bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macronutrient Supplements in Preterm and Small-for-Gestational-Age Animals: A Systematic Review and Meta-analysis
Authors: Amissah Emma , Lin Luling , Gamble Gregory D , Crowther Caroline A. , Bloomfield Frank H. , Harding Jane E. 
Published: October 2019

AbstractEarly macronutrient supplementation in preterm and/or small-for-gestational-age (SGA) infants may improve growth but have detrimental effects on later cardio-metabolic health which may be sex-specific. We systematically reviewed the long-term effects of early macronutrient supplementation in preterm and SGA animals and whether these differ by sex. Using Cochrane Neonatal and SYRCLE methodologies we included random or quasi-random studies that allocated non-human mammals to macronutrient supplements or no supplements between birth and weaning and assessed post-weaning outcomes. We used random-effects models to calculate standardized mean differences (SMD) with 95% confidence intervals (CIs). Six studies provided low to very-low-quality evidence that macronutrient supplementation increased weight in juvenile rats (SMD; 95% CI: 2.13; 1.00, 3.25; 1 study, n = 24), increased leptin concentrations in older adults (1.31; 0.12, 2.51; 1 study, n = 14 male rats), but decreased leptin concentrations in young adults (−1.13; −2.21, −0.05; 1 study, n = 16 female rats) and improved spatial learning and memory (qualitative data; 1 study). There was no evidence of sex-specific effects and no overall effect on length, serum lipids, body composition, HOMA-IR, or blood pressure. Macronutrient supplements may affect later growth, metabolism, and neurodevelopment of preterm and SGA animals, but evidence is limited and low quality.
Mitochondrial reactive oxygen species generation in blood cells is associated with disease severity and exercise intolerance in heart failure patients
Authors: Shirakawa Ryosuke , Yokota Takashi , Nakajima Takayuki , Takada Shingo , Yamane Miwako , Furihata Takaaki , Maekawa Satoshi , Nambu Hideo , Katayama Takashi , Fukushima Arata , Saito Akimichi , Ishimori Naoki , Dela Flemming , Kinugawa Shintaro , Anzai Toshihisa 
Published: October 2019

AbstractSystemic oxidative stress plays a key role in the development of chronic heart failure (CHF). We tested the hypothesis that mitochondrial reactive oxygen species (ROS) generation in circulating peripheral blood mononuclear cells (PBMCs) contributes to CHF progression. A total of 31 patients who had a history of hospital admission due to worsening HF were enrolled and grouped as having either mild CHF defined as New York Heart Association (NYHA) functional class I-II or moderate-to-severe CHF defined as NYHA functional class III. ROS levels in PBMC mitochondria were significantly increased in CHF patients with NYHA functional class III compared to those with NYHA functional class I-II, accompanied by impaired mitochondrial respiratory capacity in PBMCs. ROS generation in PBMC mitochondria was positively correlated with urinary 8-hydroxydeoxyguanosine, a systemic oxidative stress marker, in CHF patients. Importantly, mitochondrial ROS generation in PBMCs was directly correlated with plasma levels of B-type natriuretic peptide, a biomarker for severity of HF, and inversely correlated with peak oxygen uptake, a parameter of exercise capacity, in CHF patients. The study showed that ROS generation in PBMC mitochondria was higher in patients with advanced CHF, and it was associated with disease severity and exercise intolerance in CHF patients.
Ibuprofen as a corrosion inhibitor for copper in synthetic acid rain solution
Authors: Tasić Zaklina Z. , Mihajlović Marija B. Petrović , Simonović Ana T. , Radovanović Milan B. , Antonijević Milan M. 
Published: October 2019

AbstractIt is known that if unused drugs are improperly disposed, they can pollute the environment. Furthermore, researchers are still trying to find an environmentally friendly corrosion inhibitor. These factors lead to the possible application of unused pharmaceutical compounds as corrosion inhibitors. The feasibility of an anti-inflammatory, analgesic and antipyretic drug, ibuprofen, was evaluated as a potential copper corrosion inhibitor in synthetic acid rain solution. This investigation was performed by applying electrochemical and weight loss measurements and quantum chemical calculations. The results obtained by these techniques revealed the ability of ibuprofen to protect copper from corrosion. The inhibition efficiency of ibuprofen rises with increase in its concentration and can reach a value of 97.3%. The results of surface analysis of treated coupons by scanning electron microscopy and theoretical calculations are consistent with the experimental results.
Holocene vegetation patterns in southern Lithuania indicate astronomical forcing on the millennial and centennial time scales
Authors: Spiridonov Andrej , Balakauskas Lauras , Stankevič Robertas , Kluczynska Gražyna , Gedminienė Laura , Stančikaitė Miglė 
Published: October 2019

