bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of the Mean Thermosphere Circulation, O/N2 Ratio and Ne to Solar and Magnetospheric Forcing From Above and Tidal Forcing From Below
Authors: Forbes Jeffrey M. , Zhang Xiaoli , Maute Astrid , Cullens Chihoko 
Published: March 2024

AbstractThe day‐to‐day variability (“weather”) associated with the diurnal‐ and zonal‐mean (DZM) circulation, O/N2 ratio and electron density (Ne) of the I‐T system due to tidal “forcing from below” and solar flux and magnetosphere (SM) “forcing from above” during 2021 are delineated, diagnosed and quantitatively compared using a series of model simulations designed to separate these responses with respect to their origins. The external forcings are driven by actual tidal, solar wind, and solar flux observations. Both circulation systems occupy the full extent of the I‐T, and the SM‐forced DZM circulation is 2–3 times more vigorous in terms of vertical and meridional wind magnitudes. Tidal‐driven DZM Ne reductions of up to 30%–40% with respect to those of the fully forced I‐T system occur, mainly between ±30° latitude, compared to SM‐driven increases of up to 15%–20%. In terms of annual variances over this latitude range, tidal‐driven DZM Ne variances exceed or equal those of the SM‐driven variances. The former is mainly controlled by O/N2 ratio vis‐a‐vis tidal‐forced temperature variations above 150 km. While a similar cause‐effect relation exists for the latter, this is superseded by Ne variability associated with solar production. However, DZM I‐T system variability forced from below is underestimated in the simulations in two respects: the effects of gravity waves are omitted, and tidal forcing is represented by 45‐day running means, as compared with the more realistic actual daily variability of SM forcing. These shortcomings should be ameliorated once multi‐satellite missions planned for the future come to fruition.
Structural basis of the histone ubiquitination read–write mechanism of RYBP–PRC1
Authors: Ciapponi Maria , Karlukova Elena , Schkölziger Sven , Benda Christian , Müller Jürg 
Published: March 2024

AbstractHistone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP–PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.
Mechanistic study on the alleviation of postmenopausal osteoporosis by Lactobacillus acidophilus through butyrate-mediated inhibition of osteoclast activity
Authors: Dong Junjie , Shu Guizhao , Yang Jin , Wang Bing , Chen Lingqiang , Gong Zhiqiang , Zhang Xiaofeng 
Published: March 2024

AbstractIn China, traditional medications for osteoporosis have significant side effects, low compliance, and high costs, making it urgent to explore new treatment options. Probiotics have demonstrated superiority in the treatment of various chronic diseases, and the reduction of bone mass in postmenopausal osteoporosis (PMOP) is closely related to the degradation and metabolism of intestinal probiotics. It is crucial to explore the role and molecular mechanisms of probiotics in alleviating PMOP through their metabolites, as well as their therapeutic effects. We aim to identify key probiotics and their metabolites that affect bone loss in PMOP through 16srDNA sequencing combined with non-targeted metabolomics sequencing, and explore the impact and possible mechanisms of key probiotics and their metabolites on the progression of PMOP in the context of osteoporosis caused by estrogen deficiency. The sequencing results showed a significant decrease in Lactobacillus acidophilus and butyrate in PMOP patients. In vivo experiments confirmed that the intervention of L. acidophilus and butyrate significantly inhibited osteoclast formation and bone resorption activity, improved intestinal barrier permeability, suppressed B cells, and the production of RANKL on B cells, effectively reduced systemic bone loss induced by oophorectomy, with butyric acid levels regulated by L. acidophilus. Consistently, in vitro experiments have confirmed that butyrate can directly inhibit the formation of osteoclasts and bone resorption activity. The above research results indicate that there are various pathways through which L. acidophilus inhibits osteoclast formation and bone resorption activity through butyrate. Intervention with L. acidophilus may be a safe and promising treatment strategy for osteoclast related bone diseases, such as PMOP.
Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project
Authors: Gong Binsheng , Li Dan , Zhang Yifan , Kusko Rebecca , Lababidi Samir , Cao Zehui , Chen Mingyang , Chen Ning , Chen Qiaochu , Chen Qingwang , Dai Jiacheng , Gan Qiang , Gao Yuechen , Guo Mingkun , Hariani Gunjan , He Yujie , Hou Wanwan , Jiang He , Kushwaha Garima , Li Jian-Liang , Li Jianying , Li Yulan , Liu Liang-Chun , Liu Ruimei , Liu Shiming , Meriaux Edwin , Mo Mengqing , Moore Mathew , Moss Tyler J. , Niu Quanne , Patel Ananddeep , Ren Luyao , Saremi Nedda F. , Shang Erfei , Shang Jun , Song Ping , Sun Siqi , Urban Brent J. , Wang Danke , Wang Shangzi , Wen Zhining , Xiong Xiangyi , Yang Jingcheng , Yin Lihui , Zhang Chao , Zhang Ruolan , Bhandari Ambica , Cai Wanshi , Eterovic Agda Karina , Megherbi Dalila B. , Shi Tieliu , Suo Chen , Yu Ying , Zheng Yuanting , Novoradovskaya Natalia , Sears Renee L. , Shi Leming , Jones Wendell , Tong Weida , Xu Joshua 
Published: March 2024

AbstractAccurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.
Enhanced dye removal using montmorillonite modified with graphene quantum dots in sustainable salep nanocomposite hydrogel
Authors: Mohammad Sharifi Kolsum , Poursattar Marjani Ahmad , Gozali Balkanloo Peyman 
Published: March 2024

AbstractThis research investigated the utilization of graphene quantum dot/montmorillonite (GQD/MMT) as an effective nanofiller in a hydrogel composed of salep biopolymer. The semi-IPN hydrogel was synthesized using salep as the substrate, acrylamide (AAm) as the monomer, ammonium persulfate (APS) as an initiator in free radical polymerization, and N,N'-methylenebisacrylamide (MBA) as a cross-linking agent. The hydrogels were applied to remove safranin (SA), methylene blue (MB), crystal violet (CV), methyl green (MG), congo red (CR), and malachite green (MG) dyes from the water. The diverse properties were analyzed using a scanning electron microscope, fourier infrared spectroscopy, mapping, energy dispersive spectroscopy, weighing analysis, X-ray diffraction, and thermal stability analyses. The optimism of the prepared adsorbent in dye absorption was evaluated by measuring the swelling amount, pH impact, adsorbent dosage, and contact time. The adsorption calculations were described using kinetics and isotherm models. The results indicated that the Langmuir isotherm model (R2 = 99.6) and the pseudo-second-order kinetic model (R2 = 99.9) provided the best fit for the absorption process of MB. The presence of additional amounts of GQD/MMT had a reciprocal effect on the adsorption efficiency due to the accumulation of GQD/MMT in the semi-interpenetrating polymer network (semi-IPN (structure. The findings revealed that the samples exhibited high thermal stability, and the absorption process was primarily chemical. Furthermore, the nanocomposite hydrogels demonstrated distinct mechanisms for absorbing anionic dye (CR) and cationic dye (MB). Under optimal conditions, using 7 wt% GQD/MMT at a concentration of 5 ppm, pH = 7, an adsorbent dosage of 50 mg, at room temperature, and a contact time of 90 min, the maximum removal efficiencies were achieved: MB (96.2%), SA (98.2%), MG (86%), CV (99.8%), MG (95.8%), and CR (63.4%). These results highlight the adsorbent's high absorption capacity, rapid removal rate, and reusability, demonstrating its potential as an eco-friendly and cost-effective solution for removing dyes from water.
Biochemical Society support in action: experiences from our community
Authors: Ollett Lucy 
Published: March 2024

Throughout the year, the Biochemical Society offers a programme of grants for all career stages supporting research, attendance at scientific conferences and sponsorship of events. In 2023, we awarded over £320,000 towards international collaboration and the training of essential biochemistry techniques through workshops as well as the organization of independent lectures and seminar series. In this article, we are delighted to share a few insights from our community that highlight the variety of projects and opportunities made possible by our funding.
For more information about our funding opportunities and the application process, please visit our website.
A novel approach towards parametric assessment of reliability and resilience of high voltage mica‐based insulation systems by statistical analysis of experimental failure data
Authors: Negari Shahram , Esmaeil Moghadam Davoud 
Published: March 2024

AbstractInsulation systems in high‐voltage electric machines play a pivotal role in the reliable operation and longevity of the equipment. Mica‐based insulation materials have proven to possess and maintain excellent dielectric properties in the long run and prevent premature insulation degradation. Numerous qualifications tests, such as voltage endurance, are outlined in IEC and IEEE standards. The authors, however, take a different parametric approach, opting for reliability assessment of insulation systems using derived three‐parameter Weibull models. Therefore, instead of simple pass–fail criteria, empirical data is employed to determine failure rate probabilities quantitatively and objectively. Experimental data, including breakdown, dissipation factor, and partial discharge measurements, are used to construct the Weibull distribution model to predict fault and failure rates and calculate hazard functions. The rigorous examinations interpreted through the analytical model help assess insulation system resilience and particularly the impact of electrical field stress and mica content. Variation of electrical stress from 66.75 to 71.20 V/mil demonstrated how the mean time to failure of the system changed from 146.4 to 85.1 at 3 Un, hence identifying opportunities for design improvement and uncovering performance boundaries. Ultimately, the developed framework enhances comprehension of insulation system failure probabilities, guiding design decisions and ensuring a secure and reliable operation of electrical machines across applications.
Final report, On-going Key Comparison BIPM.QM-K1, Ozone at ambient level, comparison with NIM Oct.2023
Authors: Viallon Joële , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Jingkun Hao , Yiling Liu , Norris James E , Trask Peter 
Published: March 2024

