bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak
Authors: Chen Yu , Wang Amy Y. , Barkley Courtney A. , Zhang Yixin , Zhao Xinyang , Gao Min , Edmonds Mick D. , Chong Zechen 
Published: January 2023

AbstractLong-read sequencing has demonstrated great potential for characterizing all types of structural variations (SVs). However, existing algorithms have insufficient sensitivity and precision. To address these limitations, we present DeBreak, a computational method for comprehensive and accurate SV discovery. Based on alignment results, DeBreak employs a density-based approach for clustering SV candidates together with a local de novo assembly approach for reconstructing long insertions. A partial order alignment algorithm ensures precise SV breakpoints with single base-pair resolution, and a k-means clustering method can report multi-allele SV events. DeBreak outperforms existing tools on both simulated and real long-read sequencing data from both PacBio and Nanopore platforms. An important application of DeBreak is analyzing cancer genomes for potentially tumor-driving SVs. DeBreak can also be used for supplementing whole-genome assembly-based SV discovery.
Analytical solution of overlying pipe deformation caused by tunnel excavation based on Pasternak foundation model
Authors: Fu Daxi , Deng Bo , Yang Minghui , Zhen Binbin 
Published: January 2023

AbstractThe existing tunnel construction causes stratum deformation, which in turn leads to additional deformation and internal force of the overlying pipeline, thus increasing the risk of pipeline accidents. Then, how to correctly calculate the deformation and internal force of pipeline is the key to pipeline safety evaluation. To this end, this study firstly used the Pasternak foundation beam model to simulate the interaction of pipeline and soil, and divided the pipeline into the void area (i.e., pipeline-soil detachment) and the coordination area (i.e., pipeline-soil is always deformed together) between pipeline and soil. The differential equation of pipeline deflection for the void area and the coordination area were established respectively, and the solutions of pipeline deflection, the internal force of pipeline and the width of pipeline-soil void area were presented. Subsequently, the accuracy of the proposed method was verified by comparing with the available model and field test data, and it is found that the calculation results are too conservative without considering the pipeline-soil voiding phenomenon. Finally, the detailed parametric analysis was conducted. The results show that the pipeline deflection decreases with the increase of the pipeline-tunnel spacing between pipeline and tunnel, the pipeline bending stiffness and the soil elastic modulus, but increases with the increase of the formation loss rate, and the width of pipeline-soil void area increases with the increase of the pipeline-tunnel spacing, the pipeline bending stiffness and the soil elastic modulus.
Enhancement of the microwave photon-magnon coupling strength for a planar fabricated resonator
Authors: Girich Aleksey , Nedukh Sergiy , Polevoy Sergey , Sova Kateryna , Tarapov Sergey , Vakula Arthur 
Published: January 2023

AbstractPlanar resonators have a wide usage in modern microwave technologies and perspectives in novel quantum technologies development. As was demonstrated earlier, their utilization allows to achieve high values of microwave photon-magnon coupling strength—an important parameter in technologies of information coherent transfer from electromagnetic GHz range to the optical range. In the present work, the achievement of the high value of the microwave photon-magnon coupling strength by exploiting the increase of the spatial concentration of the magnetic component of the planar resonator electromagnetic field is reported. Starting from the conventional planar split-ring resonator design we increased the coupling strength up to 40% by modifying the resonator shape. The numerical simulation and experimental verification showed a predicted increase in the spatial concentration of the microwave magnetic component and showed the increased value of the microwave photon-magnon coupling strength as a sequence.
Chloroplasts evolved an additional layer of translational regulation based on non-AUG start codons for proteins with different turnover rates
Authors: Sadhu Leelavathi , Kumar Krishan , Kumar Saravanan , Dass Abhishek , Pathak Ranjana , Bhardwaj Amit , Pandey Pankaj , Van Cuu Nguyen , Rawat Bhupendra S. , Reddy Vanga Siva 
Published: January 2023

