bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual RNA-seq to catalogue host and parasite gene expression changes associated with virulence of T. annulata-transformed bovine leukocytes: towards identification of attenuation biomarkers
Authors: Elati Khawla , Tajeri Shahin , Obara Isaiah , Mhadhbi Moez , Zweygarth Erich , Darghouth Mohamed Aziz , Nijhof Ard Menzo 
Published: October 2023

AbstractThe apicomplexan parasiteTheileria annulatais transmitted byHyalommaticks and causes an acute lymphoproliferative disease that is invariably lethal in exotic cattle breeds. The unique ability of the schizont stage ofT. annulatato transform infected leukocytes to a cancer-like phenotype and the simplicity of culturing and passagingT. annulata-transformed cells in vitro have been explored for live vaccine development by attenuating the transformed cells using lengthy serial propagation in vitro. The empirical in vivo evaluation of attenuation required for each batch of long-term cultured cells is a major constraint since it is resource intensive and raises ethical issues regarding animal welfare. As yet, the molecular mechanisms underlying attenuation are not well understood. Characteristic changes in gene expression brought about by attenuation are likely to aid in the identification of novel biomarkers for attenuation. We set out to undertake a comparative transcriptome analysis of attenuated (passage 296) and virulent (passage 26) bovine leukocytes infected with a Tunisian strain ofT. annulatatermed Beja. RNA-seq was used to analyse gene expression profiles and the relative expression levels of selected genes were verified by real-time quantitative PCR (RT-qPCR) analysis. Among the 3538 T. annulatagenes analysed, 214 were significantly differentially expressed, of which 149 genes were up-regulated and 65 down-regulated. Functional annotation of differentially expressedT. annulatagenes revealed four broad categories of metabolic pathways: carbon metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum and biosynthesis of secondary metabolites. It is interesting to note that of the top 40 genes that showed altered expression, 13 were predicted to contain a signal peptide and/or at least one transmembrane domain, suggesting possible involvement in host-parasite interaction. Of the 16,514 bovine transcripts, 284 and 277 showed up-regulated and down-regulated expression, respectively. These were assigned to functional categories relevant to cell surface, tissue morphogenesis and regulation of cell adhesion, regulation of leucocyte, lymphocyte and cell activation. The genetic alterations acquired during attenuation that we have catalogued herein, as well as the accompanying in silico functional characterization, do not only improve understanding of the attenuation process, but can also be exploited by studies aimed at identifying attenuation biomarkers across different cell lines focusing on some host and parasite genes that have been highlighted in this study, such as bovine genes (CD69, ZNF618, LPAR3, and APOL3) and parasite genes such as TA03875.
China-US grain trade shapes the spatial genetic pattern of common ragweed in East China cities
Authors: Lu Siran , Luo Xiangyu , Wang Hongfang , Gentili Rodolfo , Citterio Sandra , Yang Jingyi , Jin Jing , Li Jianguang , Yang Jun 
Published: October 2023

AbstractCommon ragweed is an invasive alien species causing severe allergies in urban residents. Understanding its urban invasion pathways is crucial for effective control. However, knowledge is limited, with most studies focusing on agricultural and natural areas, and occurrence record-based studies exhibiting uncertainties. We address this gap through a study in East China cities, combining population genetics and occurrence records. Leaf samples from 37 urban common ragweed populations across 15 cities are collected. Genomic and chloroplast DNA extraction facilitate analysis of spatial genetic patterns and gene flows. Additionally, international grain trade data is examined to trace invasion sources. Results indicate spatial genetic patterns impacted by multiple introductions over time. We infer the modern grain trade between the United States and China as the primary invasion pathway. Also, cities act as transportation hubs and ports of grain importation might disperse common ragweed to urban areas. Invasive species control should account for cities as potential landing and spread hubs of common ragweed.
Structural and mechanistic insights into the inhibition of respiratory syncytial virus polymerase by a non-nucleoside inhibitor
Authors: Yu Xiaodi , Abeywickrema Pravien , Bonneux Brecht , Behera Ishani , Anson Brandon , Jacoby Edgar , Fung Amy , Adhikary Suraj , Bhaumik Anusarka , Carbajo Rodrigo J. , De Bruyn Suzanne , Miller Robyn , Patrick Aaron , Pham Quyen , Piassek Madison , Verheyen Nick , Shareef Afzaal , Sutto-Ortiz Priscila , Ysebaert Nina , Van Vlijmen Herman , Jonckers Tim H. M. , Herschke Florence , McLellan Jason S. , Decroly Etienne , Fearns Rachel , Grosse Sandrine , Roymans Dirk , Sharma Sujata , Rigaux Peter , Jin Zhinan 
Published: October 2023

