bluuebunny/crossref_metadata_2025 huggingface dataset:
Harmonic detection technology based on ant colony optimization BP neural network
Authors: Wu Jianyu , Zou Hairong
Published: May 2022

At present, ip-iq algorithm based on instantaneous reactive power theory is the most widely used in the field of harmonic detection.However, the ip-iq algorithm based on instantaneous reactive power has coordinate transformation and inverse transformation, which leads to cumbersome calculation.the existence of low-pass filter leads to delay and poor dynamic performance of the algorithm.The harmonic detection based on BP neural network has the advantages of simple calculation, fast detection speed, strong adaptive ability and good dynamic performance.However, the initial weights and thresholds are random, so it is easy for the network to fall into local optimal solution during training, resulting in low detection accuracy. This paper presents a harmonic detection method based on ant colony algorithm optimized BP neural network. ACO-BP, BP and ip-iq algorithms are compared by Simulink simulation. The results show that ACO-BP harmonic detection algorithm is feasible and superior
Formation of break-out induced by longitudinal crack of billet
Authors: Zhao Xinyu , Zhang Jianbin , Gao Feng , Wang Xianghong , Wang Litao
Published: May 2022

Due to the characteristics of large shrinkage, peritectic steel is sensitive to longitudinal crack defects. Through the analysis of the breakout shell of a domestic factory, the mechanism of longitudinal crack breakout of peritectic steel is revealed. The following conclusions are obtained: the carbon content of the steel is 0.077%, which is in the peritectic range, but Mn / S = 128, and the ratio of manganese and sulfur is relatively high. Although P + S = 0.0263%, the longitudinal crack defect still occurs when the harmful elements are very low. When breakout occurs, the superheat is 35 °C, the drawing speed is 2.5m/min, which is one of the main causes of longitudinal crack. The longitudinal crack occurs about 200-600mm away from the mold bottom and on the center of the side. After the original shell is formed, intermittent unevenness occurs. This unevenness can sometimes be repaired, but sometimes can’t. Therefore, the longitudinal crack and break-out are easy to occur after the thinner blank shell leaves the mold.
Research on Rapid Identification Method of Copper Concentrate and Its Smelting Slag
Authors: Jiang Longfa , Cai Dan , Bai LingYun , Zhang ShuMin , Zhang Heng , Tu XuMin
Published: May 2022

This research was based on the portable X-ray fluorescence spectrometer ( XRF ) to determine the content of copper and silicon in copper concentrate and its smelting slag. Taking the copper concentrate produced in typical mining areas in China and abroad and the smelting slag produced by various copper concentrate smelting processes as test samples, the content of silicon and copper was determined by XRF, and the silicon copper in copper concentrate and slag was studied. The distribution law of element content was calculated in order to realize the identification of the properties of the sample. By calculating the ratio of silicon to copper (Rsi/Cu), the rapid primary screening and identification of the solid waste property of the cargo can be realized at the port site. The results showed that: the preliminary screening of the solid material was judged as slag, suspected slag and copper concentrate when Rsi/Cu ≥5, 1≤Rsi/cu <5, and Rsi/cu <1, respectively. The established preliminary screening method had an accuracy rate of more than 95%.
Simultaneous degradation of trace antibiotics in water by adsorption and catalytic oxidation induced by N-doped reduced graphene oxide (N-rGO): synergistic mechanism
Authors: Wu Nan , Zhang Xuemin , Zhang Xue , Yang Kai , Li Yanjuan
Published: May 2022

Aimed at current difficulties in the treatment of trace antibiotics in water, an adsorption-catalytic oxidation system was established by combining persulfate and graphene, which have the dual functions of adsorption and catalysis, for simultaneous enrichment and degradation of trace antibiotics in water. The experimental results showed that over 90% sulfamethoxazole could be degraded by the proposed system. The activation energy of the proposed system was 7.9 kJ mol−1, which was significantly lower than those of typical Co catalysts and some carbon-based catalysts. Synergistic effect analysis revealed that catalytic oxidation was the key degradation kinetic of the proposed system, while adsorption showed a significant enhancement effect. Specifically, a compound with large adsorption capacity tended to be degraded preferably and rapidly. Characterization results indicated that N atoms were doped into the graphene framework, resulting in significant impacts on the activation process of potassium bisulfate by activating the sp2C system. Quenching and free radical trapping experiments revealed that degradation catalyzed by the proposed system was a non-free radical oxidation reaction dominated by singlet oxygen. In summary, the proposed design was rational, N-rGO surface provided good adsorption and catalysis sites, the synergistic effect of adsorption and catalytic oxidation led to rapid and effective enrichment andin situdegradation of trace antibiotics in water.
Facile fabrication of large-scale silver nanowire transparent conductive films by screen printing
Authors: Li Zhengliang , Zhang Xuyang , Shan Jiaqi , Liu Cuilan , Guo Xingzhong , Zhao Xiaoyu , Yang Hui
Published: May 2022

