bluuebunny/crossref_metadata_2025 huggingface dataset:
Scattering of electrons and positrons from aluminum isonuclear series
Authors: Islam M Raihan , Haque A K F , Haque M M , Billah M Masum , Khandker Mahmudul H , Islam M Rafiqul , Watabe Hiroshi , Uddin M Alfaz
Published: October 2022

The current study investigates the scattering of electrons and positrons from aluminum isonuclear series within the framework of the Dirac relativistic partial wave analysis. For the neutral aluminum atoms, the scattering phenomena are described by employing a short-range complex optical potential. For the ionic series, on the other hand, this potential is supplemented by the Coulomb potential. The calculations are reported for the differential cross-section, total cross-section, integrated elastic cross-section, inelastic cross-section, momentum transfer cross-section, viscosity cross-section, and total ionization cross-section over the energy range 1 eV ≤ E

i
≤ 1 MeV. The Sherman function S and spin asymmetry parameters T and U are also predicted for the same scattering systems over the same energy range. In addition, for the first time, we report a systematic study of the critical minima in the differential cross sections as well as the associated maximum spin polarization points in the Sherman function. We also compute the inelastic, elastic, momentum transfer, viscosity and total mean free paths for the aforesaid scattering systems. The Coulomb glory effect, the amplification of elastic backscattering of electrons from positive ions, is examined throughout the ionic series of aluminum. A comparison of our results to the reported theoretical and experimental studies reveals a good consistency over the compared energy range. The present theoretical method is thus expected to be useful for the fast generation of accurate cross-sections needed in many areas of science, technologies, and industries.
Improvement in photo-device properties of CuO thin films for opto-electronic applications: effects of (Ni, Co) co-doping
Authors: Gnanasekar T , Valanarasu S , Ade Ramesh , Vimala Juliet A , Ganesh V , AlAbdulaal T H , Bitla Yugandhar
Published: October 2022

We report co-doping effects of transition metal elements (Ni, Co) primarily on the opto-electronic properties of CuO thin films. CuO, CuO:Ni(1%), CuO:Co(1%) and CuO:Ni(1%):Co(1%) thin films were deposited via the spray pyrolysis route. Structural studies revealed the monoclinic CuO structure for all films. For all the films scanning electron microscope (SEM) images showed a crack-free and homogeneous surface. Photoluminescence (PL) spectra of all the films exhibited four emission peaks at 415, 451, 477, and 521 nm wavelengths. The optical bandgap (E
g) values were around 2.12 eV, 2.18 eV, 2.05 eV and 1.84 eV for CuO, CuO:Ni(1%), CuO:Co(1%) and CuO:Ni(1%):Co(1%)thin films, respectively. CuO:Ni(1%):Co(1%) photo-device displayed a large responsivity (R) of 0.43 AW−1, external quantum efficiency (EQE) of 100% and detectivity (D
*) of 9.55 × 109 Jones. Hence, co-doping of transition metal elements would be one of the effective approaches for enhancing opto-electronic properties of metal oxide compounds.
The amplification of cosmological magnetic fields in extended f(T,B) teleparallel gravity
Authors: Capozziello S. , Carleo A. , Lambiase G.
Published: October 2022

Observations indicate that intergalactic magnetic fields have amplitudes of the order of ∼ 10-6 G and are uniform on scales of ∼ 10 kpc. Despite their wide presence in the Universe, their origin remains an open issue. Even by invoking a dynamo mechanism or a compression effect for magnetic field amplification, the existence of seed fields before galaxy formation is still problematic. General Relativity predicts an adiabatic decrease of the magnetic field evolving as |B| ∝ 1/a
2, where a is the scale factor of the Universe. It results in very small primordial fields, unless the conformal symmetry of the electromagnetic sector is broken. In this paper, we study the possibility that a natural mechanism for the amplification of primordial magnetic field can be related to extended teleparallel gravity f(T,B) models, where T is the torsion scalar, and B the boundary term. In particular, we consider a non-minimal coupling with gravity in view to break conformal symmetry in a teleparallel background, investigating, in particular, the role of boundary term B, which can be consider as a further scalar field. We find that, after solving exactly the f(T,B) field equations both in inflation and reheating eras, a non-adiabatic behavior of the magnetic field is always possible, and a strong amplification appears in the reheating epoch. We also compute the ratio r = ρB
/ργ
between the magnetic energy density and the cosmic microwave energy density during inflation, in order to explain the present value r ≃ 1, showing that, in the slow-roll approximation, power-law teleparallel theories with Bn
have effects indistinguishable from metric theories Rn
where R is the Ricci curvature scalar.
Design and analysis of a channel drop filter and demultiplexer based on a photonic crystal super ellipse-shaped ring resonator
Authors: Radhouene Massoudi , Gharsallah Zaineb , Balaji V R , Najjar Monia , Robinson S , Janyani Vijay , Murugan M , Hegde Gopalkrishna , Sridarshini T
Published: October 2022

