bluuebunny/crossref_metadata_2025 huggingface dataset:
iRNAD: a computational tool for identifying D modification sites in RNA sequence
Authors: Xu Zhao-Chun , Feng Peng-Mian , Yang Hui , Qiu Wang-Ren , Chen Wei , Lin Hao
Published: April 2019

Motivation

Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA.

Results

We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model.

Availability and implementation

A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.
Electoral Cycles of Tax Performance in Advanced Democracies
Authors: Lami Endrit , Imami Drini
Published: April 2019

It is widely accepted that incumbents in democratic societies may use various economic policies to increase their chances of re-election. But incumbents in the most advanced democracies may be restrained in overtly manipulating economic policy instruments before elections, because more experienced voters could penalize them for such opportunistic behavior. Incumbents may embrace indirect and more ‘camouflaged’ means such as opportunistically relaxing the stance of tax revenue performance before elections, either by laxer collection efforts, additional tax exemptions or preferential treatments, or a combination of these. In this article, we present evidence of election-related cycles in the tax revenue performance of 25 Organization for Economic Co-operation and Development advanced democracies. We empirically analyze the collection effectiveness of Value Added Tax (VAT) around elections. The findings reveal significant deterioration of VAT revenue performance before elections.
Impact of age on cardiovascular drug use in patients with chronic kidney disease
Authors: Villain Cédric , Liabeuf Sophie , Metzger Marie , Combe Christian , Fouque Denis , Frimat Luc , Jacquelinet Christian , Laville Maurice , Briançon Serge , Pisoni Ronald L , Mansencal Nicolas , Stengel Bénédicte , Massy Ziad A
Published: April 2019

Background

Elderly patients with chronic kidney disease (CKD) are often excluded from clinical trials; this may affect their use of essential drugs for cardiovascular complications. We sought to assess the impact of age on cardiovascular drug use in elderly patients with CKD.

Methods

We used baseline data from the Chronic Kidney Disease-Renal Epidemiology and Information Network (CKD-REIN) cohort including 3033 adult patients with CKD Stages 3 and 4. We studied the use of recommended drugs for coronary artery disease (CAD), stroke and atrial fibrillation by age, after adjusting for socio-demographic and clinical conditions.

Results

The patients’ mean age was 66.8 years (mean estimated glomerular filtration rate 32.9 mL/min/1.73 m2). The prevalence of CAD was 24.5% [81.3% receiving antiplatelet agents, 75.6% renin–angiotensin system (RAS) blockers, 65.4% β-blockers and 81.3% lipid-lowering therapy], that of stroke 10.0% (88.8% receiving antithrombotic drugs) and that of atrial fibrillation 11.1% (69.5% receiving oral anticoagulants). Compared with patients aged <65 years, older age (≥65 years) was associated with greater use of antithrombotic drugs in stroke [adjusted odds ratio (aOR) (95% confidence interval) = 2.83 (1.04–7.73) for patients aged (75–84 years)] and less use of RAS blockers [aOR = 0.39 (0.16–0.89) for patients aged ≥85 years], β-blockers [aOR = 0.31 (0.19–0.53) for patients aged 75–84 years] and lipid-lowering therapy [aOR = 0.39 (0.15–1.02) for patients aged ≥85 years, P for trend = 0.01] in CAD. Older age was not associated with less use of antiplatelet agents in CAD or oral anticoagulants in atrial fibrillation.

Conclusions

In patients with CKD, older age per se was not associated with the underuse of antithrombotic drugs but was for other major drugs, with a potential impact on cardiovascular outcomes.
Evaluating School Connectedness of Students with Emotional and Behavioral Disorders
Authors: Marsh Robbie Jordon , Higgins Kyle , Morgan Joseph , Cumming Therese M , Brown Monica , McCreery Michael
Published: April 2019

School connectedness is the extent to which a student feels that adults and peers at school care about his or her overall well-being. Students with emotional and behavioral disorders (EBD) may experience difficulty with developing high levels of school connectedness, which may lead to engagement in health-risk behaviors. The purpose of this study was to determine the levels of school connectedness of students with EBD and compare them with their general education peers. A questionnaire was created for this study with participants attending elementary, middle, and high schools. The results of the analysis indicated that of the four factors of school connectedness (that is, school bonding, school attachment, school engagement, and school climate), the students with EBD reported significantly lower levels of school bonding than did their general education peers. The results indicate that students with EBD experience school differently than their general education peers, particularly in terms of school bonding.
Asymmetry in genitalia is in sync with lateralized mating behavior but not with the lateralization of other behaviors
Authors: Torres-Dowdall Julián , Rometsch Sina J , Aguilera Gastón , Goyenola Guillermo , Meyer Axel
Published: April 2019

