bluuebunny/crossref_metadata_2025_split huggingface dataset:
Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
Authors: Bittrich Sebastian , Midlik Adam , Varadi Mihaly , Velankar Sameer , Burley Stephen K. , Young Jasmine Y. , Sehnal David , Vallat Brinda 
Published: July 2024

AbstractWith the ever‐expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: https://molstar.org/mol‐view‐spec/, GitHub project: https://github.com/molstar/mol‐view‐spec), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view–building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball‐and‐stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python packageBasic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation filesBasic Protocol 3: Creating a MolViewSpec view with labels and other advanced featuresSupport Protocol 1: Computing rotation and translation vectorsSupport Protocol 2: Creating a MolViewSpec annotation file
CO2‐to‐CO Conversion with Over 10 % Efficiency Using Earth Abundant System in a Single‐Compartment Reactor with Oxygen Tolerant Mn Complex Catalyst
Authors: Nishi Teppei , Sakamoto Naonari , Sekizawa Keita , Morikawa Takeshi , Sato Shunsuke 
Published: July 2024

AbstractThe direct conversion of CO2 in the presence of O2 to value‐added chemicals is a potentially important cost‐effective solar‐driven CO2 reduction technology. The present work demonstrates the solar‐powered conversion of CO2 to CO with greater than 10 % efficiency using a Mn complex cathode and an Fe−Ni anode in a single‐compartment reactor without an ion exchange membrane in conjunction with a Si solar cell. Reactors separated by ion exchange membranes are typically used to prevent any effects of oxygen generated by the counter electrode. However, the present Mn complex catalyst maintained its activity even in the presence of 15 % O2. Operando surface‐enhanced Raman spectroscopy established that the present Mn catalyst preferentially reacted with CO2 without adsorbing O2. This unique characteristic enabled solar‐driven CO2 reduction using a single‐compartment reactor. In contrast, catalytic metals such as Ag tend to lose activity in such systems as a consequence of reaction with oxygen produced at the anode.
Fake news? The impact of information mismatch on mating behaviour
Authors: Rodrigues Leonor R. , Magalhães Sara 
Published: July 2024

AbstractMultiple cues are often used for mate choice in complex environments, potentially entailing mismatches in the information conveyed by different sources. We address the consequences of this information mismatch for receivers using the spider mite Tetranychus urticae, in which virgin females are highly valuable mates compared to mated females, given first male sperm precedence. Accordingly, males are known to prefer virgins and distinguish them using cues from the females themselves and that they leave on the substrate. Whereas cues from females are highly reliable, those left on the substrate may not reflect the real female mating status if females move and/or mate. Here, we tested the consequences of such mismatch by exposing males to mated or virgin females on patches previously impregnated with cues deposited by females of either mating status. Male mating attempts were solely affected by substrate cues while female acceptance and the number of mating events were independently affected by both cues. Copulation duration, in contrast, depended mainly on the mating status of the female, with the number of copulations and the total time spent mating being intermediate in environments with mismatched information. We also show that males incur mating costs, reflected in reduced survival in environments with virgin cues. These results suggest that substrate cues left by females are instrumental for males to find their mates. However, in environments with mismatched information, males may pay survival costs without the associated benefit of mating with virgins, or they may lose opportunities to mate with virgins by responding to substrate cues from mated females. The benefit of using multiple cues will then hinge upon the frequency of information mismatch, which itself should vary with the dynamics of populations.
Homologous recombination and gene‐specific selection co‐shape the vertical nucleotide diversity of mangrove sediment microbial populations
Authors: Ding Jijuan , Liu Fei , Zeng Jiaxiong , Gu Hang , Zhang Dandan , Yang Xueqin , Wu Bo , Shu Longfei , He Zhili , Wang Cheng 
Published: July 2024

AbstractMangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high‐frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0–100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome‐wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045–0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non‐synonymous mutation ratio between 0–20 and 20–100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene‐specific selection, finally resulting in the stratified differentiation occurring between 0–20 and 20–100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems.
Safety and efficacy of aficamten in patients with non‐obstructive hypertrophic cardiomyopathy: A 36‐week analysis from FOREST‐HCM
Authors: Masri Ahmad , Barriales‐Villa Roberto , Elliott Perry , Nassif Michael E. , Oreziak Artur , Owens Anjali T. , Tower‐Rader Albree , Heitner Stephen B. , Kupfer Stuart , Malik Fady I. , Melloni Chiara , Meng Lisa , Wei Jenny , Saberi Sara ,   on behalf of the FOREST‐HCM Investigators
Published: July 2024

