bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes
Authors: Li Mushan , Tu Shiqi , Li Zijia , Tan Fengxiang , Liu Jian , Wang Qian , Zhang Yuannyu , Xu Jian , Zhang Yijing , Zhou Feng , Shao Zhen 
Published: August 2019

AbstractIsotope-labeling-based mass spectrometry (MS) is widely used in quantitative proteomic studies. With this technique, the relative abundance of thousands of proteins can be efficiently profiled in parallel, greatly facilitating the detection of proteins differentially expressed across samples. However, this task remains computationally challenging. Here we present a new approach, termed Model-based Analysis of Proteomic data (MAP), for this task. Unlike many existing methods, MAP does not require technical replicates to model technical and systematic errors, and instead utilizes a novel step-by-step regression analysis to directly assess the significance of observed protein abundance changes. We applied MAP to compare the proteomic profiles of undifferentiated and differentiated mouse embryonic stem cells (mESCs), and found it has superior performance compared with existing tools in detecting proteins differentially expressed during mESC differentiation. A web-based application of MAP is provided for online data processing at http://bioinfo.sibs.ac.cn/shaolab/MAP.
Magnetic excitation of a granular gas as a bulk thermostat
Authors: Adachi Masato , Yu Peidong , Sperl Matthias 
Published: August 2019

AbstractA thermostat utilizing a varying magnetic field has been developed to agitate soft ferromagnetic particles in microgravity platforms for an investigation of an energy-dissipative granular gas. Although the method has experimentally realized a reasonably homogeneous spatial distribution of particles, the physics behind the magnetically excited particles has not been understood. Therefore, a numerical calculation based on the discrete element method is developed in this paper to explain the realization of homogeneously distributed particles. The calculation method allows considering inelastic and magnetic interactions between particles and tracking the motions due to those interactions during the excitation of the granular gas. The calculation results, compared with the experimental result, show that magnetic interactions between particles, a time-domain variation of magnetic-excitation directions, and random collisions of particles between each magnetic excitation contribute to distribute particles homogeneously.
Relationship between parity and the problems that appear in the postpartum period
Authors: Martínez-Galiano Juan Miguel , Hernández-Martínez Antonio , Rodríguez-Almagro Julián , Delgado-Rodríguez Miguel , Gómez-Salgado Juan 
Published: August 2019

AbstractParity is associated with the incidence of problems in pregnancy, delivery and the puerperium. The influence of parity in the postpartum period has been poorly studied and the results are incongruous. The objective of this study was to identify the association between parity and the existence of distinct discomfort and problems during the postpartum period. Cross-sectional study with puerperal women in Spain. Data was collected on demographic and obstetric variables and maternal manifestations of discomfort and problems during the postpartum period. An ad hoc online questionnaire was used. Crude odds ratios (ORs) and adjusted odds ratios (aORs) with 95% confidence intervals (CIs) were estimated by conditional logistic regression. 1503 primiparous and 1487 multiparous participated in the study. 53.4% (803) of the primiparous women affirmed to have feelings of sadness, as opposed to 36.2% (539) of multiparous women (aOR: 1.60; 95% CI: 1.35–1.89). 48.3% (726) of primiparous had lactation problems vs 24.7% (367) of multiparous (aOR: 2.46; 95% CI: 2.05–2.94). 37.2% (559) of primiparous reported anxiety, while the percentage in multiparous was 25.7% (382) (aOR: 1.34; 95% CI: 1.12–1.61). 22.2% (333) of primiparous had depressive symptoms, and 11.6% (172) of multiparous (aOR: 1.65; CI 95%: 1.31–2.06). Faecal incontinence was more present in primiparous than in multiparous, 6.5% (97) and 3.3% (49) respectively (aOR: 1.60; 95% CI: 1.07–2.38). Parity is associated with the presence of certain problems in the postpartum period. Thus, primiparous are more likely to have lactation problems, depressive symptoms, anxiety, sadness, and faecal incontinence.
The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia
Authors: Zwyns Nicolas , Paine Cleantha H. , Tsedendorj Bolorbat , Talamo Sahra , Fitzsimmons Kathryn E. , Gantumur Angaragdulguun , Guunii Lkhundev , Davakhuu Odsuren , Flas Damien , Dogandžić Tamara , Doerschner Nina , Welker Frido , Gillam J. Christopher , Noyer Joshua B. , Bakhtiary Roshanne S. , Allshouse Aurora F. , Smith Kevin N. , Khatsenovich Arina M. , Rybin Evgeny P. , Byambaa Gunchinsuren , Hublin Jean-Jacques 
Published: August 2019