Silver nanowire transparent conductive films (AgNW TCFs) were facilely prepared by screen printing conductive ink on a polyethylene terephthalate (PET) substrate, and the effects of ink compositions and oily stencil on the optoelectrical properties of AgNW TCFs were investigated in detail. 7.3 mg·ml−1 hydroxypropyl methylcellulose (HPMC), 4.12 mg·ml−1 AgNWs and 98T oily stencil allow the preparation of large-scale AgNW TCFs with high transmittance, low square resistance and high uniformity. The resultant screen printed AgNW TCFs possesses a sheet resistance as low as 13.0 ± 0.6 Ω sq−1, a transmittance of about 95.3% at 550 nm wavelength (deducting the background) and a haze of 3.86 (deducting the background), and can achieve a surface root mean square roughness of 3.33 nm, a film size of 15 × 20 cm2 and personalized pattern by means of the screen printing process. The transparent film heater (TFH) constructed by AgNW TCFs can rise to a usable temperature of 55 °C at a low voltage of 4 V within 80 s. This process provides a simple strategy for fabricating uniform, patterned and large size AgNW TCFs for various devices.
Majority logic based area-delay efficient 1-bit approximate adder for error-tolerant applications
Authors: Parameshwara M C , Maroof Naeem , Khan Angshuman
Published: May 2022

The complementary metal oxide semiconductor (CMOS) technology is approaching its physical limits due to lithographic issues and diminishing benefits of scaling. The new technologies such as quantum dot cellular automata (QCA), tunneling phase logic (TPL), nonmagnetic logic (NML), single electron tunneling (SET), etc are emerging as an alternative and may supersede the conventional CMOS technologies in the near future. Now days, the design of approximate computing based on QCA technologies has gaining much of recent interest. In this paper, a majority-logic (ML) based area-delay efficient novel approximate full adder (AFA) is presented. The QCA layout of proposed AFA is designed and simulated using QCADesigner tool. Further, the proposed AFA is analyzed and compared against the state-of-the-art approximate adders referred to as ‘reported AFAs’ (RAAs), in terms of error metrics (EMs), area, and time complexity. Also, analyzed its efficacy for error-tolerant applications such as image processing.
Performance and mechanism of new silicone polymer as filtrate reducer with inhibitory effect for water-based drilling fluid
Authors: Ban Guo , Xu Jiang , Zeng Jia , Zhou Shu-sheng
Published: May 2022

An organic silicon filtrate reducer (AATN) with inhibitory effect, which can resist temperature up to 180 °C, was synthesized by using acrylamide (AM), vinyl trimethoxysilane (A-171), allyltrimethylammonium chloride (TM) and N-vinyl pyrrolidone (NVP) as monomers. AATN can effectively reduce the filtration loss of drilling fluid and inhibit the hydration expansion and hydration dispersion of the clay, which was beneficial to wellbore stability. Experimental results showed that the API filtration loss (FLAPI) of the drilling fluid containing 2 wt% AATN was only 7.8 ml. The siloxane groups of AATN were hydrolyzed in aqueous solution to generate Si–OH bonds, which can react with Si–OH bonds on hydrated clay surface to form a strong chemical adsorption. It was conducive to maintaining the dispersion of clay particles in the drilling fluid. The stable grid structure was formed by AATN and clay particles to reduce mud cake permeability, which can reduce the damage of drilling fluid filtrates to borehole stability. In addition, AATN can adsorb on the surface of sodium bentonite, thus forming a hydrophobic adsorption film on its surface, which effectively enveloped bentonite and inhibited the hydration expansion of bentonite.
WDM equipped universal linear optics for programmable neuromorphic photonic processors
Authors: Totovic Angelina , Pappas Christos , Kirtas Manos , Tsakyridis Apostolos , Giamougiannis George , Passalis Nikolaos , Moralis-Pegios Miltiadis , Tefas Anastasios , Pleros Nikos
Published: May 2022

Non-von-Neumann computing architectures and deep learning training models have sparked a new computational era where neurons are forming the main architectural backbone and vector, matrix and tensor multiplications comprise the basic mathematical toolbox. This paradigm shift has triggered a new race among hardware technology candidates; within this frame, the field of neuromorphic photonics promises to convolve the targeted algebraic portfolio along a computational circuitry with unique speed, parallelization, and energy efficiency advantages. Fueled by the inherent energy efficient analog matrix multiply operations of optics, the staggering advances of photonic integration and the enhanced multiplexing degrees offered by light, neuromorphic photonics has stamped the resurgence of optical computing brining a unique perspective in low-energy and ultra-fast linear algebra functions. However, the field of neuromorphic photonics has relied so far on two basic architectural schemes, i.e., coherent linear optical circuits and incoherent WDM approaches, where wavelengths have still not been exploited as a new mathematical dimension. In this paper, we present a radically new approach for promoting the synergy of WDM with universal linear optics and demonstrate a new, high-fidelity crossbar-based neuromorphic photonic platform, able to support matmul with multidimensional operands. Going a step further, we introduce the concept of programmable input and weight banks, supporting in situ reconfigurability, forming in this way the first WDM-equipped universal linear optical operator and demonstrating different operational modes like matrix-by-matrix and vector-by-tensor multiplication. The benefits of our platform are highlighted in a fully convolutional neural network layout that is responsible for parity identification in the MNIST handwritten digit dataset, with physical layer simulations revealing an accuracy of ∼94%, degraded by only 2% compared to respective results obtained when executed entirely by software. Finally, our in-depth analysis provides the guidelines for neuromorphic photonic processor performance improvement, revealing along the way that 4 bit quantization is sufficient for inputs, whereas the weights can be implemented with as low as 2 bits of precision, offering substantial benefits in terms of driving circuitry complexity and energy savings.
Archimedean zeta integrals for 𝐺𝐿(3)×𝐺𝐿(2)
Authors: Hirano Miki , Ishii Taku , Miyazaki Tadashi
Published: May 2022

