bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome‐scale Gastrodia elata genome and large‐scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants
Authors: Xu Yuxing , Lei Yunting , Su Zhongxiang , Zhao Man , Zhang Jingxiong , Shen Guojing , Wang Lei , Li Jing , Qi Jinfeng , Wu Jianqiang 
Published: October 2021

SummaryMycoheterotrophic and parasitic plants are heterotrophic and parasitize on fungi and plants, respectively, to obtain nutrients. Large‐scale comparative genomics analysis has not been conducted in mycoheterotrophic or parasitic plants or between these two groups of parasites. We assembled a chromosome‐level genome of the fully mycoheterotrophic plant Gastrodia elata (Orchidaceae) and performed comparative genomic analyses on the genomes of G. elata and four orchids (initial mycoheterotrophs), three parasitic plants (Cuscuta australis, Striga asiatica, and Sapria himalayana), and 36 autotrophs from various angiosperm lineages. It was found that while in the hemiparasite S. asiatica and initial mycoheterotrophic orchids, approximately 4–5% of the conserved orthogroups were lost, the fully heterotrophic G. elata and C. australis both lost approximately 10% of the conserved orthogroups, indicating that increased heterotrophy is positively associated with gene loss. Importantly, many genes that are essential for autotrophs, including those involved in photosynthesis, the circadian clock, flowering time regulation, immunity, nutrient uptake, and root and leaf development, were convergently lost in both G. elata and C. australis. The high‐quality genome of G. elata will facilitate future studies on the physiology, ecology, and evolution of mycoheterotrophic plants, and our findings highlight the critical role of gene loss in the evolution of plants with heterotrophic lifestyles.
Molecular blood group screening in Omani blood donors
Authors: Al‐Riyami Arwa Z. , Al Hinai Dina , Al‐Rawahi Mohammed , Al‐Hosni Saif , Al‐Zadjali Shoaib , Al‐Marhoobi Ali , Al‐Khabori Murtadha , Al‐Riyami Hamad , Denomme Gregory A. 
Published: October 2021

AbstractBackground and ObjectivesBlood group genotyping has been used in different populations. This study aims at evaluating the genotypes of common blood group antigens in the Omani blood donors and to assess the concordance rate with obtained phenotypes.Material and MethodsBlood samples from 180 Omani donors were evaluated. Samples were typed by serological methods for the five blood group systems MNS, RH (RHD/RHCE), KEL, FY and JK. Samples were genotyped using RBC‐FluoGene vERYfy eXtend kit (inno‐train©). Predicted phenotypic variants for 70 red blood cell antigens among the MNS, RH (RHD/RHCE), KEL, FY, JK, DO, LU, YT, DI, VEL, CO and KN blood group systems were assessed.ResultsSimultaneous phenotype and genotype results were available in 130 subjects. Concordance rate was >95% in all blood group systems with exception of Fy(b+) (87%). Homozygous GATA‐1 mutation leading to erythroid silencing FY*02N.01 (resulting in the Fy(b‐)ES phenotype) was detected in 81/112 (72%) of genotyped samples. In addition, discrepant Fyb phenotype/genotype result was obtained in 14/112 samples; 13 of which has a heterozygous GATA‐1 mutation and one sample with a wild GATA genotype. D and partial e c.733C>G variants expressing the V+VS+ phenotype were found in 22/121 (18.2%) and 14/120 (11.7%) of the samples, respectively. Di(a‐b+), Js(a‐b+), Yt(a+b‐) and Kn(a+b‐) genotype frequencies were 99.4%, 95.8%, 91.9% and 97.7%, respectively.ConclusionIn conclusion, we report a high frequency of FY*02N.01 allele due to homozygous c.‐67T>C GATA‐1 single‐nucleotide variation. This is the first study reporting the detailed distribution of common and rare red cell genotypes in Omani blood donors.
Benchmark Validation Experiment of Plenum-to-Plenum Flow Through Heated Parallel Channels
Authors: Parker Austin W. , Smith Barton L. 
Published: October 2021

