bluuebunny/crossref_metadata_2025 huggingface dataset:
Endocardial HDAC3 is required for myocardial trabeculation
Authors: Jang Jihyun , Bentsen Mette , Kim Ye Jun , Kim Erick , Garg Vidu , Cai Chen-Leng , Looso Mario , Li Deqiang
Published: May 2024

Failure of proper ventricular trabeculation is often associated with congenital heart disease. Support from endocardial cells, including the secretion of extracellular matrix and growth factors is critical for trabeculation. However, it is poorly understood how the secretion of extracellular matrix and growth factors is initiated and regulated by endocardial cells. We find that genetic knockout of histone deacetylase 3 in the endocardium in mice results in early embryo lethality and ventricular hypotrabeculation. Single cell RNA sequencing identifies significant downregulation of extracellular matrix components in histone deacetylase 3 knockout endocardial cells. Secretome from cultured histone deacetylase 3 knockout mouse cardiac endothelial cells lacks transforming growth factor ß3 and shows significantly reduced capacity in stimulating cultured cardiomyocyte proliferation, which is remarkably rescued by transforming growth factor ß3 supplementation. Mechanistically, we identify that histone deacetylase 3 knockout induces transforming growth factor ß3 expression through repressing microRNA-129-5p. Our findings provide insights into the pathogenesis of congenital heart disease and conceptual strategies to promote myocardial regeneration.
Accelerating reliable multiscale quantum refinement of protein–drug systems enabled by machine learning
Authors: Yan Zeyin , Wei Dacong , Li Xin , Chung Lung Wa
Published: May 2024

Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality or even correcting the structure of biomacromolecules. However, vast computational costs and complex quantum mechanics/molecular mechanics (QM/MM) setups limit QR applications. Here we incorporate robust machine learning potentials (MLPs) in multiscale ONIOM(QM:MM) schemes to describe the core parts (e.g., drugs/inhibitors), replacing the expensive QM method. Additionally, two levels of MLPs are combined for the first time to overcome MLP limitations. Our unique MLPs+ONIOM-based QR methods achieve QM-level accuracy with significantly higher efficiency. Furthermore, our refinements provide computational evidence for the existence of bonded and nonbonded forms of the Food and Drug Administration (FDA)-approved drug nirmatrelvir in one SARS-CoV-2 main protease structure. This study highlights that powerful MLPs accelerate QRs for reliable protein–drug complexes, promote broader QR applications and provide more atomistic insights into drug development.
Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation
Authors: Staller Ecco , Carrique Loïc , Swann Olivia C. , Fan Haitian , Keown Jeremy R. , Sheppard Carol M. , Barclay Wendy S. , Grimes Jonathan M. , Fodor Ervin
Published: May 2024

Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer—the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA.
A non-canonical visual cortical-entorhinal pathway contributes to spatial navigation
Authors: Shao Qiming , Chen Ligu , Li Xiaowan , Li Miao , Cui Hui , Li Xiaoyue , Zhao Xinran , Shi Yuying , Sun Qiang , Yan Kaiyue , Wang Guangfu
Published: May 2024

Visual information is important for accurate spatial coding and memory-guided navigation. As a crucial area for spatial cognition, the medial entorhinal cortex (MEC) harbors diverse spatially tuned cells and functions as the major gateway relaying sensory inputs to the hippocampus containing place cells. However, how visual information enters the MEC has not been fully understood. Here, we identify a pathway originating in the secondary visual cortex (V2) and directly targeting MEC layer 5a (L5a). L5a neurons served as a network hub for visual processing in the MEC by routing visual inputs from multiple V2 areas to other local neurons and hippocampal CA1. Interrupting this pathway severely impaired visual stimulus-evoked neural activity in the MEC and performance of mice in navigation tasks. These observations reveal a visual cortical-entorhinal pathway highlighting the role of MEC L5a in sensory information transmission, a function typically attributed to MEC superficial layers before.
Public engagement for inclusive and sustainable governance of climate interventions
Authors: Fritz Livia , Baum Chad M. , Low Sean , Sovacool Benjamin K.
Published: May 2024

The need for public engagement is increasingly evident as discussions intensify around emerging methods for carbon dioxide removal and controversial proposals around solar geoengineering. Based on 44 focus groups in 22 countries across the Global North and Global South (N = 323 participants), this article traces public preferences for a variety of bottom-up and top-down engagement practices ranging from information recipient to broad decision authority. Here, we show that engagement practices need to be responsive to local political cultures and socio-technical environments, while attending to the global dimensions and interconnectedness of the issues at stake. Establishing public engagement as a cornerstone of inclusive and sustainable governance of climate-intervention technologies requires (i) recognizing the diversity of forms and intensities of engaging, (ii) considering national contexts and modes of engagement, (iii) tailoring to technological idiosyncrasies, (iv) adopting power-sensitive practices, (v) accounting for publics’ prior experience, (vi) establishing trust and procedural legitimacy and (vii) engaging with tensions and value disagreements.
Remote epitaxy of single-crystal rhombohedral WS2 bilayers
Authors: Chang Chao , Zhang Xiaowen , Li Weixuan , Guo Quanlin , Feng Zuo , Huang Chen , Ren Yunlong , Cai Yingying , Zhou Xu , Wang Jinhuan , Tang Zhilie , Ding Feng , Wei Wenya , Liu Kaihui , Xu Xiaozhi
Published: May 2024

