bluuebunny/crossref_metadata_2025 huggingface dataset:
Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus
Authors: Buenestado-Serrano Sergio , Martínez-Lirola Miguel , Herranz-Martín Marta , Esteban Jaime , Broncano-Lavado Antonio , Molero-Salinas Andrea , Sanz-Pérez Amadeo , Blázquez Jesús , Ruedas-López Alba , Toro Carlos , López-Roa Paula , Domingo Diego , Zamarrón Ester , Ruiz Serrano María Jesús , Muñoz Patricia , Pérez-Lago Laura , García de Viedma Darío
Published: March 2024

Mycobacterium abscessus is an opportunistic, extensively drug-resistant non-tuberculous mycobacterium. Few genomic studies consider its diversity in persistent infections. Our aim was to characterize microevolution/reinfection events in persistent infections. Fifty-three sequential isolates from 14 patients were sequenced to determine SNV-based distances, assign resistance mutations and characterize plasmids. Genomic analysis revealed 12 persistent cases (0-13 differential SNVs), one reinfection (15,956 SNVs) and one very complex case (23 sequential isolates over 192 months), in which a first period of persistence (58 months) involving the same genotype 1 was followed by identification of a genotype 2 (76 SNVs) in 6 additional alternating isolates; additionally, ten transient genotypes (88-243 SNVs) were found. A macrolide resistance mutation was identified from the second isolate. Despite high diversity, the genotypes shared a common phylogenetic ancestor and some coexisted in the same specimens. Genomic analysis is required to access the true intra-patient complexity behind persistent infections involving M. abscessus.
Catalytic polymer self-cleavage for CO2 generation before combustion empowers materials with fire safety
Authors: Luo Wei , Chen Ming-Jun , Wang Ting , Feng Jin-Feng , Fu Zhi-Cheng , Deng Jin-Ni , Yan Yuan-Wei , Wang Yu-Zhong , Zhao Hai-Bo
Published: March 2024

Polymeric materials, rich in carbon, hydrogen, and oxygen elements, present substantial fire hazards to both human life and property due to their intrinsic flammability. Overcoming this challenge in the absence of any flame-retardant elements is a daunting task. Herein, we introduce an innovative strategy employing catalytic polymer auto-pyrolysis before combustion to proactively release CO2, akin to possessing responsive CO2 fire extinguishing mechanisms. We demonstrate that potassium salts with strong nucleophilicity (such as potassium formate/malate) can transform conventional polyurethane foam into materials with fire safety through rearrangement. This transformation results in the rapid generation of a substantial volume of CO2, occurring before the onset of intense decomposition, effectively extinguishing fires. The inclusion of just 1.05 wt% potassium formate can significantly raise the limiting oxygen index of polyurethane foam to 26.5%, increase the time to ignition by 927%, and tremendously reduce smoke toxicity by 95%. The successful application of various potassium salts, combined with a comprehensive examination of the underlying mechanisms, underscores the viability of this strategy. This pioneering catalytic approach paves the way for the efficient and eco-friendly development of polymeric materials with fire safety.
Mapping cell-to-tissue graphs across human placenta histology whole slide images using deep learning with HAPPY
Authors: Vanea Claudia , Džigurski Jelisaveta , Rukins Valentina , Dodi Omri , Siigur Siim , Salumäe Liis , Meir Karen , Parks W. Tony , Hochner-Celnikier Drorith , Fraser Abigail , Hochner Hagit , Laisk Triin , Ernst Linda M. , Lindgren Cecilia M. , Nellåker Christoffer
Published: March 2024

Accurate placenta pathology assessment is essential for managing maternal and newborn health, but the placenta’s heterogeneity and temporal variability pose challenges for histology analysis. To address this issue, we developed the ‘Histology Analysis Pipeline.PY’ (HAPPY), a deep learning hierarchical method for quantifying the variability of cells and micro-anatomical tissue structures across placenta histology whole slide images. HAPPY differs from patch-based features or segmentation approaches by following an interpretable biological hierarchy, representing cells and cellular communities within tissues at a single-cell resolution across whole slide images. We present a set of quantitative metrics from healthy term placentas as a baseline for future assessments of placenta health and we show how these metrics deviate in placentas with clinically significant placental infarction. HAPPY’s cell and tissue predictions closely replicate those from independent clinical experts and placental biology literature.
SpiDe-Sr: blind super-resolution network for precise cell segmentation and clustering in spatial proteomics imaging
Authors: Chen Rui , Xu Jiasu , Wang Boqian , Ding Yi , Abdulla Aynur , Li Yiyang , Jiang Lai , Ding Xianting
Published: March 2024

