bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization and expansion of non-negative matrix factorization
Authors: Lin Xihui , Boutros Paul C. 
Published: January 2020

Abstract
Background
Non-negative matrix factorization (NMF) is a technique widely used in various fields, including artificial intelligence (AI), signal processing and bioinformatics. However existing algorithms and R packages cannot be applied to large matrices due to their slow convergence or to matrices with missing entries. Besides, most NMF research focuses only on blind decompositions: decomposition without utilizing prior knowledge. Finally, the lack of well-validated methodology for choosing the rank hyperparameters also raises concern on derived results.

Results
We adopt the idea of sequential coordinate-wise descent to NMF to increase the convergence rate. We demonstrate that NMF can handle missing values naturally and this property leads to a novel method to determine the rank hyperparameter. Further, we demonstrate some novel applications of NMF and show how to use masking to inject prior knowledge and desirable properties to achieve a more meaningful decomposition.

Conclusions
We show through complexity analysis and experiments that our implementation converges faster than well-known methods. We also show that using NMF for tumour content deconvolution can achieve results similar to existing methods like ISOpure. Our proposed missing value imputation is more accurate than conventional methods like multiple imputation and comparable to missForest while achieving significantly better computational efficiency. Finally, we argue that the suggested rank tuning method based on missing value imputation is theoretically superior to existing methods. All algorithms are implemented in the R package NNLM, which is freely available on CRAN and Github.
Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi
Authors: Bradshaw Michael , Grewe Felix , Thomas Anne , Harrison Cody H. , Lindgren Hanna , Muggia Lucia , St. Clair Larry L. , Lumbsch H. Thorsten , Leavitt Steven D. 
Published: January 2020

AbstractBackgroundRegions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in theRhizoplaca melanophthalmaspecies complex using short reads from high-throughput sequencing.ResultsWe estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny.ConclusionsThe results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For theR. melanophthalmagroup, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in theR. melanophthalmaspecies complex.
A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex
Authors: Kvist Jouni , Athanàsio Camila Gonçalves , Pfrender Michael E. , Brown James B. , Colbourne John K. , Mirbahai Leda 
Published: January 2020

AbstractBackgroundDaphniaspecies reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and femaleDaphniacan be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and maleDaphnia pulexunder controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders.ResultsIn this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, maleDaphniaare dominated with epigenetic modifications that globally promote elevated gene expression, while femaleDaphniaare dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to femaleDaphnia. Furthermore, H3K4me3 modifications are higher in male compared to femaleDaphniain more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to maleDaphniain more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes.ConclusionsThe epigenetic differences between male and female inDaphnia pulexare vast and dominated by changes that promote elevated gene expression in maleDaphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.
Regulatory roles of differentially expressed MicroRNAs in metabolic processes in negative Lens-induced myopia Guinea pigs
Authors: Guo Dadong , Ding Meihua , Song Xiaoli , Sun Yuanyuan , Li Guoping , Li Zonghong , Wei Huixia , Wu Jianfeng , Jiang Wenjun , Bi Hongsheng 
Published: January 2020

Abstract
Background
Myopia is one of the most common vision defects worldwide. microRNAs can regulate the target gene expression, influencing the development of diseases.

Results
To investigate the alterations of microRNA profiling in negative lens-induced myopia (NLIM) guinea pigs and to explore the regulatory role of microRNAs in the occurrence and the development of myopia, we first established the NLIM guinea pig model after induction for 2 weeks. Further, we isolated sclera to purify total messenger RNA (mRNA) in both NLIM and NLIM fellow sclera. Using next generation sequencing technique and bioinformatics analysis, we identified the differentially expressed microRNAs in NLIM guinea pigs, performed the bioinformatics annotation for the differentially expressed microRNAs, and validated the expression of differentially expressed microRNAs. As a result, we successfully established an NLIM model in guinea pigs, identified 27 differentially expressed microRNAs in NLIM guinea pig sclera, including 10 upregulated and 17 downregulated microRNAs. The KEGG annotation showed the main signaling pathways were closely associated with PPAR signaling, pyruvate and propanoate metabolisms, and TGF-beta signaling pathways.

