bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropathic-Like Pain Symptoms in a Community-Dwelling Sample with or at Risk for Knee Osteoarthritis
Authors: Terry Ellen L , Booker Staja Q , Cardoso Josue S , Sibille Kimberly T , Bartley Emily J , Glover Toni L , Vaughn Ivana A , Thompson Kathryn A , Bulls Hailey W , Addison Adriana S , Staud Roland , Hughes Laura B , Edberg Jeffrey C , Redden David T , Bradley Laurence A , Goodin Burel R , Fillingim Roger B 
Published: April 2019

AbstractObjectiveTo characterize neuropathic-like pain among individuals with or at risk for knee osteoarthritis.SubjectsOne hundred eighty-four individuals who self-identified as non-Hispanic black or non-Hispanic white and presented with unilateral or bilateral knee pain.DesignNeuropathic-like pain was assessed using the painDETECT, and those with high vs low neuropathic-like pain were compared on clinical pain, psychological symptoms, physical function, and quantitative sensory testing. Analyses were unadjusted, partially and fully adjusted for relevant covariates.ResultsThirty-two (17.4%) participants reported experiencing neuropathic-like pain features above the painDETECT clinical cut-score. The neuropathic-like pain group reported significantly greater pain severity on all measures of clinical pain and higher levels of psychological symptoms when fully adjusted for covariates, but no differences emerged for disability and lower extremity function. The neuropathic-like pain group also reported greater overall heat pain ratings during the heat pain threshold and increased temporal summation of heat pain in the fully adjusted model. Additionally, those with neuropathic-like pain symptoms reported greater painful after-sensations following heat pain temporal summation in all analyses. No significant group differences in pressure pain threshold emerged at any of the testing sites. In contrast, temporal summation of mechanical pain was significantly greater at both the index knee and the ipsilateral hand for the neuropathic-like pain group in all analyses.ConclusionsParticipants with or at risk for knee osteoarthritis who reported high neuropathic-like pain experienced significantly greater clinical pain and increased heat and mechanical temporal summation at the index knee and other body sites tested, suggesting central sensitization.
Iterative feature selection method to discover predictive variables and interactions for high-dimensional transplant genomic data
Authors: Huang Hu , Vierra-Green Cynthia , Spellman Stephen , Kennedy Caleb 
Published: April 2019

AbstractAfter allogeneic hematopoietic stem cell transplantation (allo-HCT), donor-derived immune cells can trigger devastating graft-versus-host disease (GVHD). The clinical effects of GVHD are well established; however, genetic mechanisms that contribute to the condition remain unclear. Candidate gene studies and genome-wide association studies have shown promising results, but they are limited to a few functionally derived genes and those with strong main effects. Transplant-related genomic studies examine two individuals simultaneously as a single case, which adds additional analytical challenges. In this study, we propose a hybrid feature selection algorithm, iterative Relief-based algorithm followed by a random forest (iRBA-RF), to reduce the SNPs from the original donor-recipient paired genotype data and select the most predictive SNP sets in association with the phenotypic outcome in question. The proposed method does not assume any main effect of the SNPs; instead, it takes into account the SNP interactions. We applied the iRBA-RF to a cohort (n=331) of acute myeloid leukemia (AML) patients and their fully 10 of 10 (HLA-A, -B, -C, -DRB1, and -DQB1) HLA-matched healthy unrelated donors and assessed two case-control scenarios: AML patients vs healthy donor as case vs control and acute GVHD group vs non-GVHD group as case vs control, respectively. The results show that iRBA-RF can efficiently reduce the size of SNPs set down to less than 0.05%. Moreover, the literature review showed that the selected SNPs appear functionally involved in the pathologic pathways of the phenotypic diseases in question, which may potentially explain the underlying mechanisms. This proposed method can effectively and efficiently analyze ultra-high dimensional genomic data and could help provide new insights into the development of transplant-related complications from a genomic perspective.
Environmental variation mediates the evolution of anticipatory parental effects
Authors: Lind Martin I. , Zwoinska Martyna K. , Andersson Johan , Carlsson Hanne , Krieg Therese , Larva Tuuli , Maklakov Alexei A. 
Published: April 2019