In advanced optical communication systems, a photonic crystal (PC) based channel drop filter (CDF) and dense wavelength division multiplexer (DWDM) demultiplexer are essential components in the design of a complete DWDM system, which offers a high transmission data rate. In the present work, a novel PC, CDF filter and demultiplexer based on a ring resonator with a super ellipse shape is designed and analyzed. To design a high-performance device, the performance parameters of the proposed components, such as transmission efficiency, spectral line width, channel spacing, Q-factor and crosstalk, are investigated. The proposed CDF is designed to drop a resonant wavelength with a high quality factor of 3955, and the ring resonator design is extended to the demultiplexer. The demultiplexer is designed to drop the four resonant wavelengths of 1579.8 nm, 1582 nm, 1583.6 nm and 1574.9 nm, respectively. The observed high quality factor (3955), bandwidth (0.4 nm) and transmission efficiency (90%) of the proposed demultiplexer will support high-performance DWDM systems
Transformation of coherent state in Hadamard gate via multi-photon catalysis
Authors: Chen Feng , Ren Gang , Yu Haijun
Published: October 2022

Based on two-mode continuous Hadamard gate (TCHG) and multi-photon catalysis, this paper presents a scheme to generate non-classical quantum states via coherent state. When considering the m-photon input and m-photon detection in a-mode, the output state is obtained for the input coherent in b-mode. An interesting finding is that as the amplitude of the output coherent state increases, both the detection efficiency and the fidelity of the output quantum state gradually approach zero. Thus, only certain low-intensity quantum light field states can pass through Hadamard gate. In addition, the quantum statistical distribution and squeezing properties of the output quantum states are also analyzed in detail. Our results show that TCHG is a powerful tool for generating non-classical quantum states under multi-photon catalysis.
Quantitative analysis of soliton interactions based on the exact solutions of the nonlinear Schrödinger equation
Authors: Zhang Xuefeng , Xu Tao , Li Min , Meng Yue
Published: October 2022

We make a quantitative study on the soliton interactions in the nonlinear Schrödinger equation (NLSE) and its variable–coefficient (vc) counterpart. For the regular two-soliton and double-pole solutions of the NLSE, we employ the asymptotic analysis method to obtain the expressions of asymptotic solitons, and analyze the interaction properties based on the soliton physical quantities (especially the soliton accelerations and interaction forces); whereas for the bounded two-soliton solution, we numerically calculate the soliton center positions and accelerations, and discuss the soliton interaction scenarios in three typical bounded cases. Via some variable transformations, we also obtain the inhomogeneous regular two-soliton and double-pole solutions for the vcNLSE with an integrable condition. Based on the expressions of asymptotic solitons, we quantitatively study the two-soliton interactions with some inhomogeneous dispersion profiles, particularly discuss the influence of the variable dispersion function f(t) on the soliton interaction dynamics.
Degradation mechanisms for polycrystalline silicon thin-film transistors with a grain boundary in the channel under negative gate bias stress
Authors: Zhang Dongli , Wang Mingxiang , Wang Huaisheng
Published: October 2022

The negative gate bias stress (NBS) reliability of n-type polycrystalline silicon (poly-Si) thin-film transistors (TFTs) with a distinct defective grain boundary (GB) in the channel is investigated. Results show that conventional NBS degradation with negative shift of the transfer curves is absent. The on-state current is decreased, but the subthreshold characteristics are not affected. The gate bias dependence of the drain leakage current at V
ds of 5.0 V is suppressed, whereas the drain leakage current at V
ds of 0.1 V exhibits obvious gate bias dependence. As confirmed via TCAD simulation, the corresponding mechanisms are proposed to be trap state generation in the GB region, positive-charge local formation in the gate oxide near the source and drain, and trap state introduction in the gate oxide.
Uncertainty quantification for wide-bin unfolding: one-at-a-time strict bounds and prior-optimized confidence intervals
Authors: Stanley Michael , Patil Pratik , Kuusela Mikael
Published: October 2022

Unfolding is an ill-posed inverse problem in particle
physics aiming to infer a true particle-level spectrum from smeared
detector-level data. For computational and practical reasons, these
spaces are typically discretized using histograms, and the smearing
is modeled through a response matrix corresponding to a discretized
smearing kernel of the particle detector. This response matrix
depends on the unknown shape of the true spectrum, leading to a
fundamental systematic uncertainty in the unfolding problem. To
handle the ill-posed nature of the problem, common approaches
regularize the problem either directly via methods such as Tikhonov
regularization, or implicitly by using wide-bins in the true space
that match the resolution of the detector. Unfortunately, both of
these methods lead to a non-trivial bias in the unfolded estimator,
thereby hampering frequentist coverage guarantees for confidence
intervals constructed from these methods. We propose two new
approaches to addressing the bias in the wide-bin setting through
methods called One-at-a-time Strict Bounds (OSB) and Prior-Optimized
(PO) intervals. The OSB intervals are a bin-wise modification of an
existing guaranteed-coverage procedure, while the PO intervals are
based on a decision-theoretic view of the problem. Importantly, both
approaches provide well-calibrated frequentist confidence intervals
even in constrained and rank-deficient settings. These methods are
built upon a more general answer to the wide-bin bias problem,
involving unfolding with fine bins first, followed by constructing
confidence intervals for linear functionals of the fine-bin
counts. We test and compare these methods to other available
methodologies in a wide-bin deconvolution example and a realistic
particle physics simulation of unfolding a steeply falling particle
spectrum.
Estimation of the effect of GNSS positioning errors on the dose rate calculation concerning aerial radiation monitoring
Authors: Mori A. , Seguchi E. , Futemma A. , Iwai T. , Sanada Y.
Published: October 2022

