bluuebunny/crossref_metadata_2025 huggingface dataset:
WHOCARES: WHOle-brain CArdiac signal REgression from highly accelerated simultaneous multi-Slice fMRI acquisitions
Authors: Colenbier Nigel , Marino Marco , Arcara Giorgio , Frederick Blaise , Pellegrino Giovanni , Marinazzo Daniele , Ferrazzi Giulio
Published: August 2022

Objective. To spatio-temporally resolve cardiac signals in functional magnetic resonance imaging (fMRI) time-series of the human brain using neither external physiological measurements nor ad hoc modelling assumptions. Approach. Cardiac pulsation is a physiological confound of fMRI time-series that introduces spurious signal fluctuations in proximity to blood vessels. fMRI alone is not sufficiently fast to resolve cardiac pulsation. Depending on the ratio between the instantaneous heart-rate and the acquisition sampling frequency (

1

/

TR

, with TR being the repetition time), the cardiac signal may alias into the frequency band of neural activation so that its removal through spectral filtering techniques is generally not possible. In this paper, we show that it is feasible to temporally and spatially resolve cardiac signals throughout the brain even when cardiac aliasing occurs by combining fMRI hyper-sampling with simultaneous multislice (SMS) imaging. The technique, which we name WHOle-brain CArdiac signal REgression from highly accelerated simultaneous multi-Slice fMRI acquisitions (WHOCARES), was developed on 695 healthy subjects selected from the Human Connectome Project and its performance validated against the RETROICOR, HAPPY and the pulse oxymeter signal regression methods. Main results. WHOCARES is capable of retrieving voxel-wise cardiac signal regressors. This is achieved without employing external physiological recordings nor through ad hoc modelling assumptions. The performance of WHOCARES was, on average, superior to RETROICOR, HAPPY and the pulse oxymeter regression methods. Significance. WHOCARES holds basis for the reliable mapping of cardiac activity in fMRI time-series. WHOCARES can be employed for the retrospective removal of cardiac noise in publicly available fMRI datasets where physiological recordings are not available. WHOCARES is freely available at https://github.com/gferrazzi/WHOCARES.
Asphalt Interface Based on Abaqus Asphalt Pavement Temperature Field and Aggregate Morphological Characteristics Measurement System
Authors: Ying Zhijun , Wang Huimin , Zhao Yunfei , Wu Zhihao , Shen Sili
Published: August 2022

To reveal the adhesion behavior of the aggregate - asphalt interface under water-temperature coupling, the temperature field of the asphalt pavement was simulated and analyzed based on Abaqus, and the morphology of the aggregate was analyzed using the Aggregate Morphological Characteristic Measurement System (AIMS II) to investigate the adhesion behavior of the asphalt interface under water-temperature coupling. The Abaqus software was used to study the temperature distribution pattern of the pavement structure of the dependent project and to construct a regional characteristic distribution model for Zhejiang Province. On this basis, aggregate texture shaping equipment was developed, aggregate morphological characteristics were tested with the aid of the Aggregate Morphological Characteristics Inspection System (AIMS II), the water immersion weighing method was used to evaluate the aggregate - asphalt interface adhesion, and the relationship between aggregate morphological characteristics and macroscopic adhesion was established. The study shows that there is a linear negative correlation between sphericity and mass loss rate, a linear positive correlation between gradient angles and mass loss rate, and an optimum value for aggregate surface texture. Using a modified 'sandwich' pulling test, four lithologies of limestone, basalt, granite and sandstone were selected to investigate the effect of environmental factors such as water and temperature on the adhesion of the aggregate to the asphalt interface. The results showed that the interfacial bonding performance of the aggregate and asphalt increased as the heating temperature of the aggregate increased, while the interfacial bonding performance of the aggregate and asphalt weakened as the water immersion time increased. The research results have certain theoretical guidance significance for enhancing the water damage resistance of asphalt mixes.
Investigation and Improvement of Switching Characteristics of SiC Optically Controlled Transistor
Authors: Zhang Yingying
Published: August 2022

