bluuebunny/crossref_metadata_2025_split huggingface dataset:
Andy’s Algorithms: new automated digital image analysis pipelines for FIJI
Authors: Law Andrew M. K. , Yin Julia X. M. , Castillo Lesley , Young Adelaide I. J. , Piggin Catherine , Rogers Samuel , Caldon Catherine Elizabeth , Burgess Andrew , Millar Ewan K. A. , O’Toole Sandra A. , Gallego-Ortega David , Ormandy Christopher J. , Oakes Samantha R. 
Published: November 2017

AbstractQuantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy’s Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3′-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy’s Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy’s algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy’s Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm.
Radiographic assessment of the skeletons of Dolly and other clones finds no abnormal osteoarthritis
Authors: Corr S. A. , Gardner D. S. , Langley-Hobbs S. , Ness M. G. , Kitchener A. C. , Sinclair K. D. 
Published: November 2017

AbstractOur recent report detailing the health status of cloned sheep concluded that the animals had aged normally. This is in stark contrast to reports on Dolly (first animal cloned from adult cells) whose diagnoses of osteoarthritis (OA) at 5½ years of age led to considerable scientific concern and media debate over the possibility of early-onset age-related diseases in cloned animals. Our study included four 8-year old ewes derived from the cell line that gave rise to Dolly, yet none of our aged sheep showed clinical signs of OA, and they had radiographic evidence of only mild or, in one case, moderate OA. Given that the only formal record of OA in Dolly is a brief mention of a single joint in a conference abstract, this led us to question whether the original concerns about Dolly’s OA were justified. As none of the original clinical or radiographic records were preserved, we undertook radiographic examination of the skeletons of Dolly and her contemporary clones. We report a prevalence and distribution of radiographic-OA similar to that observed in naturally conceived sheep, and our healthy aged cloned sheep. We conclude that the original concerns that cloning had caused early-onset OA in Dolly were unfounded.
Association of a variant in the gene encoding for ERV1/ChemR23 with reduced inflammation in visceral adipose tissue from morbidly obese individuals
Authors: López-Vicario Cristina , Rius Bibiana , Alcaraz-Quiles José , González-Périz Ana , Martínez-Puchol Ana Isabel , Casulleras Mireia , Duran-Güell Marta , Ibarzabal Ainitze , Corcelles Ricard , Laguna-Fernández Andrés , Back Magnus , Titos Esther , Clària Joan 
Published: November 2017

AbstractObesity comorbidities are closely associated with chronic low-grade adipose tissue inflammation. A number of SNPs associated with inflammation has been identified, underscoring the impact of genetic determinants on this process. Here, we screened SNPs in genes with pro-inflammatory (IL-1β, IL-6, STAT3 and JAK2), anti-inflammatory (IL-10 and SOCS3) and pro-resolving (ERV1/ChemR23) properties in 101 obese and 99 non-obese individuals. Among the SNPs analyzed, we identified that individuals carrying a C allele in the rs1878022 polymorphism of the ERV1/ChemR23 gene, which encodes for the receptor of the pro-resolving mediator RvE1, had increased ERV1/ChemR23 protein expression and reduced levels of the inflammatory cytokine IL-6 in adipose tissue. Moreover, patients carrying the C allele in homozygosity had lower plasma levels of IL-6, IFN-α2, IL-15, IL-1ra, IL-10, GM-CSF, G-CSF and VEGF and enhanced leukocyte responsiveness to RvE1. C-carriers also exhibited decreased TAG to HDL ratio, a surrogate marker of insulin resistance and a predictor of incident fatty liver. Finally, we confirmed in vivo that the ERV1/ChemR23 receptor regulates systemic and tissue inflammation since mice lacking ERV1/ChemR23 expression showed increased IL-6 levels in adipose tissue and peritoneal macrophages. Together, our study identified an ERV1/ChemR23 variant that protects patients with obesity from excessive inflammatory burden.
A novel magnet-actuated droplet manipulation platform using a floating ferrofluid film
Authors: Yang Chao , Li Gang 
Published: November 2017

