bluuebunny/crossref_metadata_2025 huggingface dataset:
The automatic identification and tracking of coronal flux ropes
Authors: Wagner A. , Kilpua E. K. J. , Sarkar R. , Price D. J. , Kumari A. , Daei F. , Pomoell J. , Poedts S.
Published: July 2023

Context.Investigating the early-stage evolution of an erupting flux rope from the Sun is important for understanding the mechanisms of how it loses its stability and its space-weather impact.

Aims.Our aim is to develop an efficient scheme for tracking the early dynamics of erupting solar flux ropes and to use the algorithm to analyse its early-stage properties. The algorithm is tested on a data-driven simulation of an eruption that took place in active region AR12473. We investigate the modelled footpoint movement and magnetic flux evolution of the flux rope and compare these with observational data from the Solar Dynamics Observatory (SDO) Atmospheric Imaging Assembly (AIA) in the 211 Å and 1600 Å channels.

Methods.We used the time-dependent data-driven magnetofrictional model (TMFM) to carry out our analysis. We also performed another modelling run, where we stop the driving of the TMFM midway through the rise of the flux rope through the simulation domain and evolve it instead with a zero-beta magnetohydrodynamic (MHD) approach.

Results.The developed algorithm successfully extracts a flux rope and its ascent through the simulation domain. We find that the movement of the modelled flux rope footpoints showcases similar trends in both the TMFM and relaxation MHD runs: the footpoints recede from their respective central location as the eruption progresses and the positive polarity footpoint region exhibits a more dynamic behaviour. The ultraviolet (UV) brightenings and extreme ultraviolet (EUV) dimmings agree well with the models in terms of their dynamics. According to our modelling results, the toroidal magnetic flux in the flux rope first rises and then decreases. In our observational analysis, we capture the descending phase of toroidal flux.

Conclusions.The extraction algorithm enables us to effectively study the early dynamics of the flux rope and to derive some of its key properties, such as footpoint movement and toroidal magnetic flux. The results generally agree well with observational data.
First-principles based study of 8-Pmmn borophene and metal interface
Authors: Vishnubhotla Vaishnavi , Mitra Sanchali , Mahapatra Santanu
Published: July 2023

Borophene, the lightest member of mono-elemental 2D materials family, has attracted much attention due to its intriguing polymorphism. Among many polymorphs, digitally discovered 8-Pmmn stands out owing to its unique tilted-Dirac fermions. However, the property of interfaces between 8-Pmmn and metal substrates has so far remained unexplored, which has critical importance of its application in any electronic devices. Here, with the help of density functional theory, we show that the unique tilted-Dirac property is completely lost when 8-Pmmn borophene is interfaced with common electrode materials such as Au, Ag, and Ti. This is attributed to the high chemical reactivity of borophene as observed from crystal orbital Hamilton population and electron localization function analysis. In an effort to restore the Dirac property, we insert a graphene/hexagonal-boron-nitride (hBN) layer between 8-Pmmn and metal, a technique used in recent experiments for other 2D materials. We show that while the insertion of graphene successfully restores the Dirac nature for all three metals, hBN fails to do so while interfacing with Ti. The quantum chemical insights presented in this work may aid in to access the Dirac properties of 8-Pmmn in experiments.
An epitaxial La2CuO4 thin film photocathode for water splitting under visible light
Authors: Kobayashi Hiroyuki , Shiratori Yosuke , Orita Masahiro , Yamada Taro , Kudo Akihiko , Domen Kazunari
Published: July 2023

A semiconductive oxide, La2CuO4 (LCO), was investigated as a potential material to compose photocathode for sunlight-driven hydrogen evolution by splitting water. LCO, despite involving partially filled Cu 3d orbitals, behaves as a semiconductor and absorbs visible light on the bandgap formed by significant Coulomb repulsion between the electronic orbitals. An epitaxial LCO film was grown on a SrRuO3/SrTiO3 (SRO/STO) single-crystal substrate by pulsed laser deposition to obtain a photocathodic specimen for water photo-splitting. An LCO photocathode dressed with a Pt cocatalyst for hydrogen evolution (Pt/LCO/SRO/STO) exhibited a cathodic photocurrent with a density of 0.4 mA cm−2 at 0 VRHE under simulated AM1.5 G sunlight. This photocathode responded to incident light up to 800 nm, which is one of the longest wavelengths so far reported for an oxide photoelectrode. Together with a counter-electrode for oxygen evolution, the Pt/LCO/SRO/STO photocathode generated hydrogen with the expected H2 : O2 = 2 : 1 stoichiometric ratio with a Faradaic efficiency of approximately 80%.
Probing C–I bond fission in the UV photochemistry of 2-iodothiophene with core-to-valence transient absorption spectroscopy
Authors: Toulson Benjamin W. , Hait Diptarka , Faccialà Davide , Neumark Daniel M. , Leone Stephen R. , Head-Gordon Martin , Gessner Oliver
Published: July 2023

