bluuebunny/crossref_metadata_2025 huggingface dataset:
A vertical wind structure that leads to extreme rainfall and major flooding in southeast Australia
Authors: Callaghan Jeff , Power Scott B.
Published: August 2021

Here we examine winds associated with extreme rainfall and major flooding in coastal catchments and more broadly over southeastern Australia. Both radio-sonde and re-analysis data are examined. In every case (i) atmospheric moisture content is high and (ii) the low-level winds are onshore, and in almost every case (iii) the wind-direction turns anti-cyclonically with increasing height up to 500 hPa. Data from Brisbane extending back more than 50 years is consistent with this behavior: winds turn anti-cyclonically with increasing height on days with heavy rainfall, whereas winds turn cyclonically with increasing height on days with light or no rainfall. In the coastal zone, extreme rainfall rarely occurs without (i), (ii) and (iii). In eastern Australia beyond the coastal zone, conditions (i) and (iii) are also associated with extreme rainfall. We found very few cases where such conditions were not associated with extreme rainfall in this broader region. This study extends previous work by showing that the link between turning winds and rainfall exists in both the tropics and subtropics, and the link applies in cases of extreme rainfall and associated major flooding.
Extreme monthly rainfall over Australia in a changing climate
Authors: Watterson Ian G. , Chua Zhi-Weng , Hope Pandora K.
Published: August 2021

Motivated by the important impacts of extreme rainfall, this study extends the CSIRO and BoM (2015) analyses and projections of 20-year means and daily extremes to rainfall on the monthly timescale. Frequency distributions for monthly rainfall rates simulated by 40 CMIP5 models for the 1986-2005 period are compared with those from the AWAP 0.25° gridded observational data. Distributions spatially-averaged over Australian regions provide a signature of seasonal rainfall. Composites of months in the top and lowest deciles for each grid point and each of the four seasons are then evaluated, along with the frequency of rainfall rates exceeding thresholds ranging from 0.5 mm d-1 to 8 mm d-1.The simulated changes by 2080-2099 under the RCP8.5 scenario for the various rainfall statistics are assessed. Maps of the ensemble mean of changes of the lowest and top deciles, as a percentage of the 1986-2005 base, partly reflect the tendency for increased mean rain in summer and autumn, with decreases in winter and spring. There is also a change in the frequency distribution, with the top decile rainfall tending to increase and the lowest decile to decrease. Bar graphs are used to represent the range of change across the models, for each of four seasons and four regions. In most cases the bars for each statistic cover both declines and increases, but there is again a shift towards the positive in the progression from lowest decile to top decile. The changes are consistent with a broadening of the distribution of monthly amounts. Model spatial resolution is not a major influence on the changes. These projections for monthly rainfall statistics should be applicable to a range of climate impacts.
Analysis of within and between-GCM uncertainties of runoff projections in Mediterranean-like catchments
Authors: Barria Pilar A. , Peel Murray C. , Walsh Kevin J.E. , Garreaud René
Published: August 2021

Streamflow reductions have been reported in mid-latitude Southern Hemisphere (SH) catchments, in particular in the southwest of Western Australia (SWA) and in central Chile (CC), following decreases in precipitation since the mid-1970s. Although projections from Global Climate Models (GCMs) indicate the observed trends are expected to continue during the rest of the 21st century, they are affected by large uncertainties that challenge informed decision making. Quantification and comparison of uncertainties in runoff projections for the period 2050-2080 relative to 1970-2000, driven by an ensemble of a single GCM with perturbed physics (CPDN) and a multi-model ensemble of different GCMs (CMIP5), were used to account for what we term “within-GCM” and “between-GCM” uncertainty in SWA catchments. Between GCM uncertainty of runoff projections was also quantified in CC catchments. Within and between-GCM uncertainties were found to be very similar (∼55 per cent) in SWA catchments. Between-GCM uncertainty for runoff projections in CC catchments is smaller than in SWA. On average, uncertainty of about 51 per cent, under RCP8.5 scenario, was simulated for the period 2050-2080 compared to 1970-2000. For CC catchments a dichotomy was observed in runoff projections under the RCP4.5 scenario, which according to our preliminary analysis might relate to how ozone is specified within different GCMs. We conclude that the number of models sampled by the CMIP5 ensemble, which includes multiple model runs from some GCMs, provides some insight into within-GCM uncertainties. Furthermore, since CMIP5 model runs report values for all regions and are easily accessible, the CMIP5 ensemble is more convenient for regional hydrological assessments than the perturbed physics experiments.
The E3 ubiquitin ligase RNF186 and
RNF186
risk variants regulate innate receptor-induced outcomes
Authors: Ranjan Kishu , Hedl Matija , Abraham Clara
Published: August 2021

Significance

This study identifies a previously undefined role for the inflammatory bowel disease–associated gene
RNF186
in innate immunity. RNF186 is expressed in human macrophages and promotes outcomes downstream of receptors responding to microbial products. Upon stimulation of microbial response receptors, RNF186 contributes to assembly and ubiquitination of the signaling complex and subsequent cytokine secretion and antimicrobial pathway induction. Importantly, through different mechanisms, both rare (through impaired ubiquitination) and common (through reduced expression) disease-risk genetic variants in
RNF186
lead to a loss in RNF186 function and impaired bacterial clearance in primary human macrophages. These studies highlight a key role for RNF186 in promoting essential innate immune functions contributing to intestinal immune homeostasis.
The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage
Authors: Garwain Osama , Sun Xiaoming , Iyer Divya Ramalingam , Li Rui , Zhu Lihua Julie , Kaufman Paul D.
Published: August 2021