AbstractThe fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.
Strontium hexaferrite platelets: a comprehensive soft X-ray absorption and Mössbauer spectroscopy study
Authors: Soria G. D. , Jenus P. , Marco J. F. , Mandziak A. , Sanchez-Arenillas M. , Moutinho F. , Prieto J. E. , Prieto P. , Cerdá J. , Tejera-Centeno C. , Gallego S. , Foerster M. , Aballe L. , Valvidares M. , Vasili H. B. , Pereiro E. , Quesada A. , de la Figuera J. 
Published: August 2019

AbstractPlatelets of strontium hexaferrite (SrFe12O19, SFO), up to several micrometers in width, and tens of nanometers thick have been synthesized by a hydrothermal method. They have been studied by a combination of structural and magnetic techniques, with emphasis on Mössbauer spectroscopy and X-ray absorption based-measurements including spectroscopy and microscopy on the iron-L edges and the oxygen-K edge, allowing us to establish the differences and similarities between our synthesized nanostructures and commercial powders. The Mössbauer spectra reveal a greater contribution of iron tetrahedral sites in platelets in comparison to pure bulk material. For reference, high-resolution absorption and dichroic spectra have also been measured both from the platelets and from pure bulk material. The O-K edge has been reproduced by density functional theory calculations. Out-of-plane domains were observed with 180° domain walls less than 20 nm width, in good agreement with micromagnetic simulations.
Transcriptomic Profiling of Adipose Derived Stem Cells Undergoing Osteogenesis by RNA-Seq
Authors: Shaik Shahensha , Martin Elizabeth C. , Hayes Daniel J. , Gimble Jeffrey M. , Devireddy Ram V. 
Published: August 2019

AbstractAdipose-derived stromal/stem cells (ASCs) are multipotent in nature that can be differentiated into various cells lineages such as adipogenic, osteogenic, and chondrogenic. The commitment of a cell to differentiate into a particular lineage is regulated by the interplay between various intracellular pathways and their resultant secretome. Similarly, the interactions of cells with the extracellular matrix (ECM) and the ECM bound growth factors instigate several signal transducing events that ultimately determine ASC differentiation. In this study, RNA-sequencing (RNA-Seq) was performed to identify the transcriptome profile of osteogenic induced ASCs to understand the associated genotype changes. Gene ontology (GO) functional annotations analysis using Database for Annotation Visualization and Integrated Discovery (DAVID) bioinformatics resources on the differentially expressed genes demonstrated the enrichment of pathways mainly associated with ECM organization and angiogenesis. We, therefore, studied the expression of genes coding for matrisome proteins (glycoproteins, collagens, proteoglycans, ECM-affiliated, regulators, and secreted factors) and ECM remodeling enzymes (MMPs, integrins, ADAMTSs) and the expression of angiogenic markers during the osteogenesis of ASCs. The upregulation of several pro-angiogenic ELR+ chemokines and other angiogenic inducers during osteogenesis indicates the potential role of the secretome from differentiating ASCs in the vascular development and its integration with the bone tissue. Furthermore, the increased expression of regulatory genes such as CTNNB1, TGBR2, JUN, FOS, GLI3, and MAPK3 involved in the WNT, TGF-β, JNK, HedgeHog and ERK1/2 pathways suggests the regulation of osteogenesis through interplay between these pathways. The RNA-Seq data was also validated by performing QPCR on selected up- and down-regulated genes (COL10A1, COL11A1, FBLN, FERMT1, FN1, FOXF1, LAMA3, LAMA4, LAMB1, IGF1, WNT10B, MMP1, MMP3, MMP16, ADAMTS6, and ADAMTS14).
Benefit of Adjuvant Chemoradiotherapy in Resected Gallbladder Carcinoma
Authors: Kim Tae Hyun , Woo Sang Myung , Lee Woo Jin , Oh Eun Sang , Youn Sang Hee , Moon Sung Ho , Kim Sang Soo , Han Sung Sik , Park Sang-Jae , Kim Dae Yong 
Published: August 2019

