bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the validity of a cross-platform retinal image segmentation tool in normal and diseased retina
Authors: Alex Varsha , Motevasseli Tahmineh , Freeman William R. , Jayamon Jefy A. , Bartsch Dirk-Uwe G. , Borooah Shyamanga 
Published: November 2021

AbstractComparing automated retinal layer segmentation using proprietary software (Heidelberg Spectralis HRA + OCT) and cross-platform Optical Coherence Tomography (OCT) segmentation software (Orion). Image segmentations of normal and diseased (iAMD, DME) eyes were performed using both softwares and then compared to the ‘gold standard’ of manual segmentation. A qualitative assessment and quantitative (layer volume) comparison of segmentations were performed. Segmented images from the two softwares were graded by two masked graders and in cases with difference, a senior retina specialist made a final independent decisive grading. Cross-platform software was significantly better than the proprietary software in the segmentation of NFL and INL layers in Normal eyes. It generated significantly better segmentation only for NFL in iAMD and for INL and OPL layers in DME eyes. In normal eyes, all retinal layer volumes calculated by the two softwares were moderate-strongly correlated except OUTLY. In iAMD eyes, GCIPL, INL, ONL, INLY, TRV layer volumes were moderate-strongly correlated between softwares. In eyes with DME, all layer volume values were moderate-strongly correlated between softwares. Cross-platform software can be used reliably in research settings to study the retinal layers as it compares well against manual segmentation and the commonly used proprietary software for both normal and diseased eyes.
Impact of spaceflight and artificial gravity on sulfur metabolism in mouse liver: sulfur metabolomic and transcriptomic analysis
Authors: Kurosawa Ryo , Sugimoto Ryota , Imai Hiroe , Atsuji Kohei , Yamada Koji , Kawano Yusuke , Ohtsu Iwao , Suzuki Kengo 
Published: November 2021

AbstractSpaceflight induces hepatic damage, partially owing to oxidative stress caused by the space environment such as microgravity and space radiation. We examined the roles of anti-oxidative sulfur-containing compounds on hepatic damage after spaceflight. We analyzed the livers of mice on board the International Space Station for 30 days. During spaceflight, half of the mice were exposed to artificial earth gravity (1 g) using centrifugation cages. Sulfur-metabolomics of the livers of mice after spaceflight revealed a decrease in sulfur antioxidants (ergothioneine, glutathione, cysteine, taurine, thiamine, etc.) and their intermediates (cysteine sulfonic acid, hercynine,N-acethylserine, serine, etc.) compared to the controls on the ground. Furthermore, RNA-sequencing showed upregulation of gene sets related to oxidative stress and sulfur metabolism, and downregulation of gene sets related to glutathione reducibility in the livers of mice after spaceflight, compared to controls on the ground. These changes were partially mitigated by exposure to 1 g centrifugation. For the first time, we observed a decrease in sulfur antioxidants based on a comprehensive analysis of the livers of mice after spaceflight. Our data suggest that a decrease in sulfur-containing compounds owing to both microgravity and other spaceflight environments (radiation and stressors) contributes to liver damage after spaceflight.
Birth order and prosociality in the early adolescent brain
Authors: Okada Naohiro , Yamamoto Yu , Yahata Noriaki , Morita Susumu , Koshiyama Daisuke , Morita Kentaro , Sawada Kingo , Kanata Sho , Fujikawa Shinya , Sugimoto Noriko , Toriyama Rie , Masaoka Mio , Koike Shinsuke , Araki Tsuyoshi , Kano Yukiko , Endo Kaori , Yamasaki Syudo , Ando Shuntaro , Nishida Atsushi , Hiraiwa-Hasegawa Mariko , Yokoyama Charles , Kasai Kiyoto 
Published: November 2021

AbstractBirth order is a crucial environmental factor for child development. For example, later-born children are relatively unlikely to feel secure due to sibling competition or diluted parental resources. The positive effect of being earlier-born on cognitive intelligence is well-established. However, whether birth order is linked to social behavior remains controversial, and the neural correlates of birth order effects in adolescence when social cognition develops remain unknown. Here, we explored the birth order effect on prosociality using a large-scale population-based adolescent cohort. Next, since the amygdala is a key region for sociality and environmental stress, we examined amygdala substrates of the association between birth order and prosociality using a subset neuroimaging cohort. We found enhanced prosociality in later-born adolescents (N = 3160), and observed the mediating role of larger amygdala volume (N = 208) and amygdala-prefrontal functional connectivity with sex-selective effects (N = 183). We found that birth order, a non-genetic environmental factor, affects adolescent social development via different neural substrates. Our findings may indicate the later-born people’s adaptive survival strategy in stressful environments.
Novel findings from family-based exome sequencing for children with biliary atresia
Authors: Tran Kien Trung , Le Vinh Sy , Dao Lan Thi Mai , Nguyen Huyen Khanh , Mai Anh Kieu , Nguyen Ha Thi , Ngo Minh Duy , Tran Quynh Anh , Nguyen Liem Thanh 
Published: November 2021

