modulates folding inside the ribosomal exit tunnel
Authors: Wruck Florian , Tian Pengfei , Kudva Renuka , Best Robert B. , von Heijne Gunnar , Tans Sander J. , Katranidis Alexandros 
Published: May 2021

AbstractProteins commonly fold co-translationally at the ribosome, while the nascent chain emerges from the ribosomal exit tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is not well understood. Here, we combine optical tweezers with single-molecule FRET and molecular dynamics simulations to investigate folding of the small zinc-finger domain ADR1a inside and at the vestibule of the ribosomal tunnel. The tunnel is found to accelerate folding and stabilize the folded state, reminiscent of the effects of chaperonins. However, a simple mechanism involving stabilization by confinement does not explain the results. Instead, it appears that electrostatic interactions between the protein and ribosome contribute to the observed folding acceleration and stabilization of ADR1a.
Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Authors: Wang Jason , Zhou Chris J. , Khodabukus Alastair , Tran Sabrina , Han Sang-Oh , Carlson Aaron L. , Madden Lauran , Kishnani Priya S. , Koeberl Dwight D. , Bursac Nenad 
Published: May 2021

AbstractIn Pompe disease, the deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA) causes skeletal and cardiac muscle weakness, respiratory failure, and premature death. While enzyme replacement therapy using recombinant human GAA (rhGAA) can significantly improve patient outcomes, detailed disease mechanisms and incomplete therapeutic effects require further studies. Here we report a three-dimensional primary human skeletal muscle (“myobundle”) model of infantile-onset Pompe disease (IOPD) that recapitulates hallmark pathological features including reduced GAA enzyme activity, elevated glycogen content and lysosome abundance, and increased sensitivity of muscle contractile function to metabolic stress. In vitro treatment of IOPD myobundles with rhGAA or adeno-associated virus (AAV)-mediated hGAA expression yields increased GAA activity and robust glycogen clearance, but no improvements in stress-induced functional deficits. We also apply RNA sequencing analysis to the quadriceps of untreated and AAV-treated GAA−/− mice and wild-type controls to establish a Pompe disease-specific transcriptional signature and reveal novel disease pathways. The mouse-derived signature is enriched in the transcriptomic profile of IOPD vs. healthy myobundles and partially reversed by in vitro rhGAA treatment, further confirming the utility of the human myobundle model for studies of Pompe disease and therapy.
Strong glacial-interglacial variability in upper ocean hydrodynamics, biogeochemistry, and productivity in the southern Indian Ocean
Authors: Tangunan Deborah , Berke Melissa A. , Cartagena-Sierra Alejandra , Flores José Abel , Gruetzner Jens , Jiménez-Espejo Francisco , LeVay Leah J. , Baumann Karl-Heinz , Romero Oscar , Saavedra-Pellitero Mariem , Coenen Jason J. , Starr Aidan , Hemming Sidney R. , Hall Ian R. ,   Expedition 361 Science Party, Barker Stephen , Brentegani Luna , Caley Thibaut , Charles Christopher D. , Crespin Julien G. , Franzese Allison M. , Han Xibin , Hines Sophia K. V. , Jimenez Espejo Francisco J. , Just Janna , Koutsodendris Andreas , Kubota Kaoru , Lathika Nambiyathodi , Norris Richard D. , dos Santos Thiago Pereira , Robinson Rebecca S. , Rolison John M. , Simon Margit H. , Tangunan Deborah , van der Lubbe Jeroen J. L. , Yamane Masako , Zhang Hucai 
Published: May 2021

AbstractIn the southern Indian Ocean, the position of the subtropical front – the boundary between colder, fresher waters to the south and warmer, saltier waters to the north – has a strong influence on the upper ocean hydrodynamics and biogeochemistry. Here we analyse a sedimentary record from the Agulhas Plateau, located close to the modern position of the subtropical front and use alkenones and coccolith assemblages to reconstruct oceanographic conditions over the past 300,000 years. We identify a strong glacial-interglacial variability in sea surface temperature and productivity associated with subtropical front migration over the Agulhas Plateau, as well as shorter-term high frequency variability aligned with variations in high latitude insolation. Alkenone and coccolith abundances, in combination with diatom and organic carbon records indicate high glacial export productivity. We conclude that the biological pump was more efficient and strengthened during glacial periods, which could partly account for the reported reduction in atmospheric carbon dioxide concentrations.
Critical evaluation of faecal microbiome preservation using metagenomic analysis
Authors: Pribyl Alena L , Parks Donovan H , Angel Nicola Z , Boyd Joel A , Hasson Alexander G , Fang Liang , MacDonald Samantha L , Wills Blake A , Wood David L A , Krause Lutz , Tyson Gene W , Hugenholtz Philip 
Published: May 2021

Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at −20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
Blood vessel and background separation for retinal image quality assessment
Authors: Liu Yi‐Peng , Lv Yajun , Li Zhanqing , Li Jing , Liu Yan , Chen Peng , Liang Ronghua 
Published: May 2021