The UV photochemistry of small heteroaromatic molecules serves as a testbed for understanding fundamental photo-induced chemical transformations in moderately complex compounds, including isomerization, ring-opening, and molecular dissociation. Here, a combined experimental-theoretical study of 268 nm UV light-induced dynamics in 2-iodothiophene (C4H3IS) is performed. The dynamics are experimentally monitored with a femtosecond extreme ultraviolet (XUV) probe that measures iodine N-edge 4d core-to-valence transitions. Experiments are complemented by density functional theory calculations of both the pump-pulse induced valence excitations and the XUV probe-induced core-to-valence transitions. Possible intramolecular relaxation dynamics are investigated by ab initio molecular dynamics simulations. Gradual absorption changes up to ∼0.5 to 1 ps after excitation are observed for both the parent molecular species and emerging iodine fragments, with the latter appearing with a characteristic rise time of 160 ± 30 fs. Comparison of spectral intensities and energies with the calculations identifies an iodine dissociation pathway initiated by a predominant π → π* excitation. In contrast, initial excitation to a nearby n⟂ → σ* state appears unlikely based on a significantly smaller oscillator strength and the absence of any corresponding XUV absorption signatures. Excitation to the π → π* state is followed by contraction of the C–I bond, enabling a nonadiabatic transition to a dissociative π→σC−I* state. For the subsequent fragmentation, a relatively narrow bond-length region along the C–I stretch coordinate between 230 and 280 pm is identified, where the transition between the parent molecule and the thienyl radical + iodine atom products becomes prominent in the XUV spectrum due to rapid localization of two singly occupied molecular orbitals on the two fragments.
Autonomous ratcheting by stochastic resetting
Authors: Ghosh Pulak K. , Nayak Shubhadip , Liu Jianli , Li Yunyun , Marchesoni Fabio
Published: July 2023

We propose a generalization of the stochastic resetting mechanism for a Brownian particle diffusing in a one-dimensional periodic potential: randomly in time, the particle gets reset at the bottom of the potential well it was in. Numerical simulations show that in mirror asymmetric potentials, stochastic resetting rectifies the particle’s dynamics, with a maximum drift speed for an optimal average resetting time. Accordingly, an unbiased Brownian tracer diffusing on an asymmetric substrate can rectify its motion by adopting an adaptive stop-and-go strategy. Our proposed ratchet mechanism can model the directed autonomous motion of molecular motors and micro-organisms.
Studying the ballistic performance of a metal target under combined KE projectile impact
Authors: Bakhtiari Amir , Sheikhi Mohammad Morad , Bani Mostafa Arab Nasrollah , Khodarahmi Hossein
Published: July 2023

In this article, using analytical, numerical and experimental methods, the range of the ballistic limit thickness (BLT) of the metal target in the impact with the combined kinematic energy (KE) projectile is investigated. The design of these types of projectiles is to achieve effective damage behind the target and they consist of two components that are coaxial and back to back. The first KE projectile (FKEP) is a filled cylinder and acts as a leading projectile, while the second KE projectile (SKEP) is a hollow cylinder carrying a fuse and explosive materials and causing damage (behind the target) is obtained by the complete passage of this projectile from the target. There is little research available in the field of penetration analysis of these projectiles, and only a semi-analytical model based on shock theory has been presented for the analysis of hollow cylindrical projectile penetration. In this research, using the shock theory, a new analytical model is presented to predict the performance of the combined KE projectile in the metal target. In parallel, experimental tests of combined KE projectile hitting a metal target (using a Gas Gun weapon) and also a 2D axisymmetric simulation (LS Dyna software) were performed in the range of 200–850 m s−1 impact velocity. The average difference between the results of experimental tests and numerical simulation with the results of the analytical model is 7 and 5% respectively.
Static and dynamic magnetization models of magnetic nanoparticles: an appraisal
Authors: Yari Parsa , Chugh Vinit Kumar , Saha Renata , Tonini Denis , Rezaei Bahareh , Mostufa Shahriar , Xu Kanglin , Wang Jian-Ping , Wu Kai
Published: July 2023

Nowadays, magnetic nanoparticles (MNPs) have been extensively used in biomedical fields such as labels for magnetic biosensors, contrast agents in magnetic imaging, carriers for drug/gene delivery, and heating sources for hyperthermia, among others. They are also utilized in various industries, including data and energy storage and heterogeneous catalysis. Each application exploits one or more physicochemical properties of MNPs, including magnetic moments, magnetophoretic forces, nonlinear dynamic magnetic responses, magnetic hysteresis loops, and others. It is generally accepted that the static and dynamic magnetizations of MNPs can vary due to factors such as material composition, crystal structure, defects, size, shape of the MNP, as well as external conditions like the applied magnetic fields, temperature, carrier fluid, and inter-particle interactions (i.e., MNP concentrations). A subtle change in any of these factors leads to different magnetization responses. In order to optimize the MNP design and external conditions for the best performance in different applications, researchers have been striving to model the macroscopic properties of individual MNPs and MNP ensembles. In this review, we summarize several popular mathematical models that have been used to describe, explain, and predict the static and dynamic magnetization responses of MNPs. These models encompass both individual MNPs and MNP ensembles and include the Stoner-Wohlfarth model, Langevin model, zero/non-zero field Brownian and Néel relaxation models, Debye model, empirical Brownian and Néel relaxation models under AC fields, the Landau–Lifshitz–Gilbert (LLG) equation, and the stochastic Langevin equation for coupled Brownian and Néel relaxations, as well as the Fokker–Planck equations for coupled/decoupled Brownian and Néel relaxations. In addition, we provide our peers with the advantages, disadvantages, as well as suitable conditions for each model introduced in this review. The shrinking size of magnetic materials brings about a significant surface spin canting effect, resulting in higher anisotropy and lower magnetization in MNPs compared to bulk materials. Accurate prediction of static and dynamic magnetizations in MNPs Requires both precise data on their magnetic properties and an accurate mathematical model. Hence, we introduced the spin canting effect and models to estimate anisotropy and saturation magnetization in MNPs.
Direct speech reconstruction from sensorimotor brain activity with optimized deep learning models
Authors: Berezutskaya Julia , Freudenburg Zachary V , Vansteensel Mariska J , Aarnoutse Erik J , Ramsey Nick F , van Gerven Marcel A J
Published: July 2023

