bluuebunny/crossref_metadata_2025 huggingface dataset:
Body Fat Percentage in Relation to Lung Function in Individuals with Normal Weight Obesity
Authors: Chen Yuan-Yuei , Kao Tung-Wei , Fang Wen-Hui , Wang Chung-Ching , Chang Yaw-Wen , Yang Hui-Fang , Wu Chen-Jung , Sun Yu-Shan , Chen Wei-Liang
Published: June 2019

Accumulating evidence indicates the association between obesity and lung function. However, no previous study has examined whether obesity affects lung function in normal weight participants with high body fat. We hypothesized that subjects with normal weight obesity (NWO) were inversely associated with lung function in Taiwan. The study sample was composed of participants who attended health examinations at the Tri-Service General Hospital from 2010 to 2016. A total of 7801 eligible participants who were classified as NWO were divided into quartiles by percentage body fat (PBF), which was measured by bioelectrical impedance analysis (BIA). A multivariable linear regression was performed to assess the association between PBF quartiles and pulmonary function. The relationship between PBF and the presence of obstructive and restrictive lung diseases was analyzed by a logistic regression. PBF quartiles were closely associated with reduced forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) in all adjusted models. This relationship remained significant in the male population, and a dose-dependent effect was observed. Increased PBF was associated with increased risks for the presence of restrictive lung diseases. These results presented a novel finding that body fat exhibited an inverse association with pulmonary function in NWO subjects. More comprehensive management of subjects with normal weight but high body fat, which might contribute to metabolic dysfunction and impaired pulmonary function, is needed.
Whole blood microRNA levels associate with glycemic status and correlate with target mRNAs in pathways important to type 2 diabetes
Authors: Mononen Nina , Lyytikäinen Leo-Pekka , Seppälä Ilkka , Mishra Pashupati P. , Juonala Markus , Waldenberger Melanie , Klopp Norman , Illig Thomas , Leiviskä Jaana , Loo Britt-Marie , Laaksonen Reijo , Oksala Niku , Kähönen Mika , Hutri-Kähönen Nina , Raitakari Olli , Lehtimäki Terho , Raitoharju Emma
Published: June 2019

We analyzed the associations between whole blood microRNA profiles and the indices of glucose metabolism and impaired fasting glucose and examined whether the discovered microRNAs correlate with the expression of their mRNA targets. MicroRNA and gene expression profiling were performed for the Young Finns Study participants (n = 871). Glucose, insulin, and glycated hemoglobin (HbA1c) levels were measured, the insulin resistance index (HOMA2-IR) was calculated, and the glycemic status (normoglycemic [n = 534]/impaired fasting glucose [IFG] [n = 252]/type 2 diabetes [T2D] [n = 24]) determined. Levels of hsa-miR-144-5p, -122-5p, -148a-3p, -589-5p, and hsa-let-7a-5p associated with glycemic status. hsa-miR-144-5p and -148a-3p associated with glucose levels, while hsa-miR-144-5p, -122-5p, -184, and -339-3p associated with insulin levels and HOMA2-IR, and hsa-miR-148a-3p, -15b-3p, -93-3p, -146b-5p, -221-3p, -18a-3p, -642a-5p, and -181-2-3p associated with HbA1c levels. The targets of hsa-miR-146b-5p that correlated with its levels were enriched in inflammatory pathways, and the targets of hsa-miR-221-3p were enriched in insulin signaling and T2D pathways. These pathways showed indications of co-regulation by HbA1c-associated miRNAs. There were significant differences in the microRNA profiles associated with glucose, insulin, or HOMA-IR compared to those associated with HbA1c. The HbA1c-associated miRNAs also correlated with the expression of target mRNAs in pathways important to the development of T2D.
Hybridization between two high Arctic cetaceans confirmed by genomic analysis
Authors: Skovrind Mikkel , Castruita Jose Alfredo Samaniego , Haile James , Treadaway Eve C. , Gopalakrishnan Shyam , Westbury Michael V. , Heide-Jørgensen Mads Peter , Szpak Paul , Lorenzen Eline D.
Published: June 2019

