bluuebunny/crossref_metadata_2025 huggingface dataset:
Modified extreme learning machine based motion control of robotic manipulators
Authors: Kapoor Neha , Ohri Jyoti
Published: January 2020

Precise trajectory tracking is a difficult task due to partially known and unknown dynamics and the disturbances present in the system. For improving the tracking performance of the robotic manipulator, this work proposes a novel PSO optimized kernel based Extreme Learning Machine (PSO-KELM) learning algorithm in which PSO is used to get the optimal values of the free kernel-parameters in KELM. The simulation results represent the good generalized performance and PSO-KELM outperforms the KELM and ELM based control techniques for the manipulator trajectory tracking. Comparative analysis of the proposed control schemes have been done with NN and SVM based controllers and various ELM based variants for the trajectory tracking problem in robotic manipulator.
Research on EEMD for vibration extreme feature preserving of rotating machinery
Authors: Li Sanhua , Tian Chunhua , Wang Chen , Ma Zaichao
Published: January 2020

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

The 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

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

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

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 >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

Pregnant 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

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

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

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

Objectives

To examine whether educational attainment and intelligence have causal effects on risk of Alzheimer’s disease (AD), independently of each other.

Design

Two-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.

Participants

17 008 AD cases and 37 154 controls from the International Genomics of Alzheimer’s Project (IGAP) consortium.

Main outcome measure

Odds ratio (OR) of AD per standardized deviation increase in years of schooling (SD = 3.6 years) and intelligence (SD = 15 points on intelligence test).

Results

There 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).

Conclusions

There 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

This 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

The 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

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.
Length-dependent accumulation of double-stranded RNAs in plastids affects RNA interference efficiency in the Colorado potato beetle
Authors: He Wanwan , Xu Wenbo , Xu Letian , Fu Kaiyun , Guo Wenchao , Bock Ralph , Zhang Jiang
Published: January 2020

Transplastomic potato plants expressing double-stranded RNA (dsRNA) targeted against essential genes of the Colorado potato beetle (CPB) can be lethal to larvae by triggering an RNA interference (RNAi) response. High accumulation levels of dsRNAs in plastids are crucial to confer an efficient RNAi response in the insects. However, whether length and sequence of the dsRNA determine the efficacy of RNAi and/or influence the level of dsRNA accumulation in plastids is not known. We compared the RNAi efficacy of different lengths of dsRNA targeted against the CPB β-Actin gene (ACT) by feeding in vitro-synthesized dsRNAs to larvae. We showed that, while the 60 bp dsRNA induced only a relatively low RNAi response in CPB, dsRNAs of 200 bp and longer caused high mortality and similar larval growth retardation. When the dsRNAs were expressed from the plastid (chloroplast) genome of potato plants, we found that their accumulation were negatively correlated with length. The level of dsRNA accumulation was positively associated with the observed mortality, suppression of larval growth, and suppression of target gene expression. Importantly, transplastomic potato plants expressing the 200 bp dsRNA were better protected from CPB than plants expressing the 297 bp dsRNA, the best-performing line in our previous study. Our results suggest that the length of dsRNAs is an important factor that influences their accumulation in plastids and thus determines the strength of the insecticidal RNAi effect. Our findings will aid the design of optimized dsRNA expression constructs for plant protection by plastid-mediated RNAi.
AON-induced splice-switching and DMPK pre-mRNA degradation as potential therapeutic approaches for Myotonic Dystrophy type 1
Authors: Stepniak-Konieczna Ewa , Konieczny Patryk , Cywoniuk Piotr , Dluzewska Julia , Sobczak Krzysztof
Published: January 2020