Objective. Development of brain–computer interface (BCI) technology is key for enabling communication in individuals who have lost the faculty of speech due to severe motor paralysis. A BCI control strategy that is gaining attention employs speech decoding from neural data. Recent studies have shown that a combination of direct neural recordings and advanced computational models can provide promising results. Understanding which decoding strategies deliver best and directly applicable results is crucial for advancing the field. Approach. In this paper, we optimized and validated a decoding approach based on speech reconstruction directly from high-density electrocorticography recordings from sensorimotor cortex during a speech production task. Main results. We show that (1) dedicated machine learning optimization of reconstruction models is key for achieving the best reconstruction performance; (2) individual word decoding in reconstructed speech achieves 92%–100% accuracy (chance level is 8%); (3) direct reconstruction from sensorimotor brain activity produces intelligible speech. Significance. These results underline the need for model optimization in achieving best speech decoding results and highlight the potential that reconstruction-based speech decoding from sensorimotor cortex can offer for development of next-generation BCI technology for communication.
Food and lifestyle impact on breath VOCs using portable mass spectrometer—pilot study across European countries
Authors: Aleksić Milena , Simeon Andrea , Vujić Djordje , Giannoukos Stamatios , Brkić Boris
Published: July 2023

In the modern world, many people are changing old dietary and lifestyle habits to improve the quality of their living—to treat or just prevent possible diseases. The main goal of this pilot study was to assess the food and lifestyle impact on exhaled breath volatile organic compounds (VOCs) in various population groups. It was done by employing a recently validated portable membrane-inlet mass spectrometer—MIMS. Thus, the obtained results would also represent the additional confirmation for the employment of the new instrument in the breath analysis. The pilot study involved 151 participants across Europe, including people with overweight, obesity, type 2 diabetes mellitus, cardiovascular disease, people with poor-quality diet and professional athletes. Exhaled breath acetone, ethanol, isoprene, and n-pentane levels were determined in samples before the meal, and 120 min after the meal. Obtained basal ppbv values were mainly in accordance with previously reported, which confirms that MIMS instrument can be used in the breath analysis. Combining the quantified levels along with the information about the participants’ lifestyle habits collected via questionnaire, an assessment of the food and lifestyle impact was obtained. Notable alteration in examined VOC levels upon meal consumption was detected in more than 70% of all participants, with exception for isoprene, which was affected in about half of participants. Lifestyle parameters impact was examined using statistical analysis of variance (ANOVA) on ranks test. Statistically significant differences in basal breath VOC levels were observed among all examined population groups. Also, n-pentane and ethanol levels significantly differed in people of different ages, as well as acetone levels in people with different physical activity habits. These findings are promising for further, more focused research using MIMS technique in breath analysis.
Is it possible to achieve High-Quality Concrete with Partial Substitution of Fly Ash?
Authors: Rahman Mohammad Junaedy , Arfandi Anas , Pangestu Gangsar
Published: July 2023

This study aims to determine the characteristics of high-quality concrete using fly ash as a partial replacement for PCC cement. Tests include slump testing, density factor and concrete compressive strength testing. Two variations of the concrete mix are made, namely the variation without fly ash and the 15% fly ash mixture. The results of this study indicate that the characteristics of concrete with fly ash substitution require the same amount of water as the concrete without fly ash to achieve the desired slump value. The density factor values obtained are also the same. In the concrete compressive strength test, the variation of the 15% fly ash mixture was higher than that of the 0% fly ash mixture.
Analysis of Bioactive Compounds Content and Toxicity Test on Mangrove Leaf Extract
Authors: Fadilah Ratnawaty , Sukainah Andi , Taufieq Nur Anny Suryaningsih , Putra Reski Praja , Adriani Mimi
Published: July 2023

Mangroves are plants that have a significant role in coastal areas, which also contain various bioactive components. Although it is rich in bioactive compounds, its utilization is still minimal. For this excuse, it is crucial to study and analyze the mixtures of bioactive compounds and toxicity tests on some mangrove leaf extracts. This research aimed to specify the content and toxicity of bioactive compounds of several mangrove leaf extracts. The procedures of the research consist of sampling and sample preparation, extraction with 70% alcohol, the Brine Shrimp Lethality Test (BSLT) toxicity testing, and data analysis using probit analysis. The bioactive compounds were measured by qualitative research. The results showed that four mangrove extracts (Avicennia sp., R.apiculata, A.illicifolius, and S.alba) had moderate toxic content. Avicennia sp. has the lowest LC50 value of 4.87 μg / ml. Four types of mangroves have a bioactive range, as well as saponins, flavonoids, alkaloids, tannins, and phenolic compounds.
Domestic Waste Management Study of Community Based in Kupang City
Authors: Ramang Ruslan , Dirawan Gufran Darma , Ruslan Rusneni
Published: July 2023