In 1990, a skull from a morphologically unusual Monodontid was found in West Greenland and collected for the Natural History Museum of Denmark, University of Copenhagen. From its intermediate morphology, the skull was hypothesized to be a beluga/narwhal hybrid. If confirmed, the specimen would, to our knowledge, represent the sole evidence of hybridization between the only two toothed whale species endemic to the Arctic. Here we present genome-wide DNA sequence data from the specimen and investigate its origin using a genomic reference panel of eight belugas and eight narwhals. Our analyses reveal that the specimen is a male, first-generation hybrid between a female narwhal and a male beluga. We use stable carbon and nitrogen isotope analysis to investigate the dietary niche of the hybrid and find a higher δ13C value than in both belugas and narwhals, suggesting a foraging strategy unlike either parental species. These results further our understanding of the interaction between belugas and narwhals, and underscore the importance of natural history collections in monitoring changes in biodiversity. In addition, our study exemplifies how recent major advances in population genomic analyses using genotype likelihoods can provide key biological and ecological insights from low-coverage data (down to 0.05x).
Principled BCI Decoder Design and Parameter Selection Using a Feedback Control Model
Authors: Willett Francis R. , Young Daniel R. , Murphy Brian A. , Memberg William D. , Blabe Christine H. , Pandarinath Chethan , Stavisky Sergey D. , Rezaii Paymon , Saab Jad , Walter Benjamin L. , Sweet Jennifer A. , Miller Jonathan P. , Henderson Jaimie M. , Shenoy Krishna V. , Simeral John D. , Jarosiewicz Beata , Hochberg Leigh R. , Kirsch Robert F. , Bolu Ajiboye A.
Published: June 2019

Decoders optimized offline to reconstruct intended movements from neural recordings sometimes fail to achieve optimal performance online when they are used in closed-loop as part of an intracortical brain-computer interface (iBCI). This is because typical decoder calibration routines do not model the emergent interactions between the decoder, the user, and the task parameters (e.g. target size). Here, we investigated the feasibility of simulating online performance to better guide decoder parameter selection and design. Three participants in the BrainGate2 pilot clinical trial controlled a computer cursor using a linear velocity decoder under different gain (speed scaling) and temporal smoothing parameters and acquired targets with different radii and distances. We show that a user-specific iBCI feedback control model can predict how performance changes under these different decoder and task parameters in held-out data. We also used the model to optimize a nonlinear speed scaling function for the decoder. When used online with two participants, it increased the dynamic range of decoded speeds and decreased the time taken to acquire targets (compared to an optimized standard decoder). These results suggest that it is feasible to simulate iBCI performance accurately enough to be useful for quantitative decoder optimization and design.
Integration of expert knowledge in the definition of Swiss pear core collection
Authors: Urrestarazu J. , Kägi C. , Bühlmann A. , Gassmann J. , Santesteban L. G. , Frey J. E. , Kellerhals M. , Miranda C.
Published: June 2019

Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.
The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinx
Authors: Yohannes Elizabeth , Kazanjian Avedis A. , Lindsay Morgan E. , Fujii Dennis T. , Ieronimakis Nicholas , Chow Gregory E. , Beesley Ronald D. , Heitmann Ryan J. , Burney Richard O.
Published: June 2019

Hydrosalpinx, the blockage of fallopian tubes, can result from pelvic inflammatory disease. Hydrosalpinx is a cause of infertility and negatively impactsin vitrofertilization. To better understand the pathobiology of hydrosalpinx, we compared the proteome of lavages from disease vs. healthy fallopian tubes. Results indicate a disruption of redox homeostasis and activation of the complement system, immune cell infiltration, and phagocytosis; pathways that may drive tubal injury. To our surprise among the most prominent proteins with hydrosalpinx was mesothelin (MSLN), which until now has only been associated with epithelial malignancies. Analogous to mesothelioma and ovarian carcinoma, a significant increase of MSLN was detected in plasma from patients with hydrosalpinx. This finding suggests MSLN may provide clinical diagnosis in lieu of the current approaches that require invasive imaging. Importantly, these findings implicate MSLN in a benign disease, indicating that the activation and role of MSLN is not restricted to cancer.
A quantitative, hierarchical approach for detecting drift dives and tracking buoyancy changes in southern elephant seals
Authors: Arce Fernando , Bestley Sophie , Hindell Mark A. , McMahon Clive R. , Wotherspoon Simon
Published: June 2019

Foraging behaviour of marine predators inferred from the analysis of horizontal or vertical movements commonly lack quantitative information about foraging success. Several marine mammal species are known to perform dives where they passively drift in the water column, termed “drift” dives. The drift rate is determined by the animal’s buoyancy, which can be used to make inference regarding body condition. Long term dive records retrieved via satellite uplink are often summarized before transmission. This loss of resolution hampers identification of drift dives. Here, we develop a flexible, hierarchically structured approach to identify drift dives and estimate the drift rate from the summarized time-depth profiles that are increasingly available to the global research community. Based on high-resolution dive data from southern elephant seals, we classify dives as drift/non-drift and apply a summarization algorithm. We then (i) automatically generate dive groups based on inflection point ordering using a ‘Reverse’ Broken-Stick Algorithm, (ii) develop a set of threshold criteria to apply across groups, ensuring non-drift dives are most efficiently rejected, and (iii) finally implement a custom Kalman filter to retain the remaining dives that are within the seals estimated drifting time series. Validation with independent data sets shows our method retains approximately 3% of all dives, of which 88% are true drift dives. The drift rate estimates are unbiased, with the upper 95% quantile of the mean squared error between the daily averaged summarized profiles using our method (SDDR) and the observed daily averaged drift rate (ODDR) being only 0.0015. The trend of the drifting time-series match expectations for capital breeders, showing the lowest body condition commencing foraging trips and a progressive improvement as they remain at sea. Our method offers sufficient resolution to track small changes in body condition at a fine temporal scale. This approach overcomes a long-term challenge for large existing and ongoing data collections, with potential application across other drift diving species. Enabling robust identification of foraging success at sea offers a rare and valuable opportunity for monitoring marine ecosystem productivity in space and time by tracking the success of a top predator.
Single-Molecule 3D Images of “Hole-Hole” IgG1 Homodimers by Individual-Particle Electron Tomography
Authors: Lei Dongsheng , Liu Jianfang , Liu Hongbin , Cleveland Thomas E. , Marino John P. , Lei Ming , Ren Gang
Published: June 2019