In this article, we give explicit formulas of archimedean Whittaker functions on

G
L
(
3
)

GL(3)

and

G
L
(
2
)

GL(2)

. Moreover, we apply those to the calculation of archimedean zeta integrals for

G
L
(
3
)
×
G
L
(
2
)

GL(3)\times GL(2)

, and show that the zeta integral for appropriate Whittaker functions is equal to the associated

L
L

-factors.
Gaussian random fields: with and without covariances
Authors: Bingham N. , Symons Tasmin
Published: May 2022

We begin with isotropic Gaussian random fields, and show how the Bochner–Godement theorem gives a natural way to describe their covariance structure. We continue with a study of Matérn processes on Euclidean space, spheres, manifolds and graphs, using Bessel potentials and stochastic partial differential equations (SPDEs). We then turn from this continuous setting to approximating discrete settings, Gaussian Markov random fields (GMRFs), and the computational advantages they bring in handling large data sets, by exploiting the sparseness properties of the relevant precision (concentration) matrices.
Extrapolation of stationary random fields via level sets
Authors: Das A. , Makogin V. , Spodarev E.
Published: May 2022

In this paper, we use the concept of excursion sets for the extrapolation of stationary random fields. Doing so, we define excursion sets for the field and its linear predictor, and then minimize the expected volume of the symmetric difference of these sets under the condition that the univariate distributions of the predictor and of the field itself coincide. We illustrate the new approach on Gaussian random fields.
Boundedness of the nodal domains of additive Gaussian fields
Authors: Muirhead S.
Published: May 2022

We study the connectivity of the excursion sets of additive Gaussian fields, i.e. stationary centred Gaussian fields whose covariance function decomposes into a sum of terms that depend separately on the coordinates. Our main result is that, under mild smoothness and correlation decay assumptions, the excursion sets{f≤ℓ}\{f \le \ell \}of additive planar Gaussian fields are bounded almost surely at the critical levelℓc=0\ell _c = 0. Since we do not assume positive correlations, this provides the first examples of continuous non-positively-correlated stationary planar Gaussian fields for which the boundedness of the nodal domains has been confirmed. By contrast, in dimensiond≥3d \ge 3the excursion sets have unbounded components at all levels.
HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer
Authors: Zhang Shanzhuo , Yan Zhiyuan , Huang Yueyang , Liu Lihang , He Donglong , Wang Wei , Fang Xiaomin , Zhang Xiaonan , Wang Fan , Wu Hua , Wang Haifeng
Published: May 2022

Motivation

Accurate ADMET (an abbreviation for ‘absorption, distribution, metabolism, excretion and toxicity’) predictions can efficiently screen out undesirable drug candidates in the early stage of drug discovery. In recent years, multiple comprehensive ADMET systems that adopt advanced machine learning models have been developed, providing services to estimate multiple endpoints. However, those ADMET systems usually suffer from weak extrapolation ability. First, due to the lack of labelled data for each endpoint, typical machine learning models perform frail for the molecules with unobserved scaffolds. Second, most systems only provide fixed built-in endpoints and cannot be customized to satisfy various research requirements. To this end, we develop a robust and endpoint extensible ADMET system, HelixADMET (H-ADMET). H-ADMET incorporates the concept of self-supervised learning to produce a robust pre-trained model. The model is then fine-tuned with a multi-task and multi-stage framework to transfer knowledge between ADMET endpoints, auxiliary tasks and self-supervised tasks.

Results

Our results demonstrate that H-ADMET achieves an overall improvement of 4%, compared with existing ADMET systems on comparable endpoints. Additionally, the pre-trained model provided by H-ADMET can be fine-tuned to generate new and customized ADMET endpoints, meeting various demands of drug research and development requirements.

Availability and implementation

H-ADMET is freely accessible at https://paddlehelix.baidu.com/app/drug/admet/train.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting protein–peptide binding residues via interpretable deep learning
Authors: Wang Ruheng , Jin Junru , Zou Quan , Nakai Kenta , Wei Leyi
Published: May 2022

Identifying the protein–peptide binding residues is fundamentally important to understand the mechanisms of protein functions and explore drug discovery. Although several computational methods have been developed, most of them highly rely on third-party tools or complex data preprocessing for feature design, easily resulting in low computational efficacy and suffering from low predictive performance. To address the limitations, we propose PepBCL, a novel BERT (Bidirectional Encoder Representation from Transformers) -based contrastive learning framework to predict the protein–peptide binding residues based on protein sequences only. PepBCL is an end-to-end predictive model that is independent of feature engineering. Specifically, we introduce a well pre-trained protein language model that can automatically extract and learn high-latent representations of protein sequences relevant for protein structures and functions. Further, we design a novel contrastive learning module to optimize the feature representations of binding residues underlying the imbalanced dataset. We demonstrate that our proposed method significantly outperforms the state-of-the-art methods under benchmarking comparison, and achieves more robust performance. Moreover, we found that we further improve the performance via the integration of traditional features and our learnt features. Interestingly, the interpretable analysis of our model highlights the flexibility and adaptability of deep learning-based protein language model to capture both conserved and non-conserved sequential characteristics of peptide-binding residues. Finally, to facilitate the use of our method, we establish an online predictive platform as the implementation of the proposed PepBCL, which is now available at http://server.wei-group.net/PepBCL/.

