bluuebunny/crossref_metadata_2025_split huggingface dataset:
How the technologies behind self‐driving cars, social networks, ChatGPT, and DALL‐E2 are changing structural biology
Authors: Bochtler Matthias 
Published: October 2024

AbstractThe performance of deep Neural Networks (NNs) in the text (ChatGPT) and image (DALL‐E2) domains has attracted worldwide attention. Convolutional NNs (CNNs), Large Language Models (LLMs), Denoising Diffusion Probabilistic Models (DDPMs)/Noise Conditional Score Networks (NCSNs), and Graph NNs (GNNs) have impacted computer vision, language editing and translation, automated conversation, image generation, and social network management. Proteins can be viewed as texts written with the alphabet of amino acids, as images, or as graphs of interacting residues. Each of these perspectives suggests the use of tools from a different area of deep learning for protein structural biology. Here, I review how CNNs, LLMs, DDPMs/NCSNs, and GNNs have led to major advances in protein structure prediction, inverse folding, protein design, and small molecule design. This review is primarily intended as a deep learning primer for practicing experimental structural biologists. However, extensive references to the deep learning literature should also make it relevant to readers who have a background in machine learning, physics or statistics, and an interest in protein structural biology.
O‐GlcNAcylation regulates osteoblast differentiation through the morphological changes in mitochondria, cytoskeleton, and endoplasmic reticulum
Authors: Weng Yao , Wang Ziyi , Sitosari Heriati , Ono Mitsuaki , Okamura Hirohiko , Oohashi Toshitaka 
Published: October 2024

AbstractTo explore the potential mechanisms which O‐linked‐N‐acetylglucosaminylation (O‐GlcNAcylation) regulates osteogenesis, a publicly RNA‐seq dataset was re‐analyzed with literature‐mining and showed the primary targets of O‐GlcNAcylation in osteoblasts are mitochondria/cytoskeleton. Although the O‐GlcNAcylation‐regulated mitochondria/cytoskeleton has been extensively studied, its specific role during osteogenesis remains unclear. To address this, we knocked out Ogt (Ogt‐KO) in MC3T3‐E1 osteoblastic cells. Then, significantly reduced osteoblast differentiation, motility, proliferation, mitochondria–endoplasmic reticulum (Mito–ER) coupling, volume of ER, nuclear tubulins, and oxygen metabolism were observed in Ogt‐KO cells. Through artificial intelligence (AI)‐predicted cellular structures, the time‐lapse live cells imaging with reactive‐oxygen‐species/hypoxia staining showed that lower cell proliferation and altered oxygen metabolism in the Ogt‐KO cells were correlated with the Mito–ER coupling. Bioinformatics analysis, combined with correlated mRNA and protein expression, suggested that Ezh2 and its downstream targets (Opa1, Gsk3a, Wnt3a, Hif1a, and Hspa9) may be involved in O‐GlcNAcylation‐regulated Mito–ER coupling, ultimately impacting osteoblast differentiation. In conclusion, our findings indicate that O‐GlcNAcylation‐regulated osteoblast differentiation is linked to morphological changes in mitochondria, cytoskeleton, and ER, with Ezh2 potentially playing a crucial role.
Effect of Acupuncture on Cognitive Function in Patients With Post‐Stroke Cognitive Impairment: A Systematic Review and Meta‐Analysis
Authors: Luo Ziyan , Li Wenxuan , Jiang Jieting , Sun Jie , Zhang Mingyue , Zhang Yaqing , Dong Lu , Li Kunpeng , Wu Caiqin 
Published: October 2024

