bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
Authors: Harringer Manuel , Alfreider Albin 
Published: February 2021

AbstractTo date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml−1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.
RasGRP2 inhibits glyceraldehyde-derived toxic advanced glycation end-products from inducing permeability in vascular endothelial cells
Authors: Takino Jun-ichi , Sato Takuma , Kanetaka Takumi , Okihara Kasumi , Nagamine Kentaro , Takeuchi Masayoshi , Hori Takamitsu 
Published: February 2021

AbstractAdvanced glycation end-products (AGEs) are formed by the non-enzymatic reaction of sugars and proteins. Among the AGEs, glyceraldehyde-derived toxic AGEs (TAGE) are associated with various diseases, including diabetic complications such as diabetic retinopathy (DR). The risk of developing DR is strongly associated with poor glycemic control, which causes AGE accumulation and increases AGE-induced vascular permeability. We previously reported that Ras guanyl nucleotide releasing protein 2 (RasGRP2), which activates small G proteins, may play an essential role in the cell response to toxicity when exposed to various factors. However, it is not known whether RasGRP2 prevents the adverse effects of TAGE in vascular endothelial cells. This study observed that TAGE enhanced vascular permeability by disrupting adherens junctions and tight junctions via complex signaling, such as ROS and non-ROS pathways. In particular, RasGRP2 protected adherens junction disruption, thereby suppressing vascular hyper-permeability. These results indicate that RasGRP2 is an essential protective factor of vascular permeability and may help develop novel therapeutic strategies for AGE-induced DR.
Differential DNA methylation in recovery from shift work disorder
Authors: Lahtinen Alexandra , Häkkinen Antti , Puttonen Sampsa , Vanttola Päivi , Viitasalo Katriina , Porkka-Heiskanen Tarja , Härmä Mikko , Paunio Tiina 
Published: February 2021

AbstractThe human DNA methylome is responsive to our environment, but its dynamics remain underexplored. We investigated the temporal changes to DNA methylation (DNAme) in relation to recovery from a shift work disorder (SWD) by performing a paired epigenome-wide analysis in an occupational cohort of 32 shift workers (25 men, age = 43.8 ± 8.8 years, 21 SWD cases). We found that the effect of vacation on DNAme was more prominent in the SWD-group as compared to controls, with respect to the amount of significantly differentially methylated positions (DMPs; Punadj < 0.05) 6.5 vs 3.7%, respectively. The vast majority (78%) of these DMPs were hypomethylated in SWD but not in controls (27%) during the work period. The Gene Ontology Cellular component “NMDA glutamate receptor” (PFDR < 0.05) was identified in a pathway analysis of the top 30 genes in SWD. In-depth pathway analyses revealed that the Reactome pathway “CREB phosphorylation through the activation of CaMKII” might underlie the recovery. Furthermore, three DMPs from this pathway, corresponding to GRIN2C, CREB1, and CAMK2B, correlated with the degree of recovery (Punadj < 0.05). Our findings provide evidence for the dynamic nature of DNAme in relation to the recovery process from a circadian disorder, with biological relevance of the emerging pathways.
The development of nonalcoholic steatohepatitis is subjected to breeder dependent variation in guinea pigs
Authors: Ipsen D. H. , Agerskov R. H. , Klaebel J. H. , Lykkesfeldt J. , Tveden-Nyborg Pernille 
Published: February 2021