Four global navigation satellite system (GNSS) receivers
were installed in a helicopter to reduce positioning errors in
aerial radiation monitoring. The effect of positioning errors on the
conversion of the counting rate of the detector to the ambient dose
equivalent rate at the ground level was evaluated. The positioning
results obtained by receiving the centimeter-class augmentation
signal known as the L-band experiment, which the Quasi-Zenith
Satellite System generates on an experimental basis for a limited
time, were used as the reference values. A comparison between
horizontal and vertical positioning errors among four receivers
demonstrated that the vertical errors were larger than the
horizontal errors. They did not differ among receivers, whereas the
horizontal errors varied according to the characteristics of the
receivers, particularly in mountainous areas; the errors tended to
be larger when the terrain change at the measurement point was
larger. The median effects of the vertical and horizontal errors on
the calculated values of the radiation dose rate at the ground level
were 3%–6% and 1%–5%, respectively, and the maximum possible
effect of the positioning error was 20%–32%. The fact that the
receiver with the highest number of available satellites had larger
errors than the other receivers indicated that the elevation angles
of satellites and the augmentation signals play an important role in
improving the positioning accuracy when the number of available
satellites reduces in mountainous areas. This study has provided
insight into selecting a suitable GNSS receiver for surveying by
vehicles such as helicopters, aircraft, and drones, which are
required to perform 3D positioning in complex terrains.
Optimization of process parameters for hot isostatic pressing of Ir–Rh alloys based on first-principles calculations
Authors: Mao Zhang , Xian Wang , Qin-qin Gao , Chang-yi Hu , Jun Zhao , Hong-zhong Cai , Gui-xue Zhang , Xing-qiang Wang , Xu-xiang Zhang , Yan Wei
Published: October 2022

In this paper, the effect of Rh content on the mechanical properties of Ir–Rh alloys was investigated based on first-principles density functional theory. The calculated results show that when the Rh content is small, the three elastic moduli (elastic modulus (B), shear modulus (G), and Young’s modulus (E)) of Ir–Rh alloy increase rapidly with the increase of Rh content. They reach a maximum value at Ir–10Rh and then decrease, before rising slowly at Ir–40Rh and then gradually decreasing again. This shows that adding a small amount of rhodium to iridium can effectively improve the strength and hardness of iridium. Among all the components of the selected Ir–Rh alloys, Ir–10Rh has the highest hardness and strength. The addition of Rh can cause the embrittlement of Ir–Rh alloys, and its brittleness first increases and then decreases with the increase of Rh content, and reaches the highest at Ir–50Rh. Considering the results obtained from theoretical calculations and experiments, Ir–20Rh was selected as the alloy composition for the study of hot isostatic pressing technology. The effects of mixing time, whether to mix powder with balls, and degassing temperature on the properties of metal powders were studied to find the best mixing and degassing process parameters. In the experiment of mixing powder for the iridium and rhodium alloy, it is found that the time required for mixing powder with balls to reach uniformity was shorter than that without balls. The oxygen content of the final mixed powder obtained by the two processes is the same. The nitrogen content of the metal powder mixed with the ball is slightly higher than that without the ball, but it can be reduced to below 0.001% after the degassing process. During the sintering process, with the increase in temperature, the mutual diffusion speed between iridium powder and rhodium powder increases, the sintering neck grows, the internal pores decrease, and the density of the sintered body increases. Therefore, the final decision process is to select mixing with balls for 10 h, degas at 1200 °C for 2 h, and then raise the temperature to 1800 °C for sintering. With the increase of hot isostatic pressing temperature and pressure, the density of the alloy increases. When the highest temperature (1300 °C) and highest pressure (140 MPa) are used for hot isostatic pressing for 2 h, the density can reach 95.7% of the theoretical density.
Performance evaluation of online motion synchronizing systems for patient-specific respiratory movements with helical tomotherapy
Authors: Chan Wing Ki Claudia , Fok Tsz Ching , Chiu Tin Lok , Yu Siu Ki
Published: October 2022