Conclusions
Our findings indicate that the development of myopia is mainly involved in the disorder of metabolic processes in NLIM guinea pigs. The PPAR signaling, pyruvate and propanoate metabolism pathways may play roles in the development of myopia.
Living alone and mortality among older people in Västerbotten County in Sweden: a survey and register-based longitudinal study
Authors: Ng Nawi , Santosa Ailiana , Weinehall Lars , Malmberg Gunnar 
Published: January 2020

Abstract
Background
Living alone is increasingly common and has been depicted as an important cause of mortality. We examined the association between living alone and mortality risks among older men and women in northern Sweden, by linking two unique longitudinal datasets.

Methods
We used the Linnaeus database, which links several population registers on socioeconomic and health. This register-based study included 22,226 men and 23,390 women aged 50 and 60 years in Västerbotten County who had participated in the Västerbotten Intervention Program (VIP) during 1990–2006, with a total of 445,823 person-years of observation. We conducted Cox-proportional hazard regression to assess the risk of living alone on the mortality that was observed between 1990 and 2015, controlling for socio-demographic factors, chronic disease risk factors and access to social capital.

Results
Older men and women who lived alone with no children at home were at a significantly higher risk of death compared to married/cohabiting couples with children at home (with an adjusted hazard ratio of 1.38, 95% CI of 1.26–1.50 in men and 1.27, 95% CI of 1.13–1.42 in women). Living alone was an even stronger factor than the well-established chronic disease risk factors and a lack of access to social capital.

Conclusions
A significant association between living alone and mortality among the older adult population in Sweden was observed. Providing good social support for older people is important in preventing the negative health impact of living alone.
Associations of sleep quality and sleep duration with frailty and pre-frailty in an elderly population Rugao longevity and ageing study
Authors: Sun Xue-Hui , Ma Teng , Yao Shun , Chen Ze-Kun , Xu Wen-Dong , Jiang Xiao-Yan , Wang Xiao-Feng 
Published: January 2020

Abstract
Background
Previous studies suggest that poor sleep quality or abnormal sleep duration may be associated with frailty. Here we test the associations of sleep disturbances with both frailty and pre-frailty in an elderly population.

Methods
Participants included 1726 community-dwelling elders aged 70–87 years. Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep disturbances. Frailty was defined using phenotype criteria. Logistic regression models were used to estimate odds ratio of the associations.

Results
The average PSQI score was 5.4 (SD, 3.1). Overall 43.6% of the participants had poor sleep quality (PSQI> 5), 8.2% had night sleep time ≤ 5 h, and 27.8% had night sleep time ≥ 9 h. The prevalence of frailty and pre-frailty was 9.2 and 52.8%, respectively. The proportions of PSQI> 5 increased with the severity of frailty status (robust: pre-frail: frail, 34.5%: 48%: 56.1%, P < 0.001). After adjustment for multiple potential confounders, poor sleep quality (PSQI> 5) was associated with higher odds of frailty (OR = 1.78, 95% CI 1.19–2.66) and pre-frailty (OR = 1.51, 95% CI 1.20–1.90). Sleep latency, sleep disturbance, and daytime dysfunction components of PSQI measurements were also associated with frailty and pre-frailty. In addition, sleep time 9 h/night was associated with higher odds of frailty and pre-frailty.

Conclusions
We provided preliminary evidences that poor sleep quality and prolonged sleep duration were associated with being frailty and pre-frailty in an elderly population aged 70–87 years. The associations need to be validated in other elderly populations.
Barriers to husbands’ involvement in maternal health care in Sidama zone, Southern Ethiopia: a qualitative study
Authors: Teklesilasie Wondwosen , Deressa Wakgari 
Published: January 2020

Abstract
Background
Husbands’ involvement in maternal care is considered as a crucial step in scaling up women’s utilization of the services. However, the factors related with how husband’s involvement in maternal health care have hardly been studied to date in the study areas. Therefore, this study aimed to explore barriers to husbands’ involvement in maternal health care, in Sidama zone, Southern Ethiopia.

Methods
The study employed a qualitative method. A pre-tested interview guide questions that prepared in English and translated in to Amharic language were used for data collection. The data were collected using focus group discussions, in-depth interviews and key-informants’ interview in April and May 2015. The data were analyzed thematically.

Results
The study identified a range of factors that-deterred husbands to involve in their female partners’ maternal health care. These are childbirth is a natural process, pregnancy and childbirth are women’s business, preference for TBAs’ care and husband’s involvement in pregnancy and birth care is a new idea were identified as barriers for husbands’ involvement in maternal health care, in this study.