AbstractBiliary atresia (BA) is a progressive inflammation and fibrosis of the biliary tree characterized by the obstruction of bile flow, which results in liver failure, scarring and cirrhosis. This study aimed to explore the elusive aetiology of BA by conducting whole exome sequencing for 41 children with BA and their parents (35 trios, including 1 family with 2 BA-diagnosed children and 5 child-mother cases). We exclusively identified and validated a total of 28 variants (17 X-linked, 6 de novo and 5 homozygous) in 25 candidate genes from our BA cohort. These variants were among the 10% most deleterious and had a low minor allele frequency against the employed databases: Kinh Vietnamese (KHV), GnomAD and 1000 Genome Project. Interestingly, AMER1, INVS and OCRL variants were found in unrelated probands and were first reported in a BA cohort. Liver specimens and blood samples showed identical variants, suggesting that somatic variants were unlikely to occur during morphogenesis. Consistent with earlier attempts, this study implicated genetic heterogeneity and non-Mendelian inheritance of BA.
A study of sex difference in infant mortality in UK pediatric intensive care admissions over an 11-year period
Authors: Almossawi Ofran , O’Brien Scott , Parslow Roger , Nadel Simon , Palla Luigi 
Published: November 2021

AbstractWithin the UK, child mortality from all causes has declined for all ages over the last three decades. However, distinct inequality remains, as child mortality rates are generally found to be higher in males. A significant proportion of childhood deaths in the UK occur in Paediatric Intensive Care Units (PICU). We studied the association of sex with infant mortality in PICUs. We included all infants (0 to 12 months old) admitted to UK PICUs from 01/01/2005 to 31/12/2015 using the Paediatric Intensive Care Audit Network (PICANet) dataset. We considered first admissions to PICU and fitted a cause-specific-hazard-ratio (CSHR) model, and a logistic model to estimate the adjusted association between sex and mortality in PICU. Pre-defined subgroups were children less than 56-days old, and those with a primary diagnosis of infection. Of 71,243 cases, 1,411/29,520 (4.8%) of females, and 1,809/41,723 (4.3%) of males died. The adjusted male/female CSHR was 0.87 (95%-CI 0.81 to 0.92) representing a 13% higher risk of death for females. The adjusted OR for male to female mortality is 0.86 (95%-CI 0.80 to 0.93). Analyses in subgroups yielded similar findings. In our analysis, female infants have a higher rate of PICU mortality compared to male infants.
Adherence to plant-based dietary patterns in relation to glioma: a case–control study
Authors: Mousavi Seyed Mohammad , Shayanfar Mehdi , Rigi Somaye , Mohammad-Shirazi Minoo , Sharifi Giuve , Esmaillzadeh Ahmad 
Published: November 2021

AbstractAvailable evidence suggests a favorable association between adherence to a plant-based diet and disease prevention, but data on the link between such dietary intakes and cancer are scarce. We examined the association between the overall plant-based diet (PDI), healthy plant-based diet (hPDI), and unhealthy plant-based diet (uPDI) and risk of glioma. This case–control study was conducted on 128 newly diagnosed glioma patients, and 256 hospital-based controls. Cases were diagnosed by pathological test and controls were selected from hospitalized people in orthopedic and surgical wards. Dietary intakes were assessed using a validated Block-format 123-items food frequency questionnaire. Scores of plant-based dietary patterns were calculated using the method suggested by Satija et al. After controlling for potential confounders, individuals with higher scores of PDI (OR: 0.54, 95% CI: 0.32–0.91,P-trend < 0.001) and hPDI (OR: 0.32, 95% CI: 0.18–0.57,P-trend < 0.001) had significantly lower odds of glioma compared with those with the lowest scores. This association did not change in the fully adjusted model; such that subjects in the highest tertile of PDI and hPDI were 69% and 71% less likely to have glioma compared with those in the lowest tertile. In contrast, higher scores of uPDI was significantly associated with a greater odds of glioma (OR: 2.85, 95% CI: 1.26–6.47,P-trend = 0.02). Adherence to PDI and hPDI was associated with a lower odds of glioma, while greater adherence to uPDI was directly associated with the likelihood of glioma. Further prospective cohort studies are needed to examine our findings.
Freeze-dried Nannochloropsis oceanica biomass protects eicosapentaenoic acid (EPA) from metabolization in the rumen of lambs
Authors: Vítor Ana C. M. , Francisco Alexandra E. , Silva Joana , Pinho Mário , Huws Sharon A. , Santos-Silva José , Bessa Rui J. B. , Alves Susana P. 
Published: November 2021