Expansion of an unstable CTG repeat in the 3′UTR of the DMPK gene causes Myotonic Dystrophy type 1 (DM1). CUG-expanded DMPK transcripts (CUGexp) sequester Muscleblind-like (MBNL) alternative splicing regulators in ribonuclear inclusions (foci), leading to abnormalities in RNA processing and splicing. To alleviate the burden of CUGexp, we tested therapeutic approach utilizing antisense oligonucleotides (AONs)-mediated DMPK splice-switching and degradation of mutated pre-mRNA. Experimental design involved: (i) skipping of selected constitutive exons to induce frameshifting and decay of toxic mRNAs by an RNA surveillance mechanism, and (ii) exclusion of the alternative exon 15 (e15) carrying CUGexp from DMPK mRNA. While first strategy failed to stimulate DMPK mRNA decay, exclusion of e15 enhanced DMPK nuclear export but triggered accumulation of potentially harmful spliced out pre-mRNA fragment containing CUGexp. Neutralization of this fragment with antisense gapmers complementary to intronic sequences preceding e15 failed to diminish DM1-specific spliceopathy due to AONs’ chemistry-related toxicity. However, intronic gapmers alone reduced the level of DMPK mRNA and mitigated DM1-related cellular phenotypes including spliceopathy and nuclear foci. Thus, a combination of the correct chemistry and experimental approach should be carefully considered to design a safe AON-based therapeutic strategy for DM1.
In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule
Authors: Dey Sougata , Sczepanski Jonathan T
Published: January 2020

The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.
Intrauterine growth restriction, preterm birth and risk of end-stage renal disease during the first 50 years of life
Authors: Gjerde Anna , Lillås Bjørn Steinar , Marti Hans-Peter , Reisæter Anna Varberg , Vikse Bjørn Egil
Published: January 2020

Background

Low birth weight (LBW) is associated with a higher risk of end-stage renal disease (ESRD). The relative impacts of absolute birth weight, birth weight in relation to gestational age and preterm birth are, however, uncertain.

Methods

The Medical Birth Registry of Norway has since 1967 recorded data on all births. All patients with ESRD since 1980 have been registered in the Norwegian Renal Registry. Data from these registries were linked. All individuals registered in the Medical Birth Registry were included and the development of ESRD was used as endpoint in Cox regression statistics. LBW and LBW for gestational age [small for gestational age (SGA)] according to the 10th percentiles were used as the main predictor variables.

Results

Of the 2 679 967 included subjects, 1181 developed ESRD. Compared with subjects without LBW, subjects with LBW had an adjusted hazard ratio (aHR) for ESRD of 1.61 (1.38–1.98). SGA had an aHR of 1.44 (1.22– 1.70). Further analyses showed that as compared with subjects who had none of the risk factors LBW, SGA and preterm birth, subjects with one risk factor had an aHR of 1.05 (0.84–1.31), subjects with two risk factors had an aHR of 1.67 (1.40–1.98) and subjects with three risk factors had an aHR of 2.96 (1.84–4.76).

Conclusions

We conclude that LBW was associated with increased risk for ESRD during the first 50 years. Our analyses add to previous knowledge showing that only subjects with at least two of the risk factors LBW, SGA or preterm birth have increased risk.
Early vascular ageing in chronic kidney disease: impact of inflammation, vitamin K, senescence and genomic damage
Authors: Dai Lu , Schurgers Leon J , Shiels Paul G , Stenvinkel Peter
Published: January 2020

Chronic kidney disease (CKD) is a clinical model of premature ageing characterized by cardiovascular disease, persistent uraemic inflammation, osteoporosis muscle wasting and frailty. The accelerated early vascular ageing (EVA) process mediated by medial vascular calcification (VC) is a hallmark of senescence as well as a strong predictor of cardiovascular morbidity and mortality in the CKD population. Current clinical therapeutic strategies and novel treatments for VC have not yet been proven to prevent or reverse VC progression in patients with CKD. Knowledge of the fundamental mechanism underlying EVA is urgently needed to identify and develop novel and efficient therapeutic targets for VC and EVA. An accumulating body of evidence indicates that deoxyribonucleic acid (DNA) damage–induced cellular senescence and ‘inflammaging’ may largely contribute to such pathological conditions characterized by accelerated EVA. Growing evidence shows that nuclear factor erythroid 2–related factor 2 (NRF2) signalling and vitamin K play a crucial role in counteracting oxidative stress, DNA damage, senescence and inflammaging, whereby NRF2 activation and vitamin K supplementation may provide a novel treatment target for EVA. In this review we discuss the link between senescence and EVA in the context of CKD, with a focus on the role of NRF2 and vitamin K in DNA damage signalling, senescence and inflammaging.
Impact of the implementation of an assisted peritoneal dialysis service on peritoneal dialysis initiation
Authors: Boyer Annabel , Solis-Trapala Ivonne , Tabinor Matthew , Davies Simon J , Lambie Mark
Published: January 2020

Background

There is limited information available on the impact that provision of an assisted peritoneal dialysis (PD) service has on the initiation of PD. The aim of this study was to assess this impact in a centre following initiation of assisted PD in 2011.

