bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Blast Resistance Gene Pi65 with LRR-RLK Domain is Required for Resistance to M. Oryzae
Authors: Wang Li-Li , Ma Zuo-Bin , Kang Hou-Xiang , Gu Shuang , Mukhina Zhanna , Wang Chang-Hua , Wang Hui , Bai Yuan-Jun , Sui Guo-Min , Zheng Wen-Jing , Ma Dian-Rong 
Published: May 2021

Abstract
Rice blast seriously threatens rice production worldwide. To control this disease, it is necessary to identify and utilize blast resistance genes to breed disease-resistant rice varieties. Here, we report a rice blast resistance gene, Pi65, isolated from the resistant variety GangYu129 (abbreviated GY129, O. sativa japonica) by map-based cloning. Pi65 overexpression in the susceptible variety LiaoXing1 (abbreviated LX1, O. sativa japonica) enhanced blast resistance, while Pi65 knockout in GY129 resulted in a decrease in its resistance to rice blast. Pi65 encodes two transmembrane regions, with 15 LRR domains and one serine/threonine protein kinase catalytic domain, conferring resistance to isolates of M. oryzae collected from northeast China. Sixteen amino acids differed between the resistance and susceptibility proteins. The Pi65 susceptibility allele had one fewer LRR duplication. Pi65 was constitutively expressed in whole plants, and M. oryzae inoculation significantly increased its expression level. Transcriptome sequencing revealed that numerous genes associated with disease resistance were specifically upregulated in GY129 24 h after M. oryzae inoculation, and photosynthesis-and carbohydrate metabolism-related genes were particularly downregulated, demonstrating disease resistance gene activation in GY129 mediated by Pi65 after rice blast fungal infection, cellular basal and energy metabolism was inhibited simultaneously. These combined factors endow GY129 with rice blast resistance. Our study provides genetic resources for improving rice blast resistance in japonica rice and enriches the study of rice blast resistance mechanisms.
Sox9+ Cell is Required for Salivary Gland Regeneration after Radiation Damage via Wnt/β-Catenin Pathway
Authors: Xu Xiuyun , Gan Xiong , Zhang Ming , Xie Jiaxiang , Chen Shuang , Li Jingting , Bao Yong , Wang Cheng , Chen Demeng 
Published: May 2021

Abstract
Background: Radiotherapy for head and neck cancer can cause serious side effects, including severe damage to the salivary glands, resulting in symptoms such as xerostomia, dental caries, oral infectious and so on. Due to lack of long-term treatment for the symptoms of saliva barren, current research has focused on finding endogenous stem cells that can differentiate into various cell lineage to replace lost tissue and restore function. Results: In our study, we identified Sox9+ cells can differentiate into various salivary epithelial cell lineages under homeostatic conditions. After ablating Sox9+ cells, the salivary glands of irradiated mice showed more severe phenotypes and reduced proliferative capacity. Analysis of online single cell RNA-sequencing data revealed enrichment of the Wnt/β-catenin pathway in Sox9+ cell population. Furthermore, treatment of Wnt/β-catenin inhibitor to irradiated mice inhibited the regenerative capability of Sox9+ cells. Finally, we showed that Sox9+ cells were able to form organoids in vitro and transplanting these organoids into salivary glands after radiation restored part of salivary gland function. Conclusions: In short, our research indicated that regenerative therapy targeting Sox9+ cells is a promising method to solve the radiation induced salivary gland injury.
Sensory and Motor Electrophysiological Mapping of the Cerebellum in Humans
Authors: Ashida Reiko , Walsh Peter , Brooks Jonathan C.W. , Cerminara Nadia L. , Apps Richard , Edwards Richard J. 
Published: May 2021

