bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prognostic index of m7G-related genes in CRC correlates with immune infiltration
Authors: Huang Xinkun , Zhu Bin , Qian Chenyu , Feng Ying 
Published: December 2022

AbstractN7-methyladenosine (m7G) modifications have been the subject of growing research interest with respect to their relationship with the progression and treatment of various cancers. This analysis was designed to examine the association between m7G-related gene expression and colorectal cancer (CRC) patient outcomes. Initial training analyses were performed using the TCGA dataset, with the GSE28722 dataset then being used to validate these results. Univariate Cox analyses were initially conducted to screen out prognostic m7G-related genes, after which a LASSO approach was used to construct an m7G risk score (MRS) model. Kaplan–Meier curves, ROC curves, and Cox analyses were subsequently used to validate the prognostic utility of this model in CRC patients. The R maftools package was further employed to assess mutational characteristics in CRC patients in different MRS subgroups, while the ESTIMATE, CIBERSORT, and ssGSEA tools were used to conduct immune infiltration analyses. A WGCNA was then performed to identify key immune-associated hub genes. The EIF4E3, GEMIN5, and NCBP2 genes were used to establish the MRS model. Patients with high MRS scores exhibited worse overall survival than patients with low scores. In Cox analyses, MRS scores were independently associated with CRC patient prognosis. Patients with low MRS scores exhibited a higher tumor mutational burden and higher levels of microsatellite instability. In immune infiltration analyses, higher immune checkpoint expression and greater immune cell infiltration were also observed in patients with low MRS scores. WGCNA analyses further identified 25 CD8+ T cell infiltration-associated genes. These findings suggest that MRS values represent a useful biomarker capable of differentiating among CRC patients with different immunological features and prognostic outcomes, offering an opportunity to better determine which patients are likely to benefit from immune checkpoint inhibitor treatment.
Metabolomics and transcriptomics reveal the effect of hetero-chitooligosaccharides in promoting growth of Brassica napus
Authors: Tang Chao , Zhai Yang , Wang Zhuo , Zhao Xin , Yang Chen , Zhao Yong , Zeng Liang-bin , Zhang De-yong 
Published: December 2022

AbstractThe hetero-chitooligosaccharide (HTCOS) is a naturally occurring biopolymer in the exoskeleton of crustaceans and insects. Although some studies have been carried out on HTCOS in inducing plant resistance and promoting growth, the molecular mechanism of HTCOS in plants is not clear. In this study, an integrated analysis of metabolomics and transcriptomics was performed to analyze the response of Brassica napus to hetero-chitooligosaccharides treatment. The levels of 26 metabolites in B. napus were significantly changed under the HTCOS treatment. Amongst these metabolites, 9 metabolites were significantly up-regulated, including pentonic acid, indole-3-acetate, and γ-aminobutyric acid. Transcriptome data showed that there were 817 significantly up-regulated genes and 1064 significantly down-regulated genes in B. napus under the HTCOS treatment. Interestingly, the indole-3-acetate (IAA) content under the HTCOS treatment was about five times higher than that under the control condition. Moreover, four genes related to plant hormone signal transduction, three AUX/IAA genes, and one ARF gene, were significantly up-regulated under the HTCOS treatment. Furthermore, the plant height, branching number, and biomass of B. napus under the HTCOS treatment were significantly increased compared to that in the control condition. This evidence indicated that the HTCOS treatment contributed to accumulating the content of plant hormone IAA in the B. napus, up-regulating the expression of key genes in the signaling pathway of plant growth and improving the agronomic traits of B. napus.
Beyond noise to function: reframing the global brain activity and its dynamic topography
Authors: Zhang Jianfeng , Northoff Georg 
Published: December 2022