Abstract
This paper documents a computational fluid dynamics (CFD) validation benchmark experiment for flow through three parallel, heated channels from one plenum to another. The test section was installed into a facility designed for natural convection benchmark validation experiments. The focus of these experiments was the highly-coupled thermal-fluid dynamics that occur between mixing jets in the upper plenum of the wind tunnel. A thermal instability in mixing jets, called thermal striping, can cause damage to structures which is a concern for high temperature gas reactors. Nine experimental cases were explored by varying the relative channel temperature or blower speed. The boundary conditions for CFD validation were measured and tabulated along with an uncertainty. Geometry measurements of the triple channel test section were used to make an as-built solid model for use in simulation. The outer tunnel and channel surface temperatures, the pressure drop across the test section, atmospheric conditions, and inflow into the upper plenum were measured or calculated for the boundary conditions. The air velocity and temperature were measured in the jet mixing region of the upper plenum as system response quantities.
Brain-Derived Neurotrophic Factor and Psychophysiological Response in Youth Badminton Athletes During the Season
Authors: Santos Arilene M.S. , Maldonado Alberto J. , de Sousa Junior Antônio V.M. , Brito Susi O.S. , de Moura Rayane C. , Figueiredo Caique , Monteiro Paula A. , Neves Lucas M. , Freitas Junior Ismael F. , dos Santos Marcos A.P. , Ribeiro Sergio L.G. , Rossi Fabrício E. 
Published: October 2021

Purpose: To analyze peripheral brain-derived neurotrophic factor (BDNF) levels and psychophysiological parameters in youth badminton athletes during the season and to determine the relationship between variables. Methods: Fourteen young badminton athletes were assessed over the season (preseason, middle season, and final season). Serum BDNF (sBDNF) was determined during the preseason and final season. Sleep time, total physical activity, and time in vigorous activity were measured using an accelerometer. The fat-free mass, skeletal muscle mass, fat mass, handgrip strength, cardiorespiratory fitness (VO2max), and dietary intake were evaluated during the season. The Stroop Color and Word Test was employed to assess cognitive tasks. To evaluate the mood, the Brunel Mood Scale was used. Results: There were lower sBDNF levels (−16.3% [46.8%]; P = .007) and sleep time (final season = 5.7 [1.1] vs preseason = 6.6 [1.1] h·night−1, P = .043) during the end of the season. The total calories and carbohydrate intake decreased across the season (P < .05). Conversely, better cognitive function was found in the final season with respect to the preseason (P < .05). There were significant correlations between BDNF and VO2max only in the preseason (r = .61, P = .027), but no significant relationship was found among sBDNF and cognitive performance, sleep time, and percentage of won games. Conclusions: Youth badminton athletes decreased their sBDNF levels, sleep time, carbohydrate, and calorie intake across the season. The athletes improved in cognitive function; however, only the females improved in body composition, and the males improved their VO2max in the middle season. The sBDNF levels were positively correlated with the VO2max in the preseason, and no correlations were observed among the sBDNF and psychological parameters, sleep time, and sport performance during the season.
Suicide among Scottish military veterans: follow-up and trends
Authors: Bergman Beverly P , Mackay Daniel F , Pell Jill P 
Published: October 2021

ObjectivesThe risk of suicide among UK military veterans remains unclear. Few recent studies have been undertaken, and most studies found no clear evidence of increased risk. We used data from the Trends in Scottish Veterans Health cohort to investigate suicides up to 2017 in order to examine whether there have been any changes in the long-term pattern of veteran suicides since our earlier study to 2012, and to compare trends in the risk of suicide among veterans with matched non-veterans.MethodRetrospective cohort study of 78 000 veterans and 253 000 non-veterans born between 1945 and 1995, matched for age, sex and area of residence, using survival analysis to examine the risk of suicide in veterans in comparison with non-veterans overall and by subgroup, and to investigate associations with specific mental health conditions.ResultsUp to 37 years of follow-up, 388 (0.5%) veterans and 1531 (0.6%) non-veterans died from suicide. The risk of suicide among veterans did not differ from non-veterans overall. Increased risk among early service leavers was explained by differences in deprivation, and the previously reported increased risk in female veterans is now confined to older women. Suicide was most common in the fifth decade of life, and around 20 years postservice. A history of mood disorder or post-traumatic stress disorder was non-significantly more common in veterans.ConclusionsVeterans are not at increased risk of suicide overall. The highest risk for both men and women is in middle age, many years after leaving service.
Disadvantage in early-life and persistent asthma in adolescents: a UK cohort study
Authors: Creese Hanna , Lai Eric , Mason Kate , Schlüter Daniela K , Saglani Sejal , Taylor-Robinson David , Saxena Sonia 
Published: October 2021