AbstractThe respiratory syncytial virus polymerase complex, consisting of the polymerase (L) and phosphoprotein (P), catalyzes nucleotide polymerization, cap addition, and cap methylation via the RNA dependent RNA polymerase, capping, and Methyltransferase domains on L. Several nucleoside and non-nucleoside inhibitors have been reported to inhibit this polymerase complex, but the structural details of the exact inhibitor-polymerase interactions have been lacking. Here, we report a non-nucleoside inhibitor JNJ-8003 with sub-nanomolar inhibition potency in both antiviral and polymerase assays. Our 2.9 Å resolution cryo-EM structure revealed that JNJ-8003 binds to an induced-fit pocket on the capping domain, with multiple interactions consistent with its tight binding and resistance mutation profile. The minigenome and gel-based de novo RNA synthesis and primer extension assays demonstrated that JNJ-8003 inhibited nucleotide polymerization at the early stages of RNA transcription and replication. Our results support that JNJ-8003 binding modulates a functional interplay between the capping and RdRp domains, and this molecular insight could accelerate the design of broad-spectrum antiviral drugs.
Coronavirus-like all-angle all-polarization broadband scatterer
Authors: Mikhailovskaya Anna , Vovchuk Dmytro , Grotov Konstantin , Kolchanov Denis S. , Dobrykh Dmitry , Ladutenko Konstantin , Bobrovs Vjačeslavs , Powell Alexander , Belov Pavel , Ginzburg Pavel 
Published: October 2023

AbstractCreeping waves traveling around a volumetric electromagnetic scatterer provide a significant contribution to its radar cross-section. While quite a few efforts were devoted to suppressing creeping waves as a part of radar countermeasures, here we utilize specially engineered creeping waves to our advantage to create broadband, all-angle, and polarization scatterers. Metalized spherical surfaces, patterned with corona virus-like spikes are designed to provide a broadband constructive interference between the specular reflection and creeping waves, elevating the scattering cross-section. The demonstrated miniature corona scatterers utilize both resonant cascading phenomena and traveling wave interference to tailor electromagnetic interactions, outperforming a resonant dipole in terms of amplitude and bandwidth quite significantly. Our experimental samples are fabricated with an additive manufacturing technique, where a 3D-printed plastic skeleton is subsequently metalized. Micron-thick layers allow governing electromagnetic interactions as if the entire object was made of solid metal. Lightweight, all-angle, all-polarization, and broadband compact scatterers such as these, reported here, have numerous applications, including radar deception, electromagnetic beckoning, and many others.
Does Movement Contextually Cue Attention During Novel Word Exposure? A Comparison of Preschool Children With Developmental Language Disorder and With Typical Language
Authors: Aljahlan Yara , Spaulding Tammie J. 
Published: October 2023

Purpose:
This study investigated the attentional tendencies of preschool children with developmental language disorder (DLD) and their typical language (TL) peers during a word learning task to examine what visual properties of novel objects capture their attention.

Method:
Twelve children with DLD and 12 children with TL completed a novel name extension task in which they selected which of three visual characteristics of referent objects (i.e., movement, color, pattern) was relevant during novel word–novel referent pairings. No visual feature was more relevant than the others; consequently, there were no correct and no incorrect responses.