AbstractHow global and local activity interact with each other is a common question in complex systems like climate and economy. Analogously, the brain too displays ‘global’ activity that interacts with local-regional activity and modulates behavior. The brain’s global activity, investigated as global signal in fMRI, so far, has mainly been conceived as non-neuronal noise. We here review the findings from healthy and clinical populations to demonstrate the neural basis and functions of global signal to brain and behavior. We show that global signal (i) is closely coupled with physiological signals and modulates the arousal level; and (ii) organizes an elaborated dynamic topography and coordinates the different forms of cognition. We also postulate a Dual-Layer Model including both background and surface layers. Together, the latest evidence strongly suggests the need to go beyond the view of global signal as noise by embracing a dual-layer model with background and surface layer.
COVID-19 instigates adipose browning and atrophy through VEGF in small mammals
Authors: Jing Xu , Wu Jieyu , Dong Caijuan , Gao Juan , Seki Takahiro , Kim Changil , Urgard Egon , Hosaka Kayoko , Yang Yunlong , Long Siwen , Huang Ping , Zheng Junnian , Szekely Laszlo , Zhang Yuanting , Tao Wei , Coquet Jonathan , Ge Minghua , Chen Yuguo , Adner Mikael , Cao Yihai 
Published: December 2022

AbstractPatients with COVID-19 frequently manifest adipose atrophy, weight loss and cachexia, which significantly contribute to poor quality of life and mortality1,2. Browning of white adipose tissue and activation of brown adipose tissue are effective processes for energy expenditure3–7; however, mechanistic and functional links between SARS-CoV-2 infection and adipose thermogenesis have not been studied. In this study, we provide experimental evidence that SARS-CoV-2 infection augments adipose browning and non-shivering thermogenesis (NST), which contributes to adipose atrophy and body weight loss. In mouse and hamster models, SARS-CoV-2 infection activates brown adipose tissue and instigates a browning or beige phenotype of white adipose tissues, including augmented NST. This browning phenotype was also observed in post-mortem adipose tissue of four patients who died of COVID-19. Mechanistically, high levels of vascular endothelial growth factor (VEGF) in the adipose tissue induces adipose browning through vasculature–adipocyte interaction. Inhibition of VEGF blocks COVID-19-induced adipose tissue browning and NST and partially prevents infection-induced body weight loss. Our data suggest that the browning of adipose tissues induced by COVID-19 can contribute to adipose tissue atrophy and weight loss observed during infection. Inhibition of VEGF signaling may represent an effective approach for preventing and treating COVID-19-associated weight loss.
Limiting grazing periods combined with proper housing can reduce nutrient losses from dairy systems
Authors: McDowell R. W. , Rotz C. A. , Oenema J. , Macintosh K. A. 
Published: December 2022

AbstractPasture-based and grass-fed branding are often associated with consumer perceptions of improved human health, environmental performance and animal welfare. Here, to examine the impacts of dairy production in detail, we contrasted global observational (n = 156) data for nitrogen and phosphorus losses from land by the duration of outdoor livestock grazing in confined, grazed and hybrid systems. Observational nitrogen losses for confined systems were lowest on a productivity—but not area—basis. No differences were noted for phosphorus losses between the systems. Modelling of the three dairy systems in New Zealand, the United States and the Netherlands yielded similar results. We found insufficient evidence that grazed dairy systems have lower nutrient losses than confined ones, but trade-offs exist between systems at farm scale. The use of a hybrid system may allow for uniform distribution of stored excreta, controlled dietary intake, high productivity and mitigation of animal welfare issues arising from climatic extremes.
Structured type III radio bursts observed in interplanetary space
Authors: Jebaraj I. C. , Magdalenic J. , Krasnoselskikh V. , Krupar V. , Poedts S. 
Published: December 2022

Context. The last few decades have seen numerous studies dedicated to fine structures of type III radio bursts observed in the meter–decameter wavelengths. Most of the explanations of the structured radio emission involve the propagation of electron beams through the strongly inhomogeneous plasma in the low corona. To date, only a few type III bursts with fine structures, observed at hecto–kilometric wavelengths, have been reported.
Aims. We report here the existence of numerous structured type III radio bursts observed during the STEREO era by all three WAVES instruments on board STEREO A, B, and Wind. The aim of the study is to report and classify structured type III bursts, and to present the characteristics of their fine structures. The final goal is to try to understand the physical mechanism responsible for the generation of structured radio emission.
Methods. In this study we used data from all available spacecraft, specifically STEREO and Wind. We employed 1D density models to obtain the speed of the source of type III radio emission, the electron beam. We also performed a spectral analysis of the fine structures in order to compare their characteristics with the metric–decametric fine structures.
Results. The presented similarities of the type III fine structures in the metric to decametric and interplanetary wavelengths indicate that the physical processes responsible for the generation of structured type III radio bursts could be the same, at heights from the low corona to the interplanetary range. We show that the observed structuring and intermittent nature of the type III bursts can be explained by the variation in the level of density fluctuations, at different distances from the Sun.
Organic detection in the near-infrared spectral Phobos regolith laboratory analogue in preparation for the Martian Moon eXploration mission
Authors: Wargnier A. , Gautier T. , Poch O. , Beck P. , Quirico E. , Buch A. , Drant T. , Perrin Z. , Doressoundiram A. 
Published: December 2022

