bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers
Authors: Qiao Yu , Cheng Qiming , Zhang Yutong , Yan Wei , Yi Fengyan , Shi Fengling 
Published: January 2021

Abstract
Background
Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin.

Results
Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin.

Conclusions
This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.
An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar
Authors: Zheng Lin , Yang Jixiu , Chen Yajuan , Ding Liping , Wei Jianhua , Wang Hongzhi 
Published: January 2021

Abstract
Background
Forest trees have important economic and ecological value. As a model tree, poplar has played a significant role in elucidating the molecular mechanisms underlying tree biology. However, a lack of mutant libraries and time-consuming stable genetic transformation processes severely limit progress into the functional characterization of poplar genes. A convenient and fast transient transformation method is therefore needed to enhance progress on functional genomics in poplar.

Methods
A total of 11 poplar clones were screened for amenability to syringe infiltration. Syringe infiltration was performed on the lower side of the leaves of young soil-grown plants. Transient expression was evaluated by visualizing the reporters β-glucuronidase (GUS) and green fluorescent protein (GFP). The experimental parameters of the syringe agroinfiltration were optimized based on the expression levels of the reporter luciferase (LUC). Stably transformed plants were regenerated from transiently transformed leaf explants through callus-induced organogenesis. The functions of Populus genes in secondary cell wall-thickening were characterized by visualizing lignin deposition therein after staining with basic fuchsin.

Results
We greatly improved the transient transformation efficiency of syringe Agrobacterium infiltration in poplar through screening for a suitable poplar clone from a variety of clones and optimizing the syringe infiltration procedure. The selected poplar clone, Populus davidiana × P. bolleana, is amenable to Agrobacterium syringe infiltration, as indicated by the easy diffusion of the bacterial suspension inside the leaf tissues. Using this technique, we localized a variety of poplar proteins in specific intracellular organelles and illustrated the protein–protein and protein–DNA interactions. The transiently transformed leaves could be used to generate stably transformed plants with high efficiency through callus induction and differentiation processes. Furthermore, transdifferentiation of the protoxylem-like vessel element and ectopic secondary wall thickening were induced in the agroinfiltrated leaves via the transient overexpression of genes associated with secondary wall formation.

Conclusions
The application of P. davidiana × P. bolleana in Agrobacterium syringe infiltration provides a foundation for the rapid and high-throughput functional characterization of Populus genes in intact poplar plants, including those involved in wood formation, and provides an effective alternative to Populus stable genetic transformation.
Heterologous expression of Arabidopsis thaliana rty gene in strawberry (Fragaria × ananassa Duch.) improves drought tolerance
Authors: Li Maofu , Yang Yuan , Raza Ali , Yin Shanshan , Wang Hua , Zhang Yuntao , Dong Jing , Wang Guixia , Zhong Chuanfei , Zhang Hong , Liu Jiashen , Jin Wanmei 
Published: January 2021

Abstract
Background
Strawberry (Fragaria × ananassa Duch.) is an important fruit crop worldwide. It was particularly sensitive to drought stress because of their fibrous and shallow root systems. Mutant rty of Arabidopsis thaliana ROOTY (RTY) results in increased endogenous auxin levels, more roots, and shoot growth. It is still unclear whether the rty gene improves stress tolerance in strawberry.

Results
rty gene was isolated from Arabidopsis thaliana and placed under the control of the cauliflower mosaic virus (CaMV) 35S promoter in the pBI121-rty binary vector carrying the selectable marker of neomycin phosphotransferase II (NPT II). Seven transgenic lines were confirmed by PCR and western blot analysis. Accumulations of IAA and ABA were significantly increased in the transgenic plants. The endogenous IAA contents were 46.5 ng g− 1 and 66.0 ng g− 1in control and transgenic plants respectively. The endogenous ABA contents in the control plant were 236.3 ng g− 1 and in transgenic plants were 543.8 ng g− 1. The production of adventitious roots and trichomes were enhanced in the transgenic plants. Furthermore, transcript levels of the genes including IAA and ABA biosynthetic, and stress-responsive genes, were higher in the transgenic plants than in the control plants under drought conditions. Water use efficiency and a reduced water loss rate were enhanced in the transgenic strawberry plants. Additionally, peroxidase and catalase activities were significantly higher in the transgenic plants than in the control plants. The experiment results revealed a novel function for rty related to ABA and drought responses.

