bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project
Authors: Roman-Reyna Veronica , Pinili Dale , Borja Frances N. , Quibod Ian L. , Groen Simon C. , Alexandrov Nickolai , Mauleon Ramil , Oliva Ricardo 
Published: October 2020

Abstract
Background
The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions.

Findings
By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities.

Conclusion
We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.
Decreased glycolysis induced dysfunction of NK cells in Henoch-Schonlein purpura patients
Authors: Chai Wenjia , Wang Xiaolin , Wang Wei , Wang Hui , Mou Wenjun , Gui Jingang 
Published: October 2020

AbstractBackgroundHenoch-Schonlein purpura (HSP) is the most common systemic vasculitis of the childhood. However, its mechanisms and pathogenesis still need more exploration. Natural killer (NK) cells are innate lymphocytes, and there is a growing appreciation that cellular metabolism is important in determining the immune responsiveness of lymphocytes. Thus, we aimed to analyze the NK cells phenotype and explore the association between glucose metabolism and NK cells function in HSP patients.ResultsA total number of 64 HSP patients and 34 healthy children were included. The HSP patients were divided into two groups according to whether accompanied with nephritis or not. NK cells in HSP patients without nephritis showed a reduced frequency in peripheral blood, a down-regulated expression of activating receptors both NKp30 and NKp46, and an attenuated cytotoxic function against tumor cells. In addition, the function impairment of NK cells was shown to exacerbate in HSPN. Our data further revealed an aberrant metabolic reprogramming of NK cells in HSP patients. Upon stimulation with cytokines (IL-15, IL-12 and IL-2), NK cells from healthy controls switched to an elevated glycolysis rate to support their effector function. By contrast, the glycolysis rate of activated NK cells in HSP group was not significantly up-regulated from the resting level possibly owing to the inhibition of mTORC1.ConclusionsOur study found that HSP patients were accompanied with dysfunction of NK cells. We concluded that the dysfunction of NK cells in HSP patients was induced with a decreased glycolysis rate and suggested that metabolic reprogramming of NK cells might be a player in the pathogenesis of HSP.
Does conserved domain SOD1 mutation has any role in ALS severity and therapeutic outcome?
Authors: Pal Surinder , Tiwari Abha , Sharma Kaushal , Sharma Suresh Kumar 
Published: October 2020

Abstract
Background
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress induced bunina and lewy bodies formation can be regulated through the action of SOD1 protein. Hence, in the present study we aim to analyse the structural and functional annotation of various reported SOD1 variants throughout and their putative correlation with the location of mutation and degree of ALS severity by inferring the structural and functional alterations in different SOD1 variants.

Methods
We have retrieved around 69 SNPs of SOD1 gene from Genecards. Structural annotation of SOD1 variants were performed using SWISS Model, I-Mutant 2.0, Dynamut, ConSurf. Similarly, the functional annotation of same variants were done using SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB. Ramachandran plot was also obtained for six synonymous SNPs to compare the amino acid distribution of wild-type SOD1 (WT SOD1) protein. Frequency analysis, Chi square analysis, ANOVA and multiple regression analysis were performed to compare the structural and functional components among various groups.

Results and conclusion
Results showed the mutations in conserved domain of SOD1 protein are more deleterious and significantly distort the tertiary structure of protein by altering Gibb’s free energy and entropy. Moreover, significant changes in SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB scores were also observed in mutations located in conserved domain of SOD1 protein. Multiple regression results were also suggesting the significant alterations in free energy and entropy for conserved domain mutations which were concordant with structural changes of SOD1 protein. Results of the study are suggesting the biological importance of location of mutation(s) which may derive the different disease phenotypes and must be dealt accordingly to provide precise therapy for ALS patients.
Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses
Authors: Tong Jiafeng , Walk Thomas C. , Han Peipei , Chen Liyu , Shen Xinjie , Li Yinshui , Gu Chiming , Xie Lihua , Hu Xiaojia , Liao Xing , Qin Lu 
Published: October 2020

Abstract
Background
High-affinity nitrate transporter 2 (NRT2) genes have been implicated in nitrate absorption and remobilization under nitrogen (N) starvation stress in many plant species, yet little is known about this gene family respond to various stresses often occurs in the production of rapeseed (Brassica napus L.).