Context.The Martian Moon eXploration mission (MMX) of the Japanese space agency (JAXA) is scheduled to take off in September 2024 to explore Phobos and Deimos – the two martian moons – by in situ observations, but also by a sampling and returning regolith samples to Earth. The origins of Phobos and Deimos are still unknown and their understanding is one of the main goals of the MMX mission. In one scenario, Phobos could be a captured asteroid, as the Phobos spectrum is similar to dark D-type asteroids.Aims.For the present work, we considered the hypothesis of Phobos being a captured D-type asteroid, and we investigated the detectability of organics on Phobos using laboratory spectral analogues.Methods.We synthesised a near-infrared spectral analogue of Phobos composed of olivine (77 vol.%, 50–125 µm), hyperfine anthracite (20 vol.%, <1 µm), and organic tholins (3 vol.%, ~400 nm) by measuring the reflectance spectrum from 0.4 to 4.75 µm with the SHADOWS spectrogonio-radiometre developped at IPAG. The best spectral match for a Phobos regolith analogue was chosen based on its reflectance level and spectral slope similarities to Phobos’ observed spectrum. Several samples were then prepared by adding a different volume content of organic matter (Titan tholins). We monitored the 3 µm band attributed toN-Hbands stretching modes absorption due to the amine function in the tholins, so as to assess the detectability of the NH-rich organics on Phobos.Results.We have demonstrated that the organic compounds become detectable for more than 5 vol.% in the mixture. We further studied the observation geometry effects on the absorption band depth and found no significant effect except at large phase angles (>80º). These results will be useful to interpret the data of the MMX Infrared Spectrometer (MIRS) onboard the MMX spacecraft, which will measure the spectral reflectance of Phobos from 0.9 to 3.6 µm.
Das Sjögren-Syndrom aus Sicht der Erfahrungsheilkunde
Authors: Noschinski Dirk-Rüdiger 
Published: December 2022

ZusammenfassungDas Sjögren-Syndrom hat sehr verschiedene Facetten, da es unterschiedliche Bereiche des Körpers befallen kann. Leitsymptome sind Xerostomie und Xerophthalmie, die in nahezu allen Fällen auftreten. Deswegen sollten Sie bei therapieresistenten Erkrankungen im Bereich des zentralen Nervensystems, des peripheren Nervensystems, des Gastrointestinaltrakts, Atmungstrakts oder Nieren, die mit Mundtrockenheit einhergehen, differenzialdiagnostisch an ein Sjögren-Syndrom denken. Eine erfolgversprechende naturheilkundliche Behandlungsstrategie kombiniert verschiedene therapeutische Elemente wie Ernährung, Mikronährstoffe, Ausleitung und anthroposophische Heilmittel im Sinne einer personalisierten Medizin.
Colonoscopy quality improvement after initial training: A cross-sectional study of intensive short-term training
Authors: Schult Anna Lisa , Hoff Geir , Holme Øyvind , Botteri Edoardo , Seip Birgitte , Ranheim Randel Kristin , Darre-Næss Ole , Owen Tanja , Nilsen Jens Aksel , Nguyen Dung Hong , Johansen Kristin , de Lange Thomas 
Published: December 2022

