bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Volcanic Aerosols on the Genesis of Tropical Cyclone Wukong (2018)
Authors: Liu Haiyang , Tang Xiaodong , Gu Jian‐Feng
Published: November 2022

The short‐range impacts of volcanic aerosols from the eruption of the Kilauea volcano on the genesis of tropical cyclone (TC) Wukong in 2018 are investigated by numerical simulations, as distinct from the studies on the aerosol climate effects. The aerosol−radiation and aerosol−cloud effects are isolated through sensitivity experiments. For the aerosol−radiation effect, the radiative cooling at the low levels and heating above by aerosols southeast of Wukong's periphery induce stable sinking and decrease latent heating in the environment far from the storm center. Therefore, the sea‐level pressure increases there, enhancing low‐level radial inflow to the storm, inner‐core convection and the release of latent heat, which is conducive to TC genesis. For the aerosol−cloud effect, volcanic aerosols in storm circulation can be converted into cloud condensation nuclei, invigorating inner‐core convection, and subsequently favoring TC genesis. However, the nonlinear effect resulting from the interaction between aerosol−radiation and aerosol−cloud effects is not conducive to TC genesis, because it weakens the aerosol−cloud effect through the deposition of aerosols and also limits the aerosol−radiation effect through the increasing of peripheral convection.
Temperature‐Precipitation Scaling Rates: A Rainfall Event‐Based Perspective
Authors: Pérez Bello Alexis , Mailhot Alain , Paquin Dominique , Paquin‐Ricard Danahé
Published: November 2022

The intensity of extreme rainfall is expected to increase in a future climate at a rate close to 7%/°C estimated from the Clausius‐Clapeyron (CC) relationship, which represents the rate of change of the atmospheric water holding capacity with temperature. Previous studies using fixed‐interval extremes (e.g., hourly or daily) have shown that extreme rainfall can also respond to temperature increases at a rate larger than the CC scaling (super CC scaling). Temperature‐precipitation scaling rates (TPSR) were estimated through an event‐based analysis for the Northeastern North American (NNA) region, using a 50‐member large ensemble of climate simulations over the 1956–2099 period. Rainfall events (REs), in which 1‐hr annual maximums (AMs) are embedded, were analyzed. Results show that the TPSR of the RE peak intensity is determined by the duration of the RE in which they are embedded. Rainfall event duration, indicative of rainfall types (large‐scale or convective), therefore plays an essential role and should be considered when estimating the TPSR. Super CC scaling observed for 1‐hr AM in southern regions of the domain was explained by a change in the dominant rainfall type. This study also confirms previously reported results that the more extreme 1‐hr AM will be part of a shorter and probably more convective dominant RE in a future climate.
Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity
Authors: Samlali Kenza , Alves Chiara Leal , Jezernik Mara , Shih Steve C. C.
Published: November 2022

Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2–4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.
Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney
Authors: Liu Shiheng , Xia Xian , Zhen James , Li Zihang , Zhou Z. Hong
Published: November 2022

The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
Generation of Fermat’s spiral patterns by solutal Marangoni-driven coiling in an aqueous two-phase system
Authors: Xiao Yang , Ribe Neil M. , Zhang Yage , Pan Yi , Cao Yang , Shum Ho Cheung
Published: November 2022

The solutal Marangoni effect is attracting increasing interest because of its fundamental role in many isothermal directional transport processes in fluids, including the Marangoni-driven spreading on liquid surfaces or Marangoni convection within a liquid. Here we report a type of continuous Marangoni transport process resulting from Marangoni-driven spreading and Marangoni convection in an aqueous two-phase system. The interaction between a salt (CaCl2) and an anionic surfactant (sodium dodecylbenzenesulfonate) generates surface tension gradients, which drive the transport process. This Marangoni transport consists of the upward transfer of a filament from a droplet located at the bottom of a bulk solution, coiling of the filament near the surface, and formation of Fermat’s spiral patterns on the surface. The bottom-up coiling of the filament, driven by Marangoni convection, may inspire automatic fiber fabrication.
Osteoblast/osteocyte-derived interleukin-11 regulates osteogenesis and systemic adipogenesis
Authors: Dong Bingzi , Hiasa Masahiro , Higa Yoshiki , Ohnishi Yukiyo , Endo Itsuro , Kondo Takeshi , Takashi Yuichi , Tsoumpra Maria , Kainuma Risa , Sawatsubashi Shun , Kiyonari Hiroshi , Shioi Go , Sakaue Hiroshi , Nakashima Tomoki , Kato Shigeaki , Abe Masahiro , Fukumoto Seiji , Matsumoto Toshio
Published: November 2022