AbstractChloroplasts have evolved from photosynthetic cyanobacteria-like progenitors through endosymbiosis. The chloroplasts of present-day land plants have their own transcription and translation systems that show several similarities with prokaryotic organisms. A remarkable feature of the chloroplast translation system is the use of non-AUG start codons in the protein synthesis of certain genes that are evolutionarily conserved from Algae to angiosperms. However, the biological significance of such use of non-AUG codons is not fully understood. The present study was undertaken to unravel the significance of non-AUG start codons in vivo using the chloroplast genetic engineering approach. For this purpose, stable transplastomic tobacco plants expressing a reporter gene i.e. uidA (GUS) under four different start codons (AUG/UUG/GUG/CUG) were generated and β-glucuronidase (GUS) expression was compared. To investigate further the role of promoter sequences proximal to the start codon, uidA was expressed under two different chloroplast gene promoters psbA and psbC that use AUG and a non-AUG (GUG) start codons, respectively, and also showed significant differences in the DNA sequence surrounding the start codon. Further, to delineate the role of RNA editing that creates AUG start codon by editing non-AUG codons, if any, which is another important feature of the chloroplast transcription and translation system, transcripts were sequenced. In addition, a proteomic approach was used to identify the translation initiation site(s) of GUS and the N-terminal amino acid encoded when expressed under different non-AUG start codons. The results showed that chloroplasts use non-AUG start codons in combination with the translation initiation site as an additional layer of gene regulation to over-express proteins that are required at high levels due to their high rates of turnover.
Plant nitrogen retention in alpine grasslands of the Tibetan Plateau under multi-level nitrogen addition
Authors: Yu Jiaoneng , Xu-Ri  , Qu Songbo , Li Fengzi , Wei Da , Borjigidai Almaz 
Published: January 2023

AbstractNitrogen (N) deposition might alleviate degradation of alpine grassland caused by N limitation on the Tibetan Plateau (TP). To determine such limitation and quantify the N-induced N retention in plant, a six-year fertilization experiment with six levels of N addition rates (0, 1, 2, 4, 8 and 16 g N m−2 yr−1) was conducted in the Namco alpine steppe and additional 89 experiments with multi-level N addition were also synthesized worldwide among which 27 sites were on the TP. In general, N addition promoted N retention in plants, and this increasing trend diminished at the critical N rate (Ncr). The maximum N retention capacity (MNRC) of plants at Ncr was strongly correlated with initial aboveground net primary productivity with a slope of 0.02, and the MNRC of grasslands globally ranged from 0.35 to 42.59 g N m−2 yr−1, approximately account for 39% of Ncr. Tibetan alpine grassland had a low average MNRC (2.24 g N m−2 yr−1) with distinct regional characteristic, which was much lower in the western TP (0.80 g N m−2 yr−1) than the eastern TP (4.10 g N m−2 yr−1). Our results inferred 0.33–1.21 Tg N yr−1 (0.22–0.79 g N m−2 yr−1) can be retained and 5.65–20.11 Tg C yr−1 (3.67–13.06 g C m−2 yr−1) can be gained by Tibetan alpine grasslands under current N deposition level. With the aggravation of N deposition, the alpine steppe ecosystem might continuously absorb N and C until N deposition reaches Ncr.
Eco-evolutionary modelling of microbial syntrophy indicates the robustness of cross-feeding over cross-facilitation
Authors: Boza G. , Barabás G. , Scheuring I. , Zachar I. 
Published: January 2023

AbstractSyntrophic cooperation among prokaryotes is ubiquitous and diverse. It relies on unilateral or mutual aid that may be both catalytic and metabolic in nature. Hypotheses of eukaryotic origins claim that mitochondrial endosymbiosis emerged from mutually beneficial syntrophy of archaeal and bacterial partners. However, there are no other examples of prokaryotic syntrophy leading to endosymbiosis. One potential reason is that when externalized products become public goods, they incite social conflict due to selfish mutants that may undermine any mutualistic interactions. To rigorously evaluate these arguments, here we construct a general mathematical framework of the ecology and evolution of different types of syntrophic partnerships. We do so both in a general microbial and in a eukaryogenetic context. Studying the case where partners cross-feed on each other’s self-inhibiting waste, we show that cooperative partnerships will eventually dominate over selfish mutants. By contrast, systems where producers actively secrete enzymes that cross-facilitate their partners’ resource consumption are not robust against cheaters over evolutionary time. We conclude that cross-facilitation is unlikely to provide an adequate syntrophic origin for endosymbiosis, but that cross-feeding mutualisms may indeed have played that role.
Characterization of diffractive bifocal intraocular lenses
Authors: Mendroch Damian , Altmeyer Stefan , Oberheide Uwe 
Published: January 2023