Methods

This retrospective, single-centre study analysed 1576 patients incident to renal replacement therapies (RRTs) between January 2002 and 2017. Adjusted Cox regression with a time-varying explanatory variable and a Fine and Gray model were used to examine the effect of assisted PD use on the rates and cumulative incidence of PD initiation, accounting for the non-linear impact of RRT starting time and the competing risks (transplant and death).

Results

Patients starting PD with assistance were older than those starting unassisted: median (interquartile range): 70.0 (61.5–78.3) versus 58.7 (43.8–69.2) years old, respectively. In the adjusted analysis assisted PD service availability was associated with an increased rate of PD initiation [cause-specific hazard ratio (cs-HR) 1.78, 95% confidence interval 1.21–2.61]. During the study period, the rate of starting PD fell before flattening out. Transplantation and death rates increased over time but this did not affect the fall in PD initiation [for each year in the study cs-HR of starting PD 0.95 (0.93–0.98), sub-distribution HR 0.95 (0.94–0.97)].

Conclusions

In a single-centre study, introducing an assisted PD service significantly increased the rate of PD initiation, benefitting older patients most. This offsets a fall in PD usage over time, which was not explained by changes in transplantation or death.
An Integrated Pain Team Model: Impact on Pain-Related Outcomes and Opioid Misuse in Patients with Chronic Pain
Authors: Gibson Carolyn J , Grasso Joseph , Li Yongmei , Purcell Natalie , Tighe Jennifer , Zamora Kara , Nicosia Francesca , Seal Karen H
Published: January 2020

Objective

Biopsychosocial integrated pain team (IPT) care models are being implemented in Veterans Health Administration (VA) and other health care systems to address chronic pain and reduce risks related to long-term opioid therapy, with little evaluation of effectiveness to date. We examined whether IPT improves self-reported pain-related outcomes and opioid misuse.

Design

Single-group quality improvement study.

Setting

Large VA health care system.

Subjects

Veterans with chronic pain (N = 99, 84% male, mean age [SD] = 60 [13] years).

Methods

Using paired t tests and Wilcoxon matched-pairs signed-ranks tests, we examined pain experience (Brief Pain Inventory, Pain Catastrophizing Scale), opioid misuse (Current Opioid Misuse Measure), treatment satisfaction (Pain Treatment Satisfaction Scale), and pain management strategies among patients with chronic pain before and after three or more IPT encounters.

Results

After an average (SD) of 14.3 (9) weeks engaged in IPT, patients reported improvement in pain interference (mean [SD] = 46.0 [15.9] vs 40.5 [16.2], P < 0.001), pain catastrophizing (mean [SD] = 22.9 [13.0] vs 19.3 [14.1], P = 0.01), treatment satisfaction (i.e., “very satisfied” = 13.1% at baseline vs 25.3% at follow-up, P = 0.01), and reduced opioid misuse (mean [SD] = 11.0 [7.5] vs 8.2 [6.1], P = 0.01). Patients reported increased use of integrative (i.e., acupuncture, 11% at baseline vs 26% at follow-up, P < 0.01) and active pain management strategies (i.e., exercise, 8% at baseline vs 16% at follow-up, P < 0.01) and were less likely to use only pharmacological pain management strategies after IPT engagement (19% at baseline vs 5% at follow-up, P < 0.01).

