bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractWe 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

AbstractIn 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

AbstractDecoders 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

AbstractCore 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

AbstractHydrosalpinx, 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

AbstractForaging 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

AbstractThe 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

AbstractProstate 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

AbstractMemory 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

AbstractCyclooxygenases 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

AbstractOpinion 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

AbstractThe 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

AbstractThe 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

AbstractOptical-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.