Background and purpose. The introduction of online motion synchronizing system on helical tomotherapy paves way for robust motion tracking. A recent upgrade launches modifications on both hardware and software of the kV tracking system. An evaluation on the kV subsystems, prior (Version1) and post upgrade (Version2), was performed to compare tracking accuracy by means of fiducial tracking error and resulted root-mean-square (RMS). Impacts influenced by various patient-specific breathing pattern regularities and target movements were also investigated to refine motion tracking error estimations upon future selection of possible candidates. Materials and methods. Respiratory patterns from twenty-five lung cases were imported individually into a commercial dynamic platform model. Situating a phantom implanted with gold fiducial markers on the platform, superior-inferior (SI) movements of corresponding targets were simulated. Each case was delivered via an identical treatment plan in Version1 and was repeated in Version2. Motion tracking accuracy, by means of discrepancies between subsystem predicted model and raw data motion recorded in patient CT simulation, was analyzed statistically. Wilcoxon signed ranked test was employed to evaluate the difference in tracking error range between the two versions. Statistical model was fitted to inspect the dependence of internal target movement towards fiducial tracking errors. Results. A small difference of ±1 mm was exhibited in 99% of fiducial tracking errors for all cases experimented under both versions. RMS errors were all below 0.5 mm. Version2 demonstrated a greater extremity in fiducial tracking error (p = 0.04). A positive correlation was depicted between internal target amplitudes and 95% interval of fiducial tracking errors (p < 0.02). Overall, irregular respiratory patterns tended to have greater fiducial tracking errors. Conclusions. The excellent tracking performance in both kV subsystem versions offers motion compensations benefits, yet Version1 outperformed Version2 in fiducial tracking accuracy. It is noticeable that greater magnitude in internal target movement and irregular breathing patterns yield greater tracking error.
Dual pulsed laser deposition of Ag nanoparticles on calcium phosphate coatings for biomedical applications
Authors: López-Álvarez M , González-Rodríguez L , Gontad F , Teixeira-Santos R , Doiro M , Álvarez-Gómez L , Mergulhão F J M , González P , Serra J
Published: October 2022

Pulsed laser deposition (PLD) represents a promising bottom-up methodology for the synthesis and transference of nanoparticles to the surface of a biomedical device. Silver (Ag) nanoparticles directly incorporated on the metallic implant emerge as an alternative strategy for local action against prosthetic joint-associated infections. In the present research, a dual sequential PLD process is proposed to obtain a bilayer coating with (1) a bio-derived calcium phosphate (CaP) layer, to provide osteointegrative properties and (2) the controlled growth of the Ag nanoparticles over it, ranging the number of laser pulses from 100 to 500. The characterization by SEM, EDS, TEM, XPS and AFM revealed the uniform deposit of Ag rounded nanoparticles, with a narrow mean size distribution, in the original non-oxidized metallic state. Moreover, given the evidences from XPS and AFM techniques, the occurrence of a coalescence phenomenon from 400 pulses onwards was proposed together with the expected positive linear relation between the number of pulses and Ag contribution with a deposition rate of 0.05 at. % of Ag per pulse. Conversely, the decrease in roughness as the Ag content increased was also verified. Finally, the expected bacteriostatic activity for these PLD deposited metallic state Ag nanoparticles against the bacterial strain Staphylococcus aureus was confirmed. Moreover, the evaluation of the osteoblast-like MG-63 cells viability on the Ag(100–500)-CaP coatings revealed a significant increased proliferation (p > 0.05) on the Ag100-CaP coating compared to the control (Ag0-CaP). When same coating was evaluated against S. aureus the effect was not significant. The possibility of modulating the amount of nanoparticles in the bilayer coating to obtain a greater or lesser effect in combination with CaP was revealed.
System requirements to improve adaptive 4-dimensional computed tomography (4D CT) imaging
Authors: Morton Natasha , O’Brien Ricky , Keall Paul , Reynolds Tess
Published: October 2022

Four-Dimensional Computed Tomography (4D CT) is of increasing importance in stereotactic body radiotherapy (SBRT) treatments affected by respiratory motion. However, 4D CT images are commonly impacted by irregular breathing, causing image artifacts that can propagate through to treatment, negatively effecting local control. REspiratory Adaptive CT (REACT) is a real-time gating method demonstrated to reduce motion artifacts by avoiding imaging during irregular respiration. Despite artifact reduction seen through in silico and clinical phantom-based studies, REACT has not been able to remove all artifacts. Here, we explore several hardware and software latencies (gantry rotation time, couch shifts, acquisition delays and phase calculation method) inherently linked to REACT and 4D CT in general and investigate their contribution to artifacts beyond those caused by irregular breathing. Imaging was simulated using the digital extended cardiac-torso (XCAT) phantom for fifty patient-measured respiratory traces. Imaging protocols included conventional cine 4D CT and five REACT scans with systematically varied parameters to test the effect of different latencies on artifacts. Artifacts were quantified by comparing the image normalized cross correlation across couch transition points and determining the volume error compared to a static phantom ground truth both as a total error and individually across pixel rows in the main plane of motion. Artifacts were determined for each lung, the whole heart and lung tumour and were compared back to conventional 4D CT and REACT with standard clinical scanning parameters. The gantry rotation time and acquisition delay were found to have the largest impact on reducing image artifacts and should be the focus of future development. The phase calculation method was also found to influence motion artifacts and should potentially be assessed on a patient-to-patient basis. Finally, the correlation between an increase in artifacts and baseline drift suggests that longer scan times allowing drift to occur may impact image quality.
Twin neural network regression is a semi-supervised regression algorithm
Authors: Wetzel Sebastian J , Melko Roger G , Tamblyn Isaac
Published: October 2022