Asymmetries in bilateral organisms attract a lot of curiosity given that they are conspicuous departures from the norm. They allow the investigation of the integration at different levels of biological organization. Here we study whether and how behavioral and asymmetrical anatomical traits co-evolved and work together. We ask if asymmetry is determined locally for each trait or at a whole individual level in a species bearing conspicuous asymmetrical genitalia. Asymmetric genitalia evolved in many species; however, in most cases the direction of asymmetry is fixed. Therefore, it has been rarely determined if there is an association between the direction of asymmetry in genitalia and other traits. In onesided livebearer fish of the genus Jenynsia (Cyprinodontiformes, Anablepidae), the anal fin of males is modified into a gonopodium, an intromittent organ that serves to inseminate females. The gonopodium shows a conspicuous asymmetry, with its tip bending either to the left or the right. By surveying 13 natural populations of Jenynsia lineata, we found that both genital morphs are equally common in wild populations. In a series of experiments in a laboratory population, we discovered asymmetry and lateralization for multiple other traits; yet, the degree of integration varied highly among them. Lateralization in exploratory behavior in response to different stimuli was not associated with genital morphology. Interestingly, the direction of genital asymmetry was positively correlated with sidedness of mating preference and the number of neuromasts in the lateral line. This suggests integration of functionally linked asymmetric traits; however, there is no evidence that asymmetry is determined at the whole individual level in our study species.
The extent of citizenship in pre-industrial England, Germany, and the Low Countries
Authors: Minns Chris , Crowston Clare H , De Kerf Raoul , De Munck Bert , Hoogenboom Marcel J , Kissane Christopher M , Prak Maarten , Wallis Patrick H
Published: April 2019

Citizenship was the main vehicle through which urban authorities granted political and economic rights to their communities. This article estimates the size of the citizenry and citizenship rates for over 30 European towns and cities between 1550 and 1849. While the extent of citizenship varied between European regions and by city size, our estimates show that citizenship was more accessible than previously thought.
Statin therapy increases lipoprotein(a) levels
Authors: Tsimikas Sotirios , Gordts Philip L S M , Nora Chelsea , Yeang Calvin , Witztum Joseph L
Published: April 2019

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 < 0.0001), with ratio >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 < 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

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

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

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 >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 (>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

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

California 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

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

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

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 <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 < .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

Intensification 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

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

Neoseiulus 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

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.
Comparative Study of the Antennal Phenotype in Species of the Belminus (Hemiptera: Triatominae) Genus Using Optical and Scanning Electron Microscopy
Authors: Sandoval Ramírez Claudia Magaly , Nieves Blanco Elsa , Esteban Adarme Lida , Angulo Silva Víctor M , Otálora-Luna Fernando , Galvão Cleber , Catalá Silvia
Published: April 2019

The genus Belminus Stål, 1859 is distinguished by markedly entomophagous species. This genus is a poorly studied group of the Triatominae (Jeannel, 1919), which includes hematophagous species that are vectors of Trypanosoma cruzi (Chagas, 1909), the etiological agent of Chagas disease. This study reports for the first time the description of the antennal sensilla of Belminus corredori (Galvão & Angulo, 2003), Belminus herreri (Lent & Wygodzinsky, 1979), and Belminus ferroae (Sandoval, Pabón, Jurberg & Galvão, 2007) nymphs and adults throughout scanning electron microscopy and optical microscopy. Nine morphological types of sensilla were identified in the three species, including bristles I and II, trichobothria, tapered hairs, thin-walled trichoid, thick-walled trichoid, basiconic, campaniform, and coeloconica sensilla. The analysis of the most abundant types of sensilla and their distribution in nymphs and adults shows similarities with the antennal phenotypes described in other Triatominae. Quantitative differences showed the important phenotypic plasticity of this morphological trait in the genus and allowed for the separation of the species in both sexes. These differences were associated with sexual dimorphism and wing condition (macropterous and brachypterous). The role of the antennal phenotype in sexual behavior, its usefulness as a taxonomic tool, and its relationship with the dispersal capacity of these species are discussed.
Effect of Bacillus thuringiensis var. israelensis Sugar Patches on Insecticide Resistant Anopheles gambiae s.l. Adults
Authors: N’do Sévérin , Bayili Koama , Bayili Bazoma , Namountougou Moussa , Sanou Roger , Ouattara Abdoulaye , Dabiré Roch K , Malone David , Ouédraogo Anicet G , Borovsky Joseph , Borovsky Dov , Diabaté Abdoulaye
Published: April 2019