Abstract
Cerebellar damage during posterior fossa surgery in children can lead to ataxia and risk of cerebellar mutism syndrome. Compartmentalisation of sensorimotor and cognitive functions within the cerebellum have been demonstrated in animal electrophysiology and human imaging studies. Electrophysiological monitoring was carried out to assess the limb sensorimotor representation within the human cerebellum for assessment of neurophysiological integrity to reduce the incidence of surgical morbidities. Thirteen adult and paediatric patients undergoing posterior fossa surgery were recruited. Sensory evoked field potentials were recorded in response to mapping (n=8): to electrical stimulation of nerves or muscles. For motor mapping (n=5), electrical stimulation was applied to the surface of the cerebellum and evoked EMG responses were sought in facial and limb muscles. Evoked potentials were found in two patients (25%). Responses were located on the surface of the right inferior posterior cerebellum to stimulation of the right leg in one patient, and on the left inferior posterior lobe in another patient to stimulation of left forearm. No evoked EMG responses were found for the motor mapping. The present study identifies challenges with using neurophysiological methods to map functional organization within the human cerebellum and considers ways to improve success.
Antibacterial Activity and Characteristics of Silver Nanoparticles Biosynthesized From Carduus Crispus
Authors: Urnukhsaikhan Enerelt , Bold Bum-Erdene , Gunbileg Aminaa , Sukhbaatar Nominchimeg , Mishig-Ochir Tsogbadrakh 
Published: May 2021

Abstract
Recently, synthesizing metal nanoparticles using plants has been extensively studied and recognized as a non-toxic and efficient way for biomedical field. The aim of this study is to investigate the role of different parts of Carduus crispus medical plant on synthesizing silver nanoparticles and their characteristics. Our study showed that silver nanoparticles (AgNP) synthesized via whole plant extract exhibited a blue shift in absorption spectra with increased optical density, which correlates to a high yield and smaller size. Also, the results of zeta potential, XRD, PCCS analysis showed the surface charge of -54.29 ±4.96 mV (AgNP-S), -42.64 ±3.762 mV (AgNP-F), -46.02 ±4.17 mV (AgNP-W), the crystallite size of 36 nm (AgNP-S), 13 nm (AgNP-F), 14 nm (AgNP-W) with face-centered cubic structure and average grain size of approximately 100 nm. Another important characteristic, such as elemental composition and constituent capping agent has been determined by EDX and FTIR. The silver nanoparticles were composed of ~80% Ag, ~15% K, and ~7.5% Ca (or ~2.8% P) elements. Moreover, the results of the FTIR measurement suggested that AgNP-F and AgNP-S contained distinct functional groups, on the other hand, AgNP-W contained all of the functional groups present in AgNP-F and AgNP-S. The silver nanoparticles showed antibacterial activity on both gram-negative bacterium Escherichia coli (5.5 ± 0.2 mm to 6.5 ± 0.3 mm) and gram-positive bacterium Micrococcus luteus (7 ± 0.4 mm to 7.7 ± 0.5 mm). Our study is meaningful as a first observation indicating the possibility of using special plant organs to control the characteristics of nanoparticles.
Application of a Novel Osteotomy Instrumentation as a Substitute Tool in Total Hip Arthroplasty
Authors: Hu Yuehao , Zhang Jingwei , Sun Ziyang , Yu Degang , Li Huiwu , Zhu Zhenan , Mao Yuanqing , Yan Mengning , Zhai Zanjing 
Published: May 2021

Abstract
Background: Mechanical failure, power shortage, and unexpected contamination of oscillating saw occasionally happened in actualizing femoral neck osteotomy during total hip arthroplasty, while no appropriate alternative solution be available presently. This study aimed to introduce a novel osteotomy instrumentation (fretsaw, jig, cable passer hook) as a substitute tool while oscillating saw was unavailable in THA.Methods: This study included 40 patients (40 hips) who underwent femoral neck osteotomy during primary THA using the new osteotomy instrumentation (n=20) and oscillating saw (n=20). Clinical data and intraoperative findings of all patients were evaluated.Results: The mean osteotomy time was 22.3 ± 3.1 s (range, 17–30 s) and 29.4 ± 3.7 s (range, 25–39 s) in the oscillating saw group and the new osteotomy instrumentation group, respectively (P<0.001). The Harris Hip Score (HHS) improved in both groups; the mean HSS was 82.3 ± 2.5 and 83.3 ± 3.5 in the oscillating saw group and new osteotomy instrumentation group at 6 months after surgery, respectively (P=0.297).Conclusion: The original osteotomy instrumentation can be an ideal substitute tool for femoral neck osteotomy in THA, especially when the oscillating saw is unavailable or malfunctional.
Nontargeted Metabolomics Analysis of Oxacillin Resistance in Staphylococcus Aureus
Authors: Liu Jingjing , Qiu Chengchao , Yuan Zichen , Wong Tin-Yan , Song Xiaofeng , Lam Henry 
Published: May 2021