AbstractTheory maintains that when future environment is predictable, parents should adjust the phenotype of their offspring to match the anticipated environment. The plausibility of positive anticipatory parental effects is hotly debated and the experimental evidence for the evolution of such effects is currently lacking. We experimentally investigated the evolution of anticipatory maternal effects in a range of environments that differ drastically in how predictable they are. Populations of the nematodeCaenorhabditis remanei, adapted to 20°C, were exposed to a novel temperature (25°C) for 30 generations with either positive or zero correlation between parent and offspring environment. We found that populations evolving in novel environments that were predictable across generations evolved a positive anticipatory maternal effect, since they required maternal exposure to 25°C to achieve maximum reproduction in that temperature. In contrast, populations evolving under zero environmental correlation had lost this anticipatory maternal effect. Similar but weaker patterns were found if instead rate-sensitive population growth was used as a fitness measure. These findings demonstrate that anticipatory parental effects evolve in response to environmental change so that ill-fitting parental effects can be rapidly lost. Evolution of positive anticipatory parental effects can aid population viability in rapidly changing but predictable environments.Impact summaryParents can help their offspring by adjusting offspring’s phenotype to match their environment. Such anticipatory parental effects would be beneficial, but only if parents can accurately predict the environment in which their offspring will develop and live. The plausibility of such anticipatory parental effects is hotly debated. The theory is clear that the predictability of the environment should play a defining role. We used an “experimental evolution” approach in a fast reproducing nematode wormCaenorhabditis remaneito tackle this question and follow the evolution of parental effects in different environments in real-time. We found that populations evolving in a novel but predictable environment indeed had anticipatory parental effects that increased fitness of their offspring in that environment. In contrast, when evolving in an unpredictable environment where such parental effects would be disadvantageous, the parental effect was rapidly lost in evolution. Our novel experimental environments were constructed by exposing worms to increased temperature. Anticipatory parental effects play an important role in adaptation to novel environments and will affect the viability of populations under climate heating.
Second-generation lung-on-a-chip array with a stretchable biological membrane
Authors: Zamprogno Pauline , Wüthrich Simon , Achenbach Sven , Stucki Janick D. , Hobi Nina , Schneider-Daum Nicole , Lehr Claus-Michael , Huwer Hanno , Geiser Thomas , Schmid Ralph A. , Guenat Olivier T. 
Published: April 2019

AbstractThe complex architecture of the lung parenchyma and the air-blood barrier is difficult to mimic in-vitro. Recently reported lung-on-a-chips used a thin, porous and stretchable PDMS membrane, to mimic the air-blood barrier and the rhythmic breathing motions. However, the nature, the properties and the size of this PDMS membrane differ from the extracellular matrix of the distal airways. Here, we present a second-generation lung-on-a-chip with an array of in vivo-like sized alveoli and a stretchable biological membrane. This nearly absorption free membrane allows mimicking in vivo functionality of the lung parenchyma at an unprecedented level. The air-blood barrier is constituted by human primary lung alveolar epithelial cells from several patients and co-cultured with primary lung endothelial cells. Typical markers of lung alveolar epithelial cells could be observed in the model, while barrier properties were preserved for up to three weeks. This advanced lung alveolar model reproduces some key features of the lung alveolar environment in terms of composition, alveolar size, mechanical forces and biological functions, which makes this model a more analogous tool for drug discovery, diseases modeling and precision medicine applications.
MAGE-3 peptide amphiphile micelle vaccine promote anti-tumor immunity in mice with stomach cancer
Authors: Windberg Joseph , Zhang Rui 
Published: April 2019

