bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary dynamics of whole-body regeneration across planarian flatworms
Authors: Vila-Farré Miquel , Rozanski Andrei , Ivanković Mario , Cleland James , Brand Jeremias N. , Thalen Felix , Grohme Markus A. , von Kannen Stephanie , Grosbusch Alexandra L. , Vu Hanh T.-K. , Prieto Carlos E. , Carbayo Fernando , Egger Bernhard , Bleidorn Christoph , Rasko John E. J. , Rink Jochen C.
Published: October 2023

Regenerative abilities vary dramatically across animals. Even amongst planarian flatworms, well-known for complete regeneration from tiny body fragments, some species have restricted regeneration abilities while others are almost entirely regeneration incompetent. Here, we assemble a diverse live collection of 40 planarian species to probe the evolution of head regeneration in the group. Combining quantification of species-specific head-regeneration abilities with a comprehensive transcriptome-based phylogeny reconstruction, we show multiple independent transitions between robust whole-body regeneration and restricted regeneration in freshwater species. RNA-mediated genetic interference inhibition of canonical Wnt signalling in RNA-mediated genetic interference-sensitive species bypassed all head-regeneration defects, suggesting that the Wnt pathway is linked to the emergence of planarian regeneration defects. Our finding that Wnt signalling has multiple roles in the reproductive system of the model speciesSchmidtea mediterranearaises the possibility that a trade-off between egg-laying, asexual reproduction by fission/regeneration and Wnt signalling drives regenerative trait evolution. Although quantitative comparisons of Wnt signalling levels, yolk content and reproductive strategy across our species collection remained inconclusive, they revealed divergent Wnt signalling roles in the reproductive system of planarians. Altogether, our study establishes planarians as a model taxon for comparative regeneration research and presents a framework for the mechanistic evolution of regenerative abilities.
The PD-1- and LAG-3-targeting bispecific molecule tebotelimab in solid tumors and hematologic cancers: a phase 1 trial
Authors: Luke Jason J. , Patel Manish R. , Blumenschein George R. , Hamilton Erika , Chmielowski Bartosz , Ulahannan Susanna V. , Connolly Roisin M. , Santa-Maria Cesar A. , Wang Jie , Bahadur Shakeela W. , Weickhardt Andrew , Asch Adam S. , Mallesara Girish , Clingan Philip , Dlugosz-Danecka Monika , Tomaszewska-Kiecana Monika , Pylypenko Halyna , Hamad Nada , Kindler Hedy L. , Sumrow Bradley J. , Kaminker Patrick , Chen Francine Z. , Zhang Xiaoyu , Shah Kalpana , Smith Douglas H. , De Costa Anushka , Li Jonathan , Li Hua , Sun Jichao , Moore Paul A.
Published: October 2023

Tebotelimab, a bispecific PD-1×LAG-3 DART molecule that blocks both PD-1 and LAG-3, was investigated for clinical safety and activity in a phase 1 dose-escalation and cohort-expansion clinical trial in patients with solid tumors or hematologic malignancies and disease progression on previous treatment. Primary endpoints were safety and maximum tolerated dose of tebotelimab when administered as a single agent (n = 269) or in combination with the anti-HER2 antibody margetuximab (n = 84). Secondary endpoints included anti-tumor activity. In patients with advanced cancer treated with tebotelimab monotherapy, 68% (184/269) experienced treatment-related adverse events (TRAEs; 22% were grade ≥3). No maximum tolerated dose was defined; the recommended phase 2 dose (RP2D) was 600 mg once every 2 weeks. There were tumor decreases in 34% (59/172) of response-evaluable patients in the dose-escalation cohorts, with objective responses in multiple solid tumor types, including PD-1-refractory disease, and in LAG-3+ non-Hodgkin lymphomas, including CAR-T refractory disease. To enhance potential anti-tumor responses, we tested margetuximab plus tebotelimab. In patients with HER2+ tumors treated with tebotelimab plus margetuximab, 74% (62/84) had TRAEs (17% were grade ≥3). The RP2D was 600 mg once every 3 weeks. The confirmed objective response rate in these patients was 19% (14/72), including responses in patients typically not responsive to anti-HER2/anti-PD-1 combination therapy. ClinicalTrials.gov identifier: NCT03219268.
Noninvasive theta-burst stimulation of the human striatum enhances striatal activity and motor skill learning
Authors: Wessel Maximilian J. , Beanato Elena , Popa Traian , Windel Fabienne , Vassiliadis Pierre , Menoud Pauline , Beliaeva Valeriia , Violante Ines R. , Abderrahmane Hedjoudje , Dzialecka Patrycja , Park Chang-Hyun , Maceira-Elvira Pablo , Morishita Takuya , Cassara Antonino M. , Steiner Melanie , Grossman Nir , Neufeld Esra , Hummel Friedhelm C.
Published: October 2023

The stimulation of deep brain structures has thus far only been possible with invasive methods. Transcranial electrical temporal interference stimulation (tTIS) is a novel, noninvasive technology that might overcome this limitation. The initial proof-of-concept was obtained through modeling, physics experiments and rodent models. Here we show successful noninvasive neuromodulation of the striatum via tTIS in humans using computational modeling, functional magnetic resonance imaging studies and behavioral evaluations. Theta-burst patterned striatal tTIS increased activity in the striatum and associated motor network. Furthermore, striatal tTIS enhanced motor performance, especially in healthy older participants as they have lower natural learning skills than younger subjects. These findings place tTIS as an exciting new method to target deep brain structures in humans noninvasively, thus enhancing our understanding of their functional role. Moreover, our results lay the groundwork for innovative, noninvasive treatment strategies for brain disorders in which deep striatal structures play key pathophysiological roles.
Anthropogenic pollen indicators: Global food plants and Latin American human indicators in the pollen record
Authors: Flantua Suzette G. A. , Hooghiemstra Henry
Published: October 2023

