bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.
Authors: Wu Di , Liu Anqi , Qu Xiaoyu , Liang Jiayi , Song Min 
Published: November 2020

Abstract

Background
Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out.

Results
In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor.

Conclusions
We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.
Small RNA sequencing of extracellular vesicles identifies circulating miRNAs related to inflammation and oxidative stress in HIV patients
Authors: Chettimada Sukrutha , Lorenz David R. , Misra Vikas , Wolinsky Steven M. , Gabuzda Dana 
Published: November 2020

Abstract

Background
Extracellular vesicles (EVs) are nano-sized particles secreted by most cells. EVs carry nucleic acids that hold promise as potential biomarkers in various diseases. Human immunodeficiency virus type 1 (HIV) infects CD4+ T cells and induces immune dysfunction, inflammation, and EV secretion, but little is known about EV small RNA cargo in relation to immune dysregulation in HIV-infected individuals. Here, we characterize small RNA carried by circulating EVs in HIV-positive subjects on antiretroviral therapy (ART) relative to uninfected controls by next-generation RNA sequencing.

Results
Plasma EVs isolated from HIV-positive and HIV-negative subjects in test (n = 24) and validation (n = 16) cohorts were characterized by electron microscopy, nanoparticle tracking analysis, and immunoblotting for exosome markers. EVs were more abundant in plasma from HIV-positive compared to HIV-negative subjects. Small RNA sequencing of plasma EVs in the test cohort identified diverse small RNA species including miRNA, piRNA, snRNA, snoRNA, tRNA, and rRNA, with miRNA being the most abundant. A total of 351 different miRNAs were detected in plasma EVs, with the top 50 miRNAs accounting for 90% of all miRNA reads. miR-26a-5p was the most abundant miRNA, followed by miR-21-5p and miR-148-3p. qRT-PCR analysis showed that six miRNAs (miR-10a-5p, − 21-5p, −27b-3p, − 122-5p, −146a-5p, − 423-5p) were significantly increased in plasma EVs from HIV-positive compared to HIV-negative subjects in the validation cohort. Furthermore, miR-21-5p, −27b-3p, −146a-5p, and − 423-5p correlated positively with metabolite markers of oxidative stress and negatively with anti-inflammatory polyunsaturated fatty acids. Over-representation and pathway enrichment analyses of miRNAs and their target genes predicted functional association with oxidative stress responses, interferon gamma signaling, Toll-like receptor signaling, TGF beta signaling, and Notch signaling.

Conclusions
HIV-positive individuals on ART have increased abundance of circulating EVs carrying diverse small RNAs, with miRNAs being the most abundant. Several miRNAs associated with inflammation and oxidative stress are increased in circulating EVs of HIV-positive individuals, representing potential biomarkers of targetable pathways that contribute to disease pathogenesis.
Simultaneous induction of mutant alleles of two allergenic genes in soybean by using site-directed mutagenesis
Authors: Sugano Shota , Hirose Aya , Kanazashi Yuhei , Adachi Kohei , Hibara Miki , Itoh Takeshi , Mikami Masafumi , Endo Masaki , Hirose Sakiko , Maruyama Nobuyuki , Abe Jun , Yamada Tetsuya 
Published: November 2020

Abstract

Background
Soybean (Glycine max) is a major protein crop, because soybean protein has an amino acid score comparable to that of beef and egg white. However, many allergens have been identified among soybean proteins. A decrease in allergenic protein levels would be useful for expanding the market for soybean proteins and processed foods. Recently, the CRISPR/Cas9 system has been adopted as a powerful tool for the site-directed mutagenesis in higher plants. This system is expected to generate hypoallergenic soybean varieties.

