bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rice plants overexpressing OsEPF1 show reduced stomatal density and increased root cortical aerenchyma formation
Authors: Mohammed U. , Caine R. S. , Atkinson J. A. , Harrison E. L. , Wells D. , Chater C. C. , Gray J. E. , Swarup R. , Murchie E. H. 
Published: April 2019

AbstractStomata are adjustable pores in the aerial epidermis of plants. The role of stomata is usually described in terms of the trade-off between CO2uptake and water loss. Little consideration has been given to their interaction with below-ground development or diffusion of other gases. We overexpressed the riceEPIDERMAL PATTERNING FACTOR1(OsEPF1)toproduce rice plants with reduced stomatal densities, resulting in lowered leaf stomatal conductance and enhanced water use efficiency. Surprisingly, we found that root cortical aerenchyma (RCA) is formed constitutively inOsEPF1OE lines regardless of tissue age and position. Aerenchyma is tissue containing air-spaces that can develop in the plant root during stressful conditions, e.g. oxygen deficiency when it functions to increase O2diffusion from shoot to root. The relationship with stomata is unknown. We conclude that RCA development and stomatal development are linked by two possible mechanisms: first that reduced stomatal conductance inhibits the diffusion of oxygen to the root, creating an oxygen deficit and stimulating the formation of RCA, second that an unknownEPFsignalling pathway may be involved. Our observations have fundamental implications for the understanding of whole plant gas diffusion and root-to-shoot signalling events.
Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas
Authors: Liu Ruishan , Mignardi Marco , Jones Robert , Enge Martin , Kim Seung K. , Quake Stephen R. , Zou James 
Published: April 2019

AbstractRecently high-throughput image-based transcriptomic methods were developed and enabled researchers to spatially resolve gene expression variation at the molecular level for the first time. In this work, we develop a general analysis tool to quantitatively study the spatial correlations of gene expression in fixed tissue sections. As an illustration, we analyze the spatial distribution of single mRNA molecules measured by in situ sequencing on human fetal pancreas at three developmental time points–80, 87 and 117 days post-fertilization. We develop a density profile-based method to capture the spatial relationship between gene expression and other morphological features of the tissue sample such as position of nuclei and endocrine cells of the pancreas. In addition, we build a statistical model to characterize correlations in the spatial distribution of the expression level among different genes. This model enables us to infer the inhibitory and clustering effects throughout different time points. Our analysis framework is applicable to a wide variety of spatially-resolved transcriptomic data to derive biological insights.
Co-regulatory Network of Oncosuppressor miRNAs and Transcription Factors for Pathology of Human Hepatic Cancer Stem Cells (HCSC)
Authors: Mohamed Rania Hassan , Abu-Shahba Nourhan , Mahmoud Marwa , Abdelfattah Ahmed M. H. , Zakaria Wael , ElHefnawi Mahmoud 
Published: April 2019

AbstractHepatic cancer stem cells (HCSCs) are considered as main players for the hepatocellular carcinoma (HCC) initiation, metastasis, drug resistance and recurrence. There is a growing evidence supporting the down-regulated miRNAs in HCSCs as key suppressors for the stemness traits, but still more details are vague about how these miRNAs modulate the HCC development. To uncover some of these miRNA regulatory aspects in HCSC, we compiled 15 down-regulated miRNA and their validated and predicted up-regulated targets in HCSC. The targets were enriched for several cancer cell stemness hallmarks and CSC pre-metastatic niche, which support these miRNAs role in suppression of HCSCs neoplastic transformation. Further, we constructed miRNA-Transcription factor (TF) regulatory networks, which provided new insights on the role of the proposed miRNA-TF co-regulation in the cancer stemness axis and its cross talk with the surrounding microenvironment. Our analysis revealed HCSC important hubs as candidate regulators for targeting hepatic cancer stemness such as, miR-148a, miR-214, E2F family, MYC and SLC7A5. Finally, we proposed a possible model for miRNA and TF co-regulation of HCSC signaling pathways. Our study identified an HCSC signature and set bridges between the reported results to give guide for future validation of HCC therapeutic strategies avoiding drug resistance.
Structure and dynamics in the lithium solvation shell of nonaqueous electrolytes
Authors: Han Sungho 
Published: April 2019