Pollen-based evidence of human presence is crucial for reconstructing human history. However, information on the morphology of pollen grains of global food plants and regional pollen-based human indicators is scattered in the literature, leading to the risk of overlooking important evidence of human presence. To address this issue, we first compiled a comprehensive overview of 354 major food plants worldwide, creating a paleoecology-friendly format that includes their family, vernacular name, earliest known use, environmental preference, and geographical region. Moreover, we identified the sources of illustrations of their pollen grains for 209 out of 273 different genera of globally relevant food plants in 10 selected pollen atlases. Secondly, we compiled all human indicators from pollen-based paleoecological literature in Latin America (based on 750 references), providing an overview of 212 single-pollen type indicators and identified 95 crucial combinations of pollen types as “human indices”, and their corresponding references. Our review datasets aids in distilling human evidence from numerous fossil pollen records worldwide.
Therapeutic potential of lactoferrin-coated iron oxide nanospheres for targeted hyperthermia in gastric cancer
Authors: Attri Komal , Chudasama Bhupendra , Mahajan Roop L. , Choudhury Diptiman
Published: October 2023

Lactoferrin (LF) is a non-heme iron-binding glycoprotein involved in the transport of iron in blood plasma. In addition, it has many biological functions, including antibacterial, antiviral, antimicrobial, antiparasitic, and, importantly, antitumor properties. In this study, we have investigated the potential of employing lactoferrin-iron oxide nanoparticles (LF-IONPs) as a treatment modality for gastric cancer. The study confirms the formation of LF-IONPs with a spherical shape and an average size of 5 ± 2 nm, embedded within the protein matrix. FTIR and Raman analysis revealed that the Fe–O bond stabilized the protein particle interactions. Further, we conducted hyperthermia studies to ascertain whether the proposed composite can generate a sufficient rise in temperature at a low frequency. The results confirmed that we can achieve a temperature rise of about 7 °C at 242.4 kHz, which can be further harnessed for gastric cancer treatment. The particles were further tested for their anti-cancer activity on AGS cells, with and without hyperthermia. Results indicate that LF-IONPs (10 µg/ml) significantly enhance cytotoxicity, resulting in the demise of 67.75 ± 5.2% of cells post hyperthermia, while also exhibiting an inhibitory effect on cell migration compared to control cells, with the most inhibition observed after 36 h of treatment. These findings suggest the potential of LF-IONPs in targeted hyperthermia treatment of gastric cancer.
The role of response conflict in concealed information detection with reaction times
Authors: klein Selle Nathalie , Or Barak , Van der Cruyssen Ine , Verschuere Bruno , Ben-Shakhar Gershon
Published: October 2023

The concealed information test (CIT) presents various probe (familiar) items amidst irrelevant (unfamiliar) items. When the probe items appear, reaction time (RT) slows down. This RT-CIT effect has been accounted for by a conflict resulting from the need to deny familiarity of the familiar probes. The present pre-registered study (n = 292) examined whether response conflict is sufficient to account for the RT-CIT effect, using city and name items. Specifically, we compared the common conflict condition, where the response buttons emphasized familiarity of CIT items (“unfamiliar” versus “familiar”), to a novel no conflict condition, where the buttons emphasized categorical membership (“city” versus “name”). In line with our expectations, the RT-CIT effect was substantially stronger in the conflict condition; yet, it remained significant even in the no conflict condition. This implies a critical role for response conflict, but also suggests that other mechanisms (e.g. orientation to significant stimuli) may contribute to the RT-CIT effect.
Relationship between body composition and pulmonary function in the general population—a cross-sectional study in Ningxia
Authors: Pi Yang-yang , Hu Wen-xuan , Jiao Zi-ming , Hou Peng-yi , Zhang Yu-hong , Zhao Yi , Li Xiao-xia , Yu Jing , Chen Fang , Jing Jin-yun , Wang Fa-xuan
Published: October 2023

Studies considering the relationship between non-obesity-related body composition and lung function are few; therefore, this study aimed to explore these correlations and effects. This cross-sectional study conducted in rural Qingtongxia City and Pingluo County, Ningxia, China, included 776 participants aged 30–75 years. Body composition and lung function were measured using direct segmental multifrequency bioelectrical impedance analysis and a digital spirometer, respectively. Their correlation was assessed using partial correlation analysis, controlling for age and smoking status, and the body composition effect on lung function was analyzed using binomial logistic regression analysis. The body components total body water content, protein content, mineral content, muscle mass, fat-free mass (FFM), skeletal muscle mass, basal metabolic volume, and chest circumference (CC) positively correlated with pulmonary function (forced vital capacity and forced expiratory volume in one second) in both sexes. Neck circumference and hip circumference positively correlated with pulmonary function in women. Additionally, lung function declines more slowly in women (odds ratio [OR] = 0.66, 95% confidence interval [CI] = 0.44–0.98, p =  0.04); CC (OR = 0.92, 95% CI = 0.86–0.98, p = 0.01) increased as a protective factor for decreased lung function. Increased waist circumference (OR = 1.04, 95% CI = 1.00–1.09, p = 0.04) was a risk factor for reduced lung function. FFM contains body composition indicators positively correlating with lung function, excluding fat-related body composition. Abdominal obesity increases the risk of decreased lung function.
Polydatin prevent lung epithelial cell from Carbapenem-resistant Klebsiella pneumoniae injury by inhibiting biofilm formation and oxidative stress
Authors: Guan Xiaodan , Jin Liang , Zhou Huifen , Chen Jing , Wan Haofang , Bao Yida , Yang Jiehong , Yu Daojun , Wan Haitong
Published: October 2023

Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes severe inflammation in various infectious diseases, such as bloodstream infections, respiratory and urinary tract infections, which leads to high mortality. Polydatin (PD), an active ingredient of Yinhuapinggan granule, has attracted worldwide attention for its powerful antioxidant, anti-inflammatory, antitumor, and antibacterial capacity. However, very little is known about the effect of PD on CRKP. In this research, we evaluated the inhibitory effects of PD on both the bacterial level and the bacterial-cell co-culture level on anti-biofilm and efflux pumps and the other was the inhibitory effect on apoptosis, reactive oxygen species (ROS), mitochondrial membrane potential (MMP) after CRKP induction. Additionally, we validated the mechanism of action by qRT-PCR and western blot in human lung epithelial cells. Firstly, PD was observed to have an inhibitory effect on the biofilm of CRKP and the efflux pump AcrAB-TolC. Mechanically, CRKP not only inhibited the activation of Nuclear Factor erythroid 2-Related Factor 2 (Nrf-2) but also increased the level of ROS in cells. These results showed that PD could inhibit ROS and activate Nrf-2 production. Together, our research demonstrated that PD inhibited bacterial biofilm formation and efflux pump AcrAB—TolC expression and inhibited CRKP-induced cell damage by regulating ROS and Nrf-2-regulated antioxidant pathways.
Developing anti-microbial peptide database version 1 to provide comprehensive and exhaustive resource of manually curated AMPs
Authors: Mondal Rajat Kumar , Sen Debarup , Arya Ankish , Samanta Sintu Kumar
Published: October 2023

Anti-Microbial Peptide Database version 1 (AMPDB v1) is a meticulously curated resource that aims to address the limitations of existing databases in the field of antimicrobial research. We have utilized the latest technology and put our best efforts into adding all relevant tools to cater to the needs of our users. AMPDB v1 is a derived database, built upon information gathered from the available resources and boasts a significant size of 59,122 entries which are classified into 88 classes. All the information in this resource was curated manually. Sequence alignment and protein feature calculation tools were integrated into the database in the form of web applications, to make them easy to use, quick, and responsive in real-time. We have included multiple types of browsing and searching options to enhance the user experience, from simple text search to a completely customizable advanced search page with intuitive options that let the user combine multiple options together to make a powerful search query. The database is accessible by a web browser athttps://bblserver.org.in/ampdb/.
Prognostic visualization model for primary pulmonary sarcoma: a SEER-based study
Authors: Huang Qian , Li Wenqiang , He Xiaoyu , He Qian , Lai Qun , Yuan Quan , Deng Zhiping
Published: October 2023

Primary pulmonary sarcoma (PPS) is a rare and poor prognostic malignancy that results from current clinical studies are lacking. Our study aimed to investigate the prognostic factors of PPS and to construct a predictive nomogram that predict the overall survival (OS) rate. We extracted data on patients diagnosed with PPS from 2010 to 2019 in the SEER database. A total of 169 patients were included after screening by inclusion and exclusion criteria. Univariate and multivariate COX regression analyses showed that age, pathological grade, liver metastasis, surgical intervention, and chemotherapy influenced the prognosis. We constructed the prediction model nomogram based on these factors. Moreover, the results of the internal and external ROC curves, calibration curves, and DCA plots confirmed that the model has good discrimination, accuracy, and clinical practice efficacy. The present study is the first population-based study to explore the factors affecting the prognosis of PPS. We established a novel prognostic nomogram to predict the OS rate, which can help to make proper clinical decisions.
Ecological assessment of Iran’s terrestrial biomes for wildlife conservation
Authors: Ansari Amir , Ghorbanpour Mansour , Kazemi Ali , Kariman Khalil
Published: October 2023

Man-made activities pose the greatest threats to wildlife in Iran's terrestrial biomes, causing significant habitat damage and fragmentation in recent years. To fully understand these threats, the present study was conducted to identify and map the Iran’s terrestrial biomes using the IDRISI TerrSet 18.31 Software, the Terrestrial Biomes Ecosystem Service Modeler on the InVEST toolkit (TBESMI), and comprehensive data sources including maps of roads, protected areas, terrestrial biomes, and country-wide land cover maps of 2017. The results showed that the largest terrestrial biome in Iran is deserts and xeric shrublands (DXS), while flooded grasslands and savannas (FGS) is the smallest biome. Roads, along with urban and agricultural developments are among the biggest threats and most destructive stressors in Iran’s terrestrial biomes. The results also revealed that there was a growth in destruction of habitats located in the temperate broadleaf and mixed forest (TBMF), temperate coniferous forest (TCF), and FGS, alongside a decrease in the DXS biome. Furthermore, we detected an increase in habitat landscape quality in the DXS, FGS and montane grasslands and shrub lands (MGS), and a decrease in the temperate grasslands, savannas and shrublands (TGSS) and TBMF biomes. Finally, the cumulative risk of habitat degradation increased in the FGS, TCF, TGSS, and TBMF biomes, whereas it decreased in the DXS biome. The FGS biome with the highest consequence cumulative score, and the MGS biome with the highest cumulative risk exposure score were found to be at the highest risk from man-made activities. Stressors associated with agriculture and urbanization had the highest cumulative exposure scores in the MGS, while roads had the highest exposure scores in the TBMF and DXS biomes. Our study underscores the critical importance of conserving Iran's terrestrial biomes and wildlife, especially in high-risk biomes like FGS and MGS, given the substantial threats posed by human activities.
Fast reconstruction algorithm based on HMC sampling
Authors: Lian Hang , Xu Jinchen , Zhu Yu , Fan Zhiqiang , Liu Yi , Shan Zheng
Published: October 2023