AbstractEicosapentaenoic acid (EPA) from freeze-dried biomass of Nannochloropsis oceanica microalgae resists ruminal biohydrogenation in vitro, but in vivo demonstration is needed. Therefore, the present study was designed to test the rumen protective effects of N. oceanica in lambs. Twenty-eight lambs were assigned to one of four diets: Control (C); and C diets supplemented with: 1.2% Nannochloropsis sp. oil (O); 12.3% spray-dried N. oceanica (SD); or 9.2% N. oceanica (FD), to achieve 3 g EPA /kg dry matter. Lambs were slaughtered after 3 weeks and digestive contents and ruminal wall samples were collected. EPA concentration in the rumen of lambs fed FD was about 50% higher than lambs fed SD or O diets. Nevertheless, the high levels of EPA in cecum and faeces of animals fed N. oceanica biomass, independently of the drying method, suggests that EPA was not completely released and absorbed in the small intestine. Furthermore, supplementation with EPA sources also affected the ruminal biohydrogenation of C18 fatty acids, mitigating the shift from the t10 biohydrogenation pathways to the t11 pathways compared to the Control diet. Overall, our results demonstrate that FD N. oceanica biomass is a natural rumen-protected source of EPA to ruminants.
A novel strategy for comprehensive optimization of structural and operational parameters in a supersonic separator using computational fluid dynamics modeling
Authors: Shoghl Sina Nabati , Naderifar Abbas , Farhadi Fatola , Pazuki Gholamreza 
Published: November 2021

AbstractIn this study, the effects of several structural and operational parameters affecting the separation efficiency of supersonic separators were investigated by numerical methods. Different turbulence models were used and their accuracies were evaluated. Based on the error analysis, the V2-f turbulence model was more accurate for describing the high swirling turbulent flow than other investigated turbulence models. Therefore, the V2-f turbulence model and particle tracing model were selected to optimize the structure of the convergence part, the diffuser, the drainage port, and the swirler. The cooling performance of three line-type in the convergent section were calculated. The simulation results demonstrated that the convergent section designed by the Witoszynski curve had higher cooling depth compared to the Bi-cubic and Quintic curves. Furthermore, the expansion angle of 2° resulted in the highest stability of fluid flow and therefore was selected in the design of the diffuser. The effect of incorporating the swirler and its structure on the separation performance of supersonic separator was also studied. Three different swirler types, including axial, wall-mounted, and helical, were investigated. It was observed that installing the swirler significantly improved the separation efficiency of the supersonic separator. In addition, the simulation results demonstrated that the separation efficiency was higher for the axial swirler compared to the wall-mounted and helical swirlers. Therefore, for the improved nozzle, the swirling flow was generated by the axial swirler. The optimized axial swirler was constructed from 12 arced vanes each of which had a swirl angle of 40°. For the optimized structure, the effects of operating parameters such as inlet temperature, pressure recovery ratio, density, and droplet size was also investigated. It was concluded that increasing the droplet size and density significantly improved the separation efficiency of the supersonic separator. For hydrocarbon droplets, the separation efficiency improved from 4.6 to 76.7% upon increasing the droplet size from 0.1 to 2 µm.
An injured pachypleurosaur (Diapsida: Sauropterygia) from the Middle Triassic Luoping Biota indicating predation pressure in the Mesozoic
Authors: Liu Qiling , Yang Tinglu , Cheng Long , Benton Michael J. , Moon Benjamin C. , Yan Chunbo , An Zhihui , Tian Li 
Published: November 2021

