Article
Computer Science, Information Systems
A. Sherly Alphonse, N. Ani Brown Mary
Summary: Accurate classification of antioxidant proteins is crucial for the development of drugs for various diseases. This study proposes a novel methodology using feature composition and dimension reduction techniques for the accurate classification of antioxidant proteins.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Review
Pharmacology & Pharmacy
Maria Gallo, Sira Defaus, David Andreu
Summary: G protein-coupled receptors (GPCRs) are usually described as monomeric transmembrane receptors, but increasing evidence shows that many GPCRs actually form higher-order assemblies. The formation, structure, physiological roles, and potential therapeutic applications of these assemblies are actively being explored. This review provides a comprehensive overview of GPCR complexes, with a focus on disrupting GPCRs using peptides mimicking transmembrane domains involved in multimerization. Recent strategies for developing drug-like versions of these transmembrane peptide candidates for therapeutic applications are also highlighted.
Article
Biochemistry & Molecular Biology
Mingcheng Qian, Zhengyang Sun, Xin Chen, Serge Van Calenbergh
Summary: This review provides an overview of the design strategy of bivalent ligands for G protein-coupled receptors (GPCRs) and mainly focuses on their application in studying and detecting GPCR dimerization in vitro and in vivo. Bivalent ligands have specific properties and are capable of binding to GPCR homodimers or heterodimers simultaneously, showing specific signal transduction compared to monovalent ligands.
BIOORGANIC CHEMISTRY
(2023)
Article
Biochemical Research Methods
Jooseong Oh, Hyi-Thaek Ceong, Dokyun Na, Chungoo Park
Summary: In this study, a machine learning model was developed to identify GPCR agonists and antagonists. The model showed high accuracy in classifying ligands and can be applied in virtual screening for potential GPCR-binding agonists and antagonists.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Bharat Poudel, T. Rajitha Rajeshwar, Juan M. Vanegas
Summary: This study demonstrates that membrane-mediated activation of the AT1 receptor produces distinct conformations compared to activation by AngII. This research provides structural insights into the mechanical activation of the AT1 receptor and its potential functional outcomes.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Ziyang Wang, Lin Yang, Yehua Sheng, Mi Shen
Summary: This paper proposes a method for segmenting pole-like objects under geometric structural constraints and combines classification results at different scales to effectively extract pole-like objects from point clouds in road scenes, achieving high-precision classification and identification.
Article
Genetics & Heredity
Wenxia Su, Shuyi Deng, Zhifeng Gu, Keli Yang, Hui Ding, Hui Chen, Zhaoyue Zhang
Summary: Apoptosis proteins play a crucial role in cellular apoptosis, regulating the balance between cell proliferation and death. The subcellular localization of these proteins is closely related to their functions and studying it is of great significance. This study proposes a novel method for predicting the subcellular location of apoptosis proteins using amphiphilic pseudo amino acid composition and support vector machine algorithm, achieving improved prediction accuracy.
FRONTIERS IN GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Muhammad Tariq, Vinitha Richard, Michael J. Kerin
Summary: This review article summarizes the current knowledge on breast tumor classification and explores the potential of transcriptomic profiling of tissue-specific microRNAs as prospective biomarkers for the diagnosis and subtyping of BLBC.
Review
Biochemistry & Molecular Biology
Libin Ye, Xudong Wang, Aidan McFarland, Jesper J. Madsen
Summary: Advances in X-ray crystallography and cryoelectron microscopy have provided insights into GPCR activation processes, but these static structures have limitations in revealing dynamics and conformational transitions. Developing NMR techniques can lead to a more comprehensive understanding of signaling processes, but challenges remain.
Article
Endocrinology & Metabolism
Shuya Shao, Dan Yao, Senya Li, Jing Li, Yufang Si, Huiping Zhang, Zhongliang Zhu, Dongli Song, Hui Li
Summary: The study found that prenatal stress can lead to gender-dependent depressive-like behavior in adolescent female rats, with the neuro-physiological mechanisms primarily involving the expression of the N-cadherin-GluA1 pathway. By administering appropriate treatments, depressive-like behavior in adolescent female offspring following PS can be improved.
NEUROENDOCRINOLOGY
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Alain B. Tchagang, Julio J. Valdes
Summary: This study proposes a new scheme for inverse design of molecules based on a classification paradigm that outputs the atomic composition of molecules given the targeted electronic properties as input. Experimental results demonstrate that this approach can achieve high accuracy. It can be extended to other drug properties, not just electronic properties of molecules.
