bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of water, CO2, ethane and their mixtures in ZSM-22 zeolite: the role of polarity and hydrogen bonding
Authors: Kummali Mohammed Musthafa , Cole David , Gautam Siddharth
Published: November 2024

Understanding the interplay between confinement effects and intermolecular interactions is essential for predicting molecular diffusion in zeolites. In this study, we investigate the diffusion behavior of ethane, CO2, and water in ZSM-22 molecular sieves, focusing on the effects of mixing these fluids. Our results reveal that while CO2 has minimal impact on ethane diffusion, water significantly slows ethane’s motion by forming molecular bridges across the pore structure, reducing ethane’s diffusion by up to 30%. Ethane, in turn, restricts water’s mobility, and reduces the water–water coordination number from 2.22 to 0.73 depending on concentration. The diffusion of CO2 in mixtures shows a 40% increase in pure state under confinement. The role of polarity and hydrogen bonding is crucial, with water molecules exhibiting 1.2 hydrogen bonds in the confined state—much lower than the 3.4 bonds in bulk water. Molecular rotation in ZSM-22 of all fluids occurs at two distinct time scales: the short-time fast rotation dominated by molecular inertia and the long-time rotation hindered by fluid-zeolite interactions. For water, hydrogen bonding further restricts full rotational freedom. These findings provide a comprehensive understanding of how ethane, water, and CO2 interact and diffuse in nanoporous materials.
Superposition of soliton, breather and lump waves in a non-painlevé integrabale extension of the Boiti-Leon-Manna-Pempinelli equation
Authors: Asadi Esmaeel , Hosseini Kamyar , Madadi Majid
Published: November 2024

In this paper, we derive general Nth-order Pfaffian solutions for a (3 + 1)-dimensional non-Painlevé integrable extension of the Boiti-Leon-Manna-Pempinelli (BLMP) equation. Specifcally, we obtain N-soliton, higher-order breather, higher-order lump and hybrid solutions, and explore the superpositions of Y-shaped and X-shaped soliton-breather waves. Moreover, we construct bilinear Bäcklund transformations, Lax pairs, and conservation laws using Bell polynomials. Finally, we identify a similar equation in the literature and demonstrate that it represents another non-Painlevé integrable extension of the BLMP equation.
Multiple surface lattice resonances in symmetric nanocuboid dimer arrays
Authors: Huang Xiaodan , Liu Mengxian
Published: November 2024

Surface lattice resonances based on nanoparticle arrays have significant characteristics such as localized field enhancement and high quality factor, and can be applied in fields such as optical sensors and lasers. In this work, we propose a symmetric Si/SiO2 nanocuboid dimer array that can generate and regulate two surface lattice resonances. One of the surface lattice resonances (named SLR1) is mainly due to the coupling between the electric dipole resonance of single Si/SiO2 nanocuboid dimers and the diffraction waves perpendicular to the applied electric field. Another surface lattice resonance (named SLR2) mainly originates from the coupling between the magnetic dipole resonance of single Si/SiO2 nanocuboid dimers and the diffraction waves parallel to the direction of the applied electric field. The research results indicate that the polarization direction of the incident field, the period of the array, the gap between the nanocuboids in the dimer, particle size, and the medium environment are all important for regulating the two surface lattice resonances. The sensing application of multiple surface lattice resonances is also investigated. The results show that under appropriate structural parameters, SLR1 can provide good stability for sensing applications, its sensitivity and figures of merit are 472 nm RIU−1 and 104, respectively. However, SLR2 is very weak or suppressed when the refractive index of the medium environment is greater than or equal to 1.2. This characteristic limits the application range of SLR2 in sensing. This work is of great significance for the design of micro-nano photonic devices based on multiple surface lattice resonances.
Electronic, optical, elastic, piezoelectric and vibrational properties of P63 KLiSO4
Authors: Lv Zhen-Long , Lv Shi-Jie , Cui Hong-Ling
Published: November 2024

KLiSO4 of the P63 symmetry is a well refined crystal at room temperature, which is a pyroelectric material with a large second harmonic generation response. However, its fundamental physical properties are still not well studied. In this work, first principles calculations are performed to study its electronic, optical, elastic, piezoelectric and vibrational properties. The results indicate that it is an ionic crystal with a large indirect band gap. Calculated optical properties imply that P63 KLiSO4 has little optical anisotropy at low frequencies. Obtained elastic constants reveal that it is mechanically stable but anisotropic, as illustrated by the directional bulk and shear moduli. Piezoelectric coefficients, dielectric constants, and Born effective charges (BECs) are computed using the density functional perturbation method. Studies disclose that it has a greater piezoelectric coefficient along the c axis. The ions have more contribution to the total dielectric constants than the electrons. The S atoms have the largest BECs. The phonon vibrational modes at the Brillouin zone center are analyzed by the factor group theory. Its infrared and Raman spectra are simulated. The causation for the vanishment of some infrared peaks in the computed infrared spectrum is uncovered. Additionally, elastic related moduli, hardness, melting point and electromechanical coupling coefficients of P63 KLiSO4 are also predicated.
Behavior of a defect in a flexible carbon nanotube
Authors: Zhang Bo , Xu Han , Liu Xiao-Jie , Yin Hai-Tao
Published: November 2024

