bluuebunny/crossref_metadata_2025 huggingface dataset:
Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe
Authors: Banerjee Samiran , Zhao Cheng , Garland Gina , Edlinger Anna , García-Palacios Pablo , Romdhane Sana , Degrune Florine , Pescador David S. , Herzog Chantal , Camuy-Velez Lennel A. , Bascompte Jordi , Hallin Sara , Philippot Laurent , Maestre Fernando T. , Rillig Matthias C. , van der Heijden Marcel G. A.
Published: January 2024

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
Production-induced seismicity indicates a low risk of strong earthquakes in the Groningen gas field
Authors: Boitz Nepomuk , Langenbruch Cornelius , Shapiro Serge A.
Published: January 2024

The maximum possible earthquake related to gas production in Western Europe’s largest gas field, Groningen, Netherlands, is an urgent practical question. Here we show how to distinguish between induced and triggered tectonic earthquakes. We estimate the maximum possible induced magnitude in the Groningen gas field to be around Mw = 4. We extend the concept of the seismogenic index to gas-production, and calculate the worst-case probability of triggering a larger-magnitude tectonic earthquake in a continuum. The probability of a Mw5.5 earthquake at Groningen is significantly higher than at Pohang Geothermal System (South Korea), where a Mw5.5 earthquake was actually triggered. Due to a long history of production in Groningen, our model estimates that strong earthquakes (Mw ≥ 4) must have occurred there several times, in disagreement with the observations. This indicates that the Groningen gas field is inherently stable and the physical conditions to trigger large tectonic earthquakes likely do not exist.
Theory predicts 2D chiral polaritons based on achiral Fabry–Pérot cavities using apparent circular dichroism
Authors: Salij Andrew H. , Goldsmith Randall H. , Tempelaar Roel
Published: January 2024

Realizing polariton states with high levels of chirality offers exciting prospects for quantum information, sensing, and lasing applications. Such chirality must emanate from either the involved optical resonators or the quantum emitters. Here, we theoretically demonstrate a rare opportunity for realizing polaritons with so-called 2D chirality by strong coupling of the optical modes of (high finesse) achiral Fabry–Pérot cavities with samples exhibiting “apparent circular dichroism” (ACD). ACD is a phenomenon resulting from an interference between linear birefringence and dichroic interactions. By introducing a quantum electrodynamical theory of ACD, we identify the design rules based on which 2D chiral polaritons can be produced, and their chirality can be optimized.
Active machine learning model for the dynamic simulation and growth mechanisms of carbon on metal surface
Authors: Zhang Di , Yi Peiyun , Lai Xinmin , Peng Linfa , Li Hao
Published: January 2024

Substrate-catalyzed growth offers a highly promising approach for the controlled synthesis of carbon nanostructures. However, the growth mechanisms on dynamic catalytic surfaces and the development of more general design strategies remain ongoing challenges. Here we show how an active machine-learning model effectively reveals the microscopic processes involved in substrate-catalyzed growth. Utilizing a synergistic approach of molecular dynamics and time-stamped force-biased Monte Carlo methods, augmented by the Gaussian Approximation Potential, we perform fully dynamic simulations of graphene growth on Cu(111). Our findings accurately replicate essential subprocesses–from the preferred diffusion of carbon monomer/dimer, chain or ring formations to edge-passivated Cu-aided graphene growth and bond breaks by ion impacts. Extending our simulations to carbon deposition on metal surfaces like Cu(111), Cr(110), Ti(001), and oxygen-contaminated Cu(111), our results align closely with experimental observations, providing a practical and efficient approach for designing metallic or alloy substrates to achieve desired carbon nanostructures and explore further reaction possibilities.
Controllable strain-driven topological phase transition and dominant surface-state transport in HfTe5
Authors: Liu Jinyu , Zhou Yinong , Yepez Rodriguez Sebastian , Delmont Matthew A. , Welser Robert A. , Ho Triet , Sirica Nicholas , McClure Kaleb , Vilmercati Paolo , Ziller Joseph W. , Mannella Norman , Sanchez-Yamagishi Javier D. , Pettes Michael T. , Wu Ruqian , Jauregui Luis A.
Published: January 2024

The fine-tuning of topologically protected states in quantum materials holds great promise for novel electronic devices. However, there are limited methods that allow for the controlled and efficient modulation of the crystal lattice while simultaneously monitoring the changes in the electronic structure within a single sample. Here, we apply significant and controllable strain to high-quality HfTe5 samples and perform electrical transport measurements to reveal the topological phase transition from a weak topological insulator phase to a strong topological insulator phase. After applying high strain to HfTe5 and converting it into a strong topological insulator, we found that the resistivity of the sample increased by 190,500% and that the electronic transport was dominated by the topological surface states at cryogenic temperatures. Our results demonstrate the suitability of HfTe5 as a material for engineering topological properties, with the potential to generalize this approach to study topological phase transitions in van der Waals materials and heterostructures.
MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer
Authors: Wang Xiaoying , Duan Maoteng , Li Jingxian , Ma Anjun , Xin Gang , Xu Dong , Li Zihai , Liu Bingqiang , Ma Qin
Published: January 2024