Conclusions
A range of factors related with clients’ and service delivery factors’ were identified as barriers to husbands’ involvement in maternal health care. Based on the study findings we recommend a contextual based awareness creation programs about husbands’ involvement in maternal health care need to be established.
Increasing utilisation of perinatal services: estimating the impact of community health worker program in Neno, Malawi
Authors: Kachimanga Chiyembekezo , Dunbar Elizabeth L. , Watson Samuel , Cundale Katie , Makungwa Henry , Wroe Emily B. , Malindi Charles , Nazimera Lawrence , Palazuelos Daniel , Drake Jeanel , Gates Thomas , van den Akker Thomas , Shea Jawaya 
Published: January 2020

Abstract
Background
By 2015, Malawi had not achieved Millennium Development Goal 4, reducing maternal mortality by about 35% from 675 to 439 deaths per 100,000 livebirths. Hypothesised reasons included low uptake of antenatal care (ANC), intrapartum care, and postnatal care. Involving community health workers (CHWs) in identification of pregnant women and linking them to perinatal services is a key strategy to reinforce uptake of perinatal care in Neno, Malawi. We evaluated changes in uptake after deployment of CHWs between March 2014 and June 2016.

Methods
A CHW intervention was implemented in Neno District, Malawi in a designated catchment area of about 3100 women of childbearing age. The pre-intervention period was March 2014 to February 2015, and the post-intervention period was March 2015 to June 2016. A 5-day maternal health training package was delivered to 211 paid and supervised CHWs. CHWs were deployed to identify pregnant women and escort them to perinatal care visits. A synthetic control method, in which a “counterfactual site” was created from six available control facilities in Neno District, was used to evaluate the intervention. Outcomes of interest included uptake of first-time ANC, ANC within the first trimester, four or more ANC visits, intrapartum care, and postnatal care follow-up.

Results
Women enrolled in ANC increased by 18% (95% Credible Interval (CrI): 8, 29%) from an average of 83 to 98 per month, the proportion of pregnant women starting ANC in the first trimester increased by 200% (95% CrI: 162, 234%) from 10 to 29% per month, the proportion of women completing four or more ANC visits increased by 37% (95% CrI: 31, 43%) from 28 to 39%, and monthly utilisation of intrapartum care increased by 20% (95% CrI: 13, 28%) from 85 to 102 women per month. There was little evidence that the CHW intervention changed utilisation of postnatal care (− 37, 95% CrI: − 224, 170%).

Conclusions
In a rural district in Malawi, uptake of ANC and intrapartum care increased considerably following an intervention using CHWs to identify pregnant women and link them to care.
A cross sectional study to determine the prevalence of cough and its impact in patients with lung cancer: a patient unmet need
Authors: Harle Amélie , Molassiotis Alex , Buffin Oliver , Burnham Jack , Smith Jaclyn , Yorke Janelle , Blackhall Fiona H. 
Published: January 2020

Abstract
Background
There is absence of literature related to cough prevalence and its characteristics in lung cancer patients, with information deriving only from broader symptoms occurrence studies. The aims of this study were to provide a snapshot of the prevalence of all-cause-cough in lung cancer patients and to characterise cough in terms of its impact and severity.

Methods
A cross-sectional study recruiting consecutive lung cancer patients over a pre-defined period of time and using cough-specific validated tools in a tertiary referral centre in the UK, including a cough severity VAS and the Manchester Cough in Lung Cancer scale (MCLCS).

Results
Data was collected from 202 patients. All-cause cough prevalence was 57% (through VAS) both in the screened (N = 223) and research (N = 202) population or 67% (through the MCLCS), and cough severity was moderate at a mean of 32 mm (in a 100 mm VAS). Age, sex, smoking status, lung cancer histology, stage and comorbidities were not associated with cough prevalence. The only variable associated with lower cough reports was being ‘on anticancer treatment’; fewer patients on treatment reported a cough (40%) compared to those off treatment (54%) (p = 0.04). The impact of cough (as measured by MCLCS) was also significant (mean score = 22). About 18% of patients felt moderate/severe distress from their cough and about 15% often or always reported disturbed sleep due to coughing. Half the patients felt their cough warranted treatment.

