bluuebunny/crossref_metadata_2025_split huggingface dataset:
A One Health framework for exploring zoonotic interactions demonstrated through a case study
Authors: Desvars-Larrive Amélie , Vogl Anna Elisabeth , Puspitarani Gavrila Amadea , Yang Liuhuaying , Joachim Anja , Käsbohrer Annemarie 
Published: July 2024

AbstractThe eco-epidemiology of zoonoses is often oversimplified to host-pathogen interactions while findings derived from global datasets are rarely directly transferable to smaller-scale contexts. Through a systematic literature search, we compiled a dataset of naturally occurring zoonotic interactions in Austria, spanning 1975–2022. We introduce the concept of zoonotic web to describe the complex relationships between zoonotic agents, their hosts, vectors, food, and environmental sources. The zoonotic web was explored through network analysis. After controlling for research effort, we demonstrate that, within the projected unipartite source-source network of zoonotic agent sharing, the most influential zoonotic sources are human, cattle, chicken, and some meat products. Analysis of the One Health 3-cliques (triangular sets of nodes representing human, animal, and environment) confirms the increased probability of zoonotic spillover at human-cattle and human-food interfaces. We characterise six communities of zoonotic agent sharing, which assembly patterns are likely driven by highly connected infectious agents in the zoonotic web, proximity to human, and anthropogenic activities. Additionally, we report a frequency of emerging zoonotic diseases in Austria of one every six years. Here, we present a flexible network-based approach that offers insights into zoonotic transmission chains, facilitating the development of locally-relevant One Health strategies against zoonoses.
Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape
Authors: Song Lele , Li Qinglan , Xia Lingbo , Sahay Arushi Eesha , Qiu Qi , Li Yuanyuan , Li Haitao , Sasaki Kotaro , Susztak Katalin , Wu Hao , Wan Liling 
Published: July 2024

AbstractHow disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL’s histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
Single-cell transcriptomics analysis of bullous pemphigoid unveils immune-stromal crosstalk in type 2 inflammatory disease
Authors: Liu Tingting , Wang Zhenzhen , Xue Xiaotong , Wang Zhe , Zhang Yuan , Mi Zihao , Zhao Qing , Sun Lele , Wang Chuan , Shi Peidian , Yu Gongqi , Wang Meng , Sun Yonghu , Xue Fuzhong , Liu Hong , Zhang Furen 
Published: July 2024

AbstractBullous pemphigoid (BP) is a type 2 inflammation- and immunity-driven skin disease, yet a comprehensive understanding of the immune landscape, particularly immune-stromal crosstalk in BP, remains elusive. Herein, using single-cell RNA sequencing (scRNA-seq) and in vitro functional analyzes, we pinpoint Th2 cells, dendritic cells (DCs), and fibroblasts as crucial cell populations. The IL13-IL13RA1 ligand–receptor pair is identified as the most significant mediator of immune-stromal crosstalk in BP. Notably, fibroblasts and DCs expressing IL13RA1 respond to IL13-secreting Th2 cells, thereby amplifying Th2 cell-mediated cascade responses, which occurs through the specific upregulation of PLA2G2A in fibroblasts and CCL17 in myeloid cells, creating a positive feedback loop integral to immune-stromal crosstalk. Furthermore, PLA2G2A and CCL17 contribute to an increased titer of pathogenic anti-BP180-NC16A autoantibodies in BP patients. Our work provides a comprehensive insight into BP pathogenesis and shows a mechanism governing immune-stromal interactions, providing potential avenues for future therapeutic research.
Engineered reversible inhibition of SpyCatcher reactivity enables rapid generation of bispecific antibodies
Authors: Hentrich Christian , Putyrski Mateusz , Hanuschka Hanh , Preis Waldemar , Kellmann Sarah-Jane , Wich Melissa , Cavada Manuel , Hanselka Sarah , Lelyveld Victor S. , Ylera Francisco 
Published: July 2024