Compared to transition metal dichalcogenide (TMD) monolayers, rhombohedral-stacked (R-stacked) TMD bilayers exhibit remarkable electrical performance, enhanced nonlinear optical response, giant piezo-photovoltaic effect and intrinsic interfacial ferroelectricity. However, from a thermodynamics perspective, the formation energies of R-stacked and hexagonal-stacked (H-stacked) TMD bilayers are nearly identical, leading to mixed stacking of both H- and R-stacked bilayers in epitaxial films. Here, we report the remote epitaxy of centimetre-scale single-crystal R-stacked WS2 bilayer films on sapphire substrates. The bilayer growth is realized by a high flux feeding of the tungsten source at high temperature on substrates. The R-stacked configuration is achieved by the symmetry breaking in a-plane sapphire, where the influence of atomic steps passes through the lower TMD layer and controls the R-stacking of the upper layer. The as-grown R-stacked bilayers show up-to-30-fold enhancements in carrier mobility (34 cm2V−1s−1), nearly doubled circular helicity (61%) and interfacial ferroelectricity, in contrast to monolayer films. Our work reveals a growth mechanism to obtain stacking-controlled bilayer TMD single crystals, and promotes large-scale applications of R-stacked TMD.
ADAM9 promotes type I interferon-mediated innate immunity during encephalomyocarditis virus infection
Authors: Bazzone Lindsey E. , Zhu Junji , King Michael , Liu GuanQun , Guo Zhiru , MacKay Christopher R. , Kyawe Pyae P. , Qaisar Natasha , Rojas-Quintero Joselyn , Owen Caroline A. , Brass Abraham L. , McDougall William , Baer Christina E. , Cashman Timothy , Trivedi Chinmay M. , Gack Michaela U. , Finberg Robert W. , Kurt-Jones Evelyn A.
Published: May 2024

Viral myocarditis, an inflammatory disease of the heart, causes significant morbidity and mortality. Type I interferon (IFN)-mediated antiviral responses protect against myocarditis, but the mechanisms are poorly understood. We previously identified A Disintegrin And Metalloproteinase domain 9 (ADAM9) as an important factor in viral pathogenesis. ADAM9 is implicated in a range of human diseases, including inflammatory diseases; however, its role in viral infection is unknown. Here, we demonstrate that mice lacking ADAM9 are more susceptible to encephalomyocarditis virus (EMCV)-induced death and fail to mount a characteristic type I IFN response. This defect in type I IFN induction is specific to positive-sense, single-stranded RNA (+ ssRNA) viruses and involves melanoma differentiation-associated protein 5 (MDA5)—a key receptor for +ssRNA viruses. Mechanistically, ADAM9 binds to MDA5 and promotes its oligomerization and thereby downstream mitochondrial antiviral-signaling protein (MAVS) activation in response to EMCV RNA stimulation. Our findings identify a role for ADAM9 in the innate antiviral response, specifically MDA5-mediated IFN production, which protects against virus-induced cardiac damage, and provide a potential therapeutic target for treatment of viral myocarditis.
Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy
Authors: Qiao Chang , Zeng Yunmin , Meng Quan , Chen Xingye , Chen Haoyu , Jiang Tao , Wei Rongfei , Guo Jiabao , Fu Wenfeng , Lu Huaide , Li Di , Wang Yuwang , Qiao Hui , Wu Jiamin , Li Dong , Dai Qionghai
Published: May 2024

Computational super-resolution methods, including conventional analytical algorithms and deep learning models, have substantially improved optical microscopy. Among them, supervised deep neural networks have demonstrated outstanding performance, however, demanding abundant high-quality training data, which are laborious and even impractical to acquire due to the high dynamics of living cells. Here, we develop zero-shot deconvolution networks (ZS-DeconvNet) that instantly enhance the resolution of microscope images by more than 1.5-fold over the diffraction limit with 10-fold lower fluorescence than ordinary super-resolution imaging conditions, in an unsupervised manner without the need for either ground truths or additional data acquisition. We demonstrate the versatile applicability of ZS-DeconvNet on multiple imaging modalities, including total internal reflection fluorescence microscopy, three-dimensional wide-field microscopy, confocal microscopy, two-photon microscopy, lattice light-sheet microscopy, and multimodal structured illumination microscopy, which enables multi-color, long-term, super-resolution 2D/3D imaging of subcellular bioprocesses from mitotic single cells to multicellular embryos of mouse andC. elegans.
Plant height as an indicator for alpine carbon sequestration and ecosystem response to warming
Authors: Quan Quan , He Nianpeng , Zhang Ruiyang , Wang Jinsong , Luo Yiqi , Ma Fangfang , Pan Junxiao , Wang Ruomeng , Liu Congcong , Zhang Jiahui , Wang Yiheng , Song Bing , Li Zhaolei , Zhou Qingping , Yu Guirui , Niu Shuli
Published: May 2024

