bluuebunny/crossref_metadata_2025 huggingface dataset:
Microseismicity Monitoring and Site Characterization With Distributed Acoustic Sensing (DAS): The Case of the Irpinia Fault System (Southern Italy)
Authors: Trabattoni A. , Festa G. , Longo R. , Bernard P. , Plantier G. , Zollo A. , Strollo A.
Published: September 2022

This paper reports the first results obtained thanks to the installation of a dedicated one‐km fiber‐optic cable, integrated within the Irpinia Near Fault Observatory regional network in Southern Italy. The cable was installed in a dry lake, located near the active faults responsible for the M6.9 earthquake that occurred in 1980. A distributed acoustic sensing (DAS) interrogator was deployed over a period of 4 months and a half and allowed to record tens of local events. To model the seismic phases observed in the recordings, simple seismic refraction experiments were conducted along with analyses of earthquakes and numerical simulations. Results show that in this peculiar geological context, DAS is mainly sensitive to waves guided horizontally by the subsurface low‐velocity layered structure of the site. This leads to considerable site amplification but also wavefront deformation and allows to detect local microearthquakes without any stacking or other array processing techniques. Magnitude estimation was performed using a dedicated amplitude correction process, along with detection threshold estimation. The benefit of using stacking of DAS channels for improving signal‐to‐noise ratio was also estimated.
Association of alpha-fetoprotein and metastasis for small hepatocellular carcinoma: A propensity-matched analysis
Authors: Wang Yu-Qi , Wang An-Jiang , Zhang Ting-Ting , Chen Si-Hai
Published: September 2022

Metastasis is crucial for the prognosis of hepatocellular carcinoma (HCC). Distinguishing the potential risk factors for distant metastasis in small HCC (diameter ≤ 5 cm) is of great significance for improving the prognosis. HCC patients in the Surveillance, Epidemiology and End Results (SEER) registry with tumors ≤ 5 cm in diameter between January 2010 and December 2015 were retrieved. Demographic and clinicopathological metrics were extracted, including age, sex, race, marital status, tumor size, histological grade, T stage, N stage, M stage, alpha-fetoprotein (AFP), and liver fibrosis score. Univariate and multivariate logistic regression analyses were used to identify independent risk factors correlated with extrahepatic metastasis in small HCC. Propensity score matching (PSM) analysis was performed to balance the confounding factors in baseline characteristics. A total of 4176 eligible patients were divided into a non-metastasis group (n = 4033) and a metastasis group (n = 143) based on metastasis status. In multivariate analysis, larger tumor size, poor histological differentiation, regional lymph node metastasis, and elevated serum AFP levels were identified as independent risk factors for distant metastasis (P < 0.05), while age, sex, race, marital status, and liver fibrosis score were not associated with extrahepatic metastasis. After propensity score analysis, the AFP level was no longer associated with metastatic risk. The present study provided no evidence for a correlation between the clinical threshold of AFP and metastasis in small hepatocellular carcinoma.
Research on a novel and improved incremental conductance method
Authors: Sun Chunhu , Ling Jing , Wang Jing
Published: September 2022

Aiming at the problem that the steady-state error and response speed cannot be taken into account in the traditional fixed-step incremental conductance method, combined with the current–voltage (I–U) characteristic curve of photovoltaic (PV) panel, this paper proposes a novel and improved variable-step incremental conductance method. The proposed tracking strategy of maximum power point (MPP) analyzes the I–U characteristic curve, and divides the I–U characteristic curve into four sections, each section has a different variable step size, thus realizing the variable step size control of global four-section. The traditional incremental conductance method and the improved incremental conductance method are simulated under the environment of Matlab/Simulink. The simulation results show that when the light intensity changes rapidly, the novel improved incremental conductance method not only has the advantages of no oscillation in steady state and fast response speed, but also improve the efficiency of photovoltaic power generation, which better realizes the fast and accurate tracking of MPP.
Two birds with one stone: large catalytic areas and abundant nitrogen sites inspired by fluorine doping contributing to CO2RR activity and selectivity
Authors: Chen Hongyu , Zhang Yi , Yang Tianfang , Shang Yizhu , Zhu Qiuying , Cao Shoufu , Lin Xiaojing , Liu Siyuan , Wei Shuxian , Wei Baojun , Wang Zhaojie , Lu Xiaoqing
Published: September 2022

Large catalytic areas and abundant nitrogen sites, inspired by fluorine doping, contribute to the activity and selectivity, respectively, of the CO2RR.
Biodegradable ZnxNi1−xS hollow nanospheres for NIR-driven photothermal antibacterial therapy
Authors: Jin Qianqian , Chen Shi , Chu Zhaoyou , Chen Benjin , Wang Wanni , Yang Juan , Jiang Yongxin , Shao Min , Qian Haisheng
Published: September 2022

Biodegradable ZnxNi1−xS hollow nanostructures coated with mPEG-PMHC18 (ZNSP) exhibit a high photothermal conversion efficiency, showing a satisfactory therapeutic performance on the healing of MRSA-infected wounds.
Data on 824 fireballs observed by the digital cameras of the European Fireball Network in 2017–2018
Authors: Borovička J. , Spurný P. , Shrbený L.
Published: September 2022