Background

Large distribution of long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) contributed to a significant decrease in malarial mortality. Unfortunately, large insecticide resistance in malaria vectors occurred and is a threat to the future use of these control approaches. The purpose of this study was to explore a new approach for vector control. Patches containing Bacillus thuringiensis var. israelensis (Bti) solubilized Cry toxins mixed with sugar were developed and tested in the laboratory with pyrethroid-resistant Anopheles gambiae s.l. using tunnel tests.

Methods

Mosquitoes were released at 6:00 p.m. into a large tunnel separated by a bed net, perforated with nine holes, from a smaller chamber with a guinea pig. Nine Bti sugar patches (BSPs) were attached to the bed net between the nine holes. Fourteen hours later (8:00 a.m.), mosquitoes were collected from the tunnel and the guinea pig chamber. Live females were kept in cups and were fed a sugar solution (5%) for 72 h and delayed mortality was followed. The results were reported as passing, blood fed and mortality rates.

Results

Mosquito populations that are resistant to the insecticides in the bed net, exhibited high mortality (60%) in the presence of the BSPs. Untreated bed nets with patches in the tunnel test killed 66–95% of the mosquitoes that landed and untreated bed nets were superior to treated bed nets.

Conclusion

BSPs efficiently kill resistant mosquitoes that land on treated and untreated bed nets and thus could ultimately reduce the number of vector-borne malarial mosquitoes.
Using syntax for improving phrase-based SMT in low-resource languages
Authors: Fadaei Hakimeh , Faili Heshaam
Published: April 2019

Data driven approaches for machine translation, such as statistical and neural machine translation, suffer from sparsity when dealing with low-resource languages. In these cases, using other sources of information including linguistic information could alleviate the problem. In this article, we focus on the problem of word ordering in translation from a high-resource to a low-resource language and try to improve the quality by using syntactic information from the high-resource side. We propose some syntactic features based on Tree Adjoining Grammar (TAG) to be employed in a phrase-based SMT model in order to improve the word ordering. In this work, a set of synchronous TAG rules is extracted and used to estimate the probability of the phrase orders suggested by the phrase-based model. The main idea of the article is to handle the word ordering by using the extended domain of locality property of TAG and abstracting the long distance dependencies into a local view, which is a TAG elementary tree. The experiments on English–Persian and English–German translation showed that, by combining the proposed TAG-based reordering features with lexical and hierarchical reordering models, we gain significant improvements over the baseline and in comparison with a neural reordering model and a pre-reordering model.
Cooling in the shade of warped transition discs
Authors: Casassus Simon , Pérez Sebastián , Osses Axel , Marino Sebastián
Published: April 2019

The mass of the gaseous reservoir in young circumstellar discs is a crucial initial condition for the formation of planetary systems, but estimates vary by orders of magnitude. In some discs with resolvable cavities, sharp inner disc warps cast two-sided shadows on the outer rings; can the cooling of the gas as it crosses the shadows bring constraints on its mass? The finite cooling time-scale should result in dust temperature decrements shifted ahead of the optical/IR shadows in the direction of rotation. However, some systems show temperature drops, while others do not. The depth of the drops and the amplitude of the shift depend on the outer disc surface density Σ through the extent of cooling during the shadow crossing time, and also on the efficiency of radiative diffusion. These phenomena may bear observational counterparts, which we describe with a simple 1D model. An application to the HD 142527 disc suggests an asymmetry in its shadows, and predicts a ≳10 deg shift for a massive gaseous disc, with peak Σ > 8.3 g cm−2. Another application to the DoAr 44 disc limits the peak surface density to Σ < 13 g cm−2.
Use of Mentholated Cigarettes and Likelihood of Smoking Cessation in the United States: A Meta-Analysis
Authors: Smith Philip H , Assefa Biruktawit , Kainth Simranpreet , Salas-Ramirez Kaliris Y , McKee Sherry A , Giovino Gary A
Published: April 2019

Introduction

Previous qualitative reviews have summarized evidence of an association between menthol cigarette use and likelihood of smoking cessation. The objective of this meta-analysis was to provide a quantitative summary of effect sizes, their variability, and factors related to the variability in effect size for the association between menthol use and likelihood of smoking cessation.