Availability and implementation

https://github.com/Ruheng-W/PepBCL.

Supplementary information

Supplementary data are available at Bioinformatics online.
PSMA5 contributes to progression of lung adenocarcinoma in association with the JAK/STAT pathway
Authors: Lu Feng , Zhou Jing , Chen Qing , Zhu Jianling , Zheng Xiaowei , Fang Na , Qiao Ling
Published: May 2022

Proteasome dysregulation is a common feature of cancer and a critical risk for tumorigenesis. However, the characteristics of proteasome components in tumor development and metastasis are poorly understood. PSMA5, an α5 subunit of the 20S core proteasome, is associated with the degradation of intracellular proteins. Increasing evidence indicated that it is involved in tumor development, but the underlying mechanism has remained unknown. Here, we show that PSMA5 is upregulated in lung adenocarcinoma (LUAD) cells and clinical LUAD tissues. Moreover, its upregulation is positively associated with lymph node metastasis and the poor prognosis of LUAD patients. PSMA5 knockdown inhibited the proliferation, invasion and metastasis of LUAD cells in vitro and in vivo, induced apoptosis of LUAD cells and sensitized LUAD cells to cisplatin. Furthermore, investigations revealed that PSMA5 overexpression inhibited cell apoptosis by activating the janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway in LUAD cells. In total, our results demonstrate that PSMA5 may function as a prognostic factor in LUAD. In addition, PSMA5 is a promising therapeutic target for LUAD, as its depletion induces cell apoptosis by inhibiting the JAK/STAT pathway.
Multimodal deep learning enhances diagnostic precision in left ventricular hypertrophy
Authors: Soto Jessica Torres , Weston Hughes J , Sanchez Pablo Amador , Perez Marco , Ouyang David , Ashley Euan A
Published: May 2022

Aims

Determining the aetiology of left ventricular hypertrophy (LVH) can be challenging due to the similarity in clinical presentation and cardiac morphological features of diverse causes of disease. In particular, distinguishing individuals with hypertrophic cardiomyopathy (HCM) from the much larger set of individuals with manifest or occult hypertension (HTN) is of major importance for family screening and the prevention of sudden death. We hypothesized that an artificial intelligence method based joint interpretation of 12-lead electrocardiograms and echocardiogram videos could augment physician interpretation.

Methods and results

We chose not to train on proximate data labels such as physician over-reads of ECGs or echocardiograms but instead took advantage of electronic health record derived clinical blood pressure measurements and diagnostic consensus (often including molecular testing) among physicians in an HCM centre of excellence. Using more than 18 000 combined instances of electrocardiograms and echocardiograms from 2728 patients, we developed LVH-fusion. On held-out test data, LVH-fusion achieved an F1-score of 0.71 in predicting HCM, and 0.96 in predicting HTN. In head-to-head comparison with human readers LVH-fusion had higher sensitivity and specificity rates than its human counterparts. Finally, we use explainability techniques to investigate local and global features that positively and negatively impact LVH-fusion prediction estimates providing confirmation from unsupervised analysis the diagnostic power of lateral T-wave inversion on the ECG and proximal septal hypertrophy on the echocardiogram for HCM.

Conclusion

These results show that deep learning can provide effective physician augmentation in the face of a common diagnostic dilemma with far reaching implications for the prevention of sudden cardiac death.
Mastigocoleidae fam. nov., a New Mesozoic Beetle Family and the Early Evolution of Dryopoidea (Coleoptera)
Authors: Tihelka Erik , Jäch Manfred A , Kundrata Robin , Li Yan-Da , Engel Michael S , Lozano-Fernandez Jesus , Huang Diying , Cai Chenyang
Published: May 2022