Results
We used two guide RNAs (gRNAs) and Agrobacterium-mediated transformation for simultaneous site-directed mutagenesis of two genes encoding the major allergens Gly m Bd 28 K and Gly m Bd 30 K in two Japanese soybean varieties, Enrei and Kariyutaka. We obtained two independent T0 Enrei plants and nine T0 Kariyutaka plants. Cleaved amplified polymorphic sequence (CAPS) analysis revealed that mutations were induced in both targeted loci of both soybean varieties. Sequencing analysis showed that deletions were the predominant mutation type in the targeted loci. The Cas9-free plants carrying the mutant alleles of the targeted loci with the transgenes excluded by genetic segregation were obtained in the T2 and T3 generations. Variable mutational spectra were observed in the targeted loci even in T2 and T3 progenies of the same T0 plant. Induction of multiple mutant alleles resulted in six haplotypes in the Cas9-free mutants derived from one T0 plant. Immunoblot analysis revealed that no Gly m Bd 28 K or Gly m Bd 30 K protein accumulated in the seeds of the Cas9-free plants. Whole-genome sequencing confirmed that a Cas9-free mutant had also no the other foreign DNA from the binary vector. Our results demonstrate the applicability of the CRISPR/Cas9 system for the production of hypoallergenic soybean plants.

Conclusions
Simultaneous site-directed mutagenesis by the CRISPR/Cas9 system removed two major allergenic proteins from mature soybean seeds. This system enables rapid and efficient modification of seed components in soybean varieties.
Stalk architecture, cell wall composition, and QTL underlying high stalk flexibility for improved lodging resistance in maize
Authors: Wang Xiaqing , Shi Zi , Zhang Ruyang , Sun Xuan , Wang Jidong , Wang Shuai , Zhang Ying , Zhao Yanxin , Su Aiguo , Li Chunhui , Wang Ronghuan , Zhang Yunxia , Wang Shuaishuai , Wang Yuandong , Song Wei , Zhao Jiuran 
Published: November 2020

Abstract

Background
Stalk fracture caused by strong wind can severely reduce yields in maize. Stalks with higher stiffness and flexibility will exhibit stronger lodging resistance. However, stalk flexibility is rarely studied in maize. Stalk fracture of the internode above the ear before tasseling will result in the lack of tassel and pollen, which is devastating for pollination in seed production. In this study, we focused on stalk lodging before tasseling in two maize inbred lines, JING724 and its improved line JING724A1 and their F2:3 population.

Results
JING724A1 showed a larger stalk fracture angle than JING724, indicating higher flexibility. In addition, compared to JING724, JING724A1 also had longer and thicker stalks, with a conical, frustum-shaped internode above the ear. Microscopy and X-ray microcomputed tomography of the internal stalk architecture revealed that JING724A1 had more vascular bundles and thicker sclerenchyma tissue. Furthermore, total soluble sugar content of JING724A1, especially the glucose component, was substantially higher than in JING724. Using an F2:3 population derived from a JING724 and JING724A1 cross, we performed bulk segregant analysis for stalk fracture angle and detected one QTL located on Chr3: 14.00–19.28 Mb. Through transcriptome data analysis and ∆ (SNP-index), we identified two candidate genes significantly associated with high stalk fracture angle, which encode a RING/U-box superfamily protein (Zm00001d039769) and a MADS-box transcription factor 54 (Zm00001d039913), respectively. Two KASP markers designed from these two candidate genes also showed significant correlations with stalk fracture angle.

Conclusions
The internode shape and glucose content are possibly correlated with stalk flexibility in maize. Two genes in the detected QTL are potentially associated with stalk fracture angle. These novel phenotypes and associated loci will provide a theoretical foundation for understanding the genetic mechanisms of lodging, and facilitate the selection of maize varieties with improved flexibility and robust lodging resistance.
Patients’ experiences of the caring encounter in health promotion practice: a qualitative study in Swedish primary health care
Authors: Lundberg Kristina , Jong Mats , Jong Miek C. , Porskrog Kristiansen Lisbeth 
Published: November 2020

