bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum field theories, Markov random fields and machine learning
Authors: Bachtis Dimitrios , Aarts Gert , Lucini Biagio
Published: March 2022

The transition to Euclidean space and the discretization of quantum field theories on spatial or space-time lattices opens up the opportunity to investigate probabilistic machine learning within quantum field theory. Here, we will discuss how discretized Euclidean field theories, such as the ϕ
4 lattice field theory on a square lattice, are mathematically equivalent to Markov fields, a notable class of probabilistic graphical models with applications in a variety of research areas, including machine learning. The results are established based on the Hammersley-Clifford theorem. We will then derive neural networks from quantum field theories and discuss applications pertinent to the minimization of the Kullback-Leibler divergence for the probability distribution of the ϕ
4 machine learning algorithms and other probability distributions.
Machine Learning the Square-Lattice Ising Model
Authors: Çivitcioğlu Burak , Römer Rudolf A. , Honecker Andreas
Published: March 2022

Recently, machine-learning methods have been shown to be successful in identifying and classifying different phases of the square-lattice Ising model. We study the performance and limits of classification and regression models. In particular, we investigate how accurately the correlation length, energy and magnetisation can be recovered from a given configuration. We find that a supervised learning study of a regression model yields good predictions for magnetisation and energy, and acceptable predictions for the correlation length.
Effect of mask-film properties on the initial GaAs nanowire growth stages
Authors: Zhikharev P V , Shwartz N L
Published: March 2022

The initial self-catalyze GaAs nanowire (NW) growth stages were studied using Monte Carlo simulation. We analyzed the effect of the mask-film etching rate with liquid gallium for different thicknesses on the initial nanowire formation stages. At a high etching rate NWs do not form on thick mask-films. A high etching rate of a thin film-mask can lead to lateral Ga drop motion over the crystalline substrate surface, which delays the nanowire formation onset. It is shown that, for the NW formation, it is necessary to maintain the correct ratio between the film thickness, etching rate, Ga and As2 flux intensities.
Linear and nonlinear optical properties of vertically coupled cylindrical double quantum dots with modified Pöschl-Teller potential
Authors: Sargsian T A , Vinnichenko M Ya , Hayrapetyan D B
Published: March 2022

Linear and third-order nonlinear absorption coefficients have been theoretically investigated in a system of vertically coupled cylindrical double quantum dots with the modified Pöschl-Teller potential in the axial direction and parabolic potential in the radial direction. Also, changes in the refractive index in these conditions were obtained. For intraband optical transitions of charge carriers in such system the selection rules have been obtained. The behaviour of the linear, nonlinear and total absorption spectra and changes in the refractive index have been theoretically observed for different lattice temperatures and illustrated by the corresponding graphs for two temperatures.
Photoluminescence temperature quenching of H2TPP and ZnTPP tetraphenylporphyrins thin films
Authors: Alimova E S , Zakharova I B , Elistratova M A
Published: March 2022

Photoluminescence temperature quenching of tetraphenylporphyrins thin films on silicon substrates have been investigated. Free-based tetraphenylporphyrin (H2TPP) and Zinc-tetraphenylporphyrin (ZnTPP) films were obtained by thermal evaporation in vacuum. The photoluminescence properties of these samples are observed in the wide temperature range from 77 to 300 K. The temperature-depended photoluminescence intensity of ZnTPP exhibits abnormal behaviour. An increase in the photoluminescence intensity is observed in the temperature range of 77-180 K. We suppose that charge carriers are trapped by non-radiative centres when the temperature decreases down to 77 K. The release of carriers occurs with a further temperature increase. In addition, there are sharp increases in the luminescence intensity of thin H2TPP and ZnTPP films at a temperature of 270 K, which are associated with a second-order phase transition.
Climate change impacts and adaptation strategies for crops in West Africa: a systematic review
Authors: Carr Tony W , Mkuhlani Siyabusa , Segnon Alcade C , Ali Zakari , Zougmoré Robert , Dangour Alan D , Green Rosemary , Scheelbeek Pauline
Published: March 2022