Rare cell populations are key in neoplastic progression and therapeutic response, offering potential intervention targets. However, their computational identification and analysis often lag behind major cell types. To fill this gap, we introduce MarsGT: Multi-omics Analysis for Rare population inference using a Single-cell Graph Transformer. It identifies rare cell populations using a probability-based heterogeneous graph transformer on single-cell multi-omics data. MarsGT outperforms existing tools in identifying rare cells across 550 simulated and four real human datasets. In mouse retina data, it reveals unique subpopulations of rare bipolar cells and a Müller glia cell subpopulation. In human lymph node data, MarsGT detects an intermediate B cell population potentially acting as lymphoma precursors. In human melanoma data, it identifies a rare MAIT-like population impacted by a high IFN-I response and reveals the mechanism of immunotherapy. Hence, MarsGT offers biological insights and suggests potential strategies for early detection and therapeutic intervention of disease.
Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake
Authors: Zinke Maximilian , Lejeune Maylis , Mechaly Ariel , Bardiaux Benjamin , Boneca Ivo Gomperts , Delepelaire Philippe , Izadi-Pruneyre Nadia
Published: January 2024

Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel’s open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
Diffusion-based generative AI for exploring transition states from 2D molecular graphs
Authors: Kim Seonghwan , Woo Jeheon , Kim Woo Youn
Published: January 2024

The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modeling their kinetics. Recently, machine learning (ML) models have shown remarkable performance for prediction of TS geometries. However, they require 3D conformations of reactants and products often with their appropriate orientations as input, which demands substantial efforts and computational cost. Here, we propose a generative approach based on the stochastic diffusion method, namely TSDiff, for prediction of TS geometries just from 2D molecular graphs. TSDiff outperforms the existing ML models with 3D geometries in terms of both accuracy and efficiency. Moreover, it enables to sample various TS conformations, because it learns the distribution of TS geometries for diverse reactions in training. Thus, TSDiff finds more favorable reaction pathways with lower barrier heights than those in the reference database. These results demonstrate that TSDiff shows promising potential for an efficient and reliable TS exploration.
Biomimetic Bouligand chiral fibers array enables strong and superelastic ceramic aerogels
Authors: Wang Hongxing , Cheng Longdi , Yu Jianyong , Si Yang , Ding Bin
Published: January 2024

Ceramic aerogels are often used when thermal insulation materials are desired; however, they are still plagued by poor mechanical stability under thermal shock. Here, inspired by the dactyl clubs of mantis shrimp found in nature, which form by directed assembly into hierarchical, chiral and Bouligand (twisted plywood) structure exhibiting superior mechanical properties, we present a compositional and structural engineering strategy to develop strong, superelastic and fatigue resistance ceramic aerogels with chiral fibers array resembling Bouligand architecture. Benefiting from the stress dissipation, crack torsion and mechanical reinforcement of micro-/nano-scale Bouligand array, the tensile strength of these aerogels (170.38 MPa) is between one and two orders of magnitude greater than that of state-of-the-art nanofibrous aerogels. In addition, the developed aerogels feature low density and thermal conductivity, good compressive properties with rapid recovery from 80 % strain, and thermal stability up to 1200 °C, making them ideal for thermal insulation applications.
Large electronegativity differences between adjacent atomic sites activate and stabilize ZnIn2S4 for efficient photocatalytic overall water splitting
Authors: Xin Xu , Li Yuke , Zhang Youzi , Wang Yijin , Chi Xiao , Wei Yanping , Diao Caozheng , Su Jie , Wang Ruiling , Guo Peng , Yu Jiakang , Zhang Jia , Sobrido Ana Jorge , Titirici Maria-Magdalena , Li Xuanhua
Published: January 2024

Photocatalytic overall water splitting into hydrogen and oxygen is desirable for long-term renewable, sustainable and clean fuel production on earth. Metal sulfides are considered as ideal hydrogen-evolved photocatalysts, but their component homogeneity and typical sulfur instability cause an inert oxygen production, which remains a huge obstacle to overall water-splitting. Here, a distortion-evoked cation-site oxygen doping of ZnIn2S4 (D-O-ZIS) creates significant electronegativity differences between adjacent atomic sites, with S1 sites being electron-rich and S2 sites being electron-deficient in the local structure of S1–S2–O sites. The strong charge redistribution character activates stable oxygen reactions at S2 sites and avoids the common issue of sulfur instability in metal sulfide photocatalysis, while S1 sites favor the adsorption/desorption of hydrogen. Consequently, an overall water-splitting reaction has been realized in D-O-ZIS with a remarkable solar-to-hydrogen conversion efficiency of 0.57%, accompanying a ~ 91% retention rate after 120 h photocatalytic test. In this work, we inspire an universal design from electronegativity differences perspective to activate and stabilize metal sulfide photocatalysts for efficient overall water-splitting.
Molecular imaging predicts lack of T-DM1 response in advanced HER2-positive breast cancer (final results of ZEPHIR trial)
Authors: Mileva Magdalena , de Vries Elisabeth G. E. , Guiot Thomas , Wimana Zéna , Deleu Anne-Leen , Schröder Carolien P. , Lefebvre Yolene , Paesmans Marianne , Stroobants Sigrid , Huizing Manon , Aftimos Philippe , Tol Jolien , Van der Graaf Winette T. A. , Oyen Wim J. G. , Vugts Danielle J. , Menke-van der Houven van Oordt C. Willemien , Brouwers Adrienne H. , Piccart-Gebhart Martine , Flamen Patrick , Gebhart Géraldine
Published: January 2024