Main text
As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of China maintained by the National Institute of Metrology (NIM) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount fraction range of 0 nmol mol−1 to 500 nmol mol−1.
To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Simulation and analysis of enhancement-mode AlGaN/GaN HEMT with P-I-N junction gate
Authors: Jia Mao , Hou Bin , Yang Ling , Zhang Meng , Chang Qingyuan , Niu Xuerui , Shi Chunzhou , Du Jiale , Wu Mei , Lu Hao , Ma Xiaohua , Hao Yue 
Published: March 2024

Abstract
To improve the threshold voltage and gate reliability of conventional enhancement-mode p-GaN-gated AlGaN/GaN high electron mobility transistors while maintaining a low on-resistance, an improved design solution for p-GaN HEMTs with P-I-N junction gate (PIN-HEMTs) has been proposed. Simulation results show that energy band modulation is achieved by adjusting the doping concentration and thickness of each layer of the PIN junction, and high-performance p-GaN gate HEMTs with adjustable threshold voltages ranging from 0.56 V to 4.75 V and gate breakdown voltages ranging from 19.8 V to 30.3 V would be prepared. The PIN-HEMT has a quasi-self-alignment property, which means that good gate control is independent of gate metal alignment. This not only improves the production efficiency but also solves the problems of weak gate control and electric field aggregation at the gate edge caused by the gate misalignment in conventional p-GaN gate HEMTs, thus realizing lower on-resistance and higher gate breakdown voltage, which demonstrates this proposed structure has excellent potentials for realizing effective and reliable high-power transistors.
Ni/Zn ratio and La substitution effect on selected structural and magnetic properties of NiZn ferrites
Authors: Šoka Martin , Ušáková Mariana , Dosoudil Rastislav , Jančárik Vladimír , Ušák Elemír , Dobročka Edmund 
Published: March 2024

Abstract
Auto-combustion process was used for synthetization of Ni1−x
Zn
x
Fe2O4 and Ni1−x
Zn
x
La0.02Fe1.98O4 (x = 0, 0.3, 0.5, 0.64 and 0.7) ferrite samples to investigate their structural and selected magnetic properties. Standard characterization method such as x-ray diffraction, magnetic susceptibility temperature dependencies measurement, low-frequency hysteresis loops recording and complex permeability spectra were used on the research samples. The monophasic ferrite compounds have been prepared. For all samples, with an increase of zinc ions in the content, a decrease of the Curie temperature and coercive field value and an increase of the complex permeability real part value were observed, together with a shift of the ferrimagnetic resonance frequency value to lower ones. Substituted samples showed some differences, such as slightly higher values of the Curie temperature and coercive field, and at the same time slightly lower values of the complex permeability real part and higher values of the ferrimagnetic resonance frequency.
Efficiently tuning the electrical performance of PBTTT-C14 thin film via in
situ controllable multiple precursors (Al2O3:ZnO) vapor phase infiltration
Authors: Jia Zhen , Wang Weike , Ma Chuang , Zhang Xuelian , Yan Ruihang , Zhu Jiankang 
Published: March 2024

Abstract
Conjugated polymer-based organic/inorganic hybrid materials become the current research frontier and show great potential to integrate flexible polymers and rigid solid materials, which have been widely used in the field of various flexible electronics and optical devices. In this study, based on the multiple vapor phase infiltration (VPI) process, various precursor molecules (diethylzinc DEZ, trimethylaluminum TMA, H2O) are applied for the in situ modification of PBTTT-C14 films. The conductivity of the PBTTT-C14/Al2O3:ZnO (AZO) film is significantly enhanced, and the maximum value of conductivity is 1.16 S cm−1, which is eight orders of magnitude higher than the undoped PBTTT-C14 thin film. Here, the change of morphologies and crystalline states are analyzed via SEM, AFM, and XRD. And the chemical changes during the VPI process of PBTTT-C14 are characterized through Raman, XPS, and UV–vis. During the AZO VPI process, the formation of new ZnS matrix in the polymer subsurface can generate new additional electron conduction pathways through the crosslinking of polymer chains with inorganic materials, and the addition of Al2O3 can bring about the increase of average grain size of ZnO crystals, which is also benefit to the conductivity increase of PBTTT-C14 thin film. Generally, the synergistic effect between the inorganic and polymer constituents results in the significantly enhancement of the conductivity of PBTTT-C14/AZO thin films.
An updated variable RBE model for proton therapy
Authors: Lyngholm Erlend , Stokkevåg Camilla Hanquist , Lühr Armin , Tian Liheng , Meric Ilker , Tjelta Johannes , Henjum Helge , Handeland Andreas Havsgård , Ytre-Hauge Kristian Smeland 
Published: March 2024

