Current Medicinal Chemistry - Volume 32, Issue 27, 2025
Volume 32, Issue 27, 2025
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Implementation of an Automated System using Machine Learning Models to Accelerate the Process of In Silico Identification of Small Molecules as Drug Candidates
More LessDrugs are commonly utilized to diagnose, cure, or prevent the occurrence of diseases, as well as to restore, alter, or change organic functions. Drug discovery is a time-consuming, costly, difficult, and inefficient process that yields very few medicinal breakthroughs. Drug research and design involves the capturing of structural information for biological targets and small molecules as well as various in silico methods, such as molecular docking and molecular dynamic simulation. This article proposes the idea of expediting computational drug development through a collaboration of scientists and universities, similar to the Human Genome Project using machine learning (ML) strategies. We envision an automated system where readily available or novel small molecules (chemical or plant-derived), as well as their biological targets, are uploaded to an online database, which is constantly updated. For this system to function, machine learning strategies have to be implemented, and high-quality datasets and high quality assurance of the ML models will be required. ML can be applied to all computational drug discovery fields, including hit discovery, target validation, lead optimization, drug repurposing, and data mining of small compounds and biomolecule structures. Researchers from various disciplines, such as bioengineers, bioinformaticians, geneticists, chemists, computer and software engineers, and pharmacists, are expected to collaborate to establish a solid workflow and certain parameters as well as constraints for a successful outcome. This automated system may help speed up the drug discovery process while also lowering the number of unsuccessful drug candidates. Additionally, this system will decrease the workload, especially in computational studies, and expedite the process of drug design. As a result, a drug may be manufactured in a relatively short time.
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Pressure Ulcers and Nutrients: From Established Evidence to Gaps in Knowledge
Pressure ulcers (PUs) are caused by continuous pressure or friction on the skin that damages tissue, especially over bony prominences. A critical factor in the development and progression of PUs is poor nutritional status, which often involves deficiencies in essential nutrients such as proteins, vitamins (A, C, D, E, K, and the B complex), and trace elements (including zinc, selenium, copper, iron, and manganese). These micronutrients are vital for effective wound healing, as they play significant roles in cellular repair, immune function, and tissue regeneration. Laboratory tests for serum albumin, prealbumin, transferrin, retinol-binding protein, and anthropometric measures like height, weight, and body mass index (BMI) are used to evaluate a patient's nutritional status. Screening tools such as the Mini Nutritional Assessment (MNA), Malnutrition Universal Screening Tool (MUST), LPZ questionnaire, and Subjective Global Assessment (SGA) are commonly employed. Emerging evidence from various studies, including in vitro, in vivo, and clinical trials, underscores the importance of personalized nutritional interventions in managing PUs. Unlike generic dietary plans, tailored nutrition that addresses the specific needs of individuals shows greater potential in promoting wound healing and improving clinical outcomes. This synthesis of existing research highlights the critical influence of micronutrients on the healing process of PUs. It suggests that a personalized approach to nutrition, which takes into account individual patient requirements and deficiencies, is likely to be more effective than a one-size-fits-all strategy in the management of these complex wounds.
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LncRNA TINCR: An Irreplaceable Biological Target in Human Malignancies
Authors: Dengke Jia, Yaping He and Yawu ZhangCurrently, malignant tumors increasingly affect young people, which has caused a catastrophic financial burden on people worldwide. lncRNA has gained considerable attention because of its importance in the early diagnosis and treatment of tumors. In addition, since terminal differentiation-induced ncRNA (abbreviated as TINCR) was reported in a Nature article, it has received focus on targeted therapy of tumors, especially in digestive system malignant tumors. This review aims to reveal and summarize its important molecular mechanisms in human malignancies. In this review, relevant research works involving the relationship between TINCR and human malignancies are gathered through systematic retrieval of PubMed. TINCR is expressed bidirectionally in human malignancies. TINCR functions primarily as a ceRNA in human malignancies, and it also functions at the transcriptional level. Moreover, lncRNA TINCR has the potential to become a novel biomolecular marker of human malignancies.