AbstractThe solvation of a lithium ion has been of great importance to understand the structure and dynamics of electrolytes. In mixed electrolytes of cyclic and linear carbonates, the lithium solvation structure and the exchange dynamics of solvents strongly depend on the mixture ratio of solvents, providing a connection of the rigidity of the lithium solvation shell with the solvent composition in the shell. Here we study the dynamical properties of solvents in the solvation sheath of a lithium ion for various solvent mixture ratios via molecular dynamics simulations. Our results demonstrate that the exchange dynamics of solvents exhibits a non-monotonic behavior with a change in the mixture ratio, which keeps preserved on both short and long time scales. As the fraction of cyclic carbonate increases, we find that the structural properties of cyclic and linear carbonates binding to a lithium ion show different responses to a change in the fraction. Furthermore, we find that the rotational dynamics of cyclic carbonate is relatively insensitive to the mixture ratio in contrast to the rotational dynamics of linear carbonate. Our results further present that an anion shows different properties in structure and dynamics from solvents upon changing the mixture ratio of solvents.
Reference genes for accurate evaluation of expression levels in Trichophyton interdigitale grown under different carbon sources, pH levels and phosphate levels
Authors: Ciesielska Anita , Oleksak Beata , Stączek Paweł 
Published: April 2019

AbstractTinea pedis is a type of dermatophytosis caused by anthropophilic keratinolytic fungi such as Trichophyton interdigitale. Quantitative reverse transcription PCR (RT-qPCR) is a reliable and reproducible technique for measuring changes in target gene expression across various biological conditions. A crucial aspect of accurate normalization is the choice of appropriate internal controls. To identify reference genes for accurate evaluation of expression levels in T. interdigitale, the transcription levels of eight candidate reference genes (adp-rf, β-act, ef1-α, gapdh, psm1, sdha, rpl2 and ubc) and one target gene (Tri m4) were analysed by RT-qPCR after growing the dermatophyte under different environmental conditions. The results obtained from expression stability evaluations with NormFinder, geNorm, BestKeeper, and RefFinder software demonstrated that adp-rf and psm1 were the most stable internal control genes across all experimental conditions. The present study constitutes the first report of the identification and validation of reference genes for RT-qPCR normalization for T. interdigitale grown under different environmental conditions resembling the conditions encountered by fungi during invasion of skin.
Benefit of second-line systemic chemotherapy for advanced biliary tract cancer: A propensity score analysis
Authors: Moik Florian , Riedl Jakob M. , Winder Thomas , Terbuch Angelika , Rossmann Christopher H. , Szkandera Joanna , Bauernhofer Thomas , Kasparek Anne-Katrin , Schaberl-Moser Renate , Reicher Andreas , Prinz Felix , Pichler Martin , Stöger Herbert , Stotz Michael , Gerger Armin , Posch Florian 
Published: April 2019

AbstractWhether 2nd-line-chemotherapy (2LCTX) + best-supportive-care (BSC) benefits patients with advanced biliary tract cancer (aBTC) more than BSC alone is unclear. We therefore conducted a propensity-score-based comparative effectiveness analysis of overall survival (OS) outcomes in 80 patients with metastatic, recurrent, or inoperable aBTC, of whom 38 (48%) were treated with BSC + 2LCTX and 42 (52%) with BSC alone. After a median follow-up of 14.8 months and 49 deaths, the crude 6-, 12-, and 18-month Kaplan-Meier OS estimates were 77%, 53% and 23% in the BSC + 2LCTX group, and 29%, 21%, and 14% in patients in the BSC group (p = 0.0003; Hazard ratio (HR) = 0.36, 95%CI:0.20–0.64, p = 0.001). An inverse-probability-of-treatment-weighted (IPTW) analysis was conducted to rigorously account for the higher prevalence of favorable prognostic variables in the 2LCTX + BSC group. After IPTW-weighting, the favorable association between 2LCTX and OS prevailed (adjusted HR = 0.40, 95%CI: 0.17–0.95, p = 0.037). IPTW-weighted 6-, 12-, and 18-month OS estimates were 77%, 58% and 33% in the BSC + 2LCTX group, and 39%, 28% and 22% in the BSC group (p = 0.037). Moreover, the benefit of 2LCTX was consistent across several clinically-relevant subgroups. Within the limitations of an observational study, these findings support the concept that 2LCTX + BSC is associated with an OS benefit over BSC alone in aBTC.
Prognostic values of signal transducers activators of transcription in gastric cancer
Authors: Zhang Yujie , Yu Chaoran 
Published: April 2019