Abstract

Objective. While a constant relative biological effectiveness (RBE) of 1.1 forms the basis for clinical proton therapy, variable RBE models are increasingly being used in plan evaluation. However, there is substantial variation across RBE models, and several new in vitro datasets have not yet been included in the existing models. In this study, an updated in vitro proton RBE database was collected and used to examine current RBE model assumptions, and to propose an up-to-date RBE model as a tool for evaluating RBE effects in clinical settings. Approach. A proton database (471 data points) was collected from the literature, almost twice the size of the previously largest model database. Each data point included linear-quadratic model parameters and linear energy transfer (LET). Statistical analyses were performed to test the validity of commonly applied assumptions of phenomenological RBE models, and new model functions were proposed for

RB

E

max

and

RB

E

min

(RBE at the lower and upper dose limits). Previously published models were refitted to the database and compared to the new model in terms of model performance and RBE estimates. Main results. The statistical analysis indicated that the intercept of the

RB

E

max

function should be a free fitting parameter and RBE estimates were clearly higher for models with free intercept.

RB

E

min

increased with increasing LET, while a dependency of

RB

E

min

on the reference radiation fractionation sensitivity (

α
/
β

x

) did not significantly improve model performance. Evaluating the models, the new model gave overall lowest RMSE and highest R2 score. RBE estimates in the distal part of a spread-out-Bragg-peak in water (

α
/
β

x

= 2.1 Gy) were 1.24–1.51 for original models, 1.25–1.49 for refits and 1.42 for the new model. Significance. An updated RBE model based on the currently largest database among published phenomenological models was proposed. Overall, the new model showed better performance compared to refitted published RBE models.
Joint reconstruction and segmentation in undersampled 3D knee MRI combining shape knowledge and deep learning
Authors: Kofler A , Wald C , Kolbitsch C , V Tycowicz C , Ambellan F 
Published: March 2024

Abstract

Objective. Task-adapted image reconstruction methods using end-to-end trainable neural networks (NNs) have been proposed to optimize reconstruction for subsequent processing tasks, such as segmentation. However, their training typically requires considerable hardware resources and thus, only relatively simple building blocks, e.g. U-Nets, are typically used, which, albeit powerful, do not integrate model-specific knowledge. Approach. In this work, we extend an end-to-end trainable task-adapted image reconstruction method for a clinically realistic reconstruction and segmentation problem of bone and cartilage in 3D knee MRI by incorporating statistical shape models (SSMs). The SSMs model the prior information and help to regularize the segmentation maps as a final post-processing step. We compare the proposed method to a simultaneous multitask learning approach for image reconstruction and segmentation (MTL) and to a complex SSMs-informed segmentation pipeline (SIS). Main results. Our experiments show that the combination of joint end-to-end training and SSMs to further regularize the segmentation maps obtained by MTL highly improves the results, especially in terms of mean and maximal surface errors. In particular, we achieve the segmentation quality of SIS and, at the same time, a substantial model reduction that yields a five-fold decimation in model parameters and a computational speedup of an order of magnitude. Significance. Remarkably, even for undersampling factors of up to R = 8, the obtained segmentation maps are of comparable quality to those obtained by SIS from ground-truth images.
Multiphysics coupled sensing mechanism of Pd/Ni alloy thin-film coated SAW hydrogen sensor
Authors: Cui Baile , Jin Jing , Hu Anyu , Ren Zixuan , Liang Yong , Wang Wen , Cheng Lina 
Published: March 2024

Abstract
Multiphysics coupled sensing mechanism of palladium/nickel (Pd/Ni) alloy thin-film coated surface acoustic wave (SAW) hydrogen (H2) sensor is demonstrated theoretically and experimentally to allow the optimization of the sensing device in this work. The resistor-capacitance circuit model is used to describe the interaction between Pd/Ni film and H2. Referring to the perturbation theory, the relationship between the changes in SAW velocity/phase and the multi-physical field quantities of the Pd/Ni film are analyzed. To verify the theoretical model, the Pd/Ni film is sputtered on the Y35°X quartz substrate to build the delay-line patterned SAW H2 sensor. Experimental results have well verified the theoretical predictions. That is, the main response mechanism is the mass loading effect, and the contribution of the acoustoelectric effect can be neglected. The expansion effect induced by hydrogen adsorption is completely different from the mass loading effect, which causes the sensing response failure, but it can be effectively improved by increasing the working temperature or decreasing the thickness of the Pd/Ni thin-film. Wide detection range (100 ppm ∼ 38 v/v %), rapid response (t
90 ∼ 7 s), and good humidity stability are achieved from the optimized SAW H2 sensor.