Spatial proteomics elucidates cellular biochemical changes with unprecedented topological level. Imaging mass cytometry (IMC) is a high-dimensional single-cell resolution platform for targeted spatial proteomics. However, the precision of subsequent clinical analysis is constrained by imaging noise and resolution. Here, we propose SpiDe-Sr, a super-resolution network embedded with a denoising module for IMC spatial resolution enhancement. SpiDe-Sr effectively resists noise and improves resolution by 4 times. We demonstrate SpiDe-Sr respectively with cells, mouse and human tissues, resulting 18.95%/27.27%/21.16% increase in peak signal-to-noise ratio and 15.95%/31.63%/15.52% increase in cell extraction accuracy. We further apply SpiDe-Sr to study the tumor microenvironment of a 20-patient clinical breast cancer cohort with 269,556 single cells, and discover the invasion of Gram-negative bacteria is positively correlated with carcinogenesis markers and negatively correlated with immunological markers. Additionally, SpiDe-Sr is also compatible with fluorescence microscopy imaging, suggesting SpiDe-Sr an alternative tool for microscopy image super-resolution.
Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA
Authors: van Soest Daan M. K. , Polderman Paulien E. , den Toom Wytze T. F. , Keijer Janneke P. , van Roosmalen Markus J. , Leyten Tim M. F. , Lehmann Johannes , Zwakenberg Susan , De Henau Sasha , van Boxtel Ruben , Burgering Boudewijn M. T. , Dansen Tobias B.
Published: March 2024

Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of chromosomal DNA mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondria can directly damage nuclear DNA is largely lacking. In this study, we investigated the effects of H2O2 released by mitochondria or produced at the nucleosomes using a titratable chemogenetic approach. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2. Nuclear H2O2 gives rise to DNA damage and mutations and a subsequent p53 dependent cell cycle arrest. Mitochondrial H2O2 release shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. We conclude that H2O2 released from mitochondria is unlikely to directly damage nuclear genomic DNA, limiting its contribution to oncogenic transformation and aging.
Pheromone-based communication influences the production of somatic extracellular vesicles in C. elegans
Authors: Szczepańska Agata , Olek Katarzyna , Kołodziejska Klaudia , Yu Jingfang , Ibrahim Abdulrahman Tudu , Adamkiewicz Laura , Schroeder Frank C. , Pokrzywa Wojciech , Turek Michał
Published: March 2024

Extracellular vesicles (EVs) are integral to numerous biological processes, yet it is unclear how environmental factors or interactions among individuals within a population affect EV-regulated systems. In Caenorhabditis elegans, the evolutionarily conserved large EVs, known as exophers, are part of a maternal somatic tissue resource management system. Consequently, the offspring of individuals exhibiting active exopher biogenesis (exophergenesis) develop faster. Our research focuses on unraveling the complex inter-tissue and social dynamics that govern exophergenesis. We found that ascr#10, the primary male pheromone, enhances exopher production in hermaphrodites, mediated by the G-protein-coupled receptor STR-173 in ASK sensory neurons. In contrast, pheromone produced by other hermaphrodites, ascr#3, diminishes exophergenesis within the population. This process is regulated via the neuropeptides FLP-8 and FLP-21, which originate from the URX and AQR/PQR/URX neurons, respectively. Our results reveal a regulatory network that controls the production of somatic EV by the nervous system in response to social signals.
Architecture and activation of human muscle phosphorylase kinase
Authors: Yang Xiaoke , Zhu Mingqi , Lu Xue , Wang Yuxin , Xiao Junyu
Published: March 2024

The study of phosphorylase kinase (PhK)-regulated glycogen metabolism has contributed to the fundamental understanding of protein phosphorylation; however, the molecular mechanism of PhK remains poorly understood. Here we present the high-resolution cryo-electron microscopy structures of human muscle PhK. The 1.3-megadalton PhK α4β4γ4δ4 hexadecamer consists of a tetramer of tetramer, wherein four αβγδ modules are connected by the central β4 scaffold. The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable enzyme activities. The α-subunit serves as a bridge between the β-subunit and the γδ subcomplex, and facilitates the γ-subunit to adopt an autoinhibited state. Ca2+-free calmodulin (δ-subunit) binds to the γ-subunit in a compact conformation. Upon binding of Ca2+, a conformational change occurs, allowing for the de-inhibition of the γ-subunit through a spring-loaded mechanism. We also reveal an ADP-binding pocket in the β-subunit, which plays a role in allosterically enhancing PhK activity. These results provide molecular insights of this important kinase complex.
Addressing the effects of gas adsorption on monolayers beyond charge population analysis: the case of WS2
Authors: Bianchi Michele Giovanni , Risplendi Francesca , Re Fiorentin Michele , Cicero Giancarlo
Published: March 2024

The optoelectronic properties of two-dimensional (2D) materials can be significantly influenced by charge transfer resulting from surface molecular adsorption. One noteworthy example is observed in WS2 monolayers, where the behavior undergoes an anomalous change when exposed to air, primarily due to the adsorption of oxygen molecules. While the acceptor nature of O2 is widely acknowledged as the underlying cause, the precise electron transfer mechanism remains in need of a comprehensive explanation at the atomistic level. Going beyond conventional charge population analysis, we develop an approach describing the process of molecular adsorption and surface charge transfer that relies on the formalism commonly adopted for charged defects in semiconductors. This method clearly identifies two key factors contributing to electron transfer upon O2 physisorption: the presence of sulphur vacancies and the intrinsic n-type nature of WS2. This approach provides an effective and general scheme to characterize the surface charge transfer in 2D materials exposed to a gas atmosphere.
Association between irritable bowel syndrome and Parkinson’s disease by Cohort study and Mendelian randomization analysis
Authors: Wang Zhi-yun , Ma Dong-rui , Li Meng-jie , Liang Yuan-yuan , Hu Zheng-wei , Li Shuang-jie , Zuo Chun-yan , Hao Chen-wei , Feng Yan-mei , Guo Meng-nan , Hao Xiao-yan , Guo Yuan-li , Ma Ke-ke , Guo Li-na , Zhang Chan , Xu Yu-ming , Mao Cheng-yuan , Shi Chang-he
Published: March 2024