Results
This report details identification of 17 NRT2 gene family members in rapeseed, as well as, assessment of their expression profiles using RNA-seq analysis and qRT-PCR assays. In this study, all BnNRT2.1 members, BnNRT2.2a and BnNRT2.4a were specifically expressed in root tissues, while BnNRT2.7a and BnNRT2.7b were mainly expressed in aerial parts, including as the predominantly expressed NRT2 genes detected in seeds. This pattern of shoot NRT expression, along with homology to an Arabidopsis NRT expressed in seeds, strongly suggests that both BnNRT2.7 genes play roles in seed nitrate accumulation. Another rapeseed NRT, BnNRT2.5 s, exhibited intermediate expression, with transcripts detected in both shoot and root tissues. Functionality of BnNRT2s genes was further outlined by testing for adaptive responses in expression to exposure to a series of environmental stresses, including N, phosphorus (P) or potassium (K) deficiency, waterlogging and drought. In these tests, most NRT2 gene members were up-regulated by N starvation and restricted by the other stresses tested herein. In contrast to this overall trend, transcription of BnNRT2.1a was up-regulated under waterlogging and K deficiency stress, and BnNRT2.5 s was up-regulated in roots subjected to waterlogging. Furthermore, the mRNA levels of BnNRT2.7 s were enhanced under both waterlogging stress and P or K deficiency conditions. These results suggest that these three BnNRT2 genes might participate in crosstalk among different stress response pathways.

Conclusions
The results presented here outline a diverse set of NRT2 genes present in the rapeseed genome that collectively carry out specific functions throughout rapeseed development, while also responding not just to N deficiency, but also to several other stresses. Targeting of individual BnNRT2 members that coordinate rapeseed nitrate uptake and transport in response to cues from multiple stress response pathways could significantly expand the genetic resources available for improving rapeseed resistance to environmental stresses.
Risk factors associated with infection of blood-borne virus among people who used methamphetamine
Authors: Cai Yilin , Dai Zheng , Wen Sijin , Bhandari Ruchi 
Published: October 2020

AbstractBackgroundThe surge of methamphetamine use has been a complicating factor compounding the steeply increasing number of drug overdose deaths in the U.S. Infection from blood-borne viruses including hepatitis B virus (HBV), hepatitis C virus (HCV) and HIV, related to methamphetamine use continue to grow. This study aims to examine the risk factors associated with HBV, HCV and HIV among people who used methamphetamine.MethodsPeople who ever used methamphetamine were identified from five National Health and Nutrition Examination Survey (NHANES) cohorts, 2007 to 2016. The outcome was either positive or negative for blood-borne viruses as identified from laboratory tests. Weighted statistics for the combined ten years of data were calculated by multiplying the weighted variable for laboratory measurements by 0.2. We examined the association of sexual activities (sexual partners, sexual identity), drug use behaviors (poly-drug use, injection drug use, frequency of drug use, age started using methamphetamine), demographics, and socio-economic status with blood-borne viruses using bivariate and multivariable logistic regression models.ResultsThere were 1132 participants representing approximately 11,996,319 persons who ever used methamphetamine in the U.S. Blood-borne viruses’ positive rate was 13.0 per 100,000. Multivariable logistic regression analyses showed significant associations of blood-borne infections with age 40–49 years (vs. age 20–29 years, adjusted odds ratio 4.77, 95% CI 1.11–20.55), age 50–59 years (vs. age 20–29 years, 10.25, 2.40–43.82), living within poverty index 1–1.9 (vs. poverty index > = 2, 2.55; 1.19–5.49), living below the poverty threshold (vs. poverty index > = 2, 2.55; 1.11–5.86), having lower than high school education (vs. equal or higher than high school education, 3.13; 1.51–6.46), sexual identity as other than heterosexual (vs. heterosexual, 5.60; 1.72–18.28), using methamphetamine and heroin and cocaine (vs. using methamphetamine alone, 4.24; 1.06–16.92), injection drug use (vs. no injection drug use, 3.15; 1.61–6.16), and started using methamphetamine at age above 25 (vs. started using methamphetamine at age between 10 and 17, 2.09; 1.01–4.35).ConclusionsAmong people who use methamphetamine, those who use polysubstance, or who inject substances, are in urgent need for vaccination and interventions to avoid further harm from blood borne infections.
The study protocol: Neuroendocrinology and (epi-) genetics of female reproductive transition phase mood disorder - an observational, longitudinal study from pregnancy to postpartum
Authors: Johann Alexandra , Ehlert Ulrike 
Published: October 2020