AbstractIn this paper, we propose a novel but versatile magnet-actuated platform for droplet manipulation, which uses a ferrofluid film floating on a liquid surface as magnetic actuator. In contrast to the traditional magnetic droplet manipulation, this platform can handle droplets without magnetically functionalizing them. Due to the immiscibility of the oil-based ferrofluid and water, the droplets desired to be manipulated can stably rest on the surface of the floating ferrofluid film (FFF) under the action of surface tension, thereby offering possibilities for magnetically-driven droplet manipulations. Such a floating, magnetically responsive liquid film not only offers an open surface for active 2D droplet manipulation, but also enables complex droplet manipulations in 3D space. Using FFF, we demonstrate a “full-space” droplet manipulation, including droplet transport/coalescence above FFF (i.e. in air), droplet transport/coalescence on FFF and droplet encapsulation/release under FFF (i.e. in liquid). Furthermore, we investigated the effects of the magnetic field intensity, the ferrofluid concentration, the droplet volume, and the FFF thickness on droplet kinematics. By finely tuning these operating conditions, the FFF strategy can enjoy more operational latitude than traditional droplet systems, thus allowing more versatile liquid handling.
Binary phase masks for easy system alignment and basic aberration sensing with spatial light modulators in STED microscopy
Authors: Klauss André , Conrad Florian , Hille Carsten 
Published: November 2017

AbstractThe use of binary phase patterns to improve the integration and optimization of spatial light modulators (SLM) in an imaging system, especially a confocal microscope, is proposed and demonstrated. The phase masks were designed to create point spread functions (PSF), which exhibit specific sensitivity to major disturbances in the optical system. This allows direct evaluation of misalignment and fundamental aberration modes by simple visual inspection of the focal intensity distribution or by monitoring the central intensity of the PSF. The use of proposed phase masks is investigated in mathematical modelling and experiment for the use in a stimulated emission depletion (STED) microscope applying wavefront shaping by a SLM. We demonstrate the applicability of these phase masks for modal wavefront sensing of low order aberration modes up to the third order of Zernike polynomials, utilizing the point detector of a confocal microscope in a ‘guide star’ approach. A lateral resolution of ~25 nm is shown in STED imaging of the confocal microscope retrofitted with a SLM and a STED laser and binary phase mask based system optimization.
Preparation and functional evaluation of collagen oligopeptide-rich hydrolysate from fish skin with the serine collagenolytic protease from Pseudoalteromonas sp. SM9913
Authors: Chen Xiu-Lan , Peng Ming , Li Jing , Tang Bai-Lu , Shao Xuan , Zhao Fang , Liu Chang , Zhang Xi-Ying , Li Ping-Yi , Shi Mei , Zhang Yu-Zhong , Song Xiao-Yan 
Published: November 2017

AbstractAlthough several serine collagenolytic proteases from bacteria were reported, none has been used to prepare bioactive collagen peptides. MCP-01 is the most abundant extracellular protease of deep-sea Pseudoalteromonas sp. SM9913 and is a serine collagenolytic protease with high efficiency on fish collagen hydrolysis. Here, we set up a pilot scale process to ferment SM9913 for extracellular protease production. With SM9913 extracellular protease as a tool, a process to prepare collagen oligopeptide-rich hydrolysate from codfish skin was set up, which was further scaled up to pilot (100 L) and plant (2000 L) levels with yields >66%. The hydrolysates from laboratory-, pilot- and plant-scales had quite similar quality, containing ~95% peptides with molecular weights lower than 3000 Da and approximately 60% lower than 1000 Da, in which collagen oilgopeptides account for approximately 95%. Bioactivity analyses showed that the hydrolysate had moisture-retention ability, antioxidant activity, and promoting effect on cell viability of human dermal fibroblasts. Safety evaluation showed that the hydrolysate was nontoxic and nonirritating to skin. Therefore, SM9913 extracellular protease is a good enzyme to prepare bioactive oligopeptides from fish skin. The results also suggest that the collagen oligopeptides-rich hydrolysate may have potentials in biomedical, functional food, pharmaceutical and cosmetic industries.
GABA concentrations in the anterior temporal lobe predict human semantic processing
Authors: Jung JeYoung , Williams Stephen R. , Sanaei Nezhad Faezeh , Lambon Ralph Matthew A. 
Published: November 2017

