bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Multi-Microbial Probiotic Formulation Bokashi on Pro- and Anti-Inflammatory Cytokines Profile in the Serum, Colostrum and Milk of Sows, and in a Culture of Polymorphonuclear Cells Isolated from Colostrum
Authors: Laskowska Ewa , Jarosz Łukasz , Grądzki Zbigniew 
Published: January 2018

Abstract
The use of probiotics in sows during pregnancy and lactation and their impact on the quality of colostrum and milk, as well as the health conditions of their offspring during the rearing period, are currently gaining the attention of researchers. The aim of the study was to determine the effect of Bokashi formulation on the concentrations of pro- and anti-inflammatory cytokines in the serum of sows during pregnancy, in their colostrum and milk, and in a culture of Con-A-stimulated polymorphonuclear cells (PMNs) isolated from the colostrum. The study was conducted on 60 sows aged 2–4 years. EM Bokashi were added to the sows’ feed. The material for the study consisted of peripheral blood, colostrum, and milk. Blood samples were collected from the sows on days 60 and 114 of gestation. Colostrum and milk samples were collected from all sows at 0, 24, 48, 72, 96, 120, 144, and 168 h after parturition. The results indicate that the use of Bokashi as feed additives resulted in increased concentrations of pro-inflammatory cytokines TNF-α and IL-6, which increase the protective capacity of the colostrum by stimulating cellular immune mechanisms protecting the sow and neonates against infection. At the same time, the increased concentrations of cytokines IL-4, IL-10, TGF-β, and of immunoglobulins in the colostrum and milk from sows in the experimental group demonstrate the immunoregulatory effect of Bokashi on Th2 cells and may lead to increased expression of regulatory T cells and polarization of the immune response from Th1 to Th2.
Authoring the identity of learner before doctor in the figured world of medical school
Authors: Stubbing Evangeline , Helmich Esther , Cleland Jennifer 
Published: January 2018

Introduction Students enter the ‘figured world’ of medical school with preconceptions of what it means to be a doctor. The meeting of these early preconceptions and their newly developing identities can create emotional tensions. The aim of this study was to advance our understanding of how such tensions were experienced and managed. Using figured worlds as a theoretical framework we explored students’ interactions of preconceptions with their newly developing professional identities in their first year at medical school. Advancing our understanding of this phenomena provided new insights into the complex process of identity formation.
Methods This was a qualitative study underpinned by a constructivist epistemology. We ran biannual focus groups with 23 first year students in one UK medical school. Data were recorded, transcribed and then template analysis used to undertake an inductive, iterative process of analysis until it was considered the template provided a detailed representation of the data.
Results Significant preconceptions associated with the identity of a doctor were ‘to help’ and ‘to be a leader’. These early preconceptions were in conflict with realities of the figured world of medical school creating the emotional tensions of ‘being unable to help’ and ‘lacking power’, with implications for interactions with patients. By the end of year one students’ negotiated tensions and ‘self-authored’ their identity as a learner as opposed to an imagined ‘as if’ identity of a doctor.
Richard Neutra's Search for the Southland: California, Latin America and Spain
Authors: Tippey Brett 
Published: January 2018

AbstractDuring the twentieth century, diverse cultures from around the globe served as vital sources for architects who attempted to merge Modernist ideas with traditional values. Richard Neutra (1892–1970) absorbed ideas from Japan, the American Middle West and his own native Austria, and eventually his study of these regions deeply affected his work. By analysing archival sources and period publications, this article reveals that even before emigrating to the United States (1923), and throughout his career, the cultures of California, Latin America and Spain were also sources for Neutra's work. He travelled extensively throughout these regions, he researched their local customs and architecture and he deftly and purposefully incorporated vernacular elements, such as sun-shading devices, ventilation strategies and interior patios, into his own work. For his Latin American and Spanish colleagues, his work exemplified a successful fusion between their own traditions and Modernist principles.
On the universality of anomalous scaling exponents of structure functions in turbulent flows
Authors: Saw E.-W. , Debue P. , Kuzzay D. , Daviaud F. , Dubrulle B. 
Published: January 2018

