bluuebunny/crossref_metadata_2025_split huggingface dataset:
Putting RFMix and ADMIXTURE to the test in a complex admixed population
Authors: Uren Caitlin , Hoal Eileen G. , Möller Marlo 
Published: April 2020

Abstract
Background
Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios.

Results
Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in admixed populations provides the opportunity for more accurate association analyses.

Conclusion
This study highlights the utility of the extension of computational tools to become more compatible to genetically structured populations, as well as the need to expand the sampling of diverse world-wide populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in world-wide complex admixture scenarios particularly when including these estimates in association studies.
Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties
Authors: Jin Jing , He Ximiao , Silva Elena 
Published: April 2020

Abstract
Background
Stable introns and intronic fragments make up the largest population of RNA in the oocyte nucleus of the frog Xenopus tropicalis. These stable intronic sequence RNAs (sisRNAs) persist through the onset of zygotic transcription when synchronous cell division has ended, and the developing embryo consists of approximately 8000 cells. Despite their abundance, the sequence properties and biological function of sisRNAs are just beginning to be understood.

Results
To characterize this population of non-coding RNA, we identified all of the sisRNAs in the X. tropicalis oocyte nucleus using published high-throughput RNA sequencing data. Our analysis revealed that sisRNAs, have an average length of ~ 360 nt, are widely expressed from genes with multiple introns, and are derived from specific regions of introns that are GC and TG rich, while CpG poor. They are enriched in introns at both ends of transcripts but preferentially at the 3′ end. The consensus binding sites of specific transcription factors such as Stat3 are enriched in sisRNAs, suggesting an association between sisRNAs and transcription factors involved in early development. Evolutionary conservation analysis of sisRNA sequences in seven vertebrate genomes indicates that sisRNAs are as conserved as other parts of introns, but much less conserved than exons.

Conclusion
In total, our results indicate sisRNAs are selected intron regions with distinct properties and may play a role in gene expression regulation.
Genome-wide identification and expression analysis of the NAC transcription factor family in tomato (Solanum lycopersicum) during aluminum stress
Authors: Jin Jian Feng , Wang Zhan Qi , He Qi Yu , Wang Jia Yi , Li Peng Fei , Xu Ji Ming , Zheng Shao Jian , Fan Wei , Yang Jian Li 
Published: April 2020

Abstract
Background
The family of NAC proteins (NAM, ATAF1/2, and CUC2) represent a class of large plant-specific transcription factors. However, identification and functional surveys of NAC genes of tomato (Solanum lycopersicum) remain unstudied, despite the tomato genome being decoded for several years. This study aims to identify the NAC gene family and investigate their potential roles in responding to Al stress.

Results
Ninety-three NAC genes were identified and named in accordance with their chromosome location. Phylogenetic analysis found SlNACs are broadly distributed in 5 groups. Gene expression analysis showed that SlNACs had different expression levels in various tissues and at different fruit development stages. Cycloheximide treatment and qRT-PCR analysis indicated that SlNACs may aid regulation of tomato in response to Al stress, 19 of which were significantly up- or down-regulated in roots of tomato following Al stress.

Conclusion
This work establishes a knowledge base for further studies on biological functions of SlNACs in tomato and will aid in improving agricultural traits of tomato in the future.
Gene expression responses to anti-tuberculous drugs in a whole blood model
Authors: Kwan Philip Kam Weng , Lin Wenwei , Naim Ahmad Nazri Mohamed , Periaswamy Balamurugan , De Sessions Paola Florez , Hibberd Martin L. , Paton Nicholas I. 
Published: April 2020