In Noisy Intermediate-Scale Quantum (NISQ) era, the scarcity of qubit resources has prevented many quantum algorithms from being implemented on quantum devices. Circuit cutting technology has greatly alleviated this problem, which allows us to run larger quantum circuits on real quantum machines with currently limited qubit resources at the cost of additional classical overhead. However, the classical overhead of circuit cutting grows exponentially with the number of cuts and qubits, and the excessive postprocessing overhead makes it difficult to apply circuit cutting to large scale circuits. In this paper, we propose a fast reconstruction algorithm based on Hamiltonian Monte Carlo (HMC) sampling, which samples the high probability solutions by Hamiltonian dynamics from state space with dimension growing exponentially with qubit. Our algorithm avoids excessive computation when reconstructing the original circuit probability distribution, and greatly reduces the circuit cutting post-processing overhead. The improvement is crucial for expanding of circuit cutting to a larger scale on NISQ devices.
Estimation of right lobe graft weight for living donor liver transplantation using deep learning-based fully automatic computed tomographic volumetry
Authors: Yang Xiaopeng , Park Seonyeong , Lee Seungyoo , Han Kyujin , Lee Mi Rin , Song Ji Soo , Yu Hee Chul , Do Yang Jae
Published: October 2023

This study aimed at developing a fully automatic technique for right lobe graft weight estimation using deep learning algorithms. The proposed method consists of segmentation of the full liver region from computed tomography (CT) images, classification of the entire liver region into the right and left lobes, and estimation of the right lobe graft weight from the CT-measured right lobe graft volume using a volume-to-weight conversion formula. The first two steps were performed with a transformer-based deep learning model. To train and evaluate the model, a total of 248 CT datasets (188 for training, 40 for validation, and 20 for testing and clinical evaluation) were used. The Dice similarity coefficient (DSC), mean surface distance (MSD), and the 95th percentile Hausdorff distance (HD95) were used for evaluating the segmentation accuracy of the full liver region and the right liver lobe. The correlation coefficient (CC), percentage error (PE), and percentage absolute error (PAE) were used for the clinical evaluation of the estimated right lobe graft weight. The proposed method achieved high accuracy in segmentation for DSC, MSD, and HD95 (95.9% ± 1.0%, 1.2 ± 0.4 mm, and 5.2 ± 1.9 mm for the entire liver region; 92.4% ± 2.7%, 2.0 ± 0.7 mm, and 8.8 ± 2.9 mm for the right lobe) and in clinical evaluation for CC, PE, and PAE (0.859, − 1.8% ± 9.6%, and 8.6% ± 4.7%). For the right lobe graft weight estimation, the present study underestimated the graft weight by − 1.8% on average. A mean difference of − 21.3 g (95% confidence interval: − 55.7 to 13.1, p = 0.211) between the estimated graft weight and the actual graft weight was achieved in this study. The proposed method is effective for clinical application.
Temporal changes in intensity and volume of external training loads during a 1 × 1 short-bout, small-sided games in elite youth soccer players
Authors: Kryściak Jakub , Tomczak Maciej , Podgórski Tomasz , Chmura Paweł , Konefał Marek , Chmura Jan , Maly Tomas , Modric Toni , Andrzejewski Marcin
Published: October 2023

This study compared external training load (ETL) and its temporal changes across repetitions during a speed endurance production (SEP) training comprised of 1 × 1 short-bout, small-sided games (SSGs) in elite youth soccer players. Twenty U18 players were divided into two groups (SEP1 and SEP2) performing six 30 s and 45 s bouts of SSG (work-to-rest ratio 1:4) on a 10 by 15 m field. ETL was characterized by the total distance covered, Player Load, the total number of accelerations/decelerations, and their relative values (per minute). Significant overall decreases in the ETL parameter values across six repetitions in both SSG groups were observed relative to the measurement in the first set beginning in 3rd (SEP1) or 4th (SEP2) repetitions. Significant greater decreases in Player Load (F(5.90) = 2.99, p < 0.05, η P2 = 0.14), Player Load per minute (F(5,90) = 11.32, p < 0.001, η P2 = 0.39), total distance per minute (F(3.43,61.73) = 7.72, p < 0.001, η P2 = 0.30) and accelerations per minute (F(5,90) = 2.59, p < 0.05, η P2 = 0.13) were observed in the 30-s games than in the 45-s games. In conclusion, the use of SSGs in SEP training is associated with a decrease in the effectiveness of physical work performed across repetitions. In practice, due to the decrease in the measured ETL indicators already in the 3rd or 4th repetition (especially in the SEP1 group), the work-to-rest ratio could be increased from the applied 1:4 to 1:6.
High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival
Authors: Storrs Erik P. , Chati Prathamesh , Usmani Abul , Sloan Ian , Krasnick Bradley A. , Babbra Ramandeep , Harris Peter K. , Sachs Chloe M. , Qaium Faridi , Chatterjee Deyali , Wetzel Chris , Goedegebuure S. Peter , Hollander Thomas , Anthony Hephzibah , Ponce Jennifer , Khaliq Ateeq M. , Badiyan Shahed , Kim Hyun , Denardo David G. , Lang Gabriel D. , Cosgrove Natalie D. , Kushnir Vladimir M. , Early Dayna S. , Masood Ashiq , Lim Kian-Huat , Hawkins William G. , Ding Li , Fields Ryan C. , Das Koushik K. , Chaudhuri Aadel A.
Published: October 2023