The engineering of immunoglobulin-G molecules (IgGs) is of wide interest for improving therapeutics, for example by modulating the activity or multiplexing the specificity of IgGs to recognize more than one antigen. Optimization of engineered IgG requires knowledge of three-dimensional (3D) structure of synthetic IgG. However, due to flexible nature of the molecules, their structural characterization is challenging. Here, we use our reported individual-particle electron tomography (IPET) method with optimized negative-staining (OpNS) for direct 3D reconstruction of individual IgG hole-hole homodimer molecules. The hole-hole homodimer is an undesired variant generated during the production of a bispecific antibody using the knob-into-hole heterodimer technology. A total of 64 IPET 3D density maps at ~15 Å resolutions were reconstructed from 64 individual molecules, revealing 64 unique conformations. In addition to the known Y-shaped conformation, we also observed an unusual X-shaped conformation. The 3D structure of the X-shaped conformation contributes to our understanding of the structural details of the interaction between two heavy chains in the Fc domain. The IPET approach, as an orthogonal technique to characterize the 3D structure of therapeutic antibodies, provides insight into the 3D structural variety and dynamics of heterogeneous IgG molecules.
Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells
Authors: Ghashghaei Maryam , Niazi Tamim M. , Aguilar-Mahecha Adriana , Klein Kathleen Oros , Greenwood Celia M. T. , Basik Mark , Muanza Thierry M.
Published: June 2019

Prostate cancer (PCa) is the most common cancer amongst men. A novel androgen receptor (AR) antagonist, enzalutamide (ENZA) has recently been demonstrated to enhance the effect of radiation (XRT) by impairing the DNA damage repair process. This study aimed to identify a radiosensitive gene signature induced by ENZA in the PCa cells and to elucidate the biological pathways which influence this radiosensitivity. We treated LNCaP (AR-positive, hormone-sensitive PCa cells) and C4-2 (AR-positive, hormone-resistant PCa cells) cells with ENZA alone and in combination with androgen deprivation therapy (ADT) and XRT. Using one-way ANOVA on the gene expression profiling, we observed significantly differentially expressed (DE) genes in inflammation-and metabolism-related genes in hormone-sensitive and hormone-resistant PCa cell lines respectively. Survival analysis in both the TCGA PRAD and GSE25136 datasets suggested an association between the expression of these genes and time to recurrence. These results indicated that ENZA alone or in combination with ADT enhanced the effect of XRT through immune and inflammation-related pathways in LNCaP cells and metabolic-related pathways in C4-2 cells. Kaplan–Meier analysis and Cox proportional hazard models showed that low expression of all the candidate genes except for PTPRN2 were associated with tumor progression and recurrence in a PCa cohort.
Sialyl Glycan Expression on T Cell Subsets in Asthma: a correlation with disease severity and blood parameters
Authors: Yeh Yu-Liang , Wu Wen-Chia , Kannagi Reiji , Chiang Bor-Luen , Liu Fu-Tong , Lee Yungling Leo
Published: June 2019

Memory T helper (Th) and regulatory T (Treg) cells play key roles in asthma. Certain sialyl carbohydrate determinants for selectins profoundly affect the migratory properties of memory Th cells, and the suppressive function of Treg cells. Previous studies have shown that the proportion of CCR4+ memory Th cells expressing sialyl 6-sulfo Lewis X (LeX) is elevated in asthma patients. We aim to investigate the roles of different sialyl glycans on T cell subsets in asthma. Using flow cytometry, we assessed the expression of three sialyl glycans, sialyl 6-sulfo LeX, cyclic sialyl 6-sulfo LeX, and sialyl LeX on memory Th and Treg cells, in the peripheral blood of asthmatic children. We also assessed the relationships between glycan-expressing cell percentages and asthma clinical parameters. Compared with controls, asthmatic children showed higher proportions of memory Th cells expressing sialyl LeX and sialyl 6-sulfo LeX. The proportions of memory Th cells with sialyl 6-sulfo LeX and cyclic sialyl 6-sulfo LeX expression in asthmatic children correlated with absolute eosinophil count and IgE level, respectively. Children with moderate-to-severe asthma had lower numbers of sialyl LeX positive Treg cells. Our study suggests that sialyl glycans on T cells may play important roles in the pathogenesis of asthma.
Overexpression of cyclooxygenase-2 in adipocytes reduces fat accumulation in inguinal white adipose tissue and hepatic steatosis in high-fat fed mice
Authors: Banhos Danneskiold-Samsøe Niels , Sonne Si Brask , Larsen Jeppe Madura , Hansen Ann Normann , Fjære Even , Isidor Marie Sophie , Petersen Sidsel , Henningsen Jeanette , Severi Ilenia , Sartini Loris , Schober Yvonne , Wolf Jacqueline , Nockher W. Andreas , Wolfrum Christian , Cinti Saverio , Sina Christian , Hansen Jacob B. , Madsen Lise , Brix Susanne , Kristiansen Karsten
Published: June 2019

