bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable Selection in the Regularized Simultaneous Component Analysis Method for Multi-Source Data Integration
Authors: Gu Zhengguo , Schipper Niek C. de , Van Deun Katrijn 
Published: December 2019

AbstractInterdisciplinary research often involves analyzing data obtained from different data sources with respect to the same subjects, objects, or experimental units. For example, global positioning systems (GPS) data have been coupled with travel diary data, resulting in a better understanding of traveling behavior. The GPS data and the travel diary data are very different in nature, and, to analyze the two types of data jointly, one often uses data integration techniques, such as the regularized simultaneous component analysis (regularized SCA) method. Regularized SCA is an extension of the (sparse) principle component analysis model to the cases where at least two data blocks are jointly analyzed, which - in order to reveal the joint and unique sources of variation - heavily relies on proper selection of the set of variables (i.e., component loadings) in the components. Regularized SCA requires a proper variable selection method to either identify the optimal values for tuning parameters or stably select variables. By means of two simulation studies with various noise and sparseness levels in simulated data, we compare six variable selection methods, which are cross-validation (CV) with the “one-standard-error” rule, repeated double CV (rdCV), BIC, Bolasso with CV, stability selection, and index of sparseness (IS) - a lesser known (compared to the first five methods) but computationally efficient method. Results show that IS is the best-performing variable selection method.
Selective autophagy, lipophagy and mitophagy, in the Harderian gland along the oestrous cycle: a potential retrieval effect of melatonin
Authors: García-Macia Marina , Santos-Ledo Adrián , Caballero Beatriz , Rubio-González Adrian , de Luxán-Delgado Beatriz , Potes Yaiza , Rodríguez-González Susana Mª. , Boga José Antonio , Coto-Montes Ana 
Published: December 2019

AbstractSexual dimorphism has been reported in many processes. However, sexual bias in favour of the use of males is very present in science. One of the main reasons is that the impact of hormones in diverse pathways and processes such as autophagy have not been properly addressed in vivo. The Harderian gland is a perfect model to study autophagic modulation as it exhibits important changes during the oestrous cycle. The aim of this study is to identify the main processes behind Harderian gland differences under oestrous cycle and their modulator. In the present study we show that redox-sensitive transcription factors have an essential role: NF-κB may activate SQSTM1/p62 in oestrus, promoting selective types of autophagy: mitophagy and lipophagy. Nrf2 activation in dioestrus, leads the retrieval phase and restoration of mitochondrial homeostasis. Melatonin’s receptors show higher expression in dioestrus, leading to decreases in pro-inflammatory mediators and enhanced Nrf2 expression. Consequently, autophagy is blocked, and porphyrin release is reduced. All these results point to melatonin as one of the main modulators of the changes in autophagy during the oestrous cycle.
The effect of orbital-lattice coupling on the electrical resistivity of YBaCuFeO5 investigated by X-ray absorption
Authors: Srivastava M. K. , Qiu X.-S. , Chin Y. Y. , Hsieh S. H. , Shao Y. C. , Liang Y.-H. , Lai C.-H. , Du C. H. , Wang H. T. , Chiou J. W. , Lai Y. C. , Tsai H. M. , Pao C. W. , Lin H. J. , Lee J. F. , Asokan K. , Pong W. F. 
Published: December 2019