AbstractMultifocal intraocular lenses incorporate a variety of design considerations, including dimensioning of the base monofocal shape and the diffraction grating. While studying three different lens models, we present a practical approach for mathematical modelling and evaluation of these geometries. Contrary to typical lens measurement methods, non-contact measurements were performed on the Alcon SN6AD1, HumanOptics MS 612 DAY and the AMO ZMA00 lenses using a confocal microscope. Subsequent data processing includes centering, tilting correction, filtering and an algorithmic decomposition into a conic and polynomial part and the diffraction grating. Lastly, evaluation of fitting parameters and grating shape is done to allow for inferences about further optical properties. Results and analysis show the confocal microscope to be a suitable imaging method for lens measurements. The processing of this data enables the reconstruction of the annular diffraction grating over the complete lens diameter. Apodization, near addition and diffraction efficiency characteristics are found utilizing the grating shape. Additionally, near-optical axis curvature, asphericity and higher order polynomials are identified qualitatively from the reconstruction of the monofocal base form. Derived properties also include the lens optical base and addition power. By making use of the surface geometries, as well as the lens’ material and thickness, a full lens model can be created for further studies. In summary, our analytical approach enables the insight to various intraocular lens design decisions. Furthermore, this procedure is suitable for lens model creation for research and simulation.
Protective effects of chitosan based salicylic acid nanocomposite (CS-SA NCs) in grape (Vitis vinifera cv. ‘Sultana’) under salinity stress
Authors: Aazami Mohammad Ali , Maleki Maryam , Rasouli Farzad , Gohari Gholamreza 
Published: January 2023

AbstractSalinity is one of the most important abiotic stresses that reduce plant growth and performance by changing physiological and biochemical processes. In addition to improving the crop, using nanomaterials in agriculture can reduce the harmful effects of environmental stresses, particularly salinity. A factorial experiment was conducted in the form of a completely randomized design with two factors including salt stress at three levels (0, 50, and 100 mM NaCl) and chitosan-salicylic acid nanocomposite at three levels (0, 0.1, and 0.5 mM). The results showed reductions in chlorophylls (a, b, and total), carotenoids, and nutrient elements (excluding sodium) while proline, hydrogen peroxide, malondialdehyde, total soluble protein, soluble carbohydrate, total antioxidant, and antioxidant enzymes activity increased with treatment chitosan-salicylic acid nanocomposite (CS-SA NCs) under different level NaCl. Salinity stress reduced Fm', Fm, and Fv/Fm by damage to photosynthetic systems, but treatment with CS-SA NCs improved these indices during salinity stress. In stress-free conditions, applying the CS-SA NCs improved the grapes' physiological, biochemical, and nutrient elemental balance traits. CS-SA NCs at 0.5 mM had a better effect on the studied traits of grapes under salinity stress. The CS-SA nanoparticle is a biostimulant that can be effectively used to improve the grape plant yield under salinity stress.
Left atrial appendage thrombus formation, potential of resolution and association with prognosis in a large real-world cohort
Authors: Hautmann Martina , Zacher Michael , Fuchs Sophia , Pérez Christian Muñoz , Ahmidou Akram , Kerber Sebastian , Barth Sebastian 
Published: January 2023

