bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cross-sectional study on the burden and impact of migraine on work productivity and quality of life in selected workplaces in the Philippines
Authors: Haw Nel Jason , Cabaluna Ian Theodore , Kaw Germaine Erika , Cortez Joanna Feliz , Chua Maria Pamela , Guce Kristel 
Published: October 2020

Abstract
Background
Migraine imposes a substantial personal and economic burden to many working age individuals. This study aimed to evaluate the burden and impact of migraine on work productivity in selected workplaces in the Philippines.

Methods
A cross-sectional survey was conducted among employees suspected or diagnosed with migraine February to May 2020. Volunteer employees were screened for migraine using the ID-Migraine™ test. Eligible employees were tested for migraine severity and impact on work productivity using the Migraine Disability Assessment (MIDAS) questionnaire. Quality of life was measured using the Short Form-36 (SF-36) questionnaire and additional questions on triggers, coping mechanisms, workplace assistance, and health care utilization were asked. Multiple logistic regression was used to identify significant predictors of migraine disability (high – MIDAS Grade III/IV vs. low – MIDAS Grade I/II). Differences in quality of life scores by migraine disability were measured using multiple linear regression. Productivity costs lost to migraine disability were calculated as the number of days lost to migraine multiplied by the self-reported wage rate, and costs according to migraine severity were measured using a two-part generalized linear model.

Results
From around 24,000 employees who were invited to participate in the survey, 954 respondents provided consent and attempted to respond to the survey resulting to a response rate of around 4.1%. A total of 511 positive migraine screens were included in the final sample. Females comprised two-thirds of all positive migraine screens and were more likely to have high migraine disability (odds ratio: 1.60, 95% CI: 1.03–2.49) than males. Those with high migraine disability scored lower on role limitations compared to those with low migraine disability. Stress and looking at computer screens were cited as the top trigger for migraine, while sleeping enough hours and getting a massage were cited as top coping mechanisms. Three in four (77%) visited their company clinic within the past 3 months, which meant that most doctors seen for migraine-related symptoms were general practitioners. Five in six (85%) took medication for migraine, almost all of which were over-the-counter medications. Mean annual productivity costs lost due to migraine disability were PHP27 794 (USD556) per person.

Conclusion
Migraine poses a significant threat to work productivity in the Philippines. Many opportunities, such as disease management and introduction of alternative options for migraine treatment, may be introduced to help address these issues.
Variable selection from a feature representing protein sequences: a case of classification on bacterial type IV secreted effectors
Authors: Zhang Jian , Lv Lixin , Lu Donglei , Kong Denan , Al-Alashaari Mohammed Abdoh Ali , Zhao Xudong 
Published: October 2020

Abstract
Background
Classification of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classification. Many computational methods (namely classifiers) are used for classification on protein sequences according to various encoding approaches. Commonly, protein sequences keep certain labels corresponding to different categories of biological functions (e.g., bacterial type IV secreted effectors or not), which makes protein prediction a fantasy. As to protein prediction, a kernel set of protein sequences keeping certain labels certified by biological experiments should be existent in advance. However, it has been hardly ever seen in prevailing researches. Therefore, unsupervised learning rather than supervised learning (e.g. classification) should be considered. As to protein classification, various classifiers may help to evaluate the effectiveness of different encoding approaches. Besides, variable selection from an encoded feature representing protein sequences is an important issue that also needs to be considered.

Results
Focusing on the latter problem, we propose a new method for variable selection from an encoded feature representing protein sequences. Taking a benchmark dataset containing 1947 protein sequences as a case, experiments are made to identify bacterial type IV secreted effectors (T4SE) from protein sequences, which are composed of 399 T4SE and 1548 non-T4SE. Comparable and quantified results are obtained only using certain components of the encoded feature, i.e., position-specific scoring matix, and that indicates the effectiveness of our method.

Conclusions
Certain variables other than an encoded feature they belong to do work for discrimination between different types of proteins. In addition, ensemble classifiers with an automatic assignment of different base classifiers do achieve a better classification result.
Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau
Authors: Chai Zhi-xin , Xin Jin-wei , Zhang Cheng-fu , Dawayangla  , Luosang  , Zhang Qiang , Pingcuozhandui  , Li Chao , Zhu Yong , Cao Han-wen , Wang Hui , Han Jian-lin , Ji Qiu-mei , Zhong Jin-cheng 
Published: October 2020

Abstract
Background
On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestication, dispersal route, and the divergence of domestic yaks from different areas are poorly understood.