Abstract
BackgroundStaphylococcus aureus has acquired resistance to antibiotics in the long-term struggle against antibiotics. Treatment of Staphylococcus aureus infection has become more difficult. In this study, based on nontargeted metabolic figure printing technique, the metabolome of a pair of isogenic methicillin-susceptible and resistant Staphylococcus aureus (MSSA and MRSA) strains treated with the sublethal dose of oxacillin was characterize to investigate the mechanism of antibiotic resistance.ResultsMassive alternations of metabolite expression were observed in both MSSA and MRSA treated with oxacillin. The results of accurate mass and mass fragmentation analysis showed that 7 and 29 metabolites of MRSA and MSSA have changed significantly after oxacillin treatment. The dysregulated metabolites suggested that CoA and fatty acids could help Staphylococcus aureus survive under antibiotic stress. Metabolic pathways engaged in antibiotic resistance were discovered through pathway enrichment analysis. The enriched pathways suggested that DNA repairing and flavin biosynthesis are universal pathways to help MSSA and MRSA survive under antibiotic stress. Compared with MSSA, MRSA systematically and effectively fight against oxacillin through precisely controlling energy producing, PBP2a substrate biosynthesis and antioxidant function. ConclusionsCoenzyme A and fatty acids help both MSSA and MRSA survive under the antibiotic stress. MSSA was susceptible to oxacillin and was forced to response. On the contrary, MRSA systematically and effectively fight against oxacillin. The different metabolome responses of MSSA and MRSA provide us with new insights into how Staphylococcus aureus develops antibiotics resistance.
A Method for Direct Estimation of Left Ventricular Global Longitudinal Strain Rate from Echocardiograms
Authors: Meyers Brett A. , Brindise Melissa C. , Kutty Shelby , Vlachos Pavlos P. 
Published: May 2021

Abstract
We present a new method for measuring global longitudinal strain and global longitudinal strain rate from 2D echocardiograms using a logarithmic-transform correlation (LTC) method. Traditional echocardiography strain analysis depends on user inputs and chamber segmentation, which yield increased measurement variability. In contrast, our approach is automated and does not require cardiac chamber segmentation and regularization, thus eliminating these issues. The algorithm was benchmarked against two conventional strain analysis methods using synthetic left ventricle ultrasound images. Measurement error was assessed as a function of contrast-to-noise ratio (CNR) using mean absolute error and root-mean-square error. LTC showed better agreement to the ground truth for strain (𝑹𝟐 = 𝟎. 𝟗1) and strain rate (𝑹𝟐 = 𝟎. 85) as compared to conventional algorithms (strain (𝑹𝟐 = 𝟎. 07), strain rate (𝑹𝟐 = 𝟎. 07)) and was unaffected by CNR. A 200% increase in strain measurement accuracy was observed compared to the conventional algorithms. Subsequently, we tested the method using a 54-subject clinical cohort (20 subjects diseased with cardiomyopathy, 34 healthy controls). Our method distinguished between normal and abnormal left ventricular function with an AUC = 0.85, a 10% improvement over the conventional GLS algorithms.
Identification of Neurodevelopmental Transition Patterns From Infancy to Early Childhood and Risk Factors Predicting Descending Transition: A Birth Cohort Study
Authors: Kato Takeo , Nishimura Tomoko , Takahashi Nagahide , Harada Taeko , Okumura Akemi , Iwabuchi Toshiki , Nomura Yoko , Tsuchiya Kenji J. , Takei Nori 
Published: May 2021

Abstract
It is unclear whether neurodevelopmental progress from infancy to early childhood remains stable. Moreover, little is known about the risk factors, if any, affecting neurodevelopmental descending transition patterns and the relationship between these patterns and later childhood adaptive behaviours. We used data of 875 children from the Hamamatsu Birth Cohort Study in Japan. Children’s neurodevelopment at 18 and 32 months and adaptive behaviours at 40 months were evaluated. Perinatal factors and infant overweight status at 18 months were investigated to identify descending-transition-associated risk factors. In the latent transition analysis, ultimately, three classes were identified for each time point, resulting in nine transition patterns; among them, 10.4% of children showed descending class shifts (normal to delayed class). Such decelerated growth was predicted by maternal pre-pregnancy overweight status (odds ratio [OR] = 2.49; 95% confidence interval [CI]: 1.23, 5.02), low maternal educational history (OR = 1.20; 95% CI: 1.04, 1.36), and infant overweight status at 18 months (OR = 5.89; 95% CI: 1.26, 27.45). Children with descending transition showed poor functioning in adaptive behaviours at the age of 40 months. Interventions targeting children with risk factors for descending transition patterns may prevent decelerated growth and subsequent poor adaptive functioning.
High-density Lipoprotein Cholesterol Negatively Correlates with Bone Mineral Density and Has Potential Predictive Value for Bone Loss
Authors: Tang Yuchen , Wang Shenghong , Yi Qiong , Xia Yayi , Geng Bin 
Published: May 2021