Abstract
Background
Postpartum depression is considered to be one of the most common health threats during pregnancy and postpartum, affecting not only the woman herself but also the offspring and the whole family system. Evidence for a conclusive etiopathological model with distinct risk and resilience factors is still broadly lacking. Therefore, the aim of the present study is to investigate numerous health-related markers to obtain greater insight into which biopsychosocial profiles render women more vulnerable to PPD or facilitate a healthy transition from pregnancy to postpartum.

Methods
The observational, longitudinal study aims to include a total of 288 physically healthy women, aged 20–45 years. A multitude of relevant parameters, of an (epi-) genetic, endocrinological, physiological and psychological nature, will be assessed over a period of 5 months, following the participants from the 3rd trimester until three months postpartum.

Discussion
The ultimate goal of the present study is to ameliorate mental health care during pregnancy and postpartum, by gaining a better understanding of the underlying biopsychosocial mechanisms that women undergo during the transition from pregnancy to postpartum.
Clinical and imaging characteristics of primary hepatic sarcomatoid carcinoma and sarcoma: a comparative study
Authors: Shi Dongli , Sun Jun , Ma Liang , Chang Jing , Li Hongjun 
Published: October 2020

Abstract
Background
Primary hepatic sarcomatous carcinoma (PHSC) and primary hepatic sarcoma (PHS) are rare malignancies with frequent overlap in both the clinic and radiology. No comparative study of these tumors for the restricted cases has previously been undertaken. The purpose of our study was to analyze the clinical and imaging features of PHSCs and PHSs, with an emphasis on particularities and similarities through a comparison of the two tumors.

Methods
We retrospectively analyzed the clinical and imaging features of 39 patients with pathologically proven PHSCs (n = 23) and PHSs (n = 16) from four university centers over a 9-year period from 2010 to 2019. Univariate analyses were performed to determine the consistent and distinctive features.

Results
The background of chronic hepatitis or cirrhosis was observed with a high frequency in both of PHSCs (73.7%) and PHSs (62.5%). Tumors with a diameter greater than 10 cm were significantly more common in PHSs than PHSCs (p = 0.043) and cystic masses were more detected in PHSs (P = 0.041). Both PHSCs and PHSs mainly presented hypovascularity (78.3% vs 81.3%). The ring hyper enhancement on the arterial phase (AP) and wash out were more frequently seen in PHSCs and the iso-hypo enhancement on the AP followed persistent or progressive enhancement was more commonly detected in PHSs (all, p < 0.05).

Conclusion
PHSC and PHS generally present as mass lesions with hypovascularity. The ring hyper enhancement on the AP and wash out favor the diagnosis of PHSC. The large size greater than 10 cm, cystic lesion, iso-hypo persistent or progressive enhancement pattern might suggest the possibility of PHSs.
Primary outcomes of combined cataract extraction technique with Ab-Interno trabeculectomy and endoscopic Cyclophotocoagulation in patients with primary open angle Glaucoma
Authors: Izquierdo Juan Carlos , Mejías Josefina , Cañola-R Laura , Agudelo Natalia , Rubio Bárbara 
Published: October 2020

Abstract
Background
Glaucoma surgery have been developed to lower intraocular pressure in a less invasive manner than traditional glaucoma surgery. The purpose of this article is to determine the outcome of using combined phacoemulsification technique, ab-interno trabeculectomy dual blade and endoscopic cyclophotocoagulation (ECP) surgeries in patients with primary open angle glaucoma.