AbstractTemperature-dependent X-ray absorption near-edge structures, X-ray linear dichroism (XLD) and extended X-ray absorption fine structure (EXAFS) spectroscopic techniques were used to investigate the valence state, preferred orbital and local atomic structure that significantly affect the electrical and magnetic properties of a single crystal of YBaCuFeO5 (YBCFO). An onset of increase of resistivity at ~180 K, followed by a rapid increase at/below 125 K, is observed. An antiferromagnetic (AFM)-like transition is close to the temperature at which the resistivity starts to increase in the ab-plane and is also observed with strong anisotropy between the ab-plane and the c-axis. The XLD spectra at the Fe L3,2-edge revealed a change in Fe 3d eg holes from the preferential $${\bf{3}}{{\boldsymbol{d}}}_{{{\bf{x}}}^{{\bf{2}}}{\boldsymbol{-}}{{\bf{y}}}^{{\bf{2}}}}$$3dx2−y2 orbital at high temperature (300–150 K) to the $${\bf{3}}{{\boldsymbol{d}}}_{{{\bf{3}}{\bf{z}}}^{{\bf{2}}}{\boldsymbol{-}}{{\bf{r}}}^{{\bf{2}}}}$$3d3z2−r2 orbital at/below 125 K. The analysis of the Fe K-edge EXAFS data of YBCFO further revealed an unusual increase in the Debye-Waller factor of the nearest-neighbor Fe-O bond length at/below 125 K, suggesting phonon-softening behavior, resulting in the breaking of lattice symmetry, particularly in the ab-plane of Fe-related square pyramids. These findings demonstrate a close correlation between electrical resistivity and coupling of the preferred Fe 3d orbital with lattice distortion of a single crystal of YBCFO.
Increased lifespan, decreased mortality, and delayed cognitive decline in osteoarthritis
Authors: Mayburd Anatoly L. , Baranova Ancha 
Published: December 2019

AbstractIn absence of therapies targeting symptomatic dementia, better understanding of the biology underlying a cognitive decline is warranted. Here we present the results of a meta-analysis of the impact of osteoarthritis (OA) on cognitive decline and overall mortality. Across 7 independent datasets obtained in studies of populations in the USA, EU and Australia (NBER, NSHAP, TILDA, NACC, Kaiser Permanente, GRIM BOOKS, OAI, with a total of >7 × 107 profiles), OA cohorts demonstrated higher cognitive scores, later dementia onset as well as longer lifespan and lower age-specific all-cause mortality. Moreover, generalized OA with multiple localizations is associated with more significant reduction of mortality and dementia than a singly localized OA or no arthritis. In OA patients with younger ages, all-cause mortality was disproportionally reduced as compared to that in controls, while exponential term of Gompert’z hazard function was increased, accelerating mortality accrual at later ages. Up to 8–10% of poly-osteoarthritic patients are predicted and observed to reach centenarian lifespan, while in matched non-OA population the same benchmark is reached by less than 1% of patients. These results point at a possibility of life-extending and cognition preserving impacts of OA-conditioned immune system.
Shedding light on melanins within in situ human eye melanocytes using 2-photon microscopy profiling techniques
Authors: Sitiwin Ephrem , Madigan Michele C. , Gratton Enrico , Cherepanoff Svetlana , Conway Robert Max , Whan Renee , Macmillan Alexander 
Published: December 2019

AbstractChoroidal melanocytes (HCMs) are melanin-producing cells in the vascular uvea of the human eye (iris, ciliary body and choroid). These cranial neural crest-derived cells migrate to populate a mesodermal microenvironment, and display cellular functions and extracellular interactions that are biologically distinct to skin melanocytes. HCMs (and melanins) are important in normal human eye physiology with roles including photoprotection, regulation of oxidative damage and immune responses. To extend knowledge of cytoplasmic melanins and melanosomes in label-free HCMs, a non-invasive ‘fit-free’ approach, combining 2-photon excitation fluorescence lifetimes and emission spectral imaging with phasor plot segmentation was applied. Intracellular melanin-mapped FLIM phasors showed a linear distribution indicating that HCM melanins are a ratio of two fluorophores, eumelanin and pheomelanin. A quantitative histogram of HCM melanins was generated by identifying the image pixel fraction contributed by phasor clusters mapped to varying eumelanin/pheomelanin ratio. Eumelanin-enriched dark HCM regions mapped to phasors with shorter lifetimes and longer spectral emission (580–625 nm) and pheomelanin-enriched lighter pigmented HCM regions mapped to phasors with longer lifetimes and shorter spectral emission (550–585 nm). Overall, we demonstrated that these methods can identify and quantitatively profile the heterogeneous eumelanins/pheomelanins withinin situHCMs, and visualize melanosome spatial distributions, not previously reported for these cells.
Clinical prognostic scores for patients with thymic epithelial tumors
Authors: Veraar Cecilia , Janik Stefan , Thanner Jürgen , Veraar Clarence , Mouhieddine Mohamed , Schiefer Ana-Iris , Müllauer Leonhard , Dworschak Martin , Klepetko Walter , Ankersmit Hendrik Jan , Moser Bernhard 
Published: December 2019