AbstractNanoparticles as a vaccine carrier can protect antigen from enzymatic hydrolysis, enhance immunogenicity, is a kind of great potential for development of new vaccine carriers. In this study, a nanometer vaccine loaded with CD4+ & CD8+ T cell epitope MAGE-3 polypeptide antigen was prepared to investigate its related properties and anti-tumor immunity. Methods: the use of self-assembly technology to prepare polypeptide / Chit2DC (chitosan - deoxycholate) drug micelles, transmission electron microscopic morphology, fluorescence spectrophotometry to calculate the loading rate, drug loading, and drug release rule. Flow cytometric detection of DC (dendritic cells) on the phagocytic rate of the drug, enzyme-linked immunosorbent spot test (ELISPOT) and cytotoxicity assay MAGE-3 polypeptide nanometer vaccine activation status of the body’s cellular immune response. In vivo tumor suppressor effect was observed in animals. Results: the peptides /Chit2DC micelles were prepared successfully. the drug encapsulation efficiency was about 37% and the drug loading was 17%. Drug-loaded nanoparticles polypeptide at pH 7.14 of the "cancer" ELISPOT and cytotoxicity experiments show that MAGE-3 polypeptide nanometer vaccine can activate the immune response in vivo to produce CTL against MAGE-3, specifically killing tumor cells expressing MAGE-3. In vivo tumor inhibition experiments showed that the relative tumor inhibition rate of polypeptide nanoparticles group was 37.181%.
Unique Features of Sub-Cortical Circuits in A Macaque Model of Congenital Blindness
Authors: Magrou Loïc , Barone Pascal , Markov Nikola T. , Scheeren Gwylan , Killackey Herbert P. , Giroud Pascale , Berland Michel , Knoblauch Kenneth , Dehay Colette , Kennedy Henry 
Published: April 2019

AbstractThere is extensive modification of the functional organization of the brain in the congenital blind human, although there is little understanding of the structural underpinnings of these changes. The visual system of macaque has been extensively characterized both anatomically and functionally. We have taken advantage of this to examine the influence of the congenital blindness in macaque resulting from the removal of the retina during in utero development. Developmental anophthalmia in macaque effectively removes the normal influence of the thalamus on cortical development leading to an induced hybrid cortex (HC) combining features of primary visual and extrastriate cortex. Here we show that retrograde tracers injected in early visual areas including hybrid cortex reveals a drastic reduction of cortical projections of the reduced lateral geniculate nucleus. In addition, there is an important expansion of projections from the pulvinar complex to the hybrid cortex, compared to the controls. These findings show that the functional consequences of congenital blindness need to be considered in terms of both modifications of the inter-areal cortical network and the ascending visual pathways.
Changes in historical typhoid transmission across 16 U.S. cities, 1889-1931: Quantifying the impact of investments in water and sewer infrastructures
Authors: Phillips Maile T. , Owers Katharine A. , Grenfell Bryan T. , Pitzer Virginia E. 
Published: April 2019

ABSTRACTBackgroundInvestments in water and sanitation systems are believed to have led to the decline in typhoid fever in developed countries, such that most cases now occur in regions lacking adequate clean water and sanitation. Exploring seasonal and long-term patterns in historical typhoid mortality in the United States can offer deeper understanding of disease drivers.MethodsWe fit modified Time-series Susceptible-Infectious-Recovered models to city-level weekly mortality counts to estimate seasonal and long-term typhoid transmission. We examined seasonal transmission separately by city and aggregated by water source. We fit regression models to measure associations between long-term transmission and financial investments in water and sewer systems.ResultsTyphoid transmission peaked in late summer/early fall. Seasonality varied by water source, with the greatest variation occurring in cities with reservoirs. Historical $1 per capita ($25.80 in 2017) investments in construction and operation of water and sewer systems were associated with 8-53% decreases in typhoid transmission, while $1 increases in total value or debt accrued to maintain them were associated with 4-7% decreases.ConclusionOur findings aid in the understanding of typhoid transmission dynamics and potential impacts of water and sanitation improvements, and can inform cost-effectiveness analyses of interventions to reduce the typhoid burden.
Is disrupted sleep a risk factor for Alzheimer’s disease? Evidence from a two-sample Mendelian randomization analysis
Authors: Anderson Emma L , Richmond Rebecca C , Jones Samuel E , Hemani Gibran , Wade Kaitlin. H , Dashti Hassan S , Lane Jacqueline M , Wang Heming , Saxena Richa , Brumpton Ben , Korologou-Linden Roxanna , Nielson Jonas B , Olav Åsvold Bjørn , Abecasis Gonçalo , Coulthard Elizabeth , Kyle Simon D. , Beaumont Robin N , Tyrrell Jessica , Frayling Timothy M , Munafò Marcus R , Wood Andrew R , Ben-Shlomo Yoav , Howe Laura D , Lawlor Debbie A , Weedon Michael N , Davey Smith George 
Published: April 2019