All previous experiments in open turbulent flows (e.g. downstream of grids, jets and the atmospheric boundary layer) have produced quantitatively consistent values for the scaling exponents of velocity structure functions (Anselmet et al., J. Fluid Mech., vol. 140, 1984, pp. 63–89; Stolovitzky et al., Phys. Rev. E, vol. 48 (5), 1993, R3217; Arneodo et al., Europhys. Lett., vol. 34 (6), 1996, p. 411). The only measurement of scaling exponents at high order (${>}6$) in closed turbulent flow (von Kármán swirling flow) using Taylor’s frozen flow hypothesis, however, produced scaling exponents that are significantly smaller, suggesting that the universality of these exponents is broken with respect to change of large scale geometry of the flow. Here, we report measurements of longitudinal structure functions of velocity in a von Kármán set-up without the use of the Taylor hypothesis. The measurements are made using stereo particle image velocimetry at four different ranges of spatial scales, in order to observe a combined inertial subrange spanning approximately one and a half orders of magnitude. We found scaling exponents (up to ninth order) that are consistent with values from open turbulent flows, suggesting that they might be in fact universal.
Maximum palinstrophy amplification in the two-dimensional Navier–Stokes equations
Authors: Ayala Diego , Doering Charles R. , Simon Thilo M. 
Published: January 2018

We derive and assess the sharpness of analytic upper bounds for the instantaneous growth rate and finite-time amplification of palinstrophy in solutions of the two-dimensional incompressible Navier–Stokes equations. A family of optimal solenoidal fields parametrized by initial values for the Reynolds number $Re$ and palinstrophy ${\mathcal{P}}$ which maximize $\text{d}{\mathcal{P}}/\text{d}t$ is constructed by numerically solving suitable optimization problems for a wide range of $Re$ and ${\mathcal{P}}$, providing numerical evidence for the sharpness of the analytic estimate $\text{d}{\mathcal{P}}/\text{d}t\leqslant (a+b\sqrt{\ln Re+c}){\mathcal{P}}^{3/2}$ with respect to both $Re$ and ${\mathcal{P}}$. This family of instantaneously optimal fields is then used as initial data in fully resolved direct numerical simulations, and the time evolution of different relevant norms is carefully monitored as the palinstrophy is transiently amplified before decaying. The peak values of the palinstrophy produced by these initial data, i.e. $\sup _{t>0}{\mathcal{P}}(t)$, are observed to scale with the magnitude of the initial palinstrophy ${\mathcal{P}}(0)$ in accord with the corresponding a priori estimate. Implications of these findings for the question of finite-time singularity formation in the three-dimensional incompressible Navier–Stokes equation are discussed.
Static rivulet instabilities: varicose and sinuous modes
Authors: Bostwick J. B. , Steen P. H. 
Published: January 2018

A static rivulet is subject to disturbances in shape, velocity and pressure fields. Disturbances to interfacial shape accommodate a contact line that is either (i) fixed (pinned) or (ii) fully mobile (free) and preserves the static contact angle. The governing hydrodynamic equations for this inviscid, incompressible fluid are derived and then reduced to a functional eigenvalue problem on linear operators, which are parametrized by axial wavenumber and base-state volume. Solutions are decomposed according to their symmetry (varicose) or anti-symmetry (sinuous) about the vertical mid-plane. Dispersion relations are then computed. Static stability is obtained by setting growth rate to zero and recovers existing literature results. Critical growth rates and wavenumbers for the varicose and sinuous modes are reported. For the varicose mode, typical capillary break-up persists and the role of the liquid/solid interaction on the critical disturbance is illustrated. There exists a range of parameters for which the sinuous mode is the dominant instability mode. The sinuous instability mechanism is shown to correlate with horizontal centre-of-mass motion and illustrated using a toy model.
A randomised study in young subjects of the effects of eating extra fruit or nuts on periodontal inflammation
Authors: Fridell Sara , Ström Edvin , Agebratt Christian , Leanderson Per , Guldbrand Hans , Nystrom Fredrik H 
Published: January 2018

Abstract
Objectives/Aims:
Fruit is often advocated as a healthy source of nutrients and vitamins. However, the high contents of sugars in many fruits could potentially counteract positive effects on the teeth.