AbstractSeveral inflammation-based prognostic scores emerged in various types of cancer to predict clinical outcomes. So far, no accurate pre-treatment scoring systems exist for patients with thymic epithelial tumors (TETs), comprising thymomas and thymic carcinomas (TCs). Therefore, we sought to test the prognostic value of different clinical composite scores and their components, identify optimal cut-off values for TETs as well as combine predictive components to new suitable prognostic scores. One hundred eighty-four patients with TETs undergoing surgical tumor resection were analyzed. A significant advantage in Freedom-from-Recurrence and/or Cause-specific survival (CSS) was evident for patients with high Advanced-Lung- Cancer-Inflammation-Index, low CRP-Fibrinogen-Score (CFS), low Glasgow-Prognostic-Score (GPS), low high-sensitivity-modified GPS, low TET-adapted GPS (TET-aGPS) and low Systemic-Immune-Inflammation Index. On multivariable analysis high TET-aGPS (HR = 14.9;p = 0.001), incomplete resection status (HR = 13.5;p = 0.001) and TC (HR = 26.0;p = 0.001) were significant independent prognostic factors for worse CSS. The CFS had the highest coefficient of determination (R2 = 0.188) to predict tumor recurrence of all composite scores, comprising CRP (R2 = 0.141) and fibrinogen (R2 = 0.158), the best single factor predictors. Inflammation-based prognostic scores and selected components are suitable to predict survival and/or tumor recurrence in TET patients undergoing primary surgery. Due to excellent long-term survival and frequent tumor recurrence, cut-off values were tailored to increase prognostic power.
Adeno-associated virus capsid protein expression in Escherichia coli and chemically defined capsid assembly
Authors: Le Dinh To , Radukic Marco T. , Müller Kristian M. 
Published: December 2019

AbstractResearch and clinical applications of recombinant adeno-associated virus (rAAV) significantly increased in recent years alongside regulatory approvals of rAAV gene therapy products. To date, all rAAV vectors as well as AAV empty capsids are produced in eukaryotic cells. We explored a new route to generate AAV capsids with the aim to analyze capsid assembly in a chemically defined setting and pave the way for new production methods and applications based on AAV virus-like particles (VLPs). We generated these empty capsids by bacterial expression and subsequent concomitant protein refolding and VLP formation. AAV serotype 2 structural protein VP3 was expressed in Escherichia coli. VLPs formed as demonstrated by dynamic light scattering, atomic force microscopy, and ELISA. Furthermore, VLPs internalized into human HeLa cells. To extend the application range of the VLPs, we tested peptide insertions, at the genetic level, in a surface loop (amino acid position 587) or at the C-terminus of VP3 and these variants also formed VLPs. VLPs developed without assembly-activating protein (AAP), but adding purified recombinant AAP to the refolding process increased capsid yield. Our findings offer a new route to understand AAV assembly biology and open a toolbox for AAV production strategies that might enable capsid display for vaccination and matching of capsids with cargoes at large scale and low cost.
Association of Dog and Cat Ownership with Incident Frailty among Community-Dwelling Elderly Japanese
Authors: Taniguchi Yu , Seino Satoshi , Nishi Mariko , Tomine Yui , Tanaka Izumi , Yokoyama Yuri , Ikeuchi Tomoko , Kitamura Akihiko , Shinkai Shoji 
Published: December 2019