Exercise results in mechanical loading of the bone and stimulates energy expenditure in the adipose tissue. It is therefore likely that the bone secretes factors to communicate with adipose tissue in response to mechanical loading. Interleukin (IL)−11 is known to be expressed in the bone, it is upregulated by mechanical loading, enhances osteogenesis and suppresses adipogenesis. Here, we show that systemic IL-11 deletion (IL-11−/−) results in reduced bone mass, suppressed bone formation response to mechanical loading, enhanced expression of Wnt inhibitors, and suppressed Wnt signaling. At the same time, the enhancement of bone resorption by mechanical unloading was unaffected. Unexpectedly, IL-11−/− mice have increased systemic adiposity and glucose intolerance. Osteoblast/osteocyte-specific IL-11 deletion in osteocalcin-Cre;IL-11fl/fl mice have reduced serum IL-11 levels, blunted bone formation under mechanical loading, and increased systemic adiposity similar to IL-11−/− mice. Adipocyte-specific IL-11 deletion in adiponectin-Cre;IL-11fl/fl did not exhibit any abnormalities. We demonstrate that osteoblast/osteocyte-derived IL-11 controls both osteogenesis and systemic adiposity in response to mechanical loading, an important insight for our understanding of osteoporosis and metabolic syndromes.
Cutmarked bone of drought-tolerant extinct megafauna deposited with traces of fire, human foraging, and introduced animals in SW Madagascar
Authors: Hixon Sean W. , Domic Alejandra I. , Douglass Kristina G. , Roberts Patrick , Eccles Laurie , Buckley Michael , Ivory Sarah , Noe Sarah , Kennett Douglas J.
Published: November 2022

People could have hunted Madagascar’s megafauna to extinction, particularly when introduced taxa and drought exacerbated the effects of predation. However, such explanations are difficult to test due to the scarcity of individual sites with unambiguous traces of humans, introduced taxa, and endemic megaherbivores. We excavated three coastal ponds in arid SW Madagascar and present a unique combination of traces of human activity (modified pygmy hippo bone, processed estuarine shell and fish bone, and charcoal), along with bones of extinct megafauna (giant tortoises, pygmy hippos, and elephant birds), extirpated fauna (e.g., crocodiles), and introduced vertebrates (e.g., zebu cattle). The disappearance of megafauna from the study sites at ~ 1000 years ago followed a relatively arid interval and closely coincides with increasingly frequent traces of human foraging, fire, and pastoralism. Our analyses fail to document drought-associated extirpation or multiple millennia of megafauna hunting and suggest that a late combination of hunting, forest clearance, and pastoralism drove extirpations.
Changes in retro-odontoid mass after upper cervical spine surgery
Authors: Shin Jae-Won , Suk Kyung-Soo , Kim Hak-Sun , Yang Jae-Ho , Lee Hwan-Mo , Moon Sung-Hwan , Lee Byung-Ho , Park Jin-Oh , Park Sang-Jun , Park Sub-ri , Kim Sun-kyu , Garcia Jane F.
Published: November 2022

A non-neoplastic mass posterior to the dens is termed a retro-odontoid mass (R-OM). This retrospective study evaluated radiographic and clinical outcomes and R-OM changes after upper cervical spine surgery. This study included 69 patients who underwent upper cervical spine surgery, including atlantoaxial fusion, occipitocervical fusion, or decompression. All patients underwent preoperative magnetic resonance imaging (MRI). Six-month follow-up MRI examinations were performed in 30 patients who had preoperative R-OMs. Radiographic outcomes of the anterior and posterior atlantodental intervals were measured using X-rays and computed tomography. The R-OM and space available for the cord (SAC) were measured using MRI. Clinical outcomes were evaluated using neck and arm pain visual analog scales, the Japanese Orthopedic Association score, the neck disability index, and the patient-reported subjective improvement rate. The anterior atlantodental interval decreased, while the posterior atlantodental interval and SAC increased postoperatively. Among the clinical outcomes, the neck and arm pain and the neck disability index decreased postoperatively, while the Japanese Orthopedic Association score increased. All clinical and radiographic outcomes improved postoperatively. The R-OM either decreased in size or disappeared after fusion surgery in all cases, except in one patient who underwent decompression surgery. In conclusion, stabilization through fusion surgery is essential for treating R-OM.
Starter culture-related changes in free amino acids, biogenic amines profile, and antioxidant properties of fermented red beetroot grown in Poland
Authors: Choińska Renata , Piasecka-Jóźwiak Katarzyna , Woźniak Łukasz , Świder Olga , Bartosiak Elżbieta , Bujak Marzena , Roszko Marek Łukasz
Published: November 2022

