bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites
Authors: Gage Hunter L. , Merrick Catherine J. 
Published: March 2020

Abstract
Background
The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium species – both Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families.

Results
The association between var genes and G4-forming motifs was conserved across Laverania, spanning ~ 1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data.

Conclusions
G4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.
Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing
Authors: Zhai Rongrong , Ye Shenghai , Zhu Guofu , Lu Yanting , Ye Jing , Yu Faming , Chu Qiren , Zhang Xiaoming 
Published: March 2020

Abstract
Background
Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire other glyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice.

Results
Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg·ml− 1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L + 1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L + 1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1).

Conclusion
Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate in rice by regulating transcription and metal ions binding. These findings provide a theoretical basis for breeding glyphosate-tolerant rice varieties and for further research on the biogenesis of glyphosate- tolerance in rice.
The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering
Authors: Wang Hongfang , Liu Chunlei , Liu Zhenguo , Wang Ying , Ma Lanting , Xu Baohua 
Published: March 2020

Abstract
Background
The health of honeybee colonies is critical for bee products and agricultural production, and colony health is closely associated with the bacteria in the guts of honeybees. Although colony loss in winter is now the primary restriction in beekeeping, the effects of different sugars as winter food on the health of honeybee colonies are not well understood. Therefore, in this study, the influence of different sugar diets on honeybee gut bacteria during overwintering was examined.

Results
The bacterial communities in honeybee midguts and hindguts before winter and after bees were fed honey, sucrose, and high-fructose syrup as winter-food were determined by targeting the V3-V4 region of 16S rDNA using the Illumina MiSeq platform.
The dominant microbiota in honeybee guts were the phyla Proteobacteria (63.17%), Firmicutes (17.61%; Lactobacillus, 15.91%), Actinobacteria (4.06%; Bifidobacterium, 3.34%), and Bacteroidetes (1.72%). The dominant taxa were conserved and not affected by season, type of overwintering sugar, or spatial position in the gut. However, the relative abundance of the dominant taxa was affected by those factors. In the midgut, microbial diversity of the sucrose group was higher than that of the honey and high-fructose syrup groups, but in the hindgut, microbial diversity of the honey and high-fructose groups was higher than that in the sucrose group. Sucrose increased the relative abundance of Actinobacteria (Bifidobacteriales Bifidobacteriaceae) and Alphaproteobacteria (Rhizobiales and Mitochondria) of honeybee midgut, and honey enriched the Bacteroidetes and Gammaproteobacteria (Pasteurellales) in honeybee hindgut. High-fructose syrup increased the relative abundance of Betaproteobacteria (Neisseriales: Neisseriaceae) of the midgut.

Conclusion
The type of sugar used as winter food affected the relative abundance of the dominant bacterial communities in honeybee guts, not the taxa, which could affect the health and safety of honeybee colonies during overwintering. The presence of the supernal Alphaproteobacteria, Bifidobacteriales, and Lactobacillaceae in the gut of honeybees fed sucrose and cheaper than honey both indicate that sucrose is very suitable as the overwintering food for honeybees.
A multi-centre, parallel-group, randomised controlled trial to assess the efficacy and safety of eurythmy therapy and tai chi in comparison with standard care in chronically ill elderly patients with increased risk of falling (ENTAiER): a trial protocol
Authors: Kienle G. S. , Werthmann P. G. , Grotejohann B. , Kaier K. , Steinbrenner I. , Voigt-Radloff S. , Huber R. 
Published: March 2020

Abstract
Background
In elderly poeple, multimorbidity and polypharmacy increase while sensory, motor and cognitive functions decrease. Falls occur in 30% of people aged 65 years and older at least once per year, with injuries at 10–20%. Reducing falls and enhancing physical, emotional and cognitive capacities are essential for healthy aging despite chronic disease. Eurythmy therapy (EYT) and Tai Chi train balance, mobility and concentrative and sensory capacities.