2022 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (IEEE CIBCB 2022)
(2022)
Article
Physics, Multidisciplinary
Mirza Mumtaz Zahoor, Shahzad Ahmad Qureshi, Asifullah Khan, Aziz ul Rehman, Muhammad Rafique
Summary: In this study, a dual-channel brain tumor detection framework is proposed to improve the detection performance by using dynamic and static features. Computer experiments on a public brain tumor dataset show that the proposed framework outperforms other existing methods with high accuracy and F-score.
WAVES IN RANDOM AND COMPLEX MEDIA
(2022)
Article
Chemistry, Multidisciplinary
Aqsa Kiran, Shahzad Ahmad Qureshi, Asifullah Khan, Sajid Mahmood, Muhammad Idrees, Aqsa Saeed, Muhammad Assam, Mohamad Reda A. Refaai, Abdullah Mohamed
Summary: This paper proposes a new deep learning-based methodology that achieves a more efficient feature database through the collaboration of two effective models without using image metadata. Experiments show that the retrieval accuracy of this method is generally 97% under different types of noise.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Physical
Faisal Hayat, Nabila Rauf, Ziaur Rehman, Francine Belanger-Gariepy
Summary: This study reports the synthesis and characterization of a series of compounds with hydroxyethyl substituents, highlighting their importance in the supramolecular organization. The compounds exhibit different coordination geometries, and H-bonding interactions play a crucial role in the crystal packing.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Multidisciplinary Sciences
Muhammad Asam, Saddam Hussain Khan, Altaf Akbar, Sameena Bibi, Tauseef Jamal, Asifullah Khan, Usman Ghafoor, Muhammad Raheel Bhutta
Summary: The interaction between devices, people, and the Internet has led to the emergence of IoT, introducing security challenges. This study proposes a CNN-based IoT malware detection architecture to address the malware detection challenge in IoT devices. The proposed architecture achieves promising malware detection capacity with 97.93% accuracy, demonstrating potential for extended applications in the future.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Shahbaz Ahmad, Umer Farooq, Mushtaq Hussain Lashari, Musadiq Idris, Zia Ur-Rehman, Nasrullah Khan, Nouman Sajjad
Summary: This study aimed to develop a portable hematological formula for estimating hemoglobin in Cholistani breed of cattle in the Cholistan desert in Pakistan. The study validated the rule of calculating hemoglobin concentration as one-third of packed cell volume (PCV) used in human medicine. The results showed a positive correlation between hemoglobin and PCV in the Cholistani cattle. The study concluded that the conventional formula used in human medicine cannot be applied to cattle, and a different equation, Hb (g/dL) = 0.13 (PCV) + 6.3, may provide reliable results for hemoglobin estimation from PCV in cattle.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Immunology
Zhewei Zhang, Ke Xiao, Sheng Wang, Abdur Rahman Ansari, Xiaoyu Niu, Wenjie Yang, Mengqi Lu, Zhi Yang, Zia ur Rehman, Weihua Zou, Weicheng Bei, Hui Song
Summary: This study investigated the regulatory mechanisms of visfatin in inflammation and apoptosis in RAW264.7 cells and mice immune organs. The results showed that visfatin can modulate inflammation and apoptosis by regulating various signaling pathways and the expression levels of cytokines.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Applied
Shaista Ramzan, Shahnaz Rahim, Syed Tasleem Hussain, Katherine B. Holt, Jeremy Karl Cockcroft, Niaz Muhammad, Zia Ur-Rehman, Asif Nawaz, Shaukat Shujah
Summary: In this study, four new diorganotin(IV) complexes were synthesized and their structures were characterized by various techniques including FT-IR, H-1 NMR, C-13 NMR, and mass spectrometry. The results confirmed the formation of tin-oxygen and tin-nitrogen bonds during complex formation, as well as the presence of penta-coordinated structures. The interaction between the complexes and DNA was found to be intercalative in nature, and the binding ability of complex 3 with SS-DNA was the highest. The electrochemical and thermodynamic parameters were also calculated, and complex 2 showed significant antioxidant activity.
APPLIED ORGANOMETALLIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Swapnil Potdar, Filipp Ianevski, Aleksandr Ianevski, Ziaurrehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli Kallioniemi, Paeivi Ostling, Tero Aittokallio, Jani Saarela
Summary: Functional precision medicine (fPM) simplifies the search for appropriate applications of existing molecules and enhances therapeutic potential. The latest version of Breeze (release 2.0) provides advanced data exploration capabilities and interactive visualization options for accurate interpretation of drug sensitivity and resistance data. It allows integration and cross-comparison of user-uploaded data with publicly available drug response datasets.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Anum Mushtaq, Irfan Ul Haq, Muhammad Azeem Sarwar, Asifullah Khan, Wajeeha Khalil, Muhammad Abid Mughal
Summary: Intelligent traffic management systems have gained significant attention in Intelligent Transportation Systems (ITS), and Reinforcement Learning (RL) based control methods have become increasingly popular in applications such as autonomous driving and traffic management solutions in ITS. This paper proposes an approach based on Multi-Agent Reinforcement Learning (MARL) and smart routing to improve the flow of autonomous vehicles on road networks. The evaluation of Multi-Agent Advantage Actor-Critic (MA2C) and Independent Advantage Actor-Critical (IA2C) shows the potential of these recently suggested techniques for traffic signal optimization. The effectiveness and reliability of the method are demonstrated through simulations using SUMO, a software modeling tool for traffic simulations.