Materials and methods:
We recruited 30 healthy non-obese participants who were randomised to either supplement their diet with extra fruits or nuts, each at +7 kcal/kg body weight/day, for 2 months.

Results:
Fructose intake increased from 9.1±6.0 to 25.6±9.6 g/day, P<0.0001, in the fruit group and was reduced from 12.4±5.7 to 6.5±5.3 g/day, P=0.007, in the nut group. Serum-vitamin C increased in both groups (fruit: P=0.017; nuts: P=0.009). α-Tocopherol/cholesterol ratio increased in the fruit group (P=0.0033) while β-carotene/cholesterol decreased in the nut group (P<0.0001). The amount of subjects with probing pocket depths ⩾4 mm in the fruit group was reduced (P=0.045) according to blinded examinations, and the difference in the changes in probing pockets ⩾4 mm was also statistically significant between the food groups (P=0.010).

Conclusion:
A large increase of fruit intake, compared with nuts, had a favourable effect on periodontal status in some respects, despite the high sugar contents. To search for potential protective micronutrients in fruit that protect the teeth could be an aim for further research.
EGBMMDA: Extreme Gradient Boosting Machine for MiRNA-Disease Association prediction
Authors: Chen Xing , Huang Li , Xie Di , Zhao Qi 
Published: January 2018

AbstractAssociations between microRNAs (miRNAs) and human diseases have been identified by increasing studies and discovering new ones is an ongoing process in medical laboratories. To improve experiment productivity, researchers computationally infer potential associations from biological data, selecting the most promising candidates for experimental verification. Predicting potential miRNA–disease association has become a research area of growing importance. This paper presents a model of Extreme Gradient Boosting Machine for MiRNA-Disease Association (EGBMMDA) prediction by integrating the miRNA functional similarity, the disease semantic similarity, and known miRNA–disease associations. The statistical measures, graph theoretical measures, and matrix factorization results for each miRNA-disease pair were calculated and used to form an informative feature vector. The vector for known associated pairs obtained from the HMDD v2.0 database was used to train a regression tree under the gradient boosting framework. EGBMMDA was the first decision tree learning-based model used for predicting miRNA–disease associations. Respectively, AUCs of 0.9123 and 0.8221 in global and local leave-one-out cross-validation proved the model’s reliable performance. Moreover, the 0.9048 ± 0.0012 AUC in fivefold cross-validation confirmed its stability. We carried out three different types of case studies of predicting potential miRNAs related to Colon Neoplasms, Lymphoma, Prostate Neoplasms, Breast Neoplasms, and Esophageal Neoplasms. The results indicated that, respectively, 98%, 90%, 98%, 100%, and 98% of the top 50 predictions for the five diseases were confirmed by experiments. Therefore, EGBMMDA appears to be a useful computational resource for miRNA–disease association prediction.
Magnetically induced transparency of a quantum metamaterial composed of twin flux qubits
Authors: Shulga K. V. , Il’ichev E. , Fistul M. V. , Besedin I. S. , Butz S. , Astafiev O. V. , Hübner U. , Ustinov A. V. 
Published: January 2018