Abstract
Background and study aims High-quality is crucial for the effectiveness of colonoscopy and can be achieved by high-quality training and verified with assessment of key performance indicators (KPIs) for colonoscopy such as cecum intubation rate (CIR), adenoma detection rate (ADR) and adequate polyp resection. Typically, trainees achieve adequate CIR after 275 procedures, but little is known about learning curves for KPIs after initial training.
Methods This cross-sectional study includes work-up colonoscopies after a positive screening test with fecal occult blood testing (FIT) or sigmoidoscopy, performed by either trainees after 300 training colonoscopies or by consultants. Outcome measures were KPIs. We assessed inter-endoscopist variation in trainees and learning curves for trainees as a group. We also compared KPIs for trainees and consultants as a group.
Results Data from 6,655 colonoscopies performed by 21 trainees and 921 colonoscopies performed by 17 consultants were included. Most trainees achieved target standards for main KPIs. With time, trainees shortened cecum intubation time and withdrawal time without decreasing their ADR, reduced the proportion of painful colonoscopies, and increased the adequate polyp resection rate (all P < 0.01). Compared to consultants, trainees had higher CIR (97.7 % vs. 96.3 %, P = 0.02), ADR after positive FIT (57.6 % vs. 50.3 %, P < 0.01), and proximal ADR after sigmoidoscopy screening (41.1 % vs. 29.8 %; P < 0.01), higher adequate polyp resection rate (94.9 % vs. 93.1 %, P = 0.01) and fewer serious adverse events (0.65 % vs. 1.41 %, P = 0.02).
Conclusions Trainees performed high-quality colonoscopies and achieved international target standards. Several KPIs continuously improved after initial training. Trainees outperformed consultants on several KPIs.
Enhancement of PIV measurements via physics-informed neural networks
Authors: Hasanuzzaman Gazi , Eivazi Hamidreza , Merbold Sebastian , Egbers Christoph , Vinuesa Ricardo 
Published: December 2022

Abstract
Physics-informed neural networks (PINN) are machine-learning methods that have been proved to be very successful and effective for solving governing equations of fluid flow. In this work we develop a robust and efficient model within this framework and apply it to a series of two-dimensional three-component stereo particle-image velocimetry (PIV) datasets, to reconstruct the mean velocity field and correct measurements errors in the data. Within this framework, the PINNs-based model solves the Reynolds-averaged-Navier–Stokes equations for zero-pressure-gradient turbulent boundary layer (ZPGTBL) without a prior assumption and only taking the data at the PIV domain boundaries. The turbulent boundary layer (TBL) data has different flow conditions upstream of the measurement location due to the effect of an applied flow control via uniform blowing. The developed PINN model is very robust, adaptable and independent of the upstream flow conditions due to different rates of wall-normal blowing while predicting the mean velocity quantities simultaneously. Hence, this approach enables improving the mean-flow quantities by reducing errors in the PIV data. For comparison, a similar analysis has been applied to numerical data obtained from a spatially-developing ZPGTBL and an adverse-pressure-gradient TBL over a NACA4412 airfoil geometry. The PINNs-predicted results have less than 1% error in the streamwise velocity and are in excellent agreement with the reference data. This shows that PINNs has potential applicability to shear-driven turbulent flows with different flow histories, which includes experiments and numerical simulations for predicting high-fidelity data.
ITB formation in gyrokinetic flux-driven ITG/TEM turbulence
Authors: Imadera Kenji , Kishimoto Yasuaki 
Published: December 2022

Abstract
The formation mechanism of internal transport barriers (ITBs) in flux-driven turbulence is studied by means of the full-f gyrokinetic code GKNET. In the adiabatic electron case with a weak magnetic shear configuration, toroidal momentum injection can change the radial mean electric field

E
r

through radial force balance, leading to a kind of driven ITB formation in which the ion thermal diffusivity by ion temperature gradient (ITG) turbulence decreases to the neoclassical transport level. Only cocurrent toroidal rotation in the outer core region can benefit the ITB formation, and this mechanism is identified to originate from a positive feedback loop between the radial

E
r

shear and resultant momentum flux. On the other hand, in the kinetic electron case with a reversed magnetic shear configuration, robust co-intrinsic rotation is driven near the

q

min

surface in ITG turbulence and sustains the

E
r

shear through the radial force balance, leading to the spontaneous reduction of ion turbulent thermal diffusivity, while this is not observed in the adiabatic electron case. In the presence of electron heating, counter-intrinsic rotation by trapped electron mode turbulence is selectively driven in the negative magnetic shear region, which provides steeper