Meteoroids impacting the Earth on a daily basis are fragments of asteroids and comets. By studying fireballs produced during their disintegration in the atmosphere, we can gain information about their source regions and the properties of their parent bodies. In this work, data on 824 fireballs presented in an accompanying paper and catalog are used. We propose a new empirical parameter for the classification of the physical properties of meteoroids, based on the maximum dynamic pressure suffered by the meteoroid in the atmosphere. We then compare the physical and orbital properties of meteoroids. We find that aphelion distance is a better indicator of asteroidal origin than the Tisserand parameter. Meteoroids with aphelia lower than 4.9 AU are mostly asteroidal, with the exception of the Taurids and α Capricornids associated with the comets 2P/Encke and 169P/NEAT, respectively. We found another population of strong meteoroids of probably asteroidal origin on orbits with either high eccentricities or high inclinations, and aphelia up to χ 7 AU. Among the meteoroid streams, the Geminids and η Virginids are the strongest, and Leonids and α Capricornids the weakest. We found fine orbital structures within the Geminid and Perseid streams. Four minor meteoroid streams from the working list of the International Astronomical Union were confirmed. No meteoroid with perihelion distance lower than 0.07 AU was detected. Spectra are available for some of the fireballs, and they enabled us to identify several iron meteoroids and meteoroids deficient in sodium. Recognition and frequency of fireballs leading to meteorite falls is also discussed.
L’histoire
mouvementée de l’EPR…
Authors: Mangeon Michaël , Roger Mathias
Published: September 2022

Depuis le projet franco-allemand conçu dans la foulée de l’accident de Tchernobyl pour répondre aux nouvelles exigences de sûreté jusqu’au réacteur qui s’apprête à renouveler le parc nucléaire national, l’EPR a connu une trentaine d’années mouvementées. Aujourd’hui les premiers réacteurs démarrent et les projets se multiplient, mais il a fallu surmonter des obstacles.
Inventory pooling and pricing decisions in multiple markets with strategic customers
Authors: Wang Xuantao , Chen Zhiming , Zhou Shaorui , Hu Mingfang , Ke Jianjie
Published: September 2022

This study considers the pricing and inventory decisions for the retailer selling in multiple markets with strategic customers. The impact of strategic customer behavior on inventory pooling is examined. The equilibrium decisions, in which strategic customers tend to purchase early, are subsequently characterized in the pooled/non-pooled systems. Our results highlight the role of the strategic customer in each market. Compared with myopic customers, the retailer is prone to reduce its inventory for strategic customers. The retailer’s optimal inventory for high-profit products is lower in the pooled system than in the non-pooled system. However, the result is reversed for low-profit products. The analytical and numerical results simultaneously demonstrate that, in the high-profit condition, the retailers’ inventory in the pooled system increases with the correlation coefficient of different markets, while the retailers’ profit decreases with the correlation coefficient. There is an opposite relationship in the low-profit condition. When the markets are less correlated, the retailer owns low inventory but high profit. Moreover, the retailers’ profit is always higher in the pooled system than in the non-pooled system.
Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 1B Inhibition Promotes Megakaryocyte Polyploidization and Platelet Production
Authors: Zhao Jiaxin , Xu Yanyan , Wang Jiqiu , Liu Junling , Zhang Ruiyan , Yan Xiaoxiang
Published: September 2022

Platelets are produced from mature megakaryocytes which undergo polyploidization and proplatelet formation. Cell-cycle regulation plays a crucial role in megakaryocyte terminal differentiation especially in polyploidization. Dual-specificity tyrosine phosphorylation-regulated kinase 1B (DYRK1B) controls cell-cycle progression in cancer cells. The objective of this study was to determine DYRK1B function in megakaryocyte maturation and platelet production. A DYRK1B knock-out mouse was generated with increased peripheral platelet count compared with the wild type mouse without affecting megakaryocyte numbers in bone marrow. Polyploidy and proplatelet formations were significantly enhanced when DYRK1B was depleted in vitro. DYRK1B inhibition promoted megakaryocyte maturation by simultaneously upregulating cyclin D1 and downregulating P27. Furthermore, there was platelet restoration in two mice disease models of transient thrombocytopenia. In summary, DYRK1B plays an important role in megakaryocyte maturation and platelet production by interacting with cyclin D1 and P27. DYRK1B inhibition has potential therapeutic value in transient thrombocytopenia treatment. Graphic Abstract
Assessment of Nutritional Status of Hospitalized Children:A Comparison of STRONGkids and Anthropometry
Authors: Elbanoni Omelkhir Ibrahim , Elabbud Hudda Abubaker Younis , Greiw Azza Elsaddiek Hussein
Published: September 2022

Introduction Malnutrition is defined as an imbalance between requirements and intake of energy and/or nutrients that affect the growth—physical and cognitive functions. It is a major public health problem worldwide especially in children under five years. It includes under-nutrition either stunting, wasting, or micronutrient deficiencies and overweight or obesity. Several nutritional screening tools had been designed to detect nutritional risk of hospitalized children at an early stage. There are six tools, however, there is no consensus on which is the best tool to be used. In clinical practice, the most frequently used screening tools are: Screening of Risk for Nutritional Status and Growth (STRONGkids) and the Subjective Global Assessment of Nutritional Status (SGA). The study aimed to assess the nutritional status of hospitalized children at the time of admission and to evaluate the usefulness of STRONGkids.