Numerous cell states are known to comprise the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME). However, the developmental stemness and co-occurrence of these cell states remain poorly defined. Here, we performed single-cell RNA sequencing (scRNA-seq) on a cohort of treatment-naive PDAC time-of-diagnosis endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) samples (n = 25). We then combined these samples with surgical resection (n = 6) and publicly available samples to increase statistical power (n = 80). Following annotation into 25 distinct cell states, cells were scored for developmental stemness, and a customized version of the Ecotyper tool was used to identify communities of co-occurring cell states in bulk RNA-seq samples (n = 268). We discovered a tumor microenvironmental community comprised of aggressive basal-like malignant cells, tumor-promoting SPP1+ macrophages, and myofibroblastic cancer-associated fibroblasts associated with especially poor prognosis. We also found a developmental stemness continuum with implications for survival that is present in both malignant cells and cancer-associated fibroblasts (CAFs). We further demonstrated that high-dimensional analyses predictive of survival are feasible using standard-of-care, time-of-diagnosis EUS-FNB specimens. In summary, we identified tumor microenvironmental and developmental stemness characteristics from a high-dimensional gene expression analysis of PDAC using human tissue specimens, including time-of-diagnosis EUS-FNB samples. These reveal new connections between tumor microenvironmental composition, CAF and malignant cell stemness, and patient survival that could lead to better upfront risk stratification and more personalized upfront clinical decision-making.
Structure of human TRPM8 channel
Authors: Palchevskyi Sergii , Czarnocki-Cieciura Mariusz , Vistoli Giulio , Gervasoni Silvia , Nowak Elżbieta , Beccari Andrea R. , Nowotny Marcin , Talarico Carmine
Published: October 2023

TRPM8 is a non-selective cation channel permeable to both monovalent and divalent cations that is activated by multiple factors, such as temperature, voltage, pressure, and changes in osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathological conditions. Here, we present a cryo-electron microscopy structure of a human TRPM8 channel in the closed state that was solved at 2.7 Å resolution. Our structure comprises the most complete model of the N-terminal pre-melastatin homology region. We also visualized several lipids that are bound by the protein and modeled how the human channel interacts with icilin. Analyses of pore helices in available TRPM structures showed that all these structures can be grouped into different closed, desensitized and open state conformations based on the register of the pore helix S6 which positions particular amino acid residues at the channel constriction.
Computing the relative binding affinity of ligands based on a pairwise binding comparison network
Authors: Yu Jie , Li Zhaojun , Chen Geng , Kong Xiangtai , Hu Jie , Wang Dingyan , Cao Duanhua , Li Yanbei , Huo Ruifeng , Wang Gang , Liu Xiaohong , Jiang Hualiang , Li Xutong , Luo Xiaomin , Zheng Mingyue
Published: October 2023

Structure-based lead optimization is an open challenge in drug discovery, which is still largely driven by hypotheses and depends on the experience of medicinal chemists. Here we propose a pairwise binding comparison network (PBCNet) based on a physics-informed graph attention mechanism, specifically tailored for ranking the relative binding affinity among congeneric ligands. Benchmarking on two held-out sets (provided by Schrödinger and Merck) containing over 460 ligands and 16 targets, PBCNet demonstrated substantial advantages in terms of both prediction accuracy and computational efficiency. Equipped with a fine-tuning operation, the performance of PBCNet reaches that of Schrödinger’s FEP+, which is much more computationally intensive and requires substantial expert intervention. A further simulation-based experiment showed that active learning-optimized PBCNet may accelerate lead optimization campaigns by 473%. Finally, for the convenience of users, a web service for PBCNet is established to facilitate complex relative binding affinity prediction through an easy-to-operate graphical interface.
A molecularly imprinted polypyrrole electrochemiluminescence sensor based on a novel zinc-based metal–organic framework and chitosan for determination of enrofloxacin
Authors: Bu Liyin , Su Chang , Song Qingyuan , Jiang Ding , Shan Xueling , Wang Wenchang , Chen Zhidong
Published: October 2023

A schematic illustration of the preparation of a Ppy-MIP/CHIT/Zn-PTC/GCE and the sensing strategy for enrofloxacin.
Surface plasmonic biosensors: principles, designs and applications
Authors: Liu Hao , Fu Yusheng , Yang Rongzhi , Guo Jiuchuan , Guo Jinhong
Published: October 2023

Recently, surface plasmon resonance (SPR) biosensors have been widely used in environmental monitoring, food contamination detection and diagnosing medical conditions due to their superior sensitivity, label-free detection and rapid analysis speed.
Detection of coca alkaloids in oral fluid from coca leaf (tea) consumers: using solid phase extraction to improve validation parameters and widen the detection window
Authors: Álvarez-Freire I. , Cabarcos-Fernández P. , Rubio N. C. , Moreda-Piñeiro A. , Tabernero-Duque M. J. , Sánchez-Sellero I. , Bermejo-Barrera P. , Bermejo-Barrera A. M.
Published: October 2023