Conclusions
The rty gene improved hormone-mediated drought tolerance in transgenic strawberry. The heterologous expression of rty in strawberry improved drought tolerance by promoting auxin and ABA accumulation. These phytohormones together brought about various physiological changes that improved drought tolerance via increased root production, trichome density, and stomatal closure. Our results suggested that a transgenic approach can be used to overcome the inherent trade-off between plant growth and drought tolerance by enhancing water use efficiency and reducing water loss rate under water shortage conditions.
Diagnostic accuracy of a liquid chromatography-tandem mass spectrometry assay in small hair samples for rifampin-resistant tuberculosis drug concentrations in a routine care setting
Authors: Metcalfe John , Bacchetti Peter , Esmail Ali , Reckers Andrew , Aguilar David , Wen Anita , Huo Shu , Muyindike Winnie R. , Hahn Judith A. , Dheda Keertan , Gandhi Monica , Gerona Roy 
Published: January 2021

Abstract
Background
Treatment monitoring of drug-resistant tuberculosis (DR-TB) in resource-limited settings is challenging. We developed a multi-analyte assay for eleven anti-TB drugs in small hair samples as an objective metric of drug exposure.

Methods
Small hair samples were collected from participants at various timepoints during directly observed RR-TB treatment at an inpatient tertiary referral facility in South Africa (DR-TB cohort). We assessed qualitative determination (i.e., detection above limit of detection) of bedaquiline, linezolid, clofazimine, pretomanid, levofloxacin, moxifloxacin, pyrazinamide, isoniazid, ethambutol, ethionamide, and prothionamide in an LC-MS/MS index panel assay against a reference standard of inpatient treatment records. Because treatment regimens prior to hospitalization were not available, we also analyzed specificity (for all drugs except isoniazid) using an external cohort of HIV-positive patients treated for latent TB infection with daily isoniazid (HIV/LTBI cohort) in Uganda.

Results
Among the 57 DR-TB patients (58% with pre-XDR/XDR-TB; 70% HIV-positive) contributing analyzable hair samples, the sensitivity of the investigational assay was 94% or higher for all drugs except ethionamide (58.5, 95% confidence interval [CI], 40.7–99.9). Assay specificity was low across all tested analytes within the DR-TB cohort; conversely, assay specificity was 100% for all drugs in the HIV/LTBI cohort.

Conclusions
Hair drug concentrations reflect long-term exposure, and multiple successive regimens commonly employed in DR-TB treatment may result in apparent false-positive qualitative and falsely elevated quantitative hair drug levels when prior treatment histories within the hair growth window are not known.
Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014
Authors: Rakau Kebareng G. , Nyaga Martin M. , Gededzha Maemu P. , Mwenda Jason M. , Mphahlele M. Jeffrey , Seheri L. Mapaseka , Steele A. Duncan 
Published: January 2021

Abstract
Background
G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.

Methods
The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.

Results
The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10− 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.

Conclusions
At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.
Prevalence and genotype distribution of group A rotavirus circulating in Shanxi Province, China during 2015–2019
Authors: Zhao Lifeng , Shi Xiaohong , Meng Dequan , Guo Jiane , Li Yiping , Liang Lirong , Guo Xiaofang , Tao Ran , Zhang Xiaohua , Gao Ruihong , Gao Li , Wang Jitao 
Published: January 2021

Abstract
Background
Group A rotavirus (RVA), despite being a leading cause of gastroenteritis in infants and young children, is less studied in Shanxi Province, China. The current study was conducted to determine the prevalence and genetic characterization of RVA in hospitalized children younger than 10 years of age with the diagnosis of acute gastroenteritis in Shanxi Province, China.

Methods
A hospital-based active surveillance of rotavirus gastroenteritis was conducted at Children’s Hospital of Shanxi from Jan 1, 2015, through Dec 31, 2019. Rotavirus was detected in stool samples by real-time quantitative reverse transcription PCR (qRT-PCR). G- and P-genotypes were determined by reverse transcription PCR (RT-PCR) and nucleotide sequencing.

Results
A total of 961 children younger than 10 years of age was enrolled over the study period, of whom 183 (19.0%) were positive for RVA. The highest RVA-infection frequency (23.7%) was found among children aged 12–23 months, and the seasonal peak was in December. G9P[8] was most prevalent (76.0%), followed by G3P[8] (7.1%), G2P[4] (3.3%), G1P[8] (0.5%) and G9P[4] (0.5%).