Methods
In eight trial sites (academic or community hospitals), 550 outpatients aged 65 years and older with chronic disease and increased risk of falling (history of imbalance, Berg Balance Scale (BBS) score ≤ 49) will be randomly assigned (1:1:1) to receive either EYT or Tai Chi (each provided in one-hour group sessions, twice, later once per week plus practice at home, for over 24 weeks) added to standard care or standard care alone. Standard care includes a detailed written recommendation on fall prevention and the visit of a primary care doctor. Seniors living a reclusive life or economically disadvantaged elderly will be particularly addressed. A motivation and communication concept supports the trial participants’ compliance with trial procedures and practicing. Public and patient representatives are involved in the planning and conduction of the trial. Falls will be documented daily in a diary by the participants. These falls as well as injuries and complications will be ascertained during monthly phone visits. The falls efficacy scale, BBS, cognition (MoCA), Mood (GDS-15), quality of life (SF12), instrumental activities of daily living (IADL), use of medical and non-medical services (FIMA) and adherence will be assessed at months 3, 6, and 12 and inner correspondence with practices (ICPH) at month 6. The trial is funded by the Federal Ministry of Education and Research (BMBF 01GL1805).

Discussion
This study will determine whether EYT and Tai Chi reduce falls, injurious falls, fear of falling and healthcare utilisation and improve mobility, cognition, mood, quality of life and functional independence. A reduction of fall risk and fear of falling and an improvement of mobility, autonomy, quality of life, mood, and cognition are highly relevant for older people to cope with aging and diseases and to reduce healthcare costs.

Trail registration
www.drks.de. DRKS00016609. Registered 30th July 2019.
Bacterial otitis media in sub-Saharan Africa: a systematic review and meta-analysis
Authors: Tesfa Tewodros , Mitiku Habtamu , Sisay Mekonnen , Weldegebreal Fitsum , Ataro Zerihun , Motbaynor Birhanu , Marami Dadi , Teklemariam Zelalem 
Published: March 2020

AbstractBackgroundOtitis media is inflammation of the middle ear, comprising a spectrum of diseases. It is the commonest episode of infection in children, which often occurs after an acute upper respiratory tract infection. Otitis media is ranked as the second most important cause of hearing loss and the fifth global burden of disease with a higher incidence in developing worlds like Sub-Saharan Africa and South Asia. Therefore, this systematic review is aimed to quantitatively estimate the current status of bacterial otitis media, bacterial etiology and their susceptibility profile in sub-Saharan Africa.MethodsA literature search was conducted from major databases and indexing services including EMBASE (Ovid interface), PubMed/MEDLINE, Google Scholar, ScienceDirect, Cochrane Library, WHO African Index-Medicus and others. All studies (published and unpublished) addressing the prevalence of otitis media and clinical isolates conducted in sub-Saharan Africa were included. Format prepared in Microsoft Excel was used to extract the data and data was exported to Stata version 15 software for the analyses. Der-Simonian-Laird random-effects model at a 95% confidence level was used for pooled estimation of outcomes. The degree of heterogeneity was presented with I2statistics. Publication bias was presented with funnel plots of standard error supplemented by Begg’s and Egger’s tests. The study protocol is registered on PROSPERO with reference number ID: CRD42018102485 and the published methodology is available fromhttp://www.crd.york.ac.uk/CRD42018102485.ResultsA total of 33 studies with 6034 patients were included in this study. All studies have collected ear swab/discharge samples for bacterial isolation. The pooled isolation rate of bacterial agents from the CSOM subgroup was 98%, patients with otitis media subgroup 87% and pediatric otitis media 86%. A univariate meta-regression analysis indicated the type of otitis media was a possible source of heterogeneity (p-value = 0.001). The commonest isolates wereP. aeruginosa(23–25%),S. aureus(18–27%),Proteusspecies (11–19%) andKlebsiellaspecies. High level of resistance was observed against Ampicillin, Amoxicillin-clavulanate, Cotrimoxazole, Amoxicillin, and Cefuroxime.ConclusionThe analysis revealed that bacterial pathogens likeP. aeruginosaandS. aureusare majorly responsible for otitis media in sub-Saharan Africa. The isolates have a high level of resistance to commonly used drugs for the management of otitis media.
ABCG2 rs2231142 variant in hyperuricemia is modified by SLC2A9 and SLC22A12 polymorphisms and cardiovascular risk factors in an elderly community-dwelling population
Authors: Liu Jia , Yang Wei , Li Yun , Wei Zhanyun , Dan Xiaojuan 
Published: March 2020

Abstract
Background
The ABCG2 rs2231142 single nucleotide polymorphism (SNP) is one of the most significant genetic variants associated with hyperuricemia (HUA) in Asian populations. However, the risk of ABCG2 rs2231142 variants for HUA could interact with other important HUA risk variants and cardiovascular factors. This study investigated the effects of the combined association among ABCG2 rs2231142 and multiple HUA genetic variants or cardiovascular risk factors on HUA risk and serum uric acid (sUA) levels in an elderly Chinese population.