This study aimed to investigate the association between irritable bowel syndrome (IBS) and Parkinson’s disease (PD) utilizing prospective cohort study and Mendelian randomization. The dataset contained a substantial cohort of 426,911 participants from the UK Biobank, discussing the association between IBS and PD with Cox proportional hazards models and case-control analysis while adjusting for covariates such as age, gender, ethnicity and education level. In univariate Cox regression model, the risk of PD was reduced in IBS patients (HR: 0.774, 95%CI: 0.625–0.956, P = 0.017), but the statistical significance diminished in the three models after adjusting for other variables. In a few subgroup analyses, IBS patients are less likely to develop into PD, and patients diagnosed with IBS after 2000 also had a lower risk (HR: 0.633, 95%CI: 0.403–0.994, P = 0.047) of subsequently developing PD. In addition, we matched five healthy control participants based on gender and age at the end of the study for each IBS patient diagnosed during the follow-up period, and logistic regression results (OR:1.239, 95%CI: 0.896–1.680, P = 0.181) showed that IBS was not associated with the risk of PD. Mendelian randomization did not find significant evidence of the causal relationship between IBS and Parkinson’s disease (OR: 0.801, 95%CI: 0.570–1.278, P = 0.204). Overall, we suggest that IBS status is not associated with the risk of developing PD, and that these findings provide valuable insights into the clinical management and resource allocation of patients with IBS.
Ion-induced field screening as a dominant factor in perovskite solar cell operational stability
Authors: Thiesbrummel Jarla , Shah Sahil , Gutierrez-Partida Emilio , Zu Fengshuo , Peña-Camargo Francisco , Zeiske Stefan , Diekmann Jonas , Ye Fangyuan , Peters Karol P. , Brinkmann Kai O. , Caprioglio Pietro , Dasgupta Akash , Seo Seongrok , Adeleye Fatai A. , Warby Jonathan , Jeangros Quentin , Lang Felix , Zhang Shuo , Albrecht Steve , Riedl Thomas , Armin Ardalan , Neher Dieter , Koch Norbert , Wu Yongzhen , Le Corre Vincent M. , Snaith Henry , Stolterfoht Martin
Published: March 2024

The presence of mobile ions in metal halide perovskites has been shown to adversely affect the intrinsic stability of perovskite solar cells (PSCs). However, the actual contribution of mobile ions to the total degradation loss compared with other factors such as trap-assisted recombination remains poorly understood. Here we reveal that mobile ion-induced internal field screening is the dominant factor in the degradation of PSCs under operational conditions. The increased field screening leads to a decrease in the steady-state efficiency, often owing to a large reduction in the current density. Instead, the efficiency at high scan speeds (>1,000 V s−1), where the ions are immobilized, is much less affected. We also show that the bulk and interface quality do not degrade upon ageing, yet the open-circuit voltage decreases owing to an increase in the mobile ion density. This work reveals the importance of ionic losses for intrinsic PSC degradation before chemical or extrinsic mechanical effects manifest.
Crimean–Congo haemorrhagic fever virus uses LDLR to bind and enter host cells
Authors: Monteil Vanessa M. , Wright Shane C. , Dyczynski Matheus , Kellner Max J. , Appelberg Sofia , Platzer Sebastian W. , Ibrahim Ahmed , Kwon Hyesoo , Pittarokoilis Ioannis , Mirandola Mattia , Michlits Georg , Devignot Stephanie , Elder Elizabeth , Abdurahman Samir , Bereczky Sándor , Bagci Binnur , Youhanna Sonia , Aastrup Teodor , Lauschke Volker M. , Salata Cristiano , Elaldi Nazif , Weber Friedemann , Monserrat Nuria , Hawman David W. , Feldmann Heinz , Horn Moritz , Penninger Josef M. , Mirazimi Ali
Published: March 2024

Climate change and population densities accelerated transmission of highly pathogenic viruses to humans, including the Crimean–Congo haemorrhagic fever virus (CCHFV). Here we report that the Low Density Lipoprotein Receptor (LDLR) is a critical receptor for CCHFV cell entry, playing a vital role in CCHFV infection in cell culture and blood vessel organoids. The interaction between CCHFV and LDLR is highly specific, with other members of the LDLR protein family failing to bind to or neutralize the virus. Biosensor experiments demonstrate that LDLR specifically binds the surface glycoproteins of CCHFV. Importantly, mice lacking LDLR exhibit a delay in CCHFV-induced disease. Furthermore, we identified the presence of Apolipoprotein E (ApoE) on CCHFV particles. Our findings highlight the essential role of LDLR in CCHFV infection, irrespective of ApoE presence, when the virus is produced in tick cells. This discovery holds profound implications for the development of future therapies against CCHFV.
Diving into the proteomic atlas of SARS-CoV-2 infected cells
Authors: Carregari Victor C. , Reis-de-Oliveira Guilherme , Crunfli Fernanda , Smith Bradley J. , de Souza Gabriela Fabiano , Muraro Stéfanie Primon , Saia-Cereda Veronica M. , Vendramini Pedro H. , Baldasso Paulo A. , Silva-Costa Lícia C. , Zuccoli Giuliana S. , Brandão-Teles Caroline , Antunes André , Valença Aline F. , Davanzo Gustavo G. , Virgillio-da-Silva João Victor , dos Reis Araújo Thiago , Guimarães Raphael Campos , Chaim Felipe David Mendonça , Chaim Elinton Adami , Kawagosi Onodera Carolina Mie , Ludwig Raissa Guimarães , Saccon Tatiana Dandolini , Damásio André R. L. , Leiria Luiz Osório S. , Vinolo Marco Aurélio R. , Farias Alessandro S. , Moraes-Vieira Pedro M. , Mori Marcelo A. , Módena José Luiz P. , Martins-de-Souza Daniel
Published: March 2024

