bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abscisic acid (ABA) signaling: Finding novel components off the beaten track
Authors: Wong Aloysius , Bi Chuyun , Pasqualini Stefania , Gehring Chris 
Published: February 2022

Abstract
The sesquiterpene abscisic acid (ABA) is an ancient universal stress response molecule. In plants, many ABA-dependent processes operate via the PYR/PYL/RCAR receptor complexes, however, there is evidence suggesting that not all plant responses operate through this mechanism. This is consistent with ABA responses in animals and humans which do not contain such receptors. We hypothesize that plant and animal proteomes harbour proteins with undiscovered ABA-binding sites and propose that carefully curated amino acid search motifs deduced from the binding sites of experimentally confirmed ABA-binding proteins can identify many more candidates in plant and animal proteomes many of which show folds that are compatible with ABA-binding. Plant candidates include annotated ABA downstream signaling components such as SnRK2.2 and SnRK2.6 and proteins with roles in protein folding and RNA polyadenylation, while candidates in the human proteome affect, among other processes, immune responses and tumor progression. If these candidates will eventually be experimentally validated, it will imply that the regulation and tuning of ABA-dependent processes is considerably more complex than hitherto suspected and it will also expand and help to clarify the role of ABA in animal systems.
Agroclimatic Zoning for the Incidence of Brown Eye Spot on Coffee Under Climate Change Scenarios
Authors: de Lima Rafael Fausto , OLIVEIRA-APARECIDO LUCAS Eduardo , Torsoni Guilherme Botega , Chiquitto Alisson Gaspar , Moraes José Reinaldo , Rolim Glauco de Souza 
Published: February 2022

Abstract
Brown eye spot (Cercospora coffeicola) is one of the main fungal diseases of coffee, leading to a significant drop in crop productivity and beverage quality in Brazil. This study aimed to elaborate an agroclimatic zoning for the incidence of brown eye spot on coffee under climate change scenarios, as suggested by IPCC (IPCC-AR5), in the main coffee-growing regions. Climate data of air temperature, precipitation, and relative humidity were collected from the National Aeronautics and Space Administration/Prediction of Worldwide Energy Resources – NASA/POWER platform from 1989 to 2020 for 46 municipalities in the states of Paraná, São Paulo, Minas Gerais, Espírito Santo, Goiás, and Bahia. The ideal climate for brown eye spot occurrence consists of an air temperature (Tmean) between 18 and 30 °C, relative humidity (RHmean) > 90%, and leaf wetness duration (LWD) > 9 hours. The number of hours of leaf wetness was determined by the sum of hours with relative humidity > 90%. Relative humidity was estimated for each hour of the day using estimated data of mean dew point temperature, maximum relative humidity, minimum relative humidity, and air temperature. Climate change scenarios were designed based on sets of climate simulations for the 21st century. Scenario S1 is the current scenario without changes, while scenarios S2 and S3 show Tmean + 1.5 °C and 3.0 °C, respectively, with RHmean without changes. Scenarios S4 and S5 present RHmean varying from −30% to +30%, respectively, with Tmean unchanged. In the current scenario (S1), Minas Gerais presented a predominance of 100% for low climate risk to brown eye spot in September. Paraná presented a medium risk in 76.15% of the state in April. Scenarios S2 and S3 showed significant changes, increasing the average fitness class in the study region, mainly in the states of São Paulo, Minas Gerais, Rio de Janeiro, and Paraná. Scenario S4 showed 100% predominance of the low-risk class. In contrast, S5 showed the occurrence of the high-risk class for the study region with a +30% increase in relative humidity. The state of Minas Gerais presented a predominance of the high-risk class for the development of C. coffeicola in 76, 100, 97.83, 89.3, 93.46, 80.64, and 57.77% from November to May, respectively. The presence of high relative humidity represents the main factor for the expansion of the high-risk class for the development of C. coffeicola.
Derivation, Comprehensive Analysis of Cancer-associated Fibroblasts and Their Correlation to Prognosis, Immune Status and Drug Sensitivity in Patients of Soft Tissue Sarcoma
Authors: Xiao Bo , Liu Liyan , Chen Zhuoyuan , Li Aoyu , Xia Yu , Wang Pingxiao , Zhao Ziyue , Xiang Cheng , Zeng Yi , Li Hui , Xiao Tao 
Published: February 2022