Aiming to the switching characteristics of SiC optically controlled transistor, SiC NPN optically controlled transistor was investigated through Silvaco TCAD. The results show that under 4500V bias voltage, the turn-on and turn-off dV/dt of the SiC transistor are 428.5V/ns and 23.9V/ns, respectively. And the tailing problem in the turn-off process is obvious. In order to improve the switching characteristics of SiC optically controlled transistor, the minority carrier lifetime in base layer is regional controlled. The simulation results indicate that, by using minority carrier lifetime control technology, the turn-off time and turn-off dV/dt are improved by about 28.2% and 39.3%, respectively. Meanwhile, turn-on time and turn-on dV/dt are only degenerated by about 3.6% and 3.4%, respectively. The overall level of switching characteristics of SiC optically controlled transistor are improved.
The silicon vertex detector of the Belle II experiment
Authors: Dujany G. , Adamczyk K. , Aggarwal L. , Aihara H. , Aziz T. , Bacher S. , Bahinipati S. , Batignani G. , Baudot J. , Behera P.K. , Bettarini S. , Bilka T. , Bozek A. , Buchsteiner F. , Casarosa G. , Corona L. , Czank T. , Das S.B. , Finck C. , Forti F. , Friedl M. , Gabrielli A. , Ganiev E. , Gobbo B. , Halder S. , Hara K. , Hazra S. , Higuchi T. , Irmler C. , Ishikawa A. , Jeon H.B. , Jin Y. , Joo C. , Kaleta M. , Kaliyar A.B. , Kandra J. , Kang K.H. , Kapusta P. , Kodyš P. , Kohriki T. , Kumar M. , Kumar R. , La Licata C. , Lalwani K. , Leboucher R. , Lee S.C. , Libby J. , Martel L. , Massaccesi L. , Mayekar S.N. , Mohanty G.B. , Morii T. , Nakamura K.R. , Natkaniec Z. , Onuki Y. , Ostrowicz W. , Paladino A. , Paoloni E. , Park H. , Polat L. , Rao K.K. , Ripp-Baudot I. , Rizzo G. , Sahoo D. , Schwanda C. , Serrano J. , Suzuki J. , Tanaka S. , Tanigawa H. , Thalmeier R. , Tiwari R. , Tsuboyama T. , Uematsu Y. , Verbycka O. , Vitale L. , Wan K. , Wang Z. , Webb J. , Wiechczynski J. , Yin H. , Zani L.
Published: August 2022

In 2019 the Belle II experiment started data taking at the asymmetric SuperKEKB collider (KEK, Japan) operating at the Y(4S) resonance. Belle II will search for new physics beyond the standard model by collecting an integrated luminosity of 50 ab−1. The silicon vertex detector (SVD), consisting of four layers of double-sided silicon strip sensors, is one of the two vertex sub-detectors. The SVD extrapolates the tracks to the inner pixel detector (PXD) with enough precision to correctly identify hits in the PXD belonging to the track. In addition the SVD has standalone tracking capability and utilizes ionization to enhance particle identification in the low momentum region. The SVD is operating reliably and with high efficiency, despite exposure to the harsh beam background of the highest peak-luminosity collider ever built. High signal-to-noise ratio and hit efficiency have been measured, as well as the spatial resolution; all these quantities show excellent stability over time. Data-simulation agreement on cluster properties has recently been improved through a careful tuning of the simulation. The precise hit-time resolution can be exploited to reject out-of-time hits induced by beam background, which will make the SVD more robust against higher levels of background. During the first three years of running, radiation damage effects on strip noise, sensor currents and depletion voltage have been observed, as well as some coupling capacitor failure due to intense radiation bursts. None of these effects cause significant degradation in the detector performance.
A 14 Gbps VCSEL driving ASIC in 55 nm for NICA multi purpose detector project
Authors: Zhao C. , Chen Q. , Guo Z. , Arteche R. , Ceballos C. , Fang N. , Gan Y. , Murin Y. , Yi L. , Guo D. , Sun X.
Published: August 2022

This paper presents the design and the test results of a 14 Gbps VCSEL driving ASIC with a novel output driver structure fabricated in a 55 nm CMOS process. It consists of an equalizer stage, a limiting amplifier stage and an output driver stage. The equalizer stage uses the CTLE structure to compensate the high frequency losses at the PCB traces, bonding wires and input pads. To meet both the gain/bandwidth requirements and the area restriction, the limiting amplifier stage adopts the inductor-shared peaking technology. To increase the voltage headroom of the output driver stage and improve the bandwidth, a novel output driver structure using the on-chip AC coupling, the stacked current source and the double feedforward compensation technique is proposed. This ASIC has been integrated with the VCSEL array in a customized optical module for the optical test. The test results show the wide-open 14 Gbps optical eye diagram with a measured RMS jitter of 2.7 ps and a peak-to-peak jitter of 17.4 ps, respectively.
Upgrade of the 4-rod radio frequency quadrupole for SARAF Phase II Linac
Authors: Kaizer B. , Barak A. , Buzaglo Y. , Dafna H. , Farber E. , Gavish I. , Goldberger N. , Kreisel A. , Pami H. , Perry A. , Rodnizki J. , Reinfeld E. , Tamim N. , Zchut T. , Weiss R. , Weissman L.
Published: August 2022

The 176 MHz 4-rod radiofrequency quadrupole (RFQ) is the crucial part of the Soreq Applied Research Accelerator Facility (SARAF) injector and must be able to operate at RF powers up to 190 kW continuous wave and transport 5 mA proton and deuteron beams. The SARAF Phase I RFQ is planned for use in Phase II. The period between the termination of Phase I and the installation of Phase II provided an opportunity to introduce RFQ improvements to fully meet the Phase II requirements. These upgrades and improvements are presented in this report together with the results of the recent conditioning campaigns.
Higher levels of no-till agriculture associated with lower PM2.5 in the Corn Belt
Authors: Behrer A Patrick , Lobell David
Published: August 2022