Methods
A total of 1206 participants over 65 years old were enrolled in this study. Physical and laboratory examinations were performed for all participants. The ABCG2 rs2231142, SLC2A9 rs3733591, and SLC22A12 rs893006 SNPs were assayed using a standardized protocol. Logistic regression analysis and liner regression were adjusted respectively to account for the association between ABCG2 rs2231142 and other genetic variants, as well as between cardiovascular risk factors and HUA risk and sUA levels.

Results
The prevalence of HUA was 14.71% in the elderly community-dwelling population. The ABCG2 rs2231142 risk T allele was associated with HUA risk (odds ratio (OR) = 1.63, 95% confidence interval (CI): 1.27–2.11; p = 1.65 × 10− 4) and with increased sUA levels (Beta = 0.16, p = 6.75 × 10− 9) in the whole study population. Linear regression analysis showed that the mean sUA level increased linearly with the number of risk alleles of the three candidate genetic variants (Beta = 0.18, p = 1.94 × 10− 12) The joint effect of the ABCG2 rs2231142 T allele and cardiovascular risk factors (obesity, hypertension and dyslipidemia) was also associated with increased HUA risk and sUA levels. Each copy of the risk T allele was significantly associated with enhanced HUA risk in patients with hypertriglyceridemia (OR = 2.52, 95% CI: 1.33–4.60; p = 0.003) compared to controls.

Conclusion
Our findings reinforce the importance of the ABCG2 rs2231143 variant as a crucial genetic locus for HUA in Chinese populations and demonstrated the combined effects of multiple genetic risk variants and cardiovascular risk exposures on HUA risk and increased sUA level.
Immunological effects of nivolumab immunotherapy in patients with oral cavity squamous cell carcinoma
Authors: Xiong Ying , Neskey David M. , Horton Joshua D. , Paulos Chrystal M. , Knochelmann Hannah M. , Armeson Kent E. , Young M. Rita I. 
Published: March 2020

Abstract
Background
Although checkpoint blockades have become widely used, the immunological impact in cancer patients, especially those with oral cavity squamous cell carcinoma (OCSCC), has not been well studied.

Methods
The present study assessed the immunological impact of anti-PD-1 (nivolumab) treatment in 10 patients with OCSCC. This involved phenotypic analyses of peripheral blood T-cell subpopulations and their expression of immune mediators prior to and following nivolumab treatment. The focus was on immunological effects of treatment without regard to possible clinical responses.

Results
Nivolumab caused a decline in the frequency of blood CD4+ cells but did not affect their expression of IFN-γ. However, nivolumab increased the proportion of CD4+ cells expressing the Treg-supporting factor Foxp3. Nivolumab treatment caused an increase in the proportion of CD8+ cells. While their expression of granzyme B increased, it did not attain significance. Analyses of CD8+ cell subpopulations showed nivolumab caused an increase in levels of unconventional CD8dimCD3+ T-cells. It also caused an increase in expression of granzyme B by these unconventional T-cells as well as by the conventional CD8hiCD3+ cells. The CD8hiCD3+ subpopulation also had a near-significant increase in IFN-γ expression. Treatment with nivolumab had no effect on the levels of the NK containing CD8dimCD3− subpopulation of cells or their expression of IFN-γ or granzyme B.

Conclusions
These results show nivolumab causes opposing effects on CD4+ and CD8+ cell populations, with CD4+ cell levels declining but increasing the proportion of Treg cells, and unconventional CD8+ T-cell levels increasing with increased expression of immune mediators by CD8+ T-cell subpopulations.
Age-related differences in breast cancer mortality according to race/ethnicity, insurance, and socioeconomic status
Authors: San Miguel Yazmin , Gomez Scarlett Lin , Murphy James D. , Schwab Richard B. , McDaniels-Davidson Corinne , Canchola Alison J. , Molinolo Alfredo A. , Nodora Jesse N. , Martinez Maria Elena 
Published: March 2020

Abstract
Background
We assessed breast cancer mortality in older versus younger women according to race/ethnicity, neighborhood socioeconomic status (nSES), and health insurance status.

Methods
The study included female breast cancer cases 18 years of age and older, diagnosed between 2005 and 2015 in the California Cancer Registry. Multivariable Cox proportional hazards modeling was used to generate hazard ratios (HR) of breast cancer specific deaths and 95% confidence intervals (CI) for older (60+ years) versus younger (< 60 years) patients separately by race/ethnicity, nSES, and health insurance status.