Growing evidence indicates that plant community structure and traits have changed under climate warming, especially in cold or high-elevation regions. However, the impact of these warming-induced changes on ecosystem carbon sequestration remains unclear. Using a warming experiment on the high-elevation Qinghai-Tibetan Plateau, we found that warming not only increased plant species height but also altered species composition, collectively resulting in a taller plant community associated with increased net ecosystem productivity (NEP). Along a 1,500 km transect on the Plateau, taller plant community promoted NEP and soil carbon through associated chlorophyll content and other photosynthetic traits at the community level. Overall, plant community height as a dominant trait is associated with species composition and regulates ecosystem C sequestration in the high-elevation biome. This trait-based association provides new insights into predicting the direction, magnitude and sensitivity of ecosystem C fluxes in response to climate warming.
Increased blood draws for ultrasensitive ctDNA and CTCs detection in early breast cancer patients
Authors: Alba-Bernal Alfonso , Godoy-Ortiz Ana , Domínguez-Recio María Emilia , López-López Esperanza , Quirós-Ortega María Elena , Sánchez-Martín Victoria , Roldán-Díaz María Dunia , Jiménez-Rodríguez Begoña , Peralta-Linero Jesús , Bellagarza-García Estefanía , Troyano-Ramos Laura , Garrido-Ruiz Guadalupe , Hierro-Martín M. Isabel , Vicioso Luis , González-Ortiz Álvaro , Linares-Valencia Noelia , Velasco-Suelto Jesús , Carbajosa Guillermo , Garrido-Aranda Alicia , Lavado-Valenzuela Rocío , Álvarez Martina , Pascual Javier , Comino-Méndez Iñaki , Alba Emilio
Published: May 2024

Early breast cancer patients often experience relapse due to residual disease after treatment. Liquid biopsy is a methodology capable of detecting tumor components in blood, but low concentrations at early stages pose challenges. To detect them, next-generation sequencing has promise but entails complex processes. Exploring larger blood volumes could overcome detection limitations. Herein, a total of 282 high-volume plasma and blood-cell samples were collected for dual ctDNA/CTCs detection using a single droplet-digital PCR assay per patient. ctDNA and/or CTCs were detected in 100% of pre-treatment samples. On the other hand, post-treatment positive samples exhibited a minimum variant allele frequency of 0.003% for ctDNA and minimum cell number of 0.069 CTCs/mL of blood, surpassing previous investigations. Accurate prediction of residual disease before surgery was achieved in patients without a complete pathological response. A model utilizing ctDNA dynamics achieved an area under the ROC curve of 0.92 for predicting response. We detected disease recurrence in blood in the three patients who experienced a relapse, anticipating clinical relapse by 34.61, 9.10, and 7.59 months. This methodology provides an easily implemented alternative for ultrasensitive residual disease detection in early breast cancer patients.
High-fidelity four-photon GHZ states on chip
Authors: Pont Mathias , Corrielli Giacomo , Fyrillas Andreas , Agresti Iris , Carvacho Gonzalo , Maring Nicolas , Emeriau Pierre-Emmanuel , Ceccarelli Francesco , Albiero Ricardo , Dias Ferreira Paulo Henrique , Somaschi Niccolo , Senellart Jean , Sagnes Isabelle , Morassi Martina , Lemaître Aristide , Senellart Pascale , Sciarrino Fabio , Liscidini Marco , Belabas Nadia , Osellame Roberto
Published: May 2024

Mutually entangled multi-photon states are at the heart of all-optical quantum technologies. While impressive progresses have been reported in the generation of such quantum light states using free space apparatus, high-fidelity high-rate on-chip entanglement generation is crucial for future scalability. In this work, we use a bright quantum-dot based single-photon source to demonstrate the high fidelity generation of 4-photon Greenberg-Horne-Zeilinger (GHZ) states with a low-loss reconfigurable glass photonic circuit. We reconstruct the density matrix of the generated states using full quantum-state tomography reaching an experimental fidelity to the target state of $${{{{\mathcal{F}}}}}_{{{{{\rm{GHZ}}}}}_{4}}=(86.0\pm 0.4)\, \%$$

F

GHZ

4

=

(

86.0
±
0.4

)

%

, and a purity of $${{{{\mathcal{P}}}}}_{{{{{\rm{GHZ}}}}}_{4}}=(76.3\pm 0.6)\, \%$$

P

GHZ

4

=

(

76.3
±
0.6

)