Methods
A retrospective case series was performed on 27 consecutive eyes with both primary open-angle glaucoma (POAG) and cataract; each eye was treated with combined phacoemulsification, ab-interno trabeculectomy-Kahook Dual Blade and Endocyclophotocoagulation at Instituto de ojos Oftalmosalud, Lima, Peru, between April 2017 and May 2017. Inclusion criteria: 1) Patients with uncontrolled mild to advanced POAG (according to Glaucoma Grading Scale HODAPP) 2) cataract condition 3) treatment with two or more glaucoma medications due to rapid progression in the visual fields (at least two in a short period of time). Intraocular pressure (IOP), best corrected visual acuity (BCVA) logMAR and number of glaucoma medications were recorded prior to the study, at day 1, week 1, and 1,3,6 and 9 months after surgery. Primary outcome measure was surgical success defined in terms of IOP < 14 mmHg either with no medications (complete success) or with medications (qualified success).

Results
A total of 27 eyes from 27 patients were included. The mean basal IOP was 17.0 ± 3.7 mmHg and postoperatively was 11.6 ± 1.9 mmHg and 11.4 ± 1.8 mmHg (P < 0.001) at 6 and 9 months respectively. Glaucoma medications decreased from 1.9 ± 1.4 to 0.56 ± 1.05 at 9 month follow-ups (P < 0.001). Preoperative best corrected visual acuity (BCVA) showed and improvement from 0.4 ± 0.4 LogMAR to 0.2 ± 0.4 logMAR at 9 months. The main complication was blood reflux intra-operatively (66.7%), which resolved without re-operation. The mean IOP was reduced by 32.9% from baseline and the surgical success was 92,6%, (complete success 70,3% and qualified success 29,6%) at 9 months.

Conclusions
In patients with POAG, combined treatment with phacoemulsification, ab-interno trabeculectomy and endoscopic cyclophotocoagulation effectively reduced IOP and glaucoma medication dependence.
Access to institutional delivery services and its associated factors among mothers in Jimma Zone, Southwest Ethiopia: a cross-sectional study
Authors: Kayrite Qaro Qanche , Salgedo Waju Beyene , Weldemarium Tesfaye Dagne , Sinkie Shimeles Ololo , Handalo Dejene Melese , Obola Teshale Dojamo , Kebene Feyera Gebissa , Garedew Muluneh Getachew , Likka Melaku Haile 
Published: October 2020

Abstract
Background
Poor access to institutional delivery services has been known as a significant contributory factor to adverse maternal as well as newborn outcomes. Previous studies measured access in terms of utilization while it has different dimensions (geographic accessibility, availability, affordability, and acceptability) that requires to be measured separately. Therefore, this study was conducted to assess the four dimensions of access and factors associated with each of these dimensions.

Methods
Community-based cross-sectional study design was used, employing both quantitative and qualitative methods. A simple random sampling technique was used to select 605 mothers who had given birth in the last 6 months preceding the study. Multi-variable binary logistic regression was used to select factors associated with the four dimensions of access by using AOR with 95% CI. Ethical approval was secured from Jimma University Institutional Review Board.

Results
Five hundred and ninety-three mothers involved in this study, resulting in a response rate of 98%. Four hundred five (68%), 273(46%), 279(47%), and 273(46%) had geographic, perceived availability, affordability, and acceptability access to institutional delivery services, respectively. Antenatal care [AOR = 3.74(1.56, 8.98)], occupation of mother [AOR = 5.10(1.63, 15.88)], and residence [AOR = 1.93(1.13, 3.29)] were independently associated with geographic accessibility. Household graduation [AOR = 1.46(1.03, 2.06)], residence [AOR = 1.74(1.17, 2.59)], and ANC [AOR = 3.80(1.38, 10.50)] were independently associated with perceived availability. Moreover, wealth quintile [AOR = 11.60(6.02, 22.35)], ANC [AOR = 3.48(1.36, 9.61)], and occupation of husband [AOR = 3.63(1.51, 8.74)] were independently associated with affordability. Lastly, mother’s education [AOR = 2.69(1.42, 5.09)], residence [AOR = 2.60(1.66, 4.08)], and household graduation [AOR = 3.12(2.16, 4.50)] were independently associated with acceptability of institutional delivery services.