Abstract
Background: Soft tissue sarcoma is among the most challenging malignancies for clinicians and associated with poor prognosis. Former studies have revealed that cancer-associated fibroblasts (CAFs) are involved in tumor development, migration, invasion and metastasis.Methods: DEGs and WGCNA were employed to obtain significant CAFs-related genes for constructing the signature. Somatic mutation, immune status, immune checkpoints and chemotherapy sensitivity were applied to define the characteristics of the identified signature. Differentially expressed genes between the distinct groups and WGCNA were employed to obtain CAFs score of each patient. Results: 35 genes were identified as CAFs-related genes in soft tissue sarcoma samples. Then, 12 CAFs-related genes were associated with overall survival in univariate Cox regression analysis and K-M method. The five genes signature was constructed based on the result from the LASSO regression analysis in train cohort. K-M curve showed that patients in the low CAFs score group had better survival, with immune infiltration and function significantly increased (P<0.05). The 1-, 3- and 5- year survival AUC values were 0.773, 0.724, and 0.726, respectively. The analysis of tumor mutations revealed that TP53, ATRX, TTN, RB1 and MUC16 were enriched in both clusters. The analysis of chemotherapy response demonstrated that most of chemotherapeutic drugs in GDSC database had lower IC50 in the high-risk group. All of the results were validated in test and whole cohorts. Conclusion: This study strongly revealed the indispensable role of CAFs in soft tissue sarcoma and constructed the prognostic signature including five CAFs-related genes.
Comparative Effects of Physical Exercise and Estradiol Therapy on Mitochondrial Density, Redox and Inflammatory Status in the Skeletal Muscle of Ovariectomized Rats
Authors: Silva Sara Barros , Honorato-Sampaio Kinulpe , Costa Sabrina Paula , Domingos Talita Emanuela , Cruz Timilly Mayra Martins da , Rodrigues Cíntia Maria , Costa Karine Beatriz , Santos Jousielle Márcia dos , Lage Vanessa Kelly da Silva , Gaiad Thais Peixoto , Santos Ana Paula , Peixoto Marco Fabrício Dias , Coimbra Cândido Celso , Reis Adelina Martha dos , Szawka Raphael Escorsim , Figueiredo Pedro Henrique Scheidt , Costa Henrique Silveira , Oliveira Murilo Xavier , Mendonça Vanessa Amaral , Lacerda Ana Cristina Rodrigues 
Published: February 2022

Abstract
Background

Previous studies have highlighted the positive effects of estrogen replacement therapy during menopause. In addition, a growing body of evidence has also proven several beneficial effects of other therapeutic strategies, especially physical exercise, to counteract the deleterious effects of menopause on skeletal muscle. However, a comparison of the effects of exercise training versus hormone replacement therapy after menopause on muscle mitochondrial profile and redox/inflammatory status has not been investigated to date. The purpose of the study was to investigate the effects of endurance training versus estradiol therapy on mitochondrial density, redox status, and inflammatory biomarkers in the skeletal muscle of ovariectomized rats.
Methods

Thirty twelve weeks-old female Wistar rats were randomly assigned into three groups: Untrained ovariectomized rats (OVX-NAT); untrained ovariectomized rats with estrogen (ES) replacement (OVX-ER); and, trained ovariectomized rats (OVX-AT). After ovariectomy, The OVX-ER rats were treated with ES (subcutaneously implanted Silastic® capsule containing 360 µg of 17β-estradiol/mL) while the OVX-AT group performed a training protocol (50~70% of maximal running speed on a treadmill, 60 min/day, five days/week for eight weeks). All animals performed a maximal treadmill test before and after the training protocol. After euthanasia, the soleus muscle was processed for histological e biochemical evaluations.
Results

The maximal oxygen consumption (VO2max), mitochondrial muscle density, total antioxidant capacity (FRAP), catalase (CAT) activity, and interleukin 10 levels improved only in the OVX-AT group, while only the OVX-ER rats presented an increase in CAT activity and a decrease in interleukin 6 levels.
Conclusions

Both endurance exercise training and estradiol therapy improve redox and inflammatory balance in the skeletal muscle of ovariectomized rats; however, only exercise increases VO2max and mitochondrial muscle density.
The hospitalization rate of cerebral venous sinus thrombosis before and during COVID-19 pandemic era: A single-center retrospective cohort study
Authors: Gharamaleki Maryam Vasaghi , Habibagahi Maryam , Hooshmandi Etrat , Tabrizi Reza , Arsang-Jang Shahram , Barzegar Zohreh , Fadakar Nima , Ostovan Vahid Reza , Rahimi-Jaberi Abbas , Ashjazadeh Nahid , Petramfar Peyman , Poursadeghfard Maryam , Izadi Sadegh , Nazeri Masoumeh , Bazrafshan Hanieh , Bahrami Zahra , Karimlu Sadigheh , Zafarmand Seyedeh Shaghayegh , Bayat Mahnaz , Salehi Mohammad Saied , Owjfard Maryam , Haghighi Saeideh Karimi , Safari Anahid , Chew Beng Lim Alvin , Worrall Bradford B , Coutinho Jonathan M. , Esperson Carlos Garcia , Spratt Neil , Levi Christopher , Azarpazhooh Mahmoud Reza , Borhani-Haghighi Afshin 
Published: February 2022