Conclusions

Biopsychosocial, integrated pain care may improve patient-centered outcomes related to opioid misuse and the subjective experience and nonpharmacological self-management of chronic pain.
Optimal Spatial Policies, Geography, and Sorting*
Authors: Fajgelbaum Pablo D , Gaubert Cecile
Published: January 2020

We study optimal spatial policies in a quantitative trade and geography framework with spillovers and spatial sorting of heterogeneous workers. We characterize the spatial transfers that must hold in efficient allocations, as well as labor subsidies that can implement them. There exists scope for welfare-enhancing spatial policies even when spillovers are common across locations. Using data on U.S. cities and existing estimates of the spillover elasticities, we find that the U.S. economy would benefit from a reallocation of workers to currently low-wage cities. The optimal allocation features a greater share of high-skill workers in smaller cities relative to the observed allocation. Inefficient sorting may lead to substantial welfare costs.
Ectopic Expression of a Cell-Wall-Degrading Enzyme-Induced OsAP2/ERF152 Leads to Resistance against Bacterial and Fungal Infection in Arabidopsis
Authors: Pillai Shakuntala E. , Kumar Chandan , Dasgupta Madhumita , Kumar Bipin K. , Vungarala Sridivya , Patel Hitendra K. , Sonti Ramesh V.
Published: January 2020

Pathogen secreted cell-wall-degrading enzymes (CWDEs) induce plant innate immune responses. The expression of rice transcription factor APETALA2/ethylene response factor-152 (OsAP2/ERF152) is enhanced in leaves upon treatment with different CWDEs and upon wounding. Ectopic expression of OsAP2/ERF152 in Arabidopsis leads to induction of immune responses such as callose deposition and upregulation of both salicylic acid- and jasmonic acid/ethylene-responsive defense genes. Arabidopsis transgenics expressing OsAP2/ERF152 exhibited resistance to infections caused by both bacterial and fungal pathogens (Pseudomonas syringae pv. tomato DC3000 and Rhizoctonia solani AG1-IA, respectively). Ectopic expression of OsAP2/ERF152 results in transient activation of mitogen-activated protein kinases 3/6 (MPK3/6), which could be leading to the induction of a broad range immunity in Arabidopsis.
The Role of Rehabilitation in Patients Receiving Hospice and Palliative Care
Authors: Montagnini Marcos , Javier Noelle Marie , Mitchinson Allison
Published: January 2020

Patients receiving palliative and hospice care experience high levels of functional loss, dependency on activities of daily living, and impairment in mobility. Physical disability affects important aspects of life, oftentimes leading to depression, poor quality of life, increased caregiver needs, increased health resource utilization, and institutionalization. Physical strength, the number of hours spent in bed, and the ability to do what one wants are important indicators of quality of life for patients with cancer and their families. Progressive debility with a sense of being a burden has been cited in the literature as a reason for desiring death among these patients. This perception of increased dependence on others serves as a strong predictor for a patient's interest in the physician aid in dying (PAD). This highlights the desire and willingness of most palliative and hospice care patients to remain physically independent during the course of their disease. Several studies have shown that maintaining the most optimal level of functional ability, especially mobility, for as long as possible is one of the main benefits of rehabilitation in the palliative and hospice care settings. Studies demonstrate that rehabilitation in patients receiving hospice and palliative care can reduce the burden of care for families and caregivers and improve patient's quality of life, sense of well-being, as well as control of pain and non-pain symptoms.
An integrated framework for the assessment of inbound supply risk and prioritization of the risk drivers
Authors: K.T. Ramesh , Sarmah Sarada P. , Tarei Pradeep Kumar
Published: January 2020

Purpose

The purpose of this paper is to present a framework for identifying various inbound supply-risk factors and analyzing its indicators considering the contextual relationship between them. This study additionally proposes a framework for developing an overall inbound supply-risk score considering a real-life case of the electronics supply chain (ESC) in the Indian context.

Design/methodology/approach

In total, 32 risk indicators are identified by a systematic literature review approach and are validated by supply chain practitioners/experts and further categorized into six main risk factors. A hybrid multi-criteria decision-making-based DANP (DEMATEL and ANP) framework is employed to develop the overall inbound-supply-risk score (ISRS) and to prioritize the risk indicators. Indian ESC is chosen as a viable case study to demonstrate the effectiveness of the proposed framework.

Findings

The outcomes from the study reveal that the overall ISRS in the ESC is 36 percent and additionally forewarns critical inbound-supply-risk factors such as supplier performance, product, and buyer organization. Further, the study also identifies the most significant risk indicators such as price margin, investment, on-time delivery, order fulfillment and design changes for ESC.

