bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statin therapy increases lipoprotein(a) levels
Authors: Tsimikas Sotirios , Gordts Philip L S M , Nora Chelsea , Yeang Calvin , Witztum Joseph L 
Published: April 2019

Abstract

Aims
Lipoprotein(a) [Lp(a)] is elevated in 20–30% of people. This study aimed to assess the effect of statins on Lp(a) levels.

Methods and results
This subject-level meta-analysis includes 5256 patients (1371 on placebo and 3885 on statin) from six randomized trials, three statin-vs.-placebo trials, and three statin-vs.-statin trials, with pre- and on-treatment (4–104 weeks) Lp(a) levels. Statins included atorvastatin 10 mg/day and 80 mg/day, pravastatin 40 mg/day, rosuvastatin 40 mg/day, and pitavastatin 2 mg/day. Lipoprotein(a) levels were measured with the same validated assay. The primary analysis of Lp(a) is based on the log-transformed data. In the statin-vs.-placebo pooled analysis, the ratio of geometric means [95% confidence interval (CI)] for statin to placebo is 1.11 (1.07–1.14) (P &lt; 0.0001), with ratio &gt;1 indicating a higher increase in Lp(a) from baseline in statin vs. placebo. The mean percent change from baseline ranged from 8.5% to 19.6% in the statin groups and −0.4% to −2.3% in the placebo groups. In the statin-vs.-statin pooled analysis, the ratio of geometric means (95% CI) for atorvastatin to pravastatin is 1.09 (1.05–1.14) (P &lt; 0.0001). The mean percent change from baseline ranged from 11.6% to 20.4% in the pravastatin group and 18.7% to 24.2% in the atorvastatin group. Incubation of HepG2 hepatocytes with atorvastatin showed an increase in expression of LPA mRNA and apolipoprotein(a) protein.

Conclusion
This meta-analysis reveals that statins significantly increase plasma Lp(a) levels. Elevations of Lp(a) post-statin therapy should be studied for effects on residual cardiovascular risk.
Human papillomavirus infection and autoimmune disorders: a tertiary center experience
Authors: Donmez Hanife Guler , Tanacan Atakan , Unal Canan , Fadiloglu Erdem , Onder Sevgen Celik , Portakal Oytun , Beksac M Sinan 
Published: April 2019

ABSTRACT
This study aimed to investigate the relationship between HPV and autoimmune disorders. We retrospectively evaluated 62 women who had HPV-DNA positivity in terms of autoimmune disorders (autoimmune antibody positivity, chronic inflammatory diseases and autoimmune diseases). The patients were divided into two groups according to autoimmune disorder positivity (autoimmune positive (n = 30), autoimmune negative (n = 32)) and compared with each other in terms of single and multiple HPV-DNA types, high and low-risk HPV-DNA types, and Pap smear findings. We determined that 48.4% of the HPV-DNA positive patients had autoimmune disorders. We found that 15 of 62 (24.2%) women had more than one type of HPV and HPV type 16 was the dominant type in this study (58.2%). A total of 27.4% of HPV-DNA positive patients had abnormal cytological findings. There was no statistically significant difference between autoimmune groups in terms of the presence of high-risk HPV types, multiple HPV types and abnormal cytological findings (P = 0.531, P = 0.558 and P = 0.234, respectively). The prevalence of autoimmune disorders was high among HPV-DNA positive women. On the other hand, the rate of high-risk HPV type positivity, multiple HPV infections and cytopathological findings were similar between the autoimmune positive and negative groups.
A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification
Authors: Chung Ren-Hua , Kang Chen-Yu 
Published: April 2019

Abstract

Background
An integrative multi-omics analysis approach that combines multiple types of omics data including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics has become increasing popular for understanding the pathophysiology of complex diseases. Although many multi-omics analysis methods have been developed for complex disease studies, only a few simulation tools that simulate multiple types of omics data and model their relationships with disease status are available, and these tools have their limitations in simulating the multi-omics data.

Results
We developed the multi-omics data simulator OmicsSIMLA, which simulates genomics (i.e., single-nucleotide polymorphisms [SNPs] and copy number variations), epigenomics (i.e., bisulphite sequencing), transcriptomics (i.e., RNA sequencing), and proteomics (i.e., normalized reverse phase protein array) data at the whole-genome level. Furthermore, the relationships between different types of omics data, such as methylation quantitative trait loci (SNPs influencing methylation), expression quantitative trait loci (SNPs influencing gene expression), and expression quantitative trait methylations (methylations influencing gene expression), were modeled. More importantly, the relationships between these multi-omics data and the disease status were modeled as well. We used OmicsSIMLA to simulate a multi-omics dataset for breast cancer under a hypothetical disease model and used the data to compare the performance among existing multi-omics analysis methods in terms of disease classification accuracy and runtime. We also used OmicsSIMLA to simulate a multi-omics dataset with a scale similar to an ovarian cancer multi-omics dataset. The neural network–based multi-omics analysis method ATHENA was applied to both the real and simulated data and the results were compared. Our results demonstrated that complex disease mechanisms can be simulated by OmicsSIMLA, and ATHENA showed the highest prediction accuracy when the effects of multi-omics features (e.g., SNPs, copy number variations, and gene expression levels) on the disease were strong. Furthermore, similar results can be obtained from ATHENA when analyzing the simulated and real ovarian multi-omics data.