Results
Here, we resequenced the genome of 91 domestic yak individuals from 31 populations and 1 wild yaks throughout China. Using a population genomics approach, we observed considerable genetic variation. Phylogenetic analysis suggested that the earliest domestications of yak occurred in the south-eastern QTP, followed by dispersal to the west QTP and northeast to SiChuang, Gansu, and Qinghai by two routes. Interestingly, we also found potential associations between the distribution of some breeds and historical trade routes such as the Silk Road and Tang-Tibet Ancient Road. Selective analysis identified 11 genes showing differentiation between domesticated and wild yaks and the potentially positively selected genes in each group were identified and compared among domesticated groups. We also detected an unbalanced pattern of introgression among domestic yak, wild yak, and Tibetan cattle.

Conclusions
Our research revealed population genetic evidence for three groups of domestic yaks. In addition to providing genomic evidence for the domestication history of yaks, we identified potential selected genes and introgression, which provide a theoretical basis and resources for the selective breeding of superior characters and high-quality yak.
Transcriptomic analysis reveals the GRAS family genes respond to gibberellin in Salvia miltiorrhiza hairy roots
Authors: Li Wenrui , Liu Chuangfeng , Liu Jingling , Bai Zhenqing , Liang Zongsuo 
Published: October 2020

Abstract
Background
Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes in plants. However, their role on the secondary metabolism regulation has not been investigated.

Results
In this study, we found that gibberellic acid (GA) can promote hairy roots growth and increase the contents of tanshinones and phenolic acids. Transcriptomic sequencing revealed that many genes involved in the secondary metabolism pathway were the GA-responsive. After further analysis of GA signaling pathway genes, which their expression profiles have significantly changed, it was found that the GRAS transcription factor family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza, which can be divided into 10 subfamilies. Thereafter, members of the same subfamily showed similar conserved motifs and gene structures, suggesting possible conserved functions.

Conclusions
Most SmGRAS genes were significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway, also participating in the GA regulation of root growth and secondary metabolism in S. miltiorrhiza.
Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11
Authors: Chen Bai-Ling , Mhuantong Wuttichai , Ho Shih-Hsin , Chang Jo-Shu , Zhao Xin-Qing , Bai Feng-Wu 
Published: October 2020

Abstract
Background
Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications.

Results
We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies.

Conclusions
The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.
Molecular signature comprising 11 platelet-genes enables accurate blood-based diagnosis of NSCLC
Authors: Goswami Chitrita , Chawla Smriti , Thakral Deepshi , Pant Himanshu , Verma Pramod , Malik Prabhat Singh , Jayadeva  , Gupta Ritu , Ahuja Gaurav , Sengupta Debarka 
Published: October 2020

Abstract
Background
Early diagnosis is crucial for effective medical management of cancer patients. Tissue biopsy has been widely used for cancer diagnosis, but its invasive nature limits its application, especially when repeated biopsies are needed. Over the past few years, genomic explorations have led to the discovery of various blood-based biomarkers. Tumor Educated Platelets (TEPs) have, of late, generated considerable interest due to their ability to infer tumor existence and subtype accurately. So far, a majority of the studies involving TEPs have offered marker-panels consisting of several hundreds of genes. Profiling large numbers of genes incur a significant cost, impeding its diagnostic adoption. As such, it is important to construct minimalistic molecular signatures comprising a small number of genes.

Results
To address the aforesaid challenges, we analyzed publicly available TEP expression profiles and identified a panel of 11 platelet-genes that reliably discriminates between cancer and healthy samples. To validate its efficacy, we chose non-small cell lung cancer (NSCLC), the most prevalent type of lung malignancy. When applied to platelet-gene expression data from a published study, our machine learning model could accurately discriminate between non-metastatic NSCLC cases and healthy samples. We further experimentally validated the panel on an in-house cohort of metastatic NSCLC patients and healthy controls via real-time quantitative Polymerase Chain Reaction (RT-qPCR) (AUC = 0.97). Model performance was boosted significantly after artificial data-augmentation using the EigenSample method (AUC = 0.99). Lastly, we demonstrated the cancer-specificity of the proposed gene-panel by benchmarking it on platelet transcriptomes from patients with Myocardial Infarction (MI).