%

. The entanglement of the generated states is certified with a semi device-independent approach through the violation of a Bell-like inequality by more than 39 standard deviations. Finally, we carry out a four-partite quantum secret sharing protocol on-chip where a regulator shares with three interlocutors a sifted key with up to 1978 bits, achieving a qubit-error rate of 10.87%. These results establish that the quantum-dot technology combined with glass photonic circuitry offers a viable path for entanglement generation and distribution.
DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing
Authors: Alper Pinar , Dĕd Vilém , Herzinger Sascha , Grouès Valentin , Peter Sarah , Lebioda Jacek , Ebermann Linda , Popleteeva Marina , Barry Nene Djenaba , Welter Danielle , Ghosh Soumyabrata , Becker Regina , Schneider Reinhard , Gu Wei , Trefois Christophe , Satagopam Venkata
Published: May 2024

The EU General Data Protection Regulation (GDPR) requirements have prompted a shift from centralised controlled access genome-phenome archives to federated models for sharing sensitive human data. In a data-sharing federation, a central node facilitates data discovery; meanwhile, distributed nodes are responsible for handling data access requests, concluding agreements with data users and providing secure access to the data. Research institutions that want to become part of such federations often lack the resources to set up the required controlled access processes. The DS-PACK tool assembly is a reusable, open-source middleware solution that semi-automates controlled access processes end-to-end, from data submission to access. Data protection principles are engraved into all components of the DS-PACK assembly. DS-PACK centralises access control management and distributes access control enforcement with support for data access via cloud-based applications. DS-PACK is in production use at the ELIXIR Luxembourg data hosting platform, combined with an operational model including legal facilitation and data stewardship.
Heart rate variability helps classify phenotype in systemic sclerosis
Authors: Delliaux Stéphane , Sow Abdou Khadir , Echcherki Anass , Benyamine Audrey , Gomes de Pinho Quentin , Brégeon Fabienne , Granel Brigitte
Published: May 2024

We aimed to develop a systemic sclerosis (SSc) subtypes classifier tool to be used at the patient’s bedside. We compared the heart rate variability (HRV) at rest (5-min) and in response to orthostatism (5-min) of patients (n = 58) having diffuse (n = 16, dcSSc) and limited (n = 38, lcSSc) cutaneous forms. The HRV was evaluated from the beat-to-beat RR intervals in time-, frequency-, and nonlinear-domains. The dcSSc group differed from the lcSSc group mainly by a higher heart rate (HR) and a lower HRV, in decubitus and orthostatism conditions. Stand-up maneuver lowered HR standard deviation (sd_HR), the major axis length of the fitted ellipse of Poincaré plot of RR intervals (SD2), and the correlation dimension (CorDim) in the dcSSc group while increased these HRV indexes in the lcSSc group (p = 0.004, p = 0.002, and p = 0.004, respectively). We identified the 5 most informative and discriminant HRV variables. We then compared 341 classifying models (1 to 5 variables combinations × 11 classifier algorithms) according to mean squared error, logloss, sensitivity, specificity, precision, accuracy, area under curve of the ROC-curves and F1-score. F1-score ranged from 0.823 for the best 1-variable model to a maximum of 0.947 for the 4-variables best model. Most specific and precise models included sd_HR, SD2, and CorDim. In conclusion, we provided high performance classifying models able to distinguish diffuse from limited cutaneous SSc subtypes easy to perform at the bedside from ECG recording. Models were based on 1 to 5 HRV indexes used as nonlinear markers of autonomic integrated influences on cardiac activity.
Relationship of oral bacterial number with medical hospitalization costs in analysis of Diagnosis Procedure Combination database from single institution in Japan
Authors: Nishi Hiromi , Kajiya Mikihito , Ohta Kouji , Shigeishi Hideo , Obayashi Taiji , Munenaga Syuichi , Obayashi Nami , Yoshioka Yukio , Konishi Masaru , Naruse Takako , Matsumoto Akihiro , Odo Ayaka , Kitagawa Masae , Ando Toshinori , Shintani Tomoaki , Tokikazu Tomoko , Ino Natsumi , Mihara Naoki , Kakimoto Naoya , Tsuga Kazuhiro , Tanimoto Kotaro , Ohge Hiroki , Kurihara Hidemi , Kawaguchi Hiroyuki
Published: May 2024