No-till approaches to agricultural soil management have been encouraged as a means of reducing soil erosion, reducing water pollution, and increasing carbon sequestration. An understudied additional benefit of no-till approaches may be improvements in local air quality. No-till approaches involve reductions in both machinery use and soil erosion, both of which could lead to improvements in air quality. We leverage recent advances in remote sensing and air pollution modelling to examine this question at a landscape scale. Combining data on daily PM2.5 levels with satellite measures of no-till uptake since 2005, we show a strong association between increasing adoption of no-till and reductions in county average PM2.5 pollution over more than 28 million hectares of cropland in the American Corn Belt. The reduction in local pollution implies substantial monetary benefits from reductions in mortality that are roughly one-fourth as large as the estimated carbon benefits. The benefits of mortality reductions are also, by themselves, nearly equal to the current monetary costs of subsidizing no-till practices.
Digital quantum simulation, learning of the Floquet Hamiltonian, and quantum chaos of the kicked top
Authors: Olsacher Tobias , Pastori Lorenzo , Kokail Christian , Sieberer Lukas M , Zoller Peter
Published: August 2022

The kicked top is one of the paradigmatic models in the study of quantum chaos (Haake et al 2018 Quantum Signatures of Chaos (Springer Series in Synergetics vol 54)). Recently it has been shown that the onset of quantum chaos in the kicked top can be related to the proliferation of Trotter errors in digital quantum simulation (DQS) of collective spin systems. Specifically, the proliferation of Trotter errors becomes manifest in expectation values of few-body observables strongly deviating from the target dynamics above a critical Trotter step, where the spectral statistics of the Floquet operator of the kicked top can be predicted by random matrix theory. In this work, we study these phenomena in the framework of Hamiltonian learning (HL). We show how a recently developed HL protocol can be employed to reconstruct the generator of the stroboscopic dynamics, i.e., the Floquet Hamiltonian, of the kicked top. We further show how the proliferation of Trotter errors is revealed by HL as the transition to a regime in which the dynamics cannot be approximately described by a low-order truncation of the Floquet–Magnus expansion. This opens up new experimental possibilities for the analysis of Trotter errors on the level of the generator of the implemented dynamics, that can be generalized to the DQS of quantum many-body systems in a scalable way. This paper is in memory of our colleague and friend Fritz Haake.
Acoustic radiation from random waves on plates
Authors: Mohammed Neekar M , Creagh Stephen C , Tanner Gregor
Published: August 2022

Controlling and simulating the sound radiating from complex structures is of importance in many engineering applications. We calculate the radiated acoustic power from plates with diffuse bending vibrations. We characterise the diffuse field by a two-point correlation function (CF) of normal velocities. Given the relation between field–field CFs and ray-dynamical phase space densities, the approach taken here offers a basis for coupling structure borne ray-tracing techniques with acoustic radiation. At the same time, it caters for stochastic, noisy driving of such systems. The results for the radiation efficiency of a plate are presented in an asymptotic form analogous to the Weyl formula for the density of states. Leading contributions from the plate interior and its boundary are derived, with corner corrections also being given for particular boundary conditions and right-angled corners. A notable feature of this analysis is that the bulk contribution vanishes below a critical frequency, and the asymptotic estimate of radiated power then leads with a boundary contribution. This is shown to agree well with a more traditional calculation based on modal analysis in the special case of a rectangular plate.
Highly durable superhydrophobic surfaces based on a protective frame and crosslinked PDMS-candle soot coatings
Authors: Sun Wenwen , Lv Kai , Lou Yisha , Zeng Dongdong , Lin Xiangde
Published: August 2022

Superhydrophobic surfaces can be applied to environmental, energy, and healthcare fields. However, the weak durability issue has significantly limited the practical industrial applications. To overcome the readily destroyed interfacial structures and chemical compositions, the superhydrophobic surfaces with high mechanical and chemical durability have been created on a stainless steel mesh (SSM) as a protective frame based on tightly crosslinked polydimethylsiloxane (PDMS)−candle soot (CS) composite coatings through simple mechanical transfer and candle burning processes, which abbreviated to SSM/PDMS−CS and showed a water contact angle (WCA) of 159.4° ± 1.6° and a sliding angle (SA) of 2.3° ± 0.5°. Harsh abrasion examinations based on sandpaper and fiber paper have been conducted by applying 100 g weight and 200 cm sliding distance. And the obtained WCAs and SAs were 155° ± 3.7°, 155.7° ± 2° and 3.7° ± 0.5°, 3.5° ± 0.3°. Scanning electron microscope showed scratches on the surface, but the superhydrophobic property has been well maintained. After 40 kHz ultrasonication treatment for 30 min, WCA and SA were 152° ± 0.9° and 4.1° ± 0.8°. Finally, SSM/PDMS−CS surfaces exhibit good chemical resistance to corrosive solutions even after pH 2, pH 10, 1 M NaCl, and toluene treatments for 15 days.
Geometrical model of 3D layer-to-layer angle-interlock woven preforms with oblique structure
Authors: Huang Zhaohua , Ma Wensuo , Jia Chenhui , Lei Xianqing , Zhang Zhuangya
Published: August 2022