Patients and Methods A cross sectional study was conducted in Benghazi Medical Center (BMC), from July 2020 to November 2020. A total of 116 under five children admitted to the hospital were included in the study.

Result and Discussion The study showed that 53.45% of children were males and 46.55% were females and showed that by using STRONGkids score, 42.2% of children were at low risk of malnutrition, 50.0% at medium risk, and 7.8% at high risk. There was an accordance between result of STRONGkids and weight for age, p = 0.000, similarly for height for age and weight for height.

conclusion The STRONGkids screening tool could be used as an initial screening tool for children on admission to provide the right intervention at the right time.
and
Authors: Holt Deborah , Giffard Philip
Published: September 2022

Staphylococcus aureus and Streptococcus pyogenes are important contributors to disease in northern Australia. Both are opportunistic pathogens, frequently carried on the skin or in the respiratory tract in the absence of disease. A large proportion of the S. aureus strains causing infection in northern Australia possess the Panton Valentine (PVL) toxin, with ST93, ST5, and ST121 being significant. PVL+ strains are associated with both community- and healthcare-associated infections, and a large proportion are methicillin-resistant S. aureus (MRSA). MRSA strains known to be healthcare associated (ST239 and ST22) are not prevalent. CC1 PVL− MRSA continue to cause infections. The diversity of S. pyogenes emm types in northern Australia is high with skin tropic and non-tropic emm types predominating. This contrasts with other parts of Australia where emm diversity is lower and rates of pharyngitis higher. The high diversity raises concerns for the likely efficacy of vaccines based on the variable region of the M protein, the nucleotide sequence of which underpins emm typing. It is likely that complex interactions occur between these two important bacterial pathogens, and other important skin pathogens in the region such as the scabies mite.
He come out and give me a beer but he never seen the bear
Authors: Jankowski Bridget L. , Tagliamonte Sali A.
Published: September 2022

In this study, we examine variation in English strong verb preterite/participle morphology in four frequent verbs:
came/come, saw/seen,
gave/give and did/done, using data from more than a dozen
Ontario communities, socially stratified by age, sex, occupation and education, representing a continuum of urban/rural locations
and spanning more than 100 years in apparent-time. Comparative sociolinguistic methods and statistical modelling permit testing of
social, geographic and linguistic factors on the variation. Despite strong social constraints, linguistic constraints are also
significant. We argue that standardization and increasing literacy have nearly eradicated the vernacular preterite forms, but they
are not moribund yet. Moreover, at least one form is stable, preterite seen. The non-standard variants endure as
sociolinguistic markers, perhaps due to locally situated prestige, particularly in non-urban communities.
Enabling matter power spectrum emulation in beyond-ΛCDM cosmologies with COLA
Authors: Brando Guilherme , Fiorini Bartolomeo , Koyama Kazuya , Winther Hans A.
Published: September 2022

We compare and validate COLA (COmoving Lagrangian Acceleration) simulations against existing emulators in the literature, namely Bacco and Euclid Emulator 2. Our analysis focuses on the non-linear response function, i.e., the ratio between the non-linear dark matter power spectrum in a given cosmology with respect to a pre-defined reference cosmology, which is chosen to be the Euclid Emulator 2 reference cosmology in this paper. We vary three cosmological parameters, the total matter density, the amplitude of the primordial scalar perturbations and the spectral index.
By comparing the COLA non-linear response function with those computed from each emulator in the redshift range 0 ≤ z ≤ 3, we find that the COLA method is in excellent agreement with the two emulators for scales up to k ∼ 1 h/Mpc as long as the deviations of the matter power spectrum from the reference cosmology are not too large.
We validate the implementation of massive neutrinos in our COLA simulations by varying the sum of neutrino masses to three different values, 0.0 eV, 0.058 eV and 0.15 eV.
We show that all three non-linear prescriptions used in this work agree at the 1% level at k ≤ 1 h/Mpc. We then introduce the Effective Field Theory of Dark Energy in our COLA simulations using the N-body gauge method. We consider two different modified gravity models in which the growth of structure is enhanced or suppressed at small scales, and show that the response function with respect to the change of modified gravity parameters depends weakly on cosmological parameters in these models.
A novel front-end amplifier for gain-less charge readout in high-pressure gas TPC
Authors: Gao C. , Feng W. , Tian X. , Sun X. , Huang G. , Qiao Y. , Hu Z. , Ye Q. , Li D.
Published: September 2022