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Research Progress in the Small Molecule Smac Mimetics in Combination Therapy of Cancer
Authors: Jiang-Ting Zhao, Xiang Zheng, Guo-Wu Rao and Quan ZhengInhibitors of Apoptosis Proteins (IAP) are inhibitors that can block programmed cell death, are expressed at high levels in various cancers, and are recognized as a therapeutic target for cancer therapy. In the past few years, several small molecule IAP protein inhibitors have been designed to mimic the endogenous IAP antagonist, but no IAP inhibitors have been approved for marketing worldwide. Previously, xevinapant has been awarded a breakthrough therapy designation by the FDA. In addition, a combination of Smac mimetics and chemotherapeutic compounds has been reported to improve anticancer efficacy. According to the phase II clinical data, xevinapant has the potential to significantly enhance the standard therapy for patients with head and neck cancer, which is expected to be approved as an innovative therapy for cancer patients. Therefore, this paper briefly describes the mechanism of IAPs (AT-406, APG-1387, GDC-0152, TL32711, and LCL161) as single or in combination for cancer treatment, their application status as well as the synthetic pathway, and explores the research prospects and challenges of IAPs antagonists in the tumor combination therapy, with the hope of providing strong insights into the further development of Smac mimics in tumor therapy.
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Nanomedicine in Management of Cerebral Infarction and Brain Cancer: Role of Inflammation
Authors: Vikas Kumar, Fahad Al. Abbasi, Firoz Anwar and Jonathan A. LalCerebral infarction, the blockage of blood vessels in the brain, is generally an age-related illness. Factors such as unhealthy diets, stressful behaviours and decreased environmental consistency with physiological barriers also contribute to increased casualties. Long-term brain function reconstruction and successful drug therapy are needed. The most frequent malignant brain tumour, glioblastoma, has been linked to variations in mitochondrial ROS, chaperone-mediated autophagy, and the interaction between lncRNA (BC200) and miRNA. Glioblastoma stem cells express high levels of ATP/P2X7 receptors, promoting survival by activating M2 muscarinic receptors.
This expert opinion provides an overview of the latest experimental drug therapies aimed at protecting against and restoring cerebral stroke.
Nanomedicine overcomes the challenges associated with traditional therapy and physiological obstacles in the treatment of cerebral infarction by improving stroke management, including diagnosis, imaging, and treatment, addressing a diverse range of associated factors.
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Unveiling the Promising Role of Substance P/Neurokinin 1 Receptor in Cancer Cell Proliferation and Cell Cycle Regulation in Human Malignancies
Authors: Soodabeh Rezaei, Hossein Javid, Sonia Iranpour, Reza Assaran Darban and Seyed Isaac HashemyNeurokinin receptors are a family of G protein-coupled receptors that were first identified in the central and peripheral nervous systems. However these receptors were later found in other types of cells, therefore, new perspectives concerning their novel roles were described. Mammalian has three neurokinin receptors, among which neurokinin-1 receptors [NK1R] have been indicated to be involved in most, if not all, intracellular functions, primarily the regulation of cell proliferation. By interacting with its potent agonist, substance P [SP], NK1R can engage a variety of signaling pathways and serve as a platform for cells to proliferate by regulating the expression of the cell cycle-related genes. Furthermore, the activity of SP/NK1R is stimulated by various oncogenes, indicating the involvement of this pathway in human cancers. As a result, numerous NK1R antagonists have been investigated in oncology trials, and the promising anti-cancer effect of these receptors has opened up new possibilities for incorporating these antagonists into cancer treatment. Considering these factors, gaining a deeper understanding of the SP/NK1R pathway could offer significant advantages for cancer patients. The more knowledge we acquire about this pathway, the greater the potential for exploiting it in the development of effective treatment strategies. Here, we present a comprehensive review of the current knowledge pertaining to the biological function of the SP/NK1R, with a specific emphasis on its recently discovered role in the regulation of cell proliferation. Moreover, we provide insights into the impact of this pathway in human cancers, along with an overview of the most significant NK1R antagonists currently utilized in cancer research studies.
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The Mechanism of Action of Exosomes Derived from Glioblastoma Cells
Authors: Ozal Beylerli, Ilgiz Gareev, Tatiana Ilyasova, Elmar Musaev and Vladimir ChekhoninGlioblastoma (GBM) is a highly aggressive and lethal brain tumor characterized by rapid growth, invasive behavior, and resistance to conventional therapies, such as surgery, radiotherapy, and chemotherapy. Despite these interventions, patient survival remains poor due to the tumor’s ability to recur and adapt to treatments. The function of GBM-derived exosomes (GBM-exosomes) as essential mediators in tumor growth has drawn attention in recent years. These small extracellular vesicles are involved in the transfer of a variety of molecules, including cytokines, miRNAs, proteins, and DNA, facilitating intercellular communication that promotes GBM cell proliferation, angiogenesis, immune evasion, and resistance to therapies. This review aims to provide an in-depth examination of the mechanisms through which GBM-exosomes contribute to these pathological processes, as well as to discuss the current methodologies for isolating and characterizing GBM exosomes. Additionally, we explore the potential of exosomes as biomarkers for diagnosis and prognosis and as novel therapeutic targets in the fight against GBM. By improving our understanding of GBM-exosomes, we can pave the way for the development of more effective, personalized treatment strategies that may improve patient outcomes and quality of life.