The COVID-19 pandemic was initiated by the rapid spread of a SARS-CoV-2 strain. Though mainly classified as a respiratory disease, SARS-CoV-2 infects multiple tissues throughout the human body, leading to a wide range of symptoms in patients. To better understand how SARS-CoV-2 affects the proteome from cells with different ontologies, this work generated an infectome atlas of 9 cell models, including cells from brain, blood, digestive system, and adipocyte tissue. Our data shows that SARS-CoV-2 infection mainly trigger dysregulations on proteins related to cellular structure and energy metabolism. Despite these pivotal processes, heterogeneity of infection was also observed, highlighting many proteins and pathways uniquely dysregulated in one cell type or ontological group. These data have been made searchable online via a tool that will permit future submissions of proteomic data (https://reisdeoliveira.shinyapps.io/Infectome_App/) to enrich and expand this knowledgebase.
Overcoming radioresistance of breast cancer cells with MAP4K4 inhibitors
Authors: Kwon Yun-Suk , Lee Min-Gu , Kim Nam-Yi , Nam Gi Suk , Nam Kyung-Soo , Jang Hyunsoo , Kim Soyoung
Published: March 2024

Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) has recently emerged as a promising therapeutic target in cancer. In this study, we explored the biological function of MAP4K4 in radioresistant breast cancer cells using two MAP4K4 inhibitors, namely PF06260933 and GNE-495. Radioresistant SR and MR cells were established by exposing SK-BR-3 and MCF-7 breast cancer cells to 48–70 Gy of radiation delivered at 4–5 Gy twice a week over 10 months. Surprisingly, although radioresistant cells were derived from two different subtypes of breast cancer cell lines, MAP4K4 was significantly elevated regardless of subtype. Inhibition of MAP4K4 with PF06260933 or GNE-495 selectively targeted radioresistant cells and improved the response to irradiation. Furthermore, MAP4K4 inhibitors induced apoptosis through the accumulation of DNA damage by inhibiting DNA repair systems in radioresistant cells. Notably, Inhibition of MAP4K4 suppressed the expressions of ACSL4, suggesting that MAP4K4 functioned as an upstream effector of ACSL4. This study is the first to report that MAP4K4 plays a crucial role in mediating the radioresistance of breast cancer by acting upstream of ACSL4 to enhance DNA damage response and inhibit apoptosis. We hope that our findings provide a basis for the development of new drugs targeting MAP4K4 to overcome radioresistance.
Cyclosporine-induced kidney damage was halted by sitagliptin and hesperidin via increasing Nrf2 and suppressing TNF-α, NF-κB, and Bax
Authors: Abd-Eldayem Ahmed M. , Makram Sohayla Mahmoud , Messiha Basim Anwar Shehata , Abd-Elhafeez Hanan H. , Abdel-Reheim Mustafa Ahmed
Published: March 2024

Cyclosporine A (CsA) is employed for organ transplantation and autoimmune disorders. Nephrotoxicity is a serious side effect that hampers the therapeutic use of CsA. Hesperidin and sitagliptin were investigated for their antioxidant, anti-inflammatory, and tissue-protective properties. We aimed to investigate and compare the possible nephroprotective effects of hesperidin and sitagliptin. Male Wistar rats were utilized for induction of CsA nephrotoxicity (20 mg/kg/day, intraperitoneally for 7 days). Animals were treated with sitagliptin (10 mg/kg/day, orally for 14 days) or hesperidin (200 mg/kg/day, orally for 14 days). Blood urea, serum creatinine, albumin, cystatin-C (CYS-C), myeloperoxidase (MPO), and glucose were measured. The renal malondialdehyde (MDA), glutathione (GSH), catalase, and SOD were estimated. Renal TNF-α protein expression was evaluated. Histopathological examination and immunostaining study of Bax, Nrf-2, and NF-κB were performed. Sitagliptin or hesperidin attenuated CsA-mediated elevations of blood urea, serum creatinine, CYS-C, glucose, renal MDA, and MPO, and preserved the serum albumin, renal catalase, SOD, and GSH. They reduced the expressions of TNF-α, Bax, NF-κB, and pathological kidney damage. Nrf2 expression in the kidney was raised. Hesperidin or sitagliptin could protect the kidney against CsA through the mitigation of oxidative stress, apoptosis, and inflammation. Sitagliptin proved to be more beneficial than hesperidin.
Pr3+-doped YPO4 nanocrystal embedded into an optical fiber
Authors: Dorosz Dominik , Kochanowicz Marcin , Valiente Rafael , Diego-Rucabado Andrea , Rodríguez Fernando , Siñeriz-Niembro Nuria , Espeso José I. , Lesniak Magdalena , Miluski Piotr , Conzendorf Sylvia , Posseckardt Juliane , Liao Zhongquan , Jimenez Gloria Lesly , Müller Robert , Lorenz Martin , Schwuchow Anka , Leich Martin , Lorenz Adrian , Wondraczek Katrin , Jäger Matthias
Published: March 2024