Research limitations/implications

Supply chain practitioners can adopt this framework as a useful inbound supply-risk assessment tool. Moreover, the hybrid framework will address subjectivity and interrelations among various factors through experts’ judgments. The results will assist the managers to have better insights on the critical risk factors and their complicated interrelationships and further strategize action plans to nullify the impact of incoming risks. This study mainly focused on risk identification and assessment of electronics inbound-supply-risk indicators in the Indian context. The framework can be used for other manufacturing and service industries, albeit the results derived are in the context of a developing country.

Originality/value

This paper provides an effective risk assessment framework for the supply chain practitioners/managers to develop a decision-support system for inbound-supply-risk quantification and prioritization of risk factors in the context of the ESC.
Parametric modeling of historical mannequins
Authors: Moskvin Aleksei , Moskvina Mariia , Kuzmichev Victor
Published: January 2020

Purpose

Digital technologies are widely used for digitization of museum and archival heritage and creation of digital, multimedia and online exhibitions, especially in terms of costume history. Digital exhibitions require historical dress forms which were used in the past for costume presentation. The purpose of this paper is to develop a new method for parametric modeling of the nineteenth century dress forms in accordance with fashionable body shape.

Design/methodology/approach

Due to limited number of body measurements in historical sizing tables, it is impossible to redesign the morphology of old fashionable body with high accuracy by means of contemporary CAD. The developed method is based on two sources of information: first, historical sizing tables with body measurements; second, historical corsets. By combining both resources and applying virtual try-on technology, the full anthropometric database about the nineteenth century fashionable body shape has been organized and the parametric model of historical dress form has been generated.

Findings

The digital replica of deformable parametric dress form was created automatically in accordance with the historical sizing systems and the corsets construction. The process of reproduction of a historical dress form has been done with high accuracy due to substantial advantages of contemporary software.

Originality/value

This study shows new way of anthropometric data generating from the construction of close-fitting and compression undergarments. The developed method and the new database can be applied for each type of dress forms which were used in the second part of the nineteenth century to generate its digital replica in virtual reality. The new approach is joining the digital technologies and the professional knowledge as an important part of cultural heritage for studying, recreating and presenting historical costume.
Strategic and operational remanufacturing mental models
Authors: Moosmayer Dirk C. , Abdulrahman Muhammad Dan-Asabe , Subramanian Nachiappan , Bergkvist Lars
Published: January 2020

Purpose

Remanufacturing is the only end-of-life (EOL) treatment process that results in as-new functional and aesthetic quality and warranty. However, applying mental model theory, the purpose of this paper is to argue that the conception of remanufacturing as an EOL process activates an operational mental model (OMM) that connects to resource reuse, environmental concern and cost savings and is thus opposed to a strategic mental model (SMM) that associates remanufacturing with quality improvements and potential price increases.

Design/methodology/approach

The authors support the argument by empirically assessing consumers’ multi-attribute decision process for cars with remanufactured or new engines among 202 car buyers in China. The authors conduct a conjoint analysis and use the results as input to simulate market shares for various markets on which these cars compete.

Findings

The results suggest that consumers on average attribute reduced utility to remanufactured engines, thus in line with the OMM. However, the authors identify a segment accounting for about 30 per cent of the market with preference for remanufactured engines. The fact that this segment has reduced environmental concern supports the SMM idea that remanufactured products can be bought for their quality.

Research limitations/implications

A single-country (China) single-brand (Volkswagen) study is used to support the conceptualised mental models. While this strengthens the internal validity of the results, future research could improve the external validity by using more representative sampling in a wider array of empirical contexts. Moreover, future work could test the theory more explicitly.

Practical implications

By selling cars with remanufactured engines to customers with a SMM that values the at least equal performance of remanufactured products, firms can enhance their profit from remanufactured products. In addition, promoting SMM enables sustainable business models for the sharing economy.

Originality/value

As a community, the authors need to more effectively reflect on shaping mental models that disconnect remanufacturing from analogies that convey inferior quality and performance associations. Firms can overcome reduced utility perceptions not only by providing discounts, i.e. sharing the economic benefits of remanufacturing, but even more by increasing the warranty, thus sharing remanufacturing’s performance benefit and reducing consumers’ risk, a mechanism widely acknowledged in product diffusion but neglected in remanufacturing so far.