This paper presents a novel low-noise front-end amplifier manufactured in a standard 130 nm CMOS process. The front-end amplifier is part of an integrated sensor, with an array of which, forms a charge readout plane in a high-pressure gaseous Time Projection Chamber (TPC) for 0νββ search. The novel front-end amplifier composed of a source-drain follower and a common-source amplifier is proposed. The potential of both the source and drain node of the input transistor follows its gate. Hence the effective input capacitance contributed by the input transistor is significantly reduced. A hexagon charge collection electrode with a diameter of 1 mm is connected to the input node of the front-end amplifier. The shielding technique is applied and the shielding metal is connected to the source or drain node of the input transistor. Therefore, the effective input capacitance contributed by the charge collection electrode is decreased. The extraction result shows that the input capacitance is decreased from the 4 pf down to 7.4 fF. A test chip has been designed and an equivalent noise charge of 33 e− is achieved from the simulations.
CEE inner TOF prototype design and preliminary test results
Authors: Wang X. , Hu D. , Shao M. , Zhao L. , Sun Y. , Lu J. , Xu H. , Zhou Y.
Published: September 2022

The Cooling Storage Ring (CSR) External-target Experiment (CEE) is the first multi-purpose nuclear physics experimental device to operate in the GeV energy range at the Heavy-Ion Research Facility (HIRFL-CSR) in Lanzhou, China.The primary goals of the CEE are to study the bulk properties of dense matter and to understand the quantum chromo-dynamic (QCD) phase diagram by measuring the charged particles produced in heavy-ion collisions at the target region with large acceptance. An inner time of flight (iTOF) system has been proposed to measure the multiplicity, angular distribution, and time information of the charged particles. Herein, we introduce the performance requirements of iTOF according to calculations and GEANT4 simulations. The proposed system is characterized by high granularity and time performance, hence, the conceptual design of the iTOF wall adopts high granularity Multi-gap Resistive Plate Chambers (MRPC) with a time resolution around 30 ps. To evaluate the MRPC design, the cosmic ray test was performed. A timing resolution better than 28 ps and an efficiency better than 98% have been achieved for MIPs, as interpreted by the cosmic ray GEANT4 simulation of time jitter components.
Exploring green gentrification in 28 global North cities: the role of urban parks and other types of greenspaces
Authors: Triguero-Mas Margarita , Anguelovski Isabelle , Connolly James J T , Martin Nick , Matheney Austin , Cole Helen V S , Pérez-Del-Pulgar Carmen , García-Lamarca Melissa , Shokry Galia , Argüelles Lucía , Conesa David , Gallez Elsa , Sarzo Blanca , Beltrán Miguel Angel , López Máñez Jesúa , Martínez-Minaya Joaquín , Oscilowicz Emilia , Arcaya Mariana C , Baró Francesc
Published: September 2022

Although cities globally are increasingly mobilizing re-naturing projects to address diverse urban socio-environmental and health challenges, there is mounting evidence that these interventions may also be linked to the phenomenon known as green gentrification. However, to date the empirical evidence on the relationship between greenspaces and gentrification regarding associations with different greenspace types remains scarce. This study focused on 28 mid-sized cities in North America and Western Europe. We assessed improved access to different types of greenspace (i.e. total area of parks, gardens, nature preserves, recreational areas or greenways [i] added before the 2000s or [ii] added before the 2010s) and gentrification processes (including [i] gentrification for the 2000s; [ii] gentrification for the 2010s; [iii] gentrification throughout the decades of the 2000s and 2010s) in each small geographical unit of each city. To estimate the associations, we developed a Bayesian hierarchical spatial model for each city and gentrification time period (i.e. a maximum of three models per city). More than half of our models showed that parks—together with other factors such as proximity to the city center—are positively associated with gentrification processes, particularly in the US context, except in historically Black disinvested postindustrial cities with lots of vacant land. We also find than in half of our models newly designated nature preserves are negatively associated with gentrification processes, particularly when considering gentrification throughout the 2000s and the 2010s and in the US. Meanwhile, for new gardens, recreational spaces and greenways, our research shows mixed results (some positive, some negative and some no effect associations). Considering the environmental and health benefits of urban re-naturing projects, cities should keep investing in improving park access while simultaneously implementing anti-displacement and inclusive green policies.
Observation of the poloidally asymmetrical density perturbation of sawtooth collapse on J-TEXT
Authors: ZHOU Yinan , ZHUANG Ge , SHI Peng , GAO Li , YANG Zhoujun , ZHANG Xiaoqing
Published: September 2022

The detailed density perturbations provided by the advanced polarimeter–interferometer system (Polaris) during sawtooth collapse on the Joint Texas Experimental Tokamak (J-TEXT) are reported in this article. During a sawtooth collapse and the crash of plasma pressure at the center, it is found that the increase in density in the region between the inversion radius and mixing radius is poloidally asymmetrical, while the increase in temperature is poloidally symmetrical. The poloidal location where the density increases is dependent on the phase of the precursory m/n = 1/1 kink mode. It is always out of phase with the hot core of the m/n = 1/1 mode. The behaviors of density perturbations during sawtooth collapse observed in J-TEXT are beyond the expectations of the standard model, and this can shed new light on the understanding of sawtooth collapse.
Risk Characteristics of Hydrogen Sulphide Exposure in Wastewater Collection and Treatment Related Occupations
Authors: Austigard Åse Dalseth , Smedbold Hans Thore , von Hirsch Svendsen Kristin
Published: September 2022

Objectives

Water and wastewater workers can be exposed to hydrogen sulphide (H2S), with an unpredictable exposure pattern, dominated by sharp peaks. These peaks can often be high above the ceiling value (CV) at 10 ppm.