Conclusions
These results report for the first time that RVA was one of the main causes of severe infectious gastroenteritis in children, and a high proportion of G9P[8] strains circulating in most areas of Shanxi Province. While the protective efficacy of the rotavirus vaccines has been demonstrated against G9P[8] strains, our results highlight that the dominant strains have not been effectively controlled in China.
Prevalence of urogenital, anal, and pharyngeal infections with Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium: a cross-sectional study in Reunion island
Authors: Calas A. , Zemali N. , Camuset G. , Jaubert J. , Manaquin R. , Saint-Pastou C. , Koumar Y. , Poubeau P. , Gerardin P. , Bertolotti A. 
Published: January 2021

Abstract
Background
Recommendations for sexually transmitted infection (STI) screening vary significantly across countries. This study evaluated the prevalence of urogenital and extragenital infections with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Mycoplasma genitalium (MG) in patients visiting a French STI clinic in the Indian Ocean region to determine whether current STI screening practices should be updated.

Methods
This cross-sectional study examined all patients who visited the STI clinic between 2014 and 2015. Triplex polymerase chain reaction screening for CT, NG, and MG was performed on urine, vaginal, pharyngeal, and anal specimens (FTD Urethritis Basic Kit, Fast Track Diagnostics, Luxembourg).

Results
Of the 851 patients enrolled in the study, 367 were women (367/851, 43.2%) and 484 were men (484/851, 56.0%). Overall, 826 urogenital specimens (826/851, 97.1%), 606 pharyngeal specimens (606/851, 71.2%), and 127 anal specimens (127/851, 14.9%) were taken from enrolled patients. The prevalence of urogenital CT and MG was high in women ≤25 years (19/186, 10.21%; 5/186, 2.69%) and in men who have sex with women ≤30 years (16/212, 7.54%; 5/212, 2.36%). Among patients with urogenital CT infection, 13.7% (7/51) had urethritis. All patients with urogenital MG infection were asymptomatic. Men who have sex with men had a high prevalence of pharyngeal CT (2/45, 4.44%) and NG (3/44, 6.81%) and a high prevalence of anal CT (2/27, 7.41%), NG (2/27, 7.40%), and MG (1/27, 3.70%). After excluding patients with concomitant urogenital infection, extragenital infections with at least 1 of the 3 pathogens were found in 20 swabs (20/91, 21.9%) taken from 16 patients (16/81, 19.7%), all of them asymptomatic.

Conclusions
Routine multisite screening for CT, NG, and MG should be performed to mitigate the transmission of STIs in high-risk sexually active populations.
An optimized segmentation and quantification approach in microvascular imaging for OCTA-based neovascular regression monitoring
Authors: Wu Sheng , Wu Shaowei , Feng Hui , Hu Zizhong , Xie Yejing , Su Yun , Feng Ting , Li Li 
Published: January 2021

Abstract
Background
Quantification of neovascularization changes in terms of neovascular complex (NVC) acquired from the optical coherence tomography angiography (OCTA) imaging is extremely important for diagnosis and treatment monitoring of proliferative diabetic retinopathy (PDR). However, only few vessel extraction methods have so far been reported to quantify neovascular changes in NVC with proliferative diabetic retinopathy PDR based on OCTA images.

Methods
Here we propose an optimized approach to segment blood vessels, which is based on an improved vascular connectivity analysis (VCA) algorithm and combined with morphological characterization and elimination of noise and artifacts. The length and width of vessels are obtained in the quantitative assessment of microvascular network. The feasibility of the proposed method is further studied by a treatment monitoring and statistical analysis process, as we have monitored and statistically analyzed the changes of NVC based on sampled OCTA images of PDR patients (N = 14) after treatment by intravitreal injection of conbercept.

Results
The proposed method has demonstrated better performance in accuracy compared with existing algorithms and can thus be used for PRD treatment monitoring. Following the PDR treatment monitoring study, our data has shown that from the 1st day to 7th day of treatment, the averaged (arithmetic mean) length of NVC has been substantially shortened by 36.8% (P < 0.01), indicating significant effects of treatment. Meanwhile, the averaged (arithmetic mean) width of NVC from the 1st day to 7th day of treatment has been increased by 10.2% (P < 0.05), indicating that most of the narrow neovascularization has been reduced.