With some 3,700 described species, Dryopoidea are a moderately diverse superfamily of beetles whose position within basal Polyphaga has been historically difficult to elucidate. Members of most extant dryopoid families are set apart from the majority of other polyphagans by their association with aquatic habitats, but little is known about the origin of these derived life habits and the phylogeny of the superfamily. Here we describe Mastigocoleidae Tihelka, Jäch, Kundrata & Cai fam. nov., a new family of Mesozoic dryopoids represented by fossils from the Cretaceous Yixian Formation in northeastern China (undescribed species; ~125 Ma), Crato Formation in northeastern Brazil (Mastigocoleus rhinoceros Tihelka & Cai gen. et sp. nov.; ~113 Ma), and amber from northern Myanmar (Mastigocoleus resinicola Tihelka & Cai gen. et sp. nov. and Cretaceocoleus saetosus Tihelka, Kundrata & Cai gen. et sp. nov.; ~99 Ma). Integrating the findings of recent molecular and morphological phylogenetic analyses, we recover Mastigocoleidae as an early-diverging dryopoid clade sister to the families Lutrochidae and Dryopidae, or less likely as a group of putative stem-dryopoids. Mastigocoleidae are most distinctly separated from all other dryopoid families by their whip-like antennae, with 11 antennomeres, reaching to the pronotal base, and with the scape broadest and longest, a short pedicel, and antennomeres II–XI more or less distinctively gradually tapering toward the apex. Mastigocoleidae indicate that the last common ancestor of Dryopoidea was likely terrestrial in the adult stage, and document character acquisitions associated with a specialization for aquatic life.
Detection of Common Copy Number of Variants Underlying Selection Pressure in Middle Eastern Horse Breeds Using Whole-Genome Sequence Data
Authors: Zandi Mohammad Bagher , Salek Ardestani Siavash , Vahedi Seyed Milad , Mahboudi Hossein , Mahboudi Fereidoun , Meskoob Ardeshir
Published: May 2022

Dareshouri, Arabian, and Akhal-Teke are 3 Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds’ development and adaptation. For this purpose, we sequenced the whole genome of 4 Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n = 3) and Akhal-Teke (n = 3) horses. Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size = 100 kb, step size = 50 kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8 837 950 single-nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and 3 quantitative trait loci, including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted P-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs that were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.
Plant cell division from the perspective of polarity
Authors: Glanc Matouš
Published: May 2022

The orientation of cell division is a major determinant of plant morphogenesis. In spite of considerable efforts over the past decades, the precise mechanism of division plane selection remains elusive. The majority of studies on the topic have addressed division orientation from either a predominantly developmental or a cell biological perspective. Thus, mechanistic insights into the links between developmental and cellular factors affecting division orientation are particularly lacking. Here, I review recent progress in the understanding of cell division orientation in the embryo and primary root meristem of Arabidopsis from both developmental and cell biological standpoints. I offer a view of multilevel polarity as a central aspect of cell division: on the one hand, the division plane is a readout of tissue- and organism-wide polarities; on the other hand, the cortical division zone can be seen as a transient polar subcellular plasma membrane domain. Finally, I argue that a polarity-focused conceptual framework and the integration of developmental and cell biological approaches hold great promise to unravel the mechanistic basis of plant cell division orientation in the near future.
Precipitation and local environment shape the geographic variation of seed size across natural populations of sand rice (Agriophyllum squarrosum)
Authors: Zhao Pengshan , Li Xiaofeng , Ran Ruilan , Sun Hong , Zhao Jiecai , Chen Guoxiong
Published: May 2022

Sand rice (Agriophyllum squarrosum) is widely distributed on dunes in the Asian interior arid zone, and its large intraspecific trait variation makes it a very good model for investigating the ecological processes underlying its adaptation to the desert environment. In this study, seed size variation across 68 natural populations was used to establish geographic patterns and to quantify the effects of the climate, soil, and collection-year weather variables. The length of the seed major axis and thousand seed weight (TSW) both showed significant longitudinal patterns. Long-term climate variables accounted for most of the explained variances for seed major axis (57.20%) and TSW (91.54%). Specifically, annual precipitation and minimum monthly precipitation had the most significantly positive and negative effects, indicating that longitudinal clines are driven by a precipitation gradient across the species’ distribution range. A substantial unique effect of soil variables (27.27%) was found for seed major axis variation, but only 3.64% of TSW variation was explained by soil variables. Two extreme groups were selected to evaluate the genetic and plastic effects on seed size in a common garden experiment. Large-seeded individuals were more competitive in semi-arid regions, and had stronger adaptive plasticity as well as better performance in early seedling establishment, and hence they have potential for use in future domestication projects.
Turbulent dynamo in the two-phase interstellar medium
Authors: Seta Amit , Federrath Christoph
Published: May 2022

Magnetic fields are a dynamically important component of the turbulent interstellar medium (ISM) of star-forming galaxies. These magnetic fields are due to a dynamo action, which is a process of converting turbulent kinetic energy to magnetic energy. A dynamo that acts at scales less than the turbulent driving scale is known as the turbulent dynamo. The ISM is a multiphase medium and observations suggest that the properties of magnetic fields differ with the phase. Here, we aim to study how the properties of the turbulent dynamo depend on the phase. We simulate the non-isothermal turbulent dynamo in a two-phase medium (most previous work assumes an isothermal gas). We show that the warm phase (T ≥ 103 K) is transsonic and the cold phase (T < 103 K) is supersonic. We find that the growth rate of magnetic fields in the exponentially growing stage is similar in both phases. We compute the terms responsible for amplification and destruction of vorticity and show that in both phases vorticity is amplified due to turbulent motions, further amplified by the baroclinic term in the warm phase, and destroyed by the term for viscous interactions in the presence of logarithmic density gradients in the cold phase. We find that the final ratio of magnetic to turbulent kinetic energy is lower in the cold phase due to a stronger Lorentz force. We show that the non-isothermal turbulent dynamo is significantly different from its isothermal counterpart and this demonstrates the need for studying the turbulent dynamo in a multiphase medium.
Disc instability and bar formation: view from the IllustrisTNG simulations
Authors: Izquierdo-Villalba David , Bonoli Silvia , Rosas-Guevara Yetli , Springel Volker , White Simon D M , Zana Tommaso , Dotti Massimo , Spinoso Daniele , Bonetti Matteo , Lupi Alessandro
Published: May 2022