Significance

Ki-67 is a clinically important tumor proliferation marker protein. Ki-67 contributes to the three-dimensional organization of heterochromatin during interphase of the cell cycle, and also coats and shapes condensed chromosomes during mitosis. Here, we show that acute depletion of Ki-67 in human cells causes DNA damage as cells traverse mitosis. When the tumor suppressor protein p53 is codepleted with Ki-67, multiple hallmarks of genome instability arise, including anaphase chromosome bridges, followed by the appearance of micronuclei. The C-terminal chromatin-binding domain of Ki-67 is sufficient for resistance to this damage. These studies uncover a factor for genome maintenance and identify a protective protein domain.
Molecular insights into differentiated ligand recognition of the human parathyroid hormone receptor 2
Authors: Wang Xi , Cheng Xi , Zhao Lihua , Wang Yuzhe , Ye Chenyu , Zou Xinyu , Dai Antao , Cong Zhaotong , Chen Jian , Zhou Qingtong , Xia Tian , Jiang Hualiang , Xu H. Eric , Yang Dehua , Wang Ming-Wei
Published: August 2021

Significance

The high-resolution cryogenic electron microscopy structure of the human parathyroid hormone receptor 2 (PTH2R), in complex with an endogenous tuberoinfundibular peptide (TIP39) and a heterotrimeric G
s
protein, reveals that the unique loop conformation at the N terminus of TIP39 is indispensable for PTH2R activation, as the deletion of which results in a potent PTH2R antagonist TIP(7-39). The naturally occurring mutation G258D impairs the receptor signaling such as cAMP accumulation. This finding provides a potential molecular mechanism for syndromic short stature.
A squalene–hopene cyclase inSchizosaccharomyces japonicusrepresents a eukaryotic adaptation to sterol-limited anaerobic environments
Authors: Bouwknegt Jonna , Wiersma Sanne J. , Ortiz-Merino Raúl A. , Doornenbal Eline S. R. , Buitenhuis Petrik , Giera Martin , Müller Christoph , Pronk Jack T.
Published: August 2021

Significance

Biosynthesis of sterols requires oxygen. This study identifies a previously unknown evolutionary adaptation in a eukaryote, which enables anaerobic growth in absence of exogenous sterols. A squalene–hopene cyclase, proposed to have been acquired by horizontal gene transfer from an acetic acid bacterium, is implicated in a unique ability of the yeastSchizosaccharomyces japonicusto synthesize hopanoids and grow in anaerobic, sterol-free media. Expression of this cyclase inSaccharomyces cerevisiaeconfirmed that at least one of its hopanoid products acts as sterol surrogate. These observations provide leads for research into the structure and function of eukaryotic membranes and into the development of sterol-independent yeast cell factories for application in anaerobic processes.
The
Brucella
effector BspL targets the ER-associated degradation (ERAD) pathway and delays bacterial egress from infected cells
Authors: Luizet Jean-Baptiste , Raymond Julie , Lacerda Thais Lourdes Santos , Barbieux Emeline , Kambarev Stanimir , Bonici Magali , Lembo Frédérique , Willemart Kévin , Borg Jean-Paul , Celli Jean , Gérard Francine C. A. , Muraille Eric , Gorvel Jean-Pierre , Salcedo Suzana P.
Published: August 2021

Significance

Intracellular bacterial pathogens rely on dedicated systems to inject effector proteins into host cells and cause disease. This is the case for
Brucella abortus
, which causes brucellosis, one of the world’s most prevalent zoonotic diseases. We have found one such effector that can control the intracellular fate of
Brucella
by hijacking the machinery of the endoplasmic reticulum generally used by our cells to degrade misfolded or unwanted proteins. This bacterial effector works to slow down the formation of a specialized vacuole that enables
Brucella
to exit from the cell and infect neighboring cells. This delay ultimately allows the bacteria extra time for extensive intracellular multiplication, an essential feature of its virulence.
Designing artificial two-dimensional landscapes via atomic-layer substitution
Authors: Guo Yunfan , Lin Yuxuan , Xie Kaichen , Yuan Biao , Zhu Jiadi , Shen Pin-Chun , Lu Ang-Yu , Su Cong , Shi Enzheng , Zhang Kunyan , HuangFu Changan , Xu Haowei , Cai Zhengyang , Park Ji-Hoon , Ji Qingqing , Wang Jiangtao , Dai Xiaochuan , Tian Xuezeng , Huang Shengxi , Dou Letian , Jiao Liying , Li Ju , Yu Yi , Idrobo Juan-Carlos , Cao Ting , Palacios Tomás , Kong Jing
Published: August 2021