AimsThe aim of this study was to report safety and efficacy of aficamten in patients with non‐obstructive hypertrophic cardiomyopathy (nHCM) over 36 weeks in the ongoing FOREST‐HCM trial.Methods and resultsPatients were started on aficamten 5 mg daily, with doses adjusted in 5‐mg increments (5–20 mg) at ≥2‐week intervals according to site‐read left ventricular ejection fraction (LVEF). Aficamten dose was increased if LVEF ≥55%, maintained if LVEF 50–54%, decreased if LVEF 40–<50%, and temporarily interrupted if LVEF <40%. Safety and efficacy were assessed over 36 weeks. Overall, 34 patients were enrolled (mean age 57.2 ± 15.3 years, 62% female, 41% in New York Heart Association [NYHA] class III). Over 36 weeks, 82.3% achieved 15–20 mg daily dose and there was a modest reduction in LVEF by −4.3% ± 5.2 from 70% ± 6.1 (p < 0.0001). At Week 36, NYHA class improved by ≥1 class in 27 (79.4%) patients. Mean Kansas City Cardiomyopathy Questionnaire clinical summary score improved by 13.8 ± 12.5 points relative to baseline. Median (interquartile range) levels of N‐terminal pro‐B‐type natriuretic peptide were significantly improved from baseline (−665.5 pg/ml [−1244.0, −232.0]; p < 0.0001), while high‐sensitivity cardiac troponin I was unchanged (−2.7 ng/L [−11.3, 1.6]; p = 0.25). There were no drug discontinuations due to adverse events. LVEF <50% occurred in 2 (5.9%) patients, one following pulmonary vein isolation and one associated with atrial fibrillation.ConclusionsOver 36 weeks, aficamten appeared safe and effective in the studied patients with nHCM.
Exploring Gas‐Solid Phase Diagrams: Novel Methods for Oxyfluorination of Mn3O4 and Mn2O3 with Molecular Fluorine
Authors: De Windt Sébastien , Auvergniot Jérémie , Cabelguen Pierre‐Etienne , Gschwind Fabienne , Dubois Marc , Guerin Katia 
Published: July 2024

AbstractFluorinated, manganese‐redox cation‐disordered rocksalts are promising candidates for high‐performance cobalt‐free Li‐ion cathode active material. A need for reactive fluorinated precursors was however identified. While manganese oxyfluorides are promising precursor candidates, none stable at room temperature was reported prior to 2023. The key to their recent synthesis by reacting molecular fluorine with MnO was a procedure to continuously scan the temperature axis in search of activation temperatures. In line with this philosophy of continuous exploration of the chemical space, two experimental procedures are reported to scan the stoichiometry axis of a gas‐solid phase diagram in search of transitions and intermediate compounds. Their application to F2 ‐ Mn3O4 and F2 ‐ Mn2O3 phase diagrams resulted in the discovery of two new ranges of stable manganese oxyfluorides of respective compositions MnO1.33‐0.13xFx with x<0.5 and MnO1.5‐0.22xFx with x<1.
Studies on supercapacitor electrode performance of novel (AlCuCoFeMnNi)3O4 high entropy spinel oxide admixed with different carbon‐based additives
Authors: Gupta Amit K. , Kumar Ankit , Marndi Mina , Giri Neeraj K. , Shahi Rohit R. 
Published: July 2024

AbstractThe present investigation aims to synthesize a novel (AlCuCoFeMnNi)3O4 type high entropy spinel oxide through the sol‐gel and investigate the effect of different carbon‐based additives on charge storage performance. The formation of the inverse spinel phase of [B(AB)O4] type inverse spinel phase was confirmed through the detailed x‐ray diffraction analysis of the synthesized sample. The synthesized spinel phase was indexed with the space group of Fd−3m and has a lattice parameter of 8.2697 Å. The synthesized high entropy oxide (HEO) phase Ni, Co, and Fe coexists in +2 and +3 states. At the same time, Cu in +2 state, Al in +3 state, and Mn in +3 and +4 states confirmed through x‐ray photoelectron spectroscopy. The electrochemical charge storage performance of synthesized HEO was measured through the three‐electrode setup in 2 M KOH aqueous electrolyte solution in two different potential windows, such as −0.2 to 0.4 V and 0.0 to 0.5 V. Different carbon‐based conducting materials such as acetylene black, reduced graphene oxide (RGO), and carbon particles obtained from 10‐hour ball‐milling of used dry cell carbon electrode (CP). The charge storage mechanism changes from electrochemical double layer capacitance to pseudocapacitive type as the potential window varies from −0.2 to 0.4 to 0 to 0.5 V. The value of specific capacitance for an electrode made of HEO with acetylene black, RGO, and CP was found to be 32.67, 7.50, and 4.58 F/g and 30.68, 16.33, and 9.05 F/g in the potential window of −0.2 to 0.4 V and 0 to 0.5 V at a scan rate of 5 mV/s, respectively. The cyclic performance of the developed three electrodes was measured at a scan rate of 100 mV/s for 1000 cycles, and it was found to be 94%, 98%, and 99% for electrodes made of HEO with acetylene black, RGO, and CP, respectively.
Numerical simulation of endovascular treatment options for cerebral aneurysms
Authors: Frank Martin , Holzberger Fabian , Horvat Medeea , Kirschke Jan , Mayr Matthias , Muhr Markus , Nebulishvili Natalia , Popp Alexander , Schwarting Julian , Wohlmuth Barbara 
Published: July 2024