AbstractTo evaluate the benefit of adjuvant treatments, such as chemoradiotherapy (CRT) and chemotherapy (CTx), compared with no adjuvant treatment (No-AT) in resected gallbladder (GB) cancer patients, 151 patients were analyzed: 98 (64.9%) patients received adjuvant treatment with CRT (n = 59, 39.1%) or CTx (n = 39, 25.8%), and the remaining 53 (35.1%) did not (No-AT). The clinicopathological factors, patterns of failure, locoregional recurrence-free survival (LRFS), recurrence-free survival (RFS) and overall survival (OS) were compared among the three groups according to tumor stage. In patients with T2-3N0M0 stage disease, the incidences of locoregional recurrence and distant recurrence and 5-year LRFS, RFS and OS rates were not significantly different among the No-AT, CTx, and CRT groups (p > 0.05 each). In those with T2-3N1-2M0 stage disease, the incidences of locoregional recurrence (11.4%, 78.1%, and 68.4%, respectively) and distant recurrence (42.8%, 73.9% and 66.7%, respectively) in the CRT group were significantly lower than those in the No-AT and CTx groups (p < 0.05), and the CRT group had significantly higher 5-year LRFS (82,1%, 26.8%, and 19.0%), RFS (53.3%, 11.6% and 16.7%) and OS rates (64.0%, 22.7% and 4.3%) than the CTx and No-AT groups (p < 0.05 each). Therefore, adjuvant CRT may improve the LRFS and RFS and subsequently improve OS in lymph node-positive resected GB cancer.
Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
Authors: Posada-Perlaza Carlos Eduardo , Ramírez-Rojas Adán , Porras Paola , Adu-Oppong Boahemaa , Botero-Coy Ana-María , Hernández Félix , Anzola Juan M. , Díaz Lorena , Dantas Gautam , Reyes Alejandro , Zambrano María Mercedes 
Published: August 2019

AbstractThe increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.
Hemoglobin S and C affect biomechanical membrane properties of P. falciparum-infected erythrocytes
Authors: Fröhlich Benjamin , Jäger Julia , Lansche Christine , Sanchez Cecilia P. , Cyrklaff Marek , Buchholz Bernd , Soubeiga Serge Theophile , Simpore Jacque , Ito Hiroaki , Schwarz Ulrich S. , Lanzer Michael , Tanaka Motomu 
Published: August 2019

AbstractDuring intraerythrocytic development, the human malaria parasite Plasmodium falciparum alters the mechanical deformability of its host cell. The underpinning biological processes involve gain in parasite mass, changes in the membrane protein compositions, reorganization of the cytoskeletons and its coupling to the plasma membrane, and formation of membrane protrusions, termed knobs. The hemoglobinopathies S and C are known to partially protect carriers from severe malaria, possibly through additional changes in the erythrocyte biomechanics, but a detailed quantification of cell mechanics is still missing. Here, we combined flicker spectroscopy and a mathematical model and demonstrated that knob formation strongly suppresses membrane fluctuations by increasing membrane-cytoskeleton coupling. We found that the confinement increased with hemoglobin S but decreases with hemoglobin C in spite of comparable knob densities and diameters. We further found that the membrane bending modulus strongly depends on the hemoglobinopathetic variant, suggesting increased amounts of irreversibly oxidized hemichromes bound to membranes.
J-PLUS: Impact of bars on quenching timescales in nearby green valley disc galaxies
Authors: Nogueira-Cavalcante J. P. , Dupke R. , Coelho P. , Dantas M. L. L. , Gonçalves T. S. , Menéndez-Delmestre K. , Lopes de Oliveira R. , Jiménez-Teja Y. , López-Sanjuan C. , Alcaniz J. , Angulo R. E. , Cenarro A. J. , Cristóbal-Hornillos D. , Hernández-Monteagudo C. , Ederoclite A. , Marín-Franch A. , Mendes de Oliveira C. , Moles M. , Sodré L. , Varela J. , Vázquez Ramió H. , Alvarez-Candal A. , Chies-Santos A. , Díaz-García L. A. , Galbany L. , Hernandez-Jimenez J. , Sánchez-Blázquez P. , Sánchez-Portal M. , Sobral D. , Telles E. , Tempel E. 
Published: August 2019

Context. Between the blue cloud and the red sequence peaks on the galaxy colour–magnitude diagram there is a region sparsely populated by galaxies called the green valley. In a framework where galaxies mostly migrate on the colour–magnitude diagram from star forming to quiescent, the green valley is considered a transitional galaxy stage. The details of the processes that drive galaxies from star-forming to passive systems still remain unknown.
Aims. We aim to measure the transitional timescales of nearby galaxies across the green valley, through the analysis of Galaxy Evolution Explorer and Javalambre Photometric of Local Universe Survey photometric data. Specifically, we seek to study the impact of bars on the quenching timescales.
Methods. We developed a method that estimates empirically the star formation quenching timescales of green valley galaxies, assuming an exponential decay model of the star formation histories and through a combination of narrow and broad bands from the Javalambre Photometric of Local Universe Survey and Galaxy Evolution Explorer. We correlated these quenching timescales with the presence of bars.
Results. We find that the Javalambre Photometric of Local Universe Survey colours F0395 −g and F0410 −g are sensitive to different star formation histories, showing, consequently, a clear correlation with the Dn(4000) and Hδ, A spectral indices. We measured quenching timescales based on these colours and we find that quenching timescales obtained with our new approach are in agreement with those determined using spectral indices. We also compared the quenching timescales of green valley disc galaxies as a function of the probability of hosting a bar. We find that galaxies with high bar probability tend to quench their star formation slowly.
Conclusions. We conclude that: (1) Javalambre Photometric of Local Universe Survey filters can be used to measure quenching timescales in nearby green valley galaxies; and (2) the resulting star formation quenching timescales are longer for barred green valley galaxies. Considering that the presence of a bar indicates that more violent processes (e.g. major mergers) are absent in host galaxies, we conclude that the presence of a bar can be used as a morphological signature for slow star formation quenching.
Linking planetesimal and dust content in protoplanetary disks via a local toy model
Authors: Gerbig Konstantin , Lenz Christian T. , Klahr Hubert 
Published: August 2019