Significance

Manipulating materials with atomic-scale precision is essential for the development of a next-generation material design toolbox. Tremendous efforts have been made to advance the compositional, structural, and spatial accuracy of material deposition and patterning. Here, we presented a new reaction pathway to implement the conversions of two-dimensional materials within the atomic-layer thickness at room temperature for electrical dipole manipulation. Not only could various Janus monolayer transition metal dichalcogenides with vertical dipole be realized, but also some heterostructures, including the dipole-nondipole heterostructures (MoS2-MoSSe) and multiheterostructures (MoS2-MoSSe-MoSeS-MoSe2) within the same monolayer host structure are developed, in which the dipoles can be selectively patterned to be zero (MoS2, MoSe2), positive (MoSSe), and negative (MoSeS).
The Medusa effect reveals levels of mind perception in pictures
Authors: Will Paris , Merritt Elle , Jenkins Rob , Kingstone Alan
Published: August 2021

Significance

Differential treatment of animate and inanimate objects often hinges on mind perception—the attribution of mental states to others. It has already been established that pictures of animate objects can elicit mind perception, albeit at reduced intensity. However, this loss of intensity is assumed to reflect an impoverishment of a rich stimulus, such as the projection of a living being into a static picture plane. The current study overturns this assumption by showing that “pure” abstraction can reduce mind perception independent of stimulus richness. Depicting things with minds raises ethical questions that have not been recognized previously. As these questions emerge from representational structure rather than representational content, they are unlikely to be quashed by improvements in image quality.
Analysis methods and quality criteria for investigating muscle physiology using x-ray diffraction
Authors: Squire John M. , Knupp Carlo
Published: August 2021

X-ray diffraction studies of muscle have been tremendously powerful in providing fundamental insights into the structures of, for example, the myosin and actin filaments in a variety of muscles and the physiology of the cross-bridge mechanism during the contractile cycle. However, interpretation of x-ray diffraction patterns is far from trivial, and if modeling of the observed diffraction intensities is required it needs to be performed carefully with full knowledge of the possible pitfalls. Here, we discuss (1) how x-ray diffraction can be used as a tool to monitor various specific muscle properties and (2) how to get the most out of the rest of the observed muscle x-ray diffraction patterns by modeling where the reliability of the modeling conclusions can be objectively tested. In other x-ray diffraction methods, such as protein crystallography, the reliability of every step of the process is estimated and quoted in published papers. In this way, the quality of the structure determination can be properly assessed. To be honest with ourselves in the muscle field, we need to do as near to the same as we can, within the limitations of the techniques that we are using. We discuss how this can be done. We also use test cases to reveal the dos and don’ts of using x-ray diffraction to study muscle physiology.
A Self-Diffraction Temporal Filter for Contrast Enhancement in Femtosecond Ultra-High Intensity Laser
Authors: Wang Xian-Zhi , Wang Zhao-Hua , Wang Yuan-Yuan , Zhang Xu , Song Jia-Jun , Wei Zhi-Yi
Published: August 2021

We demonstrated a nonlinear temporal filter based on the self-diffraction (SD) process. Temporal contrast enhancement, angular dispersion and spectrum broadening properties of the SD process are investigated in experiment and simulation. Driven by spectral phase well compensated laser pulses with bandwidth of 28 nm, the filter produced clean pulses with a temporal contrast higher than 1010 and excellent spatial profile, the spectrum of which was smoothed and broadened to 64 nm. After implementing this filter into a home-made 30 TW Ti:sapphire amplifier, temporal contrast of the amplified pulses was enhanced to 1010 within the time scale of –400 ps.
Surface-Enhanced Raman Scattering of Hydrogen Plasma-Treated Few-Layer MoTe2
Authors: Jing Xiao-Xue , Li Da-Qing , Zhang Yong , Hou Xiang-Yu , Jiang Jie , Fan Xing-Ce , Wang Meng-Chen , Feng Shao-Peng , Yu Yuan-fang , Lu Jun-Peng , Hu Zhen-Liang , Ni Zhen-Hua
Published: August 2021

Two-dimensional surface-enhanced Raman scattering (SERS) substrates have drawn intense attention due to their excellent spectral reproducibility, high uniformity and perfect anti-interference ability. However, the inferior detection sensitivity and low enhancement have limited the practical application of two-dimensional SERS substrates. To address this issue, we propose that the interaction between the MoTe2 substrate and the analyte rhodamine 6G molecules could be remarkably enhanced by the introduced p-doping effect and lattice distortion of MoTe2 via hydrogen plasma treatment. After the treatment, the SERS is greatly improved, the enhancement factor of probe molecules reaches 1.83 × 106 as well as the limit of detection concentration reaches 10−13 M. This method is anticipated to afford new enhancement probability for other 2D materials, even non-metal oxide semiconductor SERS substrates.
Computational Prediction of a Novel Superhard sp
3 Trigonal Carbon Allotrope with Bandgap Larger than Diamond
Authors: Lv Ruoyun , Yang Xigui , Yang Dongwen , Niu Chunyao , Zhao Chunxiang , Qin Jinxu , Zang Jinhao , Dong Fuying , Dong Lin , Shan Chongxin
Published: August 2021