AbstractQuantum theory is expected to govern the electromagnetic properties of a quantum metamaterial, an artificially fabricated medium composed of many quantum objects acting as artificial atoms. Propagation of electromagnetic waves through such a medium is accompanied by excitations of intrinsic quantum transitions within individual meta-atoms and modes corresponding to the interactions between them. Here we demonstrate an experiment in which an array of double-loop type superconducting flux qubits is embedded into a microwave transmission line. We observe that in a broad frequency range the transmission coefficient through the metamaterial periodically depends on externally applied magnetic field. Field-controlled switching of the ground state of the meta-atoms induces a large suppression of the transmission. Moreover, the excitation of meta-atoms in the array leads to a large resonant enhancement of the transmission. We anticipate possible applications of the observed frequency-tunable transparency in superconducting quantum networks.
A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
Authors: So Austin P. , Vilborg Anna , Bouhlal Yosr , Koehler Ryan T. , Grimes Susan M. , Pouliot Yannick , Mendoza Daniel , Ziegle Janet , Stein Jason , Goodsaid Federico , Lucero Michael Y. , De La Vega Francisco M. , Ji Hanlee P. 
Published: January 2018

AbstractNext-generation deep sequencing of gene panels is being adopted as a diagnostic test to identify actionable mutations in cancer patient samples. However, clinical samples, such as formalin-fixed, paraffin-embedded specimens, frequently provide low quantities of degraded, poor quality DNA. To overcome these issues, many sequencing assays rely on extensive PCR amplification leading to an accumulation of bias and artifacts. Thus, there is a need for a targeted sequencing assay that performs well with DNA of low quality and quantity without relying on extensive PCR amplification. We evaluate the performance of a targeted sequencing assay based on Oligonucleotide Selective Sequencing, which permits the enrichment of genes and regions of interest and the identification of sequence variants from low amounts of damaged DNA. This assay utilizes a repair process adapted to clinical FFPE samples, followed by adaptor ligation to single stranded DNA and a primer-based capture technique. Our approach generates sequence libraries of high fidelity with reduced reliance on extensive PCR amplification—this facilitates the accurate assessment of copy number alterations in addition to delivering accurate single nucleotide variant and insertion/deletion detection. We apply this method to capture and sequence the exons of a panel of 130 cancer-related genes, from which we obtain high read coverage uniformity across the targeted regions at starting input DNA amounts as low as 10 ng per sample. We demonstrate the performance using a series of reference DNA samples, and by identifying sequence variants in DNA from matched clinical samples originating from different tissue types.
Inflammatory gene expression signatures in idiopathic intracranial hypertension: possible implications in microgravity-induced ICP elevation
Authors: Zanello Susana B. , Tadigotla Vasisht , Hurley James , Skog Johan , Stevens Brian , Calvillo Eusebia , Bershad Eric 
Published: January 2018

AbstractThe visual impairment and intracranial pressure (VIIP) syndrome is a neuro–ophthalmologic condition described in astronauts returning from long duration space missions. Idiopathic intracranial hypertension (IIH), also known as pseudotumor cerebri, is characterized by a chronic elevation of intracranial pressure (ICP) in the absence of an intracranial mass lesion. Because VIIP and IIH share some neurologic and ophthalmologic manifestations, the latter might be used as a model to study some of the processes underlying VIIP. This work constitutes a preliminary investigation of the molecular pathways associated with the elevation of ICP in IIH. Gene expression signatures were obtained from exosomes collected from CSF and plasma in patients with possible signs of IIH. The gene expression targets focused on inflammatory genes and miRNAs. The results suggest that inflammatory cytokine-driven processes and immune cell migration are activated when ICP is elevated in IIH patients, either as a cause or effect of the ICP increase. Several miRNAs appear to be involved in this response, among which miR-9 and miR-16 are upregulated in CSF and plasma of higher ICP subjects. This study provides evidence in support of neurophysiological alterations and neuro-immunomodulation in this condition. If similar changes are seen in astronauts manifesting with the VIIP syndrome, an underlying pathophysiological basis may be discovered.
Majorana zero modes and long range edge correlation in interacting Kitaev chains: analytic solutions and density-matrix-renormalization-group study
Authors: Miao Jian-Jian , Jin Hui-Ke , Zhang Fu-Chun , Zhou Yi 
Published: January 2018