AbstractBackgroundPrevious studies have reported that organizational structures and cultures in primary health care are obstacles to district nurses doing successful work in health promotion practice (HPP). Because organizational structures are not easily changed, Jean Watson’s Attending Nurse Caring Model (ANCM) was introduced and piloted at a primary health care center in Sweden, aiming to transform HPP so as to empower district nurses and increase their work satisfaction.AimTo investigate patients’ experiences of the caring encounter in HPP after introduction of the ANCM in Swedish primary health care, the aim being to explore the essential components of the caring encounter between patients and district nurses.MethodsA descriptive and qualitative research design was used. Data collection was performed using individual face-to-face interviews with twelve patients at risk for developing CVD. Data analysis consisted of both deductive content analysis, using a categorization matrix based on the ANCM and, subsequently, inductive latent content analysis.ResultsThe findings were abstracted into three themes: 1.‘Feeling the deepest essence of being cared for’: to be respected and being put at the center of the encounter; 2. ‘Feeling acceptance and worth’: being treated with openness and permissive attitudes, 3. ‘Being in a supportive atmosphere that promotes hope’: to feel trust and being trusted in the encounter, and being empowered by hope. The unifying main theme of the caring encounter was abstracted as ‘Experiencing human dignity’.ConclusionThe present study revealed that the essence of the caring encounter between patients and district nurses in HPP is to be unconditionally accepted in an environment that inspires hope and encouragement. The ANCM seems to be a promising model to use for strengthening the caring encounter and supporting CVD patients in making healthy lifestyle choices. However, further studies of qualitative and quantitative designs are needed to investigate what the ANCM can contribute to HPP in Swedish primary health care.
Development, reliability and validity of the Safe Use of Mobility Aids Checklist (SUMAC) for 4-wheeled walker use in people living with dementia
Authors: Hunter Susan W. , Divine Alison , Omana Humberto , Madou Ed , Holmes Jeffrey 
Published: November 2020

AbstractBackgroundBalance and gait problems are common and progressive in dementia. Use of a mobility aid provides physical support and confidence. Yet, mobility aid use in people with dementia increases falls three-fold. An assessment tool of mobility aid safety in people with dementia does not currently exist. The objectives of this study were: 1) to develop a tool for the evaluation of physical function and safe use of a 4-wheeled walker in people with dementia, and 2) to evaluate its construct and criterion validity, inter-rater and test-retest reliability and minimal detectable change.MethodsHealthcare professionals (HCP) experienced in rehabilitation of people with dementia participated in focus groups for item generation of the new tool, The Safe Use of Mobility Aid Checklist (SUMAC). The SUMAC evaluates physical function (PF) and safe use of the equipment (EQ) on nine tasks of daily life. Reliability was evaluated by HCP (n = 5) scored participant videos of people with dementia (n = 10) using a 4-wheeled walker performing the SUMAC. Inter-rater and test-retest reliability was assessed using intra-class correlation coefficients (ICC). Construct validity evaluated scores of the HCPs to a consensus HCP panel using Spearman’s rank-order correlations. Criterion validity evaluated SUMAC-PF to the Performance-Oriented Mobility Assessment (POMA) gait subscale using Spearman’s rank-order correlations.ResultsThree focus groups (n = 17) generated a tool comprised of nine tasks and the components within each task for physical function and safe use. Inter-rater reliability was statistically significant for SUMAC-PF (ICC = 0.92, 95%CI (0.81, 0.98),p < 0.001) and SUMAC-EQ. (ICC = 0.82, 95%CI (0.54, 0.95),p < 0.001). Test-retest reliability was statistically significant for SUMAC-PF (ICC = 0.89, 95%CI (0.81, 0.94),p < 0.001) and SUMAC-EQ. (ICC = 0.88, 95%CI (0.79, 0.93),p < 0.001). As hypothesized, the POMA gait subscale correlated strongly with the SUMAC-PF (rs = 0.84), but not EQ (rs = 0.39).ConclusionsThe focus groups and research team developed a tool of nine tasks with evaluation on physical function and safe use of a 4-wheeled walker for people with dementia. The SUMAC tool has demonstrated content validity for the whole scale and good construct and criterion validity for the SUMAC-PF and SUMAC-EQ. The subscores of the SUMAC demonstrated excellent to good inter-rater and test-retest reliability.
Malaria Screener: a smartphone application for automated malaria screening
Authors: Yu Hang , Yang Feng , Rajaraman Sivaramakrishnan , Ersoy Ilker , Moallem Golnaz , Poostchi Mahdieh , Palaniappan Kannappan , Antani Sameer , Maude Richard J. , Jaeger Stefan 
Published: November 2020

Abstract

Background
Light microscopy is often used for malaria diagnosis in the field. However, it is time-consuming and quality of the results depends heavily on the skill of microscopists. Automating malaria light microscopy is a promising solution, but it still remains a challenge and an active area of research. Current tools are often expensive and involve sophisticated hardware components, which makes it hard to deploy them in resource-limited areas.