ObjectiveTo determine how early-life risk factors explain socioeconomic inequalities in persistent asthma in adolescence.MethodsWe did a causal mediation analysis using data from 7487 children and young people in the UK Millennium Cohort Study. Persistent asthma was defined as having a diagnosis reported at any two or more time points at 7, 11 or 14 years. The main exposure was maternal education, a measure of early-life socioeconomic circumstances (SECs), used to calculate the relative index of inequality. We assessed how blocks of perinatal (maternal health behaviours, infant characteristics and duration of breastfeeding, measured at 9 months) and environmental risk factors (family housing conditions; potential exposure to infections through childcare type and sibling number, and neighbourhood characteristics, measured at 3 years) mediated the total effect of childhood SECs on persistent asthma risk, calculating the proportion mediated and natural indirect effect (NIE) via blocks of mediators.ResultsAt age 14 the overall prevalence of persistent asthma was 15%. Children of mothers with lower educational qualifications were more likely to have persistent asthma, with a clear social gradient (degree plus: 12.8% vs no qualifications: 20.3%). The NIE gives the effect of SECs acting only via the mediators and shows a 31% increased odds of persistent asthma when SECs are fixed at the highest level, and mediators at the level which would naturally occur at the lowest SECs versus highest SECs (NIE OR 1.31, 95% CI 1.04 to 1.65). Overall, 58.9% (95% CI 52.9 to 63.7) of the total effect (OR 1.70, 95% CI 1.20 to 2.40) of SECs on risk of persistent asthma in adolescence was mediated by perinatal and environmental characteristics.ConclusionsPerinatal characteristics and the home environment in early life are more important in explaining socioeconomic inequalities in persistent asthma in British adolescents than more distal environmental exposures outside the home.
Quantifying status and trends from monitoring surveys: application to pygmy whitefish (Prosopium coulterii) in Lake Superior
Authors: van der Lee Adam S. , Vinson Mark R. , Koops Marten A. 
Published: October 2021

Population assessments of fish species often rely on data from surveys with different objectives, such as measuring biodiversity or community dynamics. These surveys often contain spatial–temporal dependencies that can greatly influence conclusions drawn from analyses. Pygmy whitefish (PWF, Prosopium coulterii) populations in Lake Superior were recently assessed as Threatened by the Committee on the Status of Endangered Species in Canada, which motivated a thorough analysis of available data to improve our understanding of its population status. The US Geological Survey conducts annual bottom trawl surveys in Lake Superior that commonly capture PWF. We used these data (1989–2018) to model temporal trends in PWF biomass density and make lake-wide population projections. We used a Bayesian approach, integrated nested Laplace approximation (INLA), and compared the impact of including different random structures on model fit. Inclusion of spatial structure improved model fit and conclusions differed from models omitting random effects. PWF populations have experienced periodic fluctuations in biomass density since 1989, though 2018 may represent the lowest density in the 30-year time series. Lake-wide biomass was estimated to be 71.5 t.
Nitrous oxide production and nitrogen transformations in a soil amended with biosolids
Authors: Roman-Perez Carmen C. , Hernandez-Ramirez Guillermo 
Published: October 2021

The application of organic amendments to agricultural soils enables the recycling of nutrients, further reducing the inputs of synthetic fertilizers for crop production. However, the production of N2O emissions is a concern that arises from such a practice. A 35 d incubation experiment was conducted with soils receiving three contrasting types of biosolids — mesophilic anaerobic digested (BM), composted (BC), and alkaline-stabilized (BA) — at four water-filled pore spaces (WFPS): 28%, 40%, 52%, and 64%. A zero-N-addition control was also evaluated. Across all the three types of biosolids, N2O production increased with soil moisture content, with BM and BC producing the overall highest N2O fluxes. The most intense pulses of N2O production were exhibited by BC at the beginning of the incubation. The highest cumulative N2O production was found with 64% WFPS and from BC- (409 μg N2O–N·kg−1 soil) or BM-amended soils (390 μgN2O–N·kg−1 soil), which produced more than four and two times the emissions from the control and BA-amended soils at 64% WFPS, respectively. We also found the highest nitrification rates in the BM- and BC-amended soils. The total N2O production was exponentially associated with the NO3−–N concentration present at the end of the experiment (R2 = 0.83). Changes in the concentration of the soil available N indicated the occurrence of mineralization, nitrification, and denitrification over the incubation. These results provided insight into the interacting responses of N2O production to soil moisture contents, biosolids treatment stabilization and properties, and soil N availability.
Quark stars in 4-dimensional Einstein–Gauss–Bonnet gravity
Authors: Singh Ksh. Newton , Maurya S. K. , Dutta Abhisek , Rahaman Farook , Aktar Somi 
Published: October 2021