Carbon nanotubes (CNTs) play an indispensable role in the design and application of flexible devices due to their unique physical and chemical properties. This study theoretically investigates the behavior of defects in bent CNTs. The results indicate that when the defect is under compressive strain, the conductance of the device decreases as the bending angle increases. Conversely, when the defect is under tensile strain, the conductance of the device increases with a larger bending angle.This phenomenon is primarily attributed to the enhancement of scattering states corresponding to the defect under tensile strain and the weakening of these states under compressive strain. Under bias voltage, similar patterns are observed for transmission peaks corresponding to the defect. These findings contribute to the device design process, enabling the exploitation of advantages and avoidance of disadvantages, ultimately leading to the development of flexible CNTs- devices.
Spectroscopic Study of Late-type Emission-line Stars Using the Data from LAMOST DR6
Authors: Edwin D. , Mathew Blesson , Shridharan B. , Valsan Vineeth , Nidhi S. , Bhattacharyya Suman , Kartha Sreeja S. , Robin T.
Published: November 2024

Low-mass emission-line stars belong to various evolutionary stages, from pre-main-sequence young stars to evolved stars. In this work, we present a catalog of late-type (F0 to M9) emission-line stars from the LAMOST Data Release 6. Using the scipy package, we created a Python code that finds the emission peak at Hα in all late-type stellar spectra. A data set of 38,152 late-type emission-line stars was obtained after a rigorous examination of the photometric quality flags and the signal-to-noise ratio of the spectra. Adopting well-known photometric and spectroscopic methods, we classified our sample into 438 infrared (IR) excess sources, 4669 post-main-sequence candidates, 9718 Fe/Ge/Ke sources, and 23,264 dMe sources. From a crossmatch with known databases, we found that 29,222 sources, comprising 65 IR excess sources, 7899 Fe/Ge/Ke stars, 17,533 dMe stars, and 3725 PtMS candidates, are new detections. We measured the equivalent width of the major emission lines observed in the spectra of our sample of emission-line stars. Furthermore, the trend observed in the line strengths of major emission lines over the entire late-type spectral range is analyzed. We further classified the sample into four groups based on the presence of hydrogen and calcium emission lines. This work presents a large data set of late-type emission-line stars, which can be used to study active phenomena in late-type stars.
Simultaneous reduction of tungsten and rotation in the core region induced by RMP
Authors: Sheng H. , Sun Y.W. , Zhou C.X. , Duan Y.M. , Zhang W.M. , Li Y.Y. , Zhang L. , Chen J.L. , Mao S.F. , Liu Y.Q. , Ma Q. , Shi T.H. , Ye C. , Xie P.C. , Wu X.M. , Jia M.N. , Chu N. , Wang H.H. , Zang Q. , Gu S. , Ye M.Y. ,   the EAST Team
Published: November 2024

Tungsten (W) impurity control is critical for plasma performance and a priority for ITER. The simultaneous reduction of W and rotation in the core region induced by resonant magnetic perturbations (RMPs) has been found and understood in EAST. A positive feedback loop between the W and rotation is first proposed, resulting in core W accumulation and high rotation even in low-torque plasma before the RMP application. This cycle can be reversed by the edge rotation braking induced by RMP, causing a significant simultaneous reduction of W concentration and rotation. These new mechanisms are based on several repeatable experiments and confirmed by the modeling results from TGYRO and NTVTOK. It provides a new understanding of the RMP effects on W and rotation and can be used for W and rotation control in future reactors.
4D printing of smart scaffolds for bone regeneration: a systematic review
Authors: Gharehdaghi Niusha , Nokhbatolfoghahaei Hanieh , Khojasteh Arash
Published: November 2024

As a novel emerging technology, four-dimensional (4D) printing allows the stimulation of 3D-printed materials in order to change shape, color, functionality, etc, over time. This systematic review is conducted to evaluate the purpose, materials, physiomechanical, and biological properties of 4D-printed scaffolds used for bone tissue engineering. An electronic search was conducted following the PRISMA 2020 guidelines in PubMed, Scopus, Web of Science, and Google Scholar online databases limited to English articles until April 2024. Studies in which scaffolds were fabricated through 3D printing methods responding to external stimulation were included. The quality of in vitro and in vivo studies was evaluated through the modified CONSORT checklist and SYRCLE’s risk of bias tool. The full text of 57 studies were reviewed, and 15 studies met the inclusion criteria. According to the analyzed studies, most scaffolds responded to temperature changes showing shape memory effect. Polyurethane and poly(lactic acid) were the most common shape memory polymers (SMPs), and the most common fabrication method used was fused deposition modeling. A comprehensive systematic review of the studies from the past 10 years demonstrated several findings: (1) Shape memory, drug delivery, and shape morphing are three general purposes of 4D printing for bone regeneration. (2) Smart materials used for 4D printing mostly consist of SMPs. (3) Temperature changes account for the majority of stimulation used for 4D printing. (4) incorporating 4D printing principles does not negatively impact on the physiomechanical properties of the designed scaffold. (5) The 4D-printed scaffolds show a higher osteogenic differentiation capacity than their identical 3D-printed structures in terms of bone regeneration.
Disentangling regional climate change: assessing the contribution of global- and regional-scale anthropogenic factors to observed regional warming
Authors: Barkhordarian Armineh
Published: November 2024