Conclusions
Cough is a common symptom in lung cancer with considerable impact on patients’ lives. Cough presence and severity should regularly be assessed in clinical practice. There is an urgent need to focus on developing more potent antitussive treatments and improve the management of this complex and distressing symptom.
Aqueous humor and serum 25-Hydroxyvitamin D levels in patients with cataracts
Authors: Cho Min-Chul , Kim Rock-Bum , Ahn Ja-Young , Yoo Woong-Sun , Kim Seong-Jae 
Published: January 2020

Abstract
Background
Serum 25-hydroxyvitamin D (25 (OH) D) levels are associated with various pathologic ocular conditions. Few studies have assessed 25 (OH) D concentrations in non-serum specimens, and none to date has assessed 25 (OH) D concentrations in human aqueous humor and their association with ocular diseases. This study investigated the possible correlations between 25 (OH) D concentrations in aqueous humor and serum and whether vitamin D concentrations in aqueous humor were associated with cataract.

Methods
This study prospectively enrolled 136 patients, including 87 with senile cataract and 49 with diabetic cataract, who underwent cataract surgery from January to November 2017. 25 (OH) D was measured in aqueous humor and serum specimens collected from all patients, and their correlation was analyzed statistically. Clinical and laboratory data, including the results of ophthalmologic examinations, were compared in the two groups of cataract patients.

Results
No correlation was observed between 25 (OH) D concentrations in aqueous humor and serum (P = 0.381). 25 (OH) D concentrations in aqueous humor were significantly higher in patients with diabetic than senile cataract (P = 0.006). Multivariate logistic regression analysis showed that the adjusted odds ratio for diabetic cataract for the highest compared with the lowest quartile of 25 (OH) D concentration in aqueous humor was 4.36 ng/ml (95% confidence interval [CI]: 1.33–14.34 ng/ml; P = 0.015). Multivariate linear regression analysis showed that 25(OH) D concentration in aqueous humor was 2.68 ng/ml (95% CI: 0.34–5.01 ng/ml; P = 0.025) higher in patients with diabetic than senile cataract.

Conclusions
25(OH) D concentrations in aqueous humor and serum did not correlate with each other. Higher 25(OH) D level in aqueous humor was associated with diabetic cataract. These findings suggest that studies of vitamin D levels in patients with ocular conditions should include measurements of vitamin D levels in aqueous humor.
Utilization of cervical cancer screening among migrants and non-migrants in Germany: results from a large-scale population survey
Authors: Brzoska Patrick , Aksakal Tuğba , Yilmaz-Aslan Yüce 
Published: January 2020

Abstract
Background
Studies from European and non-European countries have shown that migrants utilize cervical cancer screening less often than non-migrants. Findings from Germany are inconsistent. This can be explained by several limitations of existing investigations, comprising residual confounding and data which is restricted to only some regions of the country. Using data from a large-scale and nationwide population survey and applying the Andersen Model of Health Services Use as the theoretical framework, the aim of the present study was to examine the role that different predisposing, enabling and need factors have for the participation of migrant and non-migrant women in cervical cancer screening in Germany.

Methods
We used data from the ‘German Health Update 2014/2015’ survey on n = 12,064 women ≥20 years of age. The outcome of interest was the participation in cancer screening (at least once in lifetime vs. no participation). The outcome was compared between the three population groups of non-migrants, migrants from EU countries and migrants from non-EU countries. We employed multivariable logistic regression to examine the role of predisposing, enabling and need factors.

Results
Non-EU and EU migrant women reported a lower utilization of cervical cancer screening (50.1 and 52.7%, respectively) than non-migrant women (57.2%). The differences also remained evident after adjustment for predisposing, enabling and need factors. The respective adjusted odds ratios (OR) for non-EU and EU migrants were OR = 0.67 (95%-CI = 0.55–0.81) and OR = 0.80 (95%-CI = 0.66–0.97), respectively. Differences between migrants and non-migrants were particularly pronounced for younger age groups. Self-rated health was associated with participation in screening only in non-migrants, with a poorer health being indicative of a low participation in cancer screening.

Conclusions
The disparities identified are in line with findings from studies conducted in other countries and are indicative of different obstacles this population group encounters in the health system. Implementing patient-oriented health care through diversity-sensitive health services is necessary to support informed decision-making.