Hygrine and cuscohygrine, two coca leaf alkaloids, have been previously proposed as markers to differentiate legal and illegal cocaine consumption.
Rapidly detecting the carcinogen acetaldehyde: preparation and application of a flower-like MoS2 cataluminescence sensor at low working temperature
Authors: Wang Hongyan , Shao Ziyu , Shi Xiaoqi , Tang Zhuo , Sun Bai
Published: October 2023

A catalytic luminescence gas sensor based on flower shaped MoS2 is developed. The sensor has high sensitivity and good selectivity towards acetaldehyde.
Red-light modulated ortho-chloro azobenzene photoswitch for peptide stapling via aromatic substitution
Authors: Kapun Mia , Pérez-Areales F. Javier , Ashman Nicola , Rowling Pamela J. E. , Schober Tim , Fowler Elaine , Itzhaki Laura S. , Spring David R.
Published: October 2023

Development and proof-of-concept for a photoswitchable peptide staple with the ability to trigger a major change in binding affinity upon visible light irradiation.
How does multi-reference computation change the catalysis chemistry? DFT and CASPT2 studies of the Cu-catalysed coupling reactions between aryl iodides and β-diketones
Authors: He Nan , Nakatani Naoki , Hada Masahiko
Published: October 2023

The molecular mechanism of the Cu-catalysed coupling reaction was theoretically studied using density functional theory and multi-reference method to investigate the effects of strong electron correlation on the reaction profile.
The protometabolic nature of prebiotic chemistry
Authors: Nogal Noemí , Sanz-Sánchez Marcos , Vela-Gallego Sonia , Ruiz-Mirazo Kepa , de la Escosura Andrés
Published: October 2023

This tutorial review revises the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as the boundary conditions under which they would become protometabolic.
Surface ligand length influences kinetics of H-atom uptake in polyoxovanadate-alkoxide clusters
Authors: Peter Chari Y. M. , Schreiber Eric , Proe Kathryn R. , Matson Ellen M.
Published: October 2023

Exposing consequences of ligand sterics on H-atom uptake at surfaces with POV-alkoxide clusters.
Unexpected alkyl isomerization at the silicon ligand of an unsaturated Rh complex: combined experiment and theory
Authors: Abeynayake Niroshani S. , Le Nghia , Sanchez-Lecuona Gabriela , Donnadieu Bruno , Webster Charles Edwin , Montiel-Palma Virginia
Published: October 2023

A common intermediate was computationally identified from the reaction of [RhCl(COD)]2 and the silylphosphine [PhP(o-C6H4CH2SiHiPr2)2], L1, rendering either a Rh monomer (Rh-1) or its corresponding isomerized dimer (Rh-3) with an n-propyl on Si.
Co-MOF@MWCNTs/GCE for the sensitive detection of TBHQ in food samples
Authors: Feng Junhui , Li Chenxin , Liu Wan-nai-yi , Min Xiaoqin , Lin Xiaoyun
Published: October 2023

Herein, a novel cobalt-based metal–organic framework (Co-MOF) and multi-walled carbon nanotube (MWCNTs) composite-modified glassy carbon electrode (Co-MOF@MWCNTs /GCE) was successfully constructed and used to detect tert-butylhydroquinone (TBHQ).
Piezocatalytic degradation of 2,4-dichlorophenol in a water environment by a g-C3N4/CdS heterojunction catalyst: interfacial electric field boosting mechanism
Authors: He Qingshen , Yi Yuyan , Wang Renshu , Sun Pengfei , Dong Xiaoping
Published: October 2023

CdS modified GCN has been explored as a high-efficiency piezocatalyst for 2,4-DCP degradation.
Highly versatile and automated total ammonia nitrogen compact analyzer suitable for different types of water samples
Authors: Calvo-López Antonio , Alonso-Chamarro Julián , Puyol Mar
Published: October 2023

We present a versatile, robust, compact and automatic potentiometric analytical tool for in-field total ammonia nitrogen (TAN) monitoring in aqueous samples from different sources, with no sample pretreatment required.
White light-activated bactericidal coating using acrylic latex, crystal violet, and zinc oxide nanoparticles
Authors: Hwang Gi Byoung , Stent Joe , Noimark Sacha , Heo Ki Joon , MacRobert Alexander J. , Kay Christopher W. M. , Salvadori Enrico , Williams Charlotte K. , Pike Sebastian D. , Shaffer Milo S. P. , Allan Elaine , Parkin Ivan P.
Published: October 2023

A white light-activated bactericidal coating consisting of acrylic latex, Zinc oxide nanoparticles (ZnO NPs) and crystal violet (CV) was produced through a two-step dipping process.
An insight into synthesis, properties and applications of gelatin methacryloyl hydrogel for 3D bioprinting
Authors: Ghosh Rudra Nath , Thomas Joseph , B. R. Vaidehi , N. G. Devi , Janardanan Akshitha , Namboothiri Pramod K. , Peter Mathew
Published: October 2023

The properties and applications of GelMA bioinks in 3D bioprinting.
Frame-by-frame observations of structure fluctuations in single mass-selected Au clusters using aberration-corrected electron microscopy
Authors: Dearg Malcolm , Roncaglia Cesare , Nelli Diana , El Koraychy El Yakout , Ferrando Riccardo , Slater Thomas J. A. , Palmer Richard E.
Published: October 2023