AbstractThe precise regulation of protein function is essential in biological systems and a key goal in chemical biology and protein engineering. Here, we describe a straightforward method to engineer functional control into the isopeptide bond-forming SpyTag/SpyCatcher protein ligation system. First, we perform a cysteine scan of the structured region of SpyCatcher. Except for two known reactive and catalytic residues, none of these mutations abolish reactivity. In a second screening step, we modify the cysteines with disulfide bond-forming small molecules. Here we identify 8 positions at which modifications strongly inhibit reactivity. This inhibition can be reversed by reducing agents. We call such a reversibly inhibitable SpyCatcher “SpyLock”. Using “BiLockCatcher”, a genetic fusion of wild-type SpyCatcher and SpyLock, and SpyTagged antibody fragments, we generate bispecific antibodies in a single, scalable format, facilitating the screening of a large number of antibody combinations. We demonstrate this approach by screening anti-PD-1/anti-PD-L1 bispecific antibodies using a cellular reporter assay.
I/O-efficient iterative matrix inversion with photonic integrated circuits
Authors: Chen Minjia , Wang Yizhi , Yao Chunhui , Wonfor Adrian , Yang Shuai , Penty Richard , Cheng Qixiang 
Published: July 2024

AbstractPhotonic integrated circuits have been extensively explored for optical processing with the aim of breaking the speed and energy efficiency bottlenecks of digital electronics. However, the input/output (IO) bottleneck remains one of the key barriers. Here we report a photonic iterative processor (PIP) for matrix-inversion-intensive applications. The direct reuse of inputted data in the optical domain unlocks the potential to break the IO bottleneck. We demonstrate notable IO advantages with a lossless PIP for real-valued matrix inversion and integral-differential equation solving, as well as a coherent PIP with optical loops integrated on-chip, enabling complex-valued computation and a net inversion time of 1.2 ns. Furthermore, we estimate at least an order of magnitude enhancement in IO efficiency of a PIP over photonic single-pass processors and the state-of-the-art electronic processors for reservoir training tasks and multiple-input and multiple-output (MIMO) precoding tasks, indicating the huge potential of PIP technology in practical applications.
Legionella maintains host cell ubiquitin homeostasis by effectors with unique catalytic mechanisms
Authors: Fu Jiaqi , Li Siying , Guan Hongxin , Li Chuang , Zhao Yan-Bo , Chen Tao-Tao , Xian Wei , Zhang Zhengrui , Liu Yao , Guan Qingtian , Wang Jingting , Lu Qiuhua , Kang Lina , Zheng Si-Ru , Li Jinyu , Cao Shoujing , Das Chittaranjan , Liu Xiaoyun , Song Lei , Ouyang Songying , Luo Zhao-Qing 
Published: July 2024

AbstractThe intracellular bacterial pathogen Legionella pneumophila modulates host cell functions by secreting multiple effectors with diverse biochemical activities. In particular, effectors of the SidE family interfere with host protein ubiquitination in a process that involves production of phosphoribosyl ubiquitin (PR-Ub). Here, we show that effector LnaB converts PR-Ub into ADP-ribosylated ubiquitin, which is further processed to ADP-ribose and functional ubiquitin by the (ADP-ribosyl)hydrolase MavL, thus maintaining ubiquitin homeostasis in infected cells. Upon being activated by actin, LnaB also undergoes self-AMPylation on tyrosine residues. The activity of LnaB requires a motif consisting of Ser, His and Glu (SHxxxE) present in a large family of toxins from diverse bacterial pathogens. Thus, our study sheds light on the mechanisms by which a pathogen maintains ubiquitin homeostasis and identifies a family of enzymes capable of protein AMPylation.
Native mass spectrometry and structural studies reveal modulation of MsbA–nucleotide interactions by lipids
Authors: Zhang Tianqi , Lyu Jixing , Yang Bowei , Yun Sangho D. , Scott Elena , Zhao Minglei , Laganowsky Arthur 
Published: July 2024