While the influence of uniformly-distributed well-mixed greenhouse gas emissions on global warming is well-documented and robustly attributed through multiple lines of evidence, regional attribution remains more challenging and dependent on the performance and resolution of climate models. This study investigates the extent to which observed regional temperature trends are attributable to global-scale anthropogenic factors, mainly the direct effects of CO2, aiming to differentiate the portion of the change attributable to regional-scale drivers and local feedback mechanisms. To quantify the contribution of global- and regional-scale climate drivers to observed temperature change, I conducted regression analyses using the observed temperature change in HadCRUT4 and the global warming index derived from global radiative forcing series. Results indicate that in certain regions—specifically West Asia, East N. America, West Africa, and the Amazon—

62

±

7%, 61

±

13%, 58

±

7%, and 61

±

10% of the warming observed over 1991–2020 can be attributed to global anthropogenic warming, primarily the direct effects of CO2. The remaining portion, which represents 22

±

8%, 21

±

16%, 27

±

9%, 23

±

14% of the observed warming, is attributable to regional drivers. The Mediterranean showcases high sensitivity, with regional drivers contributing 31

±

13% of the observed 1.2

∘

C warming, amplifying the warming attributed to global anthropogenic drivers, estimated at 55 ± 10%. The Arctic Ocean along with the Russian-Arctic region exhibits a substantial contribution from regional drivers and local feedback mechanisms (the indirect effects of CO2) to the observed warming amplification, quantified at 43 ± 15% of the 3 ∘C warming over 1991–2020. Regional cooling drivers, however, are significant in East Asia and the Tibetan Plateau, with the latter experiencing a cooling contribution of

−
42

±

17%. By breaking down the contributions of climate drivers into global and regional-scale components, we gain valuable insights into the local climate mechanisms responsible for the observed regional warming, which is a crucial factor that affects agriculture, ecosystems and societies.
Non-financial reporting as an essential tool ensuring sustainable development and food security
Authors: Plaskova N S , Bogataya I N , Evstafyeva E M , Lavrov D A
Published: November 2024

The successful solution of food security problems largely depends on the joint efforts of participants in economic relations at the level of states, regions, and business entities. The results of food security policy management and the parameters of its further development should be reflected in non-financial reporting, which enterprises currently form on the basis of regulations of a recommendatory nature of various professional and public organizations. The generalization of the Russian and foreign practice of compiling non-financial reporting allowed us to substantiate the directions for improving the information support of enterprises in the field of environmental protection and the social sphere. The lack of uniform international standards for non-financial reporting is one of the main problems preventing the creation of comparable assessment information on the contribution of enterprises and States to solving environmental and social problems. A review of the survey results of various respondents regarding the importance of non-financial reporting and the convenience of its use by investors, regulatory agencies and other stakeholders showed the need to intensify work on the unification of ESG factor disclosure formats. The directions of development of the regulatory framework for non-financial reporting within the framework of the currently being developed industry-specific international standards for corporate non-financial reporting are proposed.
Measures of state regulation and support of the soybean breeding and seed production industry
Authors: Degtyareva E D , Belyshkina M E , Chutcheva Yu V , Kobozeva T P , Yu Romanovskaya A
Published: November 2024

One of the priority directions of economy in different countries of the world is the application of measures of state support and regulation of the agricultural industry, including laws and various programs that foster sustainable development of agriculture. In view of prevailing social and economic conditions in Russia, the problem of domestic supply of agricultural production with in-country selected high-yielding varieties of soybean and intensification of domestic seed production has become acute. Currently, the State is providing support to the seed industry and is intended to ensure import substitution in the seed market in the foreseeable future. However, there are also revealed some problems, which are mostly related to the functioning of state breeding and seed production centers, which include state breeding plots, breeding and seed production farms at research institutions and agrarian universities. To solve these problems, state research organizations and universities should become full-fledged participants of the seed market on a par with business. Achieving the assigned tasks should be facilitated by measures, supporting science and innovation at the state level.
Features of protection and use of biological features of protection and use of biological resources in the territory of the lower Amudarya reserve of the republic of Karakalpakstan
Authors: Kamalova K S , Kamalova R S , Kudaibergenova U K , Muhammadiyarova A
Published: November 2024

The Republic of Karakalpakstan is the focus of this article’s conservation and environmental management issues. The authors emphasize the unique characteristics of environmental management in this region in relation to the drying out of the Aral Sea and the low water level of the Amudarya River bed. Despite these environmental disasters, our country preserves the biodiversity of flora and fauna in the Badai-Tugai Nature Reserve.
Aral Environmental Disaster and Its Mitigation Through Forest Plantations
Authors: Novitskiy Z B , Hamzayev A H , Bakirov N Zh , Atadjanova G H
Published: November 2024