Abstract

Background
There are several reports of the association between SARS-CoV-2infection (COVID-19) and cerebral venous sinus thrombosis (CVST). In this study, we aimed to compare the hospitalization rate of CVST before and during the COVID-19 pandemic (before vaccination program).
Methods
In this retrospective cohort study, the hospitalization rate of adult CVST patients in Namazi hospital, a tertiary referral center in the south of Iran, was compared in two periods of time. We defined March 2018 to March 2019 as the pre-COVID-19 period and March 2020 to March 2021 as the COVID-19 period.
Results
50 and 77 adult CVST patients were hospitalized in the pre-COVID-19 and COVID-19 periods, respectively. The crude CVST hospitalization rate increased from 14.33 in the pre-COVID-19 period to 21.7 per million in the COVID-19 era (P=0.021). However, after age and sex adjustment, the incremental trend in hospitalization rate was not significant (95% CrI: -2.2, 5.14). Patients > 50-year-old were more often hospitalized in the COVID-19 period. (P=0.042) SARS-CoV-2 PCR test was done in 49.3% out of all COVID-19 period patients, which were positive in 6.5%. Modified Rankin Scale (mRS) score ≥3 at three-month follow-up was associated with age (P=0.015) and malignancy (P=0.014) in pre-COVID period; and was associated with age (P=0.025), altered mental status on admission time (P<0.001), malignancy (P=0.041) and COVID-19 infection (P=0.008) in COVID-19 period.
Conclusion
Since there was a more dismal outcome in COVID-19 associated CVST, a high index of suspicion for CVST among COVID-19 positive is recommended.
Repeated Stereotactic Body Radiotherapy With CyberKnife® in Lung Cancer: Toxicity Can Be Reduced by Sparing Irradiation to the Lungs
Authors: Watanabe Shou , Yamazaki Hideya , Kimoto Takuya , Suzuki Gen , Yamada Kei 
Published: February 2022

Abstract
Background: Data of multiple courses of stereotactic body radiotherapy (SBRT) for lung malignancies is scarce. We aimed to investigate the efficacy and safety of repeated SBRT with CyberKnife and to identify predictors of lung toxicity.Methods: We reviewed patients with primary or metastatic lung cancer who underwent repeated SBRT with CyberKnife® between December 2013 and April 2021. Local control (LC), overall survival (OS) and adverse events were analyzed. We generated a composite plan and investigated the mean lung dose (MLD), V5–V30 of the bilateral lungs, and absolute lung volumes spared from 5–30 Gy (VS5–VS30), based on equivalent dose in 2.0-Gy fractions (α / β = 3). Clinical and dosimetric predictors of Grade 2+ radiation pneumonitis (RP) were examined.Results: Twenty patients underwent repeated SBRT for 27 lesions. The most predominant dose fractionation was 60 Gy in five fractions. The median follow-up duration from the last SBRT was 18.0 months (range, 3–55 months). The 1-year and 2-year LC of lung lesions in repeated courses were 95.2% and 95.2%, respectively. The 1-year and 2-year OS rates after repeated SBRT were 88.4% and 49.7%, respectively. Five patients (25%) developed Grade 2+ RP, including a Grade 5 RP. There was no association between clinical factors and Grade 2+ RP. The Grade 2+ RP group showed higher composite MLD (p = 0.042) and lower composite VS5 (p = 0.042), VS10 (p = 0.015), VS15 (p = 0.008), and VS20 (p = 0.025), compared with the Grade 0–1 RP group.Conclusions: Repeated SBRT with CyberKnife® showed favorable LC and OS, but a high rate of Grade 2+ RP. Analysis of the composite plans showed that MLD and VS5–VS20 may predict lung toxicity of multicourse SBRT.
Ambient Noise Tomography for a High-resolution 3D S-Wave Velocity Model of the Kinki Region, Southwestern Japan, using Dense Seismic Array Data
Authors: NTHABA BOKANI , Ikeda Tatsunori , Nimiya Hiro , Tsuji Takeshi , Iio Yoshihisa 
Published: February 2022