We make use of $z\, {=}\, 0$ samples of strongly barred and unbarred disc galaxies from the TNG100 and TNG50 cosmological hydrodynamical simulations to assess the performance of the simple disc instability criterion proposed by Efstathiou, Lake & Negroponte (1982) (ELN-criterion). We find that strongly barred galaxies generally assemble earlier, are more star dominated in their central regions, and have more massive and more compact discs than unbarred galaxies. The ELN-criterion successfully identifies ${\sim }\, 75$ and ${\sim }\, 80{{ per\ cent}}$ of the strongly barred and the unbarred galaxies, respectively. Strongly barred galaxies that the criterion fails to identify tend to have more extended discs, higher spin values and bars that assembled later than is typical for the bulk of the barred population. The bars in many of these cases appear to be produced by an interaction with a close neighbour (i.e. to be externally triggered) rather than to result from secular growth in the disc. On the other hand, we find that unbarred galaxies misclassified as barred by the ELN-criterion typically have stellar discs similar to those of barred galaxies, although more extended in the vertical direction and less star-dominated in their central regions, possibly reflecting later formation times. In addition, the bulge component of these galaxies is significantly more prominent at early times than in the strongly barred sample. Thus, the ELN-criterion robustly identifies secular bar instabilities in most simulated disc galaxies, but additional environmental criteria are needed to account for interaction-induced bar formation.
The role of radio loudness in Eigenvector 1 and the Baldwin Effect of [O iii] λ5007
Authors: Wang Yongjiang , Shang Zhaohui , Brotherton Michael S
Published: May 2022

The radio emission is an important observable of quasars, but its relationship to Eigenvector 1 and the [O iii] λ5007 Baldwin Effect is not fully understood. We explore these issues based on a sample of 1800 quasars taken from the Sloan Digital Sky Survey Data Release 7. We employ a new approach of selecting subsamples in the plane of fundamental physical parameters of the black hole mass and Eddington ratio, so as to reduce variables and complexity in analyses. Based on these subsamples, we investigate the relationship between radio loudness R and Eigenvector 1 and find that radio loudness is correlated with [O iii] λ5007 emission, but has no clear relationship with optical Fe ii emission, which indicates that the radio power is probably not a driver of Eigenvector 1 but merely a secondary process. In addition, we also investigate the impact of radio loudness on the Baldwin Effect of [O iii] λ5007. We find that when the radio loudness is not strong (log R < 2), the Baldwin Effect of [O iii] λ5007 is clear, while in the samples of extreme radio loudness (log R ≥ 2), the Baldwin Effect of [O iii] λ5007 becomes weaker or even disappears. We suggest that both radio loudness and luminosity influence the relative strength of [O iii].
Detection of temozolomide-induced hypermutation and response to PD-1 checkpoint inhibitor in recurrent glioblastoma
Authors: Daniel Paul , Meehan Brian , Sabri Siham , Jamali Fatemeh , Sarkaria Jann N , Choi Dongsic , Garnier Delphine , Kitange Gaspar , Glennon Kate I , Paccard Antoine , Karamchandani Jason , Riazalhosseini Yasser , Rak Janusz , Abdulkarim Bassam
Published: May 2022

Background

Despite aggressive upfront treatment in glioblastoma (GBM), recurrence remains inevitable for most patients. Accumulating evidence has identified hypermutation induced by temozolomide (TMZ) as an emerging subtype of recurrent GBM. However, its biological and therapeutic significance has yet to be described.

Methods

We combined GBM patient and derive GBM stem cells (GSCs) from tumors following TMZ to explore response of hypermutant and non-hypermutant emergent phenotypes and explore the immune relevance of hypermutant and non-hypermutant states in vivo.

Results

Hypermutation emerges as one of two possible mutational subtypes following TMZ treatment in vivo and demonstrates distinct phenotypic features compared to non-hypermutant recurrent GBM. Hypermutant tumors elicited robust immune rejection in subcutaneous contexts which was accompanied by increased immune cell infiltration. In contrast, immune rejection of hypermutant tumors were stunted in orthotopic settings where we observe limited immune infiltration. Use of anti-PD-1 immunotherapy showed that immunosuppression in orthotopic contexts was independent from the PD-1/PD-L1 axis. Finally, we demonstrate that mutational burden can be estimated from DNA contained in extracellular vesicles (EVs).

Conclusion

Hypermutation post-TMZ are phenotypically distinct from non-hypermutant GBM and requires personalization for appropriate treatment. The brain microenvironment may be immunosuppressive and exploration of the mechanisms behind this may be key to improving immunotherapy response in this subtype of recurrent GBM.
Online Learning for Infectious Disease Fellows—A Needs Assessment
Authors: Chavez Miguel A , Nolan Nathanial S , Gleason Emily , Nematollahi Saman , Abdoler Emily , Escota Gerome
Published: May 2022

Background

Online resources and social media have become increasingly ubiquitous in medical education. Little is known about the need for educational resources aimed at infectious disease (ID) fellows.