E
r

shear formation and a resultant larger reduction of ion turbulent thermal diffusivity. This indicates that the co-existence of different modes can trigger the ‘discontinuity’ of mode structure, intrinsic rotation, and resultant mean

E
r

near

q

min

, leading to spontaneous ITB formation.
Influence of magnetic field strength on capacitively coupled CF4 discharge at different pressures
Authors: Yang Shali , Lin Hanlei , Zhang Tianxiang , Peng Yanli , Zhang Qiang 
Published: December 2022

Abstract
The influence of a homogeneous magnetic field parallel to the electrodes on the plasma properties and electron heating mode was investigated by a one-dimensional particle-in-cell/Monte Carlo simulations in electronegative CF4 discharges. The discharge conditions are Z = 3.5 cm, f = 13.56 MHz,

V

0

=
300

V, and the various gas pressure of 10 mTorr, 100 mTorr and 200 mTorr. It is found that, in the absence of a magnetic field, the discharges are electronegative at different pressures and the electronegativity is stronger at higher pressure. When a homogeneous magnetic field is applied, the electron density significantly increases and the electronegativity decreases to varying degrees at different pressures. At p = 10 mTorr and p = 100 mTorr, a transition from a hybrid combination of α and drift-ambipolar (DA) modes into a pure α mode is induced by a weak magnetic field. At p = 200 mTorr, a transition from a DA mode into a hybrid combination of α and DA modes is induced by a relatively high magnetic field. The strength of the magnetic field required to induce mode transition becomes stronger at higher gas pressures. This is because increasing the pressure reduces the mean free path and the frequent electron-neutral collisions disrupt electron gyromotion, thus the effects of the magnetic field are greatly reduced.
Electronic transport properties of Ti-supersaturated Si processed by rapid thermal annealing or pulsed-laser melting
Authors: Olea J , González-Díaz G , Pastor D , García-Hemme E , Caudevilla D , Algaidy S , Pérez-Zenteno F , Duarte-Cano S , García-Hernansanz R , del Prado A , San Andrés E , Mártil I 
Published: December 2022

Abstract
In the scope of supersaturated semiconductors for infrared detectors, we implanted Si samples with Ti at high doses and processed them by rapid thermal annealing (RTA) to recover the crystal quality. Also, for comparative purposes, some samples were processed by pulsed-laser melting. We measured the electronic transport properties at variable temperatures and analyzed the results. The results indicate that, for RTA samples, surface layers with a high Ti concentration have negligible conductivity due to defects. In contrast, the implantation tail region has measurable conductivity due to very high electron mobility. This region shows the activation of a very shallow donor and a deep donor level. While deep levels have been previously reported for Ti in Si, such a shallow level has never been measured, and we suggest that it originates from Ti-Si complexes. Finally, a decoupling effect between the implanted layer and the substrate seems to be present, and a bilayer model is applied to fit the measured properties. The fitted parameters follow the Meyer–Neldel rule. The role of the implantation tails in Si supersaturated with Ti is revealed in this work.
Adsorption of phosphate ions from water using PVA-NiO nanocomposite based on tuning influence of pulsed laser ablation method
Authors: Toghan Arafat , Mwafy Eman A , Mostafa Ayman M , Rezk Reham A 
Published: December 2022

Abstract
For the purpose of getting rid of phosphate in the direction of preserving the eco-system, nickel oxide nanoparticles (NiO NPs) have recently been used to address this issue. For that, NiO NPs were generated using a laser ablation in liquid method of PVA solution and encapsulated in a PVA matrix structure with different particle sizes using a nanosecond solid-state laser with a change in laser influence. Then, their physicochemical properties were studied using various methods. It was found that NiO NPs were distributed very well inside the PVA structure, which was confirmed by the presence of both characteristic vibrational peaks of PVA and NiO with shifting in the peak of PVA and the appearance of the main characteristic transition peaks of the d-d transition of NiO, relating to the impedance of the PVA structure with NiO NPs. The optimal conditions for the elimination of phosphate ions from water solutions were determined by examining the impacts of a number of important affected parameters. A concentration of 100 mg L−1 of phosphate can be removed from a liquid medium at pH 6 using a PVA-NiO nanocomposite. This work lays the route to getting on different nanocomposite materials to get rid of different hazardous chemical compounds.