bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research on EEMD for vibration extreme feature preserving of rotating machinery
Authors: Li Sanhua , Tian Chunhua , Wang Chen , Ma Zaichao 
Published: January 2020

Abstract
Ensemble Empirical Mode Decomposition (EEMD) has been widely used due to the more advanced processing of mode mixing than Empirical Mode Decomposition (EMD). However, EEMD still suffers mode mixing in the vibration analysis of rotating machinery. It proposes Extremum Feature Preserving Ensemble Empirical Mode Decomposition (EFPEEMD) for the feature extraction of rotor systems in rotating machinery. In the method, a fluctuant variation (FV) index is developed to quantitatively recognize the amplitude of added noise on the basis of the empirical rules in EEMD. The results of a misalignment vibration signal of a rotor system and an inner race defect signal of a rolling bearing show that, the primary vibration modes can be extracted rapidly and independently based on the elimination of the non-stationary and non-linear interference. Moreover, the fluctuant variation index removes the originally manual and empirical steps, thus enhancing the accuracy and automation of EEMD on the basis of preserving the extreme information.
Interspecific Chemical Competition Between Tribolium castaneum and Tribolium confusum (Coleoptera: Tenebrionidae) Reduces Fecundity and Hastens Development Time
Authors: Bullock Marissa , Legault Geoffrey , Melbourne Brett A 
Published: January 2020

AbstractThe flour beetles Tribolium castaneum (Herbst) and Tribolium confusum (du Val) are model organisms for studying the effects of intra- and interspecific competition. Both species are known to compete directly through egg cannibalism and indirectly through the density-dependent release of allelopathic chemicals. To better characterize these indirect interactions, recent work has focused on quantifying the per-capita effects of intraspecific chemical competition. However, the effects of interspecific chemical competition in this system have not previously been estimated. We used experimental microcosms to examine how interspecific chemical secretions affected the reproductive activity and development time of laboratory populations of T. castaneum and T. confusum. We created replicated habitats containing flour medium that had been occupied and chemically ‘conditioned’ by one of the two beetle species across a range of densities, then examined how beetles of the other species responded in terms of the number of eggs laid by females and, separately, the development time of offspring. We found that T. castaneum fecundity was reduced when beetles experienced flour conditioned by T. confusum. In contrast, fecundity of T. confusum was largely unaffected by flour conditioned by T. castaneum. Additionally, we found that interspecific conditioning decreased development times for beetles of both species, particularly the development of larvae to pupae. Our results indicate that interspecific chemical competition impacts the life history of Tribolium species and suggests that models incorporating chemical competition may more accurately describe the biology of flour beetle communities.
InterPep2: global peptide–protein docking using interaction surface templates
Authors: Johansson-Åkhe Isak , Mirabello Claudio , Wallner Björn 
Published: January 2020

Abstract

Motivation
Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability.

Results
InterPep2 is a freely available method for predicting the structure of peptide–protein interactions. Improved performance is obtained by using templates from both peptide–protein and regular protein–protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide–protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 Å LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide–protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 Å LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18).

Availability and implementation
The program is available from: http://wallnerlab.org/InterPep2.

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing
Authors: Li Yu , Wang Sheng , Bi Chongwei , Qiu Zhaowen , Li Mo , Gao Xin 
Published: January 2020

Abstract

Motivation
Nanopore sequencing is one of the leading third-generation sequencing technologies. A number of computational tools have been developed to facilitate the processing and analysis of the Nanopore data. Previously, we have developed DeepSimulator1.0 (DS1.0), which is the first simulator for Nanopore sequencing to produce both the raw electrical signals and the reads. However, although DS1.0 can produce high-quality reads, for some sequences, the divergence between the simulated raw signals and the real signals can be large. Furthermore, the Nanopore sequencing technology has evolved greatly since DS1.0 was released. It is thus necessary to update DS1.0 to accommodate those changes.

Results
We propose DeepSimulator1.5 (DS1.5), all three modules of which have been updated substantially from DS1.0. As for the sequence generator, we updated the sample read length distribution to reflect the newest real reads’ features. In terms of the signal generator, which is the core of DeepSimulator, we added one more pore model, the context-independent pore model, which is much faster than the previous context-dependent one. Furthermore, to make the generated signals more similar to the real ones, we added a low-pass filter to post-process the pore model signals. Regarding the basecaller, we added the support for the newest official basecaller, Guppy, which can support both GPU and CPU. In addition, multiple optimizations, related to multiprocessing control, memory and storage management, have been implemented to make DS1.5 a much more amenable and lighter simulator than DS1.0.

Availability and implementation
The main program and the data are available at https://github.com/lykaust15/DeepSimulator.