Methods

We conducted an educational needs assessment through a survey that aimed to describe ID fellows’ current use of online and social media tools, assess the value of online learning, and identify the educational content preferred by ID fellows. We subsequently convened focus groups with ID fellows to explore how digital tools contribute to fellow learning.

Results

A total of 110 ID fellows responded to the survey. Over half were second-year fellows (61, 55%). Although many respondents were satisfied with the educational resources provided by their fellowship program (70, 64%), the majority were interested in an online collaborative educational resource (97, 88%). Twitter was the most popular social media platform for education and the most valued online resource for learning. Focus groups identified several themes regarding social medial learning: broadened community, low barrier to learning, technology-enhanced learning, and limitations of current tools. Overall, the focus groups suggest that fellows value social media and online learning.

Conclusions

ID fellows are currently using online and social media resources, which they view as valuable educational tools. Fellowship programs should consider these resources as complementary to traditional teaching and as a means to augment ID fellow education.
Cytokine storm promoting T cell exhaustion in severe COVID-19 revealed by single cell sequencing data analysis
Authors: Yang Minglei , Lin Chenghao , Wang Yanni , Chen Kang , Han Yutong , Zhang Haiyue , Li Weizhong
Published: May 2022

Background

Evidence has suggested that cytokine storms may be associated with T cell exhaustion (TEX) in COVID-19. However, the interaction mechanism between cytokine storms and TEX remains unclear.

Methods

With the aim of dissecting the molecular relationship of cytokine storms and TEX through single-cell RNA sequencing data analysis, we identified 14 cell types from bronchoalveolar lavage fluid of COVID-19 patients and healthy people. We observed a novel subset of severely exhausted CD8 T cells (Exh T_CD8) that co-expressed multiple inhibitory receptors, and two macrophage subclasses that were the main source of cytokine storms in bronchoalveolar.

Results

Correlation analysis between cytokine storm level and TEX level suggested that cytokine storms likely promoted TEX in severe COVID-19. Cell–cell communication analysis indicated that cytokines (e.g. CXCL10, CXCL11, CXCL2, CCL2, and CCL3) released by macrophages acted as ligands and significantly interacted with inhibitory receptors (e.g. CXCR3, DPP4, CCR1, CCR2, and CCR5) expressed by Exh T_CD8. These interactions formed the cytokine–receptor axes, which were also verified to be significantly correlated with cytokine storms and TEX in lung squamous cell carcinoma.

Conclusions

Cytokine storms may promote TEX through cytokine-receptor axes and be associated with poor prognosis in COVID-19. Blocking cytokine-receptor axes may reverse TEX. Our finding provides novel insights into TEX in COVID-19 and new clues for cytokine-targeted immunotherapy development.
The digestive systems of carnivorous plants
Authors: Freund Matthias , Graus Dorothea , Fleischmann Andreas , Gilbert Kadeem J , Lin Qianshi , Renner Tanya , Stigloher Christian , Albert Victor A , Hedrich Rainer , Fukushima Kenji
Published: May 2022

To survive in the nutrient-poor habitats, carnivorous plants capture small organisms comprising complex substances not suitable for immediate reuse. The traps of carnivorous plants, which are analogous to the digestive systems of animals, are equipped with mechanisms for the breakdown and absorption of nutrients. Such capabilities have been acquired convergently over the past tens of millions of years in multiple angiosperm lineages by modifying plant-specific organs including leaves. The epidermis of carnivorous trap leaves bears groups of specialized cells called glands, which acquire substances from their prey via digestion and absorption. The digestive glands of carnivorous plants secrete mucilage, pitcher fluids, acids, and proteins, including digestive enzymes. The same (or morphologically distinct) glands then absorb the released compounds via various membrane transport proteins or endocytosis. Thus, these glands function in a manner similar to animal cells that are physiologically important in the digestive system, such as the parietal cells of the stomach and intestinal epithelial cells. Yet, carnivorous plants are equipped with strategies that deal with or incorporate plant-specific features, such as cell walls, epidermal cuticles, and phytohormones. In this review, we provide a systematic perspective on the digestive and absorptive capacity of convergently evolved carnivorous plants, with an emphasis on the forms and functions of glands.
Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters
Authors: Hajiabadi Hamideh , Mamontova Irina , Prizak Roshan , Pancholi Agnieszka , Koziolek Anne , Hilbert Lennart
Published: May 2022