AbstractThere is now considerable convergent evidence from multiple methodologies and clinical studies that the human anterior temporal lobe (ATL) is a semantic representational hub. However, the neurochemical nature of the ATL in the semantic processing remains unclear. The current study investigated the neurochemical mechanism underlying semantic processing in the ATL. We combined functional magnetic resonance imaging (fMRI) with resting-state magnetic resonance spectroscopy (MRS) to measure task-related blood-oxygen level-dependent (BOLD) signal changes during sematic processing and resting-state GABA concentrations in the ATL. Our combined fMRI and MRS investigation showed that the stronger ATL BOLD response induced by the semantic task, the lower GABA concentration in the same region. Moreover, individuals with higher GABA concentration in the ATL showed better semantic performance and stronger BOLD-related fluctuations in the semantic network. Our data demonstrated that the resting-state GABA concentration predicts neural changes in the human ATL and task performance during semantic processing. Our findings indicate that individuals with higher GABA may have a more efficient semantic processing leading to better task performance and imply that GABAergic neurochemical processes are potentially crucial to the neurobiological contribution of the ATL to semantic cognition.
Maraba virus-vectored cancer vaccines represent a safe and novel therapeutic option for cats
Authors: Hummel Jeff , Bienzle Dorothee , Morrison Annette , Cieplak Michelle , Stephenson Kyle , DeLay Josepha , Woods J. Paul , Lichty Brian D. , Bridle Byram W. 
Published: November 2017

AbstractDirect killing of malignant cells combined with induction of tumour-specific immune responses makes oncolytic vaccines attractive for cancer therapy. We previously developed a heterologous cancer immunization strategy that utilized a replication-defective adenovirus-vectored primary vaccine encoding a tumour antigen followed by boosting with a replication-competent Maraba virus expressing the same antigen. To assess the safety of oncolytic Maraba virus-based booster vaccines and inform the design of clinical trials, we conducted translational studies in cats, which have immune systems that are similar to people and spontaneously develop cancers of comparable types and etiologies. A dose of Maraba virus up to 2.5 × 1011 pfu per cat was well-tolerated, with adverse effects limited to mild, transient pyrexia, weight loss, neutropenia, lymphopenia and thrombocytopenia. Maraba viral genomes were present in some urine, stool and most plasma samples up to one week post-infection, but no infectious viruses were recovered. Post-mortem analysis showed one heart, one lung and all spleen samples contained Maraba virus genomes. No replication-competent viruses were recovered from any tissues. Post-mortem histopathological analyses revealed hyperplasia of lymphoid tissues, but no abnormal lesions were attributed to vaccination. This study demonstrated that Maraba virus-vectored cancer vaccines were well-tolerated and supports their use in treating cats.
Identification and characterization of serine protease inhibitors in a parasitic wasp, Pteromalus puparum
Authors: Yang Lei , Mei Yaotian , Fang Qi , Wang Jiale , Yan Zhichao , Song Qisheng , Lin Zhe , Ye Gongyin 
Published: November 2017

AbstractSerine protease inhibitors (SPIs) regulate protease-mediated activities by inactivating their cognate proteinases, and are involved in multiple physiological processes. SPIs have been extensively studied in vertebrates and invertebrates; however, little SPI information is available in parasitoids. Herein, we identified 57 SPI genes in total through the genome of a parasitoid wasp, Pteromalus puparum. Gene structure analyses revealed that these SPIs contain 7 SPI domains. Depending on their mode of action, these SPIs can be categorized into serpins, canonical inhibitors and alpha-2-macroglobulins (A2Ms). For serpins and canonical inhibitors, we predicted their putative inhibitory activities to trypsin/chymotrypsin/elastase-like enzymes based on the amino acids in cleaved reactive sites. Sequence alignment and phylogenetic tree indicated that some serpins similar to known functional inhibitory serpins may participate in immune responses. Transcriptome analysis also showed some canonical SPI genes displayed distinct expression patterns in the venom gland and this was confirmed by quantitative real-time PCR (qPCR) analysis, suggesting their specific physiological functions as venom proteins in suppressing host immune responses. The study provides valuable information to clarify the functions of SPIs in digestion, development, reproduction and innate immunity.
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria
Authors: Koduru Lokanand , Kim Yujin , Bang Jeongsu , Lakshmanan Meiyappan , Han Nam Soo , Lee Dong-Yup 
Published: November 2017

AbstractObligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity. With established predictive capabilities, we subsequently employed iLME620 to elucidate unique metabolic characteristics of L. mesenteroides, such as the limited ability to utilize amino acids as energy source, and to substantiate the role of malolactic fermentation (MLF) in the reduction of pH-homeostatic burden on F0F1-ATPase. We also reported new hypothesis on the MLF mechanism that could be explained via a substrate channelling-like phenomenon mainly influenced by intracellular redox state rather than the intermediary reactions. Model simulations further revealed possible proton-symporter dependent activity of the energy efficient glucose-phosphotransferase system in obligate heterofermentative LAB. Moreover, integrated transcriptomic analysis allowed us to hypothesize transcriptional regulatory bias affecting the intracellular redox state. The insights gained here about the low ATP-yielding metabolism of L. mesenteroides, dominantly controlled by the cellular redox state, could potentially aid strain design for probiotic and cell factory applications.
Heterologous expression and characterization of a new lipase from Pseudomonas fluorescens Pf0–1 and used for biodiesel production
Authors: Liu Wu , Li Menggang , Yan Yunjun 
Published: November 2017

AbstractAs a kind of important biocatalysts, Pseudomonas lipases are commonly applied in various industrial fields. Pflip1, a new extracellular lipase gene from Pseudomonas. fluorescens Pf0–1, was first cloned and respectively expressed in Escherichia coli BL21(DE3) and Pichia pastoris KM71, the recombinant proteins Pflip1a and Pflip1b were later purified separately. Then Pflip1a was further characterized. The optimum pH of Pflip1a was 8.0 and its optimal temperature was 70 °C. After incubation at 70 °C for 12 h, Pflip1a could retain over 95% of its original activity. It showed the highest activity towards p-nitrophenyl caprylate. Moreover, its activity was profoundly affected by metal ion, ionic surfactants and organic solvents. Furthermore, the two obtained recombinant lipases were immobilized on the magnetic nanoparticles for biodiesel preparation. The GC analysis showed that for the immobilized lipases Pflip1b and Pflip1a, the biodiesel yield within 24 h respectively attained 68.5% and 80.5% at 70 °C. The activities of the two immobilized lipases still remained 70% and 82% after 10 cycles of operations in non-solvent system. These characteristics and transesterification capacity of the recombinant protein indicated its great potential for organic synthesis, especially for biodiesel production.
Development and physiological effects of an artificial diet for Wolbachia-infected Aedes aegypti
Authors: Dutra Heverton Leandro Carneiro , Rodrigues Silvia Lomeu , Mansur Simone Brutman , de Oliveira Sofia Pimenta , Caragata Eric Pearce , Moreira Luciano Andrade 
Published: November 2017

AbstractThe endosymbiotic bacterium Wolbachia spreads rapidly through populations of Aedes aegypti mosquitoes, and strongly inhibits infection with key human pathogens including the dengue and Zika viruses. Mosquito control programs aimed at limiting transmission of these viruses are ongoing in multiple countries, yet there is a dearth of mass rearing infrastructure specific to Wolbachia-infected mosquitoes. One example is the lack of a blood meal substitute, which accounts for the Wolbachia-specific physiological changes in infected mosquitoes, that allows the bacterium to spread, and block viral infections. To that end, we have developed a blood meal substitute specifically for mosquitoes infected with the wMel Wolbachia strain. This diet, ADM, contains milk protein, and infant formula, dissolved in a mixture of bovine red blood cells and Aedes physiological saline, with ATP as a phagostimulant. Feeding with ADM leads to high levels of viable egg production, but also does not affect key Wolbachia parameters including, bacterial density, cytoplasmic incompatibility, or resistance to infection with Zika virus. ADM represents an effective substitute for human blood, which could potentially be used for the mass rearing of wMel-infected A. aegypti, and could easily be optimized in the future to improve performance.
Quantitative Evaluation of Nanosecond Pulsed Laser-Induced Photomodification of Plasmonic Gold Nanoparticles
Authors: Fales Andrew M. , Vogt William C. , Pfefer T. Joshua , Ilev Ilko K. 
Published: November 2017