Efficacy of the human epidermal growth factor receptor (HER)2-targeting trastuzumab emtansine (T-DM1) in breast cancer (BC) relies on HER2 status determined by immunohistochemistry or fluorescence in-situ hybridization. Heterogeneity in HER2 expression, however, generates interest in “whole-body” assessment of HER2 status using molecular imaging. We evaluated the role of HER2-targeted molecular imaging in detecting HER2-positive BC lesions and patients unlikely to respond to T-DM1. Patients underwent zirconium-89 (89Zr) trastuzumab (HER2) PET/CT and [18F]-2-fluoro-2-deoxy-D-glucose (FDG) PET/CT before T-DM1 initiation. Based on 89Zr-trastuzumab uptake, lesions were visually classified as HER2-positive (visible/high uptake) or HER2-negative (background/close to background activity). According to proportion of FDG-avid tumor load showing 89Zr-trastuzumab uptake (entire/dominant part or minor/no part), patients were classified as HER2-positive and HER2-negative, respectively. Out of 265 measurable lesions, 93 (35%) were HER2-negative, distributed among 42 of the 90 included patients. Of these, 18 (19%) lesions belonging to 11 patients responded anatomically (>30% decrease in axial diameter from baseline) after three T-DM1 cycles, resulting in an 81% negative predictive value (NPV) of the HER2 PET/CT. In combination with early metabolic response assessment on FDG PET/CT performed before the second T-DM1 cycle, NPVs of 91% and 100% were reached in predicting lesion-based and patient-based (RECIST1.1) response, respectively. Therefore, HER2 PET/CT, alone or in combination with early FDG PET/CT, can successfully identify BC lesions and patients with a low probability of clinical benefit from T-DM1.
Efficient first-principles electronic transport approach to complex band structure materials: the case of n-type Mg3Sb2
Authors: Li Zhen , Graziosi Patrizio , Neophytou Neophytos
Published: January 2024

We present an efficient method for accurately computing electronic scattering rates and transport properties in materials with complex band structures. Using ab initio simulations, we calculate a limited number of electron–phonon matrix elements, and extract scattering rates for acoustic and optical processes based on deformation potential theory. Polar optical phonon scattering rates are determined using the Fröhlich model, and ionized impurity scattering rates are derived from the Brooks-Herring theory. Subsequently, electronic transport coefficients are computed within the Boltzmann transport theory. We exemplify our approach with n-type Mg3Sb2, a promising thermoelectric material with a challenging large unit cell and low symmetry. Notably, our method attains competitive accuracy, requiring less than 10% of the computational cost compared to state-of-the-art ab initio methods, dropping to 1% for simpler materials. Additionally, our approach provides explicit information on individual scattering processes, offering an alternative that combines efficiency, robustness, and flexibility beyond the commonly employed constant relaxation time approximation with the accuracy of fully first-principles calculations.
Rotating square tessellations enabled stretchable and adaptive curved display
Authors: Deng Yang , Xu Kuaile , Jiao Rui , Liu Weixuan , Cheung Yik Kin , Li Yongkai , Wang Xiaoyi , Hou Yue , Hong Wei , Yu Hongyu
Published: January 2024

Curved displays can adjust their shape to accommodate different objects and are used in electronics and decorative lighting. Due to the immutable pixel spacing, existing commercial curved displays are flexible but not compatible with undevelopable surfaces. Inspired by kirigami and auxetic structures, we propose an approach that combines luminescent elements and rotating square tessellations to create a stretchable, arbitrary curve adaptive display. We connect square islands by vertical interconnects to relieve the stress concentration and provide extra deformation patterns. The vertical interconnects are patterned on a flexible printed circuit board (FPCB) using laser cutting and folded up via specially designed molds. Further, the freed-up space by folded interconnects allows the structure to be compressed. A prototype stretchable display is demonstrated that it can maintain electrical performance under biaxial strain and adapt to different Gaussian curvature surfaces, including cylindrical, spherical, saddle and arbitrary surfaces. Theoretical models and finite element calculations are established to describe the tensile behavior of the structures under different boundary conditions and agree with the experimental results. This proposed technology paves a feasible solution of mass production of adaptive curved displays and sets the trend for the next-generation display.
Cell-to-cell transmitted alpha-synuclein recapitulates experimental Parkinson’s disease
Authors: Prymaczok Natalia Cecilia , De Francesco Pablo Nicolas , Mazzetti Samanta , Humbert-Claude Marie , Tenenbaum Liliane , Cappelletti Graziella , Masliah Eliezer , Perello Mario , Riek Roland , Gerez Juan Atilio
Published: January 2024