Fermentation of two red beet cultivars (Wodan and Alto) with single-strain starter cultures consisting of selected strains of lactic acid bacteria (LAB) of plant origin (Weissella cibaria KKP2058, Levilactobacillus brevis ZF165) and a multi-strain culture (containing W. cibaria KKP2058, L. brevis ZF165, Lactiplantibacillus plantarum KKP1822, Limosilactobacillus fermentum KKP1820, and Leuconostoc mesenteroides JEIIF) was performed to evaluate their impact on betalains, free amino acids, formation of biogenic amines, and antioxidative properties of the juice formed. Next-generation sequencing data analysis used to identify the microbial community revealed that the starter cultures promoted the dominance of the genus Lactobacillus, and decreased the proportion of spoilage bacteria compared to spontaneously fermented juices. Generally, the fermentation process significantly influenced the amount of the analyzed compounds, leading in most cases to their reduction. The observed changes in the studied parameters depended on the starter culture used, indicating different metabolic activities of the LAB strains towards bioactive compounds. The use of multi-strain starter cultures allowed to largely prevent the reduction of betacyanins and histamine formation.
Cellulose-based hydrogels towards an antibacterial wound dressing
Authors: Guamba Esteban , Vispo Nelson Santiago , Whitehead Daniel C. , Singh Ajaya Kumar , Santos-Oliveira Ralph , Niebieskikwiat Dario , Zamora-Ledezma Camilo , Alexis Frank
Published: November 2022

Cellulose-based hydrogels with antifouling properties reduce the formation of bacterial biofilms.
Metallogels: a novel approach for the nanostructuration of single-chain magnets
Authors: Houard Felix , Cucinotta Guiseppe , Guizouarn Thierry , Suffren Yan , Calvez Guillaume , Daiguebonne Carole , Guillou Olivier , Artzner Franck , Mannini Matteo , Bernot Kevin
Published: November 2022

Supramolecular nanotubes of single-chain magnets (SCMs) can be assembled in gel phase and transferred intact on surface.
Blockchain technology based exchanged information security for demand‐side management of grid‐connected microgrid using model predictive control
Authors: Bonyani Masoud , Ghanbarian Mohammad Mehdi , Simab Mohsen
Published: November 2022

In the present study, the economic model predictive control (EMPC) scheme is presented for the time of use tariff application of photovoltaic and diesel generator backup system, which is connected to the grid‐connected microgrid. Through the use of the closed‐loop control system, the prior open‐loop optimal control is enhanced. Minimizing the grid energy and fuel costs by evaluating the fuel level restrictions in the diesel tank is the main goal of this study. To accommodate the restrictions among controllable variables, this control method fulfils the load requirements. To gain the benefits of feedback and predictions, optimal power scheduling is modelled as a control problem. Furthermore, Blockchain technology is applied to secure interchanged information in the grid to avoid manipulating data by attackers. Specifically, the analysis is divided into two scenarios. The first one takes place in the alternative style when a blackout happens between [7 am and 6 pm] h and the other occurs in a grid energy mode when the network is available over 24 h. Energy performance, cost savings, and daily revenue have all been improved by EMPC. As a result, the daily energy savings are up to 52%, whereas diesel energy does not go over 85%.
Salt‐and‐pepper denoising method for colour images based on tensor low‐rank prior and implicit regularization
Authors: Zhang Jun , Li Zhao‐yang , Wang Ling‐zhi , Chen Ying‐pin
Published: November 2022

Most of the information obtained by humans comes from colour images. However, salt‐and‐pepper noise (SPN) during signal acquisition, encoding, transmission, and decoding easily interferes with the quality of colour images. Most existing SPN denoising methods decompose a colour image into three independent matrices according to the colour channel and then recover each channel signal independently, ignoring the strong data correlation between channels. In addition, most existing SPN denoising methods apply only a single model‐driven or data‐driven approach and fail to take the advantages of their combination fully. Therefore, we first regard a colour image contaminated by SPN as the sum of an SPN tensor and a tensor with missing data. In this manner, we transform the denoising problem into a low‐rank tensor reconstruction problem. We then introduce a model‐driven‐based parallel matrix factorization low‐rank tensor reconstruction algorithm and a data‐driven‐based FFDNet denoising network to restore the colour image better. The proposed method not only enhances the similarity of the colour image channels but also explores the deep prior of the colour image to capture the image details. Finally, the proposed method is compared with some advanced denoising methods. The results show that the proposed method achieves a competitive denoising performance.
Car‐following trajectory data imputation with adversarial convolutional neural network
Authors: Zhao De , Zhang Yan , Wang Wei , Hua Xuedong , Yang Min
Published: November 2022