Conclusion
We demonstrated an end-to-end bioinformatic plus experimental workflow for identifying a minimal set of TEP associated marker-genes that are predictive of the existence of cancers. We also discussed a strategy for boosting the predictive model performance by artificial augmentation of gene expression data.
HiCHap: a package to correct and analyze the diploid Hi-C data
Authors: Luo Han , Li Xinxin , Fu Haitao , Peng Cheng 
Published: October 2020

Abstract
Background
In diploid cells, it is important to construct maternal and paternal Hi-C contact maps respectively since the two homologous chromosomes can differ in chromatin three-dimensional (3D) organization. Though previous softwares could construct diploid (maternal and paternal) Hi-C contact maps by using phased genetic variants, they all neglected the systematic biases in diploid Hi-C contact maps caused by variable genetic variant density in the genome. In addition, few of softwares provided quantitative analyses on allele-specific chromatin 3D organization, including compartment, topological domain and chromatin loop.

Results
In this work, we revealed the feature of allele-assignment bias caused by the variable genetic variant density, and then proposed a novel strategy to correct the systematic biases in diploid Hi-C contact maps. Based on the bias correction, we developed an integrated tool, called HiCHap, to perform read mapping, contact map construction, whole-genome identification of compartments, topological domains and chromatin loops, and allele-specific testing for diploid Hi-C data. Our results show that the correction on allele-assignment bias in HiCHap does significantly improve the quality of diploid Hi-C contact maps, which subsequently facilitates the whole-genome identification of diploid chromatin 3D organization, including compartments, topological domains and chromatin loops. Finally, HiCHap also supports the data analysis for haploid Hi-C maps without distinguishing two homologous chromosomes.

Conclusions
We provided an integrated package HiCHap to perform the data processing, bias correction and structural analysis for diploid Hi-C data. The source code and tutorial of software HiCHap are freely available at https://pypi.org/project/HiCHap/.
Significant progressive heterobeltiosis in banana crossbreeding
Authors: Batte Michael , Nyine Moses , Uwimana Brigitte , Swennen Rony , Akech Violet , Brown Allan , Hovmalm Helena Persson , Geleta Mulatu , Ortiz Rodomiro 
Published: October 2020

Abstract
Background
Heterobeltiosis is the phenomenon when the hybrid’s performance is superior to its best performing parent. Banana (Musa spp. AAA) breeding is a tedious, time-consuming process, taking up to two decades to develop a consumer acceptable hybrid. Exploiting heterobeltiosis in banana breeding will help to select breeding material with high complementarity, thus increasing banana breeding efficiency. The aim of this study was therefore to determine and document the level of heterobeltiosis of bunch weight and plant stature in the East African highland bananas, in order to identify potential parents that can be used to produce offspring with desired bunch weight and stature after a few crosses.

Results
This research found significant progressive heterobeltiosis in cross-bred ‘Matooke’ (highland cooking) banana hybrids, also known as NARITAs, when grown together across years with their parents and grandparents in Uganda. Most (all except 4) NARITAs exhibited positive heterobeltiosis for bunch weight, whereas slightly more than half of them had negative heterobeltiosis for stature. The secondary triploid NARITA 17 had the highest heterobeltiosis for bunch weight: 249% versus its ‘Matooke’ grandparent and 136% against its primary tetraploid parent. Broad sense heritability (across three cropping cycles) for yield potential and bunch weight were high (0.84 and 0.76 respectively), while that of plant stature was very low (0.0035). There was a positive significant correlation (P < 0.05) between grandparent heterobeltiosis for bunch weight and genetic distance between parents (r = 0.39, P = 0.036), bunch weight (r = 0.7, P < 0.001), plant stature (r = 0.38, P = 0.033) and yield potential (r = 0.59, P < 0.001). Grandparent heterobeltiosis for plant stature was significantly, but negatively, correlated to the genetic distance between parents (r = − 0.6, P < 0.001).