Twin neural network regression (TNNR) is trained to predict differences between the target values of two different data points rather than the targets themselves. By ensembling predicted differences between the targets of an unseen data point and all training data points, it is possible to obtain a very accurate prediction for the original regression problem. Since any loop of predicted differences should sum to zero, loops can be supplied to the training data, even if the data points themselves within loops are unlabelled. Semi-supervised training improves TNNR performance, which is already state of the art, significantly.
Relations between cusp forms sharing Hecke eigenvalues
Authors: Prasad Dipendra , Raghunathan Ravi
Published: October 2022

In this paper we consider the question of when the set of Hecke eigenvalues of a cusp form on

G

L
n

(

A

F

)

GL_n(\mathbb {A}_F)

is contained in the set of Hecke eigenvalues of a cusp form on

G

L
m

(

A

F

)

GL_m(\mathbb {A}_F)

for

n
≤
m

n \leq m

. This question is closely related to a question about finite dimensional representations of an abstract group, which also we consider in this work.
How Does Self-Control Promote Health Behaviors? A Multi-Behavior Test of Five Potential Pathways
Authors: Conner Mark , Wilding Sarah , Wright Charles E , Sheeran Paschal
Published: October 2022

Background

Self-control is generally defined as the capacity to override impulses and is a robust predictor of health behaviors. This paper integrates trait, reasoned action, and habit approaches to develop and test a mechanistic account of how self-control influences health actions.

Purpose

We tested five potential pathways from self-control to behavior, termed the valuation, prioritization, habituation, translation, and inhibition routes.

Methods

At baseline, participants (N = 663 adults) completed survey measures of reasoned action approach variables and habits in relation to eight health behaviors and the Brief Self-Control Scale. Three months later, participants reported their behavior. Multi-level modeling was used to test pathways across behaviors.

Results

Supporting the valuation route, affective attitude, cognitive attitude, descriptive norms, and perceived behavioral control mediated the self-control-intention relation, and intentions and perceived behavioral control mediated the relationship between self-control and health behaviors. Self-control also predicted the priority accorded to different considerations during intention formation. Higher self-control was associated with stronger prediction by cognitive attitudes and perceived behavioral control and weaker prediction by habits and injunctive norms. Self-control predicted habit formation, and habits mediated the self-control-behavior relation. Finally, self-control was associated with the improved translation of intentions into health behaviors and with greater inhibition of affective and habitual influences. Findings for the different pathways were not moderated by whether approach (health-protective behaviors) or avoidance responses (health-risk behaviors) were at issue.

Conclusions

The present research offers new insights into why self-control promotes health behavior performance, and how deficits in self-control might be offset in future behavior-change interventions.
Discovering drug–target interaction knowledge from biomedical literature
Authors: Hou Yutai , Xia Yingce , Wu Lijun , Xie Shufang , Fan Yang , Zhu Jinhua , Qin Tao , Liu Tie-Yan
Published: October 2022

Motivation

The interaction between drugs and targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from biomedical literature, which are usually triplets about drugs, targets and their interaction, becomes an urgent demand in the industry. Existing methods of discovering biological knowledge are mainly extractive approaches that often require detailed annotations (e.g. all mentions of biological entities, relations between every two entity mentions, etc.). However, it is difficult and costly to obtain sufficient annotations due to the requirement of expert knowledge from biomedical domains.

Results

To overcome these difficulties, we explore an end-to-end solution for this task by using generative approaches. We regard the DTI triplets as a sequence and use a Transformer-based model to directly generate them without using the detailed annotations of entities and relations. Further, we propose a semi-supervised method, which leverages the aforementioned end-to-end model to filter unlabeled literature and label them. Experimental results show that our method significantly outperforms extractive baselines on DTI discovery. We also create a dataset, KD-DTI, to advance this task and release it to the community.

Availability and implementation

Our code and data are available at https://github.com/bert-nmt/BERT-DTI.

Supplementary information

Supplementary data are available at Bioinformatics online.
Phytest: quality control for phylogenetic analyses
Authors: Wirth Wytamma , Mutch Simon , Turnbull Robert , Duchene Sebastian
Published: October 2022

Motivation

The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with the increase in genetic sequencing and the use of real-time pipelines e.g. in the SARS-CoV-2 era. Implementations of real-time phylogenetic analyses require automated testing to make sure that problems in the data are caught automatically within analysis pipelines and in a timely manner. Here, we present Phytest (version 1.1) a tool for automating quality control checks on sequences, trees and metadata during phylogenetic analyses.