AbstractAccumulating evidence from studies of human–animal interaction highlights the physiological, psychological, and social benefits for older owners of dogs and cats. This longitudinal study examined whether experience of dog/cat ownership protects against incident frailty in a population of community-dwelling older Japanese. Among 7881 non-frail community-dwelling adults aged 65 years or older who completed a mail survey in 2016, 6,197 (mean [SD] age, 73.6 [5.3] years; 53.6% women) were reevaluated in a 2018 follow-up survey. Frailty was assessed with the Kaigo-Yobo Checklist. Incident frailty was defined as a score of four or higher in the follow-up survey. Overall, 870 (14.0%) were current dog/cat owners, 1878 (30.3%) were past owners and 3449 (55.7%) were never owners. During the 2-year follow-up period, 918 (14.8%) developed incident frailty. Mixed-effects logistic regression models showed that the odds ratio for incident frailty among dog/cat owners, as compared with never owners, current owners were 0.87 (95% confidence interval [CI]: 0.69–1.09) and past owner were 0.84 (0.71–0.98), after controlling for important confounders at baseline. In stratified analysis, the risk of incident frailty was lower for past dog owners than for cat owners. Longer experience of caring for a dog requires physical activity and increases time outdoors spent dog walking and thus may have an important role in maintaining physical and social function and reducing frailty risk among older adults.
Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases
Authors: Šimčíková Daniela , Heneberg Petr 
Published: December 2019

AbstractPrediction methods have become an integral part of biomedical and biotechnological research. However, their clinical interpretations are largely based on biochemical or molecular data, but not clinical data. Here, we focus on improving the reliability and clinical applicability of prediction algorithms. We assembled and curated two large non-overlapping large databases of clinical phenotypes. These phenotypes were caused by missense variations in 44 and 63 genes associated with Mendelian diseases. We used these databases to establish and validate the model, allowing us to improve the predictions obtained from EVmutation, SNAP2 and PoPMuSiC 2.1. The predictions of clinical effects suffered from a lack of specificity, which appears to be the common constraint of all recently used prediction methods, although predictions mediated by these methods are associated with nearly absolute sensitivity. We introduced evidence-based tailoring of the default settings of the prediction methods; this tailoring substantially improved the prediction outcomes. Additionally, the comparisons of the clinically observed and theoretical variations led to the identification of large previously unreported pools of variations that were under negative selection during molecular evolution. The evolutionary variation analysis approach described here is the first to enable the highly specific identification of likely disease-causing missense variations that have not yet been associated with any clinical phenotype.
Control of the polarization direction of isolated attosecond pulses using inhomogeneous two-color fields
Authors: Njoroge Stephen Maina , Yuan Hua , Dickson Kinyua , Zhang Qingbin , Lan Pengfei 
Published: December 2019

AbstractWe theoretically demonstrate the control of the polarization direction of isolated attosecond pulses (IAPs) with inhomogeneous two-color fields synthesized by an 800-nm fundamental pulse and a 2000-nm control pulse having crossed linear polarizations. The results show that by using the temporally and spatially shaped field, the high-order harmonic generation (HHG) process can be efficiently controlled. An ultra-broad supercontinuum ranging from 150th to 400th harmonics which covers the water window region is generated. Such a supercontinuum supports the generation of a 64-as linearly polarized IAP, whose polarization direction is at about 45° with respect to the x axis. Moreover, we analyze the influence of the inhomogeneity parameters and the relative angle of the fundamental and control pulses on the IAP generation. It is shown that the polarization direction of the IAP can rotate in a wide range approximately from 8° to 90° relative to the x axis when the inhomogeneity parameters and the relative angle vary.
An Efficient hybrid filter-wrapper metaheuristic-based gene selection method for high dimensional datasets
Authors: Pirgazi Jamshid , Alimoradi Mohsen , Esmaeili Abharian Tahereh , Olyaee Mohammad Hossein 
Published: December 2019

AbstractFeature selection problem is one of the most significant issues in data classification. The purpose of feature selection is selection of the least number of features in order to increase accuracy and decrease the cost of data classification. In recent years, due to appearance of high-dimensional datasets with low number of samples, classification models have encountered over-fitting problem. Therefore, the need for feature selection methods that are used to remove the extensions and irrelevant features is felt. Recently, although, various methods have been proposed for selecting the optimal subset of features with high precision, these methods have encountered some problems such as instability, high convergence time, selection of a semi-optimal solution as the final result. In other words, they have not been able to fully extract the effective features. In this paper, a hybrid method based on the IWSSr method and Shuffled Frog Leaping Algorithm (SFLA) is proposed to select effective features in a large-scale gene dataset. The proposed algorithm is implemented in two phases: filtering and wrapping. In the filter phase, the Relief method is used for weighting features. Then, in the wrapping phase, by using the SFLA and the IWSSr algorithms, the search for effective features in a feature-rich area is performed. The proposed method is evaluated by using some standard gene expression datasets. The experimental results approve that the proposed approach in comparison to similar methods, has been achieved a more compact set of features along with high accuracy. The source code and testing datasets are available at https://github.com/jimy2020/SFLA_IWSSr-Feature-Selection.
The influence of multi-layered varnishes on moisture protection and vibrational properties of violin wood
Authors: Lämmlein Sarah L. , Mannes David , Van Damme Bart , Schwarze Francis W. M. R. , Burgert Ingo 
Published: December 2019