ABSTRACTAims and objectiveTo investigate the impact of acupuncture on post‐stroke cognitive impairment (PSCI).BackgroundPSCI is a major barrier to stroke patients’ rehabilitation, and acupuncture is one of the treatments. However, the benefit of acupuncture on PSCI is unclear.DesignA meta‐analysis and systematic review of randomized controlled trials (RCTs).MethodsUp to February 1, 2024, databases in PubMed, MEDLINE, Scopus, Embase, Web of Science, Cochrane Library, China National Knowledge Infrastructure, VIP, and Wanfang Data were searched. The risk of bias was investigated using the Cochrane Handbook for systematic reviews of treatments. Random‐effect and fix‐effect models were used to report the effects.ResultsThere were 29 randomized clinical trials with 2477 participants included. The findings demonstrated that the Mini‐Mental State Examination (MMSE) and the Montreal Cognitive Assessment (MoCA) scores were higher in the acupuncture group than medicine group (mean difference [MD] = 1.74, 95% confidence interval (CI) CI [1.26, 2.23], I2 = 59%, p < 0.01). Compared to medicine group, the Loewenstein Occupational Therapy Cognitive Assessment (LOTCA) score exhibited a significant decrease and demonstrated improvement in the acupuncture group. Statistically significant outcomes were observed in the Barthel Index scores and P300 event‐related potential (ERP). According to subgroup analysis, acupuncture was superior to conventional therapy for improving cognitive function in PSCI patients at 4 weeks after treatment.ConclusionAcupuncture therapy has shown promise in ameliorating cognitive deficits and enhancing daily functional abilities in individuals diagnosed with PSCI. But future research should focus on the duration and implement large sample, high‐quality RCTs.Relevance to clinical practiceClinical workers in practical clinical work can select appropriate acupoints according to the actual conditions of patients, as well as confirm the treatment course of PSCI patients, while paying attention to observing and evaluating the therapeutic efficacy of acupuncture, to improve the health outcomes of patients in a patient‐centered way.
Effect of Relaxation‐Based Virtual Reality on Psychological and Physiological Stress of Substance Abusers Under Detoxification: A Randomized Controlled Trial
Authors: Lotfinia Shahab , Yaseri Aram , Jamshidmofid Pardis , Nazari Fatemeh , Shahkaram Homa , Yaztappeh Jafar Sarani , Kianimoghadam Amir Sam 
Published: October 2024

AbstractIntroductionSubstance abuse is a widespread problem, with high rates of treatment dropout. Stress plays a crucial role in this problem, so innovative interventions with stressed patients can assist them in completing treatment.MethodsThis study is a randomized controlled trial with 60 participants who have substance abuse disorder undergoing detoxification at a residency facility in Tehran, Iran. Participants were randomly assigned to one of three groups: watching a 360° video of nature, a 360° video of a city environment, or no virtual experience. The intervention was performed only for one session. Psychological stress was measured using the Positive and Negative Affect Schedule and Perceived Stress Scale before and after the intervention. Physiological stress was assessed through respiratory rate, skin conductance, and heart rate recordings during the virtual reality (VR) experience. Data analysis was performed using R software (version 4.2).ResultsPaired t‐test results indicated significant psychological differences before and after virtual nature experiences, but not in the control and city groups. The repeated measure ANOVA showed a significant reduction in skin conductance (p < 0.01) and respiratory rate (p < 0.01) scores in the nature group.ConclusionThe findings suggest that VR relaxation could be a potentially beneficial intervention for reducing stress in patients during detoxification.
Crown‐Ether‐Based Artificial K+ Selective Ionic Filter
Authors: Xin Pengyang , Jiu Zhihui , Shi Linlin , Shu Yuqing , Song Yufei , Sun Yonghui 
Published: October 2024

AbstractIn this study, we have successfully synthesized bis (cholesterol‐dibenzo‐18‐crown‐6‐ether)‐pillar[5]arene compound 1 through a click reaction, which could spontaneously insert into lipid bilayers to form ion channel due to the membrane anchor cholesterol group and show significant transport activity of K+ superior to Na+, with a permeability ratio of K+/Na+ equal to 4.58. Compound 1 two crown ether modules act as selective filters similar to natural K+ channel, which are determined to 1 : 2 binding stoichiometry to K+ by Job's plot and NMR titration. This structurally unambiguously unimolecule artificial channel provides ideas for constructing highly K+/Na+ selective molecular filters.
Heterogenization of Palladium Trimer and Nanoparticles Through Polymerization Boosted Catalytic Efficiencies in Recyclable Coupling and Reduction Reactions
Authors: Wang Miaomiao , He Zhixin , Chen Meng , Fu Fangyu , Wang Yanlan 
Published: October 2024