Results
Risk of dying from breast cancer was higher in older than younger patients after multivariable adjustment, which varied in magnitude by race/ethnicity (P-interaction< 0.0001). Comparing older to younger patients, higher mortality differences were shown for non-Hispanic White (HR = 1.43; 95% CI, 1.36–1.51) and Hispanic women (HR = 1.37; 95% CI, 1.26–1.50) and lower differences for non-Hispanic Blacks (HR = 1.17; 95% CI, 1.04–1.31) and Asians/Pacific Islanders (HR = 1.15; 95% CI, 1.02–1.31). HRs comparing older to younger patients varied by insurance status (P-interaction< 0.0001), with largest mortality differences observed for privately insured women (HR = 1.51; 95% CI, 1.43–1.59) and lowest in Medicaid/military/other public insurance (HR = 1.18; 95% CI, 1.10–1.26). No age differences were shown for uninsured women. HRs comparing older to younger patients were similar across nSES strata.

Conclusion
Our results provide evidence for the continued disparity in Black-White breast cancer mortality, which is magnified in younger women. Moreover, insurance status continues to play a role in breast cancer mortality, with uninsured women having the highest risk for breast cancer death, regardless of age.
Study protocol of a multicenter phase III randomized controlled trial investigating the efficiency of the combination of neoadjuvant chemotherapy (NAC) and neoadjuvant laparoscopic intraperitoneal hyperthermic chemotherapy (NLHIPEC) followed by R0 gastrectomy with intraoperative HIPEC for advanced gastric cancer (AGC): dragon II trial
Authors: Beeharry Maneesh Kumarsing , Ni Zhen-Tian , Yang Zhong Yin , Zheng Ya Nan , Feng Run Hua , Liu Wen-Tao , Yan Chao , Yao Xue Xin , Li Chen , Yan Min , Zhu Zheng-Gang 
Published: March 2020

Abstract
Background
Even though treatment modalities such as adjuvant systemic radio-chemotherapy and neoadjuvant chemotherapy (NAC) have individually have improved overall survival (OS) and progression-free survival (PFS) rates in advanced Gastric Cancer (AGC), the peritoneum still presides as a common site of treatment failure and disease recurrence. The role of hyperthermic intraperitoneal chemotherapy (HIPEC) has been acknowledged as prophylaxis for peritoneal carcinomatosis (PC) in AGC patients and in this study, we aim at investigating the safety and efficacy of the combination of neoadjuvant laparoscopic HIPEC (NLHIPEC) with NAC in the neoadjuvant phase followed by surgery of curative intent with intraoperative HIPEC followed by adjuvant chemotherapy (AC).

Methods
In this multicenter Phase III randomized controlled trial, 326 patients will be randomly separated into 2 groups into a 1:1 ratio after laparoscopic exploration. The experiment arm will receive the proposed comprehensive Dragon II regimen while the control group will undergo standard R0 D2 followed by 8 cycles of AC with oxaliplatin with S-1 (SOX) regimen. The Dragon II regimen comprises of 1 cycle of NLHIPEC for 60mins at 43 ± 0.5 °C with 80 mg/m2 of Paclitaxel followed by 3 cycles of NAC with SOX regimen and after assessment, standard R0 D2 gastrectomy with intraoperative HIPEC followed by 5 cycles of SOX regimen chemotherapy. The end-points for the study are 5 year PFS, 5 year OS, peritoneal metastasis rate (PMR) and morbidity rate.

Discussion
This study is one of the first to combine NLHIPEC with NAC in the preoperative phase which is speculated to provide local management of occult peritoneal carcinomatosis or peritoneal free cancer cells while NAC will promote tumor downsizing and down-staging. The addition of the intraoperative HIPEC is speculated to manage dissemination due to surgical trauma. Where the roles of intraoperative HIPEC and NAC have individually been investigated, this study provides innovative insight on a more comprehensive approach to management of AGC at high risk of peritoneal recurrence. It is expected that the combination of NLHIPEC with NAC and HIPEC will increase PFS by 15% and decrease PMR after gastrectomy of curative intent.

Trial registration
World Health Organization Clinical Trials - International Registry Platform (WHO-ICTRP) with Registration ID ChiCTR1900024552, Registered Prospectively on the 16th July, 2019.