Parkinson’s disease is characterized by a progressive accumulation of alpha-Synuclein (αSyn) neuronal inclusions called Lewy bodies in the nervous system. Lewy bodies can arise from the cell-to-cell propagation of αSyn, which can occur via sequential steps of secretion and uptake. Here, by fusing a removable short signal peptide to the N-terminus of αSyn, we developed a novel mouse model with enhanced αSyn secretion and cell-to-cell transmission. Expression of the secreted αSyn in the mouse brain was under the control of a novel hybrid promoter in combination with adeno-associated virus serotype 9 (AAV9). This combination of promoter and viral vector induced a robust expression in neurons but not in the glia of injected mice. Biochemical characterization of the secreted αSyn revealed that, in cultured cells, this protein is released to the extracellular milieu via conventional secretion. The released αSyn is then internalized and processed by acceptor cells via the endosome–lysosome pathway indicating that the secreted αSyn is cell-to-cell transmitted. The secreted αSyn is aggregation-prone and amyloidogenic, and when expressed in the brain of wild-type non-transgenic mice, it induces a Parkinson’s disease-like phenotype that includes a robust αSyn pathology in the substantia nigra, neuronal loss, neuroinflammation, and motor deficits, all the key features of experimental animal models of Parkinson’s disease. In summary, a novel animal model of Parkinson’s disease based on enhanced cell-to-cell transmission of αSyn was developed. The neuron-produced cell-to-cell transmitted αSyn triggers all phenotypic features of experimental Parkinson’s disease in mice.
OXTR polymorphisms associated with severity and treatment responses of schizophrenia
Authors: Lv Xue , Hou Yue-Sen , Zhang Zhao-Hui , Yue Wei-Hua
Published: January 2024

The mechanisms generating specific symptoms of schizophrenia remain unclear and genetic research makes it possible to explore these issues at a fundamental level. Taking into account the associations between the oxytocin system and social functions, which are apparently impaired in schizophrenia patients, we hypothesized that the oxytocin receptor gene (OXTR) might be associated with schizophrenia symptoms in both severity and responses to antipsychotics and did this exploratory positional study. A total of 2363 patients with schizophrenia (1181 males and 1182 females) included in our study were randomly allocated to seven antipsychotic treatment groups and received antipsychotic monotherapy for 6 weeks. Their blood DNA was genotyped for OXTR polymorphisms. Their symptom severity was assessed by Positive and Negative Syndrome Scale (PANSS), and the scores were transformed into seven factors (positive, disorganized, negative symptoms apathy/avolition, negative symptoms deficit of expression, hostility, anxiety and depression). Percentage changes in PANSS scores from baseline to week 6 were calculated to quantify antipsychotic responses. We found that OXTR polymorphisms were nominally associated with the severity of overall symptoms (rs237899, β = 1.669, p = 0.019), hostility symptoms (rs237899, β = 0.427, p = 0.044) and anxiety symptoms (rs13316193, β = −0.197, p = 0.038). As for treatment responses, OXTR polymorphisms were nominally associated with the improvement in negative symptoms apathy/avolition (rs2268490, β = 2.235, p = 0.0499). No association between severity or response to treatment and OXTR polymorphisms was found with statistical correction for multiplicity. Overall, our results highlighted the possibility of nominally significant associations of the OXTR gene with the severity and improvement in schizophrenia symptoms. Given the exploratory nature of this study, these associations are indicative of the role of the OXTR gene in the pathology of schizophrenia and may contribute to further elucidate the mechanism of specific symptoms of schizophrenia and to exploit antipsychotics more effective to specific symptoms.
Sex differences in autonomic adverse effects related to antipsychotic treatment and associated hormone profiles
Authors: Johansen Ingrid T. , Steen Nils Eiel , Rødevand Linn , Lunding Synve H. , Hjell Gabriela , Ormerod Monica B. E. G. , Agartz Ingrid , Melle Ingrid , Lagerberg Trine V. , Nerhus Mari , Andreassen Ole A.
Published: January 2024

Autonomic adverse effects of antipsychotic drugs (APs) cause clinical challenges, but few studies have investigated sex differences and their underlying biological pathways. Sex-specific regulation of relevant hormones could be involved. We investigated sex differences in autonomic adverse effects related to olanzapine, quetiapine, risperidone, and aripiprazole, and the role of hormones related to APs. Patients with severe mental disorders (N = 1318) were included and grouped based on AP monotherapy: olanzapine (N = 364), quetiapine (N = 211), risperidone (N = 102), aripiprazole (N = 138), and no AP (N = 503). Autonomic symptoms from the Udvalg for Kliniske Undersøgelser (UKU) side effect scale was analyzed with logistic regression, adjusting for age, diagnosis, and polypharmacy. Further, we analyzed associations between autonomic symptoms and hormones related to APs. We found associations between autonomic adverse effects and APs, with sex-specific risk for palpitations/tachycardia associated with hormonal changes related to APs. Results showed increased salivation associated with aripiprazole, reduced salivation with quetiapine, and nausea/vomiting and palpitations/tachycardia with olanzapine, and higher risk of nausea/vomiting, diarrhea, constipation, polyuria/polydipsia, and palpitations/tachycardia in females. Significant sex x AP interaction was found for palpitations/tachycardia, with higher risk in risperidone-treated males, which was associated with different hormone profiles of prolactin, cortisol, and insulin. Our findings implicate a role of several hormones in the sex-specific autonomic adverse effects related to APs.
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming
Authors: Bruno Simone , Schlaeger Thorsten M. , Del Vecchio Domitilla
Published: January 2024