Searching for new carbon allotropes with superior properties has been a longstanding interest in material sciences and condensed matter physics. Here we identify a novel superhard carbon phase with an 18-atom trigonal unit cell in a full-sp
3 bonding network, termed tri-C18 carbon, by first-principles calculations. Its structural stability has been verified by total energy, phonon spectra, elastic constants, and molecular dynamics simulations. Furthermore, tri-C18 carbon has a high bulk modulus of 400 GPa and Vickers hardness of 79.0 GPa, comparable to those of diamond. Meanwhile, the simulated x-ray diffraction pattern of tri-C18 carbon matches well with the previously unexplained diffraction peaks found in chimney soot, indicating the possible presence of tri-C18 carbon. Remarkably, electronic band structure calculations reveal that tri-C18 carbon has a wide indirect bandgap of 6.32 eV, larger than that of cubic diamond, indicating its great potential in electronic or optoelectronic devices working in the deep ultraviolet region.
Concurrent Structural and Electronic Phase Transitions in V2O3 Thin Films with Sharp Resistivity Change
Authors: Xie Chuang , Hu Ling , Zhang Ran-Ran , Zhu Shun-Jin , Zhu Min , Wei Ren-Huai , Tang Xian-Wu , Song Wen-Hai , Zhu Xue-Bin , Sun Yu-Ping
Published: August 2021

The relationship between structural and electronic phase transitions in V2O3 thin films is of critical importance for understanding of the mechanism behind metal–insulator transition (MIT) and related technological applications. Despite being extensively studied, there are currently no clear consensus and picture of the relation between structural and electronic phase transitions so far. Using V2O3 thin films grown on r-plane Al2O3 substrates, which exhibit abrupt MIT and structural phase transition, we show that the electronic phase transition occurs concurrently with the structural phase transition as revealed by the electrical transport and Raman spectra measurements. Our result provides experimental evidence for clarifying this issue, which could form the basis of theoretical studies as well as technological applications in V2O3.
A k · p Effective Hamiltonian Generator
Authors: Jiang Yi , Fang Zhong , Fang Chen
Published: August 2021

A
k
·
p
effective Hamiltonian is important for theoretical analysis in condensed matter physics. Based on the kdotp-symmetry package, we develop an upgraded package named as kdotp-generator. This generator takes in arbitrary magnetic symmetries with their representations and returns symmetry-allowed
k
·
p
Hamiltonians. Using this package, we calculate
k
·
p
Hamiltonians for irreducible co-representations in 1651 magnetic space groups up to the third order, and their linear coupling to external fields including the electromagnetic field and the strain tensor. We hope that the package will facilitate related research in the future.
Measurement of Superconductivity and Edge States in Topological Superconductor Candidate TaSe3
Authors: Liu Shuai , Nie Si-Min , Qi Yan-Peng , Guo Yan-Feng , Yuan Hong-Tao , Yang Le-Xian , Chen Yu-Lin , Wang Mei-Xiao , Liu Zhong-Kai
Published: August 2021

Topological superconductors (TSCs) have been widely investigated in recent years due to their novel physics and ability to host Majorana fermions (MFs) which are key to topological quantum computation. Despite the great interest, only a few compounds have been proposed as candidates of intrinsic TSCs, such as iron-based superconductor FeSe0.55Te0.45 and 2M-WS2. Among them, quasi-one-dimensional superconductor TaSe3 possesses fascinating properties such as its simple stoichiometry, layered nature and chemical stability. Here, using scanning tunneling microscope/spectroscopy (STM/STS), we systematically investigate the topography and electronic structure of TaSe3. Our STM/STS measurement reveals large atomically flat, defect-free surfaces suitable for the search of MF; electronic density of states consistent with our angle-resolved photoemission result and band-structure calculations, and a uniform superconducting gap with a typical size of ∼ 0.25 meV. Remarkably, additional edge states are observed in the vicinity of the terrace edge, suggesting they may have a topological origin. Our result proves the coexistence of superconductivity and topological electronic structure in TaSe3, making it an intriguing platform to investigate topological superconductivity.
Generalized Rashba Coupling Approximation to a Resonant Spin Hall Effect of the Spin–Orbit Coupling System in a Magnetic Field
Authors: Zhang Rui , Biao Yuan-Chuan , You Wen-Long , Wang Xiao-Guang , Zhang Yu-Yu , Hu Zi-Xiang
Published: August 2021

We introduce a generalized Rashba coupling approximation to analytically solve confined two-dimensional electron systems with both the Rashba and Dresselhaus spin–orbit couplings in an external magnetic field. A solvable Hamiltonian is obtained by performing a simple change of basis, which has the same form as that with only Rashba coupling. Each Landau state becomes a new displaced-Fock state instead of the original Harmonic oscillator Fock state. Analytical energies are consistent with the numerical ones in a wide range of coupling strength even for a strong Zeeman splitting, exhibiting the validity of the analytical approximation. By using the eigenstates, spin polarization correctly displays a jump at the energy-level crossing point, where the corresponding spin conductance exhibits a pronounced resonant peak. As the component of the Dresselhaus coupling increases, the resonant point shifts to a smaller value of the magnetic field. In contrast to pure Rashba couplings, we find that the Dresselhaus coupling and Zeeman splittings tend to suppress the resonant spin Hall effect. Our method provides an easy-to-implement analytical treatment to two-dimensional electron gas systems with both types of spin–orbit couplings by applying a magnetic field.
Momentum Space Quantum Monte Carlo on Twisted Bilayer Graphene
Authors: Zhang Xu , Pan Gaopei , Zhang Yi , Kang Jian , Meng Zi Yang
Published: August 2021