Results

Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples.

Availability and implementation

Phytest source code is available on GitHub (https://github.com/phytest-devs/phytest) and can be installed via PyPI with the command ‘pip install phytest’. Extensive documentation can be found at https://phytest-devs.github.io/phytest/.

Supplementary information

Supplementary data are available at Bioinformatics online.
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data
Authors: Shehwana Huma , Kumar Shwetha V , Melott James M , Rohrdanz Mary A , Wakefield Chris , Ju Zhenlin , Siwak Doris R , Lu Yiling , Broom Bradley M , Weinstein John N , Mills Gordon B , Akbani Rehan
Published: October 2022

Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, ‘noise’, that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting.

Availability and implementation

The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE).

Supplementary information

Supplementary data are available at Bioinformatics online.
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data
Authors: Lyu Hongqiang , Liu Erhu , Wu Zhifang , Li Yao , Liu Yuan , Yin Xiaoran
Published: October 2022

Motivation

The emerging single-cell Hi-C technology provides opportunities to study dynamics of chromosomal organization. How to construct a pseudotime path using single-cell Hi-C contact matrices to order cells along developmental trajectory is a challenging topic, since these matrices produced by the technology are inherently high dimensional and sparse, they suffer from noises and biases, and the topology of trajectory underlying them may be diverse.

Results

We present scHiCPTR, an unsupervised graph-based pipeline to infer pseudotime from single-cell Hi-C contact matrices. It provides a workflow consisting of imputation and embedding, graph construction, dual graph refinement, pseudotime calculation and result visualization. Beyond the few existing methods, scHiCPTR ties to optimize graph structure by two parallel procedures of graph pruning, which help reduce the spurious cell links resulted from noises and determine a global developmental directionality. Besides, it has an ability to handle developmental trajectories with multiple topologies, including linear, bifurcated and circular ones, and is competitive with methods developed for single-cell RNA-seq data. The comparative results tell that our scHiCPTR can achieve higher performance in pseudotime inference, and the inferred developmental trajectory exhibit a reasonable biological significance.

Availability and implementation

scHiCPTR is freely available at https://github.com/lhqxinghun/scHiCPTR.

Supplementary information

Supplementary data are available at Bioinformatics online.
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites
Authors: Liu Chunting , Song Jiangning , Ogata Hiroyuki , Akutsu Tatsuya
Published: October 2022

Motivation

N4-methylcytosine (4mC) is an essential kind of epigenetic modification that regulates a wide range of biological processes. However, experimental methods for detecting 4mC sites are time-consuming and labor-intensive. As an alternative, computational methods that are capable of automatically identifying 4mC with data analysis techniques become a reasonable option. A major challenge is how to develop effective methods to fully exploit the complex interactions within the DNA sequences to improve the predictive capability.

Results

In this work, we propose MSNet-4mC, a lightweight neural network building upon convolutional operations with multi-scale receptive fields to perceive cross-element relationships over both short and long ranges of given DNA sequences. With strong imbalances in the number of candidates in different species in mind, we compute and apply class weights in the cross-entropy loss to balance the training process. Extensive benchmarking experiments show that our method achieves a significant performance improvement and outperforms other state-of-the-art methods.

Availability and implementation

The source code and models are freely available for download at https://github.com/LIU-CT/MSNet-4mC, implemented in Python and supported on Linux and Windows.

Supplementary information

Supplementary data are available at Bioinformatics online.
CAMML with the Integration of Marker Proteins (ChIMP)
Authors: Schiebout Courtney , Frost H Robert
Published: October 2022

Motivation

Cell typing is a critical task in the analysis of single-cell data, particularly when studying complex diseased tissues. Unfortunately, the sparsity and noise of single-cell data make accurate cell typing of individual cells difficult. To address these challenges, we previously developed the CAMML method for multi-label cell typing of single-cell RNA-sequencing (scRNA-seq) data. CAMML uses weighted gene sets to score each profiled cell for multiple potential cell types. While CAMML outperforms other scRNA-seq cell typing techniques, it only leverages transcriptomic data so cannot take advantage of newer multi-omic single-cell assays that jointly profile gene expression and protein abundance (e.g. joint scRNA-seq/CITE-seq).

Results

We developed the CAMML with the Integration of Marker Proteins (ChIMP) method to support multi-label cell typing of individual cells jointly profiled via scRNA-seq and CITE-seq. ChIMP combines cell type scores computed on scRNA-seq data via the CAMML approach with discretized CITE-seq measurements for cell type marker proteins. The multi-omic cell type scores generated by ChIMP allow researchers to more precisely and conservatively cell type joint scRNA-seq/CITE-seq data.