AbstractComprehensive data on factors influencing left atrial appendage (LAA) thrombus formation, resolution and impact on survival are limited. In this single-center, retrospective study 7759 (2010–2015) patients with symptomatic ongoing atrial fibrillation (AF) on admission were screened for LAA thrombi. 450 patients had LAA thrombi. 481 patients without LAA thrombi were randomly selected as controls. We assessed clinical, echocardiographic, laboratory parameters and long-term survival of both groups. Patients with LAA thrombi compared to controls were older, had more strokes, higher CHA2DS2 -VASc scores, worse renal function, less controlled diabetes, advanced heart failure, lower LAA emptying velocities, higher levels of cardiac and inflammatory markers (all p < 0.001). 56.3% of followed-up patients (304) dissolved their LAA thrombi. Chances of thrombus resolution increased with rising LAA flow velocities (OR 1.061, p = 0.022), whereas advanced age (OR 0.950, p < 0.001) and presence of permanent AF (OR 0.354, p < 0.001) decreased chances of thrombus resolution. Presence of LAA thrombi was associated with a markedly reduced 10-year survival probability (31% versus 69%). LAA thrombus formation is promoted by advanced structural heart disease, inflammation, diabetes and impaired renal function. Younger age, non-permanent AF and higher LAA flow velocities were predictors of thrombus resolution. Thrombus formation was associated with poor prognosis.
A preclinical study comparing single- and double-root 3D-printed Ti–6Al–4V implants
Authors: Chung Inna , Lee Jungwon , Li Ling , Seol Yang-Jo , Lee Yong-Moo , Koo Ki-Tae 
Published: January 2023

AbstractRecently, double-root implants have been investigated using 3D-printed technology. Here, we investigated damping capacity, microcomputed tomographic (micro-CT) and histological analyses of double-root 3D-printed implants compared with single-root 3D printed implants. Single- and double-root 3D-printed implants were fabricated and placed at both sides of mandibular third and fourth premolars in four beagle dogs. The damping capacity was measured, and periapical X-rays were taken every 2 weeks for 12 weeks. The bone volume/tissue volume (BV/TV) and bone mineral density (BMD) around the implants were measured with micro-CT. Bone-to-implant contact (BIC) and bone area fraction occupancy (BAFO) were measured in histological samples. The implant stability values between the groups were not significantly different, except at 4 and 12 weeks. The marginal bone changes were similar at the mesial and distal areas between the groups. The BV/TV and BMD values of the double-root 3D-printed implants showed no statistical difference through micro-CT analysis, but the double-root 3D-printed implants showed lower BIC and BAFO values through histomorphometric analysis compared to the single-root 3D-printed implants. Compared to single-root implants, 3D-printed double-root implants demonstrated comparable stability and bone remodeling around the fixtures, but the statistically significant bone loss in the furcation area remains problematic.
Geographical variation of common childhood illness and its associated factors among under-five children in Ethiopia: spatial and multilevel analysis
Authors: Chilot Dagmawi , Diress Mengistie , Yismaw Gela Yibeltal , Sinamaw Deresse , Simegn Wudneh , Andualem Amare Agmas , Seid Abdulwase Mohammed , Bitew Desalegn Anmut , Seid Mohammed Abdu , Eshetu Habitu Birhan , Kibret Anteneh Ayelign , Belay Daniel Gashaneh 
Published: January 2023

AbstractAlthough substantial progress has been made in reducing child mortality over the last three decades, the magnitude of the problem remains immense. Ethiopia is one of the countries with a high under-five mortality rate due to childhood illnesses including acute respiratory infections, diarrhea, and fever that varies from place to place. It is vital to have evidence of the factors associated with childhood illnesses and the spatial distribution across the country to prioritize and design targeted interventions. Thus, this study aimed to investigate the spatial cluster distribution and associated factors with common childhood illnesses. Secondary data analysis based on the 2016 Ethiopian Demographic and Health Survey data was carried out. A total weighted sample of 10,417 children was included. The study used ArcGIS and SaTScan software to explore spatial distribution. For associated factors, a multilevel binary logistic regression model was fitted using STATA V.14 software. Adjusted Odds Ratios (AOR) with a 95% Confidence Interval (CI) andp-value ≤ 0.05 in the multivariable model were used to declare significant factors associated with the problem. ICC, MOR, PCV, and deviance (−2LLR) were used to check model fitness and model comparison. In this study, the prevalence of common childhood illnesses among under-five children was 22.5% (95% CI: 21.6–23.3%). The spatial analysis depicted that common childhood illnesses have significant spatial variation across Ethiopia. The SaTScan analysis identified significant primary clusters in Tigray and Northern Amhara regions (log-likelihood ratio (LLR) = 60.19,p < 0.001). In the multilevel analysis, being rural residence [AOR = 1.39, 95% CI (1.01–1.98)], small child size at birth [AOR = 1.36, 95% CI (1.21–1.55)], high community poverty [AOR = 1.26, 95% CI (1.06–1.52)], mothers aged 35–49 [AOR = 0.81, 95% CI (0.69–0.94)], the household had electricity [AOR = 0.77, 95% CI (0.61–0.98)], the household had a refrigerator [AOR = 0.60, 95% CI (0.42–0.87)], improved drinking water [AOR = 0.82, 95% CI (0.70–0.95)], improved toilet [AOR = 0.72, 95% CI (0.54–0.94)], average child size at birth [AOR = 0.83, 95% CI (0.75–0.94)] were significantly associated with common childhood illnesses. Common childhood illnesses had spatial variations across Ethiopia. Hotspot areas of the problem were found in the Tigray, Northern Amhara, and Northeast SNNPR. Both individual and community-level factors affected common childhood illnesses distribution and prevalence in Ethiopia. Therefore, public health intervention should target the hotspot areas of common childhood illnesses to reduce their incidence in the country.
Using survey data to estimate the impact of the omicron variant on vaccine efficacy against COVID-19 infection
Authors: Rufino Jesús , Baquero Carlos , Frey Davide , Glorioso Christin A. , Ortega Antonio , Reščič Nina , Roberts Julian Charles , Lillo Rosa E. , Menezes Raquel , Champati Jaya Prakash , Fernández Anta Antonio 
Published: January 2023