AbstractViolin varnishes are known to affect both moisture absorption and vibrational properties of violin wood. However, traditional multi-layered varnish systems suffer from substantial wear as a result of intensive use, which calls for deeper understanding of the specific impact of individual layers. Using sophisticated in-situ neutron imaging and vibrational modal analysis, we show how wood sorption and vibrational behavior of tonewood depend on the build-up of the varnish system. The results demonstrate the protective effect of complete coatings and emphasize that strongly worn regions cannot accomplish the function as an effective moisture barrier, which might pose a risk for frequently played or aged string instruments. Furthermore, the build-up of the varnish system affects the vibrational properties of the tonewood, influencing its final sound quality. This delicate interplay should be considered both for the handling of antique and aged violins and for the production of modern high-quality instruments.
Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria
Authors: Batani Giampiero , Bayer Kristina , Böge Julia , Hentschel Ute , Thomas Torsten 
Published: December 2019

AbstractDespite the development of several cultivation methods, the rate of discovery of microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating novel species in the laboratory. Furthermore, no current cultivation technique is capable of selectively isolating and cultivating specific bacterial taxa or phylogenetic groups independently of morphological or physiological properties. Here, we developed a new method to isolate living bacteria solely based on their 16S rRNA gene sequence. We showed that bacteria can survive a modified version of the standard fluorescence in situ hybridization (FISH) procedure, in which fixation is omitted and other factors, such as centrifugation and buffers, are optimized. We also demonstrated that labelled DNA probes can be introduced into living bacterial cells by means of chemical transformation and that specific hybridization occurs. This new method, which we call live-FISH, was then combined with fluorescence-activated cell sorting (FACS) to sort specific taxonomic groups of bacteria from a mock and natural bacterial communities and subsequently culture them. Live-FISH represents the first attempt to systematically optimize conditions known to affect cell viability during FISH and then to sort bacterial cells surviving the procedure. No sophisticated probe design is required, making live-FISH a straightforward method to be potentially used in combination with other single-cell techniques and for the isolation and cultivation of new microorganisms.
Neonatal obstructive nephropathy induces necroptosis and necroinflammation
Authors: Popper Bastian , Rammer Marian Theodor , Gasparitsch Mojca , Singer Teresa , Keller Ursula , Döring Yvonne , Lange-Sperandio Bärbel 
Published: December 2019

AbstractUrinary tract obstruction during kidney development causes tubular apoptosis, tubular necrosis, and interstitial inflammation. Necroptosis is a subtype of programmed necrosis mediated by the receptor-interacting serine/threonine-protein kinase-3 (RIPK3) and the pseudokinase mixed lineage kinase domain-like (MLKL). Necrosis induces inflammation and stimulates cell death in an autoamplification loop named necroinflammation. Here, we studied necroptosis and necroinflammation in obstructive nephropathy induced by unilateral ureteral obstruction (UUO) in neonatal C57Bl/6J mice. Ureteral obstruction induced tubular dilatation, tubular basement membrane thickening, cast formation, and increased expression of kidney injury molecule-1 (KIM-1). Morphological investigations showed either apoptotic or necrotic cells in the tubular compartment. Biochemical analysis revealed increased caspase-8 activity and upregulation of RIPK3 as well as phosphorylated-MLKL in UUO-kidneys. Pro-inflammatory cytokines (IL-1α, INF-γ, TNF-α) were upregulated following UUO. Taken together we show that necroptosis and necroinflammation are accompanied phenomena in neonatal kidneys with obstruction. These findings may help to develop novel strategies to treat congenital obstructive nephropathy.