This research aims to find the existing waste management system and create a development model of waste technology management. Besides, this study will focus specifically on the variables that influence participatory community-based waste management technology. This study uses descriptive analysis crosstab and chi-square. The data collected using distributing questionnaires and interviews with respondents randomly. The results of this study are mostly waste generated by society and less managed well. The integration of variable dimensions of public participation can cultivate people’s willingness to reduce waste generation. Community participation can increase recycling and composting activities that waste going into a landfill can be reduced. Variable work and income results have a relationship with the waste that the people in Kupang did sorting. Simultaneously, the variables age, gender, education, type of housing, and the number of people do not have a significant relationship with waste sorting. Not all respondents addressed the garbage by the janitor, so most of them deal with their waste by burning and dispose of vacant land.
The Analysis of Mercury Concentrations of Water in Gold Mining Environment at Poboya, East Palu Subdistrict, Palu, Central Sulawesi Province
Authors: Okviyani Nur , Trimahyuni Enni , Al Faizah Ma’rif A.
Published: July 2023

Gold mining activities influence the environment, mainly the aquatic environment, due to the heavy metal and mercury detected in settling pond and river waters. Based on laboratory analysis, it is known that Mercury concentrations in settling pond water of inlet, transition, and outlet zones respectively are 0.075 mg/L, 0.042 mg/L, and 0.027 mg/L. These are shown that mercury concentration in water was not passed Government Regulation of the Minister of Environment No. 202 the year 2004 about quality standards of liquid waste, which said that the standard is 0.005 mg/L. The Heavy metal concentrations, especially mercury in river water at 1, 2, 3, 4, and 5 stations respectively, are 0.004 mg/L, 0.009 mg/L, 0.050 mg/L, and 0.006 mg/L, which do not meet the government regulation of water quality standard 0.001 mg/L.
Modeling and Simulation of High-Temperature Heat Pump Combined with Solar Energy
Authors: Djuanda  , Pasek Ari Darmawan , Tandian Nathanael P.
Published: July 2023

Heat pumps can utilize various sources of heat to increase the temperature of a room or water. This study uses solar energy as a heat source for high-temperature heat pumps. The type of heat pump used is a vapor compression heat pump and is used to produce steam. The study created a model and simulation of a heat pump combined with solar energy. System modeling is divided into three subsystems: solar collector, thermal storage, and a heat pump—the WinDali program used in heat pump simulation. The Simulation results show a close relationship between solar intensity and system performance. The maximum COP obtained is 1.32. The heat pump can generate steam for 7.25 hours, and the lifted temperature obtained is 28°C.
The Preliminary Microwave Metamaterial Absorber Based on Ring-Shaped for Stealth Technology
Authors: Yudistira Hadi Teguh , Kananda Kiki
Published: July 2023

Controlling electromagnetic waves on the material is needed by several applications such as sensors, stealth technology, and energy harvesting. An artificial material that could control electromagnetic waves is called metamaterial. Meanwhile, a metamaterial absorber can absorb the electromagnetic wave. Two concepts can be used to explain the absorbing phenomena on metamaterial absorber: the matching impedance of the air and the part of the imaginary that is high of the index of refractive collectively or the theory of interference that is destructive. The correlation of matching air impedance with destructive interference theory has been found by Yudistira in his previous works. In this study, the preliminary research of metamaterial absorbers based on ring shape is presented. The 40 mm, 35 mm, 30 mm, and 25 mm ring-shaped widths are applied to this work. We used numerical simulation work to understand the performance of metamaterial absorbers based on ring-shaped. CST microwave studio was used for numerical simulation work. The absorbance peak results for w=20, w=17.5, w=15, and w=12.5 mm are 0.92 at 3.43 GHz, 0.95 at 3.7 GHz, 0.95 at 4.04 GHz and 0.99 at 4.47 GHz, severally. The maximum absorbance is yielded to 0.99 absorbances for 25 mm of the width of the ring-shaped.
The Implementation of Classification and Spectral Transformation Methods, Based on Extraction Landsat Imagery for Growth Center Mamminasata Region
Authors: Rasyidi Emil Salim , Arief Rimba , Taking Muh. Idris
Published: July 2023

Urban growth begins from a center and affects its surrounding area, and this is due to the emergence of additional centers that will serve as a growth pole. Assessment of the dynamics of urban growth, some data, and extraction analysis methods are needed. This research examines various information by extracting of growth center area of Landsat 8 OLI / TIRS 2017 and utilizing spectral resolution on Landsat images in the Mamminasata region. The classification method tested is the OBIA classification and the Maximum Likelihood classification methods. Simultaneously, the Landsat image’s spectral resolution is maximized by spectral channel transformation sensitive to the building object. It is usually called the urban index. This study indicates that the OBIA classification method and NDBI spectral transformation proved to produce maps. It can also show center location growth with the best accuracy, especially in the Mamminasata region. Total accuracy from the accuracy-test matrix is 71.48% for building intensity and 78.57% for growth centers.
Artificial Climate Prototype for IoT-Based Vines
Authors: Fathahillah  , Zain Satria Gunawan , Andayani Dyah Darma
Published: July 2023

This climate manipulation prototype is a tool that helps monitor vine condition and automatically carries out the treatment. The design of this climate manipulation prototype can also make it easier to monitor and care for plants remotely. The plant state can be controlled with the android application which can display the condition of the plants in real-time. This type of research is research & development and uses a waterfall development model, which has stages: analysis, design, coding, and testing. Based on the results, a prototype of climate manipulation for IoT-based vines was produced. After designing the prototype, climate manipulation conducts quality testing based on functionality suitability testing. Testing aspects of functionality suitability using the black box testing method, carried out by two system experts where the test results are worth 1 with a very decent category and have met the functionality aspect.
Predicting metabolite–disease associations based on auto-encoder and non-negative matrix factorization
Authors: Gao Hongyan , Sun Jianqiang , Wang Yukun , Lu Yuer , Liu Liyu , Zhao Qi , Shuai Jianwei
Published: July 2023