Oral bacteria are known to be associated with perioperative complications during hospitalization. However, no presented reports have clarified the relationship of oral bacterial number with medical costs for inpatients. The Diagnosis Procedure Combination (DPC) database system used in Japan provides clinical information regarding acute hospital patients. The present study was conducted to determine the association of oral bacterial numbers in individual patients treated at a single institution with length of hospital stay and medical costs using DPC data. A total of 2369 patients referred by the medical department to the dental department at Hiroshima University Hospital were divided into the low (n = 2060) and high (n = 309) oral bacterial number groups. Length of hospital stay and medical costs were compared between the groups, as well as the associations of number of oral bacteria with Charlson comorbidity index (CCI)-related diseases in regard to mortality and disease severity. There was no significant difference in hospital stay length between the low (24.3 ± 24.2 days) and high (22.8 ± 20.1 days) oral bacterial number groups. On the other hand, the daily hospital medical cost in the high group was significantly greater (US$1456.2 ± 1505.7 vs. US$1185.7 ± 1128.6, P < 0.001). Additionally, there was no significant difference in CCI score between the groups, whereas the daily hospital medical costs for patients in the high group treated for cardiovascular disease or malignant tumors were greater than in the low number group (P < 0.05). Multivariate regression analysis was also performed, which showed that oral bacterial number, age, gender, BMI, cardiovascular disease, diabetes, malignant tumor, and hospital stay length were independently associated with daily hospitalization costs. Monitoring and oral care treatment to lower the number of oral bacteria in patients affected by cardiovascular disease or cancer may contribute to reduce hospitalization costs.
1D-CNN-based audio tampering detection using ENF signals
Authors: Zhao Haifeng , Ye Yanming , Shen Xingfa , Liu Lili
Published: May 2024

The extensive adoption of digital audio recording has revolutionized its application in digital forensics, particularly in civil litigation and criminal prosecution. Electric network frequency (ENF) has emerged as a reliable technique in the field of audio forensics. However, the absence of comprehensive ENF reference datasets limits current ENF-based methods. To address this, this study introduces ATD, a blind audio forensics framework based on a one-dimensional convolutional neural network (1D-CNN) model. ATD can identify phase mutations and waveform discontinuities within the tampered ENF signal, without relying on an ENF reference database. To enhance feature extraction, the framework incorporates characteristics of the fundamental harmonics of ENF signals. In addition, a denoising method termed ENF noise reduction (ENR) based on the variational mode decomposition (VMD) and robust filtering algorithm (RFA) is proposed to reduce the impact of external noise on embedded electric network frequency signals. This study investigates three distinct types of audio tampering—deletion, insertion, and replacement—culminating in the design of binary-class tampering detection scenarios and four-class tampering detection scenarios tailored to these tampering types. ATD achieves a tampering detection accuracy of over 93% in the four-class scenario and exceeds 96% in the binary-class scenario. The effectiveness, efficiency, adaptability, and robustness of ATD in the two and four classification scenarios have been confirmed by extensive experiments.
Short-term meditation training alters brain activity and sympathetic responses at rest, but not during meditation
Authors: Rusinova Anna , Volodina Maria , Ossadtchi Alexei
Published: May 2024

Although more people are engaging in meditation practices that require specialized training, few studies address the issues associated with nervous activity pattern changes brought about by such training. For beginners, it remains unclear how much practice is needed before objective physiological changes can be detected, whether or not they are similar across the novices and what are the optimal strategies to track these changes. To clarify these questions we recruited individuals with no prior meditation experience. The experimental group underwent an eight-week Taoist meditation course administered by a professional, while the control group listened to audiobooks. Both groups participated in audio-guided, 34-min long meditation sessions before and after the 8-week long intervention. Their EEG, photoplethysmogram, respiration, and skin conductance were recorded during the mediation and resting state periods. Compared to the control group, the experimental group exhibited band-specific topically organized changes of the resting state brain activity and heart rate variability associated with sympathetic system activation. Importantly, no significant changes were found during the meditation process prior and post the 8-week training in either of the groups. The absence of notable changes in CNS and ANS activity indicators during meditation sessions, for both the experimental and control groups, casts doubt on the effectiveness of wearable biofeedback devices in meditation practice. This finding redirects focus to the importance of monitoring resting state activity to evaluate progress in beginner meditators. Also, 16 h of training is not enough for forming individual objectively different strategies manifested during the meditation sessions. Our results contributed to the development of tools to objectively monitor the progress in novice meditators and the choice of the relevant monitoring strategies. According to our findings, in order to track early changes brought about by the meditation practice it is preferable to monitor brain activity outside the actual meditation sessions.
Chirality-assisted enhancement of tripartite entanglement in waveguide QED
Authors: Patrick Logan , Arshad Umar , Guo Dingyu , Mirza Imran
Published: May 2024

We study the generation and control of genuine tripartite entanglement among quantum emitters (QEs) that are side-coupled to one-dimensional spin-momentum locked (or chiral) waveguides. By applying the machinery of Fock state master equations along with the recently proposed concurrence fill measure of tripartite entanglement [S. Xie and J. H. Eberly, Phys. Rev. Lett. 127, 040403 (2021)], we analyze how three-photon Gaussian wavepackets can distribute entanglement among two and three QEs. We show that with a five times larger waveguide decay rate in the right direction as compared to the left direction, the maximum value of tripartite entanglement can be elevated by $$35\%$$