Agriculture in West Africa faces the challenge of meeting the rising demand for food as national incomes and populations increase while production becomes more uncertain due to climate change. Crop production models can provide helpful information on agricultural yields under a range of climate change scenarios and on the impact of adaptation strategies. Here, we report a systematic review of the impact of climate change on the yield of major staple crops in West Africa. Unlike earlier reviews we pay particular attention to the potential of common agricultural adaptation strategies (such as optimised planting dates, use of fertilisers and climate-resilient crop varieties) to mitigate the effects of climate change on crop yields. We systematically searched two databases for literature published between 2005 and 2020 and identified 35 relevant studies. We analysed yield changes of major staple crops (maize, sorghum, rice, millet, yam, cassava and groundnuts) caused by different climate change and field management scenarios. Yields declined by a median of 6% (−8% to +2% depending on the crop) due to climate change in all scenarios analysed. We show that the common adaptation strategies could increase crop yields affected by climate change by 13% (−4% to +19% depending on the strategy) as compared to business-as-usual field management practices, and that optimised planting dates and cultivars with longer crop cycle duration could in fact offset the negative effects of climate change on crop yields. Increased fertiliser use has not mitigated the impact of climate change on crops but could substantially increase yields now and in the future. Our results suggest that a combination of increased fertiliser use and adopting cropping practices that take advantage of favourable climate conditions have great potential to protect and enhance future crop production in West Africa.
CFD analysis of Effect of journal bearing lubricated with non-Newtonian fluid
Authors: Prakash sharma Jai , Tyagi M R , Thakre G D
Published: March 2022

The present paper deals with the CFD analysis of hydrodynamic bearing lubricated with a non-Newtonian fluid and the non-Newtonian behaviour of lubricant is represented by a power-law. Bearing parameters such as fluid film pressure and load-carrying capacity are determined by varying the power-law index (n) in terms of its viscosity from 0.8 to 1.2 under steady-state conditions through the CFX 17.2 software module and the flow model opted as Laminar based on Reynolds number calculation as per the geometry developed for the simulation. The relationship between the pressure and load-carrying capacity are also obtained for different relative clearance, revolution per minute and L/D ratio. Fluid film pressure profile was drawn by varying input parameters at different power-law index for understanding the performance of HDB under different regimes i.e. dilatant, Newtonian and pseudoplastic fluids. Plots were also created between Pressure, load carrying capacity and power law index to study the performance of HDB. This has been observed that the bearings lubricated with dilatant fluid (n >1) have higher pressure and load carrying capacity as compared to those lubricated with pseudoplastic fluid (n < 1). Occurrences of cavitation were also seen at lower angle with increases in power law index for 0.0006 relative clearance but increases at 0.0008.
Face Recognition Method Based on Residual Convolution Neural Network
Authors: Husain Arshi , Vishvakarma Virendra P.
Published: March 2022

With the advancement of information technology and societal growth, social security has become more important than ever. Face recognition, as compared to other traditional recognition methods like fingerprint recognition, palm recognition, etc, has the benefit that it is contact less, and now it is becoming one among the most prominent technologies in development. Although there are numerous recognition systems that use DNNs in the field of facial expression recognition, their accuracy and practicality are still insufficient for real-world applications. A facial recognition approach based on Resnet 152 v2 has been proposed in this work. In this paper, a residual learning approach is presented to make the training of networks that are far deeper than previously employed networks easier. The proposed method, employs the AT&T face dataset, and supposing that normalization and segmentation are complete, we concentrate on the subtask of person verification and recognition, demonstrating performance using a testing database comprising illumination, pose, expression and occlusion variations. SoftMax is the activation function that has been used, which adjusts the output sum up to one allowing it to be understood as probabilities. Then, the model would generate a judgment depending on which option has a strong likelihood. This system employs Adam as an optimizer to control the learning rate through training and categorical cross entropy as its loss function. The proposed approach has a 97 percent face recognition accuracy on AT&T dataset, showing its efficacy after a significant number of analyses and experimental verification.
Water absorption study and characterization of polymer composites developed from discarded nylon carpet
Authors: Verma Rajesh Kumar , Jaiswal Balram , Vishwakarma Rahul , Kumar Kuldeep , Kumar Kaushlendra
Published: March 2022

The scientific objective of this work is to reuse the polymer materials generated from carpet waste. The nylon obtained from the discarded carpet was used as reinforcement material into the epoxy matrix phase. A modified approach of Vacuum-assisted resin transfer molding (VARTM) was used to infuse the mixture of epoxy and hardener into the nylon carpet polymer composites. This investigates the water absorption behavior of carpet waste composite. It will justify the application of proposed composites for lightweight structural applications in a moisture environment. The nylon fiber-based-epoxy composite was dipped in water as per ASTM standard for a different duration, namely, 24, 48, 72, 144 hours. The findings demonstrate that it can effectively withstand in moisture environment, and a maximum 4.5% weight of samples increased among all the samples for a different duration. Also, the developed composite showed a lower water diffusion co-efficient than the nail head structure and linden wood. Also, the carpet waste composite samples were investigated for thermal degradation and chemical behavior using X-Ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, respectively. The finding shows that the proposed composite could be used for lightweight components such as dashboard panels, sound absorbers, panel sheets, wall tiles, etc.
A study on engine piston optimization by generative design approach
Authors: Arunkumar A , Sooriyamoorthy A , Mishael C , Giri A
Published: March 2022