AbstractPredicting the long‐term success of endovascular interventions in the clinical management of cerebral aneurysms requires detailed insight into the patient‐specific physiological conditions. In this work, we not only propose numerical representations of endovascular medical devices such as coils, flow diverters or Woven EndoBridge but also outline numerical models for the prediction of blood flow patterns in the aneurysm cavity right after a surgical intervention. Detailed knowledge about the postsurgical state then lays the basis to assess the chances of a stable occlusion of the aneurysm required for a long‐term treatment success. To this end, we propose mathematical and mechanical models of endovascular medical devices made out of thin metal wires. These can then be used for fully resolved flow simulations of the postsurgical blood flow, which in this work will be performed by means of a Lattice Boltzmann method applied to the incompressible Navier–Stokes equations and patient‐specific geometries. To probe the suitability of homogenized models, we also investigate poro‐elastic models to represent such medical devices. In particular, we examine the validity of this modeling approach for flow diverter placement across the opening of the aneurysm cavity. For both approaches, physiologically meaningful boundary conditions are provided from reduced‐order models of the vascular system. The present study demonstrates our capabilities to predict the postsurgical state and lays a solid foundation to tackle the prediction of thrombus formation and, thus, the aneurysm occlusion in a next step.
Modeling of fluid‐rigid body interaction in an electrically conducting fluid
Authors: Scherz Jan , Schlömerkemper Anja 
Published: July 2024

AbstractWe derive a mathematical model for the motion of several insulating rigid bodies through an electrically conducting fluid. Starting from a universal model describing this phenomenon in generality, we elaborate (simplifying) physical assumptions under which a mathematical analysis of the model becomes feasible. Our main focus lies on the derivation of the boundary and interface conditions for the electromagnetic fields as well as the derivation of the magnetohydrodynamic approximation carried out via a nondimensionalization of the system.
The impact of urbanisation on green total factor productivity: Exploring threshold and mediating effects of human capital
Authors: Wang Guimei , Salman Muhammad , Zhang Kuangwei 
Published: July 2024

AbstractGreen development is main direction of high‐quality economic development in China. Urbanisation and human capital (HC) are important factors affecting green development. This study examines effects of urbanisation and HC on green total factor productivity (GTFP) using least squares dummy variable model, based on provincial data in China from 2001 to 2019. This study then explored impact of urbanisation on GTFP through HC (educated HC, healthy HC, and HC structure), adopting mediating effect and threshold effect model. The results showed that urbanisation and three types of HC promote GTFP in China and coastal region. In inland region, urbanisation has insignificant impact on GTFP, while educated HC and HC structure improve it. The mediating analysis revealed that educated and healthy HC in China and coastal region enhance promotion effect of urbanisation on GTFP, whereas HC structure hinders it. In inland region, only healthy HC stimulates promotion effect of urbanisation on GTFP. Considering threshold effect of educated and healthy HC, promotion effect of urbanisation on GTFP is weaker than threshold value; but effect is stronger above threshold value. The promotion effect of urbanisation on GTFP is stronger when value of HC structure is below the threshold, while effect is weakened as value exceeds threshold value. Policy implications are documented to promote urbanisation in a differentiated manner, increase investment in HC, and strengthen coordination between urbanisation and HC.
Facile synthesis of Pt clusters decorated TiO2 nanoparticles for efficient photocatalytic degradation of antibiotics
Authors: Pan Yin , Liang Weizhen , Wang Zongpeng , Gong Junjie , Wang Yichao , Xu Aijiao , Teng Zhenyuan , Shen Shijie , Gu Lin , Zhong Wenwu , Lu Hongsheng , Chen Baofu 
Published: July 2024

AbstractTiO2 has attracted much attention in the field of photocatalytic degradation of antibiotics due to its good photostability, nontoxicity, and low cost. However, the rapid recombination of photogenerated carriers limits the further improvement of its photocatalytic activity. Here, a facile microwave‐assisted hydrothermal method has been developed to prepare Pt clusters decorated TiO2 nanoparticles. Pt clusters ranging in size from 1 to 2 nm are uniformly distributed across the surface of the TiO2 matrix. A pronounced charge transfer phenomenon is discernible between the Pt and TiO2 components. It is revealed that the charge transfer enables faster transfer and separation of photogenerated electrons and holes, which are beneficial for the improvement of photocatalytic degradation of both ofloxacin and levofloxacin. The degradation capability can be attributed to the efficient generation of •OH or •O2− species within the solution. The parallel adsorption model of TiO2 on antibiotic molecules is verified, and the degradation reaction pathway has been elucidated. This work provides a facile method for optimizing the performance of TiO2 photocatalysts, which can be extended to other oxide photocatalysts.
Silencing of FTO inhibits oxidative stress to relieve neuropathic pain by m6A modification of GPR177
Authors: Liu Li , Liu Mei , Song Zhiping , Zhang Huaigen 
Published: July 2024