35
%

as compared to the symmetric scenario where both left, and right direction decay rates are equal. Additionally, chirality can maintain the tripartite entanglement for longer than the corresponding symmetric decay rate. Finally, we study the influence of detunings and spontaneous emission on the resulting entanglement. We envision quantum networking and long-distance quantum communication as two main areas of applications of this work.
APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes
Authors: Charneau Sébastien , de Oliveira Lucas Silva , Zenonos Zenon , Hopp Christine S. , Bastos Izabela M. D. , Loew Damarys , Lombard Bérangère , Pandolfo Silveira Ariane , de Carvalho Nardeli Basílio Lobo Giovanna , Bao Sônia Nair , Grellier Philippe , Rayner Julian C.
Published: May 2024

The interaction of Plasmodium falciparum—infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or “knobs” on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer’s clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
Influence of stocking density on the growth, immune and physiological responses, and cultivation environment of white-leg shrimp (Litopenaeus vannamei) in biofloc systems
Authors: Said Mohamed Mohamed , Abo-Al-Ela Haitham G. , El-Barbary Yasmine A. , Ahmed Omaima M. , Dighiesh Hagar Sedeek
Published: May 2024

Biofloc (BF) stands out as a promising system for sustainable shrimp farming. Optimizing various culture conditions, such as stocking density, carbohydrate source, and feeding management, is crucial for the widespread adoption of the BF system. This study compares the growth performance of white-leg shrimp (Litopenaeus vannamei) in culture ponds at low density (LD) with 50 organisms/m2 and high density (HD) with 200 organisms/m2. Post-larvae of white-leg shrimp were stocked for 16 weeks in both LD and HD groups. The LD group exhibited a superior survival rate, growth rate, and feed consumption compared to the HD group. The BF from the LD system recorded a significantly higher protein content (16.63 ± 0.21%) than the HD group (15.21 ± 0.34%). Heterotrophic bacterial counts in water did not significantly differ with stocking density. However, Vibrio count in water samples was higher in the HD group (3.59 ± 0.35 log CFU/mL) compared to the LD group (2.45 ± 0.43 log CFU/mL). The whole shrimp body analysis revealed significantly higher protein and lipid content in the LD group. In contrast, the total aerobic bacterial count in shrimp from the HD group was high, with the identification of Salmonella enterica ssp. arizonae. Additionally, Vibrio counts in shrimp samples were significantly higher in the HD group (4.63 ± 0.32 log CFU/g) compared to the LD group (3.57 ± 0.22 log CFU/g). The expression levels of immune-associated genes, including prophenoloxidase, transglutaminase, penaiedin 3, superoxide dismutase, lysozyme, serine proteinase, and the growth-related gene ras-related protein (rap-2a), were significantly enhanced in the LD group. Conversely, stress-related gene expression increased significantly in the HD group. Hepatopancreases amylase, lipase, and protease were higher in the LD group, while trypsin activity did not differ significantly. Antioxidant enzyme activity (catalase, glutathione, glutathione peroxidase, and superoxide dismutase) significantly increased in the LD group. The histological structure of hepatopancreas, musculature, and female gonads remained similar in both densities. However, negative effects were observed in the gills' histology of the HD group. These results suggest that increasing stocking density is associated with significantly negative biological, microbial, and physiological effects on white-leg shrimp under the BF system.
Secretory IgA and course of COVID-19 in patients receiving a bacteria-based immunostimulant agent in addition to background therapy
Authors: Kostinov Mikhail , Svitich Oksana , Chuchalin Alexander , Osiptsov Valery , Khromova Ekaterina , Abramova Natalya , Tatevosov Vitaly , Vlasenko Anna , Gainitdinova Vilia , Pakhomov Dmitrij , Mashilov Kirill , Ospelnikova Tatyana , Mihajlova Natalya , Polishchuk Valentina , Kurbatova Ekaterina , Kostinova Aristitsa
Published: May 2024

Mucosal immunity plays a major role not only in the prevention but probably also in the outcomes of COVID-19. An enhanced production of secretory immunoglobulin A (sIgA) might contribute to the activation of the immune response mechanisms. To assess the levels of sIgA produced by epithelial cells in the nasal and pharyngeal mucosa and those measured in salivary gland secretions and to study the course of COVID-19 following the combined scheme of intranasal and subcutaneous administration of a bacteria-based immunostimulant agent. This study included 69 patients, aged between 18 and 60, who had moderate COVID-19 infection. They were divided into two groups: Group 1 (control group) included 39 patients who received only background therapy, and Group 2 was made up of 30 patients who received background therapy in combination with the Immunovac VP4 vaccine, a bacteria-based immunostimulant agent, which was given for 11 days starting from the day of admission to hospital. The levels of sIgA were measured by ELISA in epithelial, nasal and pharyngeal swabs, and salivary gland secretions at baseline and on days 14 and 30. The combined scheme of intranasal and subcutaneous administration of the Immunovac VP4 vaccine in the complex therapy of patients with COVID-19 is accompanied by increased synthesis of sIgA in nasal and pharyngeal swabs, more intense decrease in the level of C-reactive protein (CRP) and reduction in the duration of fever and length of hospitalization compared to the control group. Prescribing a immunostimulant agent containing bacterial ligands in complex therapy for COVID-19 patients helps to enhance mucosal immunity and improves the course of the disease.
Warming and shifts in litter quality drive multiple responses in freshwater detritivore communities
Authors: Benavides-Gordillo Sandra , González Angélica L. , Kersch-Becker Mônica F. , Moretti Marcelo S. , Moi Dieison A. , Aidar Marcos P. M. , Romero Gustavo Q.
Published: May 2024