Abstract
Background: In recent years, it was demonstrated that high-density lipoprotein cholesterol (HDL-C), a critical lipid for human lipid metabolism, was not completely beneficial to human health, implying that extremely high HDL-C levels may also affect human health and contribute to various diseases. The correlation between HDL-C and bone metabolism was uncertain and controversial. This study aimed to explore the correlation between HDL-C level and bone mineral density (BMD), investigating whether this relationship is different in diverse populations by stratifying age and gender.Method: The data utilized were extracted from 2005-2010 National Health and Nutrition Examination Survey (NHANES). We reviewed the data to exclude the participants aged over or equal to 20 years old or with missing core data. Multivariate linear regression analyses were conducted to estimate the association between HDL-C and BMD. A subgroup analysis was also utilized to estimate the difference in diverse populations by stratifying age and gender. Moreover, fitted smoothing curves and generalized additive models were also performed to address the nonlinear relationship between HDL-C levels and BMD.Result: Multivariable-adjusted linear regression models demonstrated that HDL-C was negatively associated with BMD, especially in females. Meanwhile, smooth curve fittings and generalized additive models also suggested an inverted U-shaped curve among females aged 30-40 or over 60. A U-shaped curve was observed for the relationship between HDL-C and BMD in femoral regions in females aged 20 to 30 or 50 to 60. Besides, female participants aged over 40 at a higher than or equal to 71 mg/dL HDL-C level were more likely to have a high risk of osteopenia or osteoporosis.Conclusion: HDL-C and BMD exhibited a negative correlation among females and different associations in diverse age groups. In addition, HDL-C can serve as a marker for osteopenia or osteoporosis.
Diagnostic accuracy of insulin-like growth factor-1 for screening growth hormone deficiency: a prospective, single-center, diagnostic accuracy study
Authors: Iwayama Hideyuki , Kitagawa Sachiko , Sada Jyun , Miyamoto Ryosuke , Hayakawa Tomohito , Kuroyanagi Yoshiyuki , Muto Taichiro , Kurahashi Hirokazu , Ohashi Wataru , Takagi Junko , Okumura Akihisa 
Published: May 2021

Abstract
Purpose
We evaluated the diagnostic accuracy of insulin-like growth factor-1 (IGF-1) for screening growth hormone deficiency (GHD) to determine the usefulness of IGF-1 as a screening test.
Methods
Among 298 consecutive children who had short stature or decreased height velocity, we measured IGF-1 levels and performed growth hormone (GH) secretion test using clonidine, arginine, and, in cases with different results of the two tests, L-dopa. Patients with congenital abnormalities were excluded. GHD was defined as peak GH ≤ 6.0 ng/mL in the two tests.
Results
We identified 60 and 238 patients with and without GHD, respectively. The mean IGF-1 (SD) was not significantly different between the GHD and non-GHD groups (p = 0.23). Receiver operating characteristic curve analysis demonstrated the best diagnostic accuracy at an IGF-1 cutoff of −1.493 SD, with 0.685 sensitivity, 0.417 specificity, 0.25 positive and 0.823 negative predictive values, and 0.517 area under the curve. Correlation analysis revealed that none of the items of patients’ characteristics increased the diagnostic power of IGF-1.
Conclusion
IGF-1 level had poor diagnostic accuracy as a screening test for GHD. Therefore, IGF-1 should not be used alone in the screening of GHD. A predictive biomarker for GHD should be developed in the future.
A super-pangenome framework of the genus Glycine unveils polyploid evolution and life-strategy transition
Authors: Zhuang Yongbin , Wang Xutong , Li Xianchong , Hu Junmei , Fan Lichuan , Jackson Scott , Doyle Jeffrey , Zhang Xian Sheng , Zhang Dajian , Ma Jianxin 
Published: May 2021