Experimental studies have shown that chromatin modifiers have a critical effect on cellular reprogramming, i.e., the conversion of differentiated cells to pluripotent stem cells. Here, we develop a model of the OCT4 gene regulatory network that includes genes expressing chromatin modifiers TET1 and JMJD2, and the chromatin modification circuit on which these modifiers act. We employ this model to compare three reprogramming approaches that have been considered in the literature with respect to reprogramming efficiency and latency variability. These approaches are overexpression of OCT4 alone, overexpression of OCT4 with TET1, and overexpression of OCT4 with JMJD2. Our results show more efficient and less variable reprogramming when also JMJD2 and TET1 are overexpressed, consistent with previous experimental data. Nevertheless, TET1 overexpression can lead to more efficient reprogramming compared to JMJD2 overexpression. This is the case when the recruitment of DNA methylation by H3K9me3 is weak and the methyl-CpG-binding domain (MBD) proteins are sufficiently scarce such that they do not hamper TET1 binding to methylated DNA. The model that we developed provides a mechanistic understanding of existing experimental results and is also a tool for designing optimized reprogramming approaches that combine overexpression of cell-fate specific transcription factors (TFs) with targeted recruitment of epigenetic modifiers.
mRNA vaccines expressing malaria transmission-blocking antigens Pfs25 and Pfs230D1 induce a functional immune response
Authors: Scaria Puthupparampil V. , Roth Nicole , Schwendt Kim , Muratova Olga V. , Alani Nada , Lambert Lynn E. , Barnafo Emma K. , Rowe Christopher G. , Zaidi Irfan U. , Rausch Kelly M. , Narum David L. , Petsch Benjamin , Duffy Patrick E.
Published: January 2024

Malaria transmission-blocking vaccines (TBV) are designed to inhibit the sexual stage development of the parasite in the mosquito host and can play a significant role in achieving the goal of malaria elimination. Preclinical and clinical studies using protein–protein conjugates of leading TBV antigens Pfs25 and Pfs230 domain 1 (Pfs230D1) have demonstrated the feasibility of TBV. Nevertheless, other promising vaccine platforms for TBV remain underexplored. The recent success of mRNA vaccines revealed the potential of this technology for infectious diseases. We explored the mRNA platform for TBV development. mRNA constructs of Pfs25 and Pfs230D1 variously incorporating signal peptides (SP), GPI anchor, and Trans Membrane (TM) domain were assessed in vitro for antigen expression, and selected constructs were evaluated in mice. Only mRNA constructs with GPI anchor or TM domain that resulted in high cell surface expression of the antigens yielded strong immune responses in mice. These mRNA constructs generated higher transmission-reducing functional activity versus the corresponding alum-adjuvanted protein-protein conjugates used as comparators. Pfs25 mRNA with GPI anchor or TM maintained >99% transmission reducing activity through 126 days, the duration of the study, demonstrating the potential of mRNA platform for TBV.
Absolute quantitation of binding antibodies from clinical samples
Authors: Tang Chan , Verwilligen Annemiek , Sadoff Jerald , Brandenburg Boerries , Sneekes-Vriese Eveline , van den Kerkhof Tom , Dillen Lieve , Rutten Lucy , Juraszek Jarek , Callewaert Katleen , Janssen Sarah , Huizingh Jeroen , Euler Zelda , Schilperoord Tom , Verhemeldonck Marc , Langedijk Johannes P. M. , Hendriks Jenny , Stieh Daniel J.
Published: January 2024

The quantitation of antibody responses is a critical requirement for the successful development of vaccines and therapeutics that often relies on the use of standardized reference materials to determine relative quantities within biological samples. The validity of comparing responses across assays using arbitrarily defined reference values is therefore limited. We developed a generalizable method known as MASCALE (Mass Spectrometry Enabled Conversion to Absolute Levels of ELISA Antibodies) for absolute quantitation of antibodies by calibrating ELISA reference sera using mass spectrometry. Levels of proteotypic peptides served as a proxy for human IgG, allowing the conversion of responses from arbitrary values to absolute amounts. Applications include comparison of binding assays at two separate laboratories and evaluation of cross-clade magnitude-breadth responses induced by an investigational HIV-1 vaccine regimen. MASCALE addresses current challenges in the interpretation of immune responses in clinical trials and expands current options available to make suitable comparisons across different settings.
Optimization and modeling of betamethasone removal from aqueous solutions using a SiO2/g-C3N5@NiFe2O4 nanophotocatalyst by RSM
Authors: Bagherlou Neda , Ghasemi Elnaz , Gharbani Parvin , Babazadeh Mirzaagha , Mehrizad Ali
Published: January 2024