Aquatic detritivores are highly sensitive to changes in temperature and leaf litter quality caused by increases in atmospheric CO2. While impacts on detritivores are evident at the organismal and population level, the mechanisms shaping ecological communities remain unclear. Here, we conducted field and laboratory experiments to examine the interactive effects of changes in leaf litter quality, due to increasing atmospheric CO2, and warming, on detritivore survival (at both organismal and community levels) and detritus consumption rates. Detritivore community consisted of the collector-gathering Polypedilum (Chironomidae), the scraper and facultative filtering-collector Atalophlebiinae (Leptophlebiidae), and Calamoceratidae (Trichoptera), a typical shredder. Our findings reveal intricate responses across taxonomic levels. At the organismal level, poor-quality leaf litter decreased survivorship of Polypedilum and Atalophlebiinae. We observed taxon-specific responses to warming, with varying effects on growth and consumption rates. Notably, species interactions (competition, facilitation) might have mediated detritivore responses to climate stressors, influencing community dynamics. While poor-quality leaf litter and warming independently affected detritivore larvae abundance of Atalophebiinae and Calamoceratidae, their combined effects altered detritus consumption and emergence of adults of Atalophlebiinae. Furthermore, warming influenced species abundances differently, likely exacerbating intraspecific competition in some taxa while accelerating development in others. Our study underscores the importance of considering complex ecological interactions in predicting the impact of climate change on freshwater ecosystem functioning. Understanding these emergent properties contributes to a better understanding of how detritivore communities may respond to future environmental conditions, providing valuable insights for ecosystem management and conservation efforts.
Technical and financial feasibility of a chemicals recovery and energy and water production from a dairy wastewater treatment plant
Authors: Basem Ali , Jasim Dheyaa J. , Ghodratallah Pooya , AbdulAmeer S. , Mahmood Ahmed Mohammed , Khudhayer Wisam J. , Dabis Hasan Khalid , Marefati Mohammad
Published: May 2024

Due to the high volume of wastewater produced from dairy factories, it is necessary to integrate a water recovery process with the treatment plant. Today, bipolar membrane electrodialysis units (BMEUs) are increasingly developed for wastewater treatment and reutilizing. This article aims to develop and evaluate (technical and cost analyses) a combined BMEU/batch reverse osmosis unit (BROU) process for the recovery of chemicals and water from the dairy wastewater plant. The combined BROU/BMEU process is able to simultaneously produce water and strong base-acid, and reduce power consumption due to the injection of concentrated feed flow into the BMEU. A comprehensive comparative analysis on the performances of two combined and stand-alone BMEU configurations are developed. The proposed combined technology for dairy factory wastewater treatment is designed on a new structure and configuration that can address superior cost analysis compared to similar technologies. Further, the optimal values of permeate flux and current density as two vital and influencing parameters on the performance of the studied dairy wastewater treatment process were calculated and discussed. From the outcomes, the total cost of production in the combined configuration has been reduced by approximately 26% compared to the stand-alone configuration. Increasing the feed concentration rate using the batch reverse osmosis process for the dairy wastewater treatment process can be an ideal solution from an economic point of view. Moreover, point (current density, feed concentration rate, total unit cost) = $$\left(328.9, 7, 14.37\right)$$

328.9
,
7
,
14.37

can be considered as an optimal point for the economic performance of the studied wastewater treatment process.
Relationship between ion currents and membrane capacitance in canine ventricular myocytes
Authors: Horváth Balázs , Kovács Zsigmond , Dienes Csaba , Barta Zalán , Óvári József , Szentandrássy Norbert , Magyar János , Bányász Tamás , Nánási Péter P.
Published: May 2024