AbstractBackgroundThere is a need for better tools to evaluate new or repurposed TB drugs. The whole blood bactericidal activity (WBA) assay has been advocated for this purpose. We investigated whether transcriptional responses in the WBA assay resemble TB responses in vivo, and whether the approach might additionally reveal mechanisms of action.Results1422 of 1798 (79%) of differentially expressed genes in WBA incubated with the standard combination of rifampicin, isoniazid, pyrazinamide and ethambutol were also expressed in sputum (P < 0.0001) obtained from patients taking the same combination of drugs; these comprised well-established treatment-response genes. Gene expression profiles in WBA incubated with the standard drugs individually, or with moxifloxacin or faropenem (with amoxicillin and clavulanic acid) clustered by individual drug exposure. Distinct pathways were detected for individual drugs, although only with isoniazid did these relate to known mechanisms of drug action.ConclusionsSubstantial agreement between whole blood cultures and sputum and the ability to differentiate individual drugs suggest that transcriptomics may add value to the whole blood assay for evaluating new TB drugs.
When gratitude and cooperation between friends affect inter-brain connectivity for EEG
Authors: Balconi Michela , Fronda Giulia , Vanutelli Maria Elide 
Published: April 2020

AbstractBackgroundRecently several studies in the psychological and social field have investigated the social function of gift exchange as a useful way for the consolidation of interpersonal and social relationships and the implementation of prosocial behaviors. Specifically, the present research wanted to explore if gift exchange, increased emotional sharing, gratitude and interpersonal cooperation, leading to an improvement in cognitive and behavioral performance. In this regard, neural connectivity and cognitive performance of 14 pairs of friends were recorded during the development of a joint attention task that involved a gift exchange at the beginning or halfway through the task. The moment of gift exchange was randomized within the pairs: for seven couples, it happened at task beginning, for the remaining seven later. Individuals’ simultaneous brain activity was recorded through the use of two electroencephalograms (EEG) systems that were used in hyperscanning.ResultsThe results showed that after gift exchange there was an improvement in behavioral performance in terms of accuracy. For what concerns EEG, instead, an increase of delta and theta activation was observed in the dorsolateral prefrontal cortex (DLPFC) when gift exchange occurred at the beginning of the task. Furthermore, an increase in neural connectivity for delta and theta bands was observed.ConclusionThe present research provides a significant contribution to the exploration of the factors contributing to the strengthening of social bonds, increasing cooperation, gratitude and prosocial behavior.
Influence of measurement principle on total hemoglobin value
Authors: Hayashi Keisuke , Hitosugi Takashi , Kawakubo Yoshifumi , Kitamoto Norihisa , Yokoyama Takeshi 
Published: April 2020

AbstractBackgroundTotal hemoglobin (tHb) measurement is indispensable for determining the patient’s condition (hemorrhagic vs. ischemic) and need for blood transfusion. Conductivity- and absorbance-based measurement methods are used for blood gas analysis of tHb. For conductivity-based measurement, tHb is calculated after converting blood conductivity into a hematocrit value, whereas absorbance measurement is based on light absorbance after red blood cell hemolysis. Due to changes in plasma electrolytes and hemolysis, there is a possibility that conductivity- and absorbance-based measurement methods may cause a difference in tHb.MethodsIn this study, test samples with controlled electrolyte changes and hemolysis were created by adding sodium chloride, distilled water or hemolytic blood to blood samples collected from healthy volunteers, and tHb values were compared between both methods.ResultsConductivity-based measurement revealed reduced tHb value (from 15.49 to 13.05 g/dl) following the addition of 10% sodium chloride, which was also reduced by the addition of hemolysate. Conversely, the addition of distilled water significantly increased tHb value than the expected value. In the absorbance method, there was no significant change in tHb value due to electrolyte change or hemolysis.ConclusionsWe have to recognize unexpected conductivity changes occur at all times when tHb is measured via conductivity- and absorbance-based measurement methods. The absorbance method should be used when measuring tHb in patients with expected blood conductivity changes. However, when using this method, the added contribution of hemoglobin from hemolytic erythrocytes lacking oxygen carrying capacity must be considered. We recognize that discrepancy can occur between conductivity- and absorbance-based measurement methods when tHb is measured.
Correlation between UGT1A1 gene polymorphism and irinotecan chemotherapy in metastatic colorectal cancer: a study from Guangxi Zhuang
Authors: Chen Shaojun , Hua Li , Feng Chengjun , Mo Qia , Wei Mengzhuan , Shen Yongqi , Lin Zhan , Li Guisheng , Xu Junyi , Guo Chengxian , Huang Haixin 
Published: April 2020