We report an implementation of the momentum space quantum Monte Carlo (QMC) method on the interaction model for the twisted bilayer graphene (TBG). The long-range Coulomb repulsion is treated exactly with the flat bands, spin and valley degrees of freedom of electrons taking into account. We prove the absence of the minus sign problem for QMC simulation when either the two valleys or the two spin degrees of freedom are considered. By taking the realistic parameters of the twist angle and interlayer tunnelings into the simulation, we benchmark the QMC data with the exact band gap obtained at the chiral limit, to reveal the insulating ground states at the charge neutrality point (CNP). Then, with the exact Green’s functions from QMC, we perform stochastic analytic continuation to obtain the first set of single-particle spectral function for the TBG model at CNP. Our momentum space QMC scheme therefore offers the controlled computation pathway for systematic investigation of the electronic states in realistic TBG model at various electron fillings.
Preparation of Superconducting Thin Films of Infinite-Layer Nickelate Nd0.8Sr0.2NiO2
Authors: Gao Qiang , Zhao Yuchen , Zhou Xing-Jiang , Zhu Zhihai
Published: August 2021

The recent observation of superconductivity in thin films of infinite-layer nickelate Nd0.8Sr0.2NiO2 has received considerable attention. Despite the many efforts to understand the superconductivity in infinite-layer nickelates, a consensus on the underlying mechanism for the superconductivity has yet to be reached, partly owing to the challenges with the material synthesis. Here, we report the successful growth of superconducting infinite-layer Nd0.8Sr0.2NiO2 films by pulsed laser deposition and soft chemical reduction. The details on the growth process are discussed.
Weakly coupled local particle detectors cannot harvest entanglement
Authors: Ruep Maximilian H
Published: August 2021

Many states of linear real scalar quantum fields (in particular Reeh–Schlieder states) on flat as well as curved spacetime are entangled on spacelike separated local algebras of observables. It has been argued that this entanglement can be ‘harvested’ by a pair of so-called particle detectors, for example singularly or non-locally coupled quantum mechanical harmonic oscillator Unruh detectors. In an attempt to avoid such imperfect coupling, we analyse a model-independent local and covariant entanglement harvesting protocol based on the local probes of a recently proposed measurement theory of quantum fields. We then introduce the notion of a local particle detector concretely given by a local mode of a linear real scalar probe field on possibly curved spacetime and possibly under the influence of external fields. In a non-perturbative analysis we find that local particle detectors cannot harvest entanglement below a critical coupling strength when the corresponding probe fields are initially prepared in quasi-free Reeh–Schlieder states and are coupled to a system field prepared in a quasi-free state. This is a consequence of the fact that Reeh–Schlieder states restrict to truly mixed states on any local mode.
Nanoliposomes co-encapsulating Ce6 and SB3CT against the proliferation and metastasis of melanoma with the integration of photodynamic therapy and NKG2D-related immunotherapy on A375 cells
Authors: Liu Huifang , Yao Cuiping , Zhang Luwei , Xin Jing , Zhang Zhenxi , Wang Sijia
Published: August 2021

Purpose. To overcome the insufficiency of conventional photodynamic therapy (PDT) for treating metastatic melanoma, the combination of smart nanoparticles and PDT with immunotherapy was used to achieve a higher efficiency by accumulating more photosensitizers in tumor areas and triggering stronger immune responses against tumors after PDT. Methods. In this study, we designed a nanoliposome co-encapsulation of chlorin E6 (Ce6) and SB-3CT to realize significant antitumoral proliferation and metastasis efficacy after laser irradiation in A375 cells. The morphology, size distribution, and loading efficiency of Ce6–SB3CT@Liposome (Lip-SC) were characterized. The reactive oxygen species (ROS) generation and cytotoxicity were evaluated in A375 cells, and the mechanisms of natural killer (NK) cell-mediated killing were assessed. Results. Lip-SC showed good stability and was well-dispersed with a diameter of approximately 140 nm in phosphate-buffered saline. The nanoliposomes could accumulate in tumor areas and induce apoptosis in cancer cells upon 660 nm light irradiation, which could trigger an immune response and induce the expression of NK group 2 member D (NKG2D) ligands. The subsequently released SB-3CT could further activate NK cells effectively and strengthen the immune system by inhibiting the shedding of soluble NKG2D ligands. Discussion. Taken together, the synergistic effects of SB-3CT on nanoliposomes for Ce6-mediated PDT were analyzed in detail to provide a new platform for future anti-melanoma treatment.
A multichannel feature-based approach for longitudinal lung CT registration in the presence of radiation induced lung damage
Authors: Stavropoulou A , Szmul A , Chandy E , Veiga C , Landau D , McClelland J R
Published: August 2021