Supplementary information
Supplementary data are available at Bioinformatics online.
Antimicrobial Treatment Patterns and Illness Outcome Among United States Patients With Plague, 1942–2018
Authors: Kugeler Kiersten J , Mead Paul S , Campbell Stefanie B , Nelson Christina A 
Published: January 2020

Abstract

Background
Plague is a rare and severe zoonotic illness with limited empiric evidence to support treatment recommendations. We summarize treatment information for all patients with plague in the United States (US) as collected under the auspices of public health surveillance.

Methods
We reviewed use of specific antimicrobials and illness outcome among cases of plague reported from 1942–2018. Antimicrobials were a priori classified into high-efficacy (aminoglycosides, tetracyclines, fluoroquinolones, sulfonamides, and chloramphenicol) and limited-efficacy classes (all others). Logistic regression models were created to describe associations between use of specific antimicrobial classes and illness outcome while controlling for potential confounding factors.

Results
Among 533 total reported plague cases during 1942–2018, 426 (80%) received high-efficacy antimicrobial therapy. Mortality differed significantly among those receiving high-efficacy therapy (9%) and only limited-efficacy therapy (51%). Aminoglycosides and tetracyclines were used more commonly than other classes, and their use was associated with increased odds of survival of plague. Gentamicin use was associated with higher mortality than streptomycin, and aminoglycoside use was linked to higher mortality than for tetracyclines. Fluoroquinolones have been used in treatment of &gt;30% of patients in recent years and limited data suggest clinical effectiveness.

Conclusions
Most US patients with plague have received effective antimicrobials. Aminoglycosides and tetracyclines substantially improve survival of plague, and fluoroquinolones may be equally as effective, yet lack sufficient data. Early recognition and early treatment with any of these antimicrobial classes remain the most important steps to improving survival of plague.
Plague and Pregnancy: Why Special Considerations Are Needed
Authors: Meaney-Delman Dana , Oussayef Nadia L , Honein Margaret A , Nelson Christina A 
Published: January 2020

AbstractPregnant women are an important at-risk population to consider during public health emergencies. These women, like nonpregnant adults, may be faced with the risk of acquiring life-threatening infections during outbreaks or bioterrorism (BT) events and, in some cases, can experience increased severity of infection and higher morbidity compared with nonpregnant adults. Yersinia pestis, the bacterium that causes plague, is a highly pathogenic organism. There are 4 million births annually in the United States, and thus the unique needs of pregnant women and their infants should be considered in pre-event planning for a plague outbreak or BT event.
A negative storage model for precise but compact storage of genetic variation data
Authors: Gonzalez-Calderon Guillermo , Liu Ruizheng , Carvajal Rodrigo , Teer Jamie K 
Published: January 2020

Abstract
Falling sequencing costs and large initiatives are resulting in increasing amounts of data available for investigator use. However, there are informatics challenges in being able to access genomic data. Performance and storage are well-appreciated issues, but precision is critical for meaningful analysis and interpretation of genomic data. There is an inherent accuracy vs. performance trade-off with existing solutions. The most common approach (Variant-only Storage Model, VOSM) stores only variant data. Systems must therefore assume that everything not variant is reference, sacrificing precision and potentially accuracy. A more complete model (Full Storage Model, FSM) would store the state of every base (variant, reference and missing) in the genome thereby sacrificing performance. A compressed variation of the FSM can store the state of contiguous regions of the genome as blocks (Block Storage Model, BLSM), much like the file-based gVCF model. We propose a novel approach by which this state is encoded such that both performance and accuracy are maintained. The Negative Storage Model (NSM) can store and retrieve precise genomic state from different sequencing sources, including clinical and whole exome sequencing panels. Reduced storage requirements are achieved by storing only the variant and missing states and inferring the reference state. We evaluate the performance characteristics of FSM, BLSM and NSM and demonstrate dramatic improvements in storage and performance using the NSM approach.
Characterization of disease-specific chondroitin sulfate nonreducing end accumulation in mucopolysaccharidosis IVA
Authors: Lawrence Roger , Prill Heather , Vachali Preejith P , Adintori Evan G , de Hart Greg , Wang Raymond Y , Burton Barbara K , Pasquali Marzia , Crawford Brett E 
Published: January 2020