Conclusions
Moderate proportions of mothers have geographic accessibility to institutional delivery services, but access to the other three dimensions was low. ANC visits of 4 or above, occupation of husband, urban residence, graduation of mother’s household as a model family, higher wealth quintiles, and maternal educational level significantly affect access to institutional delivery services. Thus, it was recommended that concerned bodies should give due attention to ANC services, female education, training of model families, and enhancement of household wealth through job creation opportunities to increase access to institutional delivery services.
Short-term effects of rainfall on childhood hand, foot and mouth disease and related spatial heterogeneity: evidence from 143 cities in mainland China
Authors: Yang Fan , Ma Yue , Liu Fengfeng , Zhao Xing , Fan Chaonan , Hu Yifan , Hu Kuiru , Chang Zhaorui , Xiao Xiong 
Published: October 2020

Abstract
Background
Numerous studies have demonstrated the potential association between rainfall and hand, foot and mouth disease (HFMD), but the results are inconsistent. This study aimed to quantify the relationship between rainfall and HFMD based on a multicity study and explore the potential sources of spatial heterogeneity.

Methods
We retrieved the daily counts of childhood HFMD and the meteorological variables of the 143 cities in mainland China between 2009 and 2014. A common time series regression model was applied to quantify the association between rainfall and HFMD for each of the 143 cities. Then, we adopted the meta-regression model to pool the city-specific estimates and explore the sources of heterogeneity by incorporating city-specific characteristics.

Results
The overall pooled estimation suggested a nonlinear exposure-response relationship between rainfall and HFMD. Once rainfall exceeded 15 mm, the HFMD risk stopped increasing linearly and began to plateau with the excessive risk ratio (ERR) peaking at 21 mm of rainfall (ERR = 3.46, 95% CI: 2.05, 4.88). We also found significant heterogeneity in the rainfall-HFMD relationships (I2 = 52.75%, P < 0.001). By incorporating the city-specific characteristics into the meta-regression model, temperature and student density can explain a substantial proportion of spatial heterogeneity with I2 statistics that decreased by 5.29 and 6.80% at most, respectively.

Conclusions
Our findings verified the nonlinear association between rainfall and HFMD. The rainfall-HFMD relationship also varies depending on locations. Therefore, the estimation of the rain-HFMD relationship of one location should not be generalized to another location.
Concomitant cemento-osseous dysplasia and aneurysmal bone cyst of the mandible: a rare case report with literature review
Authors: Yeom Han-Gyeol , Yoon Jung-Hoon 
Published: October 2020

Abstract
Background
Concomitant cemento-osseous dysplasia (COD) and aneurysmal bone cyst (ABC) are rare in the head and neck region. In our search of the English language literature, we found only one case report describing the simultaneous occurrence of COD and ABC in the head and neck region. Here, we report a case of COD associated with ABC. Further, we performed a systematic search of the literature to identify studies on patients with COD associated with nonepithelial lined cysts of the jaws.

Case presentation
The patient was a 32-year-old woman who was referred from a private dental clinic because of a cystic lesion below the mandibular right first molar. She had no pain or significant systemic disease. After performing panoramic radiography and cone-beam computed tomography, the imaging diagnosis was COD with a cystic lesion, such as ABC or solitary bone cyst. Excisional biopsy was performed, which revealed concomitant COD and ABC.

Conclusion
This case of ABC associated with COD provides insight for the diagnostic process of radiographically mixed lesions with cystic changes.