Methods

We have analyzed self-administrated H2S exposure data among 60 wastewater workers in the Municipality of Trondheim, Norway, from 2015 till 2021. The detection range of the personal alarm equipment used was 1.6 to 100 ppm H2S. The workers were divided in four similar exposed groups (SEGs): wastewater collection net, wastewater treatment plants, wastewater pumping stations and water distribution net.

Results

We identified measurements from 7083 different workdays, approximately 10% of the workdays between 2015 and 2021. Within these, 1295 days had readings above 1.6 ppm H2S, and 424 (33%) of these days had readings that exceeded the CV of 10 ppm H2S. This percentage was similar across the SEGs. Only one workday had a time weighted average (TWA) exceeding the occupational exposure limit (OEL) of 5 ppm H2S, and only 14 days exceeded 0.5 ppm H2S, 1/10th of the OEL.

Conclusions

Wastewater workers in this study are regularly exposed to short peaks of H2S, but even high peaks do not influence the 8-h TWA values significantly. A preliminary measurement program over 3 days according to EN 689 to evaluate the need for further measurements would probably not find TWA values greater than 1/10 of OEL; the EN 689 standard is not made for evaluation to peak exposures. Exceedances of CV at 10 ppm H2S occur in 6% of workdays, and in 33% of days with exposure above 1.6 ppm. The toxicity and exposure profile of H2S makes continuous exposure monitoring necessary for alarm purposes. Reliance on the 8-h occupational exposure limit as has been the normal in Norway, will not be adequately protective for wastewater workers. H2S alarm equipment should continue to be used.
A geometric deep learning framework for drug repositioning over heterogeneous information networks
Authors: Zhao Bo-Wei , Su Xiao-Rui , Hu Peng-Wei , Ma Yu-Peng , Zhou Xi , Hu Lun
Published: September 2022

Drug repositioning (DR) is a promising strategy to discover new indicators of approved drugs with artificial intelligence techniques, thus improving traditional drug discovery and development. However, most of DR computational methods fall short of taking into account the non-Euclidean nature of biomedical network data. To overcome this problem, a deep learning framework, namely DDAGDL, is proposed to predict drug-drug associations (DDAs) by using geometric deep learning (GDL) over heterogeneous information network (HIN). Incorporating complex biological information into the topological structure of HIN, DDAGDL effectively learns the smoothed representations of drugs and diseases with an attention mechanism. Experiment results demonstrate the superior performance of DDAGDL on three real-world datasets under 10-fold cross-validation when compared with state-of-the-art DR methods in terms of several evaluation metrics. Our case studies and molecular docking experiments indicate that DDAGDL is a promising DR tool that gains new insights into exploiting the geometric prior knowledge for improved efficacy.
Critical assessment of pan-genomic analysis of metagenome-assembled genomes
Authors: Li Tang , Yin Yanbin
Published: September 2022

Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi’o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi’o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition
Authors: Freestone Jack , Short Temana , Noble William Stafford , Keich Uri
Published: September 2022

Motivation

Target-decoy competition (TDC) is a commonly used method for false discovery rate (FDR) control in the analysis of tandem mass spectrometry data. This type of competition-based FDR control has recently gained significant popularity in other fields after Barber and Candès laid its theoretical foundation in a more general setting that included the feature selection problem. In both cases, the competition is based on a head-to-head comparison between an (observed) target score and a corresponding decoy (knockoff) score. However, the effectiveness of TDC depends on whether the data are homogeneous, which is often not the case: in many settings, the data consist of groups with different score profiles or different proportions of true nulls. In such cases, applying TDC while ignoring the group structure often yields imbalanced lists of discoveries, where some groups might include relatively many false discoveries and other groups include relatively very few. On the other hand, as we show, the alternative approach of applying TDC separately to each group does not rigorously control the FDR.

Results

We developed Group-walk, a procedure that controls the FDR in the target-decoy/knockoff setting while taking into account a given group structure. Group-walk is derived from the recently developed AdaPT—a general framework for controlling the FDR with side-information. We show using simulated and real datasets that when the data naturally divide into groups with different characteristics Group-walk can deliver consistent power gains that in some cases are substantial. These groupings include the precursor charge state (4% more discovered peptides at 1% FDR threshold), the peptide length (3.6% increase) and the mass difference due to modifications (26% increase).

Availability and implementation

Group-walk is available at https://cran.r-project.org/web/packages/groupwalk/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers
Authors: Liu Xin , Yu Jiale , Tao Siyu , Yang Beiyuan , Wang Shike , Wang Lin , Bai Fang , Zheng Jie
Published: September 2022

Motivation

Synthetic lethality (SL) is a type of genetic interaction in which the simultaneous inactivation of two genes leads to cell death, while the inactivation of a single gene does not affect the cell viability. It can effectively expand the range of anti-cancer therapeutic targets. SL interactions are identified mainly by experimental screening and computational prediction. Recent machine-learning methods mostly learn the representation of each gene individually, ignoring the representation of the pairwise interaction between two genes. In addition, the mechanisms of SL, the key to translating SL into cancer therapeutics, are often unclear.