Significant enterprises today favor the cooperation of generative plans in the manufacturing and assembling departments. Therefore our aim is to dwell on the more straightforward degrees of generative design to demonstrate the modification of boundary conditions and properties to exhibit modern applications. Generative Design has demonstrated to be a significant upgrade in the machine-producing side of the business because of the simplicity in changes, higher resilience, and reduced number of faults that arise. Nevertheless owing to the added complex shape of structures, the model generation and design are posed with challenges. This paper involves the examination and generative design of a 4-Stroke engine piston. The proposed method is validated through a study which closely resembles a real life prototype. The examination aims to dissect and detail a newly formed design grid for the current cylinder of the F20C 4 - stroke 4 - cylinder engine at the core of the Honda S2000. Our aim to study on piston design, which makes it lighter and more efficient while keeping the similar volume yield in the cylinder. The paper depicts the process of optimizing the component through mass reduction where the mass was reduced by close to twenty three percent.
Artificial electric field algorithm based superconducting magnetic energy storage system for damping inter area oscillations
Authors: Manzoor Aaqib , Mufti Mairaj ud Din , Nabi Mohammad Younis
Published: March 2022

This paper presents an artificial electric field algorithm (AEFA) based optimal control of superconducting magnetic energy storage (SMES) system for damping inter area oscillations. The artificial electric field algorithm is based upon Coulomb’s law of electrostatics and Newton’s law of motion. The proposed technique is used to optimize the SMES controller parameters for effective damping of inter area oscillations. Because of the potential for system damage and the subsequent constraints on power transmission along select lines, low frequency inter-area oscillations have been identified as a serious problem in utility systems. With the advancement in power electronics technologies, a new option for damping of power system oscillations has been created by integrating energy storage devices to it. The proposed scheme is tested on a two area interconnected power system which is suitably modelled and it’s modal analysis is done. The participation of each area towards the inter area mode is analyzed by using participation matrix and the suitable placement of SMES units is decided accordingly. MATLAB Simulations are carried out to prove the efficacy of proposed scheme. The simulation results show that proposed SMES controller along with the incorporation of SMES units to each generator bus effectively damps out the inter area oscillations.
Memristive effects due to charge transfer in graphene gated through ferroelectric CuInP2S6
Authors: Dey Anubhab , Yan Wenjing , Balakrishnan Nilanthy , Xie Shihong , Kudrynskyi Zakhar R , Makarovskiy Oleg , Yan Faguang , Wang Kaiyou , Patanè Amalia
Published: March 2022

Ferroelectricity at the nanometre scale can drive the miniaturisation and wide application of ferroelectric devices for memory and sensing applications. The two-dimensional van der Waals (2D-vdWs) ferroelectrics CuInP2S6 (CIPS) has attracted much attention due to its robust ferroelectricity found in thin layers at room temperature. Also, unlike many 2D ferroelectrics, CIPS is a wide band gap semiconductor, well suited for use as a gate in field-effect transistors (FETs). Here, we report on a hybrid FET in which the graphene conducting channel is gated through a CIPS layer. We reveal hysteresis effects in the transfer characteristics of the FET, which are sensitive to the gate voltage, temperature and light illumination. We demonstrate charge transfer at the CIPS/graphene interface in the dark and under light illumination. In particular, light induces a photodoping effect in graphene that varies from n- to p-type with increasing temperature. These hybrid FETs open up opportunities for electrically and optically controlled memristive devices.
Smart Piezo-bonded carbon fibre/epoxy composite structure: experiments and finite element simulation
Authors: Jerold John Britto J , Vasanthanathan A
Published: March 2022

Smart sensors patched to composite structures assist in the prediction of the mechanical behaviour of the structures. The present paper used finite element modelling and experimental procedures to conduct a detailed study on the response of composite laminate bonded with smart piezoelectric material. Fibre reinforced epoxy composite laminate was fabricated using the vacuum assisted resin transfer method. Test coupons in accordance with ASTM standards were prepared using high-speed and high-pressure abrasive water jet cutting. The mechanical properties of the composites were obtained through material characterization and the material properties were incorporated into the Finite element model. The layer-wise strain rate was computed with the ANSYS® Composite Prep Post module. A finite element model of a composite with piezoelectric sensor patch was created in ANSYS® APDL and harmonic analysis was conducted to determine the optimal frequency range for the applied load. An attempt was made to measure the strain by affixing lead zirconate titanate to a carbon fibre reinforced polymer laminate for cantilever configuration, and the LabVIEW® VI software module was integrated with the NI myDAQ system to detect the corresponding voltage for the excited frequency. The values of the generated voltage through numerical simulations were verified and validated using experimental counterparts.
Mechanochemical synthesis of stable, quantum-confined CsPbBr3 perovskite nanocrystals with blue-green emission and high PLQY
Authors: Goyal A , Andrioti E , Tang Y , Zhao Q , Zheng K , Newell K D , Schall P
Published: March 2022

