bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidation and alkylation stresses activate ribosome-quality control
Authors: Yan Liewei L. , Simms Carrie L. , McLoughlin Fionn , Vierstra Richard D. , Zaher Hani S. 
Published: December 2019

AbstractOxidation and alkylation of nucleobases are known to disrupt their base-pairing properties within RNA. It is, however, unclear whether organisms have evolved general mechanism(s) to deal with this damage. Here we show that the mRNA-surveillance pathway of no-go decay and the associated ribosome-quality control are activated in response to nucleobase alkylation and oxidation. Our findings reveal that these processes are important for clearing chemically modified mRNA and the resulting aberrant-protein products. In the absence of Xrn1, the level of damaged mRNA significantly increases. Furthermore, deletion of LTN1 results in the accumulation of protein aggregates in the presence of oxidizing and alkylating agents. This accumulation is accompanied by Hel2-dependent regulatory ubiquitylation of ribosomal proteins. Collectively, our data highlight the burden of chemically damaged mRNA on cellular homeostasis and suggest that organisms evolved mechanisms to counter their accumulation.
Global hydro-environmental sub-basin and river reach characteristics at high spatial resolution
Authors: Linke Simon , Lehner Bernhard , Ouellet Dallaire Camille , Ariwi Joseph , Grill Günther , Anand Mira , Beames Penny , Burchard-Levine Vicente , Maxwell Sally , Moidu Hana , Tan Florence , Thieme Michele 
Published: December 2019

AbstractThe HydroATLAS database provides a standardized compendium of descriptive hydro-environmental information for all watersheds and rivers of the world at high spatial resolution. Version 1.0 of HydroATLAS offers data for 56 variables, partitioned into 281 individual attributes and organized in six categories: hydrology; physiography; climate; land cover & use; soils & geology; and anthropogenic influences. HydroATLAS derives the hydro-environmental characteristics by aggregating and reformatting original data from well-established global digital maps, and by accumulating them along the drainage network from headwaters to ocean outlets. The attributes are linked to hierarchically nested sub-basins at multiple scales, as well as to individual river reaches, both extracted from the global HydroSHEDS database at 15 arc-second (~500 m) resolution. The sub-basin and river reach information is offered in two companion datasets: BasinATLAS and RiverATLAS. The standardized format of HydroATLAS ensures easy applicability while the inherent topological information supports basic network functionality such as identifying up- and downstream connections. HydroATLAS is fully compatible with other products of the overarching HydroSHEDS project enabling versatile hydro-ecological assessments for a broad user community.
Blood proteome profiling using aptamer-based technology for rejection biomarker discovery in transplantation
Authors: Shubin Andrey V. , Kollar Branislav , Dillon Simon T. , Pomahac Bohdan , Libermann Towia A. , Riella Leonardo V. 
Published: December 2019

AbstractFace transplantation is a promising solution for patients with devastating facial injuries who lack other satisfactory treatment options. At the same time, this type of transplantation is accompanied with high risks of acute transplant rejection. The limitations of traditional skin biopsy and the need to frequently monitor the condition of face transplant call for less invasive biomarkers to better diagnose and treat acute rejection. Discovery of peripheral serum proteins accurately reflecting the transplant status would represent a reasonable solution to meet this demand. However, to date, there is no clinical data available to address the feasibility of this approach. In this study, we used the next generation aptamer-based SOMAscan proteomics platform to profile 1305 proteins of peripheral blood serum in twenty-four samples taken from 6 patients during no-rejection, nonsevere rejection, and severe rejection episodes. Also, we provide a detailed description of biosample processing and all steps to generate and analyze the SOMAscan dataset with hope it will assist in performing biomarker discovery in other transplantation centers using this platform.
Culture of Methanogenic Archaea from Human Colostrum and Milk
Authors: Togo Amadou Hamidou , Grine Ghiles , Khelaifia Saber , des Robert Clotilde , Brevaut Véronique , Caputo Aurelia , Baptiste Emeline , Bonnet Marion , Levasseur Anthony , Drancourt Michel , Million Matthieu , Raoult Didier 
Published: December 2019

AbstractArchaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant’s microbiota with these neglected critical commensals from the first hour of life.
Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension
Authors: Xu Weiling , Comhair Suzy A. A. , Chen Ruoying , Hu Bo , Hou Yuan , Zhou Yadi , Mavrakis Lori A. , Janocha Allison J. , Li Ling , Zhang Dongmei , Willard Belinda B. , Asosingh Kewal , Cheng Feixiong , Erzurum Serpil C. 
Published: December 2019

AbstractPulmonary arterial endothelial cells (PAEC) are mechanistically linked to origins of pulmonary arterial hypertension (PAH). Here, global proteomics and phosphoproteomics of PAEC from PAH (n = 4) and healthy lungs (n = 5) were performed using LC-MS/MS to confirm known pathways and identify new areas of investigation in PAH. Among PAH and control cells, 170 proteins and 240 phosphopeptides were differentially expressed; of these, 45 proteins and 18 phosphopeptides were located in the mitochondria. Pathologic pathways were identified with integrative bioinformatics and human protein-protein interactome network analyses, then confirmed with targeted proteomics in PAH PAEC and non-targeted metabolomics and targeted high-performance liquid chromatography of metabolites in plasma from PAH patients (n = 30) and healthy controls (n = 12). Dysregulated pathways in PAH include accelerated one carbon metabolism, abnormal tricarboxylic acid (TCA) cycle flux and glutamate metabolism, dysfunctional arginine and nitric oxide pathways, and increased oxidative stress. Functional studies in cells confirmed abnormalities in glucose metabolism, mitochondrial oxygen consumption, and production of reactive oxygen species in PAH. Altogether, the findings indicate that PAH is typified by changes in metabolic pathways that are primarily found in mitochondria.
Early antibody response and clinical outcome in experimental canine leishmaniasis
Authors: Olías-Molero Ana Isabel , Corral María J. , Jiménez-Antón María Dolores , Alunda José Mª 
Published: December 2019

AbstractInfected dogs are the main reservoir of zoonotic visceral leishmaniasis, a widespread parasitic disease caused by Leishmania infantum. Therefore, the control of canine infections is required to reduce the incidence of human cases. Disease outcome in dogs depends on the fine balance between parasite virulence and efficacy of the immune system. Thus, knowledge of early response could yield relevant information for diagnosis and follow-up. In our study, 20 Beagle dogs were intravenously infected with 108 amastigotes of a fresh isolate of L. infantum and monitored along 16 weeks post inoculation. Specific antibody response and clinical evolution of infected animals were highly variable. Immunofluorescence antibody test (IFAT) and enzyme linked immunosorbent assay (ELISA) were useful to assess infection status, although only ELISA with promastigote-coated plates and, particularly, western blotting (WB) allowed an early diagnosis. Prominent antigens were identified by mass peptide fingerprinting. Chaperonin HSP60, 32 and 30 KDa antigens were recognized by all dogs on week 10 post infection. This suggests that these antigens may be valuable for early diagnosis. Advanced infection showed, in addition, reactivity to HSP83 and HSP70. Disease outcome did not show a clear relationship with ELISA or IFAT titers. Correlation between the clinical status and the combined reactivity to some antigens sustains their use for diagnosis and follow-up.
Association of genetic polymorphisms in CASP7 with risk of ischaemic stroke
Authors: Zheng Zhaoshi , Liu Songyan , Wang Chuheng , Wang Chunhui , Tang Dong , Shi Yuqing , Han Xuemei 
Published: December 2019