The drained bottom of the Aral Sea poses a serious threat to all living things in the Aral Sea region because it covers an area of about 6 million hectares. Nearly150 million tons of salt, dust, and sand are released into the air from it annually, which causes significant damage to agriculture and the national economy. It is possible to mitigate the ecological catastrophe by creating forest plantations on the drained bottom from desert plants. Depending on the types of bottom sediments, different technologies for creating forest plantations were tested, which made it possible to obtain highly effective plantations and minimize the negative impact of the dried bottom of the Aral Sea. Globally, the ecological problem of the Aral Sea is regarded as one of the critical issues that require immediate attention, the consequences of which are still being felt on a continental scale.
Mannose receptor (MRC1) mediates uptake of dextran by bone marrow–derived macrophages
Authors: Wollman Jared , Wanniarachchi Kevin , Pradhan Bijaya , Huang Lu , Kerkvliet Jason G , Hoppe Adam D , Thiex Natalie W
Published: November 2024

Macrophages survey their environment using receptor-mediated endocytosis and pinocytosis. Receptor-mediated endocytosis allows internalization of specific ligands, whereas pinocytosis nonselectively internalizes extracellular fluids and solutes. CRISPR/Cas9 whole-genome screens were used to identify genes regulating constitutive and growth factor–stimulated dextran uptake in murine bone marrow–derived macrophages (BMDM). The mannose receptor c-type 1 (MRC1/CD206) was a top hit in the screen. Targeted gene disruptions of Mrc1 reduced dextran uptake but had little effect on fluid-phase uptake of Lucifer yellow. Other screen hits also differentially affected the uptake of dextran and Lucifer yellow, indicating internalization by separate mechanisms. Visualization of dextran and Lucifer yellow uptake by microscopy showed enrichment of dextran in small puncta, which was inhibitable by mannan, a ligand of MRC1. In contrast, Lucifer yellow predominantly was internalized in larger macropinosomes . In addition, IL4-treated BMDMs internalized more dextran than untreated BMDM correlating with increased MRC1 expression. Therefore, dextran is not an effective marker for pinocytosis in BMDMs since it is internalized by receptor-mediated process. Numerous genes that regulate dextran internalization in primary murine macrophages were identified in the whole-genome screens, which can inform understanding of the regulation of MRC1 expression and MRC1-mediated uptake in macrophages.
DNA damage–induced EMT controlled by the PARP-dependent chromatin remodeler ALC1 promotes DNA repair efficiency through RAD51 in tumor cells
Authors: Rajabi Fatemeh , Smith Rebecca , Liu-Bordes Win-Yan , Schertzer Michael , Huet Sebastien , Londoño-Vallejo Arturo
Published: November 2024

Epithelial-to-mesenchymal transition (EMT) allows cancer cells to metastasize while acquiring resistance to apoptosis and chemotherapeutic agents with significant implications for patients’ prognosis and survival. Despite its clinical relevance, the mechanisms initiating EMT during cancer progression remain poorly understood. We demonstrate that DNA damage triggers EMT and that activation of poly (ADP-ribose) polymerase (PARP) and the PARP-dependent chromatin remodeler ALC1 (CHD1L) was required for this response. Our results suggest that this activation directly facilitates access to the chromatin of EMT transcriptional factors (TFs) which then initiate cell reprogramming. We also show that EMT-TFs bind to the RAD51 promoter to stimulate its expression and to promote DNA repair by homologous recombination. Importantly, a clinically relevant PARP inhibitor reversed or prevented EMT in response to DNA damage while resensitizing tumor cells to other genotoxic agents. Overall, our observations shed light on the intricate relationship between EMT, DNA damage response, and PARP inhibitors, providing potential insights for in cancer therapeutics.
Lawyers
Authors: He Xin
Published: November 2024

Chapter 4 delves into the roles of lawyers in Chinese courts, challenging prevailing perspectives on their treatment. Instead of criticizing the state, the chapter explores why lawyers remain marginalized. It starts by examining the presence of “unlicensed” legal workers and their interactions with judges and competitors. The discussion then shifts to licensed lawyers, exploring their contributions in civil and criminal trials and the fate of weiquan lawyers. Ultimately, the chapter poses a provocative question: Are Chinese lawyers a profession lacking professionalism? Overall, Chapter 4 offers a vivid analysis of the challenges and complexities faced by lawyers in China’s judicial system.
Litigants’ Views of the Courts
Authors: He Xin
Published: November 2024

Chapter 5 unravels the constant tension between the party-state’s reliance on the law and the public’s mistrust of the courts in China. It delves into the concept of guanxi as the prevailing belief in legal consciousness among citizens and explores the use of petitioning by dissatisfied litigants. The chapter examines the limited impact of procedural justice on Chinese litigants and their acceptance of unfavorable outcomes. It also documents measures that the courts have sought to use to improve the negative public perceptions of their work. Ultimately, it highlights the dilemma faced by Chinese courts in gaining public confidence while serving as a mechanism for governance.
Administrative Justice
Authors: He Xin
Published: November 2024