Cyclooxygenases are known as important regulators of metabolism and immune processes via conversion of C20 fatty acids into various regulatory lipid mediators, and cyclooxygenase activity has been implicated in browning of white adipose tissues. We generated transgenic (TG) C57BL/6 mice expressing thePtgs2gene encoding cyclooxygenase-2 (COX-2) in mature adipocytes. TG mice fed a high-fat diet displayed marginally lower weight gain with less hepatic steatosis and a slight improvement in insulin sensitivity, but no difference in glucose tolerance. Compared to littermate wildtype mice, TG mice selectively reduced inguinal white adipose tissue (iWAT) mass and fat cell size, whereas the epididymal (eWAT) fat depot remained unchanged. The changes in iWAT were accompanied by increased levels of specific COX-derived lipid mediators and increased mRNA levels of interleukin-33, interleukin-4 and arginase-1, but not increased expression of uncoupling protein 1 or increased energy expenditure. Epididymal WAT (eWAT) in TG mice exhibited few changes except from increased infiltration with eosinophils. Our findings suggest a role for COX-2-derived lipid mediators from adipocytes in mediating type 2 immunity cues in subcutaneous WAT associated with decreased hepatic steatosis, but with no accompanying induction of browning and increased energy expenditure.
Graph-Theoretic Analysis of Belief System Dynamics under Logic Constraints
Authors: Nedić Angelia , Olshevsky Alex , Uribe César A.
Published: June 2019

Opinion formation cannot be modeled solely as an ideological deduction from a set of principles; rather, repeated social interactions and logic constraints among statements are consequential in the construct of belief systems. We address three basic questions in the analysis of social opinion dynamics: (i) Will a belief system converge? (ii) How long does it take to converge? (iii) Where does it converge? We provide graph-theoretic answers to these questions for a model of opinion dynamics of a belief system with logic constraints. Our results make plain the implicit dependence of the convergence properties of a belief system on the underlying social network and on the set of logic constraints that relate beliefs on different statements. Moreover, we provide an explicit analysis of a variety of commonly used large-scale network models.
A systematic literature review on the European, African and Amerindian genetic ancestry components on Brazilian health outcomes
Authors: Pereira Fabiana dos Santos Carolino Firmo , Guimarães Raphael Mendonça , Lucidi Alexandre Ramos , Brum Doralina Guimarães , Paiva Carmen Lucia Antão , Alvarenga Regina Maria Papais
Published: June 2019

The variables such as race, skin colour and ethnicity have become intensely discussed in medicine research, as a response to the rising debate over the importance of the ethnic-racial dimension in the scope of health-disease processes. The aim of this study was to identify the European (EUR), African (AFR) and Amerindian (AMR) ancestries on Brazilian health outcomes through a systematic literature review. This study was carried out by searching in three electronic databases, for studies published between 2005 and 2017. A total of 13 papers were eligible. The search identified the following health outcomes: visceral leishmaniosis, malaria, Alzheimer’s disease, neuromyelitis optica, multiple sclerosis, prostate cancer, non-syndromic cleft lip/palate, chronic heart failure, sickle cell disease, primary congenital glaucoma, preterm labour, preterm premature rupture of membranes, systemic lupus erythematosus and type 1 diabetes mellitus. Research paper assessments were guided by the STROBE instrument, and agreements between results were determined by comparing the points attributed by two authors. Increased EUR ancestry was identified from preterm labour (PTL), type 1 diabetes (T1D) and non-syndromic cleft lip with or without cleft palate (NSCL), as well as in patients presenting aggressive prostate cancer prognoses. On the other hand, the highest AFR ancestral component was verified from systemic lupus erythematosus (SLE) and primary congenital glaucoma (PCG) cases, presenting worse prognoses. AMR ancestry may be a protective factor in the development of Alzheimer’s disease (AD). The worst hemodynamic parameters in cases of heart failure (HF) were identified among individuals with greater AMR and AFR ancestry indices.
Demethylation and microRNA differential expression regulate plasma-induced improvement of chicken sperm quality
Authors: Zhang Jiao Jiao , Chandimali Nisansala , Kim Nameun , Kang Tae Yoon , Kim Seong Bong , Kim Ji Su , Wang Xian Zhong , Kwon Taeho , Jeong Dong Kee
Published: June 2019