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Exosome-Machine Learning Integration in Biomedicine: Advancing Diagnosis and Biomarker Discovery
More LessExosomes, small extracellular vesicles (sEVs) secreted by various cell types, play crucial roles in intercellular communication and are increasingly recognized as valuable biomarkers for disease diagnosis and therapeutic targets. Meanwhile, machine learning (ML) techniques have revolutionized biomedical research by enabling the analysis of complex datasets and highly accurate prediction of disease outcomes. Exosomes, with their diverse cargo of proteins, nucleic acids, and lipids, offer a rich source of molecular information reflecting the physiological state of cells. Integrating exosome analysis with ML algorithms, including supervised and unsupervised learning techniques, allows for identifying disease-specific biomarkers and predicting disease outcomes based on exosome profiles. Integrating exosome biology with ML presents a promising avenue for advancing biomedical research and clinical practice. This review explores the intersection of exosome biology and ML in biomedicine, highlighting the importance of integrating these disciplines to advance our understanding of disease mechanisms and biomarker discovery.
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Research Progress on Podocyte Pyroptosis in Diabetic Nephropathy
More LessPyroptosis is a recently discovered type of lytic-programmed cell necrosis. The process involves cells assembling an inflammasome and cleaving gasdermin (GSDM) to trigger the release of pro-inflammatory cytokines that eventually induce inflammatory cell death. Diabetic nephropathy (DN) is a microvascular complication of diabetes mellitus, which leads to end-stage renal disease. Podocyte damage or loss is an important feature of diabetic kidney injury. Pyroptosis involvement in podocyte injury is closely associated with DN progression, manifesting as increased renal fibrosis, glomerulosclerosis, and tubular injury. The study aims to elucidate the mechanism of pyroptosis and summarize the pathways and potential inhibitors related to pyroptosis activation in DN podocytes. We undertook a search of bibliographic databases for peer-reviewed research literature on various aspects of pyroptosis. Multiple different pathways mediate podocyte pyroptosis to promote DN progression. Inhibition of pyroptosis can reduce podocyte damage and improve renal function in DN, suggesting that pyroptosis may help identify potential new therapeutic targets for DN treatment.
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Exploring the Therapeutic Potential of Tyrosol and its Derivatives: A Comprehensive Review
Authors: Gokul Raj DK, Milan KL and Kunka Mohanram RamkumarTyrosol (Ty) and its derivatives have gathered considerable attention in recent years due to their diverse pharmacological properties and potential therapeutic applications. This comprehensive review aims to summarize the current understanding of the therapeutic potential of Ty and its derivatives in combating various diseases, including cancer, cardiovascular disease (CVD), neurodegenerative diseases, diabetes, and obesity. This review highlights the multifaceted properties of Ty, including its pharmacokinetic profile and pharmacological actions, which contribute to its efficacy against these prevalent health conditions. Moreover, the antimicrobial and wound-healing effects of Ty are explored, elucidating its potential for broader therapeutic utilization. While existing studies provide evidence supporting the beneficial effects of Ty, gaps remain in our understanding of its molecular mechanisms of action and the exploration of novel derivatives. Future research efforts are thus critical for unraveling the full therapeutic potential of Ty and its derivatives. Moreover, the synthesis of novel derivatives with enhanced efficacy and improved bioavailability shows potential for addressing unmet medical needs. This review emphasizes the necessity for ongoing research into Ty and its derivatives, providing valuable insights into their potential as essential therapeutic agents for addressing diverse health conditions.
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FOXN3-AS1: A Candidate Prognostic Marker and Epigenetic Target with Immunotherapeutic Implications in Acute Myeloid Leukemia
AimWe focused on the FOXN3 gene and selected its antisense transcripts (FOXN3-AS1) to investigate its potential involvement in acute myeloid leukemia (AML).
BackgroundSeveral integrated multi-omics datasets have expanded the horizons of the cancer landscape. With the emergence of new high-throughput technologies, a large number of non-coding RNAs have been confirmed to be involved in the pathogenesis of different types of hematological malignancies.