Conclusions
OmicsSIMLA will be useful to evaluate the performace of different multi-omics analysis methods. Sample sizes and power can also be calculated by OmicsSIMLA when planning a new multi-omics disease study.
PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers
Authors: Johnson Travis S , Li Sihong , Franz Eric , Huang Zhi , Dan Li Shuyu , Campbell Moray J , Huang Kun , Zhang Yan 
Published: April 2019

Abstract

Background
Long thought “relics” of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene–parent gene relationships without leveraging other homologous genes/pseudogenes.

Results
We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and &gt;40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four “flavors” of CUDAlign-based databases (&gt;462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a “one stop shop” for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers.

Conclusions
Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike.
Community-based risk messaging in Inuvik, Northwest Territories, Canada
Authors: Glass Catherine T R , Giles Audrey R 
Published: April 2019

Abstract
Unintentional injuries are one of the leading causes of death worldwide, yet they are predictable and avoidable events. Community-based approaches to injury prevention are those where researchers and/or injury prevention specialists work alongside the target population to identify injury prevention issues and then co-create strategies that are relevant to the population. Community-based strategies differ from other approaches as they strive to conduct research with, rather than on marginalized groups. A community-based approach to social marketing, injury prevention and risk messaging was applied in Inuvik, Northwest Territories, Canada, to examine and address men’s boating safety behaviours. Community participants identified the need for northern-based safety resources and a community-wide education campaign. As demonstrated through this example, community-based strategies should be considered for injury prevention, as the involvement of local community members may lead to more effective risk messaging that reflects the needs, culture, and experiences of the target group, while promoting healthy behaviours.
Population trends of beach-spawning California grunionLeuresthes tenuismonitored by citizen scientists
Authors: Martin Karen L M , Pierce Emily A , Quach Vincent V , Studer Melissa 
Published: April 2019

AbstractCalifornia Grunion Leuresthes tenuis (Atherinopsidae), an indigenous endemic marine fish, makes spectacular midnight spawning runs onto sandy beaches on the Pacific coast of California and Baja California. In a unique recreational fishery, people capture the fish out of water with bare hands. Grunion hunters are not required to report their catch, and there is no bag limit. California Grunion rarely appear in trawls and do not take a hook, so population status for this species is impossible to obtain by traditional fishery methods. With citizen scientists, the “Grunion Greeters,” we monitored spawning runs along most of their habitat range. California Grunion recently underwent a northward range extension, but runs appear to be declining broadly across the core habitat. Noisy activities of recreational grunion hunters on shore disrupt spawning runs, preventing fish from reproducing before capture. Leuresthes tenuis has been identified as a Key Indicator Species for the South and Central regions of California Marine Protected Areas, and as an indicator species for climate change on beaches. Gear restrictions, license requirements, and a two-month closed season are rarely enforced late at night. We recommend continued monitoring for L. tenuis in California and increased protections for this unique charismatic fish.
Software Application Profile: The Anchored Multiplier calculator—a Bayesian tool to synthesize population size estimates
Authors: Wesson Paul D , McFarland Willi , Qin Cong Charlie , Mirzazadeh Ali 
Published: April 2019

Abstract
Estimating the number of people in hidden populations is needed for public health research, yet available methods produce highly variable and uncertain results. The Anchored Multiplier calculator uses a Bayesian framework to synthesize multiple population size estimates to generate a consensus estimate. Users submit point estimates and lower/upper bounds which are converted to beta probability distributions and combined to form a single posterior probability distribution. The Anchored Multiplier calculator is available as a web browser-based application. The software allows for unlimited empirical population size estimates to be submitted and combined according to Bayes Theorem to form a single estimate. The software returns output as a forest plot (to visually compare data inputs and the final Anchored Multiplier estimate) and a table that displays results as population percentages and counts. The web application ‘Anchored Multiplier Calculator’ is free software and is available at [http://globalhealthsciences.ucsf.edu/resources/tools] or directly at [http://anchoredmultiplier.ucsf.edu/].
International funding for mental health: a review of the last decade
Authors: Liese Bernhard H , Gribble Rebecca S F , Wickremsinhe Marisha N 
Published: April 2019