Missing values in the vehicle trajectory data undermine its application in traffic modelling and simulation. Traditional methods for missing data imputation rely on neighbor points of the missing/distorted data point and consequently can hardly handle trajectory with consecutive data loss. To fill in this research gap, external data with latent information should be considered to enhance the imputation. Hence, the primary objective of this study is to find an effective approach to impute consecutive missing data in the vehicle trajectory making use of leading vehicle trajectory. We proposed a novel imputation adversarial convolutional neural network (IACNN) by extending the CNN model with a multi‐objective loss function and adversarial learning framework for vehicle trajectory data imputation. Performance of the model is evaluated on the commonly used trajectory dataset NGSIM with comparison to other baseline models. It turns out that the proposed IACNN outperforms other baseline models in most data loss scenarios, especially with consecutive data loss.
Lightning inductive coupling characteristics of parallel cables: Computation and measurement validation
Authors: Zhou Mi , Zhao Weihan , Zheng Shengquan , Guo Yongming , Yang Zehong , Wang Jianguo , Cai Li , Fan Yadong
Published: November 2022

A simulation model composed of an interfering cable and a disturbed cable is established for studying the lightning inductive characteristics between parallel cables. Effects of the horizontal distance between cables (5–40 cm), their height difference (−6–32 cm), as well as the length of disturbed cable (1–100 m) are investigated for the cable induced voltage, which is measured at the resistive load connected between one terminal of the disturbed cable and the ground, when various lightning surge currents (8/20 μs, 5/320 μs, and 0.5 μs/100 kHz) are delivered into the interfering cable. Our findings show that an increase of horizontal distance between cables can give rise to an exponential decrease of the cable induced voltage, and that there exist linear correlations between either the height difference of two cables or the length of disturbed cable and the cable induced voltage, which reaches maximum when the cables are located at the same height and of equal length. Verification experiments for the effect of horizontal distance have also been made, and, in general, they all show a reasonable agreement with the simulations. A detailed theoretical explanation of obtained findings is provided as well.
Knowledge and Self-Reported Practice of Postnatal Mothers on Sudden Infant Death Syndrome Prevention: A Cross-Sectional Study
Authors: Antony Roseline Kallakavumkal , Saldanha Sandra Jyothi
Published: November 2022

The word “Sudden Infant Death Syndrome (SIDS)” is used for a sleeping infant, who has apparently been quite well, is found unexpectedly dead. There are varied discussions throughout the world trying to find the possible reasons and preventive measures toward these sudden deaths. However, limited studies are undertaken regarding knowledge of mothers related to SIDS. The present study aimed at identifying the knowledge gaps present among the postnatal mothers toward SIDS and assess their practices that may influence SIDS among infants. The research design was a descriptive cross-sectional design and a 107 postnatal mothers were recruited focusing on the aim of the study through purposive sampling technique. A structured knowledge questionnaire and self-reported practice checklist was prepared and validated from experts.

The findings of the study revealed that the majority of subjects 57 (53.3%) had good knowledge with a mean score of 9.34 ± 1.83 (maximum score-15). The mean practice score on prevention of SIDS among subjects was 13.76 ± 1.13 (maximum score-16). There was no significant correlation between knowledge and practice (r = −0.38, p = 0.7). However, significant association was seen between knowledge on prevention of SIDS and baseline variables such as education (p = 0.001), occupation (p = 0.001), place of residence (p = 0.001), and family income (p = 0.01). Moreover, there was a significant association between self-reported practice and age of mothers (p = 0.03).

The study findings showed good knowledge level among majority of the mothers and executed good practice toward care of the infant. However, 30.8% of the mothers had average to poor level of knowledge, which is significant and needs attention.
Adding blue to manganese-based lighting materials
Authors: Patrick Chris
Published: November 2022

Manganese-based organic-inorganic metal halides with full-spectral emission could be the future of multicolor lighting and anti-counterfeiting technology.
Sparse drifter data and mathematical approach map ocean eddies
Authors: Piccone Ashley
Published: November 2022

The scarcity of drifter data makes detecting oceanic eddies difficult, but a new mathematical tool can do the job using just a single buoy.
Facile self-assembly of sandwich-like MXene layered multiscale structure nanocomposite
Authors: Guo ZhiJin , Zhang Yan , Zhou JianPing , Sun DaQian , Li HongMei
Published: November 2022