Optical fiber with YPO4:Pr3+ nanocrystals (NCs) is presented for the first time using the glass powder—NCs doping method. The method’s advantage is separate preparation of NCs and glass to preserve luminescent and optical properties of NCs once they are incorporated into optical fiber. The YPO4:Pr3+ nanocrystals were synthesized by the co-precipitation and hydrothermal methods, optimized for size (< 100 nm), shape, Pr3+ ions concentration (0.2 mol%), and emission lifetime. The core glass was selected from the non-silica P2O5-containing system with refractive index (n = 1.788) close to the NCs (no = 1.657, ne = 1.838). Optical fiber was drawn by modified powder-in-tube method after pre-sintering of glass powder—YPO4:Pr3+ (wt 3%) mixture to form optical fiber preform. Luminescent properties of YPO4:Pr3+ and optical fiber showed their excellent agreement, including sharp Pr3+ emission at 600 nm (1D2–3H4) and 1D2 level lifetime (τ = 156 ± 5 µs) under 488 nm excitation. The distribution of the YPO4:Pr3+ NCs in optical fiber were analyzed by TEM-EDS in the core region (FIB-SEM-prepared). The successful usage of glass powder—NCs doping method was discussed in the aspect of promising properties of the first YPO4:Pr3+ doped optical fiber as a new way to develop active materials for lasing applications, among others.
Reliable Tilt-depth estimates based on the stable computation of the tilt angle using robust vertical derivatives
Authors: Abdelrahman Kamal , Pham Luan Thanh , Oliveira Saulo Pomponet , Duong Van-Hao , Duy Thong Kieu , Gomez-Ortiz David , Fnais Mohammed S. , Eldosouky Ahmed M.
Published: March 2024

The Tilt-depth is a popular approach for determining depths of magnetic sources. As this method is based on the distance between contour levels of the tilt angle, it can lead to inaccurate depth estimates when the contour lines are distorted by the presence of noise. In this paper, we stabilize the Tilt-depth method based on the computation of stable vertical derivative obtained by the β-VDR method. The presented method is demonstrated on synthetic magnetic anomalies and real magnetic data from the Arabian Shield. The results obtained from the synthetic examples coincide well with the actual depths. These results proved the utility of the presented method in cases where the field is corrupted by noise. The real example shows that the presented method can provide valuable information on subsurface structures of the area where the Tilt-depth estimates are consistent with the result of the horizontal tilt angle. The findings show that the presented method is less sensitive to noise and can provide source edges and depths more clearly and with higher accuracy.
Fatty liver classification via risk controlled neural networks trained on grouped ultrasound image data
Authors: Yen Tso-Jung , Yang Chih-Ting , Lee Yi-Ju , Chen Chun-houh , Yang Hsin-Chou
Published: March 2024

Ultrasound imaging is a widely used technique for fatty liver diagnosis as it is practically affordable and can be quickly deployed by using suitable devices. When it is applied to a patient, multiple images of the targeted tissues are produced. We propose a machine learning model for fatty liver diagnosis from multiple ultrasound images. The machine learning model extracts features of the ultrasound images by using a pre-trained image encoder. It further produces a summary embedding on these features by using a graph neural network. The summary embedding is used as input for a classifier on fatty liver diagnosis. We train the machine learning model on a ultrasound image dataset collected by Taiwan Biobank. We also carry out risk control on the machine learning model using conformal prediction. Under the risk control procedure, the classifier can improve the results with high probabilistic guarantees.
PCB defect detection algorithm based on CDI-YOLO
Authors: Xiao Gaoshang , Hou Shuling , Zhou Huiying
Published: March 2024

During the manufacturing process of printed circuit boards (PCBs), quality defects can occur, which can affect the performance and reliability of PCBs. Existing deep learning-based PCB defect detection methods are difficult to simultaneously achieve the goals of high detection accuracy, fast detection speed, and small number of parameters. Therefore, this paper proposes a PCB defect detection algorithm based on CDI-YOLO. Firstly, the coordinate attention mechanism (CA) is introduced to improve the backbone and neck network of YOLOv7-tiny, enhance the feature extraction capability of the model, and thus improve the accuracy of model detection. Secondly, DSConv is used to replace part of the common convolution in YOLOv7-tiny to achieve lower computing costs and faster detection speed. Finally, Inner-CIoU is used as the bounding box regression loss function of CDI-YOLO to speed up the bounding box regression process. The experimental results show that the method achieves 98.3% mAP on the PCB defect dataset, the detection speed is 128 frames per second (FPS), the parameters is 5.8 M, and the giga floating-point operations per second (GFLOPs) is 12.6 G. Compared with the existing methods, the comprehensive performance of this method has advantages.
Real-time analysis of osteoclast resorption and fusion dynamics in response to bone resorption inhibitors
Authors: Panwar Preety , Olesen Jacob Bastholm , Blum Galia , Delaisse Jean-Marie , Søe Kent , Brömme Dieter
Published: March 2024

