Article
Multidisciplinary Sciences
Mohammed A. Al-masni, Dong-Hyun Kim
Summary: An end-to-end deep learning segmentation method called CMM-Net, incorporating global contextual features and dilated convolution module, achieved superior performance on multiple medical imaging datasets. The method showed excellent segmentation results for skin lesions, retinal blood vessels, and brain tumors, demonstrating high generalizability.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai, Yu Wang, Wenbin Ma
Summary: Through analyzing data from multiple sources and utilizing various algorithms and methods, immune phenotypes in glioblastoma patients were classified, revealing distinct immune characteristics and clinicopathological features. The study also identified differences in drug sensitivity and prognosis among different immune phenotypes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Plant Sciences
Joan Marquez-Molins, Pascual Villalba-Bermell, Julia Corell-Sierra, Vicente Pallas, Gustavo Gomez
Summary: This study provides an integrative analysis of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd). The results show that HSVd causes a reconfiguration of the cucumber regulatory pathways, predominantly affecting specific regulatory layers at different infection phases. The initial response involves differential exon usage, followed by transcriptional downregulation modulated by epigenetic changes. The alterations in endogenous small RNAs are limited and mainly occur at the late stage. The significant host alterations are primarily related to the downregulation of plant defense mechanisms and the systemic spreading of defense signals.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Lohit Kumar Srinivas Gujjala, Wangyun Won
Summary: This manuscript discusses the development process for synthesizing lignin hydrogel (LH) with biomedical applications. Two synthesis strategies, single and two-step processes, were studied and categorized as grade A and B LHs respectively. The raw material (native vs. methacrylated lignin) was analyzed for its impact on the overall technoeconomic analysis and life-cycle assessment of the process. The study found that the hydrogel production sub-system was the major contributor to the cost of LH production. Sensitivity analysis and uncertainty analysis were conducted to identify key parameters and evaluate the influence of market uncertainties. The proposed strategy of lignin upgradation was found to be cleaner in grade A compared to grade B, suggesting its potential integration in lignocellulosic biorefinery for eco-friendly processes.
Article
Multidisciplinary Sciences
Naga Raju Gudhe, Hamid Behravan, Mazen Sudah, Hidemi Okuma, Ritva Vanninen, Veli-Matti Kosma, Arto Mannermaa
Summary: In this study, a novel multi-level dilated residual neural network is proposed for biomedical image segmentation. By replacing convolutional blocks of the classical U-Net with multi-level dilated residual blocks and incorporating non-linear multi-level residual blocks into skip connections, enhanced segmentation performance is achieved.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Inuk Jung, Minsu Kim, Sungmin Rhee, Sangsoo Lim, Sun Kim
Summary: MONTI is a multi-omics analysis method that selects multi-omics features representing specific traits, demonstrating improved cancer subtype classification accuracy through integrating different omics data.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
EIena I. Usova, Asiiat S. Alieva, Alexey N. Yakovlev, Madina S. Alieva, Alexey A. Prokhorikhin, Alexandra O. Konradi, Evgeny V. Shlyakhto, Paolo Magni, Alberico L. Catapano, Andrea Baragetti
Summary: Genetics, environmental and lifestyle factors greatly impact cardiovascular diseases, with atherosclerosis as the etiopathological factor. Novel omic approaches can enhance accurate prediction and risk assessment of ACVD, with the use of genomics expanding therapeutic potential and omics presenting a forward step in this direction. AI/ML strategies are essential for analyzing data and developing predictive models for ACVD diagnosis and prediction.
Review
Chemistry, Analytical
Maria A. Woerheide, Jan Krumsiek, Gabi Kastenmueller, Matthias Arnold
Summary: Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, generating vast amounts of data that can be integrated in multi-omics studies. Integrative analysis of such datasets is complicated by the high dimensionality, heterogeneity, and lack of universal protocols. While previous reviews focused on integrating two omics layers with a phenotype, this review highlights methods to combine metabolomics data with two or more omics layers without focusing on a specific phenotype.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biology
Jaclyn Smith, Yao Shi, Michael Benedikt, Milos Nikolic
Summary: In the field of biomedicine, there is a need for scalable data integration solutions due to limitations in large-scale data processing frameworks in analyzing complex data types. TraNCE is an automated framework designed to address the challenges of designing distributed analyses with complex biomedical data types, demonstrating its ability to outperform common alternatives.