Methods

We systematically searched Medline, PsycINFO, and Embase for prospective and cross-sectional studies of the association between menthol use and smoking cessation. We analyzed data with random effects meta-analyses and meta-regression.

Results

Our review identified 22 reports from 19 studies of the association between menthol use and cessation. All identified study samples included only US smokers, with one exception that included both Canadian and US smokers. Our overall model did not demonstrate a significant association between menthol use and cessation; however, menthol users were significantly less likely to quit among blacks/African American smokers (odds ratio = 0.88).

Conclusions

Among blacks/African Americans predominantly in the US menthol users have approximately 12% lower odds of smoking cessation compared to non-menthol users. This difference is likely the result of the tobacco industry’s ongoing marketing influence on the black/African American Community, suggesting that a menthol ban may have a unique public health benefit for black/African American smokers by encouraging quitting behavior.

Implications

This study adds a quantitative summary of the association between menthol cigarette use and smoking cessation in the United States. Findings of an association with lower likelihood of cessation among black/African American smokers, likely resulting from the tobacco industry’s marketing influence, support the ban of menthol flavoring as part of a comprehensive tobacco control effort to increase cessation among black/African American smokers.
Smoking Across the Menopausal Transition in a 10-Year Longitudinal Sample: The Role of Sex Hormones and Depressive Symptoms
Authors: Peltier MacKenzie R , Flores José M , Smith Philip H , Roberts Walter , Verplaetse Terril L , Moore Kelly E , Hacker Robyn , Oberleitner Lindsay M , McKee Sherry A
Published: April 2019

Introduction

Current cigarette smoking rates among older women remain problematic, especially given that this population experiences increased smoking-related health consequences. Despite these increased health concerns, little research to date has explored smoking patterns across the menopausal transition (pre-, early-peri-, late-peri-, and postmenopausal) or the effect of unique factors such as sex hormones and depression during this transition.

Methods

This study used 10 yearly waves of data from the Study of Women’s Health Across the Nation, a longitudinal dataset. Data included 1397 women endorsing ever smoking regularly at baseline. Random-effects logistic regression models were used to examine smoking transitions.

Results

Although there were no associations between menopausal transition stage and smoking behavior, increased estradiol was associated with an increased likelihood of quitting regular smoking (eg, transitioning from regular smoking to non-regular or no smoking; odds ratio [OR] = 1.28), whereas increased testosterone was associated with an increased likelihood of relapsing to regular smoking (eg, transitioning from former or nonregular smoking to regular smoking OR = 2.56). Depression was associated with increased likelihood of continued smoking (OR = 0.97) and relapse (OR = 1.03).

Conclusions

The results emphasize the need to develop interventions to target initiated or continued smoking among women across the menopausal transition and specifically highlight the importance of developing treatments that target depressive symptoms in this population. In addition, although singular hormone measures were associated with smoking behavior, there is a need for future study of dynamic changes in hormones, as well as the impact of progesterone on smoking behaviors across the menopausal transition.

Implications

To date, no studies have examined smoking behaviors across the menopausal transition. In this study, although menopausal transition status was not significantly related to transitions in smoking behavior, important relationships between sex hormones and depression were observed. Increased estradiol was associated with an increased likelihood of quitting regular smoking, whereas increased testosterone was associated with an increased likelihood of relapsing to regular smoking behavior. Higher depression scores were related to continued smoking and relapse to regular smoking behavior. These results highlight the need to develop interventions to target smoking cessation among women across the menopausal transition.
Lund’s Fly Myiasis
Authors: Potters Idzi , Huits Ralph
Published: April 2019