Cathepsin K (CatK), an essential collagenase in osteoclasts (OCs), is a potential therapeutic target for the treatment of osteoporosis. Using live-cell imaging, we monitored the bone resorptive behaviour of OCs during dose-dependent inhibition of CatK by an ectosteric (Tanshinone IIA sulfonate) and an active site inhibitor (odanacatib). CatK inhibition caused drastic reductions in the overall resorption speed of OCs. At IC50 CatK-inhibitor concentration, OCs reduced about 40% of their trench-forming capacity and at fourfold IC50 concentrations, a > 95% reduction was observed. The majority of CatK-inhibited OCs (~ 75%) were involved in resorption-migration-resorption episodes forming adjacent pits, while ~ 25% were stagnating OCs which remained associated with the same excavation. We also observed fusions of OCs during the resorption process both in control and inhibitor-treated conditions, which increased their resorption speeds by 30–50%. Inhibitor IC50-concentrations increased OC-fusion by twofold. Nevertheless, more fusion could not counterweigh the overall loss of resorption activity by inhibitors. Using an activity-based probe, we demonstrated the presence of active CatK at the resorbing front in pits and trenches. In conclusion, our data document how OCs respond to CatK-inhibition with respect to movement, bone resorption activity, and their attempt to compensate for inhibition by activating fusion.
The immunoglobulin heavy chain super enhancer controls class switch recombination in developing B cells
Authors: Dauba Audrey , Näser Emmanuelle , Andrieux Dylan , Cogné Michel , Denizot Yves , Khamlichi Ahmed Amine
Published: March 2024

Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to replace the initial IgM by another antibody class (IgG, IgE or IgA). CSR is preceded by transcription of theIgHconstant genes and is controlled by the super-enhancer 3′ regulatory region (3′RR) in an activation-specific manner. The 3’RR is composed of four enhancers (hs3a, hs1-2, hs3b and hs4). In mature B cells, 3’RR activity correlates with transcription of its enhancers. CSR can also occur in primary developing B cells though at low frequency, but in contrast to mature B cells, the transcriptional elements that regulate the process in developing B cells are ill-known. In particular, the role of the 3’RR in the control of constant genes’ transcription and CSR has not been addressed. Here, by using a mouse line devoid of the 3’RR and a culture system that highly enriches in pro-B cells, we show that the 3’RR activity is indeed required for switch transcription and CSR, though its effect varies in an isotype-specific manner and correlates with transcription of hs4 enhancer only.
Air pollutant prediction model based on transfer learning two-stage attention mechanism
Authors: Ma Zhanfei , Wang Bisheng , Luo Wenli , Jiang Jing , Liu Dongxiang , Wei Hui , Luo HaoYe
Published: March 2024

Atmospheric pollution significantly impacts the regional economy and human health, and its prediction has been increasingly emphasized. The performance of traditional prediction methods is limited due to the lack of historical data support in new atmospheric monitoring sites. Therefore, this paper proposes a two-stage attention mechanism model based on transfer learning (TL-AdaBiGRU). First, the first stage of the model utilizes a temporal distribution characterization algorithm to segment the air pollutant sequences into periods. It introduces a temporal attention mechanism to assign self-learning weights to the period segments in order to filter out essential period features. Then, in the second stage of the model, a multi-head external attention mechanism is introduced to mine the network's hidden layer key features. Finally, the adequate knowledge learned by the model at the source domain site is migrated to the new site to improve the prediction capability of the new site. The results show that (1) the model is modeled from the data distribution perspective, and the critical information within the sequence of periodic segments is mined in depth. (2) The model employs a unique two-stage attention mechanism to capture complex nonlinear relationships in air pollutant data. (3) Compared with the existing models, the mean absolute error (MAE), root mean square error (RMSE), and mean absolute percentage error (MAPE) of the model decreased by 14%, 13%, and 4%, respectively, and the prediction accuracy was greatly improved.
An atomistic study of sticking, bouncing, and aggregate destruction in collisions of grains with small aggregates
Authors: Nietiadi Maureen L. , Urbassek Herbert M. , Rosandi Yudi
Published: March 2024