AbstractVariability in disease development due to differences in strains and breeders constitutes a substantial challenge in preclinical research. However, the impact of the breeder on non-alcoholic steatohepatitis (NASH) is not yet fully elucidated. This retrospective study investigates NASH development in guinea pigs from Charles River or Envigo fed a high fat diet (20% fat, 15% sucrose, 0.35% cholesterol) for 16 or 24/25 weeks. Charles River animals displayed more severe NASH, with higher steatosis (p < 0.05 at week 16), inflammation (p < 0.05 at both week), fibrosis (p < 0.05 at week 16) and disease activity (p < 0.05 at both weeks). Accordingly, alanine and aspartate aminotransferase were increased at week 24/25 (p < 0.01). Hepatic expression of inflammatory (Ccl2, Cxcl8) and fibrotic (Pdgf, Serpine1, Col1a1) genes was also increased (p < 0.05). Differences were observed in healthy chow (4% fat, 0% sucrose, 0% cholesterol) fed animals: Envigo animals displayed higher relative liver weights (p < 0.01 at both weeks), liver cholesterol (p < 0.0001 at week 24/25) and aspartate aminotransferase (p < 0.05 at week 16), but lower levels of alkaline phosphatase (p < 0.0001 at week 24/25). These findings accentuates the importance of the breeder and its effect on NASH development and severity. Consequently, this may affect reproducibility, study comparison and limit the potential of developing novel therapies.
ALMA/NICER observations of GRS 1915+105 indicate a return to a hard state
Authors: Koljonen K. I. I. , Hovatta T. 
Published: February 2021

Context. GRS 1915+105 is a transient black hole X-ray binary consistently emitting 10–100% of the Eddington luminosity in the X-ray band over the last three decades until mid-2018 when the source luminosity suddenly decreased by an order of magnitude. This phase was followed by a change to a state with even lower average X-ray fluxes never seen before during the outburst but presenting renewed flaring activity at different wavelengths, albeit with mean fluxes still in decline.
Aims. GRS 1915+105 has the longest orbital period known among low-mass X-ray binaries, the largest accretion disk size, and therefore the largest mass supply for accretion. The high inclination of the disk allows the study of geometrical effects of the accretion flow such as changes in the height-to-radius ratio or the effect of accretion disk winds on the intrinsic emission that is expected during the outburst decay. In addition, the transient jet is expected to change to a compact, self-absorbed, steady jet.
Methods. We conducted two full polarization Atacama Large Millimeter Array observations to study the jet properties during the outburst decay by analyzing the spectral, polarization, and intra-epoch variability for both observation epochs. In addition, we analyzed almost daily Neutron Star Interior Composition Explorer pointing observations, modeling X-ray power spectral densities, spectral energy distributions, and light curves with a physically motivated model to follow the changing accretion disk properties throughout the outburst decay and relating them to the jet emission.
Results. We show that the X-ray and millimeter (mm) spectral, timing, and polarization properties are consistent with those of a typical decaying X-ray binary outburst and that GRS 1915+105 has descended into the low-luminosity hard X-ray state. The jet emission in the mm is consistent with a compact, steady jet with ∼1% linear polarization, and the magnetic field is likely aligned with the jet position angle. Relating the mm emission to the X-ray emission reveals that the source has changed from a higher radio/X-ray correlation index to a lower one; Lradio ∝ LX0.6.
RHOBTB2 p.Arg511Trp Mutation in Early Infantile Epileptic Encephalopathy-64: Review and Case Report
Authors: Fonseca Jacinta , Melo C. , Ferreira C. , Sampaio M. , Sousa R. , Leão M. 
Published: February 2021

AbstractEarly infantile epileptic encephalopathy-64 (EIEE 64), also called RHOBTB2-related developmental and epileptic encephalopathy (DEE), is caused by heterozygous pathogenic variants (EIEE 64; MIM#618004) in the Rho-related BTB domain-containing protein 2 (RHOBTB2) gene. To date, only 13 cases with RHOBTB2-related DEE have been reported. We add to the literature the 14th case of EIEE 64, identified by whole exome sequencing, caused by a heterozygous pathogenic variant in RHOBTB2 (c.1531C > T), p.Arg511Trp. This additional case supports the main features of RHOBTB2-related DEE: infantile-onset seizures, severe intellectual disability, impaired motor functions, postnatal microcephaly, recurrent status epilepticus, and hemiparesis after seizures.
Seizure Semiology in Focal and Generalized Epilepsies: Distinctive and Overlapping Features
Authors: Marashly Ahmad 
Published: February 2021