Review
Chemistry, Analytical
Syed Niaz Ali Shah, Eman Gul, Faisal Hayat, Ziaur Rehman, Mashooq Khan
Summary: This review provides a detailed summary of sulfite-based chemiluminescence (CL) systems, focusing on the impact of various enhancers. The role of metal ions, solvents, nanomaterials, and carbon dots in the CL system is discussed, along with recent developments and strategies employed to enhance the system. The study highlights the importance of understanding the mechanisms and effects of enhancers on the efficiency of the sulfite CL system for designing selective and sensitive detection systems.
Review
Chemistry, Inorganic & Nuclear
Haseeb Ullah, Zahid Haneef, Abrar Ahmad, Ian S. Butler, Rebwar Nasir Dara, Ziaur Rehman
Summary: Semiconductor photocatalytic technology driven by solar energy is an attractive strategy to address environmental pollution issues. MoS2 and CdS, as semiconductor-based photocatalysts, have unique properties such as tunable bandgap, high absorption of visible light, and efficient charge transfer, making them ideal for water decontamination. This review covers the mechanism of semiconductor photocatalysis, synthesis strategies for MoS2 and CdS nanostructured photocatalysts, and their applications in wastewater treatment. It also discusses potential approaches to enhance their photocatalytic performance, including morphology modification, heteroatom doping, and nanocomposite formation with metal sulfides, metal oxides, or carbon compounds.
INORGANIC CHEMISTRY COMMUNICATIONS
(2023)
Article
Computer Science, Information Systems
Faiza Babar Khan, Muhammad Hanif Durad, Asifullah Khan, Farrukh Aslam Khan, Sajjad Hussain Chauhdary, Mohammed Alqarni
Summary: Malware is a significant threat to information security, and efficient anti-malware software is crucial for protection. However, identifying malware remains challenging, especially with unknown samples. In this paper, a novel architecture based on the Relation Network is proposed for Few-Shot Learning (FSL) implementation, achieving improved classification accuracy by up to 94% with only one training instance.
Article
Biochemistry & Molecular Biology
Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Katrina Exter, Sven Fahrner, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjoern Gruening, Kim Tamara Gurwitz, John M. Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Carla Lancelotti, Jessica Klemeier, Jean-Luc Legras, Allyson L. Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Michaela Th Mayrhofer, Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
Summary: The main goals of the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows. This article presents key findings and recommendations for generating and establishing sustainable life science resources based on the work done within the EOSC-Life consortium. The article also highlights the challenges to sustainability in the life sciences and how EOSC-Life provides a model for sustainable data management according to FAIR principles.
Article
Multidisciplinary Sciences
Yinyin Wang, Jehad Aldahdooh, Yingying Hu, Hongbin Yang, Markus Vaha-Koskela, Jing Tang, Ziaurrehman Tanoli
Summary: The drug development process is time-consuming and costly, leading to the popularity of repurposing old drugs for cancer and rare diseases. This study presents a novel scoring algorithm based on chemical and genomic data to repurpose drugs for various diseases. The algorithm is strengthened by integrating comprehensive manually curated datasets for each data type.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Eugene F. Douglass, Robert J. Allaway, Bence Szalai, Wenyu Wang, Tingzhong Tian, Adria Fernandez-Torras, Ron Realubit, Charles Karan, Shuyu Zheng, Alberto Pessia, Ziaurrehman Tanoli, Mohieddin Jafari, Fangping Wan, Shuya Li, Yuanpeng Xiong, Miquel Duran-Frigola, Martino Bertoni, Pau Badia-I-Mompel, Lidia Mateo, Oriol Guitart-Pla, Verena Chung, Jing Tang, Jianyang Zeng, Patrick Aloy, Julio Saez-Rodriguez, Justin Guinney, Daniela S. Gerhard, Andrea Califano
Summary: The Columbia Cancer Target Discovery and Development Center is developing a resource called PANACEA to study tumor-specific drug mechanisms of action. This resource is used as the basis for a DREAM Challenge to assess the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions.
CELL REPORTS MEDICINE
(2022)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)