Context. If planetesimal formation is an efficient process, as suggested by several models involving gravitational collapse of pebble clouds, then, not before long, a significant part of the primordial dust mass should be absorbed in many km-sized objects. A good understanding of the total amount of solids in the disk around a young star is crucial for planet formation theory. However, as the mass of particles above the mm size cannot be assessed observationally, one must ask how much mass is hidden in bigger objects.
Aims. We performed 0-d local simulations to study how the planetesimal to dust and pebble ratio evolves in time and to develop an understanding of the potentially existing mass in planetesimals for a certain amount of dust and pebbles at a given disk age.
Methods. We performed a parameter study based on a model considering dust growth, planetesimal formation, and collisional fragmentation of planetesimals, while neglecting radial transport processes.
Results. While at early times, dust is the dominant solid particle species, there is a phase during which planetesimals make up a significant portion of the total mass starting at approximately 104–106 yr. The time of this phase and the maximal total planetesimal mass strongly depend on the distance to the star R, the initial disk mass, and the efficiency of planetesimal formation ɛ. Planetesimal collisions are more significant in more massive disks, leading to lower relative planetesimal fractions compared to less massive disks. After approximately 106 yr, our model predicts planetesimal collisions to dominate, which resupplies small particles.
Conclusions. In our model, planetesimals form fast and everywhere in the disk. For a given ɛ, we are able to relate the dust content and mass of a given disk to its planetesimal content, providing us with some helpful basic intuition about mass distribution of solids and its dependence on underlying physical processes.
Carbon-rich (DQ) white dwarfs in the Sloan Digital Sky Survey
Authors: Koester D. , Kepler S. O. 
Published: August 2019

Context.Among the spectroscopically identified white dwarfs, a fraction smaller than 2% have spectra dominated by carbon lines, mainly molecular C2, but also a smaller group dominated by C Iand C IIlines. These are together called DQ white dwarfs.Aims.We want to derive atmospheric parametersTeff, logg, and carbon abundances for a large sample of these stars and discuss implications for their spectral evolution.Methods.Sloan Digital Sky Survey spectra andugrizphotometry were used, together withGaiaData Release 2 parallaxes andGband photometry. These were fitted to synthetic spectra and theoretical photometry derived from model atmospheres.Results.We found that the DQ hotter thanTeff~ 10 000 K have masses ~ 0.4M⊙larger than the classical DQ, which have masses typical for the majority of white dwarfs (~ 0.6M⊙). We found some evidence that the peculiar DQ below 10 000 K also have significantly larger masses and may thus be the descendants of the hot and warm DQ above 10 000 K. A significant fraction of the hotter objects withTeff> 14 500 K have atmospheres dominated by carbon.
Exhaled air speed measurements of respiratory air flow, generated by ten different human subjects, under uncontrolled conditions
Authors: Ivanov Martin 
Published: August 2019

The presented study reveals a multi-point experimental measurement of the airflow speed, generated in the exhalation phase from the human respiratory cycle, based on data from 10 real human subjects. The results obtained demonstrate the exceptional irregularity and the transient character of the human respiratory cycle, in terms of measured speed at different points of man-generated exhalation air flow. The presented exponential trend lines show as expected, that there is a reduction in the exhalation speed, with the increase of the distance from the nose.
The summary analysis shows that at 10 cm distance from the nose the maximum as well as the average measured speeds are higher than the one, measured at 5 cm distance. This suggests that due to the physiology of the human nose, 5 cm distance is not enough to characterize the fully developed exhalation jet flow. It is suggested that at this distance the exhalation jets are still two, issuing from each nostril, with different flowrate ratio.
The obtained flow characteristics can be used to compare, validate and verify data from conducted numerical studies of the breathing process, via virtual models or real breathing thermal mannikins.