V2CT
x
shows a low ion diffusion barrier, while the multiple oxidation states of vanadium allow V2CT
x
to participate in multi-electron redox reactions, which demonstrates a greater potential for electrochemical energy storage applications. However, the lateral arrangement of V2CT
x
lamellae tends to cause the accumulation and collapse of the structure. Herein, the two-dimensional layered V2CT
x
is modified with Ag+ and Cu2+, the V2CT
x
/Ag/Cu composite is successfully prepared. The Ag nanoparticles (NPs) and Cu NPs grown between the layers of V2CT
x
can effectively suppress the accumulation of the lamellae and ensure the smooth transfer of electrolyte ions and electrons between the layers. Meanwhile, the doping of Ag NPs and Cu NPs can enlarge the interlayer spacing of V2CT
x
, which can expose more active contact sites for electrolyte ions, shorten the diffusion path of electrolyte ions, and effectively improve the electrochemical performance of V2CT
x
. The Ag NPs and Cu NPs agglomerate in the delamination of V2CT
x
to form a conductive channel covering multiple layers, which facilitates cross-layer electron transfer and reduces the internal resistance of the V2CT
x
/Ag/Cu composite. Basis on the above reasonable structural designs, the internal resistance of the V2CT
x
/Ag/Cu composite is only 0.72 Ω, showing excellent diffusion ability of K+. The result represents a new step forward in exploring the electrochemical properties of two dimensional materials of V2CT
x
.
QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data
Authors: Ssekagiri Alfred , Jjingo Daudi , Lujumba Ibra , Bbosa Nicholas , Bugembe Daniel L , Kateete David P , Jordan I King , Kaleebu Pontiano , Ssemwanga Deogratius
Published: November 2022

Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%.

Availability and implementation

QuasiFlow and corresponding documentation are publicly available at https://github.com/AlfredUg/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces
Authors: Réau Manon , Renaud Nicolas , Xue Li C , Bonvin Alexandre M J J
Published: November 2022

Motivation

Gaining structural insights into the protein–protein interactome is essential to understand biological phenomena and extract knowledge for rational drug design or protein engineering. We have previously developed DeepRank, a deep-learning framework to facilitate pattern learning from protein–protein interfaces using convolutional neural network (CNN) approaches. However, CNN is not rotation invariant and data augmentation is required to desensitize the network to the input data orientation which dramatically impairs the computation performance. Representing protein–protein complexes as atomic- or residue-scale rotation invariant graphs instead enables using graph neural networks (GNN) approaches, bypassing those limitations.

Results

We have developed DeepRank-GNN, a framework that converts protein–protein interfaces from PDB 3D coordinates files into graphs that are further provided to a pre-defined or user-defined GNN architecture to learn problem-specific interaction patterns. DeepRank-GNN is designed to be highly modularizable, easily customized and is wrapped into a user-friendly python3 package. Here, we showcase DeepRank-GNN’s performance on two applications using a dedicated graph interaction neural network: (i) the scoring of docking poses and (ii) the discriminating of biological and crystal interfaces. In addition to the highly competitive performance obtained in those tasks as compared to state-of-the-art methods, we show a significant improvement in speed and storage requirement using DeepRank-GNN as compared to DeepRank.

Availability and implementation

DeepRank-GNN is freely available from https://github.com/DeepRank/DeepRank-GNN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Feasible weighted projected principal component analysis for semi-parametric factor models
Authors: Choi Sung Hoon
Published: November 2022

Various factor estimation procedures have been developed, based on the latent factor model. They often consider general conditions that allow for correlations and heteroscedasticity. However, the conventional principal components method does not efficiently estimate the parameters. It also does not accommodate additional covariates, which explain the unknown factors, even if they are available. In particular, a few aggregated macroeconomic variables can be used as covariates in diffusion index forecasts. To account for these features, I propose the feasible weighted projected principal component (WPPC) analysis, based on semi-parametric factor models, and also establish its asymptotic properties. In addition, I apply the WPPC method to the diffusion index forecasting model. Finally, I investigate the performance of the WPPC estimator in forecasting excess bond returns using US bond market and macroeconomic data.
Modeling the thermal analysis of the uncovered solar collectors using perforated absorbent plate
Authors: Anupong Wongchai , Treve Mark , Muda Iskandar , Sapaev I B , Arana Julio Francisco Jimenez , Alfilh Raed H C , Alvarez José Ricardo Nuñez , Almassi Morteza
Published: November 2022