The sperm quality is a vital economical requisite of poultry production. Our previous study found non-thermal dielectric barrier discharge plasma exposure on fertilized eggs could increase the chicken growth and the male reproduction. However, it is unclear how plasma treatment regulates the reproductive capacity in male chickens. In this study, we used the optimal plasma treatment condition (2.81 W for 2 min) which has been applied on 3.5-day-incubated fertilized eggs in the previous work and investigated the reproductive performance in male chickens aged at 20 and 40 weeks. The results showed that plasma exposure increased sperm count, motility, fertility rate, and fertilization period of male chickens. The sperm quality-promoting effect of plasma treatment was regulated by the significant improvements of adenosine triphosphate production and testosterone level, and by the modulation of reactive oxygen species balance and adenosine monophosphate-activated protein kinase and mammalian target of rapamycin pathway in the spermatozoa. Additionally, the plasma effect suggested that DNA demethylation and microRNA differential expression (a total number of 39 microRNAs were up-regulated whereas 53 microRNAs down-regulated in the testis) regulated the increases of adenosine triphosphate synthesis and testosterone level for promoting the chicken sperm quality. This finding might be beneficial to elevate the fertilization rate and embryo quality for the next generation in poultry breeding.
Interference effects in quantum-optical coherence tomography using spectrally engineered photon pairs
Authors: Graciano Pablo Yepiz , Martínez Alí Michel Angulo , Lopez-Mago Dorilian , Castro-Olvera Gustavo , Rosete-Aguilar Martha , Garduño-Mejía Jesús , Alarcón Roberto Ramírez , Ramírez Héctor Cruz , U’Ren Alfred B.
Published: June 2019

Optical-coherence tomography (OCT) is a technique that employs light in order to measure the internal structure of semitransparent, e.g. biological, samples. It is based on the interference pattern of low-coherence light. Quantum-OCT (QOCT), instead, employs the correlation properties of entangled photon pairs, for example, generated by the process of spontaneous parametric downconversion (SPDC). The usual QOCT scheme uses photon pairs characterised by a joint-spectral amplitude with strict spectral anti-correlations. It has been shown that, in contrast with its classical counterpart, QOCT provides resolution enhancement and dispersion cancellation. In this paper, we revisit the theory of QOCT and extend the theoretical model so as to include photon pairs with arbitrary spectral correlations. We present experimental results that complement the theory and explain the physical underpinnings appearing in the interference pattern. In our experiment, we utilize a pump for the SPDC process ranging from continuous wave to pulsed in the femtosecond regime, and show that cross-correlation interference effects appearing for each pair of layers may be directly suppressed for a sufficiently large pump bandwidth. Our results provide insights and strategies that could guide practical implementations of QOCT.
Empathizing associates with mean diffusivity
Authors: Takeuchi Hikaru , Taki Yasuyuki , Nouchi Rui , Yokoyama Ryoichi , Kotozaki Yuka , Nakagawa Seishu , Sekiguchi Atsushi , Iizuka Kunio , Yamamoto Yuki , Hanawa Sugiko , Araki Tsuyoshi , Miyauchi Carlos Makoto , Sakaki Kohei , Sassa Yuko , Nozawa Takayuki , Ikeda Shigeyuki , Yokota Susumu , Daniele Magistro , Kawashima Ryuta
Published: June 2019

Empathizing is defined as “the drive to identify another’s mental states and to respond to these with an appropriate emotion” and systemizing is defined as “the drive to the drive to analyze and construct rule-based systems”. While mean diffusivity (MD) has been robustly associated with several cognitive traits and disorders related with empathizing and systemizing, its direct correlation with empathizing and systemizing remains to be investigated. We undertook voxel-by-voxel investigations of regional MD to discover microstructural correlates of empathizing, systemizing, and the discrepancy between them (D score: systemizing − empathizing). Whole-brain analyses of covariance revealed that across both sexes, empathizing was positively correlated with MD of (a) an anatomical cluster that primarily spreads in the areas in and adjacent to the left dorsolateral prefrontal cortex, left anterior to the middle cingulate cortex, and left insula and (b) an anatomical cluster of the left postcentral gyrus and left rolandic operculum. The former overlaps with positive MD correlates of cooperativeness. The D score and systemizing did not show significant correlations. In conclusion, while increased MD has generally been associated with reduced neural tissues and possibly area function, higher empathizing and cooperativeness were commonly reflected by greater MD values in areas (a) that mainly overlap with areas that play a key role in emotional salience and empathy. In addition, higher empathizing was correlated with greater MD values in areas (b) that play a key role in the mirror neuron system.
Combating viral contaminants in CHO cells by engineering innate immunity
Authors: Chiang Austin W. T. , Li Shangzhong , Kellman Benjamin P. , Chattopadhyay Gouri , Zhang Yaqin , Kuo Chih-Chung , Gutierrez Jahir M. , Ghazi Faezeh , Schmeisser Hana , Ménard Patrice , Bjørn Sara Petersen , Voldborg Bjørn G. , Rosenberg Amy S. , Puig Montserrat , Lewis Nathan E.
Published: June 2019

Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited activation of cellular immune responses and increased resistance to the RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.
Effects of geometry on large-scale tube-shear exfoliation of graphite to multilayer graphene and nanographite in water
Authors: Blomquist Nicklas , Alimadadi Majid , Hummelgård Magnus , Dahlström Christina , Olsen Martin , Olin Håkan
Published: June 2019

Industrially scalable methods for the production of graphene and other nanographites are needed to achieve cost-efficient commercial products. At present, there are several available routes for the production of these materials but few allow large-scale manufacturing and environmentally friendly low-cost solvents are rarely used. We have previously demonstrated a scalable and low-cost industrial route to produce nanographites by tube-shearing in water suspensions. However, for a deeper understanding of the exfoliation mechanism, how and where the actual exfoliation occurs must be known. This study investigates the effect of shear zone geometry, straight and helical coil tubes, on this system based on both numerical simulation and experimental data. The results show that the helical coil tube achieves a more efficient exfoliation with smaller and thinner flakes than the straight version. Furthermore, only the local wall shear stress in the turbulent flow is sufficient for exfoliation since the laminar flow contribution is well below the needed range, indicating that exfoliation occurs at the tube walls. This explains the exfoliation mechanism of water-based tube-shear exfoliation, which is needed to achieve scaling to industrial levels of few-layer graphene with known and consequent quality.
Live yeast in juvenile diet induces species-specific effects on Drosophila adult behaviour and fitness
Authors: Murgier Juliette , Everaerts Claude , Farine Jean-Pierre , Ferveur Jean-François
Published: June 2019

The presence and the amount of specific yeasts in the diet of saprophagous insects such as Drosophila can affect their development and fitness. However, the impact of different yeast species in the juvenile diet has rarely been investigated. Here, we measured the behavioural and fitness effects of three live yeasts (Saccharomyces cerevisiae = SC; Hanseniaspora uvarum = HU; Metschnikowia pulcherrima = MP) added to the diet of Drosophila melanogaster larvae. Beside these live yeast species naturally found in natural Drosophila populations or in their food sources, we tested the inactivated “drySC” yeast widely used in Drosophila research laboratories. All flies were transferred to drySC medium immediately after adult emergence, and several life traits and behaviours were measured. These four yeast diets had different effects on pre-imaginal development: HU-rich diet tended to shorten the “egg-to-pupa” period of development while MP-rich diet induced higher larval lethality compared to other diets. Pre- and postzygotic reproduction-related characters (copulatory ability, fecundity, cuticular pheromones) varied according to juvenile diet and sex. Juvenile diet also changed adult food choice preference and longevity. These results indicate that specific yeast species present in natural food sources and ingested by larvae can affect their adult characters crucial for fitness.
High frequency GPS bursts and path-level analysis reveal linear feature tracking by red foxes
Authors: Bischof Richard , Gjevestad Jon Glenn Omholt , Ordiz Andrés , Eldegard Katrine , Milleret Cyril
Published: June 2019

There is a need to quantify and better understand how wildlife interact with linear features, as these are integral elements of most landscapes. One potentially important aspect is linear feature tracking (LFT), yet studies rarely succeed in directly revealing or quantifying this behavior. In a proof-of-concept study, we employed short-term intensive GPS monitoring of red foxes (Vulpes vulpes) in a multiple-use landscape in southern Norway. Using periodic bursts of high frequency GPS position fixes, we performed modified path selection analyses to estimate the propensity of foxes to track natural and man-made linear features (roads, forest edges, and streams) once they are encountered. Foxes in our study tracked primarily forest edges and roads. Forty-three percent of bursts that encountered any linear feature resulted in LFT. LFT, although prominent, was manifested as a short-lived behavior, with overall median times to linear feature abandonment around two minutes. Movement speeds were highest along roads, perhaps due to greater ease of travel or higher perceived risk. In the highly heterogeneous habitats that characterize human-dominated landscapes, LFT may be manifested at such a fine spatio-temporal scale that it would remain hidden during telemetry studies employing conventional position fix frequencies. The approach described here may aid others studying spatial behaviors that are manifested over very short durations, yet are biologically significant.
Probing the effect(s) of the microwaves’ electromagnetic fields in enzymatic reactions
Authors: Horikoshi Satoshi , Nakamura Kota , Yashiro Mikio , Kadomatsu Kanae , Serpone Nick
Published: June 2019