The original configuration of 3D layer-to-layer angle-interlock (LLA) woven fibers cannot be maintained during matrix impregnation and is unstable when the composite is subjected to loading. The fibers in the yarn are susceptible to lateral sliding, resulting in deformation of the textile geometry. The initial modulus of the composite in the warp direction is smaller and can be inconsistent owing to the unstable geometry of the fabric. A stable 3D layer-to-layer angle-interlock (SLLA) fabric was devised by constructing a denser yarn arrangement, and the properties of this new structure were investigated in this study. The geometric parameters of this novel reinforcing structure were mathematically modeled, and the results were validated experimentally. The results showed that the SLLA structure was more stable than that of the LLA fabric. The experimentally determined structural parameters were in good agreement with the theoretically calculated values.
Entangled microwave photons generation using cryogenic low noise amplifier (transistor nonlinearity effects)
Authors: Salmanogli Ahmad
Published: August 2022

This article mainly focuses on important quantum phenomenon called entanglement arising the nonlinearity property. This study uses a unique approach in which transistor nonlinearity effect (third-order nonlinearity) entangled microwave photons are created in a cryogenic low-noise amplifier (LNA). For entanglement analysis, the Hamiltonian of the designed cryogenic LNA (containing two coupled oscillators) is derived, and then, using the dynamic equation of motion, the oscillator’s number of photons and the phase-sensitive cross-correlation factor are calculated in the Fourier domain to calculate the entanglement metric. The oscillators are coupled to each other through the gate–drain capacitor, and nonlinear transconductance is as an important factor strongly manipulating the entanglement. As a main conclusion, the study shows that the designed circuit using transistor third-order nonlinearity has the ability to generate the entangled microwave photons at very low intrinsic transconductance and more importantly when the noise figure (NF) is strongly minimized. As a complementary task, the printed circuit board of the cryogenic LNA is designed and simulated to verify the ability of the circuit to achieve an ultralow NF, by which the probability of the generation of entangled microwave photons is increased.
Geometrical interpretation of the argument of weak values of general observables in N-level quantum systems
Authors: Ballesteros Ferraz Lorena , Lambert Dominique L , Caudano Yves
Published: August 2022

Observations in quantum weak measurements are determined by complex numbers called weak values. We present a geometrical interpretation of the argument of weak values of general Hermitian observables in N-dimensional quantum systems in terms of geometric phases. We formulate an arbitrary weak value in terms of three real vectors on the unit sphere in N
2 − 1 dimensions,

S

N

2

−
2

. These vectors are linked to the initial and final states, and to the weakly measured observable, respectively. We express pure states in the complex projective space of N − 1 dimensions,

C

P

N
−
1

, which has a non-trivial representation as a 2N − 2 dimensional submanifold of

S

N

2

−
2

(a generalization of the Bloch sphere for qudits). The argument of the weak value of a projector on a pure state of an N-level quantum system describes a geometric phase associated to the symplectic area of the geodesic triangle spanned by the vectors representing the pre-selected state, the projector and the post-selected state in

C

P

N
−
1

. We then proceed to show that the argument of the weak value of a general observable is equivalent to the argument of an effective Bargmann invariant. Hence, we extend the geometrical interpretation of projector weak values to weak values of general observables. In particular, we consider the generators of SU(N) given by the generalized Gell–Mann matrices. Finally, we study in detail the case of the argument of weak values of general observables in two-level systems and we illustrate weak measurements in larger dimensional systems by considering projectors on degenerate subspaces, as well as Hermitian quantum gates. To conclude, we discuss the interpretation and usefulness of geometric phases in weak values in connection to weak measurements.
Effect of various discontinuities present in a plate on stress concentration: a review
Authors: Patel Rashmiben H , Patel Bhaveshkumar P
Published: August 2022

The stress concentration factor is one of the most significant factors in design engineering in the modern era with lots of objectives across the world. Stress concentration is the localization of high stresses primarily due to discontinuities within the time, abrupt changes in cross-section, and contact with stresses. This paper focuses on a problem with different discontinuities as specially holes present in a plate like isotropic, anisotropic and orthotropic etc. The different methods used by various authors to evaluate stress concentration with different related parameters, and describes the study related to their results carried out by them. Finite plate with polygonal, circular, inclined circular, elliptical types holes has been considered as one of the most important design application in present era. In the present work, the analysis and reviews are based on the following (a) types of discontinuities, (b) types of loading, (c) material/composites/plies (d) orientation of discontinuities in a finite plate. Finally, the scope of this research work is incorporated.
A geometric study for determining the optimum volume fraction of pre-embedded capsules for self-healing of cracks in a cementitious matrix
Authors: Alghamri R , Jahjouh M , Alastal K , Al-Tabbaa A
Published: August 2022