Abstract
Morquio syndrome type A, also known as MPS IVA, is a rare autosomal recessive disorder caused by deficiency of N-acetylgalactosamine-6-sulfatase, a lysosomal hydrolase critical in the degradation of keratan sulfate (KS) and chondroitin sulfate (CS). The CS that accumulates in MPS IVA patients has a disease-specific nonreducing end (NRE) terminating with N-acetyl-D-galactosamine 6-sulfate, which can be specifically quantified after enzymatic depolymerization of CS polysaccharide chains. The abundance of N-acetyl-D-galactosamine 6-sulfate over other possible NRE structures is diagnostic for MPS IVA. Here, we describe an assay for the liberation and measurement of N-acetyl-D-galactosamine 6-sulfate and explore its application to MPS IVA patient samples in pilot studies examining disease detection, effects of age and treatment with enzyme-replacement therapy. This assay complements the existing urinary KS assay by quantifying CS-derived substrates, which represent a distinct biochemical aspect of MPS IVA. A more complete understanding of the disease could help to more definitively detect disease across age ranges and more completely measure the pharmacodynamic efficacy of therapies. Larger studies will be needed to clarify the potential value of this CS-derived substrate to manage disease in MPS IVA patients.
Key Performance Indicators for program scale-up and divergent practice styles: a study from NSW, Australia
Authors: Grøn Sisse , Loblay Victoria , Conte Kathleen P , Green Amanda , Innes-Hughes Christine , Milat Andrew , Mitchell Jo , Persson Lina , Thackway Sarah , Williams Mandy , Hawe Penelope 
Published: January 2020

Abstract
Implementing programs at scale has become a vital part of the government response to the continuing childhood obesity epidemic. We are studying the largest ever scale-up of school and child care obesity prevention programs in Australia. Health promotion teams support primary schools and early childhood services in their area to achieve a number of specified, evidence-based practices aimed at organizational changes to improve healthy eating and physical activity. Key performance indicators (KPIs) were devised to track program uptake across different areas—measuring both the proportion of schools and early childhood services reached and the proportion of practices achieved in each setting (i.e. the proportion of sites implementing programs as planned). Using a ‘tight–loose–tight’ model, all local health districts receive funding and are held accountable to reaching KPI implementation targets. However, local teams have independent discretion over how to best use funds to reach targets. Based on 12 months of ethnographic fieldwork and interviews across all districts, this study examines variations in the decision making and strategizing processes of the health promotion teams. We identified three distinct styles of practice: KPI-driven practice (strategic, focussed on targets); relationship-driven practice (focussed on long-term goals); and equity-driven practice (directing resources to sites most in need). In adapting to KPIs, teams make trade-offs and choices. Some teams struggled to balance a moral imperative to attend to equity issues, with a practical need to meet implementation targets. We discuss how models of program scale-up and tracking could possibly evolve to recognize this complexity.
Education, intelligence and Alzheimer’s disease: evidence from a multivariable two-sample Mendelian randomization study
Authors: Anderson Emma L , Howe Laura D , Wade Kaitlin H , Ben-Shlomo Yoav , Hill W David , Deary Ian J , Sanderson Eleanor C , Zheng Jie , Korologou-Linden Roxanna , Stergiakouli Evie , Davey Smith George , Davies Neil M , Hemani Gibran 
Published: January 2020

AbstractObjectivesTo examine whether educational attainment and intelligence have causal effects on risk of Alzheimer’s disease (AD), independently of each other.DesignTwo-sample univariable and multivariable Mendelian randomization (MR) to estimate the causal effects of education on intelligence and vice versa, and the total and independent causal effects of both education and intelligence on AD risk.Participants17 008 AD cases and 37 154 controls from the International Genomics of Alzheimer’s Project (IGAP) consortium.Main outcome measureOdds ratio (OR) of AD per standardized deviation increase in years of schooling (SD = 3.6 years) and intelligence (SD = 15 points on intelligence test).ResultsThere was strong evidence of a causal, bidirectional relationship between intelligence and educational attainment, with the magnitude of effect being similar in both directions [OR for intelligence on education = 0.51 SD units, 95% confidence interval (CI): 0.49, 0.54; OR for education on intelligence = 0.57 SD units, 95% CI: 0.48, 0.66]. Similar overall effects were observed for both educational attainment and intelligence on AD risk in the univariable MR analysis; with each SD increase in years of schooling and intelligence, odds of AD were, on average, 37% (95% CI: 23–49%) and 35% (95% CI: 25–43%) lower, respectively. There was little evidence from the multivariable MR analysis that educational attainment affected AD risk once intelligence was taken into account (OR = 1.15, 95% CI: 0.68–1.93), but intelligence affected AD risk independently of educational attainment to a similar magnitude observed in the univariate analysis (OR = 0.69, 95% CI: 0.44–0.88).ConclusionsThere is robust evidence for an independent, causal effect of intelligence in lowering AD risk. The causal effect of educational attainment on AD risk is likely to be mediated by intelligence.
Citizen-Consumers Wanted: Revitalizing the American Dream in the Face of Economic Recessions, 1981–2012
Authors: Coskuner-Balli Gokcen 
Published: January 2020