This paper examines the effects that electromagnetic fields from microwave radiation have in enzymatic reactions. Hydrolysis of proteins in beef (in vivo case) and casein (in vitro case) by the papain enzyme, a major industrial enzyme, is used herein as a model reaction to assess, under highly controlled conditions, the various parameters of microwave radiation (electric field, magnetic field, pulsed microwave irradiation, continuous microwave irradiation) as they might influence these in vivo and in vitro enzymatic reactions. The effect(s) of the microwaves’ electromagnetic fields was clearly evidenced in the in vivo case, contrary to the in vitro case where no such effect was observed, likely due to the nature of the hydrolysis reaction and to the autolysis (self-digestion) of the papain enzyme. Additionally, the effect of pulsed versus continuous microwave irradiation was further assessed by examining the catalase-assisted decomposition of hydrogen peroxide.
Nucleation in confinement generates long-range repulsion between rough calcite surfaces
Authors: Dziadkowiec Joanna , Zareeipolgardani Bahareh , Dysthe Dag Kristian , Røyne Anja
Published: June 2019

Fluid-induced alteration of rocks and mineral-based materials often starts at confined mineral interfaces where nm-thick water films can persist even at high overburden pressures and at low vapor pressures. These films enable transport of reactants and affect forces acting between mineral surfaces. However, the feedback between the surface forces and reactivity of confined solids is not fully understood. We used the surface forces apparatus (SFA) to follow surface reactivity in confinement and measure nm-range forces between two rough calcite surfaces in NaCl, CaCl2, or MgCl2 solutions with ionic strength of 0.01, 0.1 or 1 M. We observed long-range repulsion that could not be explained by changes in calcite surface roughness, surface damage, or by electrostatic or hydration repulsion, but was correlated with precipitation events which started at µm-thick separations. We observed a submicron-sized precipitate that formed in the confined solution. This liquid-like viscous precipitate did not undergo any spontaneous ripening into larger crystals, which suggested that confinement prevented its dehydration. Nucleation was significantly postponed in the presence of Mg2+. The long-range repulsion generated by nucleation between confined mineral surfaces can have a crucial influence on evolution of the microstructure and therefore the macroscopic strength of rocks and materials.
Down regulation of p-coumarate 3-hydroxylase in petunia uniquely alters the profile of emitted floral volatiles
Authors: Kim Joo Young , Swanson Robert T. , Alvarez Maria I. , Johnson Timothy S. , Cho Keun H. , Clark David G. , Colquhoun Thomas A.
Published: June 2019

Petunia × hybrida cv ‘Mitchell Diploid’ floral volatile benzenoid/phenylpropanoid (FVBP) biosynthesis ultimately produces floral volatiles derived sequentially from phenylalanine, cinnamic acid, and p-coumaric acid. In an attempt to better understand biochemical steps after p-coumaric acid production, we cloned and characterized three petunia transcripts with high similarity to p-coumarate 3-hydroxylase (C3H), hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT), and caffeoyl shikimate esterase (CSE). Transcript accumulation of PhC3H and PhHCT was highest in flower limb tissue during open flower stages. PhCSE transcript accumulation was also highest in flower limb tissue, but it was detected earlier at initial flower opening with a bell-shaped distribution pattern. Down regulation of endogenous PhC3H transcript resulted in altered transcript accumulation of many other FVBP network transcripts, a reduction in floral volatiles, and the emission of a novel floral volatile. Down regulation of PhHCT transcript did not have as large of an effect on floral volatiles as was observed for PhC3H down regulation, but eugenol and isoeugenol emissions were significantly reduced on the downstream floral volatiles. Together these results indicate that PhC3H is involved in FVBP biosynthesis and the reduction of PhC3H transcript influences FVBP metabolism at the network level. Additional research is required to illustrate PhHCT and PhCSE functions of petunia.
Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen
Authors: Bedre Renesh , Irigoyen Sonia , Schaker Patricia D. C. , Monteiro-Vitorello Claudia B. , Da Silva Jorge A. , Mandadi Kranthi K.
Published: June 2019

Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane’s large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain
Authors: Schott-Verdugo Stephan , Müller Lena , Classen Elisa , Gohlke Holger , Groth Georg
Published: June 2019

The structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained elusive, hampering the understanding on how the perception of the plant hormone ethylene is transformed into a downstream signal. We generated the first structural model of the transmembrane sensor domain of ETR1 by integrating ab initio structure prediction and coevolutionary information. To refine and independently validate the model, we determined protein-related copper stoichiometries on purified receptor preparations and explored the helix arrangement by tryptophan scanning mutagenesis. All-atom molecular dynamics simulations of the dimeric model reveal how ethylene can bind proximal to the copper ions in the receptor, illustrating the initial stages of the ethylene perception process.
Divergent behavioural responses of gypsy moth (Lymantria dispar) caterpillars from three different subspecies to potential host trees
Authors: Clavijo McCormick Andrea , Arrigo Luca , Eggenberger Helen , Mescher Mark C. , De Moraes Consuelo M.
Published: June 2019