Changes in cluster structure have been observed via dynamic imaging in the scanning transmission electron microscope. This opens up the possibility of measuring the potential energy surface of metal clusters of different sizes.
Nucleophilic sulfur controlled efficient ketothioamide synthesis from tribromomethyl carbinols
Authors: Tiwari Shubham , Chandrashekharappa Sandeep , Gururaja Guddeangadi N.
Published: October 2023

A greener approach towards diverse α-ketothioamides is demonstrated with a broad substrate scope. The presented protocol establishes the reactivity of the polysulfide derived from elemental sulfur and amines in an aqueous medium.
Branched polyesters from radical ring-opening polymerization of cyclic ketene acetals: synthesis, chemical hydrolysis and biodegradation
Authors: Mousa Maryam , Jonsson Magnus , Wilson Olivia , Geerts Roy , Bergenudd Helena , Bengtsson Christoffer , Larsson Kron Anna , Malmström Eva
Published: October 2023

A new synthetic route to the cyclic ketene acetal, 2-methylene-4-methyl-1,3-dioxepane (Me-MDO) is reported. The introduction of side-groups to the polyester affects its degradability.
Composite ligand shells on gold nanoprisms – an ensemble and single particle study
Authors: Zámbó Dániel , Kovács Dávid , Südi Gergely , Zolnai Zsolt , Deák András
Published: October 2023

The composition of mixed thiol ligand layer prepared on gold nanoprisms can be fine-tuned by controlling molecule concentration levels and addition sequence.
Chiral fluid membranes with orientational order and multiple edges
Authors: Ding Lijie , Pelcovits Robert A. , Powers Thomas R.
Published: October 2023

We carry out Monte Carlo simulations on fluid membranes with orientational order and multiple edges in the presence and absence of external forces.
A geometric probabilistic approach to random packing of hard disks in a plane
Authors: Brouwers H. J. H.
Published: October 2023

In this paper, the random packing fraction of hard disks in a plane is analyzed, following a geometric probabilistic approach.
Cholinium-based ionic liquid catalysts for polyethylene terephthalate glycolysis: understanding the role of solvent and a reappraisal of the cation contribution
Authors: Bura Diana , Pedrini Lorenzo , Trujillo Cristina , Connon Stephen J.
Published: October 2023

A combined computational and experimental study has identified a new PET degradation pathway using cholinium-based ionicliquids, leading to a re-evaluation of the cholinium unit's role in catalysis and improved catalyst design.
Tribological characteristics of dimpled surfaces filled with dopamine‐modified MoS2
Authors: Qin Tuo , Yu Aibing , Zhao Shuo , Li Kefan , Qi Shaochun , Ye Jiawang
Published: October 2023

To improve the tribological characteristics of dimples on the surface of 45 steel, the dimples were filled with MoS2 and MoS2 modified by dopamine (MoS2 @ DA), and ball‐disk friction and wear tests were conducted. Specifically, the dimple filling gap, abrasion depth, and surface cross‐sectional area of 45 steel were measured. The wear morphology of the friction ball and exfoliation of MoS2 in the dimples and the bending characteristics of the specimens were studied. The surface friction coefficient of MoS2 @ DA‐filled specimen was 17.9% lower than MoS2‐filled specimen, and the dimple filling gap was 70.1% lower, the surface abrasion depth was 5.8% lower, and the abrasion cross‐sectional area was 17.7% smaller. Moreover, the bending strength of the MoS2 @ DA specimen was 3.27 times greater than that of the MoS2 specimen, and the exfoliation of MoS2 was slowed by filling with the MoS2 @ DA. Finally, the tribological characteristics were also superior for the specimens prepared with MoS2 @ DA.
Semi‐blind demodulation algorithm for short burst FM‐MFSK based on STFT
Authors: Gao Chunfang , Lee Choong Hyun , Wei Xiaoji , Gong Yong
Published: October 2023

In the blind reception of non‐cooperative signals in short‐time burst communication, signal time domain detection is the premise and key of signal modulation parameter estimation, signal demodulation, decoding, interpretation, information acquisition and interference guidance. In this paper, the semi‐blind demodulation method of short‐time burst FM‐MFSK signal is studied under the condition of low signal‐to‐noise ratio. A short‐time burst FM‐MFSK semi‐blind demodulation method based on STFT is proposed. When SNR is higher than 3 dB, the correct demodulation probability for FM‐MFSK signal can reach 90%.
A robust watermarking algorithm against JPEG compression based on multiscale autoencoder
Authors: Zhang Wei , Chen Rongrong , Wang Bin
Published: October 2023

The network structure of digital watermarking algorithm based on deep learning is usually encoder‐noise layer‐decoder. Most of the existing encoders suffer from the problem of insufficient feature extraction, and the introduction of simulated differentiable joint photographic experts group (JPEG) compression in the noise layer cannot ensure the robustness under real JPEG. In this paper, a watermarking algorithm based on multi‐scale auto‐encoder is proposed, which can effectively extract the image feature information by combining with the channel attention mechanism. At the same time, some parameters of decoder and encoder are shared to reduce redundant feature embedding and improve extraction accuracy. This paper also proposes a robust training scheme against JPEG compression, which can guide the model to store the watermark in the low‐frequency region needed for decoding. Experimental results show that the peak signal‐to‐noise ratio (PSNR) of the proposed algorithm is above 48 and the decoding rate is above 99% under JPEG compression with quality factor Q = 50. Moreover, this scheme can effectively promote the combination of noise layer in training. In addition, the proposed algorithm is also robust to other common network noises.
Investigation of cell damage of periodontopathic bacteria exposed to silver, zirconium oxide, and silicon oxide nanoparticles as antibacterial agents
Authors: Dağlıoğlu Yeşim , Yavuz Mustafa Cihan , Ertürk Omer , Ameen Fuad , Khatami Mehrdad
Published: October 2023