Article
Statistics & Probability
Wendong Li, Dongdong Xiang, Gongtao Chen, Peihua Qiu
Summary: This article investigates the problem of signal classification in the context of large-scale multiple testing and proposes two prediction procedures for controlling misclassification rates. The asymptotic properties of these procedures are derived. The results show that considering the dependence structure among features can significantly improve signal classification.
Article
Green & Sustainable Science & Technology
Cheng Wang, Tao Lv, Rongjiang Cai, Jianfeng Xu, Liya Wang
Summary: This study provides a global overview of multi-level perspective (MLP) research using bibliometrics. The results indicate a continuous growth in MLP research literature, with an increasing number of journals and countries involved. The research mainly focuses on transition, sustainability transition, socio-technical transition, energy transition, innovation, and governance, and is expected to shift towards agency, power, and policy. MLP research will further explore interactions between multi-niche, multi-regime, and multi-landscape levels. The findings help scholars gain a systematic understanding of the current research status, frontiers, and future trends of MLP from a macro perspective.
Article
Mechanics
Cong Guo, Ji He
Summary: This study investigates the mechanical performance of a bio-inspired helicoidal structure, and finds that it exhibits excellent load-bearing capacity and damage resistance through indentation tests and simulation analysis. The small rotation angle between adjacent layers in the helicoidal structure enables a more uniform stress distribution and the generation of a twisted crack path, enhancing its load-bearing capacity and damage resistance.
COMPOSITE STRUCTURES
(2022)
Article
Computer Science, Information Systems
Mingwen Shao, Gaozhi Zhang, Wangmeng Zuo, Deyu Meng
Summary: This paper investigates the impact of adversarial examples on biomedical image segmentation models, proposing a multi-scale gradient-based attack method. Experimental results demonstrate that the predicted masks generated by this method have high intersection over union and pixel accuracy with the target masks, while reducing the distances between adversarial and clean examples compared to the state-of-the-art method.
INFORMATION SCIENCES
(2021)
Article
Automation & Control Systems
Huisi Wu, Baiming Zhang, Junquan Pan, Jing Qin
Summary: This paper proposes a novel biomedical image segmentation network MOG-Net, which introduces a new object-aware module (OAM) and a pyramid context encoder module (PCEM) to address the lack of global dependencies and semantic information dilution in existing models, achieving satisfactory segmentation performance by establishing global dependencies at multiple levels and compensating high-level semantic information dilution.
IEEE TRANSACTIONS ON AUTOMATION SCIENCE AND ENGINEERING
(2023)
Article
Engineering, Civil
Byeonghwa Goh, Joonmyung Choi
Summary: This study developed a multilevel scalable spatial-coarsening method for diamond structures to selectively scale the space represented by the particles. The bonding relationship between the particles of different spatial regions was explained by the combination of the potential energies dominating each side. The proposed method accurately reproduces the tensor properties of diamond crystal material and successfully predicts the all-atom model and experimental results.