AbstractThe Middle Triassic Luoping Biota in south-west China represents the inception of modern marine ecosystems, with abundant and diverse arthropods, fishes and marine reptiles, indicating recovery from the Permian–Triassic mass extinction. Here we report a new specimen of the predatory marine reptileDiandongosaurus, based on a nearly complete skeleton. The specimen is larger than most other known pachypleurosaurs, and the body shape, caniniform teeth, clavicle with anterior process, and flat distal end of the anterior caudal ribs show its affinities withDiandongosaurus acutidentatus, while the new specimen is approximately three times larger than the holotype. The morphological characters indicate that the new specimen is an adult ofD. acutidentatus, allowing for ontogenetic variation. The fang-like teeth and large body size confirm it was a predator, but the amputated hind limb on the right side indicate itself had been predated by an unknown hunter. Predation on such a large predator reveals that predation pressure in the early Mesozoic was intensive, a possible early hint of the Mesozoic Marine Revolution.
Separation of some vitamins in reversed-phase thin-layer chromatography and pressurized planar electrochromatography with eluent containing surfactant
Authors: Polak Beata , Pajurek Emilia 
Published: November 2021

AbstractThe separation of some water- and fat-soluble vitamins via micellar systems of reversed-phase high-performance thin-layer chromatography (HPTLC) and pressurized planar electrochromatography (PPEC) was subjected to research. Hence, the influence of the mobile phase composition (surfactant and acetonitrile concentration, eluent buffer pH) on the migration distances and zone separation of some vitamins (thiamine, riboflavin, niacin, pyridoxine, cyanocobalamin, folic acid, ergocalciferol and α-tocopherol) was investigated. Our results indicated that the applied technique has an impact on the solute order. Comparing the system capacity of HPLC and PPEC (measured as height of the theoretical plate) for the mobile phase systems with and without surfactant shows differences, especially for fat-soluble vitamin. The variances and reproducibilities (% RDS) values of the vitamin are less in PPEC than in TLC. Moreover, the migration distances of water-soluble vitamins are longer than fat-soluble ones. Overall, eluent consisting of 50% acetonitrile, 18.75 mM SDS, the buffer of pH 6.99 via the PPEC technique was most appropriate for determining the investigated vitamins in the artificial mixture and the two commercially available vitamin combinations.
Enzymatic ligation of an antibody and arginine 9 peptide for efficient and cell-specific siRNA delivery
Authors: Ando Yu , Nakazawa Hikaru , Miura Daisuke , Otake Maho , Umetsu Mitsuo 
Published: November 2021

AbstractA fusion protein comprising an antibody and a cationic peptide, such as arginine-9 (R9), is a candidate molecule for efficient and cell-specific delivery of siRNA into cells in order to reduce the side effects of nucleic acid drugs. However, their expression in bacterial hosts, required for their development, often fails, impeding research progress. In this study, we separately prepared anti-EGFR nanobodies with the K-tag sequence MRHKGS at the C-terminus and R9 with the Q-tag sequence LLQG at the N-terminus, and enzymatically ligated them in vitro by microbial transglutaminase to generate Nanobody-R9, which is not expressed as a fused protein in E. coli. Nanobody-R9 was synthesized at a maximum binding efficiency of 85.1%, without changing the binding affinity of the nanobody for the antigen. Nanobody-R9 successfully delivered siRNA into the cells, and the cellular influx of siRNA increased with increase in the ratio of Nanobody-R9 to siRNA. We further demonstrated that the Nanobody-R9–siRNA complex, at a 30:1 ratio, induced an approximately 58.6% reduction in the amount of target protein due to RNAi in mRNA compared to lipofectamine.
Characterization of subcellular localization of eukaryotic clamp loader/unloader and its regulatory mechanism
Authors: Park Su Hyung , Kim Seong-jung , Myung Kyungjae , Lee Kyoo-young 
Published: November 2021

AbstractProliferating cell nuclear antigen (PCNA) plays a critical role as a processivity clamp for eukaryotic DNA polymerases and a binding platform for many DNA replication and repair proteins. The enzymatic activities of PCNA loading and unloading have been studied extensively in vitro. However, the subcellular locations of PCNA loaders, replication complex C (RFC) and CTF18-RFC-like-complex (RLC), and PCNA unloader ATAD5-RLC remain elusive, and the role of their subunits RFC2-5 is unknown. Here we used protein fractionation to determine the subcellular localization of RFC and RLCs and affinity purification to find molecular requirements for the newly defined location. All RFC/RLC proteins were detected in the nuclease-resistant pellet fraction. RFC1 and ATAD5 were not detected in the non-ionic detergent-soluble and nuclease-susceptible chromatin fractions, independent of cell cycle or exogenous DNA damage. We found that small RFC proteins contribute to maintaining protein levels of the RFC/RLCs. RFC1, ATAD5, and RFC4 co-immunoprecipitated with lamina-associated polypeptide 2 (LAP2) α which regulates intranuclear lamin A/C. LAP2α knockout consistently reduced detection of RFC/RLCs in the pellet fraction, while marginally affecting total protein levels. Our findings strongly suggest that PCNA-mediated DNA transaction occurs through regulatory machinery associated with nuclear structures, such as the nuclear matrix.
Translatory and rotatory motion of exchange-bias capped Janus particles controlled by dynamic magnetic field landscapes
Authors: Huhnstock Rico , Reginka Meike , Tomita Andreea , Merkel Maximilian , Dingel Kristina , Holzinger Dennis , Sick Bernhard , Vogel Michael , Ehresmann Arno 
Published: November 2021