Antibiotic resistance is one of the biggest public health problems of our time. The nanoparticles are a powerful alternative to these antibiotics. Engineered nanoparticles show toxic effects on bacteria by different mechanisms. The bacteria–cell interaction of engineered nanoparticles exerts their toxic effects through changes in cell wall, cell membrane, and cytoplasm content/density. Thus, death occurs as a result of cell deformation. In this study, the cellular damage of silver nanoparticles, which are known to have strong antibacterial properties, and zirconium oxide and silicon oxide engineering nanoparticles, which are less known, on periodontopathic (Prevotella intermedia and Aggregatibacter actinomycetemcomitans) bacteria, were investigated by ultrastructural changes. The lysis of the cytoplasm and separation of the membrane cytoplasm were observed. Both types of bacteria treated with Ag ENP show more hollow cytoplasm than bacteria treated with the other two nanoparticles.
Wind-mass transfer in S-type symbiotic binaries
Authors: Skopal A. , Shagatova N.
Published: October 2023

Context. Observational indications of wind-mass transfer from an evolved giant to its distant white dwarf (WD) companion in symbiotic binaries are rare. Here, we present a way to examine the neutral wind from the giant in symbiotic binaries, which is temporarily observable throughout the orbital plane during outbursts.

Aims. We find that the mass-loss rate from giants in the orbital plane of S-type symbiotic binaries is high, indicating a high wind-mass-transfer efficiency in these systems.

Methods. We modeled hydrogen column densities in the orbital plane between the observer and the WD for all suitable eclipsing S-type symbiotic binaries during outbursts in any orbital phase.

Results. The mass-loss rate from the giant in the orbital plane is on the order of 10−6 M⊙ yr−1, which is a factor of ∼10 higher than rates derived from nebular emission produced by the ionized wind from normal giants in symbiotic stars. This finding suggests a substantial focusing of the giant’s wind toward the orbital plane and, thus, its effective transfer onto the WD companion.

Conclusions. Our finding suggests that wind focusing on the orbital plane may be a common property of winds from giants in S-type symbiotic stars. Such wind-focusing resolves a long-standing problem of the large energetic output from their burning WDs and deficient fueling by the giant via a standard Bondi–Hoyle accretion. It also allows the WD to grow faster in mass, which lends support to the possibility that S-type symbiotic binaries are progenitors of Type Ia supernovae.
Solitonic Neural Network: A novel approach of Photonic Artificial Intelligence based on photorefractive solitonic waveguides
Authors: Bile Alessandro , Tari Hamed , Pepino Riccardo , Nabizada Arif , Fazio Eugenio
Published: October 2023

Neuromorphic models are proving capable of performing complex machine learning tasks, overcoming the structural limitations imposed by software systems and electronic neuromorphic models. Unlike computers, the brain uses a unified geometry whereby memory and computation occur in the same physical location. The neuromorphic approach tries to reproduce the functional blocks of biological neural networks. In the photonics field, one possible and efficient way is to use integrated circuits based on soliton waveguides, ie channels self-written by light. Thanks to the nonlinearity of some crystals, propagating light can write waveguides and then can modulate them according to the information it carries. Thus, the created structures are not static but they can self-modify by varying the input information pattern. These hardware systems show a neuroplasticity which is very close to the one which characterize the brain functioning. The solitonic neuromorphic paradigm this work introduces is based on X-junction solitonic neurons as the fundamental elements for complex neural networks. These solitonic units are able to learn information both in supervised and unsupervised ways by unbalancing the X-junction. The storage of information coincides with the evolution of structure that changes plastically. Thus, complex solitonic networks can store information as propagation trajectories and use them for reasoning.
Non-returning deterministic and nondeterministic finite automata with translucent letters
Authors: Mráz František , Otto Friedrich
Published: October 2023

Here, we propose a variant of the nondeterministic finite automaton with translucent letters (NFAwtl), which, after reading and deleting a letter, does not return to the left end of its tape, but instead continues from the position of the letter just deleted. When the end-of-tape marker is reached, our automaton can decide whether to accept, reject, or continue, which means that it reads the remaining tape contents again from the beginning. This type of automaton, called a non-returning finite automaton with translucent letters or an nrNFAwtl, is strictly more expressive than the NFAwtl. We study the expressive capacity of this type of automaton and that of its deterministic variant, comparing them to various other types of finite automata that do not simply read their input from left to right. Also, we are interested in the closure properties of the resulting classes of languages and in the complexity of the fixed membership problem.
Advocating for an open communication culture in perfusion and cardiothoracic community: a call to action
Authors: Butt Salman Pervaiz , Saleem Yasir , Cook Bill
Published: October 2023

This article advocates for an open communication culture in the perfusion and cardiothoracic community to enhance patient safety during surgery. All team members, including nurses, anesthesiologists, and perfusionists, should actively contribute their insights. Empowering perfusionists to voice concerns without fear of repercussions is crucial. Involvement in debriefs, root cause analyses and data management systems aids continuous improvement. A robust speak-up culture prevents unsafe practices and elevates perfusion care standards, leading to better patient outcomes.