A traveler presented with a furuncular skin abscess and periorbital edema. A larva was surgically removed from the abscess and identified as a larva of Cordylobia rodhaini. Myiasis caused by C. rodhaini is called Lund’s fly myiasis and only rarely is reported in humans. After disinfection, the remaining lesion healed without further intervention and the edema resolved.
Innate Immunity Acts as the Major Regulator in Talaromyces marneffei Coinfected AIDS Patients: Cytokine Profile Surveillance During Initial 6-Month Antifungal Therapy
Authors: Dong Rong-Jing , Zhang Yun-Gui , Zhu Lei , Liu Heng-Li , Liu Jun , Kuang Yi-Qun , Wang Rui-Rui , Li Yu-Ye
Published: April 2019

Background

Talaromycosis caused by Talaromyces marneffei infection is a fatal systemic mycosis in immunosuppressed individuals, such as patients with AIDS. Cytokines and immunocytes play a central role against fungus infection. However, how the host immune system responds to infection and treatment has not been reported to date.

Methods

Forty-one Talaromyces marneffei coinfected AIDS patients were followed up, their immunocytes and cytokine profiles were obtained at different antifungal treatment stages, and data on clinical features and laboratory examinations were collected. Correlation analysis was used to identify factors associated with host immunity against Talaromyces marneffei infection in AIDS patients.

Results

Common diseases and conditions of these 41 patients were lymphadenopathy, hepatomegaly, and splenomegaly. CD4+ T cells were extremely low in all of them. Moreover, significant increases of proinflammatory cytokines (IL-12, IL-17A, TNF-α, IFN-γ, IL-18, and IL-1β), anti-inflammatory cytokines (IL-10), and chemokines (IP-10) were observed in talaromycosis before treatment (P < .05), comparing to both AIDS patients and healthy controls. The cytokines IL-6, IL-8, TNF-α, IL-18, IL-17A, IL-7, IP-10, and IL-1β reached peak levels 3 days after initial antifungal therapy, and then gradually decreased. The symptoms of the patients gradually decreased. Furthermore, patients who died showed the highest levels of IL-6, TNF-α, IL-8, IL-1β, and IP-10, which were 1.4- to 164-fold higher than in surviving patients.

Conclusions

Our findings indicate that innate immune-cell-derived cytokines are critical for host defense against AIDS-associated Talaromyces marneffei infection; furthermore, excessive inflammatory cytokines are associated with poor outcomes.
Biosynthesis of Long Chain Alkyl Diols and Long Chain Alkenols inNannochloropsisspp. (Eustigmatophyceae)
Authors: Balzano Sergio , Villanueva Laura , de Bar Marijke , Sahonero Canavesi Diana X , Yildiz Caglar , Engelmann Julia C , Marechal Eric , Lupette Josselin , Sinninghe Damst� Jaap S , Schouten Stefan
Published: April 2019

We investigated potential biosynthetic pathways of long chain alkenols (LCAs), long chain alkyl diols (LCDs), and long chain hydroxy fatty acids (LCHFAs) in Nannochloropsis oceanica and Nannochloropsis gaditana, by combining culturing experiments with genomic and transcriptomic analyses. Incubation of Nannochloropsis spp. in the dark for 1 week led to significant increases in the cellular concentrations of LCAs and LCDs in both species. Consistently, 13C-labelled substrate experiments confirmed that both LCA and LCD were actively produced in the dark from C14–18 fatty acids by either condensation or elongation/hydroxylation, although no enzymatic evidence was found for the former pathway. Nannochloropsis spp. did, however, contain (i) multiple polyketide synthases (PKSs) including one type (PKS-Clade II) that might catalyze incomplete fatty acid elongations leading to the formation of 3-OH-fatty acids, (ii) 3-hydroxyacyl dehydratases (HADs), which can possibly form Δ2/Δ3 monounsaturated fatty acids, and (iii) fatty acid elongases (FAEs) that could elongate 3-OH-fatty acids and Δ2/Δ3 monounsaturated fatty acids to longer products. The enzymes responsible for reduction of the long chain fatty acids to LCDs and LCAs are, however, unclear. A putative wax ester synthase/acyl coenzyme A (acyl-CoA): diacylglycerol acyltransferase is likely to be involved in the esterification of LCAs and LCDs in the cell wall. Our data thus provide useful insights in predicting the biosynthetic pathways of LCAs and LCDs in phytoplankton suggesting a key role of FAE and PKS enzymes.