Abstract
The signal transducers and activators of transcription genes family (STATs) have been well studied as prognostic predictors for various solid tumors, but their prognostic values in gastric cancer (GC) patients have not been fully elucidated. The ‘Kaplan–Meier plotter’ and multiple public available databases were used for the characterization of the prognostic roles of STATs family in GC. The results indicated that high mRNA expression of all individual STATs, except STAT3 and STAT6, were significantly associated with favorable overall survival (OS) in GC. Moreover, the prognostic values of STATs were further characterized in subtypes, including HER2 status, Lauren’s classification, differentiation, and clinical stages. Moreover, the prognostic value of STATs signature was also characterized. Low risk group displayed a significantly favorable OS than high risk (HR: 1.71; 95% CI: 1.09–2.66, P=0.0184). In addition, STATs showed distinct expression between GC and normal groups. Meanwhile, comparable high correlation between STATs and tumor immune infiltrating cells (TIICs) was also observed. STAT4 displayed highest correlation with dendritic cells (correlation = 0.716, P=1.63e-59) and CD8+ T cells (correlation = 0.697, P=5.02e-55). In conclusion, our results suggest that all individual STATs, except STAT3 and STAT6, may act as prognostic markers in GC.
Exploration of Metrics for Quantifying Formant Space: Implications for Clinical Assessment of Parkinson Disease
Authors: Whitfield Jason A. 
Published: April 2019

Purpose
Speakers with Parkinson disease (PD) often exhibit hypokinetic dysarthria, which affects speech articulation. Vowel space metrics based on formant frequencies have been used to examine vowel articulation in speakers with PD. Although data from a number of studies suggest that speakers with PD exhibit smaller acoustic vowel space areas than control speakers, a handful of studies did not observe differences in vowel space area between speakers with and without PD. One potential factor explaining the inconsistent performance of traditional vowel space metrics is that these point-based metrics undersample the formant space to adequately capture between-groups and within-group differences in articulation. This article discusses recent advances in vowel space assessment that augment traditional vowel space metrics by examining the distribution of the entire formant frequency trace.

Conclusion
A general approach to obtaining these metrics is discussed along with clinical implications for vowel space assessment in speakers with PD.
DeepRange: deep‐learning‐based object detection and ranging in autonomous driving
Authors: Parmar Yashrajsinh , Natarajan Sudha , Sobha Gayathri 
Published: April 2019

Autonomous driving is an emerging area of intelligent transport systems. It necessitates automatic detection, classification, and ranging of on‐road obstacles. Current autonomous driving systems rely largely on LiDAR and radar units to gather information of distance to obstacles. LiDAR units are, in general, expensive. Alternatives such as stereo image processing for obtaining distance estimates are computationally intensive. Here, the authors explore the power of a deep‐learning‐based approach for range finding. The proposed approach is based on perception and requires only a low‐cost image sensor. Estimating the range of objects from a monocular image captured by a passive cost‐effective image sensor is, however, a challenging task. The authors propose an enhancement to classical convolutional neural networks based on addition of a range estimation layer for obtaining the distance to detected objects. The proposed strategy accomplishes object detection, classification and ranging simultaneously. The approach has been studied on the KITTI Vision Benchmark Suite, and experimental results indicate a detection speed of 61 fps, with mAP of 96.92% in recognition performance on an NVIDIA RTX 2080Ti GPU platform. Further, the proposed approach leads to an average error of only 0.915 m in range estimation which is quite acceptable in highway scenarios.
Influence of surface roughness on diffraction in the externally occulted Lyot solar coronagraph
Authors: Rougeot R. , Flamary R. , Mary D. , Aime C. 
Published: April 2019