Uncovered solar collectors using perforated absorbent plates are a variety of reception collectors that are used for solar heating of air for consumption in air conditioning systems and dryers. The thermal performance of these collectors is subject to various factors including diameter and step holes, air suction velocity and solar radiation. Using modeling, a proper evaluation of the effect of each of these parameters on the thermal performance of the collector can be obtained. In this paper, by using heat transfer and energy balance modeling in different components of the sample collector, the effect of each of these parameters is estimated by using the preheatment of building air, thermal efficiency and output temperature of the collector according to the parameters of solar radiation, air suction velocity, diameter and step of the holes of the absorbent plate. Also, the efficiency of heat exchange of perforated plates is estimated for air suction velocity, diameter and step of holes. The results show that increasing the suction rate of air and solar radiation increases the thermal efficiency of the collector. Also, efficiency of the heat exchange (εHX), which decreases with increasing suction speed, is due to the decrease in the output temperature of the collector because of the increase in the amount of inlet air to it, increasing the suction rate from 60 m/h to 160 m/h reduces the efficiency of the heat exchange by 30%.
International Standardized Nomenclature for Outbred Stocks of Laboratory Animals
Authors: Festing M , Kondo K , Loosli R , Poiley S M , Spiegel A
Published: November 2022

Preface by the Secretary-General of ICLA

In accordance with the «Aims of ICLA» (ICLA Bulletin No. 26, March 1970) the Governing Board established in 1969 a Working Party to prepare an International Nomenclature System for Outbred Animals.

The members were: Professor, Dr. A. Spiegel, Federal Republic of Germany, chairman.Dr. M. Festing, United KingdomDr. K. Kondo, JapanDr. R. Loosli, SwitzerlandMr. S. Poiley, U.S.A.

The nomenclature rules, completed and approved by the ICLA Governing Board on 8 December 1971, are published herewith. I am convinced that this system will bring order out of the existing chaos. The system is an offer to the world laboratory animal science, particularly the breeders and users. Editors of scientific journals, catalogues, and indices all over the world are also encouraged to require and use animal stock identification by this system for outbred animals used in experimentation.

The ICLA Governing Board would have preferred to have seen an international centralization of symbol registration. However, the ICLA Secretariat has not got the capacity necessary for such a task and some practical solution to the registration problem will have to be found by the Governing Board. A final aim should then be for ICLA to publish a comprehensive world list of breeder symbols at intervals.

Oslo, January 1972

Stian Erichsen 

Secretary-General
Finite difference schemes for a size structured coagulation-fragmentation model in the space of Radon measures
Authors: Ackleh Azmy S , Lyons Rainey , Saintier Nicolas
Published: November 2022

We study a size-structured coagulation-fragmentation model formulated in the space of Radon measures. We reformulate this model as a mass conservation law on this space and establish its well-posedness. We develop and compare multiple finite difference schemes. In particular, we develop a fully explicit scheme and a semi-implicit scheme for the structured coagulation-fragmentation model, and we develop an explicit scheme based on the conservation law formulation. We prove convergence for each scheme and test the schemes against multiple well-known examples. We analyze and compare important properties of each scheme, such as mass conservation, order of convergence and computation time.
Virtual element method for the Navier–Stokes equation coupled with the heat equation
Authors: Antonietti Paola F , Vacca Giuseppe , Verani Marco
Published: November 2022

We consider the virtual element discretization of the Navier–Stokes equations coupled with the heat equation where the viscosity depends on the temperature. We present the virtual element discretization of the coupled problem, show its well-posedness and prove optimal error estimates. Numerical experiments that confirm the theoretical error bounds are also presented.
One Minute of EEG Data Provides Sufficient and Reliable Data for Identifying Lewy Body Dementia
Authors: Jin Lucy , Nawaz Huma , Ono Kenichiro , Nowell Justin , Haley Erik , Berman Brian D. , Mukhopadhyay Nitai D. , Barrett Matthew J.
Published: November 2022

Objective:

To determine the minimum duration of electroencephalography (EEG) data necessary to differentiate EEG features of Lewy body dementia (LBD), that is, dementia with Lewy bodies and Parkinson disease dementia, from non-LBD patients, that is, Alzheimer disease and Parkinson disease.

Methods:

We performed quantitative EEG analysis for 16 LBD and 14 non-LBD patients. After artifact removal, a fast Fourier transform was performed on 90, 60, and thirty 2-second epochs to derive dominant frequency; dominant frequency variability; and dominant frequency prevalence.

Results:

In LBD patients, there were no significant differences in EEG features derived from 90, 60, and thirty 2-second epochs (all P>0.05). There were no significant differences in EEG features derived from 3 different groups of thirty 2-second epochs (all P>0.05). When analyzing EEG features derived from ninety 2-second epochs, we found that LBD had significantly reduced dominant frequency, reduced dominant frequency variability, and reduced dominant frequency prevalence alpha compared with the non-LBD group (all P<0.05). These same differences were observed between the LBD and non-LBD groups when analyzing thirty 2-second epochs.