Molecular dynamics simulations are used to study central collisions between spherical grains and between grains and small grain aggregates (up to 5 grains). For a model material (Lennard-Jones), grain–grain collisions are sticking when the relative velocity v is smaller than the so-called bouncing velocity and bouncing for higher velocities. We find a similar behavior for grain–aggregate collisions. The value of the bouncing velocity depends only negligibly on the aggregate size. However, it is by 35% larger than the separation velocity needed to break a contact; this is explained by energy dissipation processes during the collision. The separation velocity follows the predictions of the macroscopic Johnson–Kendall–Roberts theory of contacts. At even higher collision velocities, the aggregate is destroyed, first by the loss of a monomer grain and then by total disruption. In contrast to theoretical considerations, we do not find a proportionality of the collision energy needed for destruction and the number of bonds to be broken. Our study thus sheds novel light on the foundations of granular mechanics, namely the energy needed to separate two grains, the difference between grain–grain and grain–aggregate collisions, and the energy needed for aggregate destruction.
Detecting defects that reduce breakdown voltage using machine learning and optical profilometry
Authors: Gallagher James C. , Mastro Michael A. , Jacobs Alan G. , Kaplar Robert. J. , Hobart Karl D. , Anderson Travis J.
Published: March 2024

Semiconductor wafer manufacturing relies on the precise control of various performance metrics to ensure the quality and reliability of integrated circuits. In particular, GaN has properties that are advantageous for high voltage and high frequency power devices; however, defects in the substrate growth and manufacturing are preventing vertical devices from performing optimally. This paper explores the application of machine learning techniques utilizing data obtained from optical profilometry as input variables to predict the probability of a wafer meeting performance metrics, specifically the breakdown voltage (Vbk). By incorporating machine learning techniques, it is possible to reliably predict performance metrics that cause devices to fail at low voltage. For diodes that fail at a higher (but still below theoretical) breakdown voltage, alternative inspection methods or a combination of several experimental techniques may be necessary.
Discrepancy of flowering time between genetically close sublineages of Aegilops umbellulata Zhuk.
Authors: Son In , Kasazumi Nozomi , Okada Moeko , Takumi Shigeo , Yoshida Kentaro
Published: March 2024

Aegilops umbellulata Zhuk., a wild diploid wheat-related species, has been used as a genetic resource for several important agronomic traits. However, its genetic variations have not been comprehensively studied. We sequenced RNA from 114 accessions of Ae. umbellulata to evaluate DNA polymorphisms and phenotypic variations. Bayesian clustering and phylogenetic analysis based on SNPs detected by RNA sequencing revealed two divergent lineages, UmbL1 and UmbL2. The main differences between them were in the sizes of spikes and spikelets, and culm diameter. UmbL1 is divided into two sublineages, UmbL1e and UmbL1w. These genetic differences corresponded to geographic distributions. UmbL1e, UmbL1w, and UmbL2 are found in Turkey, Iran/Iraq, and Greece, respectively. Although UmbL1e and UmbL1w were genetically similar, flowering time and other morphological traits were more distinct between these sublineages than those between the lineages. This discrepancy can be explained by the latitudinal and longitudinal differences in habitats. Specifically, latitudinal clines of flowering time were clearly observed in Ae. umbellulata, strongly correlated with solar radiation in the winter season. This observation implies that latitudinal differences are a factor in differences in the flowering times of Ae. umbellulata. Differences in flowering time could influence other morphological differences and promote genetic divergence between sublineages.
Assessing the accuracy and reliability of application-based audiometry for hearing evaluation
Authors: Lee Seung Yeol , Seo Hee Won , Jung Seon Min , Lee Seung Hwan , Chung Jae Ho
Published: March 2024

Pure-tone audiometry (PTA) is the gold standard for assessing hearing loss. However, traditional PTA tests require specialized equipment, trained personnel, and a soundproof environment. Recently, smartphone-based PTA tests have been developed as an alternative method for hearing assessment. The aim of this study was to validate the accuracy and reliability of a smartphone application-based audiometry test. This study was conducted to assess the performance of application-based audiometry from November 2021 to January 2022. Pure-tone thresholds were measured using a smartphone application-based PTA test and compared with results obtained using a traditional audiometer in a sound-treated booth. The smartphone application used in this study was the "Care4Ear (Care4ear, version 1.0.6, MIJ Co., Ltd.)". Hearing thresholds less than 35 dB HL were classified as group A, 35-64 dB HL as group B, and 65 dB HL or greater as group C for the classification of hearing levels. We evaluated the accuracy of smartphone audiometry for each group and compared the results of frequency-specific hearing tests. Additionally, we examined the results of smartphone audiometry in individuals (n = 27) with asymmetric hearing loss. Seventy subjects completed both conventional audiometry and smartphone application-based hearing tests. Among the ears assessed, 55.7% were classified as group A, while 25.7% and 18.6% were classified as group B and group C, respectively. The average hearing threshold obtained from conventional pure-tone audiometry was 37.7 ± 25.2 dB HL, whereas the application-based hearing test yielded thresholds of 21.0 ± 23.0 dB HL. A significant correlation (r = 0.69, p < 0.01) was found between the average hearing thresholds obtained from the application-based and conventional pure-tone audiometry tests. The application-based test achieved a 97.4% hit rate for classifying hearing thresholds as class A, but lower rates of 22.2% for class B and 38.5% for class C. Notably, a discrepancy was observed between the hearing threshold measured by the application and the conventional audiometry for the worse ear with asymmetric hearing. The smartphone-based audiometry is a feasible method for hearing evaluation especially in persons with normal hearing. In cases of hearing loss or asymmetric hearing loss, the results of the application-based audiometry may be inaccurate, limiting its diagnostic utility.
Taurine reduces microglia activation in the brain of aged senescence-accelerated mice by increasing the level of TREM2
Authors: Ahmed Sharif , Ma Ning , Kawanokuchi Jun , Matsuoka Keiya , Oikawa Shinji , Kobayashi Hatasu , Hiraku Yusuke , Murata Mariko
Published: March 2024