Results
We designed an Android mobile application called Malaria Screener, which makes smartphones an affordable yet effective solution for automated malaria light microscopy. The mobile app utilizes high-resolution cameras and computing power of modern smartphones to screen both thin and thick blood smear images for P. falciparum parasites. Malaria Screener combines image acquisition, smear image analysis, and result visualization in its slide screening process, and is equipped with a database to provide easy access to the acquired data.

Conclusion
Malaria Screener makes the screening process faster, more consistent, and less dependent on human expertise. The app is modular, allowing other research groups to integrate their methods and models for image processing and machine learning, while acquiring and analyzing their data.
Molecular identification of Actinomadura madurae isolated from a patient originally from Algeria; observations from a case report
Authors: Izri Arezki , Aljundi Mohanad , Billard-Pomares Typhaine , Fofana Youssouf , Marteau Anthony , Ferreira Theo Ghelfenstein , Brun Sophie , Caux Frederic , Akhoundi Mohammad 
Published: November 2020

Abstract

Background
Mycetoma is a chronic granulomatous subcutaneous infection caused by anaerobic pseudofilamentous bacteria or fungi. It is commonly prevalent in tropical and subtropical countries. Men are more susceptible to the disease due to greater participation in agricultural works. Mycetoma commonly involves lower extremities, wherein untreated cases lead to aggressive therapeutic choices, such as amputation of the affected body organs and consequently lifelong disability.

Case presentation
In this report, we present the rare case of a 58-year-old man, originally from Algeria with a left foot chronic tumefaction of 5 years. In the initial clinical examination, mycetoma was diagnosed based on tumefaction and the presence of multiple sinuses with the emission of white grains. The latter was observed via direct examination. The histopathological analysis demonstrated an actinomycetoma caused by bacteria, as the etiological agent. Imaging showed a bone involvement with osteolysis at the levels of 2nd to 4th metatarsal diaphysis. The mycological and bacterial cultures were both negative. For an accurate diagnosis, the obtained grains were subjected to molecular analysis, targeting the 16S-rDNA gene. Molecular identification yielded Actinomadura madurae as the causal agent, and 800/160 mg of trimethoprim/sulfamethoxazole was prescribed twice a day for 1 year, as a treatment.

Conclusion
Considering low information about this disease, especially in non-endemic areas, it is of high importance to enhance the knowledge and awareness of clinicians and healthcare providers, in particular in the countries with immigration issues.
Treating male partners of women with bacterial vaginosis (StepUp): a protocol for a randomised controlled trial to assess the clinical effectiveness of male partner treatment for reducing the risk of BV recurrence
Authors:   on behalf of the StepUp RCT Team, Vodstrcil Lenka A. , Plummer Erica L. , Doyle Michelle , Fairley Christopher K. , McGuiness Colette , Bateson Deborah , Hocking Jane S. , Law Matthew G. , Petoumenos Kathy , Donovan Basil , Chow Eric P. F. , Bradshaw Catriona S. 
Published: November 2020

Abstract
Background
Bacterial vaginosis (BV) is estimated to affect 1 in 3 women globally and is associated with obstetric and gynaecological sequelae. Current recommended therapies have good short-term efficacy but 1 in 2 women experience BV recurrence within 6 months of treatment. Evidence of male carriage of BV-organisms suggests that male partners may be reinfecting women with BV-associated bacteria (henceforth referred to as BV-organisms) and impacting on the efficacy of treatment approaches solely directed to women. This trial aims to determine the effect of concurrent male partner treatment for preventing BV recurrence compared to current standard of care.