AbstractStudying seizure semiology is the first step in evaluating any patient with epilepsy which leads the way to further investigations and management, particularly in differentiating focal and generalized epilepsies. While the usefulness of semiological analysis has been confirmed through decades' worth of research and clinical practice, there remains some instances when the line between focal and generalized semiological features is blurred leading to difficulties identifying the type of epilepsy at hand. This in turn can lead to delayed or wrong diagnoses with significant implications.In this review article, we explain the role of semiology in epilepsy, specifically in differentiating focal versus generalized epilepsies and cover the semiological features for both groups. We also discuss the occasional overlapping semiology between the two groups and provide case examples.
Embryology of the Orbit
Authors: Cho Raymond I. , Kahana Alon 
Published: February 2021

AbstractThe orbit houses and protects the ocular globe and the supporting structures, and occupies a strategic position below the anterior skull base and adjacent to the paranasal sinuses. Its embryologic origins are inextricably intertwined with those of the central nervous system, skull base, and face. Although the orbit contains important contributions from four germ cell layers (surface ectoderm, neuroectoderm, neural crest, and mesoderm), a significant majority originate from the neural crest cells. The bones of the orbit, face, and anterior cranial vault are mostly neural crest in origin. The majority of the bones of the skull base are formed through endochondral ossification, whereas the cranial vault is formed through intramembranous ossification. Familiarity with the embryology and fetal development of the orbit can aid in understanding its anatomy, as well as many developmental anomalies and pathologic conditions that affect the orbit.
High-energy x-ray nanotomography introducing an apodization Fresnel zone plate objective lens
Authors: Takeuchi Akihisa , Uesugi Kentaro , Uesugi Masayuki , Toda Hiroyuki , Hirayama Kyosuke , Shimizu Kazuyuki , Matsuo Koichi , Nakamura Takashi 
Published: February 2021

In this study, high-energy x-ray nanotomography (nano-computed tomography, nano-CT) based on full-field x-ray microscopy was developed. Fine two-dimensional and three-dimensional (3D) structures with linewidths of 75 nm–100 nm were successfully resolved in the x-ray energy range of 15 keV–37.7 keV. The effective field of view was ∼60 µm, and the typical measurement time for one tomographic scan was 30 min–60 min. The optical system was established at the 250-m-long beamline 20XU of SPring-8 to realize greater than 100× magnification images. An apodization Fresnel zone plate (A-FZP), specifically developed for high-energy x-ray imaging, was used as the objective lens. The design of the A-FZP for high-energy imaging is discussed, and its diffraction efficiency distribution is evaluated. The spatial resolutions of this system at energies of 15 keV, 20 keV, 30 keV, and 37.7 keV were examined using a test object, and the measured values are shown to be in good agreement with theoretical values. High-energy x-ray nano-CT in combination with x-ray micro-CT is applied for 3D multiscale imaging. The entire bodies of bulky samples, ∼1 mm in diameter, were measured with the micro-CT, and the nano-CT was used for nondestructive observation of regions of interest. Examples of multiscale CT measurements involving carbon steel, mouse bones, and a meteorite are discussed.
Electronic structure and thermoelectric properties of half-Heusler alloys NiTZ
Authors: Jaishi Dhurba R. , Sharma Nileema , Karki Bishnu , Belbase Bishnu P. , Adhikari Rajendra P. , Ghimire Madhav P. 
Published: February 2021