AbstractCaspase 7 (CASP7) is located on chromosome 10q25.3 that has been identified to be a susceptibility locus of ischaemic stroke (IS) by genome-wide association study. Elevated CASP7 was observed in IS, acting as a key apoptotic mediator in the development of IS. The aim of this study was to investigate the association between genetic polymorphisms in CASP7 and risk of IS. The CASP7 polymorphisms were genotyped using a TaqMan allelic discrimination assay. The expression levels of CASP7 mRNA were examined using quantitative polymerase chain reaction and luciferase activity was analyzed using the Dual Luciferase reporter assay. The rs12415607 in the promoter of CASP7 was associated with a reduced risk of IS (AA vs. CC: adjusted OR = 0.55, 95% CI: 0.38–0.80, P = 0.002; CA/AA vs. CC: adjusted OR = 0.70, 95% CI: 0.54–0.91, P = 0.007; AA vs. CC/CA: adjusted OR = 0.64, 95% CI: 0.46–0.90, P = 0.01; A vs. C: adjusted OR = 0.74, 95% CI: 0.62–0.89, P = 0.001). Moreover, the rs12415607 AA genotype carriers exhibited lower levels of CASP7 mRNA and the rs12415607 A allele decreased the promoter activity. These findings indicate that the rs12415607 A allele induces lower levels of transcriptional activity and CASP7 mRNA, and thus is associated with a reduced risk of IS.
Persistent Neurobehavioral Markers of Developmental Morphosyntax Errors in Adults
Authors: Wagley Neelima , Perrachione Tyler K. , Ostrovskaya Irina , Ghosh Satrajit S. , Saxler Patricia K. , Lymberis John , Wexler Kenneth , Gabrieli John D. E. , Kovelman Ioulia 
Published: December 2019

Purpose

Child language acquisition is marked by an optional infinitive period (ages 2–4 years) during which children use nonfinite (infinitival) verb forms and finite verb forms interchangeably in grammatical contexts that require finite forms. In English, children's errors include omissions of past tense /–
ed
/ and 3rd-person singular /–
s
/. This language acquisition period typically ends by the age of 4 years, but it persists in children with language impairments. It is unknown if adults still process optional infinitives differently than other kinds of morphosyntax errors.

Method
We compared behavior and functional brain activation during grammaticality judgments across sentences with developmental optional infinitive tense/agreement errors (“Yesterday I play the song”), nondevelopmental agreement errors (“He am tall”) that do not occur in typical child language acquisition, and grammatically correct sentences.

Results

Adults (
N
= 25) were significantly slower and less accurate in judging sentences with developmental errors relative to other sentences. Sentences with developmental errors yielded greater activation in bilateral inferior frontal gyri relative to nondevelopmental error sentences in both auditory and visual modalities.

Conclusions
These findings suggest that the heightened computational demands for finiteness extend well beyond early childhood and continue to exert their influence on grammatical mental and brain function in adulthood.
Deriving star cluster parameters with convolutional neural networks
Authors: Bialopetravičius J. , Narbutis D. 
Published: December 2019

Context. Convolutional neural networks (CNNs) have been established as the go-to method for fast object detection and classification of natural images. This opens the door for astrophysical parameter inference on the exponentially increasing amount of sky survey data. Until now, star cluster analysis was based on integral or resolved stellar photometry, which limit the amount of information that can be extracted from individual pixels of cluster images.
Aims. We aim to create a CNN capable of inferring star cluster evolutionary, structural, and environmental parameters from multiband images and to demonstrate its capabilities in discriminating genuine clusters from galactic stellar backgrounds.
Methods. A CNN based on the deep residual network (ResNet) architecture was created and trained to infer cluster ages, masses, sizes, and extinctions with respect to the degeneracies between them. Mock clusters placed on M 83 Hubble Space Telescope images utilizing three photometric passbands (F336W, F438W, and F814W) were used. The CNN is also capable of predicting the likelihood of the presence of a cluster in an image and quantifying its visibility (S/N).
Results. The CNN was tested on mock images of artificial clusters and has demonstrated reliable inference results for clusters of ages ≲100 Myr, extinctions AV between 0 and 3 mag, masses between 3 × 103 and 3 × 105 M⊙, and sizes between 0.04 and 0.4 arcsec at the distance of the M 83 galaxy. Real M 83 galaxy cluster parameter inference tests were performed with objects taken from previous studies and have demonstrated consistent results.
Search for spectral features in extragalactic background light with gamma-ray telescopes
Authors: Korochkin A. , Neronov A. , Semikoz D. 
Published: December 2019