Metabolism refers to a series of orderly chemical reactions used to maintain life activities in organisms. In healthy individuals, metabolism remains within a normal range. However, specific diseases can lead to abnormalities in the levels of certain metabolites, causing them to either increase or decrease. Detecting these deviations in metabolite levels can aid in diagnosing a disease. Traditional biological experiments often rely on a lot of manpower to do repeated experiments, which is time consuming and labor intensive. To address this issue, we develop a deep learning model based on the auto-encoder and non-negative matrix factorization named as MDA-AENMF to predict the potential associations between metabolites and diseases. We integrate a variety of similarity networks and then acquire the characteristics of both metabolites and diseases through three specific modules. First, we get the disease characteristics from the five-layer auto-encoder module. Later, in the non-negative matrix factorization module, we extract both the metabolite and disease characteristics. Furthermore, the graph attention auto-encoder module helps us obtain metabolite characteristics. After obtaining the features from three modules, these characteristics are merged into a single, comprehensive feature vector for each metabolite–disease pair. Finally, we send the corresponding feature vector and label to the multi-layer perceptron for training. The experiment demonstrates our area under the receiver operating characteristic curve of 0.975 and area under the precision–recall curve of 0.973 in 5-fold cross-validation, which are superior to those of existing state-of-the-art predictive methods. Through case studies, most of the new associations obtained by MDA-AENMF have been verified, further highlighting the reliability of MDA-AENMF in predicting the potential relationships between metabolites and diseases.
Durability of the First Biologic in Patients with Crohn’s Disease: A Nationwide Study from the epi-IIRN
Authors: Atia Ohad , Friss Chagit , Focht Gili , Magen Rimon Ramit , Ledderman Natan , Greenfeld Shira , Ben-Tov Amir , Loewenberg Weisband Yiska , Matz Eran , Gorelik Yuri , Chowers Yehuda , Dotan Iris , Turner Dan
Published: July 2023

Background

In this nationwide study we aimed to compare the durability of the first initiated biologic in Crohn’s disease [CD], stratified by monotherapy and combotherapy.

Methods

We used data from the epi-IIRN cohort, which includes 98% of the Israeli inflammatory bowel disease population [2005–2020]. Durability was defined as consistent treatment without surgery or added medications [except for combination therapy with thiopurines or methotrexate]. All comparisons were based on stringent propensity-score matching and paired time-to-event analyses.

Results

A total of 19 264 patients with CD were included, of whom 7452 [39%] received biologics with a median follow-up of 6.8 years (interquartile range [IQR] 3.6–10.7). Time to biologics decreased gradually from 6.7 years [IQR 2.7–10.4] in 2005 to 0.2 years [0.07–0.23] in 2020. The durability of the first biologic after 1 and 3 years was higher with adalimumab monotherapy [88%/61%] than vedolizumab monotherapy [81%/59%; n = 394 matched patients, p = 0.04] and similar between infliximab monotherapy and vedolizumab monotherapy [65%/43%; n = 182 matched patients, p = 0.1]. Durability was higher in adalimumab monotherapy vs infliximab monotherapy [83%/62% vs 71%/48% at 1/3 years; p <0.001] and it was similar in adalimumab monotherapy vs infliximab combotherapy [87%/63% vs 80%/58%, respectively; p = 0.1]. Durability was higher in combotherapy compared with monotherapy for both infliximab [85%/64% vs 67%/43%, respectively; n = 496 matched pairs, p <0.001], and adalimumab [93%/76% vs 82%/62%, respectively; n = 540 matched pairs, p <0.001].

Conclusion

Durability of the first biologic in CD was highest for adalimumab monotherapy. Combotherapy further increased the durability of adalimumab and infliximab. Unless otherwise indicated, our data may support using anti-tumour necrosis factors [TNFs] as first-line biologics in CD, particularly adalimumab if monotherapy is advised.
Domains and residues of the Saccharomyces cerevisiae hnRNP protein Hrp1 important for transcriptional autoregulation and noncoding RNA termination
Authors: Goguen Emma C , Brow David A
Published: July 2023

Proteins that bind the nascent transcript exiting RNA polymerase II can regulate transcription elongation. The essential Saccharomyces cerevisiae hnRNP protein Hrp1 is one such protein and participates in both cleavage and polyadenylation-coupled and Nrd1-Nab3-Sen1-dependent RNA polymerase II termination. Prior evidence that Hrp1 is a positive RNA polymerase II elongation factor suggests that its release from the elongation complex promotes termination. Here we report the effects of deletions and substitutions in Hrp1 on its autoregulation via an Nrd1-Nab3-Sen1-dependent transcription attenuator in the 5′-UTR of its mRNA and on the function of an Hrp1-dependent Nrd1-Nab3-Sen1 terminator in the SNR82 snoRNA gene. Deletion of either of two central RNA recognition motifs or either of the flanking low-sequence complexity domains is lethal. Smaller, viable deletions in the amino-terminal low-sequence complexity domain cause readthrough of both the HRP1 attenuator and SNR82 terminator. Substitutions that cause readthrough localized mostly to the RNA recognition motifs, although not always to the RNA-binding face. We found that autoregulation of Hrp1 mRNA synthesis is surprisingly robust, overcoming the expected lethal effects of the start codon and frameshift mutations via overexpression of the mRNA up to 40-fold. Our results suggest a model in which binding of attenuator or terminator elements in the nascent transcript by RNA recognition motifs 1 and 2 disrupts interactions between RNA recognition motif 2 and the RNA polymerase II elongation complex, increasing its susceptibility to termination.
Lipid metabolism in the immune niche of tumor-prone liver microenvironment
Authors: Chen Jintian , Chan Thomas T H , Zhou Jingying
Published: July 2023