MethodsWe conducted experimental validation using quantitative polymerase chain reaction (qPCR) with bone marrow specimens from AML patients. Then, Kaplan-Meier (KM) and Receiver Operating Characteristic (ROC) curves were used to substantiate the prognostic association between FOXN3-AS1 and AML patients within the TCGA database. Correlation between FOXN3-AS1 expression and gene mutation, immune, and immune function using Spearman correlation analysis. To explore the physical and functional interaction between FOXN3-AS1 and the DNMT1 protein, we utilized the RPISeq web tool from Iowa State University. Subsequently, we performed qPCR experiments to test the effect of 5AzaC (DNMT1 inhibitor) on FOXN3-AS1 expression AML cell lines (THP1 and OCI-AML3). We leveraged the “OncoPredict” R package in conjunction with the Genomics of Drug Sensitivity (GDSC) database to predict drug response in AML patients expressing FOXN3-AS1.
ResultsWe observed a significant upregulation of FOXN3-AS1 expression in AML patients compared to healthy controls using clinical samples. The TCGA database revealed an association between high FOXN3-AS1 expression and adverse prognosis. In our subsequent analysis, genes with poor prognostic implications in AML patients were exclusively identified in the FOXN3-AS1 high-expression group, further corroborating this relationship. AML patients with higher FOXN3-AS1 expression levels may respond less optimally to immunotherapy than patients with lower levels. Besides, we computationally predicted the interaction of FOXN3-AS1 and DNMT1 protein and experimentally confirmed that DNMT1i (GSK-3484862) affects the expression level of FOXN3-AS1. We also found that the chemotherapy drugs (5-Fluorouralic, Cisplatin, Dactolisib, Sapitinib, Temozolomide, Ulixertinib, Vinorelbine, Ruxolitinib, Osimertinib and Cisplatin) showed favorable responses in AML patients with high FOXN3-AS1 expression levels.
ConclusionOur candidate approach identifies FOXN3-AS1 as a prognostic indicator of survival in AML with a potential immune-related role. The preliminary observations we made on FOXN3-AS1/DNMT1 crosstalk warrant more in-depth invested immunotherapeutic approaches in AML.
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Identifying and Validating an Angiogenesis-related Signature for the Prognosis of Head and Neck Squamous Cell Carcinoma
Authors: Yueting Hou, Haifeng Pang, Xuemei Xu and Dong ZhaoAimsThe present study aimed todevelop a prognostic model for HNSCC treatment on the basis of angiogenesis-related signatures.
BackgroundHead and Neck Squamous Cell Carcinoma (HNSCC) is the most frequent malignancy with poor prognostic outcomes in the head and neck. Angiogenesis plays a critical role in tumorigenesis and is expected to be an effective therapeutic target.
ObjectiveThe RNA-seq dataset TCGA-HNSCC and the hallmark gene set were used for angiogenesis-related RiskScore model construction.
MethodsThe RNA-seq data was downloaded from The Cancer Genome Atlas (TCGA), and the hallmark gene set was used to measure the angiogenesis score using the GSVA R package. Then, the optimal cutoff point for prognostic classification was calculated by the survminer package, and Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify angiogenesis gene modules. Multi/univariable and Lasso Cox analyses were performed to develop the RiskScore model, and the classifier efficiency was evaluated by the Receiver Operating Characteristic curve (ROC). Furthermore, a nomogram was designed for survival probability prediction, and the immune infiltration and immunotherapy differences among different risk patients were assessed.
ResultsAfter calculating the angiogenesis score, we found that this indicator and patients’ prognosis were closely correlated, especially when patients with a high angiogenesis score had a poor prognosis. Then, WGCNA identified a blue gene module positively correlated with angiogenesis. Multivariate and Lasso Cox analysis further identified 9 risk model genes for developing a RiskScore, which was used to divide low- and high-risk groups of patients. Those with a high risk tended to show poor prognosis, immune infiltration, and higher immune escape. Finally, a nomogram was developed to optimize the risk model, and it exhibited excellent short- and long-term survival prediction performance.
ConclusionWe constructed a reliable RiskScore model for the prognostic prediction of HNSCC patients, contributing to precise therapeutic intervention of the cancer.
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Exploring a Desirable Quadr-mRNAs Panel for Non-invasive and Ultrasensitive Bladder Cancer Diagnosis: In-silico and Clinical Studies
BackgroundMost patients with non-muscle invasive bladder cancer (NMIBC) have a high direction for recurrence and disease progression, which remains a significant unresolved challenge in bladder cancer patients. Therefore, a constant search is necessary for identifying appropriate and reliable biomarkers for early diagnosis of NMIBC. The current study has aimed to search for valuable diagnostic biomarkers in the tissue and urine specimens of NMIBC patients.