Autonomous healing of cracks using capsule-based systems is emerging as a promising solution to restore durability and strength of damaged structures. For satisfactory self-healing efficiency, both capsule geometry and dosage are to be determined for the concrete mix proportion. With previous research being performed on self-healing efficiency using different capsule shapes and crack patterns, this paper introduces quantitative numerical solutions on the optimal dosage of the capsules required to completely repair cracks in a three-dimensional model of a cementitious matrix. Four different sizes of spherical capsules ranging between 0.6 mm to 4.75 mm embedded within a mortar matrix were tested in the model and the model results were validated using previous experimental findings. As the cargo of capsules could be powder or liquid self-healing agents, three different scenarios were considered in this work to calculate the volume of the healing agent in the crack. It was found that the smaller the capsules the more homogenous and uniform the distribution of capsules is. However, the bigger sizes of the capsules are much preferable in terms of the amount of self-healing materials supplied to the cracked vicinity. For instance, capsules of 2–4 mm size could fill 80% of the crack volume but were localised and unevenly distributed on the planes of the crack. Overall, the developed model in this study provides a robust and efficient tool to quantitively design the proportions of cement-based self-healing systems. Based on the results of the geometric model, an ANN model was also developed to calculate healing volume in terms of the volume fraction of the healing agents and the size of capsules. Results showed very close values to those obtained by the numerical model.
Exceptional surgeries in 3-manifolds
Authors: Baker Kenneth , Hoffman Neil
Published: August 2022

Myers shows that every compact, connected, orientable

3
3

-manifold with no

2
2

-sphere boundary components contains a hyperbolic knot. We use work of Ikeda with an observation of Adams-Reid to show that every

3
3

-manifold subject to the above conditions contains a hyperbolic knot which admits a non-trivial non-hyperbolic surgery, a toroidal surgery in particular. We conclude with a question and a conjecture about reducible surgeries.
Plants and water: the search for a comprehensive understanding
Authors: Rockwell Fulton , Sage Rowan F
Published: August 2022

We learn early in life sciences classes that water is the solution of life, working in tandem with carbon to make life as we know it possible. Globally, the abundance of water can be misleading, as most of this water is unavailable, being overly salinized in the oceans or locked in deep underground reserves. On land, the critical supply is of freshwater, which is unevenly distributed in space and time. Even the wettest environments can experience episodic water deficit, and flash flooding periodically occurs in arid landscapes. While humanity can capture, store and transport freshwater over large distances to ensure sustained supply, such options are not apparent for plants except in an immediate local context. Plants must make do with the water in their immediate surroundings, whether it be abundant or scarce. How they do this has led to a myriad of adaptive solutions, involving capturing, storing and transporting water. The traits that enable them to optimize water use in a range of hydraulic environments, subject to multivariate selective constraints, are the essence of the discipline of plant–water relations.
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data
Authors: Zhang Shuangquan , Yang Lili , Wu Xiaotian , Sheng Nan , Fu Yuan , Ma Anjun , Wang Yan
Published: August 2022

Motivation

Transcription factor binding sites (TFBSs) prediction is a crucial step in revealing functions of transcription factors from high-throughput sequencing data. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) provides insight on TFBSs and nucleosome positioning by probing open chromatic, which can simultaneously reveal multiple TFBSs compare to traditional technologies. The existing tools based on convolutional neural network (CNN) only find the fixed length of TFBSs from ATAC-seq data. Graph neural network (GNN) can be considered as the extension of CNN, which has great potential in finding multiple TFBSs with different lengths from ATAC-seq data.

Results

We develop a motif predictor called MMGraph based on three-layer GNN and coexisting probability of k-mers for finding multiple motifs from ATAC-seq data. The results of the experiment which has been conducted on 88 ATAC-seq datasets indicate that MMGraph has achieved the best performance on area of eight metrics radar score of 2.31 and could find 207 higher-quality multiple motifs than other existing tools.

Availability and implementation

MMGraph is wrapped in Python package, which is available at https://github.com/zhangsq06/MMGraph.git

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting cancer drug response using parallel heterogeneous graph convolutional networks with neighborhood interactions
Authors: Peng Wei , Liu Hancheng , Dai Wei , Yu Ning , Wang Jianxin
Published: August 2022

Motivation

Due to cancer heterogeneity, the therapeutic effect may not be the same when a cohort of patients of the same cancer type receive the same treatment. The anticancer drug response prediction may help develop personalized therapy regimens to increase survival and reduce patients’ expenses. Recently, graph neural network-based methods have aroused widespread interest and achieved impressive results on the drug response prediction task. However, most of them apply graph convolution to process cell line-drug bipartite graphs while ignoring the intrinsic differences between cell lines and drug nodes. Moreover, most of these methods aggregate node-wise neighbor features but fail to consider the element-wise interaction between cell lines and drugs.

Results

This work proposes a neighborhood interaction (NI)-based heterogeneous graph convolution network method, namely NIHGCN, for anticancer drug response prediction in an end-to-end way. Firstly, it constructs a heterogeneous network consisting of drugs, cell lines and the known drug response information. Cell line gene expression and drug molecular fingerprints are linearly transformed and input as node attributes into an interaction model. The interaction module consists of a parallel graph convolution network layer and a NI layer, which aggregates node-level features from their neighbors through graph convolution operation and considers the element-level of interactions with their neighbors in the NI layer. Finally, the drug response predictions are made by calculating the linear correlation coefficients of feature representations of cell lines and drugs. We have conducted extensive experiments to assess the effectiveness of our model on Cancer Drug Sensitivity Data (GDSC) and Cancer Cell Line Encyclopedia (CCLE) datasets. It has achieved the best performance compared with the state-of-the-art algorithms, especially in predicting drug responses for new cell lines, new drugs and targeted drugs. Furthermore, our model that was well trained on the GDSC dataset can be successfully applied to predict samples of PDX and TCGA, which verified the transferability of our model from cell line in vitro to the datasets in vivo.