AbstractThe ATP-binding cassette (ABC) transporter, MsbA, plays a pivotal role in lipopolysaccharide (LPS) biogenesis by facilitating the transport of the LPS precursor lipooligosaccharide (LOS) from the cytoplasmic to the periplasmic leaflet of the inner membrane. Despite multiple studies shedding light on MsbA, the role of lipids in modulating MsbA-nucleotide interactions remains poorly understood. Here we use native mass spectrometry (MS) to investigate and resolve nucleotide and lipid binding to MsbA, demonstrating that the transporter has a higher affinity for adenosine 5’-diphosphate (ADP). Moreover, native MS shows the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL) can tune the selectivity of MsbA for adenosine 5’-triphosphate (ATP) over ADP. Guided by these studies, four open, inward-facing structures of MsbA are determined that vary in their openness. We also report a 2.7 Å-resolution structure of MsbA in an open, outward-facing conformation that is not only bound to KDL at the exterior site, but with the nucleotide binding domains (NBDs) adopting a distinct nucleotide-free structure. The results obtained from this study offer valuable insight and snapshots of MsbA during the transport cycle.
DBScope as a versatile computational toolbox for the visualization and analysis of sensing data from deep brain stimulation
Authors: Oliveira Andreia M. , Carvalho Eduardo , Barros Beatriz , Soares Carolina , Ferreira-Pinto Manuel J. , Vaz Rui , Aguiar Paulo 
Published: July 2024

AbstractDifferent neurostimulators for deep brain stimulation (DBS) come already with the ability to chronically sense local field potentials during stimulation. This invaluable new data has the potential to increase our understanding of disease-related brain activity patterns, their temporal evolution, and their modulation in response to therapies. It also gives the opportunity to unveil new electrophysiological biomarkers and ultimately bring adaptive stimulation therapies closer to clinical practice. Unfortunately, there are still very limited options on how to visualize, analyze, and exploit the full potential of the sensing data from these new DBS neurostimulators. To answer this need, we developed a free open-source toolbox, named DBScope, that imports data from neurostimulation devices and can be operated in two ways: via user interface and programmatically, as a library of functions. In this way, it can be used by both clinicians during clinical sessions (for instance, to visually inspect data from the current or previous in-clinic visits), and by researchers in their research pipelines (e.g., for pre-processing, feature extraction and biomarker search). All in all, the DBScope toolbox is set to facilitate the clinical decision-making process and the identification of clinically relevant biomarkers. The toolbox is already being used in clinical and research environments, and it is freely available to download at GitHub (where it is also fully documented).
Sputtered thin film deposited laser induced graphene based novel micro-supercapacitor device for energy storage application
Authors: Sain Sourav , Chowdhury Suman , Maity Sayantan , Maity Gurupada , Roy Susanta Sinha 
Published: July 2024

AbstractPioneering flexible micro-supercapacitors, designed for exceptional energy and power density, transcend conventional storage limitations. Interdigitated electrodes (IDEs) based on laser-induced graphene (LIG), augmented with metal-oxide modifiers, harness synergies with layered graphene to achieve superior capacitance. This study presents a novel one-step process for sputtered plasma deposition of HfO2, resulting in enhanced supercapacitance performance. Introducing LIG-HfO2 micro-supercapacitor (MSC) devices with varied oxygen flow rates further boosts supercapacitance performance by introducing oxygen functional groups. FESEM investigations demonstrate uniform coating of HfO2 on LIG fibers through sputtering. Specific capacitance measurements reveal 6.4 mF/cm2 at 5 mV/s and 4.5 mF/cm2 at a current density of 0.04 mA/cm2. The LIG-HfO2 devices exhibit outstanding supercapacitor performance, boasting at least a fourfold increase over pristine LIG. Moreover, stability testing indicates a high retention rate of 97% over 5000 cycles, ensuring practical real-time applications.
Impact of bedaquiline regimen on the treatment success rates of multidrug-resistant tuberculosis patients in Egypt
Authors: Afifi Magda , Amin Wagdy , Helal Dina , Ashmawy Rasha , El-Maradny Yousra A. , Khalifa Noha , Ghazy Ramy Mohamed 
Published: July 2024