Abstract
Research interest in the Kinki region, southwestern Japan, has been aroused by the frequent occurrence of microearthquake activity that do not always coincide with documented active fault locations. Previous studies in the Kinki region focused mainly on deep, large-scale structures and could not efficiently resolve fine-scale (~10 km) shallow crustal structures. Hence, characterization of the upper crustal structure of this region at an improved spatial resolution is required. From the cross-correlation of the vertical components of the ambient seismic noise data recorded by a densely-distributed seismic array, we estimated Rayleigh wave phase velocities using a frequency domain method. Then, we applied a direct surface wave tomographic method for the measured phase velocity dispersion data to obtain the 3D S-wave velocity model of the Kinki region. The estimated velocity model reveals a NE-SW trending low-velocity structure coinciding with the Niigata-Kobe Tectonic Zone (NKTZ) and the active Biwako-seigan Fault Zone (BSFZ). Also, we identified fine-scale low-velocity structures coinciding with known active faults on the eastern side of the NKTZ, as well as sets of low-velocity structures across the Tanba region, that may be attributable to the weathering effects or activity of unidentified concealed fault zones. Furthermore, sedimentary basins manifest as low-velocity zones extending to depths ranging from ~1.5 to 2 km, correlating with those reported in previous studies. Our results therefore contribute towards fundamental understanding of earthquake faulting as well as tectonic boundary and will be useful for hazard assessment and disaster mitigation.
Modulatory Role of Garlic (Allium Sativum) Extract Against Cisplatin- Induced Nephrotoxicity In Female Albino Rats And Their Offspring.
Authors: El-Beltagy Abd El-Fattah , Mohamed Gamal , Akeel Mohammed A , K.Abdelaziz Karoline , Elbakry Kadry A , Elsayed Ahmed Ahmed I A 
Published: February 2022

Abstract
This work is mainly designed to evaluate the potential therapeutic role of garlic extract against cisplatin induced nephrotoxicity in pregnant rats and their offspring. Twenty-four pregnant rats were used in the current study. They were randomly allocated into four equal groups (n=6): control, garlic, and CP + Garlic group. At the end of the weaning period, the mothers and the offsprings of all groups were sacrificed, the kidneys were immediately excised, and processed for histological and biochemical investigations. Also, blood samples were withdrawn and processed for estimation of the assigned biochemical parameters. The renal histological sections from CP-treated mother rats displayed pronounced histopathological lesions however; their offsprings showed mild renal histopatological lesions if compared with those of their mothers. The levels of renal tissue SOD), CAT and GPx enzymes were significantly decreased .On the contrary, the levels of MDA, serum urea and creatinine were significantly increased in CP-treated mother rats and their offsprings as compared with control. The percentage value of caspase 3 activity was markedly elevated in the renal tissues of CP-treated mother rats and their offspring compared to the control group. Supplementation of garlic extract to the rats of group 4, the over-all histological lesions as well as biochemical parameters were restored nearly to the control ones. It is concluded that garlic (Allium sativum) extract has a powerful ameliorative role against CP induced nephrotoxicity in preganat rats and their offspring.
Modelling Risk Behaviour: The use of Behaviour Change Assumptions in Cost-Effectiveness Studies for Oral PrEP in the United Kingdom and United States
Authors: Koshkouei Mona , Whitacre Ryan , Paparini Sara 
Published: February 2022

Abstract
Background
HIV prevention policy and program implementation rely heavily on cost-effectiveness studies. They involve the use of some uncertain variables, serving as proxies for complex, emergent and unpredictable scientific, social and behavioural issues. The ongoing implementation and scale-up of oral pre-exposure prophylaxis (PrEP) requires the improvement and refinement of cost-effectiveness calculations, and the measures on which they are based.
Methods
We conducted a framework synthesis of the literature on cost-effectiveness for oral PrEP for men who have sex with men (MSM) in the US and UK between 2009 and 2021.
Results
Reviewing how behavioural risk variables were used in the studies, we found both significant increases and decreases in projected risk behaviour in MSM starting PrEP, and limited use of evidence for these variables. Studies that included increased ‘risk compensation’ scenarios inferred quantitative estimates from qualitative measures, appeared to group risk variables with assumptions about low adherence, and projected estimates of increased HIV incidence associated with PrEP use. Conversely, studies that included lower risk behaviour cited related research about behavioural risk reduction associated with treatment-as-prevention and referenced discussions about the importance of changing risk behaviour, rather than empirical evidence of changed behaviour.
Conclusion
Increased accuracy of cost-effectiveness models can be achieved through refining the use of behavioural risk variables, including reference to a common evidence base.
A Numerical Study of Automotive Body Panel Draw Dies Defects Using Finite Element Simulation
Authors: Yadegari Farzad , Sehhat M. Hossein , Mahdianikhotbesara Ali 
Published: February 2022