Quantifying parenchymal tissue changes in the lungs is imperative in furthering the study of radiation induced lung damage (RILD). Registering lung images from different time-points is a key step of this process. Traditional intensity-based registration approaches fail this task due to the considerable anatomical changes that occur between timepoints. This work proposes a novel method to successfully register longitudinal pre- and post-radiotherapy (RT) lung computed tomography (CT) scans that exhibit large changes due to RILD, by extracting consistent anatomical features from CT (lung boundaries, main airways, vessels) and using these features to optimise the registrations. Pre-RT and 12 month post-RT CT pairs from fifteen lung cancer patients were used for this study, all with varying degrees of RILD, ranging from mild parenchymal change to extensive consolidation and collapse. For each CT, signed distance transforms from segmentations of the lungs and main airways were generated, and the Frangi vesselness map was calculated. These were concatenated into multi-channel images and diffeomorphic multichannel registration was performed for each image pair using NiftyReg. Traditional intensity-based registrations were also performed for comparison purposes. For the evaluation, the pre- and post-registration landmark distance was calculated for all patients, using an average of 44 manually identified landmark pairs per patient. The mean (standard deviation) distance for all datasets decreased from 15.95 (8.09) mm pre-registration to 4.56 (5.70) mm post-registration, compared to 7.90 (8.97) mm for the intensity-based registrations. Qualitative improvements in image alignment were observed for all patient datasets. For four representative subjects, registrations were performed for three additional follow-up timepoints up to 48 months post-RT and similar accuracy was achieved. We have demonstrated that our novel multichannel registration method can successfully align longitudinal scans from RILD patients in the presence of large anatomical changes such as consolidation and atelectasis, outperforming the traditional registration approach both quantitatively and through thorough visual inspection.
Deep learning multimodal fNIRS and EEG signals for bimanual grip force decoding
Authors: Ortega Pablo , Faisal A Aldo
Published: August 2021

Objective. Non-invasive brain-machine interfaces (BMIs) offer an alternative, safe and accessible way to interact with the environment. To enable meaningful and stable physical interactions, BMIs need to decode forces. Although previously addressed in the unimanual case, controlling forces from both hands would enable BMI-users to perform a greater range of interactions. We here investigate the decoding of hand-specific forces. Approach. We maximise cortical information by using electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS) and developing a deep-learning architecture with attention and residual layers (cnnatt) to improve their fusion. Our task required participants to generate hand-specific force profiles on which we trained and tested our deep-learning and linear decoders. Main results. The use of EEG and fNIRS improved the decoding of bimanual force and the deep-learning models outperformed the linear model. In both cases, the greatest gain in performance was due to the detection of force generation. In particular, the detection of forces was hand-specific and better for the right dominant hand and cnnatt was better at fusing EEG and fNIRS. Consequently, the study of cnnatt revealed that forces from each hand were differently encoded at the cortical level. Cnnatt also revealed traces of the cortical activity being modulated by the level of force which was not previously found using linear models. Significance. Our results can be applied to avoid hand-cross talk during hand force decoding to improve the robustness of BMI robotic devices. In particular, we improve the fusion of EEG and fNIRS signals and offer hand-specific interpretability of the encoded forces which are valuable during motor rehabilitation assessment.
Ferroelectric semiconductor junctions based on graphene/In2Se3/graphene van der Waals heterostructures
Authors: Xie Shihong , Dey Anubhab , Yan Wenjing , Kudrynskyi Zakhar R , Balakrishnan Nilanthy , Makarovsky Oleg , Kovalyuk Zakhar D , Castanon Eli G , Kolosov Oleg , Wang Kaiyou , Patanè Amalia
Published: August 2021

The miniaturization of ferroelectric devices offers prospects for non-volatile memories, low-power electrical switches and emerging technologies beyond existing Si-based integrated circuits. An emerging class of ferroelectrics is based on van der Waals (vdW) two-dimensional materials with potential for nano-ferroelectrics. Here, we report on ferroelectric semiconductor junctions (FSJs) in which the ferroelectric vdW semiconductor α-In2Se3 is embedded between two single-layer graphene electrodes. In these two-terminal devices, the ferroelectric polarization of the nanometre-thick In2Se3 layer modulates the transmission of electrons across the graphene/In2Se3 interface, leading to memristive effects that are controlled by applied voltages and/or by light. The underlying mechanisms of conduction are examined over a range of temperatures and under light excitation revealing thermionic injection, tunnelling and trap-assisted transport. These findings are relevant to future developments of FSJs whose geometry is well suited to miniaturization and low-power electronics, offering opportunities to expand functionalities of ferroelectrics by design of the vdW heterostructure.
Preparation of high temperature sensible heat storage materials from reduced vanadium tailings and graphite
Authors: Piao Rongxun , Li Xuan , Zhao Peng
Published: August 2021