AbstractThe development of heterogeneous palladium catalysts has shown continuous vitality in the field of catalysis and materials. In this work, we report one concise free radical polymerization approach to accomplish the aromatic palladium trimer functionalized polymers PSSy‐[Pd3]+ (2) and its derived palladium nanoparticles (3). Full characterizations could confirm the successful combination of cationic [Pd3]+ or nanoparticles with poly(p‐sulfonated styrene) skeleton. Compared to their monomeric tri‐palladium precursor (1) and common Pd(dba)2, Pd(PPh3)4, Pd(OAc)2, heterogeneous PSSy‐[Pd3]+ (2) shows much superior catalytic activities (0.15 mol %, TOF=1333.3 h−1) in the SMCC reaction. The identically ligated PdNPs (3) are formed in‐suit in the presence of NaBH4 and accomplish quantitative reduction of 4‐nitrophenol in just 320 s (0.50 mol %, TOF=2250 h−1). Moreover, these heterogeneous catalysts are reused for 5–6 times without significant loss of catalytic activity. Their superior catalytic ability is probably attributed to the synergistic effect of polymer entanglement and the tri‐palladium fragment. This work enlightens that the immobilization of palladium clusters or nanoparticles by polymerization could offer multiple advantages in stability, efficiency and recyclability for their involved catalyses and show far‐reaching future implications.
De Novo Design of Tryptophan Containing Broad‐Spectrum Cationic Antimicrobial Octapeptides
Authors: Sarkar Tanumoy , Vignesh S. R. , Kumar Sundaravadivelu Pradeep , Thummer Rajkumar P. , Satpati Priyadarshi , Chatterjee Sunanda 
Published: October 2024

AbstractWith the advent of antibiotic resistant organisms, development of alternate classes of molecules other than antibiotics to combat microbial infections, have become extremely important. In this context, antimicrobial peptides have taken center stage of antimicrobial therapeutic research. In this work, we have reported two cationic antimicrobial octapeptides WRL and LWRF, with broad spectrum antimicrobial activities against several strains of ESKAPE pathogens. Both the peptides were membrane associative and induced microbial cell death through membranolysis, being selective towards microbial membranes over mammalian membranes. The AMPs were unstructured in water, adopting partial helical conformation in the presence of microbial membrane mimics. Electrostatic interaction formed the primary basis of peptide‐membrane interactions. WRL was more potent, salt tolerant and faster acting of the two AMPs, owing to the presence of two tryptophan residues against that of one in LWRF. Increased tryptophan number in WRL enhanced its membrane association ability, resulting in higher antimicrobial potency but lower selectivity. This experimental and computational work, established that an optimum number of tryptophan residues and their position was critical for obtaining high antimicrobial potency and selectivity simultaneously in the designed cationic AMPs. Understanding the peptide membrane interactions in atomistic details can lead to development of better antimicrobial therapeutics in future.
Utility of The Paris System for Reporting Urinary Cytology in patients with HPV‐positive urinary tract carcinoma
Authors: Tanaka Kara , Kayraklioglu Neslihan , Chan Emily , Ding Chien‐Kuang C. , Vohra Poonam 
Published: October 2024

AbstractBackgroundHuman papillomavirus (HPV)‐positive urinary tract carcinomas (UTCas) have distinct morphology and molecular features with potential treatment implications. Cytomorphologic analysis of these tumors on urine cytology specimens has not yet been reported. The authors evaluated the cytomorphologic findings of HPV‐positive UTCa on urine cytology using The Paris System for Reporting Urinary Cytology (TPS) criteria.MethodsHPV‐positive cases were identified by a retrospective review of surgical specimens that had UTCa confirmed by HPV in situ hybridization. Cases that had concurrent urine cytology were reviewed using TPS. Cytomorphologic features of high‐grade urothelial carcinoma (HGUC) were evaluated as well as the presence of atypical squamous cells (ASCs) and basaloid features.ResultsSixteen cytology specimens from eight patients with HPV‐positive UTCa were included. On original diagnosis, none of the cytology specimens were suggested to be HPV‐associated. TPS diagnostic criteria identified eight cases with at least atypical findings, including five HGUC cases, one case that was suspicious for HGUC, and two atypical urothelial cases. Common cytomorphologic features included basaloid clusters (six of eight cases; 75%) and ASCs (four of eight cases; 50%) that matched the corresponding surgical specimens. Most cases exhibited urothelial cell hyperchromasia (seven of eight cases; 88%), and hypochromasia was a frequently observed variant (four of eight cases; 50%), either alone or in addition to hyperchromasia.ConclusionsHPV‐positive UTCa can be identified reliably as HGUC by using TPS criteria; however, these cases may not be recognized as HPV‐associated. The presence of basaloid cells or ASCs can help suggest screening for HPV in urine specimens. Larger scale studies are warranted to validate cytomorphologic differences and determine the impact of HPV infection on clinical outcomes for patients with UTCa.
Trichosanthes Cucumerina Derived Activated Carbon: The Potential Electrode material for High Energy Symmetric Supercapacitor
Authors: Joseph Anit , Mathew Arshitha , Thomas Tiju 
Published: October 2024