Abstract
Polyploidy and life strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and genetic bases of such transitions remain elusive. We assembled plantum genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. The perennials exhibited greater genome stability than the annuals, with few centromere repeats abundant in the latter. Biased subgenome fractionation has occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting local genomic differentiation. A gene annotated to modulate vegetative to reproductive phase transition was identified to have undergone adaptive evolution underlying the perenniality-annuality transition. Our study provides mechanistic insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.
Investigating COVID-19 in Low-income Settings: Protocol for a Multidisciplinary Mixed Methods Research in Burkina Faso
Authors: Traoré Isidore , Ouedraogo Samiratou , Kania Dramane , Firmin Nongodo , Kaboré Blahima Konaté , Médah Rachel , Badolo Hermann , de Rekeneire Nathalie , Kamga Ariane Mamguem , Poda Armel , Diendere Arnaud Eric , Ouédraogo Boukary , Ouédraogo Esperance , Billa Oumar , Tinto Halidou , Dabakuyo-Yonli Tienhan Sandrine 
Published: May 2021

Abstract
Background: The world has high hopes of vaccination against COVID-19 to protect the population, boost economies and return to normal life. Vaccination programmes are being rolled out in high income countries, but the pandemic continues to rage in many low-income countries (LICs) despite implementation of strict hygiene measures. We aim to present a comprehensive research protocol that will generate epidemiological, sociological, and anthropological data about the COVID-19 epidemic in Burkina Faso a landlocked country in West Africa with scares resources. Methods: We will perform a multidisciplinary research using mixed methods in the two main cities in Burkina Faso (Ouagadougou and Bobo-Dioulasso). Data will be collected in general population and in COVID-19 patients, caregivers and health care professional in reference care centers: (i) to determine cumulative incidence of SARS-CoV-2 infection in the Burkinabe population using blood samples collected from randomly selected households according to the WHO-recommended protocol; (ii) develop a score to predict severe complications of COVID-19 in persons infected with SARS-CoV-2 using retrospective and prospective data; (iii) perform semi-structured interviews and direct observation on site, to describe and analyze the healthcare pathways and experiences of patients with COVID-19 attending reference care centers, and to identify the perceptions, acceptability and application of preventive strategies among the population. Discussion: This study will generate comprehensive data that will contribute to improve COVID-19 response strategies in Burkina Faso. The lessons learned from the management of the epidemic may serve as examples to the country authorities to better design preventive strategies in the case of future epidemics or pandemics.Ethics and disseminationThis project was approved by the Ministry for Health (N° 2020 - 00952/MS/CAB/INSP/CM) and the Ethics Committee for Health Research of Burkina Faso (N° 2020-8-140).
Negative Correlations Between Cultivable Pyrene-degrading Sphingomonas and Active Soil Pyrene Degraders Explain Bioaugmentation Postpone or Failure
Authors: Jiang Bo , Chen Yating , Xing Yi , Lian Luning , Shen Yaoxin , Zhang Baogang , Zhang Han , Sun Guangdong , Li Junyi , Wang Xinzi , Zhang Dayi 
Published: May 2021

Abstract
Background: Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbon (PAHs), but suffers from unsatisfactory performance in engineering practices. It is hypothetically explained by the complicated interactions between indigenous microbes and introduced degrading consortium. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium consisting of Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira by magnetic-nanoparticle mediated isolation (MMI) from soils.Results: Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, explained by its negative correlations with the active pyrene degraders. In contrast, amendment with the active pyrene degrading consortium, pyrene degradation efficiency increased by 30.17%. In addition, pyrene degradation efficiency was positively correlated with the abundance of pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP), which significantly increased in MMI-isolated consortium. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas the MMI-isolated pyrene degrading consortium exhibited both phthalate and salicylate pathways. The results indicated that Sphingomonas sp. YT1005 was not the actual pyrene degrader in soils, and MMI could successfully isolate the active pyrene degraders that were suitable for bioaugmentation.Conclusion: This work revealed the microbial intra-correlations during the bioaugmentation process, uncovered the underlying mechanisms of bioaugmentation postpone with cultivable degraders, and provided a deeper insight into the actual pyrene degraders and degradation pathways in PAHs contaminated soils. Our findings gave new explanations for bioaugmentation postpone or failure, and offered clues to enhance bioaugmentation performance by the active degraders using MMI.