Cesium lead halides are a family of bright, visible-light emitting materials with near-unity photoluminescence quantum yield (PLQY) in nanocrystals (NCs). The usual way to achieve visible light-emission tunability is by mixing halides, which often leads to phase separation and poor stability. While the NCs should also show size-dependent PL emission, reports on strong quantum confinement in these materials are scarce. Here, we report the synthesis of quantum-confined cesium lead bromide (CsPbBr3) NCs via a facile, environment-friendly, and scalable high-energy mechanochemical synthesis route. The PLQY measured is ∼85%, even after 90 days of synthesis, and the emission wavelength is shifted from green, 520 nm, to blue, 460 nm by quantum confinement in NCs of size 3–5 nm. Micro-PL optical spectroscopy and atomic force microscopy confirm the size tunability of PL on a single-dot scale. Our work demonstrates the potential of mechanochemical synthesis in the medium-scale production of bright luminescent quantum-confined NCs that could be extended to other materials as well.
Liquid cooling of stacked piezoelectric actuators for high-power operation
Authors: Zhong Jianpeng , Nishida Rina , Shinshi Tadahiko
Published: March 2022

In this article, we propose a liquid cooling solution to reduce the temperature rise and expand the working range of stacked piezoelectric actuators (PEAs) for high-frequency and large-stroke operation. Based on an analysis and preliminary testing of the power dissipation and temperature rise, a specific liquid cooling solution for a single PEA is designed and its effectiveness is verified through experiments. To incorporate liquid cooling into a high-bandwidth fast steering mirror (FSM) system driven by PEAs, a compact and self-contained cooling unit is proposed and evaluated. Subsequent experimental results validate its effectiveness, but also show some deficiencies for this cooling solution. To further improve the cooling efficiency, two new coolants are adopted based on an analysis of the heat transfer coefficient, and a suitable direct liquid cooling solution is established. Experimental results show that the cooled PEA can operate continuously over 8 kHz with a peak-to-peak voltage of 100 V whilst its maximum temperature is restricted to around 40 °C using this cooling solution. The reliability and coolant insulation properties have been verified by a 3-month long continuously operational test.
RCX—an R package adapting the Cytoscape Exchange format for biological networks
Authors: Auer Florian , Kramer Frank
Published: March 2022

Motivation

The Cytoscape Exchange (CX) format is a JSON-based data structure designed for the transmission of biological networks using standard web technologies. It was developed by the network data exchange, which itself serves as online commons to share and collaborate on biological networks. Furthermore, the Cytoscape software for the analysis and visualization of biological networks contributes structure elements to capture the visual layout within the CX format. However, there is a fundamental difference between data handling in web standards and R. A manual conversion requires detailed knowledge of the CX format to reproduce and work with the networks.

Results

Here, we present a software package to create, handle, validate, visualize and convert networks in CX format to standard data types and objects within R. Networks in this format can serve as a source for biological knowledge and also capture the results of the analysis of those while preserving the visual layout across all platforms. The RCX package connects the R environment for statistical computing with outside platforms for storage and collaboration, as well as further analysis and visualization of biological networks.

Availability

RCX is a free and open-source R package, available on Bioconductor from release 3.15 (https://bioconductor.org/packages/RCX) and via GitHub (https://github.com/frankkramer-lab/RCX).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation
Authors: Wei Yu , Li Shanshan , Li Zhonglin , Wan Ziwei , Lin Jianping
Published: March 2022

Motivation

In the process of discovery and optimization of lead compounds, it is difficult for non-expert pharmacologists to intuitively determine the contribution of substructure to a particular property of a molecule.

Results

In this work, we develop a user-friendly web service, named interpretable-absorption, distribution, metabolism, excretion and toxicity (ADMET), which predict 59 ADMET-associated properties using 90 qualitative classification models and 28 quantitative regression models based on graph convolutional neural network and graph attention network algorithms. In interpretable-ADMET, there are 250 729 entries associated with 59 kinds of ADMET-associated properties for 80 167 chemical compounds. In addition to making predictions, interpretable-ADMET provides interpretation models based on gradient-weighted class activation map for identifying the substructure, which is important to the particular property. Interpretable-ADMET also provides an optimize module to automatically generate a set of novel virtual candidates based on matched molecular pair rules. We believe that interpretable-ADMET could serve as a useful tool for lead optimization in drug discovery.