Context. Cumulative optical and infrared emission from galaxies accumulated over cosmological time scales, the extragalactic background light (EBL), could be probed by complementary techniques of direct observations and source counting in the visible and infrared as well as via its imprint on the signal of distant active galactic nuclei in γ-rays.
Aims. We compare the visible and infrared measurements with the γ-ray constraints and study if the discrepancies of the measurements with different methods could be due to the presence of features in the EBL spectrum that are localised in the micron wavelength range.
Methods. We combined data on time-averaged spectra of selected blazars that were obtained by Fermi and ground-based gamma-ray telescopes. We also modelled the effect of absorption on EBL while allowing for the existence of a previously unaccounted spectral feature.
Results. We show that a previously reported “excess” in EBL flux in the ∼1 micron wavelength range is consistent with γ-ray measurements, that is, if the excess has the form of a narrow feature of the width δλ <  λ and an overall flux of up to 15 nW m−2 sr−1 above the “minimal” EBL, which is estimated from the visible and infrared source counts. Such ’bump-like’ spectral features could originate, for example, from decaying dark-matter particles, or either axions or peculiar astrophysical processes in the course of star-formation history. We discuss the possibilities for the search of spectral features in the EBL with the Cherenkov Telescope Array.
Co-spatial velocity and magnetic swirls in the simulated solar photosphere
Authors: Liu Jiajia , Carlsson Mats , Nelson Chris J. , Erdélyi Robert 
Published: December 2019

Context.Velocity or intensity swirls have now been shown to be widely present throughout the photosphere and chromosphere. It has been suggested that these events could contribute to the heating of the upper solar atmosphere, via exciting Alfvén pulses, which could carry significant amounts of energy. However, the conjectured necessary physical conditions for their excitation, that the magnetic field rotates co-spatially and co-temporally with the velocity field, has not been verified.Aims.We aim to understand whether photospheric velocity swirls exist co-spatially and co-temporally with photospheric magnetic swirls, in order to demonstrate the link between swirls and pulses.Methods.The automated swirl detection algorithm (ASDA) is applied to the photospheric horizontal velocity and vertical magnetic fields obtained from a series of realistic numerical simulations using the radiative magnetohydrodynamics (RMHD) code Bifrost. The spatial relationship between the detected velocity and magnetic swirls is further investigated via a well-defined correlation index (CI) study.Results.On average, there are ∼63 short-lived photospheric velocity swirls (with lifetimes mostly less than 20 s, and average radius of ∼37 km and rotating speeds of ∼2.5 km s−1) detected in a field of view (FOV) of 6 × 6 Mm−2, implying a total population of velocity swirls of ∼1.06 × 107in the solar photosphere. More than 80% of the detected velocity swirls are found to be accompanied by local magnetic concentrations in intergranular lanes. On average, ∼71% of the detected velocity swirls have been found to co-exist with photospheric magnetic swirls with the same rotating direction.Conclusions.The co-temporal and co-spatial rotation in the photospheric velocity and magnetic fields provide evidence that the conjectured condition for the excitation of Alfvén pulses by photospheric swirls is fulfilled.
Gebissfunktion bei Totalprothesen
Authors: Karakuş Ghezal , Wöstmann Bernd , Rehmann Peter 
Published: December 2019