MethodsThe changes of twelve candidate mRNAs in a screening phase (40 tissue samples of NMIBC patients and their corresponding 40 urine specimens) and a subsequent independent validation phase (40 urine specimens) were estimated using real-time polymerase chain reaction (RT-qPCR). The receiver operating characteristic (ROC) analysis was executed to determine the potential diagnostic values of mRNAs.
ResultsThe mRNA levels of seven candidate genes were markedly higher in tissue specimens relative to their neighboring tissues. Among them, four mRNAs, including ERBB2, CCND1, MKI67, and MAGEA6, were differentially expressed in urine samples of NMIBC patients relative to control subjects. Further, the expression of these four mRNAs was validated in the validation step. Combining these biomarkers showed better diagnostic performance than single biomarkers in the urine sample for non-invasive NMIBC detection. The combination of these mRNAs and cytology enhanced the sensitivity of cytology from 37% to 87%.
ConclusionOur findings suggested that a four-mRNA panel may be promising in the non-invasive diagnosis of NMIBC, which deserves further investigation.
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Pioglitazone Alleviates β1-adrenergic Receptor Antibody-induced Atrial Fibrillation Susceptivity via Mitigation of PPAR-γ-mediated Metabolic Inflexibility
Authors: Linqiang Xi, Huaxin Sun, Na Yang, Qianhui Wang, Ling Zhang, Jie Song, Dilare Taiwaikuli, Luxiang Shang and Xian Hui ZhouBackgroundBeta-1-adrenergic receptor antibodies (β1-AAbs) function as arrhythmogenic molecules in autoimmune-related atrial fibrillation (AF). This study examined the potential impact of pioglitazone, an agonist for peroxisome proliferator-activated receptor-γ (PPAR-γ), on atrial remodeling induced by β1-AAbs.
MethodsAn in vivo study was performed to confirm the protective effects of pioglitazone on β1-AAbs-induced atrial remodeling. GW9662, a PPAR-γ antagonist, was employed to identify the potential therapeutic target of pioglitazone. The rats were administered subcutaneous injections of the second extracellular loop peptide for 8 weeks to establish active immunization models. Pioglitazone was then administered orally for 2 weeks. Epicardial electrophysiologic studies, multielectrode array measurements, and echocardiography were conducted to examine atrial remodeling. Glucose metabolism products and key metabolic molecules were measured to evaluate the atrial substrate metabolism. Mitochondrial morphologies and function indices were tested to depict the underlying links between atrial metabolism and mitochondrial homeostasis under the pioglitazone treatment.
ResultsPioglitazone significantly reversed β1-AAbs-induced AF susceptibility, ameliorated atrial structural remodeling, decreased the global insulin resistance reflected in the plasma glucose and insulin levels, and increased the protein expressions of glycolipid uptake and transportation (GLUT1, CD36, and CPT1a). These trends were counterbalanced by the GW9662 intervention. Mechanistically, pioglitazone mitigated the atrial mitochondrial network damage and partly renovated the mitochondrial biogenesis, even the mitochondrial dynamics, which were reversed by inhibiting the PPAR-γ target.
ConclusionPioglitazone effectively reduced the AF vulnerability and recovered the atrial myocardial metabolism and mitochondrial damage. The potential anti-remodeling effect of pioglitazone on the atrium was associated with the moderately increased expression of key membrane proteins related to glucose transporter and fatty acid uptake, which may promote the increased myocardial preference for utilization of FA as the key cardiac oxidative fuel and ameliorate the atrial metabolic inflexibility.
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Volumes & issues
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Volume 32 (2025)
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Volume (2025)
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Volume 31 (2024)
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Volume 30 (2023)
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Volume 29 (2022)
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Volume 28 (2021)
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Volume 27 (2020)
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Volume 26 (2019)
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Volume 25 (2018)
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Volume 24 (2017)
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Volume 23 (2016)
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Volume 22 (2015)
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Volume 21 (2014)
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Volume 20 (2013)
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Volume 19 (2012)
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Volume 18 (2011)
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Volume 17 (2010)
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Volume 16 (2009)
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Volume 15 (2008)
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Volume 14 (2007)
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Volume 13 (2006)
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Volume 12 (2005)
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Volume 11 (2004)
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Volume 10 (2003)
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Volume 9 (2002)
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Volume 8 (2001)
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Volume 7 (2000)
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