The experimental study on the preparation of high temperature (>500 °C) sensible heat storage materials (SHS) was conducted through the means of sintering method, in which vanadium tailings after carbothermic reduction used as the main matrix, graphite as the thermal conductivity modifier, and clay as the auxiliary material. The phase analysis by XRD shows that the main phases of the SHS materials without clay addition are aluminosilicate, sodium aluminoslicate, ilmenite and graphite, while additional phases of quartz and carbonate were observed if clay is added. With the graphite addition ranging from 0 to 15%, the density and hardness of the SHS materials without clay addition generally shows decreasing tendency while both properties behave increasing first and then decreasing in the SHS materials with clay addition. In addition, with increase of graphite, thermal conductivity of material without adding clay gradually increases in a range of 0.54 ∼ 1.54 W·m−1·K−1, while thermal conductivity of materials with adding clay remains unchanged first and then increases in the range of 0.754 ∼ 1.922 W·m−1·K−1.Thermal analysis shows that when the graphite content is 3 ∼ 5%, both SHS materials without or with clay have moderate specific heat capacity and high thermal capacity (>1.2 MJ m−3·K) at temperate above 500 °C, and high heat storage density (>200 kJ kg−1) in the temperature range of 500 °C ∼ 750 °C, indicating SHS materials prepared in this study can be considered for application in high temperature storage system.
Ce and Fe doped LaNiO3 synthesized by micro-emulsion route: Effect of doping on visible light absorption for photocatalytic application
Authors: Ghafoor Aamir , Bibi Ismat , Majid Farzana , Kamal Shagufta , Ata Sadia , Nazar Nosheen , Iqbal Munawar , Raza Muhammad A S , Almoneef Maha M
Published: August 2021

A series of La1−xCexNi1−yFeyO3 (x, y = 0.00–0.25) NPs was fabricated via micro-emulsion route and effect of doping was investigated on the basis of optical, photocatalytic and structural properties. The as-synthesized NPs were characterized via XRD, Raman analysis, SEM and UV–visible techniques. The XRD results confirmed the rhombohedral perovskite phase particles with particles of 60–80 nm range. UV–vis absorption edge showed significant red shift thereby tuning the band gap from 2.77 to 2.64 eV. The photocatalytic effectiveness of LaNiO3 and La0.80Ce0.20Ni0.80Fe0.20O3 catalysts was performed by degrading Congo red (CR) dye under visible light exposure. Substituted catalyst exhibited superior photodegradation by showing 97% degradation in comparison to pristine LaNiO3 (63% only) in 120 min. Degradation of CR followed the pseudo fist order kinetics. In addition, the catalyst dose effect, dye concentration and pH variation was studied for Cr dye degradation. Enhanced photocatalytic activity and narrow bandgap of Ce and Fe doped LaNiO3 introduce such materials as efficient visible active photocatalysts to be utilized in dye removal application from waste water and in photovoltaic applications, respectively.
Effects of surface activation time on Si-Si direct wafer bonding at room temperature
Authors: Yang Song , Qu Yongfeng , Deng Ningkang , Wang Kang , He Shi , Yuan Yuan , Hu Wenbo , Wu Shengli , Wang Hongxing
Published: August 2021

Surface activated bonding (SAB) based on argon ion beam irradiation was used to directly bond Si and Si wafers at room temperature, and the effects of the surface activation time on the Si-Si bonding were investigated. The experimental results show that the surface activation treatment with a proper duration is beneficial to the reduction of surface roughness of Si wafers and the realization of high bonding strength. The Si-Si wafers bonded after the surface activation of 420 s has an extremely low percentage of area covered by voids (0.08%) and a high bonding strength (9.45 MPa). Meanwhile, the annealing at 500 °C does not lead to a significant change in the percentage of area covered by voids for Si-Si bonding. Besides, the transmission electron microscope characterization indicates that the argon ion beam irradiation of 180 s can result in the formation of an amorphous Si layer with a thickness of approximately 10.6 nm at the Si-Si bonding interface, and the whole cross-section structure of the Si-Si bonding consists of a Si substrate, an amorphous Si layer and a Si substrate.
Sunscreens With High Versus Low Sun Protection Factor and Cutaneous Squamous Cell Carcinoma Risk: A Population-Based Cohort Study
Authors: Lergenmuller Simon , Ghiasvand Reza , Robsahm Trude E , Green Adele C , Lund Eiliv , Rueegg Corina S , Veierød Marit B
Published: August 2021

Evidence on sunscreen use and cutaneous squamous cell carcinoma (cSCC) risk is limited. Most studies have not taken sun protection factor (SPF) into consideration and used nonusers of sunscreen as the reference group. Nonusers are likely a priori at lower cSCC risk than users. No study has investigated the effect of high- versus low-SPF sunscreens on cSCC, appropriately adjusting for time-varying confounding. Using data from the Norwegian Women and Cancer Study (1991–2016), we investigated whether use of SPF ≥15 versus SPF <15 sunscreens reduces cSCC risk. We used a marginal structural Cox proportional hazards model with inverse probability of treatment and censoring weights to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). During follow-up of 148,781 women (mean follow-up, 14.3 years), 653 women were diagnosed with cSCC. The effect on cSCC risk of sunscreens with SPF ≥15 versus SPF <15 was close to the null when used at any latitudes (HR = 1.02, 95% CI: 0.82, 1.27) and when used in lower-latitude settings (HR = 1.05, 95% CI: 0.84, 1.32). In conclusion, we found no indication that sunscreens with SPF ≥15 reduced Norwegian women’s cSCC risk more than sunscreens with SPF <15, suggesting that either there is no difference in their effects long-term or the difference is diluted by incorrect application.
Prospects and challenges of cancer systems medicine: from genes to disease networks
Authors: Karimi Mohammad Reza , Karimi Amir Hossein , Abolmaali Shamsozoha , Sadeghi Mehdi , Schmitz Ulf
Published: August 2021

It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.
LipiDisease: associate lipids to diseases using literature mining
Authors: More Piyush , Bindila Laura , Wild Philipp , Andrade-Navarro Miguel , Fontaine Jean-Fred
Published: August 2021