Availability and implementation

An implementation of this work is available on CRAN at https://cran.r-project.org/web/packages/CAMML/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cortical neuronal hyperexcitability and synaptic changes in SGCE mutation-positive myoclonus dystonia
Authors: Sperandeo Alessandra , Tamburini Claudia , Noakes Zoe , de la Fuente Daniel Cabezas , Keefe Francesca , Petter Olena , Plumbly William , Clifton Nicholas E , Li Meng , Peall Kathryn J
Published: October 2022

Myoclonus dystonia is a childhood-onset hyperkinetic movement disorder with a combined motor and psychiatric phenotype. It represents one of the few autosomal dominant inherited dystonic disorders and is caused by mutations in the ε-sarcoglycan (SGCE) gene. Work to date suggests that dystonia is caused by disruption of neuronal networks, principally basal ganglia-cerebello-thalamo-cortical circuits. Investigation of cortical involvement has primarily focused on disruption to interneuron inhibitory activity, rather than the excitatory activity of cortical pyramidal neurons. Here, we have sought to examine excitatory cortical glutamatergic activity using two approaches: the CRISPR/Cas9 editing of a human embryonic cell line, generating an SGCE compound heterozygous mutation, and three patient-derived induced pluripotent stem cell lines, each gene edited to generate matched wild-type SGCE control lines. Differentiation towards a cortical neuronal phenotype demonstrated no significant differences in either early- (PAX6, FOXG1) or late-stage (CTIP2, TBR1) neurodevelopmental markers. However, functional characterization using Ca2+ imaging and microelectrode array approaches identified an increase in network activity, while single-cell patch clamp studies found a greater propensity towards action potential generation with larger amplitudes and shorter half-widths associated with SGCE mutations. Bulk RNA sequencing analysis identified gene ontological enrichment for ‘neuron projection development’, ‘synaptic signalling’ and ‘synaptic transmission’. Examination of dendritic morphology found SGCE mutations to be associated with a significantly higher number of branches and longer branch lengths, together with longer ion-channel dense axon initial segments, particularly towards the latter stages of differentiation (Days 80 and 100). Gene expression and protein quantification of key synaptic proteins (synaptophysin, synapsin and PSD95), AMPA and NMDA receptor subunits found no significant differences between the SGCE mutation and matched wild-type lines. By contrast, significant changes to synaptic adhesion molecule expression were identified, namely higher presynaptic neurexin-1 and lower postsynaptic neuroligin-4 levels in the SGCE mutation carrying lines. Our study demonstrates an increased intrinsic excitability of cortical glutamatergic neuronal cells in the context of SGCE mutations, coupled with a more complex neurite morphology and disruption to synaptic adhesion molecules. These changes potentially represent key components to the development of the hyperkinetic clinical phenotype observed in myoclonus dystonia, as well a central feature to the wider spectrum of dystonic disorders, potentially providing targets for future therapeutic development.
Gone with the wind: The consequences of US drone strikes in Pakistan
Authors: Mahmood Rafat , Jetter Michael
Published: October 2022

Employing day-to-day wind conditions as an identification strategy, we explore the consequences of the 420 US drone strikes in Pakistan between 2006 and 2016. Results suggest that drone strikes encourage terrorism over the upcoming days and weeks, causing up to 19% of all terror attacks with more than 3,000 terror deaths in Pakistan during that period. Studying a leading Pakistani newspaper, we identify a polarised response to drone strikes as negative emotions and anger, but also positive emotions, in drone-related articles increase. Finally, anti-US protests and online searches exhibiting radical Islamist concepts increase as a consequence of drone strikes.
The impact of machine-learning-derived lean psoas muscle area on prognosis of type B aortic dissection patients undergoing endovascular treatment
Authors: Liu Jitao , Su Sheng , Liu Weijie , Xie Enmin , Hu Xiaolu , Lin Wenhui , Ding Huanyu , Luo Songyuan , Liu Yuan , Huang Wenhui , Li Jie , Yang Fan , Luo Jianfang
Published: October 2022

OBJECTIVES

The aim of this work was to investigate the impact of machine-learning-derived baseline lean psoas muscle area (LPMA) for patients undergoing thoracic endovascular aortic repair.

METHODS

A retrospective study was undertaken of acute and subacute complicated type B aortic dissection patients who underwent endovascular treatment from 2010 to 2017. LPMA (a marker of frailty) was calculated by multiplying psoas muscle area and density measured at L3 level from the computed tomography. The optimal cut-off value of LPMA was determined by the Cox hazard model with restricted cubic spline.

RESULTS

A total of 428 patients who met the inclusion criteria were included in this study. Patients were classified into low LPMA group (n = 218) and high LPMA group (n = 210) using the cut-off value of 395 cm2 Hounsfield unit. An automatic muscle segmentation algorithm was developed based on U-Net architecture. There was high correlation between machine-learning method and manual measurement for psoas muscle area (r = 0.91, P < 0.001) and density (r = 0.90, P < 0.001). Multivariable regression analyses revealed that baseline low LPMA (<395 cm2 Hounsfield unit) was an independent positive predictor for 30-day (odds ratio 5.62, 95% confidence interval 1.20–26.23, P = 0.028) and follow-up (hazard ratio 5.62, 95% confidence interval 2.68–11.79, P < 0.001) mortality. Propensity score matching and subgroup analysis based on age (<65 vs ≥65 years) confirmed the independent association between baseline LPMA and follow-up mortality.