Context. The solar coronagraph ASPIICS will fly on the future ESA formation flying mission Proba-3. The instrument combines an external occulter of diameter 1.42 m and a Lyot solar coronagraph of 5 cm diameter, located downstream at a distance of 144 m.
Aims. The theoretical performance of the externally occulted Lyot coronagraph has been computed by assuming perfect optics. In this paper, we improve related modelling by introducing roughness scattering effects from the telescope. We have computed the diffraction at the detector, that we compare to the ideal case without perturbation to estimate the performance degradation. We have also investigated the influence of sizing the internal occulter and the Lyot stop, and we performed a sensitivity analysis on the roughness.
Methods. We have built on a recently published numerical model of diffraction propagation. The micro-structures of the telescope are built by filtering a white noise with a power spectral density following an isotropic ABC function, suggested by Harvey scatter theory. The parameters were tuned to fit experimental data measured on ASPIICS lenses. The computed wave front error was included in the Fresnel wave propagation of the coronagraph. A circular integration over the solar disk was performed to reconstruct the complete diffraction intensity.
Results. The level of micro-roughness is 1.92 nm root-mean-square. Compared to the ideal case, in the plane of the internal occulter, the diffraction peak intensity is reduced by ≃0.001%. However, the intensity outside the peak increases by 12% on average, up to 20% at 3 R⊙, where the mask does not filter out the diffraction. At detector level, the diffraction peak remains ≃10−6 at 1.1 R⊙, similar to the ideal case, but the diffraction tail at large solar radius is much higher, up to one order of magnitude. Sizing the internal occulter and the Lyot stop does not improve the rejection, as opposed to the ideal case.
Conclusions. Besides these results, this paper provides a methodology to implement roughness scattering in the wave propagation model for the solar coronagraph.
Physics architecture. Part two
Authors: Konopleva Nelly 
Published: April 2019

Physics architecture. Part two.
The talk is devoted to the jubilee of academician M.A. Markov, who was born in 1908. Now we have also the 100th anniversary of the gauge invariance principle proposed by Weyl in 1918. During the period from 1967 to 1988 M.A. Markov was Academician Secretary of Nuclear Physics Department of AN USSR. He organized the series of conferences dedicated to the topical problems of theoretical, nuclear and elementary particle physics. One of them was international seminar “Vector mesons and electromagnetic interactions” under A.M. Baldin direct leadership. It went off in JINR in September of 1969. This very that seminar gave birth to the conferences series named “Baldin autumn”. Thanks to the discussions at the A.M. Baldin seminar many critical situations in theoretical and experimental physics were subsequently settled.
The first plenary session of the seminar included L.D. Faddeev talk about gauge field quantization, which cleared the way to develop the renormalized quantum gauge field theory. My talk was dedicated to the transformation of the classical gauge field theory into geometrical one. As a result the unified geometrical theory was obtained, which could include any interactions together with Einsteinian gravity. In this connection both formulations of Weyl’s local gauge invariance principle (of 1918 and 1929) as well as Einsteinian principle of general relativity were used. This approach was based on the fibre bundle geometry, which was developed by mathematicians at that time. This theory gives a realizable classification of interactions according to the local Lie’s symmetry groups associated with them. This approach leads to the VIth Hilbert’s problem solution.
To obtain further development of the gauge field theory, it is necessary to decide the question of the gauge field mass origin. It is the key moment both in quantum and geometrical classical theories of the gauge fields. Therefore it is very important to analyze the experiments, where massive and massless particles are converted in each other (similar Baldin experiments in JINR in 1967).
Np-237 transmutation efficiency dependence on beam particle, energy and sample position in QUINTA setup
Authors: Kilim S. , Strugalska-Gola E. , Szuta M. , Bielewicz M. , Tyutyunnikov S. , Adam J. , Stegailov V.I. 
Published: April 2019