Methods
StepUp is an open-label, multicentre, parallel group randomised controlled trial for women diagnosed with BV and their male partner. Women with clinical-BV defined using current gold standard diagnosis methods (≥3 Amsel criteria and Nugent score (NS) = 4–10) and with a regular male partner will be assessed for eligibility, and couples will then be consented. All women will be prescribed oral metronidazole 400 mg twice daily (BID) for 7 days, or if contraindicated, a 7-day regimen of topical vaginal 2% clindamycin. Couples will be randomised 1:1 to either current standard of care (female treatment only), or female treatment and concurrent male partner treatment (7 days of combined antibiotics - oral metronidazole tablets 400 mg BID and 2% clindamycin cream applied topically to the glans penis and upper shaft [under the foreskin if uncircumcised] BID). Couples will be followed for up to 12 weeks to assess BV status in women, and assess the adherence, tolerability and acceptability of male partner treatment. The primary outcome is BV recurrence defined as ≥3 Amsel criteria and NS = 4–10 within 12 weeks of enrolment. The estimated sample size is 342 couples, to detect a 40% reduction in BV recurrence rates from 40% in the control group to 24% in the intervention group within 12 weeks.

Discussion
Current treatments directed solely to women result in unacceptably high rates of BV recurrence. If proven to be effective the findings from this trial will directly inform the development of new treatment strategies to impact on BV recurrence.

Trial registration
The trial was prospectively registered on 12 February 2019 on the Australian and New Zealand Clinical Trial Registry (ACTRN12619000196145, Universal Trial Number: U1111–1228-0106, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=376883&isReview=true).
Adequate antenatal care and ethnicity affect preterm birth in pregnant women living in the tropical rainforest of Suriname
Authors: Baldewsingh G. K. , Jubitana B. C. , van Eer E. D. , Shankar A. , Hindori-Mohangoo A. D. , Covert H. H. , Shi L. , Lichtveld M. Y. , Zijlmans C. W. R. 
Published: November 2020

Abstract

Background
Adequate antenatal care (ANC) services are key for early identification of pregnancy related risk factors and maintaining women’s health during pregnancy. This study aimed to assess the influence of ANC provided by the Medical Mission Primary Health Care Suriname (MMPHCS) and of ethnicity on adverse birth outcomes in Tribal and Indigenous women living in Suriname’s remote tropical rainforest interior.

Method
From April 2017 to December 2018 eligible Tribal and Indigenous women with a singleton pregnancy that received ANC from MMPHCS were included in the study. Data on low birth weight (LBW < 2500 g), preterm birth (PTB < 37 weeks), low Apgar score (< 7 at 5 min), parity (≤1 vs. > 1) and antenatal visits utilization (≥8 vs. < 8) in 15 interior communities were retrospectively analyzed using descriptive statistics, crosstabs and Fisher’s exact tests.

Results
A total of 204 women were included, 100 (49%) were Tribal, mean age was 26 ± 7.2 years and 126 women (62%) had 8 or more ANC visits. One participant had a miscarriage; 22% had adverse birth outcomes: 16 (7.9%) LBW and 30 (14.8%) PTB; 7 women had a child with both PTB and LBW; 5 women had stillbirths. None of the newborns had low Apgar scores. Maternal age, ethnicity, ANC and parity were associated with PTB (χ2 = 8,75, p = 0.003, χ2 = 4,97, p = 0.025, χ2 = 17,45, p < 0.001, χ2 = 11,93, p < 0.001 respectively).

Conclusion
Despite an almost 100% study adherence over one fifth of women that received ANC in the interior of Suriname had adverse birth outcomes, in particular PTB and LBW. Younger nulliparous Indigenous women with less than the recommended 8 ANC visits had a higher risk for PTB. The rate of adverse birth outcomes highlights the need for further research to better assess factors influencing perinatal outcomes and to put strategies in place to improve perinatal outcomes. Exposure assessment of this sub-cohort and neurodevelopment testing of their children is ongoing and will further inform on potential adverse health effects associated with environmental exposures including heavy metals such as mercury and lead.