Results:
Children with DLD were systematically different from their TL peers in which visual features of objects they attended to during nonword–novel referent pairings in that they selected movement as the relevant feature of novel objects more often than TL children. There was also a significant negative correlation between chronological age and the propensity for movement selections.

Conclusions:
In most cases, word learning involves mapping the auditory signal onto visual information. Identifying what children with DLD naturally attend to when exposed to novel word–novel referent pairings is an important first step in order to better understand how to design effective and efficient word learning interventions with this population.
Leader‐following consensus and qualitative analysis of a new multi‐agent‐based epidemic model
Authors: Amiri Mehra Amir Hossein , Shafieirad Mohsen , Zamani Iman 
Published: October 2023

AbstractThis paper addresses an investigation into a leader‐following consensus problem in a novel multi‐agent‐based SIS (Susceptible‐Infected‐Susceptible) epidemic model. As infectious diseases are easily spread through travel, the model considers each agent to represent a city in an infected country, interacting with neighbouring cities towards achieving disease eradication through consensus. To make the model more realistic, the Effect Terms (ETs) arising from the effects of agent states on each other are also considered. The differential equations' positivity and existence of solutions are examined, and the proposed model's equilibrium points are obtained, with stability analysed using new local and global basic reproduction numbers defined in this study. Additionally, a leader‐following consensus control for the multi‐agent‐based system is proposed to drive each agent to follow a virtual leader agent. Finally, numerical simulations are included to validate the theoretical findings corresponding to the proposed scheme.
Direction‐of‐arrival estimation via coarray‐domain RELAX algorithm with source number estimation
Authors: Ahmad Fauzia , Amin Moeness G. 
Published: October 2023

AbstractA modified RELAX algorithm based on iterative coarray‐domain beamforming for fast source direction‐of‐arrival (DOA) estimation with fully augmentable sparse arrays is proposed. The authors exploit the deterministic centralised nature of the noise in the coarray domain and the Hermitian symmetry of the spatial autocorrelation function to efficiently incorporate source number estimation within the iterative framework. In doing so, the proposed algorithm allows low‐complexity, fast DOA estimation of more sources than sensors, without resorting to computationally expensive implementations of source number estimation using information theoretic criteria. Three variants of the proposed algorithm are presented, each differing in terms of the specific method employed for source number estimation. Extensive simulations are performed with a minimum redundancy array to compare and contrast the performance of the three variants in terms of their accuracy in estimating the number of sources in the field‐of‐view of the array. The results demonstrate that the modified RELAX algorithm can provide accurate estimates of the number and directions of sources, especially when the number of uncorrelated sources is equal to or higher than the number of sensors.
Direct laser synthesis and patterning of high entropy oxides from liquid precursors
Authors: Castonguay Alexander C , Nova Nabila Nabi , Dueñas Lauren M , McGee Shannon , Lodhi M J K , Yang Yang , Zarzar Lauren D 
Published: October 2023

Abstract
High entropy oxides are a class of materials distinguished by the use of configurational entropy to drive material synthesis. These materials are being examined for their exciting physiochemical properties and hold promise in numerous fields, such as chemical sensing, electronics, and catalysis. Patterning and integration of high entropy materials into devices and platforms can be difficult due to their thermal sensitivity and incompatibility with many conventional thermally-based processing techniques. In this work, we present a laser-based technique, laser-induced thermal voxels, that combines the synthesis and patterning of high entropy oxides into a single process step, thereby allowing patterning of high entropy materials directly onto substrates. As a proof-of-concept, we target the synthesis and patterning of a well-characterized rock salt-phase high entropy oxide, (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O, as well as a spinel-phase high entropy oxide, (Mg0.2Ni0.2Co0.2Cu0.2Zn0.2)Cr2O4. We show through electron microscopy and x-ray analysis that the materials created are atomically homogenous and are primarily of the rock salt or spinel phase. These findings show the efficacy of laser induced thermal voxel processing for the synthesis and patterning of high entropy materials and enable new routes for integration of high entropy materials within microscale platform and devices.
Neural network Gaussian processes as efficient models of potential energy surfaces for polyatomic molecules
Authors: Dai J , Krems R V 
Published: October 2023