ABSTRACTINTRODUCTIONIt is established that Alzheimer’s disease (AD) patients experience sleep disruption. However, it remains unknown whether disruption in the quantity, quality or timing of sleep is a risk factor for the onset of AD.METHODSMendelian randomization (MR) was used to estimate the causal effect of self-reported and accelerometer-measured sleep parameters (chronotype, duration, fragmentation, insomnia, daytime napping and daytime sleepiness) on AD risk.RESULTSOverall, there was little evidence that sleep traits affect the risk of AD. There was some evidence to suggest that self-reported daytime napping was associated with lower AD risk (odds ratio [OR]: 0.70, 95% confidence interval [CI]: 0.50 to 0.99). Some other sleep traits (accelerometer-measured eveningness and sleep duration, and self-reported daytime sleepiness) had ORs for AD risk of a similar magnitude to daytime napping, but were less precisely estimated.DISCUSSONOur findings provide tentative evidence that daytime napping may reduce AD risk. However, findings should be replicated using independent samples.
The “amphi”-brains of amphipods: New insights from the neuroanatomy ofParhyale hawaiensis(Dana, 1853)
Authors: Wittfoth Christin , Harzsch Steffen , Wolff Carsten , Sombke Andy 
Published: April 2019

ABSTRACTBackgroundOver the last years, the amphipod crustaceanParhyale hawaiensishas developed into an attractive marine animal model for evolutionary developmental studies that offers several advantages over existing experimental organisms. It is easy to rear in laboratory conditions with embryos available year-round and amenable to numerous kinds of embryological and functional genetic manipulations. However, beyond these developmental and genetic analyses, research on the architecture of its nervous system is fragmentary. In order to provide a first neuroanatomical atlas of the brain, we investigatedP. hawaiensisusing immunohistochemical labelings combined with laser-scanning microscopy, X-ray microcomputed tomography, histological sectioning and 3D reconstructions.ResultsAs in most amphipod crustaceans, the brain is dorsally bent out of the body axis with downward oriented lateral hemispheres of the protocerebrum. It comprises almost all prominent neuropils that are part of the suggested ground pattern of malacostracan crustaceans (except the lobula plate and projection neuron tract neuropil). Beyond a general uniformity of these neuropils, the brain ofP. hawaiensisis characterized by a modified lamina (first order visual neuropil) and, compared to other Amphipoda, an elaborated central complex. The lamina displays a chambered appearance that, in the light of a recent analysis on photoreceptor projections inP. hawaiensis, corresponds to specialized photoreceptor terminals. The presence of a poorly differentiated hemiellipsoid body is indicated and critically discussed.ConclusionsAlthough amphipod brains show a general uniformity, when compared with each other, there is also a certain degree of variability in architecture and size of different neuropils. In contrast to other amphipods, the brain ofP. hawaiensisdoes not display any striking modifications or bias towards one particular sensory modality. Thus, we conclude that its brain may represent a common type of an amphipod brain.
Shared morphological consequences of global warming in North American migratory birds
Authors: Weeks Brian C. , Willard David E. , Ellis Aspen A. , Witynski Max L. , Hennen Mary , Winger Benjamin M. 
Published: April 2019

ABSTRACTIncreasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four-decade specimen series of 70,716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40-year period drove consistent reductions in body size across these diverse taxa. Concurrently, wing length – which impacts nearly all aspects of avian ecology and behavior – has consistently increased across taxa. Our findings suggest that warming-induced body size reduction is a general response to climate change, and reveal a similarly consistent shift in an ecologically-important dimension of body shape. We hypothesize that increasing wing length represents a compensatory adaptation to maintain migration as reductions in body size have increased the metabolic cost of flight. An improved understanding of warming-induced morphological changes, and their limits, are important for predicting biotic responses to global change.
Genotyping-by-sequencing based cytoplasmic markers underpin population structural variation of perennial ryegrass
Authors: Cao Mingshu , Faville Marty , Jacobs Jeanne , Carena Marcelo 
Published: April 2019

AbstractChloroplast and mitochondrial genomes provide unique information in studying plant populations because cytoplasmic genes exhibit a different mode of inheritance and a different rate of gene mutation compared to nuclear genes. Despite this, cytoplasmic genomic contributions to plant population performance are largely unexplored because few methods are available to characterize and evaluate cytoplasmic genome-wide variations. Here we have developed cytoplasmic markers based on genotyping-by-sequencing (GBS), which enable us to characterize thousands of samples, to survey gene variants across cytoplasmic genomes, and to monitor within-population variations of chloroplast or mitochondrial origin. Using these cytoplasmic genome-wide markers we have found that within-population differentiations are evident in ryegrass (Lolium perenne), beyond the explanation of nuclear markers. Moreover, chloroplast and mitochondrial variations exhibit different patterns, with mitochondrial markers more readily reflecting the maternal origins. Application of GBS-based cytoplasmic markers should facilitate quantifying the contribution of cytoplasmic inheritance to plant performance through selective breeding or under natural selection pressure.
Overcoming tissue scattering in wide-field deep imaging by extended detection and computational reconstruction
Authors: Zhang Yuanlong , Zhou Tiankuang , Hu Xuemei , Xie Hao , Fang Lu , Kong Lingjie , Dai Qionghai 
Published: April 2019

AbstractCompared to the golden technique of point‐scanning multiphoton microscopy, line‐scanning temporal focusing microscopy (LTFM) is competitive in high imaging speed while maintaining tight axial confinement. However, considering its wide‐field detection mode, LTFM suffers from shallow penetration depth as a result of crosstalk induced by tissue scattering. In contrast to the spatial filtering based on confocal slit detection, we propose the extended detection LTFM (ED‐LTFM), the first technique to extract signals from scattered photons and thus effectively extend the imaging depth. By recording a succession of line‐shape excited signals in 2D and reconstructing signals under Hessian regularization, we can push the depth limitation in scattering tissue imaging. We valid the concept with numerical simulations, and demonstrate the performance of enhanced imaging depth in in vivo imaging of mouse brains.
Epigenetic regulation of unique genes and repetitive elements by the KRAB zinc finger protein ZFP57
Authors: Shi Hui , Strogantsev Ruslan , Takahashi Nozomi , Kazachenka Anastasiya , Lorincz Matthew C. , Hemberger Myriam , Ferguson-Smith Anne C. 
Published: April 2019

AbstractBackgroundKRAB-zinc finger proteins (KZFPs) represent one of the largest families of DNA binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental-origin at genomic imprints along with ZFP445 which is specific for imprints. However, ZFP57 has multiple methylated genomic targets. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at unique and repetitive regions of the genome.ResultsOver 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibiting alterations in expression. Comparison with DNA methyltransferase-deleted ES cells (TKO) identifies remarkably similar losses of H3K9me3 and changes in expression, defining regions where H3K9me3 is secondary to DNA methylation. We show that ZFP57 is the principal methylation-sensitive KZFP recruiting KAP1 and H3K9me3 in ES cells. Finally, like imprints, other unique targets of ZFP57 are enriched for germline-derived DNA methylation including oocyte-specific methylation that is resistant to post-fertilisation epigenetic reprogramming.ConclusionOur analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline derived imprinting control regions.