AbstractThe Earth’s biota originated and developed to its current complex state through interacting with multilevel physical forcing of our planet’s climate and near and outer space phenomena. In the present study, we focus on the time scale of hundreds to thousands of years in the most recent time interval – the Holocene. Using a pollen paleocommunity dataset from southern Lithuania (Čepkeliai bog) and applying spectral analysis techniques, we tested this record for the presence of statistically significant cyclicities, which can be observed in past solar activity. The time series of non-metric multidimensional scaling (NMDS) scores, which in our case are assumed to reflect temperature variations, and Tsallis entropy-related community compositional diversity estimates q* revealed the presence of cycles on several time scales. The most consistent periodicities are characterized by periods lasting between 201 and 240 years, which is very close to the DeVries solar cycles (208 years). A shorter-term periodicity of 176 years was detected in the NMDS scores that can be putatively linked to the subharmonics of the Gleissberg solar cycle. In addition, periodicities of ≈3,760 and ≈1,880 years were found in both parameters. These periodic patterns could be explained either as originating as a harmonic nonlinear response to precession forcing, or as resulting from the long-term solar activity quasicycles that were reported in previous studies of solar activity proxies.
Detecting the impact of subject characteristics on machine learning-based diagnostic applications
Authors: Chaibub Neto Elias , Pratap Abhishek , Perumal Thanneer M. , Tummalacherla Meghasyam , Snyder Phil , Bot Brian M. , Trister Andrew D. , Friend Stephen H. , Mangravite Lara , Omberg Larsson 
Published: October 2019

AbstractCollection of high-dimensional, longitudinal digital health data has the potential to support a wide-variety of research and clinical applications including diagnostics and longitudinal health tracking. Algorithms that process these data and inform digital diagnostics are typically developed using training and test sets generated from multiple repeated measures collected across a set of individuals. However, the inclusion of repeated measurements is not always appropriately taken into account in the analytical evaluations of predictive performance. The assignment of repeated measurements from each individual to both the training and the test sets (“record-wise” data split) is a common practice and can lead to massive underestimation of the prediction error due to the presence of “identity confounding.” In essence, these models learn to identify subjects, in addition to diagnostic signal. Here, we present a method that can be used to effectively calculate the amount of identity confounding learned by classifiers developed using a record-wise data split. By applying this method to several real datasets, we demonstrate that identity confounding is a serious issue in digital health studies and that record-wise data splits for machine learning- based applications need to be avoided.
Alpha-synuclein stepwise aggregation reveals features of an early onset mutation in Parkinson’s disease
Authors: de Oliveira Guilherme A. P. , Silva Jerson L. 
Published: October 2019

AbstractAmyloid formation is a process involving interconverting protein species and results in toxic oligomers and fibrils. Aggregated alpha-synuclein (αS) participates in neurodegenerative maladies, but a closer understanding of the early αS polymerization stages and polymorphism of heritable αS variants is sparse still. Here, we distinguished αS oligomer and protofibril interconversions in Thioflavin T polymerization reactions. The results support a hypothesis reconciling the nucleation-polymerization and nucleation-conversion-polymerization models to explain the dissimilar behaviors of wild-type and the A53T mutant. Cryo-electron microscopy with a direct detector shows the polymorphic nature of αS fibrils formed by heritable A30P, E46K, and A53T point mutations. By showing that A53T rapidly nucleates competent species, continuously elongates fibrils in the presence of increasing amounts of seeds, and overcomes wild-type surface requirements for growth, our findings place A53T with features that may explain the early onset of familial Parkinson’s disease cases bearing this mutation.
EphB2 receptor cell-autonomous forward signaling mediates auditory memory recall and learning-driven spinogenesis
Authors: Talebian Asghar , Henkemeyer Mark 
Published: October 2019