Chapter 9 highlights the significant changes in administrative litigation following the 2014 amendment to the Administrative Litigation Law (ALL). Although the traditional three difficulties—“to file the lawsuit, to adjudicate cases, and to enforce judgments”—have improved, the courts’ political status remains relatively weak. Administrative litigation is a minor instrument in governance, and its development is influenced by its interaction with administrative reconsideration and the continued popularity of administrative mediation. The chapter also explores the development of administrative mediation and the outcomes of administrative litigation. It argues that understanding the relationship between courts and other state agents is crucial to comprehending the trajectory of administrative litigation and its role in governance.
The Impact of Cognitive Behavioral Therapy for Insomnia on Neurofilament Light and Phosphorylated Tau in Individuals with a Concussion
Authors: Ludwig Rebecca , Rippee Michael , D’Silva Linda , Radel Jeff , Eakman Aaron M , Morris Jill , Beltramo Alvin , Drerup Michelle , Siengsukon Catherine
Published: November 2024

Background

Concussions damage neurologic tissue, increasing release of intercellular proteins including phosphorylated Tau (pTau) and neurofilament light (NfL). Disrupted sleep from a concussion negatively impacts the ability of the glymphatic system to remove cellular waste from the brain.

Objective

The purpose of this study was to determine if enhancing sleep using Cognitive Behavioral Therapy for Insomnia (CBT-I) impacts pTau and NFL levels following a concussion.

Methods

This is pre/post intervention analysis of a larger wait-list control study. Participants had their blood sampled pre/post the CBT-I intervention which was analyzed using SIMOA analytics. Paired sampling statistics and linear regression models were used to examine how insomnia severity impacts pTau181 and NfL.

Results

Twenty-eight participants were enrolled in this study. Age and baseline protein level were significantly associated with post-intervention protein levels, but post-intervention insomnia severity was not associated with post-intervention protein levels. About 50% of participants that had clinically meaningful change in insomnia and had a reduction in their NfL and pTau181 values.

Conclusions

Post-intervention insomnia was not associated with post-intervention NfL or pTau. Yet, on an individual level, ~50% of participants had a clinically meaningful change in insomnia and reduced level of NfL and pTau 18.1.

Clinical Trial Registration

NCT04885205 https://clinicaltrials.gov
Eugenol and basil essential oil as priming agents for enhancing Arabidopsis immune response
Authors: Hirose Shogo , Horiyama Soyoka , Morikami Atsushi , Fujiwara Kazuki , Tsukagoshi Hironaka
Published: November 2024

Plants, as sessile organisms, must adapt to environmental changes and defend themselves against biotic stress, including pathogen attack. Their immune responses entail recognition of pathogen patterns, activation of defense mechanisms, and accumulation of various antimicrobial compounds. Eugenol, abundant in basil, has antibacterial properties and enhances plant resistance to viruses. However, its priming effects on biotrophic pathogens remain unclear. Thus, we investigated whether eugenol and basil essential oils could prime Arabidopsis thaliana immunity against the hemi-biotroph Pseudomonas syringae pv. maculicola (Psm) MAFF302723. Our study revealed that both eugenol and basil essential oils functioned as priming agents, mitigating disease symptoms upon Psm infection. This priming effect occurred via NPR1-dependent but salicylic acid-independent signaling. Moreover, our gene expression analysis suggested that priming might influence jasmonic acid/ethylene signaling. These findings underscore the potential of employing natural compounds such as basil essential oil to bolster plant immune responses in sustainable agricultural practices.
Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses
Authors: Campelo Felipe , de Oliveira Ana Laura Grossi , Reis-Cunha João , Fraga Vanessa Gomes , Bastos Pedro Henrique , Ashford Jodie , Ekárt Anikó , Adelino Talita Emile Ribeiro , Silva Marcos Vinicius Ferreira , de Melo Iani Felipe Campos , de Jesus Augusto César Parreiras , Bartholomeu Daniella Castanheira , de Souza Trindade Giliane , Fujiwara Ricardo Toshio , Bueno Lilian Lacerda , Lobo Francisco Pereira
Published: November 2024

We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.
IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction
Authors: Kushwaha Anjana , Duroux Patrice , Giudicelli Véronique , Todorov Konstantin , Kossida Sofia
Published: November 2024