Almost all previous work on host-plant selection by insect herbivores has focused on adult behaviour; however, immature life stages can also play an active role in host discrimination. The important forest pest Lymantria dispar (gypsy moth) has three recognised subspecies: the European, Asian, and Japanese gypsy moth. Unlike the other two subspecies, the European subspecies is characterised by a loss of female flight ability, which might impose a selective pressure on larvae to actively engage in host-plant selection. We therefore explored the interactions of early-instar larvae from laboratory colonies of each subspecies with four potential hosts of differing quality: oak, beech, maple, and pine—measuring larval survival and performance, feeding preferences, responses to host-derived odour cues, and the propensity to disperse from hosts via ballooning. Compared to larvae from the Asian and Japanese subspecies, larvae from the (American-originated) European gypsy moth colony exhibited (i) significantly lower survival on the poorest quality host (pine), (ii) an ability to discriminate among hosts via olfactory cues; and (iii) higher propensity to disperse from sub-optimal hosts. These results are consistent with the hypothesis that larvae from flightless female European Gypsy moth subspecies play a more active role in host-plant selection.
Land use and land cover change effect on surface temperature over Eastern India
Authors: Gogoi Partha Pratim , Vinoj V. , Swain D. , Roberts G. , Dash J. , Tripathy S.
Published: June 2019

Land use and land cover (LULC) change has been shown to have significant effect on climate through various pathways that modulate land surface temperature and rainfall. However, few studies have illustrated such a link over the Indian region using observations. Through a combination of ground, satellite remote sensing and reanalysis products, we investigate the recent changes to land surface temperature in the Eastern state of Odisha between 1981 and 2010 and assess its relation to LULC. Our analysis reveals that the mean temperature of the state has increased by ~0.3 °C during the past three decades with the most accelerated warming (~0.9 °C) occurring during the recent decade (2001 to 2010). Our study shows that 25 to 50% of this observed overall warming is associated with LULC. Further we observe that the spatial pattern of LULC changes matches well with the independently estimated warming associated with LULC suggesting a physical association between them. This study also reveals that the largest changes are linked to changing vegetation cover as evidenced by changes to both LULC classes and normalized difference vegetation index (NDVI). Our study shows that the state has undergone an LULC induced warming which accounts for a quarter of the overall temperature rise since 2001. With the expected expansion of urban landscape and concomitant increase in anthropogenic activities along with changing cropping patterns, LULC linked changes to surface temperature and hence regional climate feedback over this region necessitates additional investigations.
A Hybrid Gene Selection Method Based on ReliefF and Ant Colony Optimization Algorithm for Tumor Classification
Authors: Sun Lin , Kong Xianglin , Xu Jiucheng , Xue Zhan’ao , Zhai Ruibing , Zhang Shiguang
Published: June 2019

For the DNA microarray datasets, tumor classification based on gene expression profiles has drawn great attention, and gene selection plays a significant role in improving the classification performance of microarray data. In this study, an effective hybrid gene selection method based on ReliefF and Ant colony optimization (ACO) algorithm for tumor classification is proposed. First, for the ReliefF algorithm, the average distance among k nearest or k non-nearest neighbor samples are introduced to estimate the difference among samples, based on which the distances between the samples in the same class or the different classes are defined, and then it can more effectively evaluate the weight values of genes for samples. To obtain the stable results in emergencies, a distance coefficient is developed to construct a new formula of updating weight coefficient of genes to further reduce the instability during calculations. When decreasing the distance between the same samples and increasing the distance between the different samples, the weight division is more obvious. Thus, the ReliefF algorithm can be improved to reduce the initial dimensionality of gene expression datasets and obtain a candidate gene subset. Second, a new pruning rule is designed to reduce dimensionality and obtain a new candidate subset with the smaller number of genes. The probability formula of the next point in the path selected by the ants is presented to highlight the closeness of the correlation relationship between the reaction variables. To increase the pheromone concentration of important genes, a new phenotype updating formula of the ACO algorithm is adopted to prevent the pheromone left by the ants that are overwhelmed with time, and then the weight coefficients of the genes are applied here to eliminate the interference of difference data as much as possible. It follows that the improved ACO algorithm has the ability of the strong positive feedback, which quickly converges to an optimal solution through the accumulation and the updating of pheromone. Finally, by combining the improved ReliefF algorithm and the improved ACO method, a hybrid filter-wrapper-based gene selection algorithm called as RFACO-GS is proposed. The experimental results under several public gene expression datasets demonstrate that the proposed method is very effective, which can significantly reduce the dimensionality of gene expression datasets, and select the most relevant genes with high classification accuracy.