Abstract
Background
There are obviously ethnic differences between the UGT1A1 gene polymorphisms. Due to the difference of genetic background and environment, the treatment with colorectal cancer patients of Guangxi Zhuang should not completely follow the Euramerican or Chinese han patients. The study aimed to explore the correlation of UGT1A1 gene polymorphism of Guangxi Zhuang metastatic colorectal cancer (mCRC) with irinotecan -based chemotherapy, in order to develop an individualized irinotecan regimen for mCRC patients of Guangxi Zhuang.

Methods
From June 2013 and June 2015, a total of 406 patients of Guangxi who were histologically diagnosed as metastatic colorectal cancer with 102 patients of this cohort with three generations of Zhuang, and 86 patients that conformed to inclusion and exclusion criteria were competitively enrolled. The distribution of UGT1A1 gene polymorphism was analyzed-retrospectively in all patients. Pyrosequencing method was used to detect the UGT1A1*28 and*6 gene polymorphism in the 86 Guangxi Zhuang mCRC patients. After first-line chemotherapy with FOLFIRI regimen, the relationship between gene polymorphism of UGT1A1 and adverse reactions, and efficacy of Irinotecan were analyzed with χ2 test and Kaplan-Meier method.

Results
UGT1A1*28 wild-type (TA6/6), heterozygous mutant (TA6/7) and homozygous mutant (TA7/7) accounted for 69.8, 30.2 and 0%, respectively. UGT1A1*6 wild type (G/G), heterozygous mutation type (G/A) and homozygous mutant (A/A) accounted for 76.7%, 20.9 and 2.3%, respectively. UGT1A1*28 TA6/7 type could increase the risk of grade 3~4 diarrhea (p = 0.027), which did not increase the risk of grade 3~4 neutropenia (p = 0.092). UGT1A1*6G/A and A/A type could increase the risk of grade 3~4 diarrhea and neutropenia (p = 0.001; p = 0.017). After chemotherapy with FOLFIRI, there was no significant difference in response rate (RR) (p = 0.729; p = 0.745) or in median progression-free survival (mPFS) between the wild-type, mutant treatment of UGT1A1*28 and UGT1A1*6 (7.0 m vs 7.4 m, p = 0.427; 6.9 m vs 7.0 m p = 0.408).

Conclusions
The distribution of UGT1A1*28 and UGT1A1*6 gene polymorphism in Guangxi Zhuang patients were differed from the existing reported of European people and Chinese Han population. The UGT1A1 gene polymorphism with irinotecan chemotherapy-associated diarrhea and neutropenia were closely related. There was no significant association between UGT1A1 gene polymorphism and therapeutic efficacy of irinotecan.
What hinders and facilitates the implementation of nurse-led interventions in dementia care? A scoping review
Authors: Karrer Melanie , Hirt Julian , Zeller Adelheid , Saxer Susi 
Published: April 2020