AbstractBackgroundNeuropathic pain (NP) is a challenging health condition owing to its complex nature and associated multiple etiologies. The occurrence of NP involves the abnormal activity of neurons mediated by oxidative stress (OS). Previous research has demonstrated that m6A methylation plays a role in the regulatory pathway of NP. This study aimed to investigate the specific molecular pathways through which m6A methylation modifiers alleviate NP.MethodsFor this purpose, an NO rat model was developed via spared nerve injury (SNI), followed by quantifying the animal's pain assessment via paw withdrawal threshold (PWT) and paw withdrawal latency (PWL). The OS in SNI rats was evaluated by measuring reactive oxygen species, superoxide dismutase, and catalase (CAT) in spinal cord tissues. Moreover, quantitative‐real‐time polymerase chain reaction and western blot analysis were employed for detecting fat mass and obesity‐associated (FTO) and GPR177 levels, while m6A levels of GPR117 were analyzed via MeRIP.ResultsThe results indicated an enhanced OS with highly expressed FTO in spinal cord tissue samples, where knocking down Fto effectively relieved NP and OS in SNI rats. Mechanistic investigations revealed that Fto‐mediated reduction of Grp177 m6A modification was involved in the WNT5a/TRPV1 axis‐mediated OS remission of NP. Moreover, in vitro experiment results indicated that YTHDF2 was an important m6A methylated reading protein for this process.ConclusionsFto silencing leads to increased m6A methylation of Grp177 through a YTHDF2‐dependent mechanism, resulting in decreased Grp177 stability and ultimately reducing NP in rats by OS suppression.
Preconception underweight and the risk of offspring congenital heart diseases in young pregnant women: Evidence from the China Birth Cohort Study
Authors: Yan Ruohua , Liu Xiaohang , Peng Yaguang , Peng Xiaoxia 
Published: July 2024

AbstractObjectiveMaternal obesity is a highly suggestive risk factor of offspring congenital heart diseases (CHD). However, the risk of offspring CHD associated with maternal underweight has rarely been mentioned. Therefore, this study aimed to explore the effect of preconception underweight on offspring CHD.MethodsFrom November 2017 to August 2021, 132 386 pregnant women were enrolled in a birth cohort study in China in early pregnancy, and completed follow‐up until delivery (or miscarriage/termination). Offspring CHD was diagnosed by prenatal ultrasound examination in both live births and stillbirths. Log‐binomial regression and restricted cubic spline were used to estimate the risk of offspring CHD associated with preconception body mass index (BMI). A generalized additive model was used to explore the modification effect of maternal age on the association between preconception BMI and offspring CHD.ResultsA total of 129 096 pregnant women were included in the analysis. The incidence of CHD in the underweight, normal weight, overweight, and obesity groups were 117/17 313 (0.68%), 556/85 695 (0.65%), 128/19 936 (0.64%), 47/6152 (0.76%), respectively. Both underweight and obesity before pregnancy marginally increased the risk of offspring CHD. The association between preconception BMI and offspring CHD varied by maternal age, with low preconception BMI associated with a significantly higher risk of offspring CHD in women <24 years (RR 2.32, 95% CI: 1.07–5.01 for 17 vs 21 kg/m2).ConclusionPreconception underweight was associated with an increased risk of offspring CHD in young pregnant women. Therefore, weight gain is important to prevent offspring CHD, especially for young women with low preconception BMI.
Screening of Chagas disease in pregnant women—Recommendation by the Italian National Institute of Health, 2023
Authors: Ornaghi Sara , Corsi Decenti Edoardo , Zammarchi Lorenzo , Bartoloni Alessandro , Angheben Andrea , Nava Chiara , Tommasella Margherita , Carletti Valerio , Colciago Elisabetta , Dell'Oro Stefania , Farsetti Daniele , Finale Enrico , Fumagalli Simona , Giovinale Silvia , Iannuzzi Laura , Maellaro Filomena , Maggiora Elena , Pometti Francesca , Sampaolo Letizia , Basevi Vittorio , Donati Serena 
Published: July 2024

SynopsisAll pregnant women at risk should be screened for Chagas disease, as recommended by the Italian National Institute of Health.