Availability and implementation

Interpretable-ADMET is available at http://cadd.pharmacy.nankai.edu.cn/interpretableadmet/.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Neurogenetics Collection: emerging themes and future considerations for the field in Brain
Authors: Traynor Bryan J , Al-Chalabi Ammar
Published: March 2022

Genomics has emerged over the last two decades as a fundamental approach to understanding the molecular basis of human diseases. This Collection brings together some recent articles published in Brain, selected to illustrate the impact of genomics on neurology and to highlight emerging themes in the neurogenetics space.
The role of critical immune genes in brain disorders: insights from neuroimaging immunogenetics
Authors: Bian Beilei , Couvy-Duchesne Baptiste , Wray Naomi R. , McRae Allan F.
Published: March 2022

Genetic variants in the human leukocyte antigen and killer cell immunoglobulin-like receptor regions have been associated with many brain-related diseases, but how they shape brain structure and function remains unclear. To identify the genetic variants in HLA and KIR genes associated with human brain phenotypes, we performed a genetic association study of ∼30 000 European unrelated individuals using brain MRI phenotypes generated by the UK Biobank (UKB). We identified 15 HLA alleles in HLA class I and class II genes significantly associated with at least one brain MRI-based phenotypes (P < 5 × 10−8). These associations converged on several main haplotypes within the HLA. In particular, the human leukocyte antigen alleles within an ancestral haplotype 8.1 were associated with multiple MRI measures, including grey matter volume, cortical thickness (TH) and diffusion MRI (dMRI) metrics. These alleles have been strongly associated with schizophrenia. Additionally, associations were identified between HLA-DRB1*04∼DQA1*03:01∼DQB1*03:02 and isotropic volume fraction of diffusion MRI in multiple white matter tracts. This haplotype has been reported to be associated with Parkinson’s disease. These findings suggest shared genetic associations between brain MRI biomarkers and brain-related diseases. Additionally, we identified 169 associations between the complement component 4 (C4) gene and imaging phenotypes. We found that C4 gene copy number was associated with cortical TH and dMRI metrics. No KIR gene copy numbers were associated with image-derived phenotypes at genome-wide threshold. To address the multiple testing burden in the phenome-wide association study, we performed a multi-trait association analysis using trait-based association test that uses extended Simes procedure and identified MRI image-specific associations. This study contributes to insight into how critical immune genes affect brain-related traits as well as the development of neurological and neuropsychiatric disorders.
Performing “Realness” in a Transnational Ethnic Imaginary: Starring Dilraba on Post-2010 Chinese TV
Authors: Zhao Jamie J
Published: March 2022

This research examines the rising and televisual mediation of Xinjiang ethnic minority female celebrities within Han-centric China’s heteropatriarchal, nationalistic cultural imaginaries in the post-2010 years. Specifically, my analysis focuses on one of the most popular Uyghur female TV celebrities in China, Dilraba Dilmurat. By identifying a popular cultural discourse of “transnational ethnic imaginary” surrounding her celebrity images, I explore the ways in which her geo-cultural-ethnic-gender identity has been capitalized on by the Chinese TV industry and subjectively performed by herself within official and popular fantasies about a global, harmonious China. Ultimately, I argue that her success as a TV star in the post-2010 years exposes the artificiality and contingency of the self-imagined dimorphism of the dominant Han Chinese and ethnic minorities within the party-state’s interethnic, transnational, heteropatriarchal-structured fantasies about a global China and a homogenous Chineseness.
A shared brain system forming confidence judgment across cognitive domains
Authors: Rouault Marion , Lebreton Maël , Pessiglione Mathias
Published: March 2022

Confidence is typically defined as a subjective judgment about whether a decision is right. Decisions are based on sources of information that come from various cognitive domains and are processed in different brain systems. An unsettled question is whether the brain computes confidence in a similar manner whatever the domain or in a manner that would be idiosyncratic to each domain. To address this issue, human participants performed two tasks probing confidence in decisions made about the same material (history and geography statements), but based on different cognitive processes: semantic memory for deciding whether the statement was true or false, and duration perception for deciding whether the statement display was long or short. At the behavioral level, we found that the same factors (difficulty, accuracy, response time, and confidence in the preceding decision) predicted confidence judgments in both tasks. At the neural level, we observed using functional magnetic resonance imaging that confidence judgments in both tasks were associated to activity in the same brain regions: positively in the ventromedial prefrontal cortex and negatively in a prefronto-parietal network. Together, these findings suggest the existence of a shared brain system that generates confidence judgments in a similar manner across cognitive domains.
CarbArrayART: a new software tool for carbohydrate microarray data storage, processing, presentation, and reporting
Authors: Akune Yukie , Arpinar Sena , Silva Lisete M , Palma Angelina S , Tajadura-Ortega Virginia , Aoki-Kinoshita Kiyoko F , Ranzinger René , Liu Yan , Feizi Ten
Published: March 2022

Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
CarboGrove: a resource of glycan-binding specificities through analyzed glycan-array datasets from all platforms
Authors: Klamer Zachary L , Harris Chelsea M , Beirne Jonathan M , Kelly Jessica E , Zhang Jian , Haab Brian B
Published: March 2022

Glycan arrays continue to be the primary resource for determining the glycan-binding specificity of proteins. The volume and diversity of glycan-array data are increasing, but no common method and resource exist to analyze, integrate, and use the available data. To meet this need, we developed a resource of analyzed glycan-array data called CarboGrove. Using the ability to process and interpret data from any type of glycan array, we populated the database with the results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies. In meta-analyses of glycan-binding proteins, we observed glycan-binding specificities that were not uncovered from single sources. In addition, we confirmed the ability to efficiently optimize selections of glycan-binding proteins to be used in experiments for discriminating between closely related motifs. Through descriptive reports and a programmatically accessible Application Programming Interface, CarboGrove yields unprecedented access to the wealth of glycan-array data being produced and powerful capabilities for both experimentalists and bioinformaticians.
Implementing active play standards: a qualitative study with licensed childcare providers in British Columbia, Canada
Authors: Buckler E Jean , Mâsse Louise C , Faulkner Guy E , Puterman Eli , McConnell-Nzunga Jennifer , Naylor Patti-Jean
Published: March 2022

With an increasing number of children attending regular early childhood education and care (ECEC), this setting presents an opportunity to develop physical activity habits and movement skills of children. These behaviours play an important role in the development and well-being of children. In 2017, an Active Play Standard was introduced in British Columbia, Canada, to mandate practices related to physical activity, screen time and movement skill development in licensed ECEC. A capacity-building initiative including training and online resources was released alongside these guidelines to support implementation. The purpose of this study was to qualitatively examine the barriers and facilitators ECEC practitioners faced in implementing the standard, and to explore the role of the capacity-building initiative. Data were collected via semi-structured telephone interviews with educators (n = 23). Data were coded using thematic analysis and sorted into three major themes influencing provision of physical activity opportunities: attributes and impact of the Active Play standard and capacity-building workshop, characteristics of providers and characteristics of ECEC settings. Future studies should consider targeting factors including organizational culture and climate, and provider capacity to provide physical activity and fundamental movement skill programming, and support for facility level policies and collaborative planning processes that create a positive physical activity culture.
Genetic and phenotypic links between obesity and extracellular vesicles
Authors: Zhai Ranran , Pan Lu , Yang Zhijian , Li Ting , Ning Zheng , Pawitan Yudi , Wilson James F , Wu Di , Shen Xia
Published: March 2022

Obesity has a highly complex genetic architecture, making it difficult to understand the genetic mechanisms, despite the large number of discovered loci via genome-wide association studies (GWAS). Omics techniques have provided a better resolution to view this problem. As a proxy of cell-level biology, extracellular vesicles (EVs) are useful for studying cellular regulation of complex phenotypes such as obesity. Here, in a well-established Scottish cohort, we utilized a novel technology to detect surface proteins across millions of single EVs in each individual’s plasma sample. Integrating the results with established obesity GWAS, we inferred 78 types of EVs carrying one or two of 12 surface proteins to be associated with adiposity-related traits such as waist circumference. We then verified that particular EVs’ abundance is negatively correlated with body adiposity, while no association with lean body mass. We also revealed that genetic variants associated with protein-specific EVs capture 2–4-fold heritability enrichment for blood cholesterol levels. Our findings provide evidence that EVs with specific surface proteins have phenotypic and genetic links to obesity and blood lipids, respectively, guiding future EV biomarker research.
Identifying factors contributing to increased susceptibility to COVID-19 risk: a systematic review of Mendelian randomization studies
Authors: Luo Shan , Liang Ying , Wong Tommy Hon Ting , Schooling Catherine Mary , Au Yeung Shiu Lun
Published: March 2022

Background

To summarize modifiable factors for coronavirus disease 2019 (COVID-19) suggested by Mendelian randomization studies.

Methods

In this systematic review, we searched PubMed, EMBASE and MEDLINE, from inception to 15 November 2021, for Mendelian randomization studies in English. We selected studies that assessed associations of genetically predicted exposures with COVID-19-related outcomes (severity, hospitalization and susceptibility). Risk of bias of the included studies was evaluated based on the consideration of the three main assumptions for instrumental variable analyses.