This study presents the preparation of SiO2/g-C3N5@NiFe2O4 nanophotocatalyst for the removal of betamethasone from aqueous solutions. The SiO2/g-C3N5@NiFe2O4 nanophotocatalyst was synthesized using the solvothermal method, and its structure and optical properties were characterized and confirmed through XRD, FESEM, EDX, DRS, BET, VSM and PL analysis. Photocatalytic removal of betamethasone was optimized using a central composite design. The band gap of pure g-C3N5, NiFe2O4, and SiO2/g-C3N5@NiFe2O4 was obtained 2.4 eV, 2.7 eV, and 1.4 eV, respectively using the Tauc plot. The F-value of 909.88 and Lack of Fit F-value of 0.41 confirm the obtained model is significant. Also, the value of R2 = 0.9988 along with R2adja = 09977 demonstrates excellent model performance. Maximum removal efficiency of betamethasone was approximately 87.15% under the following optimal conditions: nanophotocatalyst dosage of 0.005 g/50 mL, a betamethasone concentration of 20 mg/L, and an irradiation time of 40 min under visible light. This performance closely aligns with the actual value of 80.65%. In conclusion, the SiO2/g-C3N5@NiFe2O4 nanophotocatalyst demonstrates excellent photocatalytic ability for the removal of betamethasone from aqueous solutions.
Constructing a finer-grained representation of clinical trial results from ClinicalTrials.gov
Authors: Shi Xuanyu , Du Jian
Published: January 2024

Randomized controlled trials are essential for evaluating clinical interventions; however, selective reporting and publication bias in medical journals have undermined the integrity of the clinical evidence system. ClinicalTrials.gov serves as a valuable and complementary repository, yet synthesizing information from it remains challenging. This study introduces a curated dataset that extends beyond the traditional PICO framework. It links efficacy with safety results at the experimental arm group level within each trial, and connects them across all trials through a knowledge graph. This novel representation effectively bridges the gap between generally described searchable information and specifically detailed yet underutilized reported results, and promotes a dual-faceted understanding of interventional effects. Adhering to the “calculate once, use many times” principle, the structured dataset will enhance the reuse and interpretation of ClinicalTrials.gov results data. It aims to facilitate more systematic evidence synthesis and health technology assessment, by incorporating both positive and negative results, distinguishing biomarkers, patient-reported outcomes, and clinical endpoints, while also balancing both efficacy and safety outcomes for a given medical intervention.
Quantitative catalogue of mammalian mitotic chromosome-associated RNAs
Authors: Zhang Le , Hu Chuansheng , Xu Zeqian , Li Hua , Ye Bishan , Li Xinhui , Czajkowsky Daniel M. , Shao Zhifeng
Published: January 2024

The faithful transmission of a cell’s identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.
An RNA-seq atlas of mouse brain areas during fasting and diet-induced obesity
Authors: Todorov Petar V. , Klein Anders Bue , Egerod Kristoffer L. , Clemmensen Christoffer , Pers Tune H.
Published: January 2024

Mammalian energy homeostasis is primarilly regulated by the hypothalamus and hindbrain, with the hippocampus, midbrain nuclei, and other regions implicated by evidence from human genetics studies. To understand how these non-canonical brain regions respond to imbalances in energy homeostasis, we performed two experiments examining the effects of different diets in male C57BL6 mice. In our first study, groups of six pair-housed mice were given access to chow, high-fat diet or fasted for 16 hours. In our subsequent study, two groups of 10 mice were single-housed and given access to chow or fasted for 24 h. We recorded food intake for each cage, the change in body weight for each animal, and collected hypothalamus, hippocampus, superior colliculus, inferior colliculus, frontal cortex, and zona incerta-centric samples. We performed bulk RNA sequencing on 185 samples and validated them by a series of quality control assessments including alignment quality and gene expression profiling. We believe these studies capture the transcriptomic effects of acute fasting and high-fat diet in the rodent brain and provide a valuable reference.
Physical–chemical analysis of different types of flours available in the Romanian market
Authors: Bodor Katalin , Szilágyi József , Salamon Brigitta , Szakács Orsolya , Bodor Zsolt
Published: January 2024

The physical–chemical characteristics of different types of flours are essential for understanding their composition, nutritional value, and functional properties as well. The aim of this research was to identify the variability of the different wheat flours available in Romania. In this study 39 different wheat flours were selected and the following parameters were analyzed in the laboratory: moisture content, ash content, gluten content (wet and dry) and wet gluten spreading. The tested flours were classified into four different classes according to their ash content: 480 (ash content 0.48%) (N = 11), 550 (0.55%) (N = 9), 650 (0.65%) (N = 8), 1100 (1.1%) (N = 11). Mathematical and statistical methods were used to analyze the obtained results: descriptive statistics, box-plot, Spearman correlation and hierarchical cluster analysis. The results revealed that moisture content varied between 9.5 and 11.8%. In terms of ash content, the lowest and highest measured values were 0.427–2.04 g/100 g. The average wet gluten content of the studied flours varied between 30 and 32%, while the average dry gluten content was 12.8%. The findings indicate that the moisture content of all examined flour samples was within permissible levels for extended storage, aligning with established standards. Gluten is a key and essential parameter for bread making because influences the dough mixing and baking properties. The mineral content, represented by ash content, is influenced by cereal type and milling process, with wheat's ash content ranging between 1.5 and 2%. Flours with high wet gluten content (> 34%) can be used to improve the properties of lower quality flours. Further studies are necessary in order to determine the possible health effects of different cereal varieties.
Differentiating behavioral impact with or without vaccination certification under mass vaccination and non-pharmaceutical interventions on mitigating COVID-19
Authors: Cao Hu , Cao Longbing
Published: January 2024