ZusammenfassungZur prothetischen Rehabilitation zahnloser Kiefer ist gebissfunktionell eine störungsfreie Okklusion anzustreben, wobei in der Totalprothetik die Okklusionskonzepte der bilateral balancierten und der Front-Eckzahn-geführten Okklusion kontrovers diskutiert werden. Ziel der vorliegenden klinischen Untersuchung war es, im intraindividuellen Vergleich zu ermitteln, ob die Patienten eines der beiden Okklusionskonzepte bevorzugen. Insgesamt 38 Patienten erhielten 1 Oberkiefer- und 2 nahezu identische Unterkiefertotalprothesen, deren Unterschied lediglich in der Art des Okklusionskonzepts lag. Die Patienten wurden nicht über den Unterschied informiert. Nach einer 2-wöchigen Tragedauer beider Prothesen wurde die Präferenz der Patienten anhand eines Fragebogens ermittelt. Zwischenzeitlich wurden die Unterkiefertotalprothesen in das jeweils andere Okklusionskonzept überführt und die Patienten nach 2 Wochen erneut befragt. Nach 2 Wochen bevorzugten 63% der Patienten die balancierten Prothesen, 5% favorisierten die Front-Eckzahn-geführten Prothesen und 32% konnten keine Unterschiede feststellen. Nach 4 Wochen bevorzugten noch 47% der Patienten die balancierten Prothesen, 11% die Front-Eckzahn-geführten Prothesen und 42% konnten keine Unterschiede feststellen. Die Ergebnisse deuten darauf hin, dass in der initialen Phase der Prothesenadaptation das Konzept der bilateral balancierten Okklusion vorteilhafter zu sein scheint.
C-terminal of ABCA1 separately regulates cholesterol floppase activity and cholesterol efflux activity
Authors: Okamoto Yusuke , Tomioka Maiko , Ogasawara Fumihiko , Nagaiwa Kota , Kimura Yasuhisa , Kioka Noriyuki , Ueda Kazumitsu 
Published: December 2019

ABSTRACT
ATP-Binding Cassette A1 (ABCA1) is a key lipid transporter for cholesterol homeostasis. We recently reported that ABCA1 not only exports excess cholesterol in an apoA-I dependent manner, but that it also flops cholesterol from the inner to the outer leaflet of the plasma membrane. However, the relationship between these two activities of ABCA1 is still unclear. In this study, we analyzed the subcellular localization of ABCA1 by using a newly generated monoclonal antibody against its extracellular domain and the functions of eleven chimera proteins, in which the C-terminal domain of ABCA1 was replaced with those of the other ABCA subfamily members. We identified two motifs important for the functions of ABCA1. Three periodically repeated leucine residues were necessary for the cholesterol floppase activity but not the cholesterol efflux activity, while a VFVNFA motif was essential for both activities of ABCA1. These results suggest that the C-terminal of ABCA1 separately regulates the cholesterol floppase activity and the cholesterol efflux activity.
Optical far-field extinction of a single GaAs nanowire towards in situ size control of aerotaxy nanowire growth
Authors: Chen Yang , Anttu Nicklas , Sivakumar Sudhakar , Gompou Eleni , Magnusson Martin H 
Published: December 2019

Abstract
A substrate-free approach of semiconductor nanowire growth has been achieved by the aerotaxy technique previously. In this work, we propose an in situ method to monitor the size of nanowires through non-destructive optical-extinction measurements. Our work aims to build a theoretical look-up database of extinction spectra for a single nanowire of varying dimensions. We describe the origin of possible peaks in the spectra, for example due to nanowire-length dependent Fabry–Perot resonances and nanowire-diameter dependent TM and TE mode resonances. Furthermore, we show that the Au catalyst on top of the nanowire can be ignored in the simulations when the volume of the nanowire is an order of magnitude larger than that of the Au catalyst and the diameter is small compared to the incident wavelength. For the calculation of the extinction spectra, we use the finite element method, the discrete dipole approximation and the Mie theory. To compare with experimental measurements of randomly oriented nanowires, we perform an averaging over nanowire orientation for the modeled results. However, in the experiments, nanowires are accumulating on the quartz window of the measurement setup, which leads to increasing uncertainty in the comparison with the experimental extinction spectra. This uncertainty can be eliminated by considering both a sparse and a dense collection of nanowires on the quartz window in the optical simulations. Finally, we create a database of extinction spectra for a GaAs nanowire of varying diameters and lengths. This database can be used to estimate the diameter and the length of the nanowires by comparing the position of a peak and the peak-to-shoulder difference in the extinction spectrum. Possible tapering of nanowires can be monitored through the appearance of an additional peak at a wavelength of 700–800 nm.