AbstractBackgroundThe implementation of evidence-based interventions for people with dementia is complex and challenging. However, successful implementation might be a key element to ensure evidence-based practice and high quality of care. There is a need to improve implementation processes in dementia care by better understanding the arising challenges. Thus, the aim of this study was to identify recent knowledge concerning barriers and facilitators to implementing nurse-led interventions in dementia care.MethodsWe performed a scoping review using the methodological framework of Arksey and O’Malley. Studies explicitly reporting on the implementation process and factors influencing the implementation of a nurse-led intervention in dementia care in all settings were included. We searched eight databases from January 2015 until January 2019. Two authors independently selected the studies. For data analysis, we used an inductive approach to build domains and categories.ResultsWe included 26 studies in the review and identified barriers as well as facilitators in five domains: policy (e.g. financing issues, health insurance), organisation (e.g. organisational culture and vision, resources, management support), intervention/implementation (e.g. complexity of the intervention, perceived value of the intervention), staff (e.g. knowledge, experience and skills, attitude towards the intervention), and person with dementia/family (e.g. nature and stage of dementia, response of persons with dementia and their families).ConclusionsBesides general influencing factors for implementing nursing interventions, we identified dementia-specific factors reaching beyond already known barriers and facilitators. A pre-existing person-centred culture of care as well as consistent team cultures and attitudes have a facilitating effect on implementation processes. Furthermore, there is a need for interventions that are highly flexible and sensitive to patients’ condition, needs and behaviour.
Cytokine response in human leptospirosis with different clinical outcomes: a systematic review
Authors: Senavirathna Indika , Rathish Devarajan , Agampodi Suneth 
Published: April 2020

Abstract
Background
Leptospirosis is a neglected zoonotic disease which is a major challenge for clinicians and public health professionals in tropical countries. The cytokine storm during the second (immune) phase is thought to be a major contributory factor for the leptospirosis disease severity. We aim to summarize evidence for cytokine response in leptospirosis at different clinical outcomes.

Methods
A systematic review was carried out to examine the cytokine response in leptospirosis patients using relevant scientific databases. Reference lists of the selected articles were also screened. Quality of the selected studies was assessed by using the National Institutes of Health Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies.

Results
Of the 239 articles retrieved in the initial search, 18 studies fulfilled the selection criteria. India and Thailand have produced the highest number of studies (17% each, n = 3). The majority were comparative cross-sectional studies (72%, n = 13). Overall the quality of the selected studies was fair regardless of few drawbacks such as reporting of sample size and the lack of adjustment for confounders. Microscopic agglutination test (67% - 12/18) and enzyme-linked immunosorbent assay (50% - 9/18) were commonly used for the confirmation of leptospirosis and the measurement of cytokines respectively. IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10 and TNF-α levels were found to be significantly higher in severe than in mild leptospirosis. There were equivocal findings on the association between IL-1β, TNF-α and IL-10/TNF-α ratio and disease severity.

Conclusions
Leptospirosis had a wide-range of elevated cytokines. However, prospective studies in-relation to the onset of the symptom are required to better understand the pathophysiology of cytokine response in leptospirosis.
Diagnosis of severe scrub typhus infection by next-generation sequencing:a case report
Authors: Chen Jie , Zheng Xu-dong , Dai Qi-he , Hong Wei-li , Li You-peng , Chen Rui , Ye Bing-bing , Mo Xiao-jie , Cui Peng , Ruan Zhan-wei 
Published: April 2020

Abstract
Background
Scrub typhus is an acute febrile illness, which was caused by Orientia tsutsugamushi and transmitted through the bite of chiggers. The diagnosis of scrub typhus could be missed diagnosis due to the absence of the pathognomonic eschar.

Case presentation
A 76-year-old man was hospitalized with fever and kidney injury and was diagnosed of hemorrhagic fever with renal syndrome first. However, the situation of the illness deteriorated into refractory septic shock and multiple organ dysfunction rapidly,although the treatment of anti-sepsis was used in 3rd-5th day. Orientia tsutsugamushi was determined to be the causative pathogen by Next-generation sequencing of his plasma sample in 6th day. Then, the patient was treated with doxycycline and azithromycin and recovered quickly.

Conclusions
Next-generation sequencing was a new diagnostic technology and could identify scrub typhus in accurately and fast without the pathognomonic eschar.
Health behaviors of caregivers of childhood cancer survivors: a cross-sectional study
Authors: Cho In Young , Chung Nack-Gyun , Baek Hee Jo , Lee Ji Won , Sung Ki Woong , Shin Dong Wook , Yoo Jung Eun , Song Yun-Mi 
Published: April 2020

Abstract
Background
Caregiving for childhood cancer survivors may be burdensome for caregivers and affect their physical health and health behaviors. However, studies examining health behaviors in caregivers of childhood cancer survivors are scarce. This study aimed to examine health behaviors of caregivers of childhood cancer survivors by comparing them with those of the general population, and analyze associated factors.