AbstractWe study Kitaev model in one-dimension with open boundary condition by using exact analytic methods for non-interacting system at zero chemical potential as well as in the symmetric case of Δ = t, and by using density-matrix-renormalization-group method for interacting system with nearest neighbor repulsion interaction. We suggest and examine an edge correlation function of Majorana fermions to characterize the long range order in the topological superconducting states and study the phase diagram of the interating Kitaev chain.
The effect of image position on the Independent Components of natural binocular images
Authors: Hunter David W. , Hibbard Paul B. 
Published: January 2018

AbstractHuman visual performance degrades substantially as the angular distance from the fovea increases. This decrease in performance is found for both binocular and monocular vision. Although analysis of the statistics of natural images has provided significant insights into human visual processing, little research has focused on the statistical content of binocular images at eccentric angles. We applied Independent Component Analysis to rectangular image patches cut from locations within binocular images corresponding to different degrees of eccentricity. The distribution of components learned from the varying locations was examined to determine how these distributions varied across eccentricity. We found a general trend towards a broader spread of horizontal and vertical position disparity tunings in eccentric regions compared to the fovea, with the horizontal spread more pronounced than the vertical spread. Eccentric locations above the centroid show a strong bias towards far-tuned components, eccentric locations below the centroid show a strong bias towards near-tuned components. These distributions exhibit substantial similarities with physiological measurements in V1, however in common with previous research we also observe important differences, in particular distributions of binocular phase disparity which do not match physiology.
Stratification-induced reorientation of disk settling through ambient density transition
Authors: Mrokowska Magdalena M. 
Published: January 2018

AbstractSettling due to gravity force is a basic transport mechanism of solid particles in fluids in the Earth. A large portion of particles occurring in nature and used in technical applications are non-spherical. Settling of particles is usually studied in homogeneous ambient conditions, however, stratification is inherent of natural fluids. It has been acknowledged that stratification modifies the velocity of settling spheres and amorphous aggregates. However, the effect of particle shape on the dynamics of settling through density-stratified ambient fluid has not been recognized well enough. Here I show experimental evidence that continuous density transition markedly modifies the settling dynamics of a disk in terms of settling velocity and orientation of a particle. Settling dynamics of a disk are more complex than dynamics of spheres and aggregates studied previously. I found that in a two-layer ambient with density transition, a disk settling in a low Reynolds number regime undergoes five phases of settling with the orientation varying from horizontal to vertical, and it may achieve two local minimum settling velocities in the density transition layer. Moreover, I found that the settling dynamics depends on a density difference between upper and lower homogeneous layers, stratification strength and thickness of density transition.
Reference gene identification and validation for quantitative real-time PCR studies in developing Xenopus laevis
Authors: Mughal Bilal B. , Leemans Michelle , Spirhanzlova Petra , Demeneix Barbara , Fini Jean-Baptiste 
Published: January 2018

AbstractReference genes are essential for gene expression analysis when using real-time quantitative PCR (RT-qPCR). Xenopus laevis is a popular amphibian model for studying vertebrate embryogenesis and development. Further, X. laevis is ideal for studying thyroid signaling due to its thyroid dependent metamorphosis, a stage comparable to birth in humans. When using PCR based studies, a primary concern is the choice of reference genes. Commonly used references are eef1a1, odc1, rpl8, and actnB, although there is a lack of ad hoc reference genes for X. laevis. Here, we used previously published RNA-seq data on different X. laevis stages and identified the top 14 candidate genes with respect to their expression levels as a function of developmental stage and degree of variation. We further evaluated the stability of these and other candidate genes using RT-qPCR on various stages including the unfertilised eggs, whole embryos during early development and brains during late development. We used four different statistical software packages: deltaCT, geNorm, NormFinder and BestKeeper. We report optimized reference gene pair combinations for studying development (early whole embryos), brains at later stages (metamorphosis and adult), and thyroid signalling. These reference gene pairs are suitable for studying different aspects of X. laevis development and organogenesis.