Abstract
Kernel models of potential energy surfaces (PESs) for polyatomic molecules are often restricted by a specific choice of the kernel function. This can be avoided by optimizing the complexity of the kernel function. For regression problems with very expensive data, the functional form of the model kernels can be optimized in the Gaussian process (GP) setting through compositional function search guided by the Bayesian information criterion. However, the compositional kernel search is computationally demanding and relies on greedy strategies, which may yield sub-optimal kernels. An alternative strategy of increasing complexity of GP kernels treats a GP as a Bayesian neural network (NN) with a variable number of hidden layers, which yields NNGP models. Here, we present a direct comparison of GP models with composite kernels and NNGP models for applications aiming at the construction of global PES for polyatomic molecules. We show that NNGP models of PES can be trained much more efficiently and yield better generalization accuracy without relying on any specific form of the kernel function. We illustrate that NNGP models trained by distributions of energy points at low energies produce accurate predictions of PES at high energies. We also illustrate that NNGP models can extrapolate in the input variable space by building the free energy surface of the Heisenberg model trained in the paramagnetic phase and validated in the ferromagnetic phase. By construction, composite kernels yield more accurate models than kernels with a fixed functional form. Therefore, by illustrating that NNGP models outperform GP models with composite kernels, our work suggests that NNGP models should be a preferred choice of kernel models for PES.
A Simple HPLC-UV Method for Ivosidenib Determination in Human Plasma
Authors: Gando Yoshito , Yasu Takeo 
Published: October 2023

Abstract
Ivosidenib is used for the treatment of acute myeloid leukemia (AML) with isocitrate dehydrogenase 1 (IDH1) mutations. However, increased blood concentrations of ivosidenib are associated with a risk of a prolonged QT interval in patients with AML. Therapeutic drug monitoring in patients with AML with IDH1 mutation offers the potential to improve treatment efficacy while minimizing toxicity. In this study, we developed an efficient high-performance liquid chromatography–ultraviolet (HPLC-UV) method for the quantification of ivosidenib in plasma. Human plasma samples (50 μL) were processed by protein precipitation using acetonitrile, followed by chromatographic separation on a reversed-phase column with an isocratic mobile phase of 0.5% KH₂PO₄ (pH 4.5) and acetonitrile (45:55, v/v) at a flow rate of 1.0 mL/min, with ultraviolet detection at 245 nm. Calibration curves were linear over the range of 0.25–20 μg/mL with a coefficient of determination (r2) of 0.99999. Intra-day and inter-day precision were 1.20–8.04% and 0.69–4.20%, respectively. The assay accuracy was −2.00% to 1.93% and recovery was &gt;91.2%. These findings support the effectiveness of the newly developed HPLC-UV method for the quantification of ivosidenib in human plasma. This simple and cost-effective method is expected to expand ivosidenib monitoring in laboratories lacking LC–MS/MS instruments.
The vector error correction index model: representation, estimation and identification
Authors: Cubadda Gianluca , Mazzali Marco 
Published: October 2023

SummaryThis paper extends the multivariate index autoregressive model to the case of cointegrated time series of order (1,1). In this new modelling, namely the vector error-correction index model (VECIM), the first differences of series are driven by some linear combinations of the variables, namely the indexes. When the indexes are significantly fewer than the variables, the VECIM achieves a substantial dimension reduction with reference to the vector error correction model. We show that the VECIM allows one to decompose the reduced-form errors into sets of common and uncommon shocks, and that the former can be further decomposed into permanent and transitory shocks. Moreover, we offer a switching algorithm for optimal estimation of the VECIM. Finally, we document the practical value of the proposed approach by both simulations and an empirical application, where we search for the shocks that drive the aggregate fluctuations at different frequency bands in the US.
The impact of COVID-19 on health service utilization in sub-Saharan Africa: a scoping review
Authors: Tannor E , Quentin W , Busse R , Opoku D , Amuasi J H 
Published: October 2023