Current density, the membrane current value divided by membrane capacitance (Cm), is widely used in cellular electrophysiology. Comparing current densities obtained in different cell populations assume that Cm and ion current magnitudes are linearly related, however data is scarce about this in cardiomyocytes. Therefore, we statistically analyzed the distributions, and the relationship between parameters of canine cardiac ion currents and Cm, and tested if dividing original parameters with Cm had any effect. Under conventional voltage clamp conditions, correlations were high for IK1, moderate for IKr and ICa,L, while negligible for IKs. Correlation between Ito1 peak amplitude and Cm was negligible when analyzing all cells together, however, the analysis showed high correlations when cells of subepicardial, subendocardial or midmyocardial origin were analyzed separately. In action potential voltage clamp experiments IK1, IKr and ICa,L parameters showed high correlations with Cm. For INCX, INa,late and IKs there were low-to-moderate correlations between Cm and these current parameters. Dividing the original current parameters with Cm reduced both the coefficient of variation, and the deviation from normal distribution. The level of correlation between ion currents and Cm varies depending on the ion current studied. This must be considered when evaluating ion current densities in cardiac cells.
Clear effects on root system architecture of winter wheat cultivars (Triticum aestivum L.) from cultivation environment and practices
Authors: Cope Jonathan E. , Berckx Fede , Lundmark Johan , Henriksson Tina , Karlsson Ida , Weih Martin
Published: May 2024

Roots play a pivotal role in the adaption of a plant to its environment, with different root traits adapting the plant to different stresses. The environment affects the Root System Architecture (RSA), but the genetic factors determine to what extent, and whether stress brought about by extreme environmental conditions is detrimental to a specific crop. This study aimed to identify differences in winter wheat RSA caused by cultivation region and practice, in the form of preceding crop (precrop), and to identify if modern cultivars used in Sweden differ in their reaction to these environments. This was undertaken using high-throughput phenotyping to assess the RSA. Clear differences in the RSA were observed between the Swedish cultivation regions, precrop treatments, and interaction of these conditions with each other and the genetics. Julius showed a large difference between cultivars, with 9.3–17.1% fewer and 12–20% narrower seminal roots. Standardized yield decreased when grown after wheat, 23% less compared to oilseed rape (OSR), and when grown in the Southern region, 14% less than the Central region. Additionally, correlations were shown between the root number, angle, and grain yield, with different root types being correlated depending on the precrop. Cultivars on the Swedish market show differences that can be adapted to the region-precrop combinations. The differences in precrop effect on RSA between regions show global implications and a need for further assessment. Correlations between RSA and yield, based on root-type × precrop, indicate different needs of the RSA depending on the management practices and show the potential for improving crop yield through targeting genotypic and environmental conditions in a holistic manner. Understanding this RSA variance, and the mechanisms of conditional response, will allow targeted cultivar breeding for specific environments, increasing plant health and food security.
Mathematical model of dry stack structural elements with geometric imperfections under a cyclic bending moment
Authors: Smolana Mateusz , Gromysz Krzysztof
Published: May 2024

Dry stack structural elements are characterized by nonlinear stiffness that arises from geometric imperfections of their components and the absence of any bonding between them. Moreover, such elements dissipate energy under cyclic loading because of their internal structure. The authors considered dry stack structural elements loaded with a bending moment to propose a relatively simple mathematical model of dry stacks composed of only three elements. The model consists of a linear spring, a nonlinear spring, and a spring with hysteresis in series. In this model, the first element describes the idealized properties of a dry stack element, while the second and third elements correspond to the influence of geometric imperfections and the behaviour of dry joints. Furthermore, the authors described a procedure for determining the parameters of the model based on test results. The proposed solution was verified via experimental studies of temporary support structures consisting of a stack of cuboid elements and a hydraulic jack typically used in the process of building rectification. This study showed that the proposed model adequately describes both the nonlinearity and the energy dissipation under a cyclic bending moment.
CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase
Authors: Wakabayashi Taiki , Oide Mao , Nakasako Masayoshi
Published: May 2024

Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis–Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.
A novel model incorporating quantitative contrast-enhanced ultrasound into PI-RADSv2-based nomogram detecting clinically significant prostate cancer
Authors: Huang Kaifeng , Luo Li , Hong Ruixia , Zhao Huai , Li Ying , Jiang Yaohuang , Feng Yujie , Fu Qihuan , Zhou Hang , Li Fang
Published: May 2024

The diagnostic accuracy of clinically significant prostate cancer (csPCa) of Prostate Imaging Reporting and Data System version 2 (PI-RADSv2) is limited by subjectivity in result interpretation and the false positive results from certain similar anatomic structures. We aimed to establish a new model combining quantitative contrast-enhanced ultrasound, PI-RADSv2, clinical parameters to optimize the PI-RADSv2-based model. The analysis was conducted based on a data set of 151 patients from 2019 to 2022, multiple regression analysis showed that prostate specific antigen density, age, PI-RADSv2, quantitative parameters (rush time, wash-out area under the curve) were independent predictors. Based on these predictors, we established a new predictive model, the AUCs of the model were 0.910 and 0.879 in training and validation cohort, which were higher than those of PI-RADSv2-based model (0.865 and 0.821 in training and validation cohort). Net Reclassification Index analysis indicated that the new predictive model improved the classification of patients. Decision curve analysis showed that in most risk probabilities, the new predictive model improved the clinical utility of PI-RADSv2-based model. Generally, this new predictive model showed that quantitative parameters from contrast enhanced ultrasound could help to improve the diagnostic performance of PI-RADSv2 based model in detecting csPCa.