Conclusion
The results and analysis have confirmed that the proposed optimization process by the improved VCA method is both effective and feasible to segment and quantify the NVC with lower noise and fewer artifacts. Thus, it can be potentially applied to monitor the fibrovascular regression during the treatment period.
Clinical Trial Registration This trial is registered with the Chinese Clinical Trial Registry (Registered 27 December 2017, http://www.chictr.org.cn, registration number ChiCTR-IPR-17014160).
Perceived barriers to and suggested interventions for physical activity during pregnancy among participants of the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in Southern California
Authors: Koleilat Maria , Vargas Nancy , vanTwist Victoria , Kodjebacheva Gergana Damianova 
Published: January 2021

Abstract
Background
The American College of Obstetricians and Gynecologists (ACOG) recommends that pregnant women engage in at least 20 to 30 min of moderate-intensity physical activity on most days of the week. Regular exercise during pregnancy is associated with many benefits for the mother and the developing fetus; yet, a large number of pregnant women do not engage in the recommended amounts. This study aimed to investigate barriers to and interventions for physical activity among pregnant WIC participants in Southern California.

Methods
We conducted four focus groups (FGs) with pregnant low-income women aged 18 years or older in either their second or third trimester. FGs were conducted at a WIC center in Southern California. The FGs were held according to language (English vs. Spanish-speaking) and BMI category (normal weight vs. overweight and obese). A total of 28 women participated. We used ATLAS. ti. to analyze the focus group transcripts. The study adhered to the Consolidated Criteria for Reporting Qualitative Research.

Results
The mean age of focus group participants was 28.9 years (SD = 6.6), and the majority were Latina. Intrapersonal barriers to physical activity were fatigue and lack of energy, pain and swelling, lack of childcare, medical restrictions and safety concerns, lack of knowledge about exercise safety, and lack of time. Interpersonal barriers included concerns and lack of support from partners and families, conflicting advice from friends and neighbors, and lack of advice on safe exercise from physicians. Women in all four groups suggested a community-based intervention where they can mingle with each other and share their challenges and concerns. Other suggestions to interventions differed among groups and reflected the women’s experiences and backgrounds. Specifically, to promote education, English-speaking women preferred a brochure while Spanish-speaking women preferred a video. Overweight women emphasized including children in their exercise activities to promote healthy behavior in youth.

Conclusions
Interventions should be tailored to pregnant women’s needs. Primary care providers should provide reassurance and information to pregnant women and their partners on the type and frequency of safe exercise.
OB Nest randomized controlled trial: a cost comparison of reduced visit compared to traditional prenatal care
Authors: Theiler Regan N. , Butler-Tobah Yvonne , Hathcock Matthew A. , Famuyide Abimbola 
Published: January 2021

Abstract
Background
Traditional prenatal care includes up to 13 in person office visits, and the cost of this care is not well-described. Alternative models are being explored to better meet the needs of patients and providers. OB Nest is a telemedicine-enhanced program with a reduced frequency of in-person prenatal visits. The cost implications of connected care services added to prenatal care packages are unclear.

Methods
Using data from the OB Nest randomized, controlled trial we analyzed the provider and staff time associated with prenatal care in the traditional and OB Nest models. Fewer visits were required for OB Nest, but given the compensatory increase in connected care activity and supplies, the actual cost difference is not known. Nursing and provider staff time was prospectively recorded for all patients enrolled in the OB Nest clinical trial. Published 2015 national wages for healthcare workers were used to calculate the actual labor cost of providing either traditional or OB Nest prenatal care in 2015 US dollars. Overhead expenses and opportunity costs were not considered.

Results
Total provider cost was decreased caring for the OB Nest participants, but nursing cost was increased. OB Nest care required an average of 160.8 (+/− 45.0) minutes provider time and 237 (+/− 25.1) minutes nursing time, compared to 215.0 (+/− 71.6) and 99.6 (+/− 29.7) minutes for traditional prenatal care (P < 0.01). This translated into decreased provider cost and increased nursing cost (P < 0.01). Supply costs increased, travel costs declined, and overhead costs declined in the OB Nest model.

Conclusions
In this trial, labor cost for OB Nest prenatal care was 34% higher than for traditional prenatal care. The increased cost is largely attributable to additional nursing connected care time, and in some practice settings may be offset by decreased overhead costs and increased provider billing opportunities. Future efforts will be focused on development of digital solutions for some routine nursing tasks to decrease the overall cost of the model.

Trial registrations
ClinicalTrials.gov Identifier: NCT02082275.