AbstractThis article brings the sociological theory of governmentality to bear on a longitudinal analysis of American presidential speeches to theorize the formation of the citizen-consumer subject. This 40-year historical analysis—which extends through four economic recessions and the presidential terms of Ronald Reagan, Bill Clinton, George W. Bush, and Barack Obama—illustrates the ways in which the national mythology of the American Dream has been linked to the political ideology of the state to create the citizen-consumer subject in the United States. The quantitative and qualitative analysis of the data demonstrates 1) the consistent emphasis on responsibility as a key moral value, albeit meshed with ideals of liberalism and libertarianism at different presidential periods; 2) that the presidents iteratively link the neoliberal political ideology and the national mythology of the American Dream through a sophisticated morality play myth, wherein they cast the citizen-consumer as a responsible moral hero on a journey to achieve the American Dream; and 3) that the presidents use three main dispositives—disciplinary, legal, and security—to craft the citizen-consumer subject in their response to economic recessions. These findings extend prior consumer research on consumer subjectivity, consumer moralism, marketplace mythology, and politics of consumption.
Artemisia frigida (Asterales: Asteraceae) Improves the Growth of Grasshopper Calliptamus abbreviatus and Increases the Risk of Damaging Populations
Authors: Huang Xunbing , Ullah Hidayat , Zhang Zehua , Lv Shenjin 
Published: January 2020

AbstractThe grasshopper Calliptamus abbreviatus Ikonn is a significant pest species distributed across the northern Asian grasslands. Grasshopper plagues often result in significant loss to plant biomass and subsequent deterioration of grass quality that leads to economic depletion. To better understand the close relationship between C. abbreviatus and host plant species, a 2-yr study was conducted. Results showed that the relative density of C. abbreviatus was positively correlated with aboveground biomass of the plant Artemisia frigida. We hypothesized that A. frigida, the most favorable food resource, was optimal for growth performance and that the presence of this plant species led to C. abbreviatus plagues. A controlled feeding trial showed that C. abbreviatus had better growth performance (i.e., survival rate, body mass, and growth rate) when fed on A. frigida and this host was preferred over other plant species since the consumption and food utilization efficiency on plant was comparatively greater. These results were consistent with the distribution of C. abbreviatus in the grassland and suggested that the presence of A. frigida significantly improved C. abbreviatus growth performance. These findings will be useful for designing improved pest management strategies in response to grassland vegetation succession due to grazing, climate change, or human interference.
Testing of behavioral and cognitive development in rats after prenatal exposure to 1800 and 2400 MHz radiofrequency fields
Authors: Li Zhi-qiang , Zhang Yuan , Wan Yue-Meng , Zhou Qiong , Liu Chang , Wu Hui-Xin , Mu Yun-Zheng , He Yue-Feng , Rauniyar Ritika , Wu Xi-Nan 
Published: January 2020

Abstract
The objective of the study was to explore the effects of behavioral and cognitive development in rats after prenatal exposure to 1800 and 2400 MHz radiofrequency fields. Pregnant female rats were exposed to radiofrequency fields beginning on the 21st day of pregnancy. The indicators of physiological and behavioral development were observed and measured in the offspring rats: Y maze measured at 3-weeks postnatal, open field at 7-weeks postnatal, and the expression of N-methyl-D-aspartate receptors (NMDARs) measured by reverse transcription-PCR in the hippocampus at 9-weeks postnatal. The body weight of the 1800 MHz group and the 1800 MHz + WiFi group showed a downward trend. The eye opening time of newborn rats was much earlier in the WiFi group than in the control group. Compared to the control group, the overall path length of the 1800 MHz + WiFi group was shortened and the stationary time was delayed. The path length of the WiFi group was shortened and the average velocity was increased in the error arm. The 1800 MHz + WiFi group displayed an increased trend in path length, duration, entry times and stationary time in the central area. In both the 1800 MHz + WiFi and WiFi groups, NR2A and NR2B expression was down-regulated, while NR2D, NR3A and NR3B were up-regulated. Moreover, NR1 and NR2C in the WiFi group were also up-regulated. Prenatal exposure to 1800 MHz and WiFi radiofrequency may affect the behavioral and cognitive development of offspring rats, which may be associated with altered mRNA expression of NMDARs in the hippocampus.
Isolated muscular cystic echinococcosis mimicking neoplasia
Authors: Grandjean Lapierre Simon , Barkati Sapha , Desjardins Michael , Ndao Momar , Libman Michael , Poirier Louise , Mottard Sophie , Désy Delphine , Dufresne Simon-Frédéric 
Published: January 2020

Highlight
Musculoskeletal cystic echinococcosis can present as an isolated disease mimicking neoplasia. Along with albendazole therapy, complete excision avoiding cyst rupture is essential to prevent disease dissemination and hypersensitivity reactions. Conventional epidemiology and molecular typing can help differentiate between domestic and sylvatic strains of echinococcosis in the traveler and migrant population.