Abstract
Among the advantages of the sheets used in the car body, it can mention the high strength, low thickness and suitable ductility. crack and wrinkling of the sheet are the most common types of defects in the drawing process. Therefore, it seems necessary to know the process factors that affect the sheet metal forming behavior. One of the critical tools of simulation and subsequent process optimization is the finite element method. In this research, with the help of AutoForm software, finite element simulation of the process is performed. After designing the appropriate Taguchi experiment, the parameters affecting the outputs, including thickness strain and surface strain on the production part, are investigated, and optimal values ​​are introduced. The known effective parameters on the process output include the forming limit diagram, sheet strength, friction coefficient, die balancers, and used sheet thickness.
Genome-level analysis of BpR2R3-MYB family genes transcribed in seedlings of Betula platyphylla and BpR2R3- MYB15 enhanced flavonoid production
Authors: zheng baojiang , liu huimin , yu zhongyang , fan guizhi 
Published: February 2022

Abstract
Background: Flavonoids have a wide range of biological activities in plant development, stress resistance and human health, etc. R2R3-MYBs are one of the key elements in regulation of flavonoid production, but their functional importance in Betula platyphylla remains elusive.Methods: The full-length transcriptome data of 30-day-old seedlings of Betula platyphylla were used to identify BpR2R3-MYB family genes, and their gene structure, chromosome distribution and syntenic relationships were predicted by bioinformatics methods. Agrobacterium-mediated transient transformation was used to verify the function of BpR2R3-pMYB15 in flavonoid production.Results: 44 BpR2R3-MYB family genes expressed in seedlings of Betula platyphylla were identified and found to be unevenly distributed in 11 chromosomes. Among them, 90.90% of the BpR2R3-MYBs had introns, and only four genes had no introns. Five gene pairs with segment duplication were found, and their Ka/Ks ratios were less than 1. Thirty orthologs between Betula platyphylla and Arabidopsis thaliana and 68 orthologs between Betula platyphylla and Populus trichocarpa were detected. Five BpR2R3-MYBs were clustered with R2R3-MYB genes related to flavonoid synthesis, and BpR2R3-pMYB15 had the highest correlation coefficients between the value of gene expression and flavonoid content. BpR2R3-pMYB15 was cloned, and its transient overexpression obtained using Agrobacterium-mediated transformation positively regulated flavonoid production.Conclusion: This work enriches the collection of R2R3-MYBs related to flavonoid production in seedlings of Betula platyphylla.
Integrated Bioinformatics Analysis Identifies Pyroptosis-related Genes in Alzheimer’s Disease
Authors: Guo Tong , Wang YuFen 
Published: February 2022

Abstract
Background: Recent studies have shown the association between Alzheimer’s disease (AD) and inflammation. Pyroptosis is an inflammatory type of programmed cell death, and it has been associated with AD. Herein, we aimed to explore the potential role of pyroptosis-related genes in AD, advancing the understanding of pyroptosis-related genes in AD pathogenesis.Methods: Based on the gene expression profile in GSE5281, we screened for differentially expressed genes (DEGs), performed a weighted gene correlation analysis (WGCNA), and identified the most AD-related module. After intersecting the hub genes in this module with 52 pyroptosis-related genes, we obtained the key genes to construct a least absolute shrinkage and selection operator (LASSO) model for AD. We also constructed a CASP6-focused interaction network including several hub genes. The LASSO model and expression of CASP6 were evaluated in GSE122063 and GSE132903.Results: Through WGCNA, four functional modules were identified, of which the brown module is most significantly related to AD (correlation coefficient=0.93, P=4e-13). CASP6 is aberrantly highly expressed in AD and closely connected with hub genes in the brown module. Seven genes (CASP6, BAK1, CASP5, CHMP4B, CHMP4C, IRF2, PLCG1) were identified as key genes, and the LASSO model based on key genes can predict AD with medium-to-high accuracy in train, test and validation set (AUC=0.898, 0.811, 0.857, respectively). Conclusions: Highly expressed CASP6 interact with other pyroptosis-related genes in AD, shedding light on the potential role of pyroptosis in AD pathogenesis.