AbstractHigh surface area porous activated carbons obtained from sustainable biomass are excellent functional materials for energy storage applications. This is the first report on snake gourd (Trichosanthes cucumerina) pericarp as a raw material of activated carbon and supercapacitor electrode material. Herein, a simple KOH activation and carbonisation method is used. The obtained SGC900 sample has a surface area of 1841 m2/g and an average pore volume of 0.52 cm3/g. SGC900 based supercapacitor exhibits good electrochemical storage capacity in 1 M H2SO4 with a specific capacitance of 206 F/g at 1 A/g. The symmetric device delivered an energy density of 11 Wh/kg at a power density of 1.6 kW/kg. It provides a series resistance (Rs) of 1.2 Ω and a charge transfer resistance Rct of 1.9 Ω. Furthermore, the device retains 95 % of capacitance over 5000 cycles. This work presents an easy and feasible approach for producing value‐added activated carbon from sustainable biomass, potentially used in high‐performance energy storage.
Genetic Modification of Mice Using Prime Editing
Authors: Salem Amr R. , Xie Xiaoling , Griffin Susan H. , Gan Lin , Miano Joseph M 
Published: October 2024

AbstractGenetically modifying mice traditionally involved complex methods of designing and validating targeting constructs, embryonic stem cell electroporation and selection, blastocyst injection, and breeding chimeras for germline transmission. Such arduous steps were best carried out by specialized gene targeting cores in academia or through expensive commercial vendors. Further, the time from initiation to completion of a project often took at least 1 year and, in some cases, much longer (or never), with no guarantees of success. The RNA‐programmable CRISPR system of gene editing has greatly streamlined the generation of gene modifications (e.g., small substitutions, insertions, and deletions) in the mouse with high rates of success. Several editing platforms exist for gene/genome targeting in mice and other animal models previously difficult or impossible to alter. Here, we provide a simplified method of generating genetically modified mice using the prime editing platform. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Design, cloning, and synthesis of engineered pegRNA (epegRNA)Basic Protocol 2: Microinjection of PE2 components into mouse zygoteBasic Protocol 3: Genotyping founder mice and breeding for germline transmission
Preparation and Photophysical Properties of Znq2 Metallic Nanomaterials
Authors: Li Fulian , Long Yunshuai , Huang Xin , Ma Penghui , Huang Guiyi , Song Yumin 
Published: October 2024

AbstractBis(8‐hydroxyquinolates) Zinc (Znq2) can be used as a light‐emitting layer material in OLED devices to achieve its efficient electroluminescence effect. In this paper, Znq2 powder has been successfully synthesized and modified by the physical vapor deposition (PVD) method. Precursors and nano‐materials are characterized by XRD, SEM, PL, and so on. The performance of the modified material has been significantly improved. The emission intensity and absorption intensity in the deposited products increased with the increase in PVD temperature. At 453 K, luminous properties such as luminous intensity reach the optimal value including its fluorescence lifetime. Fluorescence lifetime values vary from 13 to 17 ns with the increase in temperature. The luminescence mechanism is also discussed. The energy gap and absorption spectrum of HOM‐LUMO are calculated by the DFT/UB3LYP method. The experimental values agree well with the theoretical values. The nanomaterial crystals modified by PVD technology are more orderly, impurities are reduced, and the luminous stability of the material is improved, which may be one of the reasons for the relatively slow decline in product life. The research combined with theoretical simulation is expected to be helpful to the research and promotion of such materials.
Repotrectinib: Redefining the therapeutic landscape for patients with ROS1 fusion‐driven non‐small cell lung cancer
Authors: Desilets Antoine , Repetto Matteo , Drilon Alexander 
Published: October 2024

AbstractThe ROS1 proto‐oncogene encodes a receptor tyrosine kinase with structural homology to other oncogenic drivers, including ALK and TRKA‐B‐C. The FDA‐approved tyrosine kinase inhibitors (TKIs) crizotinib and entrectinib have demonstrated efficacy in treating ROS1 fusion‐positive NSCLC. However, limitations such as poor blood‐brain barrier penetration and acquired resistance, particularly the ROS1 G2032R solvent‐front mutation, hinder treatment durability. Repotrectinib, a next‐generation macrocyclic TKI, was rationally designed to overcome on‐target resistance mutations and improve brain distribution through its low molecular weight. In the TRIDENT‐1 clinical trial, repotrectinib demonstrated significant efficacy in both TKI‐naïve and TKI‐pretreated patients with ROS1‐rearranged NSCLC, including those with CNS metastases and G2032R resistance mutations. In the TKI‐naïve cohort (n = 71), 79% of patients achieved an objective response, with a median progression‐free survival (PFS) of 35.7 months, surpassing all previously approved ROS1 TKIs. In patients who had received one prior ROS1 TKI but were chemotherapy‐naïve (n = 56), objective responses were observed in 38%, and median PFS was 9.0 months. The safety profile of repotrectinib was consistent with earlier‐generation ROS1 TKIs and common adverse events included anemia, neurotoxicity, increased creatine kinase levels, and weight gain. These findings underscore the potential of repotrectinib to address unmet needs in ROS1‐rearranged NSCLC, offering durable responses and improved intracranial activity. Future research should prioritize developing next‐generation, selective ROS1 inhibitors to reduce Trk‐mediated toxicities and improve treatment tolerance.
MDM‐Incorporated Quad Donut Modes OCDMA‐FSO Scheme for Secure High‐Altitude Platforms‐To‐Satellite Scenarios
Authors: Kumari Meet , Mishra Satyendra K. 
Published: October 2024