AbstractBedaquiline (BDQ), an innovative anti-tuberculous (TB) agent, has attracted attention for its potential effectiveness against drug-resistant TB. This study investigated the impact of BDQ-containing regimens on treatment success rates among multi-drug resistant tuberculosis (MDR-TB) patients in Egypt. We conducted a prospective cohort study that included all adult non-pregnant patients treated in MDR-TB centers in Egypt from April 1, 2020, to June 30, 2021, with follow-up extended until December 31, 2022. The study compared patients prescribed BDQ according to national protocols with those receiving conventional treatments for MDR-TB. Treatment success rates, mortality rates, and adverse events were analyzed using descriptive statistics, chi-square tests, logistic regression, and Kaplan–Meier survival curves. Adjustment for potential confounders was conducted using propensity score matching and Cox-hazard regressions. A total of 84 patients were included in this study. The median age of the study participants was 39 years; 22.6% were women, 57.1% were unemployed or housewives, and 1.2% had human immunodeficiency virus (HIV). Regarding the treatment regimen, 67.8% were exposed to BDQ-based treatment. Among the 55 patients (65.5%) with treatment success, a significantly higher success rate was observed in the BDQ group (73.7%) compared to the conventional group (48.1%), P = 0.042. Additionally, the incidence of skin discoloration was significantly higher in the BDQ group compared to the conventional group (38.6% versus 0.0%, P < 0.001). Despite the lower mortality incidence in the BDQ-group (14.0% versus 22.2% in the conventional group), the Kaplan–Meier survival analysis revealed no excess mortality associated with the BDQ-group, with a hazard ratio (HR) of 0.62 (95% CI 0.21–1.78, P = 0.372). Propensity score matching, while considering factors such as lesion site, diabetes mellitus, hepatitis C virus, and smoking, revealed a significant increase in the success rate associated with BDQ inclusion, with an HR of 6.79 (95% CI 1.8–25.8). In conclusion, BDQ is an effective and tolerable medication for treating MDR-TB, associated with lower mortality rates compared to conventional treatment.
Differential expression of “Candidatus Liberibacter solanacearum” genes and prophage loci in different life stages of potato psyllid
Authors: Saberi Esmaeil , Qureshi Jawwad A. , Brown Judith K. 
Published: July 2024

AbstractPsyllid species, including the potato psyllid (PoP) Bactericera cockerelli (Sulc) (Triozidae) serve as host and vector of “Candidatus Liberibacter spp.” (“Ca. Liberibacter”), which also infects diverse plant hosts, including citrus and tomato. Psyllid transmission of “Ca. Liberibacter” is circulative and propagative. The time of “Ca. Liberibacter” acquisition and therefore vector life stage most competent for bacterial transmission varies by pathosystems. Here, the potato psyllid-“Ca. Liberibacter solanacearum” (CLso) pathosystem was investigated to dissect CLso-prophage interactions in the tomato plant and PoP-psyllid host by real-time quantitative reverse transcriptase amplification of CLso genes/loci with predicted involvement in host infection and psyllid-CLso transmission. Genes/loci analyzed were associated with (1) CLso-adhesion, -invasion, -pathogenicity, and -motility, (2) prophage-adhesion and pathogenicity, and (3) CLso-lysogenic cycle. Relative gene expression was quantified by qRT-PCR amplification from total RNA isolated from CLso-infected 1st–2nd and 4th–5th nymphs and teneral adults and CLso-infected tomato plants in which CLso infection is thought to occur without SC1-SC2 replication. Gene/loci expression was host-dependent and varied with the psyllid developmental stage. Loci previously associated with repressor-anti-repressor regulation in the “Ca Liberibacter asiaticus”-prophage pathosystem, which maintains the lysogenic cycle in Asian citrus psyllid Diaphorina citri, were expressed in CLso-infected psyllids but not in CLso-infected tomato plants.
Real-time deep learning-based model predictive control of a 3-DOF biped robot leg
Authors: El-Hussieny Haitham 
Published: July 2024

AbstractOur research utilized deep learning to enhance the control of a 3 Degrees of Freedom biped robot leg. We created a dynamic model based on a detailed joint angles and actuator torques dataset. This model was then integrated into a Model Predictive Control (MPC) framework, allowing for precise trajectory tracking without the need for traditional analytical dynamic models. By incorporating specific constraints within the MPC, we met operational and safety standards. The experimental results demonstrate the effectiveness of deep learning models in improving robotic control, leading to precise trajectory tracking and suggesting potential for further integration of deep learning into robotic system control. This approach not only outperforms traditional control methods in accuracy and efficiency but also opens the way for new research in robotics, highlighting the potential of utilizing deep learning models in predictive control techniques.
Magnetic yolk-shell structured periodic mesoporous organosilica supported palladium as a powerful and highly recoverable nanocatalyst for the reduction of nitrobenzenes
Authors: Norouzi Meysam , Elhamifar Dawood , Kargar Shiva 
Published: July 2024