Abstract
Mental health represents one of the most significant and increasing burdens to global public health. Over the past decade, the once invisible field has gained recognition on the global health agenda and this increased recognition is expected to increase international funding for mental health. Our review found that few studies have been conducted as to the level of international funding for mental health and there is a need for a differentiated assessment. We conducted such an assessment of global development-related assistance for mental health between 2006 and 2016 and established categories to serve as a baseline for future measurement. We found that development assistance specifically dedicated to mental health accounted for just 0.3% of all development assistance for health. Given the limited public expenditure on mental health by national governments in low- and middle-income countries, renewed efforts by the international community and development partners to substantially increase funding for mental health are critical.
Integration of physical abuse clinical decision support at 2 general emergency departments
Authors: Rosenthal Bruce , Skrbin Janet , Fromkin Janet , Heineman Emily , McGinn Tom , Richichi Rudolph , Berger Rachel P 
Published: April 2019

Abstract

Objective
The study sought to develop and evaluate an electronic health record–based child abuse clinical decision support system in 2 general emergency departments.

Materials and Methods
A combination of a child abuse screen, natural language processing, physician orders, and discharge diagnoses were used to identify children &lt;2 years of age with injuries suspicious for physical abuse. Providers received an alert and were referred to a physical abuse order set whenever a child triggered the system. Physician compliance with clinical guidelines was compared before and during the intervention.

Results
A total of 242 children triggered the system, 86 during the preintervention and 156 during the intervention. The number of children identified with suspicious injuries increased 4-fold during the intervention (P &lt; .001). Compliance was 70% (7 of 10) in the preintervention period vs 50% (22 of 44) in the intervention, a change that was not statistically different (P = .55). Fifty-two percent of providers said that receiving the alert changed their clinical decision making. There was no relationship between compliance and provider or patient demographics.

Conclusions
A multifaceted child abuse clinical decision support system resulted in a marked increase in the number of young children identified as having injuries suspicious for physical abuse in 2 general emergency departments. Compliance with published guidelines did not change; we hypothesize that this is related to the increased number of children identified with suspicious, but less serious injuries. These injuries were likely missed preintervention. Tracking compliance with guidelines over time will be important to assess whether compliance increases as physician comfort with evaluation of suspected physical abuse in young children improves.
Evaluation of net protein contribution, methane production, and net returns from beef production as duration of confinement increases in the cow–calf sector1
Authors: Baber Jessica R , Sawyer Jason E , Wickersham Tryon A 
Published: April 2019

AbstractIntensification of cow–calf production may provide a sustainable solution for meeting increasing beef demand in the face of diminishing resources. However, intensification with its greater reliance on cereal grains potentially decreases the upcycling of human-inedible protein into beef. A previously described model was used to evaluate cow–calf intensification on beef’s ability to meet human protein requirements. Four scenarios were compared, based on a 1,000 cow herd: 1) Conventional cow–calf production system (0CON), 2) cows limit-fed in confinement for 4 mo after weaning (4CON), 3) cows limit-fed in confinement for 8 mo after breeding (8CON), or 4) cows limit-fed in confinement year-round (12CON). Changes were not made to either the stocker or feedlot segments of the beef value chain. Net protein contribution (NPC) was calculated by multiplying the ratio of human-edible protein (HeP) in beef produced to HeP in feed by the protein quality ratio. A NPC >1 indicates that the production system is positively contributing to meeting human requirements, whereas a NPC <1 indicates the sector or value chain is competing with humans for HeP. Methane was estimated based on proportion of forage in diet and total methane production was reported per kg HeP. In the cow–calf sector, HeP conversion efficiency (HePCE) decreased from 2,640.83 to 0.37 while methane production decreased from 4.53 to 1.82 kg/kg HeP produced as the length of intensification increased from 0CON to 12CON. Decreased HePCE resulted in NPC values for cow–calf sector of 8,036.80, 4.93, 2.19, and 1.28 for 0CON, 4CON, 8CON, and 12CON, respectively. Protein quality ratio of the entire beef value chain increased from 3.15 to 3.33, while HePCE decreased from 0.99 to 0.39 as length of intensification increased from 0CON to 12CON. For the beef value chain, NPC was 3.11, 2.30, 1.73, and 1.31 for 0CON, 4CON, 8CON, and 12CON, respectively. Across the value chain, confinement of cows for 12 mo decreased enteric methane from 3.05 to 1.53 kg/kg HeP (0CON and 12CON, respectfully). Additionally, profitability of the cow–calf operation decreased from $249.34 to $102.16 per cow as intensification increased. Of confinement scenarios, probability of loss to an operation was least (4%) for 4CON. Feed costs increased by $260.79 per cow for 0CON when drought conditions existed (0COND). Total methane production was reduced by intensification and none of the scenarios evaluated competed with humans for HeP.
The impact of reducing the frequency of animals genotyped at higher density on imputation and prediction accuracies using ssGBLUP1
Authors: Sollero Bruna P , Howard Jeremy T , Spangler Matthew L 
Published: April 2019