Np-237 samples were irradiated with spallation neutrons produced at the ADS setup QUINTA. Six experiments were carried out at the JINR, in Dubna – one in carbon (C6+), three in deuteron, and two in proton beams. The energy in carbon was 24 GeV, in deuteron – 2, 4 and 8 GeV, respectively, and 660 MeV in the proton beam. In five cases the sample was located in a side window in a lead shield. In one case (660 MeV proton beam) two samples were located on the top of the QUINTA setup, one – on the top of section 2, and the second one – on the top of section 4. The transmutation study method was based on gamma-ray spectrometry. During the analysis of the spectra several fission products and one actinide were identified. Fission product activities yielded the number of fissions. The actinide (Np-238), a result of neutron capture by Np-237, yielded the number of captures.
The main goal of this work was to find out if and how the transmutation rate depended on the accelerator beam and sample location during the irradiation.
FCC-ee and the CR effects
Authors: Pukhaeva Nelli 
Published: April 2019

The proposed new FCC-ee e+e– colliders will be hosted in the Geneva area as the new 100 km tunnel will allow producing collisions at centre-of-mass energies from 90 to 350 GeV and beyond at several interaction points and will be used for a precision measurement at the Z pole, WW threshold, HZ cross section maximum and tt̅ threshold with an unequaled accuracy.
New measurements, which will be realized with large amount of data and at high energies accessible at the FCC-ee would allow a detailed study of the Color Reconnection phenomenon, especially in the hadronic WW decays, and would be helpful for other studies, for example in search for these effects in tt̅ and in Higgs decays.
Deuteron breakup at zero angle in the Coulomb nuclear field
Authors: Sitnik Igor 
Published: April 2019

Deuteron breakup cross sections on the C and CH2 targets have been measured up to the proton internal momenta of 0.3 GeV/c. The cross-sections 12C(d, p)X and 1H(d, p)X reactions have been obtained with high precision. The obtained data are compared with previous measurements.
The behavior features in the vicinity of the cross section maximum were studied in dependence on the transversal momentum in the region of 0.01 < pt < 0.16 GeV/c.
The measurements have been performed at the Veksler Baldin Laboratory of High Energy Physics of the Joint Institute for Nuclear Research.
Effectiveness of digital feedback on patient experience and 30-day complications after screening colonoscopy: a randomized health services study
Authors: Bugajski M. , Wieszczy P. , Pisera M. , Rupinski M. , Hoff G. , Huppertz-Hauss G. , Regula J. , Bretthauer M. , Kaminski M. 
Published: April 2019

Abstract
Background and study aims European guidelines (ESGE) recommend measuring patient experience and 30-day complication rate after colonoscopy. We compared digital and paper-based feedback on patients’ experience and 30-day complications after screening colonoscopy.
Patients and methods Screenees attending for primary screening colonoscopies in two centers from September 2015 to December 2016 were randomized (1:1) to an intervention arm (choice of feedback method) or control arm (routine paper-based feedback). Participants in the intervention arm could choose preferred feedback method (paper-based, automated telephone or online survey) and were contacted by automated telephone 30 days after colonoscopy to assess complications. Control group participants self-reported complications. Primary and secondary endpoints were response rates to feedback and complications questionnaire, respectively.
Results There were 1,281 and 1,260 participants in the intervention and control arms, respectively. There was no significant difference in response rate between study groups (64.8 % vs 61.5 %; P = 0.08). Free choice of feedback improved response for participants identified as poor responders: younger than 60 years (60.8 % vs 54.7 %; P = 0.031), male (64.0 % vs 58.6 %; P = 0.045) and in small non-public center (56.2 % vs 42.5 %; P = 0.043).In the intervention arm, 1,168 participants (91.2 %) answered the phone call concerning complications. A total of 79 participants (6.2 %) reported complications, of which two (0.2 %) were verified by telephone as clinically relevant. No complications were self-reported in the control group.
Conclusion The overall response rate was not significantly improved with digital feedback, yet the technology yielded significant improvement in participants defined as poor responders. Our study demonstrated feasibility and efficacy of digital patient feedback about complications after colonoscopy.