The liver is a common primary site not only for tumorigenesis, but also for cancer metastasis. Advanced cancer patients with liver metastases also show reduced response rates and survival benefits when treated with immune checkpoint inhibitors. Accumulating evidence has highlighted the importance of the liver immune microenvironment in determining tumorigenesis, metastasis-organotropism, and immunotherapy resistance. Various immune cells such as T cells, natural killer and natural killer T cells, macrophages and dendritic cells, and stromal cells including liver sinusoidal endothelial cells, Kupffer cells, hepatic stellate cells, and hepatocytes are implicated in contributing to the immune niche of tumor-prone liver microenvironment. In parallel, as the major organ for lipid metabolism, the increased abundance of lipids and their metabolites is linked to processes crucial for nonalcoholic fatty liver disease and related liver cancer development. Furthermore, the proliferation, differentiation, and functions of hepatic immune and stromal cells are also reported to be regulated by lipid metabolism. Therefore, targeting lipid metabolism may hold great potential to reprogram the immunosuppressive liver microenvironment and synergistically enhance the immunotherapy efficacy in the circumstance of liver metastasis. In this review, we describe how the hepatic microenvironment adapts to the lipid metabolic alterations in pathologic conditions like nonalcoholic fatty liver disease. We also illustrate how these immunometabolic alterations promote the development of liver cancers and immunotherapy resistance. Finally, we discuss the current therapeutic options and hypothetic combination immunotherapies for the treatment of advanced liver cancers.
A short fragment of mitochondrial DNA for the taxonomic identification of blow flies (Diptera: Calliphoridae) in northwestern South America
Authors: Amat Eduardo , Gómez Giovan F , López-Rubio Andrés , Gómez-Piñerez Luz M , Albertino Rafael Jose
Published: July 2023

Blow flies are of medical, sanitary, veterinary, and forensic importance. Their accurate taxonomic identification is essential for their use in applied research. However, neotropical fauna has not been completely studied or described, and taxa identification without the required training is a difficult task. Additionally, the current morphological keys are not fitting to all extant taxa. Molecular-based approaches are widely used to overcome these issues, including the standard 5ʹ COI barcode fragment (~650 base pairs [bp]) for identification at the species level. Here, a shorter sequence of 5ʹ COI fragment (~342 bp) was assessed for the identification of 28 blow fly species inhabiting the northwest of South America. One tree-based (the generalized mixed Yule-coalescent—GMYC) and 3 distance-based approaches (automatic barcode gap discover – ABGD, the best close match – BCM, and the nearest neighbor – NN) analyses were performed. Noticeably, the amplification and sequencing of samples that had been preserved for up to 57 years were successful. The tree topology assigned 113 sequences to a specific taxon (70% effectiveness), while the distance approach assigned to 95 (59% effectiveness). The short fragment allowed the molecular identification of 19 species (60% of neotropical species except for the Lucilia species and Hemilucilia semidiaphana). According to these findings, the taxonomic and faunistic considerations of the blow fly fauna were provided. Overall, the short fragment approach constitutes an optimal species confirmation tool for the most common blow flies in northwestern South America.
Molecular and phenotypical findings of a novel de novo SYNGAP1 gene variant in an 11-year-old Iranian boy with intellectual disability
Authors: Mir Atefeh , Song Yongjun , Lee Hane , Nadeali Zakiye , Akbarian Fahimeh , Tabatabaiefar Mohammad Amin
Published: July 2023

Objective

Intellectual developmental disorder (IDD) type 5 is an autosomal dominant (AD) disorder and is characterized by intellectual disability (ID), psychomotor developmental delay, variable autism phenotypes, microcephaly, and seizure. IDD can be caused by mutations in the SYNGAP1 gene, which encodes a Ras GTPase-activating protein. This study revealed a novel de novo nonsense variant in SYNGAP1. The identification of such variants is essential for genetic counseling in patients and their families.

Methods

Exome sequencing implicated the causative variant. Sanger sequencing and cosegregation analyses were used to confirm the variant. Multiple in silico analysis tools were applied to interpret the variant using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines.

Results

The de novo NM_006772.3(SYNGAP1):c.3685C>T variant was identified in an 11-year-old boy with severe intellectual disability, neurodevelopmental delay, speech disorder, ataxia, specific dysmorphic facial features, and aggressive behavior.

Conclusion

The current study findings expand the existing knowledge of variants in SYNGAP1 that have been previously associated with nonsyndromic intellectual disability and autism, extending the spectrum of phenotypes associated with this gene. The data have implications for genetic diagnosis and counseling in similar phenotypic presentations.
Prime spectrums of EQ-algebras
Authors: Zhao Bin , Wang Wei
Published: July 2023