Abstract
The largest gains in accuracy in a genomic selection program come from genotyping young selection candidates who have not yet produced progeny and who might, or might not, have a phenotypic record recorded. To reduce genotyping costs and to allow for an increased amount of genomic data to be available in a population, young selection candidates may be genotyped with low-density (LD) panels and imputed to a higher density. However, to ensure that a reasonable imputation accuracy persists overtime, some parent animals originally genotyped at LD must be re-genotyped at a higher density. This study investigated the long-term impact of selectively re-genotyping parents with a medium-density (MD) SNP panel on the accuracy of imputation and on the genetic predictions using ssGBLUP in a simulated beef cattle population. Assuming a moderately heritable trait (0.25) and a population undergoing selection, the simulation generated sequence data for a founder population (100 male and 500 female individuals) and 9,000 neutral markers, considered as the MD panel. All selection candidates from generation 8 to 15 were genotyped with LD panels corresponding to a density of 0.5% (LD_0.5), 2% (LD_2), and 5% (LD_5) of the MD. Re-genotyping scenarios chose parents at random or based on EBV and ranged from 10% of male parents to re-genotyping all male and female parents with MD. Ranges in average imputation accuracy at generation 15 were 0.567 to 0.936, 0.795 to 0.985, and 0.931 to 0.995 for the LD_0.5, LD_2, and LD_5, respectively, and the average EBV accuracies ranged from 0.453 to 0.735, 0.631 to 0.784, and 0.748 to 0.807 for LD_0.5, LD_2, and LD_5, respectively. Re-genotyping parents based on their EBV resulted in higher imputation and EBV accuracies compared to selecting parents at random and these values increased with the size of LD panels. Differences between re-genotyping scenarios decreased when the density of the LD panel increased, suggesting fewer animals needed to be re-genotyped to achieve higher accuracies. In general, imputation and EBV accuracies were greater when more parents were re-genotyped, independent of the proportion of males and females. In practice, the relationship between the density of the LD panel used and the target panel must be considered to determine the number (proportion) of animals that would need to be re-genotyped to enable sufficient imputation accuracy.
Residual Toxicity of Insecticides to Neoseiulus fallacis (Acari: Phytoseiidae) in Apples
Authors: Jamil Raja Zalinda Raja , Vandervoort Christine , Wise John C 
Published: April 2019

AbstractNeoseiulus fallacis (Garman) is a predatory mite that is common in apple orchards and distributed throughout North America. However, N. fallacis may be susceptible to pesticides used for the management of crop pests. This study aimed to evaluate the temporal effects of commonly used insecticides on N. fallacis survival. Neoseiulus fallacis adults were exposed to field-aged residues, and mortality and lethal time were measured over 96 h of exposure. Carbaryl caused high mortality to N. fallacis and the shortest lethal time values (LT50), followed by spinetoram, with moderate lethal time values. Esfenvalerate, acetamiprid, chlorantraniliprole, and novaluron showed little to no lethality to N. fallacis following exposure to dry field-aged residues. The results of this study provide important field-relevant knowledge that is often void from laboratory-based studies, which can aid integrated pest management (IPM) decision-makers in apple production systems.
“Alone in a Sea of Rib-Tips”: Alvenia Fulton, Natural Health, and the Politics of Soul Food1
Authors: Weisse Travis A 
Published: April 2019

Abstract
While the intersection between alternative medicine and the natural food movement in radical white communities of the 1960s and 1970s is well known, the connection between these traditions and the simultaneous revolution in the black foodscape has not received adequate attention. This paper addresses this gap by exploring how an alternative healer and minister from the rural South, Alvenia Fulton, rose to prominence in Chicago during the 1960s and 1970s as one of the major figures in the transformation of the black diet by harnessing the star power of her celebrity clients. Fulton hybridized her apprenticeship in slave herbalism with concepts from white Protestant health food lectures into a corrective nutrition program to bring health and renewal to black communities that were struggling under the burden of structural and medical racism. When, in the 1960s, coronary heart disease peaked for black Americans, soul food became the iconic diet of the civil rights movement. To help her community while respecting their culture, Fulton struck a careful bargain to encourage more black Americans to eat raw, natural, vegetarian food by subtly reimagining the historical contents of the slave diet.