AbstractRetinal image analysis has become an intuitive and standard aided diagnostic technique for eye diseases. The good image quality is essential support for doctors to provide timely and accurate disease diagnosis. This paper proposes an end‐to‐end learning based method for evaluating the retinal image quality. First, blood vessels of the input image are segmented by U‐Net, and the fundus image is divided into two parts: blood vessels and background. Then, we design a dual branch network module which extracts global features that influence the image quality and suppress the interference of blood vessels and local textures to achieve better performance. The proposed module can be embedded in various advanced network structures. The experimental results show the more efficient convergence rate for the network with the module. The best network accuracy rate is 85.83%, the AUC is 0.9296, and the F1‐score is 0.7967 on the collected local dataset. Additionally, the model generalization is tested on the public DRIMDB dataset. The accuracy, AUC, and F1‐score reach 97.89%, 0.9978, and 0.9688, respectively. Compared with the state‐of‐the‐art networks, the performance of the proposed method is proven to be accurate and effective for retinal image quality assessment.
Retracted: Selection of intermediate routes for secure data communication systems using graph theory application and grey wolf optimization algorithm in MANETs
Authors: Balaji Subbiah , Obaidat Mohammad S. , Suthir Sriram , Rajesh Manoharan , Suresh Koneri Chandrasekaran 
Published: May 2021

AbstractRetraction: “Selection of intermediate routes for secure data communication systems using graph theory application and grey wolf optimization algorithm in MANETs” by authors Subbiah Balaji, Mohammad S. Obaidat, Sriram Suthir, Manoharan Rajesh and Koneri Chandrasekaran Suresh, IET Netw. 2021;1–7. https://doi.org/10.1049/ntw2.12026.The above article, published online on 5 May 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor‐in‐Chief, Han‐Chieh Chao and John Wiley and Sons Ltd. The retraction has been agreed due to evidence indicating that the peer review of this paper was compromised.
The ionized heart of a molecular disk
Authors: Moscadelli L. , Cesaroni R. , Beltrán M. T. , Rivilla V. M. 
Published: May 2021

Context. Hyper-compact (HC) or ultra-compact H II regions are the first manifestations of the radiation feedback from a newly born massive star. Therefore, their study is fundamental to understanding the process of massive (≥8 M⊙) star formation.
Aims. We employed Atacama Large Millimeter/submillimeter Array (ALMA) 1.4 mm Cycle 6 observations to investigate at high angular resolution (≈0.′′050, corresponding to 330 au) the HC H II region inside molecular core A1 of the high-mass star-forming cluster G24.78+0.08.
Methods. We used the H30α emission and different molecular lines of CH3CN and 13CH3CN to study the kinematics of the ionized and molecular gas, respectively.
Results. At the center of the HC H II region, at radii ≲500 au, we observe two mutually perpendicular velocity gradients, which are directed along the axes at PA = 39° and PA = 133°, respectively. The velocity gradient directed along the axis at PA = 39° has an amplitude of 22 km s−1 mpc−1, which is much larger than the other’s, 3 km s−1 mpc−1. We interpret these velocity gradients as rotation around, and expansion along, the axis at PA = 39°. We propose a scenario where the H30α line traces the ionized heart of a disk-jet system that drives the formation of the massive star (≈20 M⊙) responsible for the HC H II region. Such a scenario is also supported by the position-velocity plots of the CH3CN and 13CH3CN lines along the axis at PA = 133°, which are consistent with Keplerian rotation around a 20 M⊙ star.
Conclusions. Toward the HC H II region in G24.78+0.08, the coexistence of mass infall (at radii of ~5000 au), an outer molecular disk (from ≲4000 au to ≳500 au), and an inner ionized disk (≲500 au) indicates that the massive ionizing star is still actively accreting from its parental molecular core. To our knowledge, this is the first example of a molecular disk around a high-mass forming star that, while becoming internally ionized after the onset of the H II region, continues to accrete mass onto the ionizing star.
Simulation of choroidal neovascularization in rabbits using indirect transpupillary laser coagulation
Authors: Prudnikova E.V. , Katelnikova A.E. , Ustenko Zh. Yu. 
Published: May 2021

Objective: to identify the applicability of indirect transpupillary laser coagulation (ITLC) for modeling choroidal neovascularization (CN) in rabbits and its optimal parameters.
Materials and methods: 12 rabbits, divided into 2 equal groups, were subjected to single- and double-sided ITLC, respectively, using a laser device with a wavelength of 810 nm (using different powers), an indirect ophthalmoscope and a lens. The time spent on coagulation, ophthalmoscopic signs on the 1st, 8th, 15th, 22nd and 29th days of the study, the severity of CN (histological and immunohistochemical (IHC) studies), body weight and general condition of the animals were also evaluated. Results: in all cases, it was possible to apply the coagulants using ITLC. During ophthalmoscopy, peripheral vascularization was detected on the 8th-29th day. Histological and IHC studies revealed significant tissue damage at a power of 700, 1000 mW, as well as signs of CN when using a power of 500 mW on the 15th day of the study.
Conclusion: ITLC is a safe method and can be used to simulate CN in rabbits at a power of no more than 500 mW.