As COVID-19 vaccines became widely available worldwide, many countries implemented vaccination certification, also known as a “green pass”, to promote and expedite vaccination on containing virus spread from the latter half of 2021. This policy allowed those vaccinated to have more freedom in public activities compared to more constraints on the unvaccinated in addition to existing non-pharmaceutical interventions (NPIs). Accordingly, the vaccination certification also induced heterogeneous behaviors of unvaccinated and vaccinated groups. This makes it essential yet challenging to model the behavioral impact of vaccination certification on the two groups and the transmission dynamics of COVID-19 within and between the groups. Very limited quantitative work is available for addressing these purposes. Here we propose an extended epidemiological model SEIQRD$$^2$$

2

to effectively distinguish the behavioral impact of vaccination certification on unvaccinated and vaccinated groups through incorporating two contrastive transmission chains. SEIQRD$$^2$$

2

also quantifies the impact of the green pass policy. With the resurgence of COVID-19 in Greece, Austria, and Israel in 2021, our simulation results indicate that their implementation of vaccination certification brought about more than a 14-fold decrease in the total number of infections and deaths as compared to a scenario with no such a policy. Additionally, a green pass policy may offer a reasonable practical solution to strike the balance between public health and individual’s freedom during the pandemic.
Long-lasting blocking of interoceptive effects of cocaine by a highly efficient cocaine hydrolase in rats
Authors: Wei Huimei , LeSaint Johnathan E. , Jin Zhenyu , Zhan Chang-Guo , Zheng Fang
Published: January 2024

Cocaine dependence is a serious world-wide public health problem without an FDA-approved pharmacotherapy. We recently designed and discovered a highly efficient long-acting cocaine hydrolase CocH5-Fc(M6). The present study examined the effectiveness and duration of CocH5-Fc(M6) in blocking interoceptive effects of cocaine by performing cocaine discrimination tests in rats, demonstrating that the duration of CocH5-Fc(M6) in blocking cocaine discrimination was dependent on cocaine dose and CocH5-Fc(M6) plasma concentration. Particularly, a dose of 3 mg/kg CocH5-Fc(M6) effectively attenuated discriminative stimulus effects of 10 mg/kg cocaine, cumulative doses of 10 and 32 mg/kg cocaine, and cumulative doses of 10, 32 and 56 mg/kg cocaine by ≥ 20% for 41, 19, and 10 days, and completely blocked the discriminative stimulus effects for 30, 13, and 5 days with corresponding threshold plasma CocH5-Fc(M6) concentrations of 15.9, 72.2, and 221 nM, respectively, under which blood cocaine concentration was negligible. Additionally, based on the data obtained, cocaine discrimination model is more sensitive than the locomotor activity to reveal cocaine effects and that CocH5-Fc(M6) itself has no long-term toxicity regarding behavioral activities such as lever pressing and food consumption in rats, further demonstrating that CocH5-Fc(M6) has the desired properties as a promising therapeutic candidate for prevenance of cocaine dependence.
CDMO: Chaotic Dwarf Mongoose Optimization Algorithm for feature selection
Authors: Abdelrazek Mohammed , Abd Elaziz Mohamed , El-Baz A. H.
Published: January 2024

In this paper, a modified version of Dwarf Mongoose Optimization Algorithm (DMO) for feature selection is proposed. DMO is a novel technique of the swarm intelligence algorithms which mimic the foraging behavior of the Dwarf Mongoose. The developed method, named Chaotic DMO (CDMO), is considered a wrapper-based model which selects optimal features that give higher classification accuracy. To speed up the convergence and increase the effectiveness of DMO, ten chaotic maps were used to modify the key elements of Dwarf Mongoose movement during the optimization process. To evaluate the efficiency of the CDMO, ten different UCI datasets are used and compared against the original DMO and other well-known Meta-heuristic techniques, namely Ant Colony optimization (ACO), Whale optimization algorithm (WOA), Artificial rabbit optimization (ARO), Harris hawk optimization (HHO), Equilibrium optimizer (EO), Ring theory based harmony search (RTHS), Random switching serial gray-whale optimizer (RSGW), Salp swarm algorithm based on particle swarm optimization (SSAPSO), Binary genetic algorithm (BGA), Adaptive switching gray-whale optimizer (ASGW) and Particle Swarm optimization (PSO). The experimental results show that the CDMO gives higher performance than the other methods used in feature selection. High value of accuracy (91.9–100%), sensitivity (77.6–100%), precision (91.8–96.08%), specificity (91.6–100%) and F-Score (90–100%) for all ten UCI datasets are obtained. In addition, the proposed method is further assessed against CEC’2022 benchmarks functions.
Jurassic paleosurfaces with fecal mounds reveal the last supper of arenicolid worms
Authors: Mángano M. Gabriela , Buatois Luis A. , Piñuela Laura , Volkenborn Nils , Rodríguez-Tovar Francisco J. , García-Ramos José C.
Published: January 2024