Availability and implementation

The source code can be obtained from https://github.com/weiba/NIHGCN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Isoform function prediction by Gene Ontology embedding
Authors: Qiu Sichao , Yu Guoxian , Lu Xudong , Domeniconi Carlotta , Guo Maozu
Published: August 2022

Motivation

High-resolution annotation of gene functions is a central task in functional genomics. Multiple proteoforms translated from alternatively spliced isoforms from a single gene are actual function performers and greatly increase the functional diversity. The specific functions of different isoforms can decipher the molecular basis of various complex diseases at a finer granularity. Multi-instance learning (MIL)-based solutions have been developed to distribute gene(bag)-level Gene Ontology (GO) annotations to isoforms(instances), but they simply presume that a particular annotation of the gene is responsible by only one isoform, neglect the hierarchical structures and semantics of massive GO terms (labels), or can only handle dozens of terms.

Results

We propose an efficacy approach IsofunGO to differentiate massive functions of isoforms by GO embedding. Particularly, IsofunGO first introduces an attributed hierarchical network to model massive GO terms, and a GO network embedding strategy to learn compact representations of GO terms and project GO annotations of genes into compressed ones, this strategy not only explores and preserves hierarchy between GO terms but also greatly reduces the prediction load. Next, it develops an attention-based MIL network to fuse genomics and transcriptomics data of isoforms and predict isoform functions by referring to compressed annotations. Extensive experiments on benchmark datasets demonstrate the efficacy of IsofunGO. Both the GO embedding and attention mechanism can boost the performance and interpretability.

Availabilityand implementation

The code of IsofunGO is available at http://www.sdu-idea.cn/codes.php?name=IsofunGO.

Supplementary information

Supplementary data are available at Bioinformatics online.
Streaming books: confluencers, Kindle Unlimited and the platform imaginary
Authors: Larson Christine
Published: August 2022

The Kindle’s 2007 launch transformed one of the oldest breeds of creative workers—authors—into one of the newest: platformized cultural producers. Although most research on such workers focuses on careers birthed by social media (i.e., influencers, YouTube creators), many cultural producers work in legacy industries where traditional and platformized practices coexist, come together and influence each other (i.e., publishing, music, film). Both groups—born-digital and “confluencers”—must negotiate precarious labor conditions, but confluencers can draw on both digital and pre-digital networks and traditions to do so. This project shows how one such group—indie romance authors—draws on its history to create collective imaginaries regarding Kindle Unlimited (KU). These imaginaries offer an emergent, if weak, base of resistance to Amazon’s platform power. I contribute to literature on platformized cultural production by: (a) distinguishing among groups of platformized producers; and (b) showing how historic context informs strategies for negotiating platform power.
Comparison of safety and outcomes related to remdesivir treatment among dialysis patients hospitalized with COVID-19
Authors: Zaki Kirollos E , Huang Cheng-Wei , Zhou Hui , Chung Joanie , Selevan David C , Rutkowski Mark P , Sim John J
Published: August 2022

Background

Patients with end-stage kidney disease (ESKD) are highly susceptible to coronavirus disease 2019 (COVID-19) infection and its complications. Remdesivir has improved outcomes in COVID-19 patients but its use has been limited among ESKD patients due to insufficient data regarding safety outcomes. We sought to evaluate the safety of remdesivir among dialysis patients hospitalized with COVID-19.

Methods

This retrospective cohort study was conducted among patients age ≥18 years on maintenance dialysis and hospitalized with COVID-19 between 1 May 2020 and 31 January 2021 within an integrated health system who were treated or not treated with remdesivir. The primary outcome was 30-day all-cause mortality. Secondary outcomes were intensive care unit (ICU) stay, and transaminitis (AST/ALT >5× normal). Pseudo-populations were created using inverse probability of treatment weights with propensity scoring to balance patient characteristics among the two groups. Multivariable Poisson regression with robust error was performed to estimate 30-day mortality risk ratio.

Results

A total of 486 (407 hemodialysis and 79 peritoneal dialysis) patients were hospitalized with COVID-19, among which 112 patients (23%) were treated with remdesivir [median treatment four days (interquartile range 2–5)]. The 30-day mortality rate was 24.1% among remdesivir-treated and 27.8% among non-treated patients. The estimated 30-day mortality rate was 0.74 (95% confidence interval 0.52–1.05) among remdesivir treated compared with non-treated patients. Liver injury and ICU admission rates were 1.8% and 14.3% among remdesivir-treated patients compared with 2.4% and 16% among non-treated patients.