Conclusions:

There were no differences in EEG features derived from 1 minute versus 3 minutes of EEG data, and both durations of EEG data equally differentiated LBD from non-LBD.
The Influence of Vaginal Microbiome and Clinical Factors on HPV Clearance: A Prospective Study
Authors: Yang Zhongzhou , Wu Hao , Wang Xiaohan , Tong Guoqing , Huang Zhuoqi , Wang Jie , Jiang Yuxin , Cao Min , Wang Yue , Deng Xingxing , Liu Na , Qi Le , Liu Mengping , Hutchins Andrew , Yao Bin , Shi Mang , Li Yantao , Zhu Shida
Published: November 2022

Background

Although the microbiome and lifestyle factors are associated with HPV clearance, few studies have systematically explored the relevant factors. This formal follow-up prospective study aims to predict HPV clearance based on vaginal microbiota and lifestyle clinical factors.

Participants and Methods

Participants were recruited through a digital eHealth platform. Participants were unvaccinated for HPV and were assessed at baseline and a follow-up consultation between August 2021 and January 2022. Both clinical factors and cervicovaginal mucus (CVM) samples were collected from each participant. CVM samples were used to detect HPV and characterize vaginal microbiome by metagenomics. Lifestyle clinical factors were grouped into low-, middle-, and high-risk to operate the stratified analysis as well as survival analysis for HPV clearance.

Results

We recruited 141 HPV-positive women at baseline. For the first follow-up, there were 116 HPV persistent infection and 25 HPV clearance participants. Among 28 clinical factors, six factors were identified as significantly associated: age, age of first sexual intercourse, diet balance, marital status, abortion and physical activity under the stratified analysis. Those with a middle-risk diet balance had an odds ratio (OR) (3.91, 95% CI: 1.02-28.03). Those with extremely high-risk diet balance also had a high OR (11.26, 95% CI: 1.35-122.14), but with a faster and higher proportion of HPV clearance. Conversely, clinical factors with low risk and correspondingly faster HPV clearance were physical activity, sleep quality, depression, and anxiety. Although HPV clearance was unrelated to each microbiome specie, HPV clearance was related to the lower overall diversity of species in the vaginal microbiome and the larger abundance oflactobacillus inners.

Conclusions

This study systematically depicts HPV clearance influenced by clinical factors and its relationship with the vaginal microbial ecosystem. HPV clearance can be improved by modulation of lifestyle habits and marital relationship. The findings from this prospective study have implications for the future design of guidelines to control cervical cancer or other HPV-related cancer, and therefore might be beneficial to women infected with HPV.
A three-step pathway from (2-aminophenyl)chalcones to novel styrylquinoline–chalcone hybrids: synthesis and spectroscopic and structural characterization of three examples
Authors: Vera Diana R. , Mantilla Juan P. , Palma Alirio , Díaz Costa Iván , Cobo Justo , Glidewell Christopher
Published: November 2022

Three new styrylquinoline–chalcone hybrids have been synthesized using a three-step pathway starting with Friedländer cyclocondensation between (2-aminophenyl)chalcones and acetone to give 2-methyl-4-styrylquinolines, followed by selective oxidation to the 2-formyl analogues, and finally Claisen–Schmidt condensation between the formyl intermediates and 1-acetylnaphthalene. All intermediates and the final products have been fully characterized by IR and 1H/13C NMR spectroscopy, and by high-resolution mass spectrometry, and the three products have been characterized by single-crystal X-ray diffraction. The molecular conformations of (E)-3-{4-[(E)-2-phenylethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H21NO, (IVa), and (E)-3-{4-[(E)-2-(4-fluorophenyl)ethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H20FNO, (IVb), are very similar. In each compound, the molecules are linked into a three-dimensional array by hydrogen bonds, of the C—H...O and C—H...N types in (IVa), and of the C—H...O and C—H...π types in (IVb), and by two independent π–π stacking interactions. By contrast, the conformation of the chalcone unit in (E)-3-{4-[(E)-2-(2-chlorophenyl)ethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H20ClNO, (IVc), differs from those in (IVa) and (IVb). There are only weak hydrogen bonds in the structure of (IVc), but a single rather weak π–π stacking interaction links the molecules into chains. Comparisons are made with some related structures.
The Open Language Archives Community: a 20-year update
Authors: Bird Steven , Simons Gary F.
Published: November 2022

Purpose

This paper reports on the first 20 years of the Open Language Archives Community (OLAC), comprehensive infrastructure for indexing and discovering language resources.