AbstractSymptoms-based detection of SARS-CoV-2 infection is not a substitute for precise diagnostic tests but can provide insight into the likely level of infection in a given population. This study uses symptoms data collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID. This work, conducted in January of 2022 during the emergence of the Omicron variant (subvariant BA.1), aims to improve the quality of infection detection from the available symptoms and to use the resulting estimates of infection levels to assess the changes in vaccine efficacy during a change of dominant variant; from the Delta dominant to the Omicron dominant period. Our approach produced a new symptoms-based classifier, Random Forest, that was compared to a ground-truth subset of cases with known diagnostic test status. This classifier was compared with other competing classifiers and shown to exhibit an increased performance with respect to the ground-truth data. Using the Random Forest classifier, and knowing the vaccination status of the subjects, we then proceeded to analyse the evolution of vaccine efficacy towards infection during different periods, geographies and dominant variants. In South Africa, where the first significant wave of Omicron occurred, a significant reduction of vaccine efficacy is observed from August-September 2021 to December 2021. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses (of Pfizer/BioNTech), and from 0.51 to 0.09 for those vaccinated with one dose (of Pfizer/BioNTech or Johnson & Johnson). We also extended the study to other countries in which Omicron has been detected, comparing the situation in October 2021 (before Omicron) with that of December 2021. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around − 0.6 between the measured prevalence of Omicron in several countries and the vaccine efficacy in those same countries. This prediction, in January of 2022, of the decreased vaccine efficacy towards Omicron is in line with the subsequent increase of Omicron infections in the first half of 2022.
Validation of a motion model for soccer players’ sprint by means of tracking data
Authors: Narizuka Takuma , Takizawa Kenta , Yamazaki Yoshihiro 
Published: January 2023

AbstractIn soccer game analysis, the widespread availability of play-by-play and tracking data has made it possible to test mathematical models that have been discussed mainly theoretically. One of the essential models in soccer game analysis is a motion model that predicts the arrival point of a player ints. Although many space evaluation and pass prediction methods rely on motion models, the validity of each has not been fully clarified. This study focuses on the motion model proposed by Fujimura and Sugihara (Fujimura–Sugihara model) under sprint conditions based on the equation of motion. A previous study indicated that the Fujimura–Sugihara model is ineffective for soccer games because it generates a circular arrival region. This study aims to examine the validity of the Fujimura–Sugihara model using soccer tracking data. Specifically, we quantitatively compare the arrival regions of players between the model and real data. We show that the boundary of the player’s arrival region is circular rather than elliptical, which is consistent with the model. We also show that the initial speed dependence of the arrival region satisfies the solution of the model. Furthermore, we propose a method for estimating valid kinetic parameters in the model directly from tracking data and discuss the limitations of the model for soccer games based on the estimated parameters.