We investigated the electronic and thermoelectric properties of half-Heusler alloys NiTZ (T = Sc and Ti; Z = P, As, Sn, and Sb) having an 18 valence electron count. Calculations were performed by means of density functional theory and the Boltzmann transport equation with constant relaxation time approximation, validated by NiTiSn. The chosen half-Heuslers were found to be indirect bandgap semiconductors, and the lattice thermal conductivity was comparable with the state-of-the-art thermoelectric materials. The estimated power factor for NiScP, NiScAs, and NiScSb revealed that their thermoelectric performance can be enhanced by an appropriate doping rate. The value of ZT found for NiScP, NiScAs, and NiScSb is 0.46, 0.35, and 0.29, respectively, at 1200 K.
Buffer layer engineering of L1 FePd thin films with large perpendicular magnetic anisotropy
Authors: Wang Xinjun , Krylyuk Sergiy , Josell Daniel , Zhang Delin , Lyu Deyuan , Wang Jian-Ping , Gopman Daniel B. 
Published: February 2021

Development of L10 FePd thin films with large bulk perpendicular magnetic anisotropy and a low damping constant may permit superior scaling of next-generation ultra-high density magnetic memory elements. The buffer layer influences the L10-order parameter, static and dynamic magnetic properties of FePd and demands consideration for the design of high anisotropy strength and low damping films. In this report, we systematically investigate the perpendicular magnetic anisotropy and damping constant of the FePd thin films engineered through the Cr/(Pt, Ru, Ir, Rh), Mo/Ir, and Ir buffer layers. We observed that the Ir(001), Cr(001)/Ir(001), Cr(001)/Pt(001), Cr(001)/Rh(001), and Cr(001)/Ru(001) buffer layers can induce highly oriented (001) FePd films while the Mo/Ir buffer layer does not. Of all the buffer layers, the largest perpendicular magnetic anisotropy Ku ∼ 1.2 MJ/m3 and damping constant α ∼ 0.005 were achieved for the Cr/Pt buffered FePd sample, consistent with a high ordering parameter S ∼ 0.82. The Cr/Ru buffered FePd sample shows the lowest α ∼ 0.008, despite having a lower S ∼ 0.64 and a lower Ku ∼ 0.9 MJ/m3. These film-level properties would be sufficient for the engineering of devices that require thermally stable, sub-10 nm lateral size elements with low damping for applications of low energy-delay magnetic memory devices.
Broadband optical absorption enhancement in hybrid organic–inorganic perovskite metasurfaces
Authors: Wang Chenzhe , Zhang Zhifeng 
Published: February 2021

The hybrid organic–inorganic perovskite (HOIP) becomes a promising candidate for ultra-thin photoelectric batteries and skin-like sensors. However, homogeneous thin films of the material usually provide low absorption efficiency. In this work, by engineering the nanohole arrays on a HOIP ultrathin film, we successfully design an all-dielectric HOIP metasurface with broadband optical absorption enhancement through the finite-difference time-domain technique. The absorption enhancement arises from the Mie resonance, which can be tuned by varying the geometrical parameters and the spatial periodicity of the nanoholes. Compared with a uniform HOIP film, the HOIP metasurface significantly enhances the absorption over the entire visible regime, and the maximum absorption rate reaches 90%. Moreover, our design with multiple nanohole sizes provides consistently high absorption efficiency up to 51%–87% in a broad wavelength range of 400 nm–770 nm. Furthermore, the external quantum efficiency of a solar cell with our HOIP metasurface is 44% higher than that of a uniform HOIP film by assuming the ideal process with infinite carrier lifetime and negligible recombination. Our findings may provide a route for effective light trapping and efficient photoelectric conversion with ultrathin HOIP metasurfaces.
Gestures in patients’ presentation of medically unexplained symptoms (MUS)
Authors: Sowińska Agnieszka , Boruta-Żywiczyńska Monika 
Published: February 2021