The main purpose of this paper is to study prime spectrums of EQ-algebras and to solve two open problems about $\wedge $-prime spectrums of involutive and prelinear EQ-algebras, which were proposed by N. Akhlaghinia, R.A. Borzooei and M. A. Kologani. In order to do so, we first give some characterizations of preideals, prime preideals and maximal preideals on (good) EQ-algebras, respectively. Then we introduce the notion of quasi De Morgan EQ-algebras (MEQ-algebras for short) and obtain that $\wedge $-prime preideals coincide with prime preideals for MEQ-algebras, and each involutive EQ-algebra is an MEQ-algebra. Following, we show that the prime spectrum space of a good EQ-algebra is a compact topological space and obtain that for any involutive EQ-algebra the prime spectrum space is connected if and only if its Boolean center is indeed 2-element. Also, we prove that the maximal spectrum space of a good and prelinear EQ-algebra (or an involutive and prelinear EQ-algebra) is a normal Hausdorff space. These results totally answer the above two open problems. Finally, we give some characterizations of the spectrum space of an MEQ-algebra by its reticulation.
Chemical homogeneity and sulfur deficiency in the early B-type stars of the λ Orionis group
Authors: Elmaslı Aslı , Ünal Kübra Özge
Published: July 2023

We present a detailed abundance analysis of nine early B-type stars in the λ Orionis group. High- and medium-resolution spectra of the target stars were observed at the Ankara University Kreiken Observatory or acquired from the European Southern Observatory and Observatoire de Haute-Provence archives. The atmospheric parameters of each star were estimated from the hydrogen Balmer, ionized silicone, and helium lines. Non-LTE model atmosphere calculations determined the precise abundances of helium, carbon, nitrogen, oxygen, neon, magnesium, silicon, sulfur, and iron from the spectra of each target star. While the abundances of the light elements He, C, N, O, Ne, Si, and also Fe are close to solar, Mg, Al, and S are deficient, and Ar is overabundant compared to the Sun. The phosphorus absorption lines were only accessible on the optical spectra of HD 43112, HD 34989, 37 Ori, and HD 36895. The phosphorus mean abundance values of these four stars are underabundant compared to the Sun. Argon was only detected on the spectra of HD 43112 and HD 36262 and showed an overabundance of 0.33 dex. The sulfur element deficiency was detected in all stars except for 35 Orionis. Sulfur may be a good signature to distinguish the λ Orionis group members from the Orion star-forming complex. Overall, chemical homogeneity was detected in all B-type star members of the λ Orionis group. Furthermore, the mass and age of each member were calculated and plotted on the H–R diagram.
Characterizing three-dimensional magnetic field, turbulence, and self-gravity in the star-forming region L1688
Authors: Hu Yue , Lazarian A
Published: July 2023

Interaction of three-dimensional magnetic fields, turbulence, and self-gravity in the molecular cloud is crucial in understanding star formation but has not been addressed so far. In this work, we target the low-mass star-forming region L1688 and use the spectral emissions of 12CO, 13CO, C18O, and H i, as well as polarized dust emissions. To obtain the 3D direction of the magnetic field, we employ the novel polarization fraction analysis. In combining with the plane-of-the-sky (POS) magnetic field strength derived from the Davis–Chandrasekhar–Fermi (DCF) method and the new differential measure analysis (DMA) technique, we present the first measurement of L1688’s three-dimensional magnetic field, including its orientation and strength. We find that L1688’s magnetic field has two statistically different inclination angles. The low-intensity tail has an inclination angle ≈55° on average, while that of the central dense clump is ≈30°. We find the global mean value of total magnetic field strength is Btot ≈ $135 \,\mathrm{\mu }{\rm G}$ from DCF and Btot ≈ $75 \,\mathrm{\mu }{\rm G}$ from DMA. We use the velocity gradient technique (VGT) to separate the magnetic fields’ POS orientation associated with L1688 and its foreground/background. The magnetic fields’ orientations are statistically coherent. The probability density function of H2 column density and VGT reveal that L1688 is potentially undergoing gravitational contraction at large scale ≈1.0 pc and gravitational collapse at small scale ≈0.2 pc. The gravitational contraction mainly along the magnetic field resulting in an approximate power-law relation $B_{\rm tot}\propto n_{\rm H}^{1/2}$ when volume density nH is less than approximately 6.0 × 103 cm−3.
Favorable Loci Identified for Stripe Rust Resistance in Chinese Winter Wheat Accessions via Genome-Wide Association Study
Authors: Wang Wenli , Jin Pengfei , Zhang Jia , Tang Yaqi , Zhao Bingjie , Yue Weiyun , Cheng Peng , Li Qiang , Wang Baotong
Published: July 2023

Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Currently, the utilization of resistant cultivars is the most viable way to reduce yield losses. In this study, a panel of 188 wheat accessions from China was evaluated for stripe rust resistance, and genome-wide association studies were performed using high-quality Diversity Arrays Technology markers. According to the phenotype and genotype data, a total of 26 significant marker–trait associations were identified, representing 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3A, 3B, 5A, 5B, 6B, 7B, and 7D. Of the 18 QTLs, almost all were associated with adult plant resistance (APR) except QYr.nwsuaf-6B.2, which was associated with all-stage resistance (also known as seedling resistance). Three of the 18 QTLs were mapped far from previously identified Pst resistance genes and QTLs and were considered potentially new loci. The other 15 QTLs were mapped close to known resistance genes and QTLs. Subsequent haplotype analysis for QYr.nwsuaf-2A and QYr.nwsuaf-7B.3 revealed the degrees of resistance of the panel in the APR stage. In summary, the favorable alleles identified in this study may be useful in breeding for disease resistance to stripe rust.
Combined Mcl-1 and YAP1/TAZ inhibition for treatment of metastatic uveal melanoma
Authors: Glinkina Kseniya A. , Teunisse Amina F.A.S. , Gelmi Maria Chiara , de Vries Jelle , Jager Martine J. , Jochemsen Aart G.
Published: July 2023