Fluorescence microscopy, a central tool of biological research, is subject to inherent trade-offs in experiment design. For instance, image acquisition speed can only be increased in exchange for a lowered signal quality, or for an increased rate of photo-damage to the specimen. Computational denoising can recover some loss of signal, extending the trade-off margin for high-speed imaging. Recently proposed denoising on the basis of neural networks shows exceptional performance but raises concerns of errors typical of neural networks. Here, we present a work-flow that supports an empirically optimized reduction of exposure times, as well as per-image quality control to exclude images with reconstruction errors. We implement this work-flow on the basis of the denoising tool Noise2Void and assess the molecular state and 3D shape of RNA polymerase II (Pol II) clusters in live zebrafish embryos. Image acquisition speed could be tripled, achieving 2-s time resolution and 350-nm lateral image resolution. The obtained data reveal stereotyped events of approximately 10 s duration: initially, the molecular mark for recruited Pol II increases, then the mark for active Pol II increases, and finally Pol II clusters take on a stretched and unfolded shape. An independent analysis based on fixed sample images reproduces this sequence of events, and suggests that they are related to the transient association of genes with Pol II clusters. Our work-flow consists of procedures that can be implemented on commercial fluorescence microscopes without any hardware or software modification, and should, therefore, be transferable to many other applications.
Functional connectivity signatures of political ideology
Authors: Yang Seo Eun , Wilson James D , Lu Zhong-Lin , Cranmer Skyler
Published: May 2022

Emerging research has begun investigating the neural underpinnings of the biological and psychological differences that drive political ideology, attitudes, and actions. Here, we explore the neurological roots of politics through conducting a large sample, whole-brain analysis of functional connectivity (FC) across common fMRI tasks. Using convolutional neural networks, we develop predictive models of ideology using FC from fMRI scans for nine standard task-based settings in a novel cohort of healthy adults (n = 174, age range: 18 to 40, mean = 21.43) from the Ohio State University Wellbeing Project. Our analyses suggest that liberals and conservatives have noticeable and discriminative differences in FC that can be identified with high accuracy using contemporary artificial intelligence methods and that such analyses complement contemporary models relying on socio-economic and survey-based responses. FC signatures from retrieval, empathy, and monetary reward tasks are identified as important and powerful predictors of conservatism, and activations of the amygdala, inferior frontal gyrus, and hippocampus are most strongly associated with political affiliation. Although the direction of causality is unclear, this study suggests that the biological and neurological roots of political behavior run much deeper than previously thought.
Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response
Authors: Shalamova Lyudmila , Felgenhauer Ulrike , Wilhelm Jochen , Schaubmar Andreas R , Büttner Kathrin , Schoen Andreas , Widera Marek , Ciesek Sandra , Weber Friedemann
Published: May 2022

The new variant of concern (VOC) of SARS-CoV-2, Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype (wt) strain (B.1) with respect to their interactions with the antiviral interferon (IFN-alpha/beta) response in infected cells. Our data indicate that IFN induction by Omicron is low and comparable to the wt, whereas Delta showed an increased IFN induction. However, Omicron exceeded both the wt and the Delta strain with respect to the ability to withstand the antiviral state imposed by IFN-alpha.
All-cementless Revision Total Knee Arthroplasty Using a Constrained Condylar Design With Porous Tantalum: Technique and Clinical Results
Authors: Tye Erik Y. , Bryman Jason A. , Kay Robert D. , Taylor Adam J. , Andrawis John P. , Kwong Louis M.
Published: May 2022

Introduction:

Contemporary differences exist with regards to revision total knee arthroplasty (TKA) fixation philosophy. The use of an all-cementless constrained condylar knee (CCK) design for revision TKA with porous tantalum has not been described in the recent peer-reviewed literature. Our rationale for using an all-cementless design in the revision setting includes the theoretical decrease in aseptic loosening and enhanced preservation of bone stock.

Methods:

We report the surgical technique and clinical results of 28 patients who underwent revision TKA utilizing an all-cementless CCK design and review the complications, rerevisions, and survivorship free of aseptic loosening. All subjects were included in the survivorship analysis.

Results:

The mean age of patients was 62.8 years. The average length of follow-up was 3.6 years (range: 2 to 6 y). Seventeen patients underwent revision TKA for periprosthetic joint infection as the second stage of a 2-stage reconstruction, 7 for aseptic loosening, and 4 for instability. There were 6 failures defined as the removal of any components for any reason; 5 of the 6 failures were due to recurrent periprosthetic joint infection. There were no failures that were revised for aseptic loosening.

Discussion:

If we consider those patients lost to follow-up to represent a failure (5/28), our series would have an 82.1% survivorship free from aseptic loosening and a failure rate 17.9% at an average of 3.6 years. Early results suggest the use of an all-cementless CCK design with porous tantalum for revision TKA may provide an acceptable alternative to cemented and hybrid techniques in selected patients.
Infective Endocarditis After Transcatheter Aortic Valve Implantation: A Systematic Review
Authors: Hassanin Ahmed , Afify Hesham , Zook Salma , Frishman William H. , Aronow Wilbert S.
Published: May 2022

Infective endocarditis (IE) after transcatheter aortic valve implantation (TAVI) is a rare but potentially fatal event. In this systematic review, we searched PubMed and Embase for large TAVI studies and registries to identify the incidence, presentation, microbiology, risk factors, and outcomes of IE in this population. After application of the selection criteria and quality assessment, 8 studies representing 255,310 TAVR cases and 4218 cases of IE qualified for this review. IE following TAVI is uncommon with an incidence of 0.87 to 1.7 events per 100 person-years. Most events occur in the first year following valve implantation. Staphylococcus, Enterococcus, and Streptococcus species are the most common pathogens. Risk factors include age, sex, concomitant comorbidities, and procedural factors. Outcomes are dismal, and surgical intervention is rare in this population.