CONCLUSIONS

Baseline LPMA could profoundly affect the prognosis of patients undergoing thoracic endovascular aortic repair. It was feasible to integrate the automatic muscle measurements into clinical routine.
When Is a Potassium Channel Not a Potassium Channel?
Authors: Accili Eric
Published: October 2022

Ever since they were first observed in Purkinje fibers of the heart, funny channels have had close connections to potassium channels. Indeed, funny channels were initially thought to produce a potassium current in the heart called IK2. However, funny channels are completely unlike potassium channels in ways that make their contributions to the physiology of cells unique. An important difference is the greater ability for sodium to permeate funny channels. Although it does not flow through the funny channel as easily as does potassium, sodium does permeate well enough to allow for depolarization of cells following a strong hyperpolarization. This is critical for the function of funny channels in places like the heart and brain. Computational analyses using recent structures of the funny channels have provided a possible mechanism for their unusual permeation properties.
Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana
Authors: Andrade Pedro , Lyra Mariana L , Zina Juliana , Bastos Deivson F O , Brunetti Andrés E , Baêta Délio , Afonso Sandra , Brunes Tuliana O , Taucce Pedro P G , Carneiro Miguel , Haddad Célio F B , Sequeira Fernando
Published: October 2022

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.
Clinical outcomes of asymptomatic low-grade esophagitis: results from a multicenter Chinese cohort
Authors: Chen Songfeng , Xiang Xuelian , Zhang Xiaohao , Zhuang Qianjun , Tan Niandi , Hou Xun , Zhang Mengyu , Hu Junnan , Duan Chaofan , Cui Yi , Wang Jinhui , Xing Xiangbin , Zhang Nina , Xiao Yinglian
Published: October 2022

Background

Asymptomatic low-grade (Los Angeles Classification Grades A and B) esophagitis is common in clinical practice with unclear clinical outcomes. This study aimed to explore the clinical outcomes of asymptomatic low-grade esophagitis.

Methods

This was a multicenter cohort study conducted by three academic hospitals in China. Asymptomatic low-grade esophagitis patients between January 2015 and December 2019 were included. Mucosal healing condition 1 year after initial diagnosis, symptom outcomes, and proton-pump inhibitor (PPI) use within 1 year after initial diagnosis were studied and compared.

Results

A total of 248 asymptomatic low-grade esophagitis patients were included. Esophagitis disappeared in 76.2% of patients 1 year after initial diagnosis. In terms of symptom outcomes, 89.9% of patients did not present gastroesophageal reflux disease (GERD) symptoms within 1 year after initial diagnosis. No significant difference was found in the proportion of patients who presented GERD symptoms and in the proportion of patients with persistent esophagitis between the PPI group and the non-PPI group (all P > 0.05). Patients with initial Grade B esophagitis were more likely to present follow-up GERD symptoms (16.0% vs 7.5%, P = 0.041) and had more severe follow-up esophagitis than those with Grade A (P < 0.001). Patients with follow-up GERD symptoms were more likely to have persistent esophagitis than those without.

Conclusions

This study demonstrated that asymptomatic low-grade esophagitis had relatively benign clinical outcomes. Patients with initial Grade B esophagitis and patients with follow-up GERD symptoms were more likely to be those who are in genuine need of further follow-up and treatments.
The Role of Adverse Childhood Experiences in Multidimensional Nature of Subjective Age
Authors: Xie Donghong , Wang Jiwen , Huang Fan
Published: October 2022

Objectives

Age stereotypes and expectations about one’s own aging commence in childhood, while most research focuses on predictive associations with midlife cognition and health outcomes in later life. This study instead aims to examine adverse childhood experiences (ACEs) contributing to multiple measures of subjective age (SA) among Chinese older adults and test whether these relationships differ by household registration (hukou).

Methods

In a representative sample of Chinese older adults aged 60 and older from the 2018 China Longitudinal Aging and Social Survey (n = 7,815), ordinary least squares is used to examine the associations between ACEs and 3 facets of SA: felt age, look age, and self-defined aging standard.

Results

Childhood starvation experience and limited health care access predict older felt age and look age, while parental death is associated with lower self-defined aging standard. Zooming in on hukou-specific associations shows that the dose–response relationship on older adults with rural hukou is particularly pronounced.

Discussion

Findings provide empirical support for views of aging from a life-course perspective and highlight the enduring impact of ACEs for late-adulthood SA, as well as their differential influence on multiple indicators of SA. Interventions that focus on promoting health and development in childhood could potentially have effects beyond the childhood phase, and benefit for their positive aging attitude in later life.