AbstractWhile ephrin-B ligands and EphB receptors are expressed to high levels in the learning centers of the brain, it remains largely unknown how their trans-synaptic interactions contribute to memory. We find that EphB2 forward signaling is needed for contextual and sound-evoked memory recall and that constitutive over-activation of the receptor’s intracellular tyrosine kinase domain results in enhanced memory. Loss of EphB2 expression does not affect the number of neurons activated following encoding, although a reduction of neurons activated after the sound-cued retrieval test was detected in the auditory cortex and hippocampal CA1. Further, spine density and maturation was reduced in the auditory cortex of mutants especially in the neurons that were dual-activated during both encoding and retrieval. Our data demonstrates that trans-synaptic ephrin-B-EphB2 interactions and forward signaling facilitate neural activation and structural plasticity in learning-associated neurons involved in the generation of memories.
Reproduction of vesicles coupled with a vesicle surface-confined enzymatic polymerisation
Authors: Kurisu Minoru , Aoki Harutaka , Jimbo Takehiro , Sakuma Yuka , Imai Masayuki , Serrano-Luginbühl Sandra , Walde Peter 
Published: October 2019

AbstractMolecular assembly systems that have autonomous reproduction and Darwinian evolution abilities can be considered as minimal cell-like systems. Here we demonstrate the reproduction of cell-sized vesicles composed of AOT, i.e., sodium bis-(2-ethylhexyl) sulfosuccinate, coupled with an enzymatic polymerisation reaction occurring on the surface of the vesicles. The particular reaction used is the horseradish peroxidase-catalysed polymerisation of aniline with hydrogen peroxide as oxidant, which yields polyaniline in its emeraldine salt form (PANI-ES). If AOT micelles are added during this polymerisation reaction, the AOT - PANI-ES vesicles interact with the AOT molecules in the external solution and selectively incorporate them in their membrane, which leads to a growth of the vesicles. If the AOT vesicles also contain cholesterol, the vesicles not only show growth, but also reproduction. An important characteristic of this reproduction system is that the AOT-based vesicles encourage the synthesis of PANI-ES and PANI-ES promotes the growth of AOT vesicles.
Nanobolometer with ultralow noise equivalent power
Authors: Kokkoniemi Roope , Govenius Joonas , Vesterinen Visa , Lake Russell E. , Gunyhó András M. , Tan Kuan Y. , Simbierowicz Slawomir , Grönberg Leif , Lehtinen Janne , Prunnila Mika , Hassel Juha , Lamminen Antti , Saira Olli-Pentti , Möttönen Mikko 
Published: October 2019

AbstractSince the introduction of bolometers more than a century ago, they have been used in various applications ranging from chemical sensors, consumer electronics, and security to particle physics and astronomy. However, faster bolometers with lower noise are of great interest from the fundamental point of view and to find new use-cases for this versatile concept. We demonstrate a nanobolometer that exhibits roughly an order of magnitude lower noise equivalent power, $$20\,{\mathrm{zW}}/\sqrt {{\mathrm{Hz}}}$$
20

zW
∕

Hz

, than previously reported for any bolometer. Importantly, it is more than an order of magnitude faster than other low-noise bolometers, with a time constant of 30 μs at $$60\,{\mathrm{zW}}/\sqrt {{\mathrm{Hz}}}$$
60

zW
∕

Hz

. These results suggest a calorimetric energy resolution of 0.3 zJ = h × 0.4 THz with a time constant of 30 μs. Further development of this nanobolometer may render it a promising candidate for future applications requiring extremely low noise and high speed such as those in quantum technology and terahertz photon counting.
Interactions between plants and soil shaping the root microbiome under abiotic stress
Authors: Hartman Kyle , Tringe Susannah G. 
Published: October 2019

Abstract
Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.
Identification of novel non-synonymous variants associated with type 2 diabetes-related metabolites in Korean population
Authors: Park Tae-Joon , Lee Heun-Sik , Kim Young Jin , Kim Bong-Jo 
Published: October 2019