The accurate prediction of peptide-major histocompatibility complex (MHC) class I binding probabilities is a critical endeavor in immunoinformatics, with broad implications for vaccine development and immunotherapies. While recent deep neural network based approaches have showcased promise in peptide-MHC (pMHC) prediction, they have two shortcomings: (i) they rely on hand-crafted pseudo-sequence extraction, (ii) they do not generalize well to different datasets, which limits the practicality of these approaches. While existing methods rely on a 34 amino acid pseudo-sequence, our findings uncover the involvement of 147 positions in direct interactions between MHC and peptide. We further show that neural architectures can learn the intricacies of pMHC binding using even full sequences. To this end, we present PerceiverpMHC that is able to learn accurate representations on full-sequences by leveraging efficient transformer based architectures. Additionally, we propose IMGT/RobustpMHC that harnesses the potential of unlabeled data in improving the robustness of pMHC binding predictions through a self-supervised learning strategy. We extensively evaluate RobustpMHC on eight different datasets and showcase an overall improvement of over 6% in binding prediction accuracy compared to state-of-the-art approaches. We compile CrystalIMGT, a crystallography-verified dataset presenting a challenge to existing approaches due to significantly different pMHC distributions. Finally, to mitigate this distribution gap, we further develop a transfer learning pipeline.
STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data
Authors: Ran Peng , Wang Yunzhi , Li Kai , He Shiman , Tan Subei , Lv Jiacheng , Zhu Jiajun , Tang Shaoshuai , Feng Jinwen , Qin Zhaoyu , Li Yan , Huang Lin , Yin Yanan , Zhu Lingli , Yang Wenjun , Ding Chen
Published: November 2024

Mass spectrometry (MS)-based proteomics has become instrumental in comprehensively investigating complex biological systems. Data-independent acquisition (DIA)-MS, utilizing hybrid spectral library search strategies, allows for the simultaneous quantification of thousands of proteins, showing promise in enhancing protein identification and quantification precision. However, low-quality profiles can considerably undermine quantitative precision, resulting in inaccurate protein quantification. To tackle this challenge, we introduced STAVER, a novel algorithm that leverages standardized benchmark datasets to reduce non-biological variation in large-scale DIA-MS analyses. By eliminating unwanted noise in MS signals, STAVER significantly improved protein quantification precision, especially in hybrid spectral library searches. Moreover, we validated STAVER’s robustness and applicability across multiple large-scale DIA datasets, demonstrating significantly enhanced precision and reproducibility of protein quantification. STAVER offers an innovative and effective approach for enhancing the quality of large-scale DIA proteomic data, facilitating cross-platform and cross-laboratory comparative analyses. This advancement significantly enhances the consistency and reliability of findings in clinical research. The complete package is available at https://github.com/Ran485/STAVER.
Zygotic activin A is dispensable for the mouse preimplantation embryo development and for the derivation and pluripotency of embryonic stem cells
Authors: Winek Eliza , Wolińska-Nizioł Lidia , Szczepańska Katarzyna , Szpakowska Anna , Gewartowska Olga , Wysocka Izabela , Grzesiak Magdalena , Suwińska Aneta
Published: November 2024

In this work, we aimed to determine the role of activin A during crucial events of mouse embryogenesis and distinguish the function of the protein of zygotic origin and the one secreted by the maternal reproductive tract. To this end, we recorded the progression of development and phenotype of Inhba knockout embryos and compared them with the heterozygotes and wild-type embryos using time-lapse imaging and detection of lineage-specific markers. We revealed that the zygotic activin A deficiency does not impair the course and rate of development of embryos to the blastocyst stage. Inhba knockout embryos form functional epiblast, as evidenced by their ability to give rise to embryonic stem cells. Our study is the first to show that derivation, maintenance in culture, and pluripotency of embryo-derived embryonic stem cells are exogenous and endogenous activin A independent. However, the implantation competence of activin A–deficient embryos may be compromised as indicated in the outgrowth assay.
Outcomes of elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms in Sweden
Authors: Yu Harry H Y , Asciutto Giuseppe , Dias Nuno , Wanhainen Anders , Karelis Angelos , Sonesson Björn , Mani Kevin
Published: November 2024

Background

A juxtarenal abdominal aortic aneurysm is defined as a short (less than 4 mm) or no-neck aneurysm, which is often treated with open or complex endovascular repair. The evidence to support the best treatment strategy is scarce. The aim of this study was to assess the short- and mid-term outcomes of elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms in Sweden.

Methods

Patients who underwent elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms between 2018 and 2021 were identified in the Swedish Vascular Registry. Demographics, practice patterns, and operative details were assessed. The primary outcome was 30-day mortality. Secondary outcomes included perioperative complications and mid-term survival.

Results

Among 3777 aortic aneurysm repairs performed, 418 involved juxtarenal abdominal aortic aneurysms (open surgical repair 228 (54.5%), fenestrated endovascular aneurysm repair 176 (42.1%), chimney endovascular aneurysm repair 6 (1.4%), and branched endovascular aneurysm repair 8 (1.9%)). Some 25 centres performed juxtarenal abdominal aortic aneurysm repairs with open surgical repair and fenestrated endovascular aneurysm repair. The caseload varied from 2 to 54 repairs per centre. The mean aneurysm diameter was 61 mm. Endovascularly treated patients were older and had more pulmonary co-morbidities. The 30-day mortality rate was 2.2% (open surgical repair 2.6% and fenestrated endovascular aneurysm repair 1.7%; P = 0.397). Perioperative major complications occurred in 14.1% of patients (open surgical repair 19.3% and fenestrated endovascular aneurysm repair 7.4%; P < 0.001) and perioperative vascular complications occurred in 12.1% of patients (open surgical repair 8.8% and fenestrated endovascular aneurysm repair 11.9%; P = 0.190). The survival rate (estimated using Kaplan–Meier analysis) at 1 year and 3 years was 93.1% and 85.9% respectively for open surgical repair and 95.2% and 80.9% respectively for fenestrated endovascular aneurysm repair (P = 0.477).