ABSTRACTThe next generation of communication networks is envisioned to be driven by high‐altitude platform (HAP)‐to‐satellite systems. License‐free narrow beam free space optics (FSO) can provide uninterrupted connectivity in satellite‐enabled Internet of Things scenarios. This work proposes a HAP‐to‐satellite hybrid mode division multiplexing–optical code division multiple access (MDM‐OCDMA) scheme employing zero cross‐correlation (ZCC) and multidiagonal (MD) codes. In high‐speed satellite communications, a 12 × 10‐Gbps hybrid MDM‐OCDMA scheme carrying four donut modes (0, 1, 2, and 3) enables high channel capacity, sufficient spectral efficiency, and data security under severe link conditions. Based on simulations, the hybrid MDM‐OCDMA scheme using the ZCC code achieves a greater FSO link distance of 420 m compared with when using the MD code at a 10e‐9 error correction limit under clear air and weak turbulent scenario. The reliable transmission distance of 250 m is achievable with the 120‐Gbps proposed system, assuming pointing errors of 2 mrad, 1‐dB receiver, and 2.5‐dB transmitter losses. The results also show that the system can sustain an additional loss of 1.5–2 dB over 250 m for all donut modes. Additionally, the system using ZCC code contributes to low power consumption over MD and variable weight ZCC code and thus requires a minimum received power of −4.02 dBm. It also offers high optical signal to noise of 42–52 dB, −11.58 to −22.20 dB of gain, 11.58–22.20 dB of noise figure, and −48.11 to −58.73 dBm of signal power at output over 200–700 m range up to 2 dB of additional loss. Comparative analysis indicates that the proposed system is more efficient, less complex, adequately distance‐friendly (=420 m), and capable of higher data rates (=120 Gbps) compared with other works. This makes it a promising solution for future high‐speed satellite communications considering the impact of link losses and atmospheric conditions.
RecQ protein‐like 4 drives cisplatin chemosensitivity of cervical cancer cells by modulating annexin A2
Authors: Wang Ruixue , Zhang Yunyan 
Published: October 2024

AbstractCervical cancer is a common malignant tumor in women with high morbidity and mortality. Chemotherapy drugs such as cisplatin (DDP) are easy to cause chemotherapy resistance and affect the therapeutic effect. Hence, it is critical to design new therapies that can reverse chemotherapy resistance and increase sensitivity to chemotherapy drugs. This study investigated the function of RecQ protein‐like 4 (RECQL4) in DDP‐resistant cervical cancer cells and its regulatory mechanism. By constructing DDP‐resistant Hela and CaSki cell lines, it was found that RECQL4 expression was elevated. RECQL4 knockdown is able to promote apoptosis, DNA damage, and increase the DDP sensitivity in cervical cancer cells. In vivo experiments have demonstrated that knockdown of RECQL4 suppresses tumor growth and promotes tumor apoptosis. Next, we investigated the potential regulatory relationship of RECQL4 to Annexin A2 (ANXA2). The results demonstrated that RECQL4 binds to ANXA2. Knockdown of RECQL4 downregulates the ANXA2 expression via promoting ubiquitination. Furthermore, we also found that ANXA2 overexpression partially abolished the role of RECQL4 knockdown in promoting apoptosis and DNA damage of cervical cancer cells, suggesting that RECQL4 plays a role in DDP sensitivity of cervical cancer cells by mediating ANXA2. In conclusion, the present study suggests that knocking down RECQL4 reduces DDP sensitivity in cervical cancer cells by modulating ANXA2. Targeting RECQL4 therapy may be a new strategy to improve chemosensitivity of cervical cancer cells.