Abstract
The aim of this paper is to explore speech-accompanying gesture use in presentation of medically unexplained
symptoms (MUS). The data are 19 video-filmed semi-structured interviews with patients presenting MUS. Four patterns of gestural
behaviors are established in symptom presentation: (1) No gesturing; (2) Overall low gesture rate; (3) Overall high gesture rate
with low rate for symptoms; (4) Overall high gesture rate with high rate for symptoms. The patients with overall low gesture rate
tend to perform deictic gestures, pointing to exact locations of the symptoms; those with overall high gesture rate and low
symptom rate produce metaphorics, and those who gesticulate at high rates – mainly iconics and metaphorics. Although exact factors
that lead to the four types of gesturing patterns are unclear, the findings encourage medical professionals to attend to the
information in gesture use in order to obtain a better understanding of the patient’s experience of MUS.
Spatial characterization of edge zonal flows in the TJ-II stellarator: the roles of plasma heating and isotope mass
Authors: Losada U , Kobayashi T , Ohshima S , Cappa A , Van Milligen B , Liniers M , López-Miranda B , Liu B , Pastor I , Silva C , Hidalgo C 
Published: February 2021

Abstract
In this article, we report the latest results for the impacts of the isotope mass and the plasma heating scenario on the spatiotemporal characteristics of the low-frequency zonal flow (ZF)-like electrostatic oscillation found in the plasma edge of the TJ-II stellarator. The radial profile of the toroidal cross-coherence in low-frequency floating potential fluctuations (1 < f < 25 kHz), known as long-range correlations (LRCs), was explored along the plasma boundary region by a dual Langmuir probe system. The study was performed using electron cyclotron resonance heating (ECRH)- and neutral beam injection (NBI)-heated plasmas with two different isotope concentrations: pure hydrogen plasmas and plasmas dominated by deuterium (

≈
70
%

D

). The highest toroidal coherence levels are detected for floating potential oscillations at less than 10 kHz in hydrogen and deuterium plasmas, in both the ECRH and NBI heating schemes. The radial extent of the LRC profile is clearly larger in the ECRH than in the NBI-heated plasma scenarios. While the maximum amplitude of the LRC does not show a significant dependence on isotope mass, the relation between the LRCs’ radial sizes in plasmas and different isotope masses increases with the isotope mass in NBI-heated scenarios. These results provide the first experimental observation of ZFs with a larger radial size in deuterium than in hydrogen plasmas.
EMI-GCN: a hybrid model for real-time monitoring of multiple bolt looseness using electromechanical impedance and graph convolutional networks
Authors: Zhou Lu , Chen Si-Xin , Ni Yi-Qing , Choy Alex Wai-Hing 
Published: February 2021

Abstract
Electro-mechanical impedance (EMI) has been proved as an effective non-destructive evaluation indicator in monitoring the looseness of bolted joints. Yet due to the complex electro-mechanical coupling mechanism, EMI-based methods in most cases are considered as qualitative approaches and are only applicable for single-bolt monitoring. These issues limit practical applications of EMI-based methods in industrial and transportation sectors where real-time and reliable monitoring of multiple bolted joints in a localized area is desired. Previous research efforts have integrated various machine learning (ML) algorithms in EMI-based monitoring to enable quantitative diagnosis, but only one-to-one (single sensor single bolt) case was considered, and the EMI–ML integrations are basically unnatural and ingenious by learning the EMI measurements from isolated sensors. This paper presents a novel EMI-based bolt looseness monitoring method incorporating both physical mechanism (acoustic attenuation) and data-driven analysis, by implementing a lead zirconate titanate (PZT) sensor network and a built-in graph convolutional network (GCN) model. The GCN model is constructed in such a way that the structure of the PZT network is fully represented, with the sensor-bolt distance and sweeping frequency encoded in the propagation function. The proposed method takes into account not only the EMI signature but also the relationship between the sensing nodes and the bolted joints and can quantitatively infer the torque loss of multiple bolts through node-level outputs. A proof-of-concept experiment was conducted on a twin-bolt plate, and results show that the proposed method outperforms other baseline models either without a graph network structure or does not consider sensor-bolt distance. The developed hybrid model provides new thinking in interpreting sensor networks which are widely adopted in structural health monitoring, and the approach is expected to be applicable in practical scenarios such as rail insulated joints and aircraft wings where bolt joints are clustered.