Exceptional paleosurfaces preserving fecal casting mounds occur in the Upper Jurassic Lastres Formation of Spain. As in modern shorelines, these biogenic structures are associated with straight to sinuous-crested ripples showing the interplay of biological and physical processes in a low-energy marine environment. These trace fossils display characteristics, distribution, and densities like those of modern arenicolid populations (approximately 35 specimens per m2). Under close examination, these fecal casting mounds are morphologically undistinguishable from those produced by recent arenicolids (e.g. Arenicola marina, Abarenicola pacifica), providing evidence of the presence of these polychaetes in the Late Jurassic. As their modern counterparts, fossil arenicolids very likely modified their environment generating a seabed topography and impacting ancient benthic communities, sediment characteristics, and sediment biogeochemistry. Although the presence of oxic microhabitats and biogeochemical processes cannot be accurately measured in the fossil record, comparison with the work of modern populations allows to make inferences on sediment reworking and bioirrigation potential. In addition, association with grazing trails supports the idea of fertilization and modulation of food resources to other species. These paleosurfaces underscore the significance of high-fidelity snapshots in the fossil record (true substrates) to reconstruct past ecologies and sediment biogeochemistry. A new ichnotaxon, Cumulusichnus asturiensis n. igen. and n. isp., is defined.
Land subsidence analysis along high-speed railway based on EEMD-Prophet method
Authors: Dongwei Qiu , Yuci Tong , Yuzheng Wang , Keliang Ding , Tiancheng Liu , Shanshan Wan
Published: January 2024

Environmental changes and ground subsidence along railway lines are serious concerns during high-speed railway operations. It is worth noting that AutoRegressive Integrated Moving Average (ARMA), Long Short-Term Memory (LSTM), and other prediction methods may present limitations when applied to predict InSAR time series results. To address this issue, this study proposes a prediction method that decomposes the nonlinear settlement time series of feature points obtained through InSAR technology using Ensemble Empirical Mode Decomposition (EEMD). Subsequently, multiple Intrinsic Mode Functions (IMFs) are generated, and each IMF is individually predicted using the Prophet forecasting model. Finally, we employ an equal-weight superimposition method to combine the results, resulting in the prediction of the InSAR settlement time series. The predicted values of each component are subsequently weighted equally and combined to derive the final prediction outcome. This paper selects InSAR monitoring data along a high-speed railway in inland China and uses the proposed method and ARMA and Prophet models to carry out comparative experiments. The experimental results show that compared with the ARMA and Prophet models, the method in this paper improves the root mean square error by 58.01% and 32.3%, and increases the mean absolute error by 62.69% and 33.78%, respectively. The predicted settlement values generated by our method exhibit better agreement with the actual InSAR monitoring values.
Machine learning-based prediction model for myocardial ischemia under high altitude exposure: a cohort study
Authors: Chen Yu , Zhang Xin , Ye Qing , Zhang Xin , Cao Ning , Li Shao-Ying , Yu Jie , Zhao Sheng-Tao , Zhang Juan , Xu Xin-Ming , Shi Yan-Kun , Yang Li-Xia
Published: January 2024

High altitude exposure increases the risk of myocardial ischemia (MI) and subsequent cardiovascular death. Machine learning techniques have been used to develop cardiovascular disease prediction models, but no reports exist for high altitude induced myocardial ischemia. Our objective was to establish a machine learning-based MI prediction model and identify key risk factors. Using a prospective cohort study, a predictive model was developed and validated for high-altitude MI. We consolidated the health examination and self-reported electronic questionnaire data (collected between January and June 2022 in 920th Joint Logistic Support Force Hospital of china) of soldiers undergoing high-altitude training, along with the health examination and second self-reported electronic questionnaire data (collected between December 2022 and January 2023) subsequent to their completion on the plateau, into a unified dataset. Participants were subsequently allocated to either the training or test dataset in a 3:1 ratio using random assignment. A predictive model based on clinical features, physical examination, and laboratory results was designed using the training dataset, and the model's performance was evaluated using the area under the receiver operating characteristic curve score (AUC) in the test dataset. Using the training dataset (n = 2141), we developed a myocardial ischemia prediction model with high accuracy (AUC = 0.86) when validated on the test dataset (n = 714). The model was based on five laboratory results: Eosinophils percentage (Eos.Per), Globulin (G), Ca, Glucose (GLU), and Aspartate aminotransferase (AST). Our concise and accurate high-altitude myocardial ischemia incidence prediction model, based on five laboratory results, may be used to identify risks in advance and help individuals and groups prepare before entering high-altitude areas. Further external validation, including female and different age groups, is necessary.