AbstractThe article explores the first exact solution in a four-dimensional EGB-gravity with an anisotropic matter source. The solution has been found by two assumptions, a metric potential and the MIT-bag equation of state. Further, the solution has been tested with several physical constraints. Finally, using the boundary condition we have also estimated the range of bag constant $$\mathcal {B}$$
B
by varying the mass of the structure and the Gauss-Bonnet coupling constant $$\alpha $$
α
. This allows us to check the physical viability of the solution by comparing it with the existing accepted range of bag constant $$\mathcal {B}$$
B
.
Comparison of selected general-purpose event generators for particle fluence simulation in LHC silicon trackers
Authors: Oblakowska-Mucha Agnieszka , Szumlak Tomasz 
Published: October 2021

AbstractAt the LHC era, the detector systems are operating at the harsh hadronic environment with the unprecedentedly high particle flux. Position-sensitive silicon devices are usually positioned at the innermost regions of the experimental setups and must cope with highly non-uniform radiation fields. At the end of LHC Run 2, fluence in silicon trackers reached 10$$^{15}$$

15

n$$_{\mathrm{eq}}$$

eq

/cm$$^2$$

2

. Initial simulation studies predict that the maximal fluence for the HL-LHC may be up to two orders of magnitude higher than the one seen in LHC Run 1 and Run 2. In this paper, two general-purpose physics event generators used for simulation of proton–proton collisions for the radiation damage studies at LHC energies: PYTHIA 8.2 and Dpmjet-III are compared. Fluences obtained using these models, with the latest tuning to the LHC data, in detectors situated close to the proton–proton interaction point are determined as well. We also indicate a potential new method for actual fluence estimation using experiment real-time data monitoring system.
Ideal structure of rings of analytic functions with non-Archimedean metrics
Authors: Bruno Nicholas 
Published: October 2021

The work of Helmer [Divisibility properties of integral functions, Duke Math. J. 6(2) (1940) 345–356] applied algebraic methods to the field of complex analysis when he proved the ring of entire functions on the complex plane is a Bezout domain (i.e. all finitely generated ideals are principal). This inspired the work of Henriksen [On the ideal structure of the ring of entire functions, Pacific J. Math. 2(2) (1952) 179–184. On the prime ideals of the ring of entire functions, Pacific J. Math. 3(4) (1953) 711–720] who proved a correspondence between the maximal ideals within the ring of entire functions and ultrafilters on sets of zeroes as well as a correspondence between the prime ideals and growth rates on the multiplicities of zeroes. We prove analogous results on rings of analytic functions in the non-Archimedean context: all finitely generated ideals in the ring of analytic functions on an annulus of a characteristic zero non-Archimedean field are two-generated but not guaranteed to be principal. We also prove the maximal and prime ideal structure in the non-Archimedean context is similar to that of the ordinary complex numbers; however, the methodology has to be significantly altered to account for the failure of Weierstrass factorization on balls of finite radius in fields which are not spherically complete, which was proven by Lazard [Les zeros d’une function analytique d’une variable sur un corps value complet, Publ. Math. l’IHES 14(1) (1942) 47–75].
Meso-substituted cationic 3- and 4-N-Pyridylporphyrins and their Zn(II) derivatives for antibacterial photodynamic therapy
Authors: Gyulkhandanyan Aram G. , Paronyan Marina H. , Gyulkhandanyan Anna G. , Ghazaryan Karapet R. , Parkhats Marina V. , Dzhagarov Boris M. , Korchenova Maria V. , Lazareva Ekaterina N. , Tuchina Elena S. , Gyulkhandanyan Grigor V. , Tuchin Valery V. 
Published: October 2021