Abstract
Metabolome-genome wide association studies (mGWASs) are useful for understanding the genetic regulation of metabolites in complex diseases, including type 2 diabetes (T2D). Numerous genetic variants associated with T2D-related metabolites have been identified in previous mGWASs; however, these analyses seem to have difficulty in detecting the genetic variants with functional effects. An exome array focussed on potentially functional variants is an alternative platform to obtain insight into the genetics of biochemical conversion processes. In the present study, we performed an mGWAS using 27,140 non-synonymous variants included in the Illumina HumanExome BeadChip and nine T2D-related metabolites identified by a targetted metabolomics approach to evaluate 2,338 Korean individuals from the Korea Association REsource (KARE) cohort. A linear regression analysis controlling for age, sex, BMI, and T2D status as covariates was performed to identify novel non-synonymous variants associated with T2D-related metabolites. We found significant associations between glycine and CPS1 (rs1047883) and PC ae C36:0 and CYP4F2 (rs2108622) variants (P&lt;2.05 × 10−7, after the Bonferroni correction for multiple testing). One of the two significantly associated variants, rs1047883 was newly identified whereas rs2108622 had been previously reported to be associated with T2D-related traits. These findings expand our understanding of the genetic determinants of T2D-related metabolites and provide a basis for further functional validation.
Engineering anti-cancer nanovaccine based on antigen cross-presentation
Authors: Warrier Vaishnavi U. , Makandar Amina I. , Garg Manoj , Sethi Gautam , Kant Ravi , Pal Jayanta K. , Yuba Eiji , Gupta Rajesh Kumar 
Published: October 2019

AbstractDendritic cells (DCs) present exogenous antigens on major histocompatibility complex (MHC) class I molecules, thereby activating CD8+ T cells, contributing to tumor elimination through a mechanism known as antigen cross-presentation. A variety of factors such as maturation state of DCs, co-stimulatory signals, T-cell microenvironment, antigen internalization routes and adjuvants regulate the process of DC-mediated antigen cross-presentation. Recently, the development of successful cancer immunotherapies may be attributed to the ability of DCs to cross-present tumor antigens. In this review article, we focus on the underlying mechanism of antigen cross-presentation and ways to improve antigen cross-presentation in different DC subsets. We have critically summarized the recent developments in the generation of novel nanovaccines for robust CD8+ T-cell response in cancer. In this context, we have reviewed nanocarriers that have been used for cancer immunotherapeutics based on antigen cross-presentation mechanism. Additionally, we have also expressed our views on the future applications of this mechanism in curing cancer.
Structural dynamics of P-type ATPase ion pumps
Authors: Dyla Mateusz , Basse Hansen Sara , Nissen Poul , Kjaergaard Magnus 
Published: October 2019

Abstract
P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.
Endoplasmic reticulum stress and mitochondrial biogenesis are potential therapeutic targets for abdominal aortic aneurysm
Authors: Miyao Masashi , Cicalese Stephanie , Cooper Hannah A. , Eguchi Satoru 
Published: October 2019

Abstract
Endoplasmic reticulum (ER) and mitochondria are crucial organelles for cell homeostasis and alterations of these organelles have been implicated in cardiovascular disease. However, their roles in abdominal aortic aneurysm (AAA) pathogenesis remain largely unknown. In a recent issue of Clinical Science, Navas-Madronal et al. ((2019), 133(13), 1421–1438) reported that enhanced ER stress and dysregulation of mitochondrial biogenesis are associated with AAA pathogenesis in humans. The authors also proposed that disruption in oxysterols network such as an elevated concentration of 7-ketocholestyerol in plasma is a causative factor for AAA progression. Their findings highlight new insights into the underlying mechanism of AAA progression through ER stress and dysregulation of mitochondrial biogenesis. Here, we will discuss the background, significance of the study, and future directions.
Mathematical modelling of cell migration
Authors: Butler George , Rudge Jonathan , Dash Philip R. 
Published: October 2019

Abstract
The complexity of biological systems creates challenges for fully understanding their behaviour. This is particularly true for cell migration which requires the co-ordinated activity of hundreds of individual components within cells. Mathematical modelling can help understand these complex systems by breaking the system into discrete steps which can then be interrogated in silico. In this review, we highlight scenarios in cell migration where mathematical modelling can be applied and discuss what types of modelling are most suited. Almost any aspect of cell migration is amenable to mathematical modelling from the modelling of intracellular processes such as chemokine receptor signalling and actin filament branching to larger scale processes such as the movement of individual cells or populations of cells through their environment. Two common ways of approaching this modelling are the use of models based on differential equations or agent-based modelling. The application of both these approaches to cell migration are discussed with specific examples along with common software tools to facilitate the process for non-mathematicians. We also highlight the challenges of modelling cell migration and the need for rigorous experimental work to effectively parameterise a model.
DNA methylation dynamics at transposable elements in mammals
Authors: Jansz Natasha 
Published: October 2019

Abstract
Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.