Conclusion

This nationwide study reveals considerable variations in volume and treatment strategy between Swedish centres performing juxtarenal abdominal aortic aneurysm repairs. Survival is comparable for open surgical repair and fenestrated endovascular aneurysm repair, although there are significant baseline demographic differences between patients selected for the two treatment modalities.
Focal brain administration of antiseizure medications improves outcomes and reduces side effects
Authors: Vezzani Annamaria
Published: November 2024

This scientific commentary refers to ‘Intracerebral delivery of antiseizure medications by microinvasive neural implants’ by Jackson et al. (https://doi.org/10.1093/brain/awae282).
Tau, synapse loss and gliosis progress in an Alzheimer’s mouse model after amyloid-β immunotherapy
Authors: Welikovitch Lindsay A , Mate de Gerando Anastasie , Khasnavis Anita , Bhavsar Harshil , Meltzer Jonah C , Buée Luc , Chibnik Lori B , Bussiere Thierry , Hyman Bradley T
Published: November 2024

Preclinical studies assessing drugs for Alzheimer’s disease (AD) are conducted in animal models that usually display only one neuropathological feature of AD, whereas patients present with a complex combination of comorbidities and neuropathologies. Importantly, it is well established that amyloid-β (Aβ) plaque and tau tangle accumulation interact in a phase-dependent manner, making it difficult to predict how targeting one might influence the other, as well as downstream degeneration.

We developed a transgenic mouse model, APP/PS1xTau22, with progressive cortical Aβ deposition and hippocampal tau neurofibrillary inclusions, to investigate how both neuropathologies act jointly to bring about neural degeneration, synapse loss and glial phenotypes. We then assessed whether applying murine chimeric aducanumab, an anti-amyloid immunotherapy, could impact the synergistic relationship between amyloid and tau.

Drug treatment resulted in a ∼70% reduction in Aβ deposition in hippocampal and cortical areas and produced a robust peri-plaque microglial and astrocytic response. Removing amyloid from the brain did not reverse or slow tau pathology or alter synapse loss.

Our findings suggest that, once the interaction between amyloid and tau is set in motion, reducing plaque burden by Aβ immunotherapy may stimulate glial responses, but is insufficient to curb degenerative phenotypes in this model.
Luminescent anthracene-based elastic mixed molecular crystals for flexible and FRET-assisted optical waveguides
Authors: Ikeda Koki , Matsuo Takumi , Yano Keigo , Hayashi Shotaro
Published: November 2024

Optical waveguides based on elastic molecular crystals are of interest as flexible and compact optical communication materials. Low emission efficiency is often a problem in terms of communication signal strength, and an increase in the loss factor α due to fluorescence reabsorption in the crystal reduces the photon transport efficiency. Here, we report the development and improvement of Förster resonance energy transfer (FRET)-assisted optical waveguides using anthracene-based elastic mixed molecular crystals. 9,10-Dicyanoanthracene was selected as the dopant for solution-grown crystallization of 9,10-dibromoanthracene. 1H NMR measurements of the obtained crystals showed that the acceptor doping to be 1% to 5%. Elastic behavior was observed even when doped with a few percent of the acceptor. The quantum efficiency was 0.016, a dramatic improvement over the previous luminescent elastic mixed molecular crystals (0.004). The α value (92 dB/cm) of this crystal containing 1%-doped 9,10-dicyanoanthracene is much lower than that of the crystal consisting of only 9,10-dibromoanthracene (1258 dB/cm) due to the reduced reabsorption in the FRET system. We have demonstrated a practical approach toward developing improved fluorescent, highly efficient, and flexible optical waveguides by constructing the mixed crystal structure by selecting appropriate acceptor molecules and their low doping ratios.
Preliminary assessment of the accuracy of cutaneous T-cell lymphoma diagnosis through deep sequencing of the TRG gene
Authors: Hong Jin-Bon , Hsieh Tyng-Shiuan , Tsai Tsen-Fang , Liau Jau-Yu , Chiu Hsien-Ching , Lee Tung-Lung , Huang Tai-Chung
Published: November 2024

Background

The diagnostic challenges in early mycosis fungoides (MF) and other cutaneous T-cell lymphomas (CTCLs) persist despite advancements in molecular methods.

Objectives

To provide a preliminary assessment of next-generation sequencing (NGS) in analysing TRG (T-cell receptor gamma locus) sequences for distinguishing CTCLs from benign inflammatory skin disorders.