Design/methodology/approach

We begin with the original vision, assess progress relative to the original requirements, and identify ongoing challenges.

Findings

Based on the overview of OLAC history and recent developments and on the analysis of the situation in the language archives area as a whole, the authors propose an agenda for a more sustainable future for open language archiving.

Originality/value

This paper examines the progress of OLAC and discusses improvements in such areas as participation, access, and sustainability.
You have kids? How being a parent influences status and trust in the workplace
Authors: Zhang Teng , Soderberg Andrew T.
Published: November 2022

Purpose

This paper aims to examine how individuals are perceived by their coworkers, specifically how individuals’ gender and parental status affect how much social status they are accorded in the workplace, and the extent to which they are trusted by their coworkers.

Design/methodology/approach

The authors recruited an online sample of adults across North America to respond to survey questions about one of their current or former coworkers. Information was collected to determine the gender and parental status of this coworker and their perceptions of this person’s social status and how much they trusted this person.

Findings

The results showed that having children can affect how individuals are perceived by their coworkers. Specifically, compared with working men without children, working fathers were perceived to have higher status and were trusted more by their coworkers. In addition, working mothers were perceived by their coworkers to have higher status than, and trusted as much as, working women without children. Exploratory analyses revealed that working fathers were also perceived to be warmer than working men without children.

Originality/value

This study examines important workplace perceptions of parents from the perspective of their coworkers rather than from the employer perspective that is largely based on hypothetical scenarios as used in previous research.
The effect of anti-money laundering regulations on earnings management: evidence of Iran
Authors: Abdi Shima , Soroushyar Afsaneh
Published: November 2022

Purpose

The purpose of this study is to examine the impact of anti-money laundering (AML) regulations on accrual earnings management (AEM) and real earnings management (REM) in Iran’s emerging capital market.

Design/methodology/approach

The panel data regression is used to testing hypotheses. The sample includes 2,020 data and 202 companies listed on the Tehran Stock Exchange (TSE) over a period of ten years from 2012 to 2021. Also, the companies covered in this study include financial and nonfinancial companies. Furthermore, the data related to the research variables were extracted from the annual financial statements and the TSE database.

Findings

The results show that compliance with AML regulations leads to a reduction in AEM and REM. In other words, companies with higher money laundering (ML) tend to manage their earnings, which is in line with agency theory.

Practical implications

This study has implication for policymakers and regulators, auditors and managers. Considering the negative impact of AML regulations on earnings management (EM), Iranian auditing firms need to emphasize on the full implementation of AML regulations in TSE. Also, the results of this research may aid policymakers and regulators to detect financial crimes through accounting signals.

Originality/value

To the best of the authors’ knowledge, this is the first study in an Iran capital market to examine the impact of AML regulations on EM in financial and nonfinancial companies. Previous research has not controlled for the effects of financial companies. Prior studies have not examined the effects of financial companies. In addition, this study differentiates itself from previous studies by introducing a new method for measuring the independent ML variable based on auditor opinions. The obtained data can aid international bodies to better understand compliance with ML regulations in Iran and can reduce their concerns in negotiations.
Systematically Detecting Patterns of Social, Historical and Linguistic Change: The Framing of Poverty in Times of Poverty
Authors: Schneider Gerold
Published: November 2022

The linguistic DNA project seeks to understand the evolution of philosophy, society and language during the Modern English period. Corpora like Early English Books Online (EEBO), Corpus of Late Modern English Texts (CLMET) and Corpus of Historical American English (COHA) allow us to apply statistical data‐driven models extracting patterns to confirm our expectations. As systems biology has revolutionised biology by systematically searching for all patterns, we detect patterns in our data systematically with contextual and distributional semantic approaches, an approach that could be called systems history. We uncover semantic patterns with methods from text mining, computational linguistics and digital humanities. We normalise the spelling automatically to present‐day variants and use bottom‐up analyses to step from words to concepts: collocations, topic modelling and distributional semantics. We illustrate the approaches with two case studies: associations of poverty changing across time, and Charles Dickens social criticism, his vision of helping to improve the situation of the poor. As no gold standard for our task exists, our approaches are exploratory, which entails considerable manual intervention, e.g. sifting candidate lists, reading excerpts and interpreting topic models. A fully automatic approach is currently neither feasible nor envisaged: semi‐automatic approaches give researchers the inspiring opportunity to interact with the texts in a constant move between distant and close reading. The different characteristics of the various statistical methods offer complementary perspectives.