Results

To fill the gaps, we propose a pairwise interaction learning-based graph neural network (GNN) named PiLSL to learn the representation of pairwise interaction between two genes for SL prediction. First, we construct an enclosing graph for each pair of genes from a knowledge graph. Secondly, we design an attentive embedding propagation layer in a GNN to discriminate the importance among the edges in the enclosing graph and to learn the latent features of the pairwise interaction from the weighted enclosing graph. Finally, we further fuse the latent features with explicit features extracted from multi-omics data to obtain powerful gene representations for SL prediction. Extensive experimental results demonstrate that PiLSL outperforms the best baseline by a large margin and generalizes well under three realistic scenarios. Besides, PiLSL provides an explanation of SL mechanisms via the weighted paths in the enclosing graphs by attention mechanism.

Availability and implementation

Our source code is available at https://github.com/JieZheng-ShanghaiTech/PiLSL.
Conversion therapy for initially unresectable hepatocellular carcinoma using a combination of toripalimab, lenvatinib plus TACE: real-world study
Authors: Qu Wei-Feng , Ding Zhen-Bin , Qu Xu-Dong , Tang Zheng , Zhu Gui-Qi , Fu Xiu-Tao , Zhang Zi-Han , Zhang Xin , Huang Ao , Tang Min , Tian Meng-Xin , Jiang Xi-Fei , Huang Run , Tao Chen-Yang , Fang Yuan , Gao Jun , Wu Xiao-Ling , Zhou Jian , Fan Jia , Liu Wei-Ren , Shi Ying-Hong
Published: September 2022

Background

Combination conversion therapies afforded curative surgery chance for initially unresectable hepatocellular carcinoma (uHCC). This study aimed to evaluate the conversion rate and clinical outcomes of a first-line conversion regimen of lenvatinib combined with transarterial chemoembolization (TACE) plus immunotherapy for initial uHCC by interpreting real-world data.

Methods

Conversion therapy data of patients with uHCC from November 2018 to January 2021 were analysed. The regimens included triple combination therapy (t-CT: lenvatinib, TACE, plus toripalimab) and dual combination therapy (d-CT: lenvatinib plus TACE). Another study population diagnosed with hepatocellular carcinoma of macrovascular invasion disease were included as the upfront surgery cohort. Treatment responses and conversion rate were primary outcomes. Survival and adverse events were analysed.

Results

Fifty-one patients receiving t-CT (n = 30) and d-CT (n = 21) were enrolled. Higher overall response rates (76.7 per cent versus 47.6 per cent, P = 0.042) and disease control rates (90.0 per cent versus 57.1 per cent, P = 0.042) were observed via t-CT than d-CT. Both median overall survival and event-free survival were not reached in the t-CT cohort. A higher rate of curative conversion resection was achieved through t-CT than d-CT (50.0 per cent versus 19.0 per cent, P = 0.039). The disease-free survival of patients undergoing conversion resection in the t-CT cohort (n = 15) was higher than that in the upfront surgery cohort (n = 68, P = 0.039). Both t-CT and d-CT regimens were tolerable.

Conclusions

Better treatment responses and conversion rate for patients with uHCC were obtained with first-line t-CT. Neoadjuvant t-CT before surgery should be recommended for patients with macrovascular invasion.
Character-Based Value Factorization For MADRL
Authors: Liqin Xiong , Lei Cao , Xiliang Chen , Jun Lai , Xijian Luo
Published: September 2022

Value factorization is a popular method for cooperative multi-agent deep reinforcement learning. In this method, agents generally have the same ability and rely only on individual value function to select actions, which is calculated from total environment reward. It ignores the impact of individual characteristics of heterogeneous agents on actions selection, which leads to the lack of pertinence during training and the increase of difficulty in learning effective policies. In order to stimulate individual awareness of heterogeneous agents and improve their learning efficiency and stability, we propose a novel value factorization method based on Personality Characteristics, PCQMIX, which assigns personality characteristics to each agent and takes them as internal rewards to train agents. As a result, PCQMIX can generate heterogeneous agents with specific personality characteristics suitable for specific scenarios. Experiments show that PCQMIX generates agents with stable personality characteristics and outperforms all baselines in multiple scenarios of the StarCraft II micromanagement task.
Comparison of the Risk of Crohn’s Disease Postoperative Recurrence Between Modified Rutgeerts Score i2a and i2b Categories: An Individual Patient Data Meta-analysis
Authors: Rivière Pauline , Pekow Joel , Hammoudi Nassim , Wils Pauline , De Cruz Peter , Wang Christina Pu , Mañosa Míriam , Ollech Jacob , Allez Matthieu , Nachury Maria , Kamm Michael A , Ahanori Maya , Ferrante Marc , Buisson Anthony , Singh Siddarth , Laharie David , Diouf Momar , Fumery Mathurin
Published: September 2022

Background

The modified Rutgeerts’ score [RS] differentiates i2a—lesions confined to the anastomosis—and i2b—more than five aphthous ulcers in the neoterminal ileum with normal intervening mucosa, with or without anastomotic lesions—categories. Its relevance for the therapeutic management of Crohn’s disease [CD] patients after ileocolic resection is still debated. Our objective was to compare the postoperative recurrence risk in patients with an i2a or i2b score, using an individual patient data meta-analysis.