Conclusion

Among dialysis patients hospitalized with COVID-19, remdesivir was not associated with higher rates of liver injury or ICU admissions, and demonstrated a trend toward lower 30-day mortality.
Chronic kidney disease as cardiovascular risk factor in routine clinical practice: a position statement by the Council of the European Renal Association
Authors: Ortiz Alberto , Wanner Christoph , Gansevoort Ron ,   ERA Council, Ortiz Alberto , Wanner Christoph , Gansevoort Ron T , Cozzolino Mario , Fliser Danilo , Gambaro Giovanni , Ong Albert , Rosenkranz Alexander R , Rychlık Ivan , Sarafidis Pantelis , Torra Roser , Tuglular Serhan
Published: August 2022

The European Society of Cardiology 2021 guideline on cardiovascular (CV) disease (CVD) prevention in clinical practice has major implications for both CV risk screening and kidney health of interest to primary care physicians, cardiologists, nephrologists, and other professionals involved in CVD prevention. The proposed CVD prevention strategies require as first step the categorization of individuals into those with established atherosclerotic CVD, diabetes, familiar hypercholesterolaemia, or chronic kidney disease (CKD), i.e. conditions that are already associated with a moderate to very-high CVD risk. This places CKD, defined as decreased kidney function or increased albuminuria as a starting step for CVD risk assessment. Thus, for adequate CVD risk assessment, patients with diabetes, familiar hypercholesterolaemia, or CKD should be identified by an initial laboratory assessment that requires not only serum to assess glucose, cholesterol, and creatinine to estimate the glomerular filtration rate, but also urine to assess albuminuria. The addition of albuminuria as an entry-level step in CVD risk assessment should change clinical practice as it differs from the current healthcare situation in which albuminuria is only assessed in persons already considered to be at high risk of CVD. A diagnosis of moderate of severe CKD requires a specific set of interventions to prevent CVD. Further research should address the optimal method for CV risk assessment that includes CKD assessment in the general population, i.e. whether this should remain opportunistic screening or whether systematic screening.
Genome assembly of the chemosynthetic endosymbiont of the hydrothermal vent snailAlviniconcha adamantisfrom the Mariana Arc
Authors: Breusing Corinna , Klobusnik Nathan Hagen , Hauer Michelle A , Beinart Roxanne A
Published: August 2022

Chemosynthetic animal-microbe symbioses sustain hydrothermal vent communities in the global deep sea. In the Indo-Pacific Ocean, hydrothermal ecosystems are often dominated by gastropod species of the genus Alviniconcha, which live in association with chemosynthetic Gammaproteobacteria or Campylobacteria. While the symbiont genomes of most extant Alviniconcha species have been sequenced, no genome information is currently available for the gammaproteobacterial endosymbiont of Alviniconcha adamantis—a comparatively shallow living species that is thought to be the ancestor to all other present Alviniconcha lineages. Here, we report the first genome sequence for the symbiont of A. adamantis from the Chamorro Seamount at the Mariana Arc. Our phylogenomic analyses show that the A. adamantis symbiont is most closely related to Chromatiaceae endosymbionts of the hydrothermal vent snails Alviniconcha strummeri and Chrysomallon squamiferum, but represents a distinct bacterial species or possibly genus. Overall, the functional capacity of the A. adamantis symbiont appeared to be similar to other chemosynthetic Gammaproteobacteria, though several flagella and chemotaxis genes were detected, which are absent in other gammaproteobacterial Alviniconcha symbionts. These differences might suggest potential contrasts in symbiont transmission dynamics, host recognition, or nutrient transfer. Furthermore, an abundance of genes for ammonia transport and urea usage could indicate adaptations to the oligotrophic waters of the Mariana region, possibly via recycling of host- and environment-derived nitrogenous waste products. This genome assembly adds to the growing genomic resources for chemosynthetic bacteria from hydrothermal vents and will be valuable for future comparative genomic analyses assessing gene content evolution in relation to environment and symbiotic lifestyles.
Estimated Pulse Wave Velocity and All-Cause Mortality: Findings From the Health and Retirement Study
Authors: Heffernan Kevin S , Wilmoth Janet M , London Andrew S
Published: August 2022

Background and Objectives

The gold standard method for the assessment of vascular aging is carotid–femoral pulse wave velocity (cfPWV). cfPWV can be estimated from 2 commonly assessed clinical variables—age and blood pressure. This analysis uses data from the Health and Retirement Study to examine the relationship between estimated pulse wave velocity (ePWV) and mortality among 9,293 middle age and older adults.

Research Design and Methods

Cox proportional hazard models were used to predict mortality occurring over a 10- to 12-year period. Controls were included for sociodemographic characteristics (age, gender, race, ethnicity, wealth, income, and education), health status (history of cardiovascular disease [CVD], diabetes, and stroke and related medication use), health behaviors (smoking, physical activity, and body mass index), and CVD-related biomarkers (systolic and diastolic blood pressure, C-reactive protein, cystatin c, hemoglobin A1c, total cholesterol, and high-density lipoprotein cholesterol).

Results

By 2018, 26.19% of the weighted analytic sample were reported as deceased. In the fully specified models that control for age, age-squared, systolic and diastolic blood pressure, sociodemographic variables, health status and behaviors, and biomarkers, ePWV was associated with a greater likelihood of mortality.