Lipids exhibit an essential role in cellular assembly and signaling. Dysregulation of these functions has been linked with many complications including obesity, diabetes, metabolic disorders, cancer and more. Investigating lipid profiles in such conditions can provide insights into cellular functions and possible interventions. Hence the field of lipidomics is expanding in recent years. Even though the role of individual lipids in diseases has been investigated, there is no resource to perform disease enrichment analysis considering the cumulative association of a lipid set. To address this, we have implemented the LipiDisease web server. The tool analyzes millions of records from the PubMed biomedical literature database discussing lipids and diseases, predicts their association and ranks them according to false discovery rates generated by random simulations. The tool takes into account 4270 diseases and 4798 lipids. Since the tool extracts the information from PubMed records, the number of diseases and lipids will be expanded over time as the biomedical literature grows.

Availability and implementation

The LipiDisease webserver can be freely accessed at http://cbdm-01.zdv.uni-mainz.de:3838/piyusmor/LipiDisease/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting correlated outcomes from molecular data
Authors: Rauschenberger Armin , Glaab Enrico
Published: August 2021

Motivation

Multivariate (multi-target) regression has the potential to outperform univariate (single-target) regression at predicting correlated outcomes, which frequently occur in biomedical and clinical research. Here we implement multivariate lasso and ridge regression using stacked generalization.

Results

Our flexible approach leads to predictive and interpretable models in high-dimensional settings, with a single estimate for each input–output effect. In the simulation, we compare the predictive performance of several state-of-the-art methods for multivariate regression. In the application, we use clinical and genomic data to predict multiple motor and non-motor symptoms in Parkinson’s disease patients. We conclude that stacked multivariate regression, with our adaptations, is a competitive method for predicting correlated outcomes.

Availability and implementation

The R package joinet is available on GitHub (https://github.com/rauschenberger/joinet) and cran (https://cran.r-project.org/package=joinet).

Supplementary information

Supplementary data are available at Bioinformatics online.
Data Proliferation, Reconciliation, and Synthesis in Viral Ecology
Authors: Gibb Rory , Albery Gregory F , Becker Daniel J , Brierley Liam , Connor Ryan , Dallas Tad A , Eskew Evan A , Farrell Maxwell J , Rasmussen Angela L , Ryan Sadie J , Sweeny Amy , Carlson Colin J , Poisot Timothée
Published: August 2021

The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synthesis of host–virus data is a central challenge to characterize the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open database of mammal host–virus associations that reconciles four published data sets. We show that this offers a substantially richer view of the known virome than any individual source data set but also that databases such as these risk becoming out of date as viral discovery accelerates. We argue for a shift in practice toward the development, incremental updating, and use of synthetic data sets in viral ecology, to improve replicability and facilitate work to predict the structure and dynamics of the global virome.
Differential inflammatory profile of mesenteric and omental fat in patients with colorectal cancer
Authors: Ismaiel M. , Murphy B. , Hayes C. , O’Connell L. V. , Winter D. C.
Published: August 2021

Visceral obesity (mesenteric and omental adipose tissue) is a risk factor for colorectal cancer (CRC) and weight loss can reduce risk. This study examined mesenteric and omental fat activity in patients with CRC.
Surgical repair of diastasis recti abdominis provides long-term improvement of abdominal core function and quality of life: a 3-year follow-up
Authors: Olsson Anders , Kiwanuka Olivia , Wilhelmsson Sofia , Sandblom Gabriel , Stackelberg Otto
Published: August 2021

Background

Diastasis recti abdominis (DRA) is a condition affecting many post-partum women. The aim of this study was to evaluate long-term results of surgical repair of DRA in a cohort of post-partum women.

Methods

Sixty post-partum women with DRA and training-resistant core dysfunctions were included. Surgical repair was performed with suture plication of the linea alba. Abdominal core function was evaluated with the abdominal trunk function protocol (ATFP) including a self-report questionnaire and seven functional tests. Urinary incontinence and quality of life were evaluated with the Urogenital Distress Inventory (UDI-6), the Incontinence Impact Questionnaire (IIQ-7) and the SF-36 questionnaire. Follow-up was performed at 1 and 3 years after surgery.

Results

Response rate at the 3-year follow-up was 86.7 per cent for the disability rating index (DRI) questionnaire; and 71.7 per cent for the ATFP, UDI-6, IIQ-7 and SF-36 questionnaires. All DRI parameters were improved (P < 0.001) after 3 years of follow-up compared with preoperative values. The functional tests in the ATFP showed an improvement in core muscle strength and stability (P < 0.001), back muscle strength (P < 0.001) and abdominal muscle strength (P = 0.002) compared to preoperative values as well as an improvement of core muscle strength and stability compared with the 1-year follow-up values (P = 0.003). UDI-6 and IIQ-7 results were improved (P < 0.001 and P = 0.004) compared with preoperative values and showed consistent values compared with the 1-year follow-up (P = 0.09 and P = 1.0). Quality of life measured with SF-36 was improved compared with preoperative values and showed consistent values compared with the 1-year follow-up.

Conclusion

The functional improvement of surgical reconstruction of the DRA persisted for 3 years in this series of post-partum women with DRA.