Methods

We conducted a systematic literature search until July 2020, to identify all relevant studies reporting the i2a/i2b status in the year following ileocolic resection and clinical and/or surgical postoperative CD recurrence in their follow-up. Individual patient-level data were obtained from the corresponding authors. The association between the modified RS and time-to-event was evaluated using a mixed Cox model with the centre as the random effect.

Results

Seven studies published between 2008 and 2019 were included, corresponding to 400 patients: 189 [47%] i2a and 211 [53%] i2b. Median [interquartile range, IQR] time from ileocolic resection to ileocolonoscopy was 6.2 [5.5, 7.9] months and median [IQR] follow-up time after ileocolonoscopy was 4.5 [2.9, 7.3] years. The risk of clinical postoperative recurrence at 1 and 3 years was 11% [6–15%], and 25% [18–32%] in the i2a group versus 9% [5–13%] and 33% [26–41%] in the i2b group [p = 0.63 and p = 0.12, respectively]. No significant difference was observed in terms of time to clinical postoperative recurrence [p = 0.16] or surgical postoperative recurrence [p = 0.87]. Results did not change after excluding patients having initiated an immunosuppressant or a biologic in the 3 months after endoscopy [remaining cohort, n = 361].

Conclusions

In this individual patient data meta-analysis, no difference was observed between i2a and i2b subcategories with regards to clinical or surgical postoperative recurrence. As we wait for prospective trials, the same treatment strategy could be applied to all patients classified as i2 on the Rutgeerts score.
Artificial intelligence–derived cardiac ageing is associated with cardiac events post-heart transplantation
Authors: Ozcan Ilke , Toya Takumi , Cohen-Shelly Michal , Park Hyun Woong , Ahmad Ali , Ozcan Alp , Noseworthy Peter A , Kapa Suraj , Lerman Lilach O , Attia Zachi I , Kushwaha Sudhir S , Friedman Paul A , Lerman Amir
Published: September 2022

Aims

An artificial intelligence algorithm detecting age from 12-lead electrocardiogram (ECG) has been suggested to reflect ‘physiological age’. An increased physiological age has been associated with a higher risk of cardiac mortality in the non-transplant population. We aimed to investigate the utility of this algorithm in patients who underwent heart transplantation (HTx).

Methods and results

A total of 540 patients were studied. The average ECG ages within 1 year before and after HTx were used to represent pre- and post-HTx ECG ages. Major adverse cardiovascular event (MACE) was defined as any coronary revascularization, heart failure hospitalization, re-transplantation, and mortality. Recipient pre-transplant ECG age (mean 63 ± 11 years) correlated significantly with recipient chronological age (mean 49 ± 14 years, R = 0.63, P < 0.0001), while post-transplant ECG age (mean 54 ± 10 years) correlated with both the donor (mean 32 ± 13 years, R = 0.45, P < 0.0001) and the recipient ages (R = 0.38, P < 0.0001). During a median follow-up of 8.8 years, 307 patients experienced MACE. Patients with an increase in ECG age post-transplant showed an increased risk of MACE [hazard ratio (HR): 1.58, 95% confidence interval (CI): (1.24, 2.01), P = 0.0002], even after adjusting for potential confounders [HR: 1.58, 95% CI: (1.19, 2.10), P = 0.002].

Conclusion

Electrocardiogram age-derived cardiac ageing after transplantation is associated with a higher risk of MACE. This study suggests that physiological age change of the heart might be an important determinant of MACE risk post-HTx.
The Regulation of Environmentally Harmful Fossil Fuel Subsidies: From Obscurity to Prominence in the Multilateral Trading System
Authors: Asmelash Henok
Published: September 2022

Environmentally harmful fossil fuel subsidies were notably absent from efforts to enhance the mutual supportiveness of trade and environment in the multilateral trading system. However, a combination of factors has recently propelled the regulation of such subsidies up the trade and environment agenda. The recently launched initiative to negotiate a plurilateral Agreement on Climate Change, Trade and Sustainability (ACCTS) represents the latest and most ambitious of the growing number of initiatives to discipline fossil fuel subsidies. This article examines the factors that brought the regulation of fossil fuel subsidies to prominence and the prospects of the ACCTS initiative to introduce binding rules on fossil fuel subsidies. The article argues that such an initiative is long overdue, but it faces significant hurdles to succeed. Drawing on past and present intergovernmental initiatives to tackle environmentally harmful subsidies, the article highlights the key challenges on the road ahead and suggests possible ways forward.
Forum: Gendered Dynamics of Academic Networks
Authors: Scalera Elliott Jamie , Mitchell Sara McLaughlin , Dion Michelle L , Vargas Thomas R , Krupnikov Yanna , Milita Kerri , Barry Ryan John , Smith Victoria , Style Hillary , Crawford Kerry F , Windsor Leah C , Fattore Christina , Breuning Marijke , Ramos Jennifer
Published: September 2022