Conclusions
Such significant heterobeltiosis exhibited for bunch weight is to our knowledge the largest among main food crops. Since bananas are vegetatively propagated, the effect of heterobeltiosis is easily fixed in the hybrids and will not be lost over time after the release and further commercialization of these hybrids.
Hepatic predominant presentation of Kawasaki disease in adolescence case report and review of literature
Authors: Pratap Krishan , Gardner Logan S. , Gillis David , Newman Martin , Wainwright Dana , Prentice Roger 
Published: October 2020

AbstractBackgroundKawasaki Disease (KD) is the most common paediatric vasculitis affecting small to medium arteries. Although the average age of diagnosis is 3.4 years with a well-defined clinical presentation, older patients with KD including adolescent and adult patients demonstrate a less classical presentation with prominent findings including hepatitis, cervical lymphadenopathy, and arthralgia. We describe a case of an adolescent presentation of Kawasaki Disease presenting with a predominantly cholestatic hepatic picture.Case presentationWe describe a case of KD in a 16-year-old Caucasian female with predominately hepatic disease that showed resistance to intravenous immunoglobulin (IVIG). The formal diagnosis of KD was made on her 8th day of symptoms. She displayed classical symptoms commencing with fever, followed by peripheral desquamation, strawberry tongue, cervical lymphadenopathy. She became clinically jaundiced with evidence of hepatic artery narrowing on ultrasound that resolved with treatment. Her disease was biphasic and required further IVIG for non-hepatic symptoms. She did not develop coronary aneurysms.ConclusionSignificant hepatic dysfunction with clinical jaundice is rare in KD without associated gall bladder hydrops and tends to occur in older patients. We describe such a case and review the five described cases in the literature. Diagnostic delay is more common in adolescent patients and given that the prognosis of KD is closely correlated to diagnostic timing and provision of care, it is important to consider Kawasaki Disease in older demographics especially with undiagnosed hepatic disease.
Prospective GERiatric Observational (ProGERO) study: cohort design and preliminary results
Authors: Saraiva Marcos Daniel , Rangel Luís Fernando , Cunha Julia Lusis Lassance , Rotta Thereza Cristina Ariza , Douradinho Christian , Khazaal Eugênia Jatene Bou , Aliberti Márlon Juliano Romero , Avelino-Silva Thiago Junqueira , Apolinario Daniel , Suemoto Claudia Kimie , Jacob-Filho Wilson 
Published: October 2020

Abstract
Background
The demographic changes in Brazil as a result of population aging is one of the fastest in the world. The far-reaching new challenges that come with a large older population are particularly disquieting in low- and middle-income countries (LMICs). Longitudinal studies must be completed in LMICs to investigate the social and biological determinants of aging and the consequences of such demographic changes in their context. Therefore, we designed the Prospective GERiatric Observational (ProGERO) study, a longitudinal study of outpatient older adults in São Paulo, Brazil, to collect data both on aging and chronic diseases, and investigate characteristics associated with adverse outcomes in this population.

Methods
The ProGERO study takes place in a geriatric outpatient clinic in the largest academic medical center in Latin America. We performed baseline health examinations in 2017 and will complete subsequent in-person visits every 3 years when new participants will also be recruited. We will use periodic telephone interviews to collect information on the outcomes of interest between in-person visits. The baseline evaluation included data on demographics, medical history, physical examination, and comprehensive geriatric assessment (CGA; including multimorbidity, medications, social support, functional status, cognition, depressive symptoms, nutritional status, pain assessment, frailty, gait speed, handgrip strength, and chair-stands test). We used a previously validated CGA-based model to rank participants according to mortality risk (low, medium, high). Our selected outcomes were falls, disability, health services utilization (emergency room visits and hospital admissions), institutionalization, and death. We will follow participants for at least 10 years.

Results
We included 1336 participants with a mean age of 82 ± 8 years old. Overall, 70% were women, 31% were frail, and 43% had a Charlson comorbidity index score ≥ 3. According to our CGA-based model, the incidence of death in 1 year varied significantly across categories (low-risk = 0.6%; medium-risk = 7.4%; high-risk = 17.5%; P < 0.001).

Conclusion
The ProGERO study will provide detailed clinical data and explore the late-life trajectories of outpatient older patients during a follow-up period of at least 10 years. Moreover, the study will substantially contribute to new information on the predictors of aging, senescence, and senility, particularly in frail and pre-frail outpatients from an LMIC city.