AbstractMagnetic Janus particles (MJPs), fabricated by covering a non-magnetic spherical particle with a hemispherical magnetic in-plane exchange-bias layer system cap, display an onion magnetization state for comparably large diameters of a few microns. In this work, the motion characteristics of these MJPs will be investigated when they are steered by a magnetic field landscape over prototypical parallel-stripe domains, dynamically varied by superposed external magnetic field pulse sequences, in an aqueous medium. We demonstrate, that due to the engineered magnetization state in the hemispherical cap, a comparably fast, directed particle transport and particle rotation can be induced. Additionally, by modifying the frequency of the applied pulse sequence and the strengths of the individual field components, we observe a possible separation between a combined or an individual occurrence of these two types of motion. Our findings bear importance for lab-on-a-chip systems, where particle immobilization on a surface via analyte bridges shall be used for low concentration analyte detection and a particle rotation over a defined position of a substrate may dramatically increase the immobilization (and therefore analyte detection) probability.
Numerical analysis of the precursory information of slope instability process with constant resistance bolt
Authors: Chen Feng , Wang Xue-bin , Du Yan-hong , Tang Chun-an 
Published: November 2021

AbstractThe instability of slope has already threatened life and property safety of the people, and improving the monitoring method of slope stability has important theoretical and practical significance for disaster prevention and reduction. According to the idea of “Newton force sudden drop and catastrophic occurrence” proposed by M.C. He in the landslide monitoring, a numerical model with constant resistance bolt has been established. Through numerical simulation research, it is found that the maximum principal stress, minimum principal stress and shear stress of the intersection point P of landslide surface and constant resistance bolt are sudden growth and sudden decrease, the vertical displacement and lateral displacement of this point P appear rise and fall before three kinds of stress. When loading to the next step of the step where three stress have reduced to a minimum value the slope is unstable and destroyed. At this time, the constant resistance bolt has undergone larger plastic deformation and damaged. Finally, comparing the stress curves and the acoustic emission (AE) curves, it can be seen that stress decreases from the maximum value and the AE curves begin to show a significant rise, the two curves display opposite law. It can be seen from the AE diagram that the failure mode of the slope is a combined tension and shear failure. The numerical test results provide a new idea for real-time monitoring and forecasting of slope.
Quantification of the effects of climatic conditions on French hospital admissions and deaths induced by SARS-CoV-2
Authors: d’Albis Hippolyte , Coulibaly Dramane , Roumagnac Alix , de Carvalho Filho Eurico , Bertrand Raphaël 
Published: November 2021

AbstractAn estimation of the impact of climatic conditions—measured with an index that combines temperature and humidity, the IPTCC—on the hospitalizations and deaths attributed to SARS-CoV-2 is proposed. The present paper uses weekly data from 54 French administrative regions between March 23, 2020 and January 10, 2021. Firstly, a Granger causal analysis is developed and reveals that past values of the IPTCC contain information that allow for a better prediction of hospitalizations or deaths than that obtained without the IPTCC. Finally, a vector autoregressive model is estimated to evaluate the dynamic response of hospitalizations and deaths after an increase in the IPTCC. It is estimated that a 10-point increase in the IPTCC causes hospitalizations to rise by 2.9% (90% CI 0.7–5.0) one week after the increase, and by 4.1% (90% CI 2.1–6.4) and 4.4% (90% CI 2.5–6.3) in the two following weeks. Over ten weeks, the cumulative effect is estimated to reach 20.1%. Two weeks after the increase in the IPTCC, deaths are estimated to rise by 3.7% (90% CI 1.6–5.8). The cumulative effect from the second to the tenth weeks reaches 15.8%. The results are robust to the inclusion of air pollution indicators.