Results

We identified 700 studies through systematic search, of which 50 Mendelian randomization studies were included. Included studies have explored a wide range of socio-demographic factors, lifestyle attributes, anthropometrics and biomarkers, predisposition to diseases and druggable targets in COVID-19 risk. Mendelian randomization studies suggested that increases in smoking, obesity and inflammatory factors were associated with higher risk of COVID-19. Predisposition to ischaemic stroke, combined bipolar disorder and schizophrenia, attention-deficit and hyperactivity disorder, chronic kidney disease and idiopathic pulmonary fibrosis was potentially associated with higher COVID-19 risk. Druggable targets, such as higher protein expression of histo-blood group ABO system transferase (ABO), interleukin (IL)-6 and lower protein expression of 2′-5′ oligoadenylate synthetase 1 (OAS1) were associated with higher risk of COVID-19. There was no strong genetic evidence supporting the role of vitamin D, glycaemic traits and predisposition to cardiometabolic diseases in COVID-19 risk.

Conclusion

This review summarizes modifiable factors for intervention (e.g. smoking, obesity and inflammatory factors) and proteomic signatures (e.g. OAS1 and IL-6) that could help identify drugs for treating COVID-19.
Persistence of a multidrug-resistant worldwide-disseminated methicillin-resistant Staphylococcus epidermidis clone harbouring the cfr linezolid resistance gene in a French hospital with evidence of interspecies transfer to several Staphylococcus aureus lineages
Authors: Côrtes Marina Farrel , André Camille , Martins Simões Patricia , Corvec Stéphane , Caillon Jocelyne , Tristan Anne , Bes Michèle , Vandenesch François , Figueiredo Agnes Marie Sá , Dupieux Céline , Laurent Frédéric
Published: March 2022

Background

Resistance to linezolid has become a worldwide concern since it is one of the last-resort antibiotics to treat multidrug-resistant staphylococcal and enterococcal infections.

Objectives

We investigated staphylococcal infections caused by 16 cfr-positive linezolid-resistant Staphylococcus epidermidis and Staphylococcus aureus isolates in a French university hospital from 2015 to 2018.

Methods

Antimicrobial susceptibility of isolates was tested by broth microdilution and gradient strips. Genetic determinants of linezolid resistance (including cfr gene and 23S rRNA mutations) were assessed by PCR and WGS; the latter was also used to characterize the cfr-carrying plasmids in S. epidermidis and S. aureus, and to explore the clonal relationship of isolates.

Results

All linezolid-resistant staphylococcal isolates harboured the same cfr-carrying plasmid, sharing 99% identity with the previously described pSA737. The three S. aureus isolates belonged to different STs (ST8, ST72, ST2416); the 13 methicillin-resistant S. epidermidis (MRSE) belonged to ST2 and harboured both cfr and mutations in genes encoding 23S rRNA and ribosomal proteins. Phylogenetic analysis grouped the MRSE isolates into two clusters, one of which (n = 12 isolates) belonged to the recently reported multidrug-resistant worldwide-disseminated S. epidermidis lineages.

Conclusions

The results presented herein highlight the persistence and efficient spread of a cfr-carrying plasmid in a hospital related both to the dissemination of a multidrug-resistant S. epidermidis clone and the in vivo interspecies transfer of cfr between S. epidermidis and S. aureus. The emergence of linezolid-resistant strains should be closely monitored, and the mechanisms involved systematically explored in order to limit the spread of plasmid-mediated resistance.
Resolving the Cohenian paradox in judicial probability theory
Authors: Du Wenjing , Niu Zihan , Xiong Minghui
Published: March 2022

The Cohenian paradox is one of the main themes of judicial probability theory and one of the core topics discussed by the new evidence scholarship. To resolve this paradox, evidence scholars nowadays have proposed various solutions, including legal probabilism, judicial Bayesian decision theory and relative plausibility theory. These three solutions can be classified into two approaches, i.e. the probabilism and the explanationism. Among them, the former includes legal probabilism and judicial Bayesian decision theory, and the latter includes the relative plausibility theory. However, the two approaches have recently begun to converge and become more understandable to each other. For example, Welch (2020, Int. J. Evid. Proof, 24, 351–373) has recently defended and improved the relative plausibility theory by substantially improving it with the help of Bayesian decision theory. In this paper, by contrast, we attempt to defend the probabilistic approach—legal probabilism and Bayesian decision theory on the basis of relative plausibility theory.
Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases
Authors: Zivkovic Igor , Ivkovic Kate , Cvetesic Nevena , Marsavelski Aleksandra , Gruic-Sovulj Ita
Published: March 2022

Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. This ensures faithful protein synthesis and cellular fitness. Using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we demonstrated that the class I editing domain clears the non-cognate amino acids well-discriminated at the synthetic site with the same rates as the weakly-discriminated fidelity threats. This unveiled low selectivity suggests that evolutionary pressure to optimize the rates against the amino acids that jeopardize translational fidelity did not shape the editing site. Instead, we propose that editing was shaped to safeguard cognate aminoacyl-tRNAs against hydrolysis. Misediting is prevented by the residues that promote negative catalysis through destabilisation of the transition state comprising cognate amino acid. Such powerful design allows broad substrate acceptance of the editing domain along with its exquisite specificity in the cognate aminoacyl-tRNA rejection. Editing proceeds by direct substrate delivery to the editing domain (in cis pathway). However, we found that class I IleRS also releases misaminoacyl-tRNAIle and edits it in trans. This minor editing pathway was up to now recognized only for class II AARSs.
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion
Authors: Serna-Pujol Núria , Salinas-Pena Mónica , Mugianesi Francesca , Le Dily François , Marti-Renom Marc A , Jordan Albert
Published: March 2022

Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
Prognostic Value of Pretreatment Red Blood Cell Distribution Width in Patients With Esophageal Cancer Who Underwent Esophagectomy
Authors: Yoshida Naoya , Horinouchi Tomo , Eto Kojiro , Harada Kazuto , Sawayama Hiroshi , Imamura Yu , Iwatsuki Masaaki , Ishimoto Takatsugu , Baba Yoshifumi , Miyamoto Yuji , Watanabe Masayuki , Baba Hideo
Published: March 2022

Objective:

This comprehensive analysis aimed to elucidate the mechanism underlying how high pretreatment red blood cell distribution width (RDW) reflects poor prognosis after esophagectomy for esophageal cancer.

Background:

Several cohort studies have reported that preoperative RDW might be a predictive marker for poor prognosis after esophagectomy; however, the underlying mechanism of this relationship has not been elucidated.

Methods:

This study included 626 patients with esophageal cancer who underwent esophagectomy between April 2005 and November 2020. A retrospective investigation of the association between pretreatment RDW and clinicopathological features, blood data, short-term outcomes, and prognosis was conducted using a prospectively entered institutional clinical database and the latest follow-up data.

Results:

Of 626 patients, 87 (13.9%) had a high pretreatment RDW. High RDW was significantly associated with several disadvantageous characteristics regarding performance status, the American Society of Anesthesiologists physical status, respiratory comorbidity, and nutritional status. Similarly, high RDW correlated with frequent postoperative morbidities (respiratory morbidity and reoperation; P = 0.022 and 0.034, respectively), decreased opportunities for adjuvant chemotherapy (P = 0.0062), and increased death from causes other than esophageal cancer (P = 0.046). Finally, RDW could be an independent predictor of survival after esophagectomy (hazard ratio, 1.47; 95% confidence interval, 1.009–2.148; P = 0.045).

Conclusion:

High pretreatment RDW reflected various adverse backgrounds and it could be a surrogate marker of poor prognosis in patients who have undergone esophagectomy for esophageal cancer.
Simulated Bundled Payments for 4 Common Surgical Approaches to Treat Degenerative Cervical Myelopathy
Authors: Jain Nikhil , Sharma Mayur , Wang Dengzhi , Ugiliweneza Beatrice , Drazin Doniel , Boakye Maxwell
Published: March 2022

Study Design:

Retrospective cohort study.

Objective:

The aim was to compare 90-day and 2-year reimbursements for ≥2-level anterior cervical discectomy and fusion (mACDF), anterior cervical corpectomy and fusion (ACCF), posterior laminectomy and fusion (LF) and laminoplasty (LP) done for degenerative cervical myelopathy (DCM).

Summary of Background Data:

In DCM pathologies where there exists a clinical equipoise in approach selection, a randomized controlled trial found that an anterior approach did not significantly improve patient-reported outcomes over posterior approaches. In the era of value and bundled payments initiatives, cost profile of various approaches will form an important consideration for decision making.

Materials and Methods:

IBM MarketScan Research Database (2005–2018) was used to study beneficiaries (30–75 y) who underwent surgery (mACDF, ACCF, LF, LP) for DCM. Index hospital stay (operating room, surgeon, hospital services) and postdischarge inpatient, outpatient and prescription medication payments have been used to simulate 90-day and 2-year bundled payment amounts, along with their distribution for each procedure.

Results:

A total of 10,834 patients with median age of 54 years were included. The median 90-day payment was $46,094 (interquartile range: $34,243–$65,841) for all procedures, with LF being the highest ($64,542) and LP the lowest ($37,867). Index hospital was 62.4% (operating room: 46.6) and surgeon payments were 17.5% of the average 90-day bundle. There was significant difference in the index, 90-day and 2-year reimbursements and their distribution among procedures.

Conclusion:

In a national cohort of patients undergoing surgery for DCM, LP had the lowest complication rate, and simulated bundled reimbursements at 90 days and 2 years postoperatively. The lowest quartile 90-day payment for LF was more expensive than median amounts for mACDF, ACCF, and LP. If surgeons encounter scenarios of clinical equipoise in practice, LP is likely to result in maximum value as it is on an average 70% less expensive than LF over 90 days.