Methods
This study included 326 caregivers of childhood cancer survivors recruited from 3 major hospitals in South Korea and 1304 controls from the Korean National Health and Nutritional Examination Survey matched for age, sex, and education level. We compared health behaviors between the two groups by using conditional logistic regression analyses, and investigated factors associated with unhealthy behaviors in caregivers by using multiple logistic regression analyses.

Results
Caregivers were less likely to be physically inactive (aOR: 0.69, 95% CI: 0.51, 0.92) compared to controls, and this was more evident in women (aOR: 0.65, 95% CI: 0.45, 0.94). However, caregivers were more likely to be binge drinkers (aOR: 2.26, 95% CI: 1.73, 2.97), especially if they were men (aOR: 13.59, 95% CI: 8.09, 22.82). Factors associated with unhealthy behaviors in caregivers differed by the type of behavior. Current smoking risk was lower in female caregivers and in those with more comorbidities. Increasing age, female sex, higher education level, and lower household income were associated with lower risk of binge drinking. Higher household income and anxiety were associated with lower risk of physical inactivity, while depression was associated with higher risk of physical inactivity.

Conclusions
Caregivers of childhood cancer survivors were more likely to engage in binge drinking, but less likely to be physically inactive. Strategies to promote adherence to desirable health behaviors in caregivers are needed with consideration of their socioeconomic and clinical factors, such as number of comorbidities.
Trend of disparity between coastland and inland in medical expenditure burden for rural inpatients with malignant tumor in southeast of China from 2007 to 2016
Authors: Fu Rong , Lin Zheng , He Fei , Jiang Yixian , Zheng Zhenquan , Hu Zhijian 
Published: April 2020

Abstract
Background
New Rural Cooperative Medical Scheme (NRCMS) was developed to improve the health security for rural residents. This study aimed to assess the trend of disparity between coastland and inland in medical expenditure burden for rural inpatients with malignant tumor from 2007 to 2016 under the effect of NRCMS.

Methods
The data from medical records of 1,306,895 patients with malignant tumor who had NRCMS in 2932 hospitals was collected. The relative differences [95% confidence intervals (CIs)] between coastland and inland in four medical expense indicators were calculated using generalized linear models to assess the trend of disparity over time.

Results
In total, there were 769,484 (58.88%) coastland patients and 537,411 (41.12%) inland patients. Male and patients aged older than 44 years accounted for 56.87 and 80% of 1,306,895 patients, respectively. After adjusting for gender, age, tumor site and hospital level, coastland patients had higher hospitalization expenses which were all medical expenses incurred during the hospitalization, lower reimbursement ratio and ratio of out-of-pocket expenses to disposable income than inland patients in most years. The surgery expenses of coastland patients were lower than those of inland patients in 2016. The relative differences (95% CIs) between coastland and inland in medical expense indicators were moving closer to 1.0 from 2007 to 2010 among patients without surgery, implying that the disparity between two areas significantly narrowed. The range of change was similar between two areas from 2011 to 2016 whether among patients without or with surgery, implying that the disparity did not significantly change. The disparity between coastland and inland depended on the household income situation. For low-income patients, the differences between two areas in medical expense indicators were not statistically significance in most cases and the disparity between two areas did not significantly change over time.

Conclusions
Under the effect of NRCMS, the medical expenditure burden of rural inpatients reduced but suffering from malignant tumor was still catastrophic. As a whole, the inland patients had heavier medical expenditure burden than coastland patients. Because of economic factors and medical assistance policies, the medical expenditure burden was similar between coastland and inland low-income patients.