AbstractA novel palladium-loaded yolk-shell structured nanomaterial with magnetite core and phenylene-based periodic mesoporous organosilica (PMO) shell (Fe3O4@YS-Ph-PMO/Pd) nanocatalyst was synthesized for the reduction of nitrobenzenes. The Fe3O4@YS-Ph-PMO/Pd was prepared through cetyltrimethylammonium bromide (CTAB) directed condensation of 1,4-bis(triethoxysilyl)benzene (BTEB) around Fe3O4@silica nanoparticles followed by treatment with palladium acetate. This nanocatalyst was characterized by using Fourier transform infrared (FT-IR) spectroscopy, thermal gravimetric analysis (TGA), low-angle and wide-angle powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and vibrating sample magnetometer (VSM) analyses. These analyses showed a magnetic nanomaterial with high chemical and thermal stability for the designed composite. The Fe3O4@YS-Ph-PMO/Pd nanocomposite was employed as a powerful and highly recoverable catalyst in the green reduction of nitroarenes in H2O at room temperature. A variety of nitroarene derivatives were applied as substrate in the presence of 0.9 mol% of Fe3O4@YS-Ph-PMO/Pd catalyst. All nitroarenes were selectively converted to their corresponding amines with high to excellent yields (92–96%) within short reaction times (10–18 min). This catalyst was recovered and reused at least 11 times without significant decrease in efficiency and stability.
A new DES-mediated synthesis of Henna-based benzopyranophenazines and benzoxanthenetriones
Authors: Monem Arezo , Habibi Davood , Goudarzi Hadis 
Published: July 2024

AbstractMTPPBr/THFTCA-DES was prepared as a new deep eutectic solvent (DES) from a mixture (molar ratio 7:3) of methyltriphenyl-phosphonium bromide (MTPPBr) and tetrahydrofuran-2,3,4,5-tetra-carboxylic acid (THFTCA), and characterized with various spectroscopic techniques, densitometer, and eutectic point. Then, it was used as a new and powerful catalyst for the synthesis of two sets of biologically important compounds, namely the Henna-based benzopyranophenazines and benzoxan-thenetriones. Solvent-free conditions, short reaction time, high efficiency, and easy recycling and separation of the DES catalyst are among the most important features of the presented method. Also, there is a nice consistency between the proposed structure of the DES compound, the integration values of the 1H NMR peaks, and the ratio of MTPPBr to THFTCA obtained from the eutectic point phase diagram. In addition, the reduction of peak splitting patterns in DES compared to the two primary materials can be good evidence of the formation of hydrogen bonds between the two components.
Deep learning application of vertebral compression fracture detection using mask R-CNN
Authors: Paik Seungyoon , Park Jiwon , Hong Jae Young , Han Sung Won 
Published: July 2024

AbstractVertebral compression fractures (VCFs) of the thoracolumbar spine are commonly caused by osteoporosis or result from traumatic events. Early diagnosis of vertebral compression fractures can prevent further damage to patients. When assessing these fractures, plain radiographs are used as the primary diagnostic modality. In this study, we developed a deep learning based fracture detection model that could be used as a tool for primary care in the orthopedic department. We constructed a VCF dataset using 487 lateral radiographs, which included 598 fractures in the L1-T11 vertebra. For detecting VCFs, Mask R-CNN model was trained and optimized, and was compared to three other popular models on instance segmentation, Cascade Mask R-CNN, YOLOACT, and YOLOv5. With Mask R-CNN we achieved highest mean average precision score of 0.58, and were able to locate each fracture pixel-wise. In addition, the model showed high overall sensitivity, specificity, and accuracy, indicating that it detected fractures accurately and without misdiagnosis. Our model can be a potential tool for detecting VCFs from a simple radiograph and assisting doctors in making appropriate decisions in initial diagnosis.