Uveal melanoma is the most common intraocular tumor in adults, representing approximately 5% of all melanoma cases. Up to 50% of uveal melanoma patients develop metastases that are resistant to most of the commonly used antineoplastic treatments. Virtually all uveal melanoma tumors harbor activating mutations in GNAQ or GNA11, encoding Gαq and Gα11, respectively. Constant activity of these proteins causes deregulation of multiple downstream signaling pathways including PKC, MAPK and YAP1/TAZ. While the importance of YAP1 signaling for the proliferation of uveal melanoma has recently been demonstrated, much less is known about the paralog of YAP1 transcriptional coactivator, named TAZ; however, similar to YAP1, TAZ is expected to be a therapeutic target in uveal melanoma. We performed a small-scale drug screen to discover a compound synergistically inhibiting uveal melanoma proliferation/survival in combination with YAP1/TAZ inhibition. We found that the combination of genetic depletion of YAP1/TAZ together with Mcl-1 inhibition demonstrates a synergistic inhibitory effect on the viability of uveal melanoma cell lines. Similarly, indirect attenuation of the YAP1/TAZ signaling pathway with an inhibitor of the mevalonate pathway, that is, the geranyl-geranyl transferase inhibitor GGTI-298, synergizes with Mcl-1 inhibition. This combination could be potentially used as a treatment for metastatic uveal melanoma.
Quinapril treatment curtails decline of global longitudinal strain and mechanical function in hypertensive rats
Authors: Wilson Alexander J. , Sands Gregory B. , Wang Vicky Y. , Pontre Beau , Ennis Daniel B. , Young Alistair A. , LeGrice Ian J. , Nash Martyn P.
Published: July 2023

Background:

Left ventricular (LV) global longitudinal strain (GLS) has been proposed as an early imaging biomarker of cardiac mechanical dysfunction.

Objective:

To assess the impact of angiotensin-converting enzyme (ACE) inhibitor treatment of hypertensive heart disease on LV GLS and mechanical function.

Methods:

The spontaneously hypertensive rat (SHR) model of hypertensive heart disease (n = 38) was studied. A subset of SHRs received quinapril (TSHR, n = 16) from 3 months (mo). Wistar Kyoto rats (WKY, n = 13) were used as controls. Tagged cardiac MRI was performed using a 4.7 T Varian preclinical scanner.

Results:

The SHRs had significantly lower LV ejection fraction (EF) than the WKYs at 3 mo (53.0 ± 1.7% vs. 69.6 ± 2.1%, P < 0.05), 14 mo (57.0 ± 2.5% vs. 74.4 ± 2.9%, P < 0.05) and 24 mo (50.1 ± 2.4% vs. 67.0 ± 2.0%, P < 0.01). At 24 mo, ACE inhibitor treatment was associated with significantly greater LV EF in TSHRs compared to untreated SHRs (64.2 ± 3.4% vs. 50.1 ± 2.4%, P < 0.01). Peak GLS magnitude was significantly lower in SHRs compared with WKYs at 14 months (7.5% ± 0.4% vs. 9.9 ± 0.8%, P < 0.05). At 24 months, Peak GLS magnitude was significantly lower in SHRs compared with both WKYs (6.5 ± 0.4% vs. 9.7 ± 1.0%, P < 0.01) and TSHRs (6.5 ± 0.4% vs. 9.6 ± 0.6%, P < 0.05).

Conclusions:

ACE inhibitor treatment curtails the decline in global longitudinal strain in hypertensive rats, with the treatment group exhibiting significantly greater LV EF and GLS magnitude at 24 mo compared with untreated SHRs.
Acute inhibition of nicotinamide adenine dinucleotide phosphate oxidase in the commissural nucleus of the solitary tract reduces arterial pressure and renal sympathetic nerve activity in renovascular hypertension
Authors: Marques Stefanne M. , Melo Mariana R. , Zoccal Daniel B. , Menani José V. , Colombari Débora S.A. , Ferreira-Neto Marcos L. , Xavier Carlos H. , Colombari Eduardo , Pedrino Gustavo R.
Published: July 2023

Background:

A growing body of evidence suggests that oxidative stress plays a role in the pathophysiology of hypertension. However, the involvement of the reactive oxygen species (ROS) in the commissural nucleus of the solitary tract (commNTS) in development the of hypertension remains unclear.

Method:

We evaluated the hemodynamic and sympathetic responses to acute inhibition of NADPH oxidase in the commNTS in renovascular hypertensive rats. Under anesthesia, male Holtzman rats were implanted with a silver clip around the left renal artery to induce 2-kidney 1-clip (2K1C) hypertension. After six weeks, these rats were anesthetized and instrumented for recording mean arterial pressure (MAP), renal blood flow (RBF), renal vascular resistance (RVR), and renal sympathetic nerve activity (RSNA) during baseline and after injection of apocynin (nicotinamide adenine dinucleotide phosphate oxidase inhibitor), NSC 23766 (RAC inhibitor) or saline into the commNTS.

Results:

Apocynin into the commNTS decreased MAP, RSNA, and RVR in 2K1C rats. NSC 23766 into the commNTS decreased MAP and RSNA, without changing RVR in 2K1C rats.

Conclusion:

These results demonstrate that the formation of ROS in the commNTS is important to maintain sympathoexcitation and hypertension in 2K1C rats and suggest that NADPH oxidase in the commNTS could be a potential target for therapeutics in renovascular hypertension.