bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractComputational 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

AbstractGrowing 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

AbstractEarly 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

AbstractMutually 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

AbstractThe 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

AbstractWe 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

AbstractOral 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

AbstractThe 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

AbstractAlthough 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

AbstractWe 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

AbstractThe 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

AbstractBiofloc (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.