Methods

NGS was used to assess TRG sequences in skin samples from clinicopathologically proven CTCLs and benign inflammatory skin disorders.

Results

Our study analysed skin samples from a total of 36 participants, comprising 22 cases of CTCL, including 14 MF and 8 other CTCLs, alongside 14 cases of benign inflammatory skin disorders. According to LymphoTrack® criteria, monoclonality was detected in 16 (73%) of the 22 patients with CTCL. Specifically, in cases of MF, 10 of 14 (71%) were identified as monoclonal, with all 4 non-monoclonal cases being in the patch stage. For the other cases of CTCL, six of eight displayed monoclonality. Among the 22 patients with CTCL, 10 (45%) had multiple biopsies, with 8 (36%) displaying the same dominant clone across different sites. Among the 14 benign cases, only the case of erythrodermic psoriasis exhibited monoclonality. Our decision tree analysis suggests that a high frequency of the most abundant clone, its ratio to the third most abundant clone and TRG VγI segment usage are effective markers that can help in the diagnosis of CTCL.

Conclusions

A combination of the clone frequencies and TRG V segment usage may enhance diagnosis of MF and other CTCLs, helping to differentiate them from benign conditions. However, molecular diagnosis for patch-stage MF remains challenging.
Clinical mechanism of muscle mass loss during neoadjuvant chemotherapy in older patients with esophageal cancer: a prospective cohort study
Authors: Harada Tsuyoshi , Tsuji Tetsuya , Ueno Junya , Konishi Nobuko , Yanagisawa Takumi , HIjikata Nanako , Ishikawa Aiko , Hashimoto Kakeru , Kagaya Hitoshi , Tatematsu Noriatsu , Zenda Sadamoto , Kotani Daisuke , Kojima Takashi , Fujita Takeo
Published: November 2024

In older patients with locally advanced esophageal cancer (LAEC), loss of skeletal muscle mass during neoadjuvant chemotherapy (NAC) is associated with poor clinical outcomes. This study aimed to investigate factors associated with loss of skeletal muscle mass during NAC in older patients with LAEC. This was a single-center exploratory prospective cohort study. Consecutive patients aged ≥65 years with LAEC scheduled for curative esophagectomy after NAC were enrolled between October 2021 and December 2023. As a primary endpoint, loss of skeletal muscle mass index (ΔSMI: pre-NAC minus post-NAC value) was calculated from computed tomography images before and after NAC. Significant pre-NAC and during-NAC factors with ΔSMI were detected with a multivariate regression model. Statistical significance was considered as two-tailed P <0.05. A total of 69 patients were analyzed. The mean age was 72.9 years, and 53 (77%) were male. Mean SMI before and after NAC was 43.1 and 40.9 cm2/m2, and mean ΔSMI was 2.2 cm2/m2. In multivariate analysis, ΔSMI was associated with increased sitting time during NAC (per 1 min/day, adjusted coefficient 0.007, 95% confidence interval [CI] 0.001 to 0.013, P = 0.016), decreased Geriatric Nutritional Risk Index during NAC (per 1 score, adjusted coefficient −0.146, 95% CI −0.213 to −0.013, P = 0.002), and worsening decreased appetite during NAC (vs. no worsening, adjusted coefficient 1.571, 95% CI 0.279 to 2.862, P = 0.018). It was hypothesized that the inactivity-related mechanism and malnutrition-related mechanism are important for skeletal muscle mass loss during NAC in older patients with LAEC.
Employer Screening and Optimal Unemployment Insurance
Authors: Meier Mario , Obermeier Tim
Published: November 2024

Field experiments show that employers are less likely to consider long-term unemployed job seekers for interviews. We study the implications for optimal unemployment insurance. Based on a structural model of job search and recruitment, estimated with German data, we analyse the optimal two-tier unemployment system. We find that screening makes the optimal initial benefit level 4 percentage points higher and the potential benefit duration seven months longer. Using an extended Baily–Chetty formula, we study the mechanisms through which screening affects the consumption smoothing gain and moral hazard cost of providing unemployment insurance and highlight the role of the externality from endogenous firm behaviour.
Can survey design reduce anchoring bias in recall data? Evidence from smallholder farmers in Malawi
Authors: Godlonton Susan , Hernandez Manuel A , Paz Cynthia
Published: November 2024

Recall biases in retrospective self-reported survey data have important implications for empirical research. We leverage the survey design literature and test three strategies to attenuate mental anchoring in retrospective data collection: question ordering, retrieval cues and aggregate (community) anchoring. We focus on maize production and happiness reports among smallholder farmers in Malawi. Asking for retrospective before concurrent data on average reduces recall bias (i.e. the deviation of the recalled versus the concurrent outcome reported in the previous period) by 34 per cent for maize production, a meaningful improvement with no increase in data collection costs. Retrieval cues are less successful and community anchors can exacerbate the bias. None of the strategies help to ease the recall bias for happiness reports.
Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China
Authors: Hu Xueqian , Bi Jie , Yu Qiaoling , Li Huan
Published: November 2024

Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.