Discussion and Implications

An estimate of PWV derived from age and blood pressure is independently associated with an increased likelihood of death in a representative sample of middle age and older adults in the United States.
Association between SLICC/ACR damage index and outcomes for lupus patients after cardiac valve surgery
Authors: Hu Szu-Yen , Cheng Chiao-Feng , Yang Kelvin Jeason , Wang Chih-Hsien , Chi Nai-Hsin , Hsu Ron-Bin , Chen Yih-Sharng , Yu Hsi-Yu
Published: August 2022

Systemic lupus erythematosus (SLE) is associated with multi-organ damage including cardiac valve, which may need valvular operation. However, methods for outcome prediction and prosthetic valve selection are unclear in SLE patients undergoing cardiac valve surgery. Twenty-five SLE patients receiving valvular operation in a single institute between 2002 and 2020 were enrolled. Systemic Lupus International Collaborative Clinics/American College of Rheumatology Damage Index (SLICC/ACR damage index, SDI) was applied to evaluate the damage severity. Clinical outcomes were compared between patients with different SDI. The hospital survival rate was 88%, and long-term survival rate was 59.5% and 40.2% at 5 and 10 years. The median SDI was 4 (interquartile range 3–6) in our study, patients were then grouped into higher SDI (defined as SDI ≥ 5, n = 11) and lower SDI group (defined as SDI < 5, n = 14). The in-hospital survival rate (72.2% vs 100%, P = 0.074) and 5-year survival rate (18.2% vs 92.9%, P < 0.001) were lower in higher SDI group, compared to lower SDI group. SDI score was associated with long-term outcome for SLE patients receiving cardiac valve surgery. SDI ≥ 5 was associated with very poor long-term outcomes. This finding implicates that xenograft might be a reasonable choice for SLE patients with SDI ≥ 5.
Carbon sink price prediction based on radial basis kernel function support vector machine regression model
Authors: Yang Xing , Mi Jun-long , Jiang Jin , Li Jia-wen , Zhang Quan-shen , Geng Meng-meng
Published: August 2022

At present, the main pricing methods for carbon sink trading are marginal cost pricing, shadow price pricing and physical option pricing. The most serious defect of these three methods is that their theoretical basis is the extremely idealized effective market hypothesis, which obviously does not conform to the fractal and chaotic behavior characteristics of the actual carbon sink trading market. It is particularly important to study new pricing technologies and methods for a complex, nonlinear and dissipative system. Therefore, this paper constructs a carbon sink price prediction method based on the radial basis kernel function support vector machine (RBF-SVM) model. The main findings are the following:

• Compared with the build nonlinear support vector machine (SVM) models by the three kernel functions: linear kernel function (LF), radial basis function (RBF) and sigmoid kernel function, the RBF-SVM has the highest prediction accuracy.

• The adaptability of the RBF-SVM model is tested by using the price fluctuation data of EU allowance (EUA). It is proved that the adaptability of the RBF-SVM model for the price predictions of heterogeneous carbon products is also excellent.

• The forecast results of the RBF-SVM model for carbon sink price for the period of September 2021 to August 2022 show that the lowest carbon sink price of 20 euros is expected to occur around November 2021 and the highest price of 38.5 euros around August 2022.

Therefore, the established RBF-SVM model can be used for carbon sink trading market price prediction, which is more scientific and applicable than the previous three methods.
Genomic insights into the conservation and population genetics of two Chinese native goat breeds
Authors: Wang Xiaopeng , Li Guixin , Jiang Yongchuang , Tang Jianhong , Fan Yin , Ren Jun
Published: August 2022

Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats.
Purification and characterization of protease M, a yeast mitochondrial nucleotide-stimulated metal protease: its identification as CYM1 gene product, a mitochondrial presequence peptidase
Authors: Yasuhara Toshimasa , Nakai Toshiki , Fujiki Yukio
Published: August 2022

A chelator-sensitive protease in the mitochondrial matrix of the yeast, Saccharomyces cerevisiae (Biochem. Biophys. Res. Commun. 144, 277, 1987), was purified and characterized. The purified enzyme, termed protease M, specifically hydrolyzes peptide substrates on the N-side of the paired basic residues. When mastoparan was used as substrate, it cleaved Ala8-Leu9 and Lys11-Lys12 bonds as well as the N-side of Lys11-Lys12 residues. Nucleotide triphosphates stimulated the activity 3-fold at 2.5 mM. The genomic DNA sequence showed that protease M was a gene product of CYM1 known as mitochondrial presequence protease homologue in S. cerevisiae, encoding a 989-amino acid-long precursor protein. The N-terminal sequence of the purified enzyme indicated that protease M has 16-residue signal sequence and the ‘mature’ protein consists of 973 amino acids with a molecular mass of 110 kDa. Protease M contained consensus sequence motifs of ATP-binding site very near the carboxyl terminus. The alignment of the two ATP-binding motifs is an inverted version of the common alignment. Gene disruption of the enzyme generates mixed subunits in tetrameric MnSOD formed with 23-kDa mature and 24-kDa partial presequence-containing subunits. This report describes newly identified enzyme properties of the CYM1 gene product, protease M and abnormal MnSOD complex formation of the disruption mutant.