Alzheimer’s disease (AD), a chronic neurodegenerative disorder, is the leading cause of dementia. Over-activated microglia is related to amyloid-beta (Aβ) and phosphorylated tau (phospho-tau) accumulation in the AD brain. Taurine is an amino acid with multiple physiological functions including anti-inflammatory effects, and has been reported to be neuroprotective in AD. However, the role of taurine in microglia-mediated AD remains unclear. Here, we examined the effects of taurine on the brains of senescence-accelerated mouse prone 8 (SAMP8) mice by comparing those administered 1% taurine water with those administered distilled water (DW). We observed increased levels of taurine and taurine transporter (TAUT) in the brains of the taurine-treated mice compared with those of control mice. Immunohistochemical and Western blot analyses revealed that taurine significantly reduced the number of activated microglia, levels of phospho-tau and Aβ deposit in the hippocampus and cortex. Triggering receptors expressed on myeloid cells-2 (TREM2) are known to protect against AD pathogenesis. Taurine upregulated TREM2 expression in the hippocampus and cortex. In conclusion, the present study suggests that taurine treatment may upregulate TREM2 to protect against microglia over-activation by decreasing the accumulation of phospho-tau and Aβ; providing an insight into a novel preventive strategy in AD.
Population status and genetic assessment of mugger (Crocodylus palustris) in a tropical regulated river system in North India
Authors: Sharma Surya Prasad , Ghazi Mirza Ghazanfarullah , Katdare Suyash , Badola Ruchi , Hussain Syed Ainul
Published: March 2024

For rewilding the depleted crocodylian populations in India, a targeted ‘one-species one area’ based conservation approach was adopted in the early-1970s. Suitable habitats were identified and designated as protected areas, specifically targeted to recover a particular crocodylian species. A ~ 610 km stretch of Chambal River in the Ganga River Basin was declared as National Chambal Sanctuary to restore the ‘Critically Endangered’ gharial (Gavialis gangeticus), where active management of mugger (Crocodylus palustris) was discouraged. In the present study, we examined the population trends, occupancy, and genetic status of mugger by conducting population monitoring and genetic assessment to understand the status of potentially competitive mugger in the Sanctuary. Our finding suggests that the mugger population has notably increased and colonised the Sanctuary. We observed a moderate level of genetic diversity in the mugger, which was relatively higher compared to the gharial in the Sanctuary. The rapid colonization of ecological generalist mugger raises concerns about potential competition with ecological specialist gharial threatening its long-term sustainability. Considering the coexistence dynamics between the species, it is essential to extend adaptive management strategies for mugger to ensure successful recovery of gharial population in the Sanctuary.
Mechanism of plasma electrolytic oxidation in Mg3ZnCa implants: a study of double-layer formation and properties through nanoindentation
Authors: Lashkarara S. , fazlali A. , Ghaseminezhad K. , Fleck C. , Salavati M.
Published: March 2024

Plasma electrolytic oxidation (PEO), applied to light metals such as titanium, aluminum, and magnesium, creates a two-layer coating and has become increasingly important in metal coatings. However, due to the high voltage and temperature of the process, no online instrument could monitor the underlying mechanism. This paper presents a new image proving that the surface of PEO-coated Mg3ZnCa boiled during the process and argues that three hypotheses are involved in the PEO mechanism based on boiling caused by tolerating high voltage during the PEO process, which could explain the current‒voltage diagram of the process. Finally, nanoindentation was used to measure the elastic module and hardness of the PEO layers. The nanoindentation test results revealed the similarity of the elastic module of the outer porous layer and the primary alloy, with values of 40.25 GPa and 41.47 GPa, respectively, confirming that the outer porous layer corresponds to the cold plasma-gas phase formed during the PEO process.
Effects of macroprudential policies on ecological footprint: the moderating role of environmental policy stringency in the top 11 largest countries
Authors: Luo Heng , Sun Ying , Zhang Li
Published: March 2024

This study investigates the impact of macroprudential policies on ecological footprint (EF) in the top 11 largest countries. This study uses country-level panel data from these countries, covering the period from 1992 to 2020. Findings indicate that macroprudential policies alleviates ecological footprint in the sample. Macroprudential policies primarily reduce the ecological footprint before medium quantile (50%) while the environmental benefits of the policies end in the later quantiles. Moreover, environmental policy stringency (EPS) amplifies the positive influence of macroprudential policies on environmental sustainability. Estimate results stay the same with basic regression results in the post-global financial crisis (GFC) period while the impact is positive in the pre-GFC period. Finally, other robust tests validate the findings reported in basic regression model. This study suggests that governments should customize various types of macroprudential policies while also considering environmental concerns. The achievement of a sustainable environment can be facilitated by the combined effects of macroprudential policies and EPS.
Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity
Authors: Moraes Zenker Maurício , Portella Tatiana Pineda , Pessoa Felipe Arley Costa , Bengtsson-Palme Johan , Galetti Pedro Manoel
Published: March 2024

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4–30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.