Photodynamic inactivation of microorganisms known as antibacterial photodynamic therapy (APDT) is one of the most promising and innovative approaches for the destruction of pathogenic microorganisms. Among the photosensitizers (PSs), compounds based on cationic porphyrins/metalloporphyrins are most successfully used to inactivate microorganisms. Series of meso-substituted cationic pyridylporphyrins and metalloporphyrins with various peripheral groups in the third and fourth positions of the pyrrole ring have been synthesized in Armenia. The aim of this work was to determine and test the most effective cationic porphyrins and metalloporphyrins with high photoactivity against Gram negative and Gram positive microorganisms. It was shown that the synthesized cationic pyridylporphyrins/metalloporphyrins exhibit a high degree of phototoxicity towards both types of bacteria, including the methicillin-resistant S. aureus strain. Zinc complexes of porphyrins are more phototoxic than metal-free porphyrin analogs. The effectiveness of these Zn–metalloporphyrins on bacteria is consistent with the level of singlet oxygen generation. It was found that the high antibacterial activity of the studied cationic porphyrins/metalloporphyrins depends on four factors: the presence in the porphyrin macrocycle of a positive charge (+4), a central metal atom (Zn[Formula: see text] and hydrophobic peripheral functional groups as well as high values of quantum yields of singlet oxygen. The results indicate that meso-substituted cationic pyridylporphyrins/metalloporphyrins can find wider application in photoinactivation of bacteria than anionic or neutral PSs usually used in APDT.
Copy-and-patch compilation: a fast compilation algorithm for high-level languages and bytecode
Authors: Xu Haoran , Kjolstad Fredrik 
Published: October 2021

Fast compilation is important when compilation occurs at runtime, such as query compilers in modern database systems and WebAssembly virtual machines in modern browsers. We present copy-and-patch, an extremely fast compilation technique that also produces good quality code. It is capable of lowering both high-level languages and low-level bytecode programs to binary code, by stitching together code from a large library of binary implementation variants. We call these binary implementations stencils because they have holes where missing values must be inserted during code generation. We show how to construct a stencil library and describe the copy-and-patch algorithm that generates optimized binary code.
We demonstrate two use cases of copy-and-patch: a compiler for a high-level C-like language intended for metaprogramming and a compiler for WebAssembly. Our high-level language compiler has negligible compilation cost: it produces code from an AST in less time than it takes to construct the AST. We have implemented an SQL database query compiler on top of this metaprogramming system and show that on TPC-H database benchmarks, copy-and-patch generates code two orders of magnitude faster than LLVM -O0 and three orders of magnitude faster than higher optimization levels. The generated code runs an order of magnitude faster than interpretation and 14% faster than LLVM -O0. Our WebAssembly compiler generates code 4.9X-6.5X faster than Liftoff, the WebAssembly baseline compiler in Google Chrome. The generated code also outperforms Liftoff's by 39%-63% on the Coremark and PolyBenchC WebAssembly benchmarks.
Epstein-Barr Virus Induces Lymphangiogenesis and Lympth Node Metastasis via Upregulation of VEGF-C in Nasopharyngeal Carcinoma
Authors: Li Deng-Ke , Chen Xing-Rui , Wang Li-Na , Wang Jia-Hong , Wen Yue-Ting , Zhou Zi-Ying , Li Ji-Ke , Liu Jing-Xian , Cai Lin-Bo , Zhong Shui-Sheng , Lyu Xiao-Ming , Damola Faleti Oluwasijibomi , Li Min-Ying , Zhang Jing-Jing , Zeng Yu-Mei , Wang Qian-Li , Zhang Qian-Bing , Lyu Hao , Fu Xiao-Yan , Wang Wei , Li Xin , Huang Zhong-Xi , Yao Kai-Tai 
Published: October 2021

Abstract

Lymphatic metastasis is a common clinical symptom in nasopharyngeal carcinoma (NPC), the most common Epstein-Barr virus (EBV)-associated head and neck malignancy. However, the effect of EBV on NPC lymph node (LN) metastasis is still unclear. In this study, we demonstrated that EBV infection is strongly associated with advanced clinical N stage and lymphangiogenesis of NPC. We found that NPC cells infected with EBV promote LN metastasis by inducing cancer-associated lymphangiogenesis, whereas these changes were abolished upon clearance of EBV genomes. Mechanistically, EBV-induced VEGF-C contributed to lymphangiogenesis and LN metastasis, and PHLPP1, a target of miR-BART15, partially contributed to AKT/HIF1a hyperactivity and subsequent VEGF-C transcriptional activation. In addition, administration of anti-VEGF-C antibody or HIF1α inhibitors attenuated the lymphangiogenesis and LN metastasis induced by EBV. Finally, we verified the clinical significance of this prometastatic EBV/VEGF-C axis by determining the expression of PHLPP1, AKT, HIF1a, and VEGF-C in NPC specimens with and without EBV. These results uncover a reasonable mechanism for the EBV-modulated LN metastasis microenvironment in NPC, indicating that EBV is a potential therapeutic target for NPC with lymphatic metastasis.

Implications:
This research demonstrates that EBV induces lymphangiogenesis in NPC by regulating PHLPP1/p-AKT/HIF1a/VEGF-C, providing a new therapeutic target for NPC with lymphatic metastasis.