AbstractThe rapid growth of gold nanoparticle applications in laser therapeutics and diagnostics has brought about the need for establishing innovative standardized test methods for evaluation of safety and performance of these technologies and related medical products. Furthermore, given the incomplete and inconsistent data on nanoparticle photomodification thresholds provided in the literature, further elucidation of processes that impact the safety and effectiveness of laser-nanoparticle combination products is warranted. Therefore, we present a proof-of-concept study on an analytical experimental test methodology including three approaches (transmission electron microscopy, dynamic light scattering, and spectrophotometry) for experimental evaluation of damage thresholds in nanosecond pulsed laser-irradiated gold nanospheres, and compared our results with a theoretical model and prior studies. This thorough evaluation of damage threshold was performed based on irradiation with a 532 nm nanosecond-pulsed laser over a range of nanoparticle diameters from 20 to 100 nm. Experimentally determined damage thresholds were compared to a theoretical heat transfer model of pulsed laser-irradiated nanoparticles and found to be in reasonably good agreement, although some significant discrepancies with prior experimental studies were found. This study and resultant dataset represent an important foundation for developing a standardized test methodology for determination of laser-induced nanoparticle damage thresholds.
Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children
Authors: Muurinen Mari , Hannula-Jouppi Katariina , Reinius Lovisa E. , Söderhäll Cilla , Merid Simon Kebede , Bergström Anna , Melén Erik , Pershagen Göran , Lipsanen-Nyman Marita , Greco Dario , Kere Juha 
Published: November 2017

AbstractSilver-Russell syndrome (SRS) is a growth retardation syndrome in which loss of methylation on chromosome 11p15 (11p15 LOM) and maternal uniparental disomy for chromosome 7 [UPD(7)mat] explain 20–60% and 10% of the syndrome, respectively. To search for a molecular cause for the remaining SRS cases, and to find a possible common epigenetic change, we studied DNA methylation pattern of more than 450 000 CpG sites in 44 SRS patients. Common to all three SRS subgroups, we found a hypomethylated region at the promoter region of HOXA4 in 55% of the patients. We then tested 39 patients with severe growth restriction of unknown etiology, and found hypomethylation of HOXA4 in 44% of the patients. Finally, we found that methylation at multiple CpG sites in the HOXA4 promoter region was associated with height in a cohort of 227 healthy children, suggesting that HOXA4 may play a role in regulating human growth by epigenetic mechanisms.
Frailty is an independent predictor of incident dementia: Evidence from the English Longitudinal Study of Ageing
Authors: Rogers Nina T. , Steptoe Andrew , Cadar Dorina 
Published: November 2017

AbstractThe aim of this study was to determine whether frailty in older adults is associated with the risk of subsequent dementia. A total of 8,722 older adults from the English Longitudinal Study of Ageing were followed-up every two years until they reported a diagnosis of dementia, died, or were right censored. Frailty was defined using a frailty index comprised of 47 health deficits. To test if cognitive function influences the relationship between frailty and incident dementia, the analyses were repeated according to lower or upper three quartiles of baseline cognitive function. Competing risks regression and Cox proportional hazard models were used to evaluate whether the degree of baseline frailty was associated with incident dementia. Compared with non-frail participants, pre-frail (HR: 1.51 95%CI [1.12–2.02]) and frail participants (HR: 1.73 95%CI [1.22–2.43]) had a higher risk of developing dementia, after adjustment for covariates. The association between frailty and incident dementia was significant for adults in the upper three quartiles of global cognitive function (HR: 3.48 95%CI [1.98–6.12]), but not for adults who were in the lowest quartile of cognitive function (HR: 1.13 95%CI [0.74–1.71]). Frailty should be monitored alongside cognitive functioning when assessing risk factors for dementia in older adults.