This forum examines whether scholars’ access to networks in the international studies profession is gendered and if so, the consequences of those networks for personal and professional success. Academic networks that encompass both professional and personal connections have been proposed as one solution to chilly climate issues because they provide a dual function of enhancing scholarly productivity and inclusion in the profession. The articles in the forum consider both professional (e.g., citation) and personal (e.g., mentorship, friendship) networks, as well as traditional (e.g., invited talks) and nontraditional (e.g., social media) networks. The authors show that biases that arise through the gendered nature of academic networks can be mitigated through social media, mentoring, and friendship networks. However, we must also be cognizant of other factors that create barriers for women in the profession (e.g., university prestige, parenthood, COVID-19).
Effect of Bed Bug (Hemiptera: Cimicidae) Aldehydes on Efficacy of Fungal Biopesticides
Authors: Dery Mark , Choe Dong-Hwan
Published: September 2022

The use of the entomopathogenic fungus Beauveria bassiana (Bals. – Criv.) Vuill. (Hypocreales: Cordycipitaceae) has been recently incorporated in the management of bed bugs, Cimex lectularius L. (Hemiptera: Cimicidae). Bed bugs produce a set of aldehydes that are known to affect the growth of some fungi. Considering that bed bugs or their exuviae release these aldehydes, it was suspected that the bed bugs’ aggregation sites would contain an increased level of the bed bug aldehydes. The current study examined if elevated levels of the bed bug aldehydes in the microhabitats would impact the efficacy of B. bassiana. Following a brief exposure to the residues of commercial products containing B. bassiana, the treated bed bugs were kept in a vial with or without a natural or artificial blend of bed bug aldehydes (i.e., exuviae or synthetic compounds). For a B. bassiana product that is not currently registered for bed bugs control, the presence of aldehydes significantly reduced 15-d mortality (61–62%) compared to the no aldehydes control (97.7%). However, when tested with a B. bassiana formulation designed for bed bug control, the aldehydes only caused delayed mortality for the treated bed bugs. When tested in culture, the growth rate of B. bassiana on a medium was significantly reduced when the bed bug aldehydes were provided in the headspace. Implications on practical bed bug management using fungal biopesticides are discussed.
Evaluation of Lethal and Sublethal Effects of Methyl Benzoate on the Generalist PredatorOrius laevigatus(Fieber)
Authors: Mostafiz Md Munir , Güncan Ali , Lee Kyeong-Yeoll
Published: September 2022

Methyl benzoate (MBe), a volatile organic molecule, has been shown to have insecticidal effects on a variety of agricultural, stored products, and urban arthropod pests in recent investigations. However, the toxicity of MBe against nontarget organisms has rarely been investigated. This study investigated the lethal and sublethal effects of MBe on the generalist predator Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) via different exposure routes. This species is an important natural enemy of thrips, aphids, and mites in biological control programs globally. Acute toxicity bioassays conducted on O. laevigatus showed that the lethal median concentration (LC50) values of MBe for topical and residual toxicity were 0.73 and 0.94%, respectively, after 24 hr of exposure. Importantly, a sublethal concentration of MBe (LC30 = 0.51%) did not affect the survival and reproduction of O. laevigatus. In addition, prey consumption by O. laevigatus under different exposure conditions with varying densities of Aphis gossypii (Glover) (Hemiptera: Aphididae) adults demonstrated a good fit for a Type II functional response. The sublethal concentration of MBe did not affect the attack rate and handling time of O. laevigatus compared to untreated insects, nor did it affect the longevity and fecundity of O. laevigatus females. Thus, according to the International Organization for Biological Control, the sublethal MBe concentration for O. laevigatus is categorized as harmless and may be used in conjunction with this predator species for integrated control of many agricultural insect pests.
Molecular Studies of Relationships and Identifications Among Insects of the Subfamily Panchaetothripinae (Thysanoptera, Thripidae)
Authors: Xie Yan Lan , Mound Laurence A , Lima Élison Fabrício Bezerra , He Shu Qi , Zhang Hong Rui , Li Ya Jin
Published: September 2022

The Panchaetothripinae comprises 42 genera and 146 species of leaf-feeding thrips, some of which are horticultural pests. We examined representatives of the 18 genera that include most of these pests. For species delimitation, we used DNA barcoding to produce171 sequences for 40 morphospecies. Most species were found to be monophyletic, although cryptic diversity was evident in 8 presumptive species. A multilocus molecular phylogenetic assessment was based on one mitochondrial (COI) and three nuclear loci (EF-1α, ITS2, and 28S) from 132 specimens (18 genera and 33 species), representing all genera and ~82% of species in China. Maximum likelihood (ML) and Bayesian inference (BI) confirmed monophyly of each genus with strong support. Monophyly of tribes Panchaetothripini and Monilothripini were refuted, but the well supported tribe Tryphactothripini was confirmed. Rhipiphorothrips was recovered as a sister to the remainder of the genera of Panchaetothripinae combined. Both analyses revealed two major clades. Clade A comprised the majority of the genera, including tribe Tryphactothripini. Clade B included only four genera of which two, Helionothrips and Caliothrips, are particularly species rich. The relationships of some genera remain unresolved.