Abstract

Background
The COVID-19 pandemic has affected health systems and impacted health service utilization (HSU) globally. The aim of this scoping review is to synthesize the available evidence on HSU in sub-Saharan Africa during the COVID-19 pandemic focusing on (1) changes in HSU compared to the pre-pandemic period, (2) changes in HSU amongst particular patient groups studied, and (3) identify factors determining changes in HSU as a result of the COVID-19 pandemic.

Methods
The Scoping review is guided by the methodological framework developed by Arskey and O'Malley. We have searched for relevant studies in PubMed(MEDLINE), EMBASE, Scopus and Web of Science and for grey literature on governmental and organizational websites. Search terms combined synonyms for three main concepts: (1) ‘COVID-19 pandemic’, (2) ‘health service utilization’, and (3) ‘sub-Saharan Africa’. Two reviewers independently screened articles at the title and abstract stage for inclusion into full text screening for data extraction. We provide a general descriptive overview, tabular summaries and thematic analysis of the extracted data.

Results
We identified a total of 21,440 titles. After removal of duplicates, 14,626 titles and abstracts are currently being screened. Data extraction and analysis will be completed before the conference. We will provide a comprehensive overview of studies on health service utilization during the COVID-19 pandemic conducted in sub-Saharan Africa. We will describe the settings and methods used by identified studies, analyze the types of diseases studied (communicable, non-communicable, and injuries), and present the discussed reasons for changes in health service utilization.

Conclusions
This review is the first to describe the impact of the COVID-19 pandemic on HSU in sub-Saharan Africa. Understanding the effects of the pandemic on HSU is important to support the development of better policies for pandemic preparedness and response in the region.
“Health is a serious game”: Gamification as a tool for primary prevention in Public Health
Authors: Tesi B , Donia P , Covelli A , Aloise I , Renzi E , Massimi A , Villari P 
Published: October 2023

Abstract

Background
Gamification, according to literature, is the use of game design elements in non-game contexts. Rewards (e.g. points, badges and rankings) are a gamification strategy to entice users to complete required tasks and could be useful for Public Health (PH) interventions to promote healthy lifestyles. This study aims to find out which gamification approaches are most useful in PH.

Methods
We investigated PubMed, Scopus and Web of Science databases to conduct our systematic review, including articles published up to February 3, 2023. Prisma Statement 2020 guidelines were used. No time limits were included. Only articles in Italian or English that discussed gamification interventions in PH, effectiveness and user satisfaction were taken into account. The quality of the studies will be assessed using the NIH quality assessment tool.

Results
327 articles were found, 27 of which were included in the review. Pre-post studies were the most included (n = 12), conducted in Europe (n = 7) and USA (n = 6). The target population was mainly young adults and teens (n = 7). Most gamification interventions involved physical activity (n = 13), nutrition (n = 5) and smoking cessation (n = 2). Overall, the interventions proved to be all effective, but the ones about physical activity were the most useful, engaging and with longer-lasting results over time. Where satisfaction was assessed (n = 16), users gave positive feedback.

Conclusions
The research outcomes have shown how gamification may engage not only individuals, but masses, using game design elements in different Public Health areas. The implementation of gamification tools in PH is an innovative intervention that often uses graphic language to simplify and deliver messages to all kinds of users. Gamification is easy to use and could be a good strategy for primary prevention, to support a sustainable behavior change following the game period. More large scale controlled trials are needed in order to confirm these results.

Key messages
• Gamification is an important tool in public health useful for primary prevention.
• The mass appeal of gamification can reach many users leading to healthier lifestyles, especially among young adults.