THIN-WALLED STRUCTURES
(2023)
Article
Biochemical Research Methods
Tony Pan, Rahul Nihalani, Srinivas Aluru
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2020)
Article
Geosciences, Multidisciplinary
D. Khider, J. Emile-Geay, N. P. McKay, Y. Gil, D. Garijo, V Ratnakar, M. Alonso-Garcia, S. Bertrand, O. Bothe, P. Brewer, A. Bunn, M. Chevalier, L. Comas-Bru, A. Csank, E. Dassie, K. DeLong, T. Felis, P. Francus, A. Frappier, W. Gray, S. Goring, L. Jonkers, M. Kahle, D. Kaufman, N. M. Kehrwald, B. Martrat, H. McGregor, J. Richey, A. Schmittner, N. Scroxton, E. Sutherland, K. Thirumalai, K. Allen, F. Arnaud, Y. Axford, T. Barrows, L. Bazin, S. E. Pilaar Birch, E. Bradley, J. Bregy, E. Capron, O. Cartapanis, H-W Chiang, K. M. Cobb, M. Debret, R. Dommain, J. Du, K. Dyez, S. Emerick, M. P. Erb, G. Falster, W. Finsinger, D. Fortier, Nicolas Gauthier, S. George, E. Grimm, J. Hertzberg, F. Hibbert, A. Hillman, W. Hobbs, M. Huber, A. L. C. Hughes, S. Jaccard, J. Ruan, M. Kienast, B. Konecky, G. Le Roux, V Lyubchich, V. F. Novello, L. Olaka, J. W. Partin, C. Pearce, S. J. Phipps, C. Pignol, N. Piotrowska, M-S Poli, A. Prokopenko, F. Schwanck, C. Stepanek, G. E. A. Swann, R. Telford, E. Thomas, Z. Thomas, S. Truebe, L. von Gunten, A. Waite, N. Weitzel, B. Wilhelm, J. Williams, M. Winstrup, N. Zhao, Y. Zhou
PALEOCEANOGRAPHY AND PALEOCLIMATOLOGY
(2019)
Review
Oncology
Mohamed Amgad, Elisabeth Specht Stovgaard, Eva Balslev, Jeppe Thagaard, Weijie Chen, Sarah Dudgeon, Ashish Sharma, Jennifer K. Kerner, Carsten Denkert, Yinyin Yuan, Khalid AbdulJabbar, Stephan Wienert, Peter Savas, Leonie Voorwerk, Andrew H. Beck, Anant Madabhushi, Johan Hartman, Manu M. Sebastian, Hugo M. Horlings, Jan Hudecek, Francesco Ciompi, David A. Moore, Rajendra Singh, Elvire Roblin, Marcelo Luiz Balancin, Marie-Christine Mathieu, Jochen K. Lennerz, Pawan Kirtani, I-Chun Chen, Jeremy P. Braybrooke, Giancarlo Pruneri, Sandra Demaria, Sylvia Adams, Stuart J. Schnitt, Sunil R. Lakhani, Federico Rojo, Laura Comerma, Sunil S. Badve, Mehrnoush Khojasteh, W. Fraser Symmans, Christos Sotiriou, Paula Gonzalez-Ericsson, Katherine L. Pogue-Geile, Rim S. Kim, David L. Rimm, Giuseppe Viale, Stephen M. Hewitt, John M. S. Bartlett, Frederique Penault-Llorca, Shom Goel, Huang-Chun Lien, Sibylle Loibl, Zuzana Kos, Sherene Loi, Matthew G. Hanna, Stefan Michiels, Marleen Kok, Torsten O. Nielsen, Alexander J. Lazar, Zsuzsanna Bago-Horvath, Loes F. S. Kooreman, Jeroen A. W. M. van der Laak, Joel Saltz, Brandon D. Gallas, Uday Kurkure, Michael Barnes, Roberto Salgado, Lee A. D. Cooper
Article
Medicine, General & Internal
Apurva Agrawal, Chandan Singh Chauhan, Krishna Boliwal, Ashish Sharma
Summary: The development of new antibiotics has been slow in recent decades, but it is crucial for future prescribers to have proper knowledge and attitude towards antibiotic prescription to address antibiotic resistance effectively. This study aimed to assess the knowledge and attitude of medical students regarding antimicrobials and antibiotic resistance, with majority having basic knowledge yet areas of concern identified.
JOURNAL OF LABORATORY PHYSICIANS
(2022)
Article
Transplantation
Nripesh Sadasukhi, Ketul Patel, T. Sadasukhi, Manish Gupta, H. Gupta, Ashish Sharma, Sandeep Malik
Summary: This study compares the difference in length loss of the renal artery and vein between open and laparoscopic renal donor nephrectomy, and finds that there is no significant difference between the two surgical methods.
INDIAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Transplantation
Ashish Sharma, Nripesh Sadasukhi, Sandeep Malik, T. C. Sadasukhi, H. L. Gupta, Manish Gupta
Summary: This study presented a case series of 15 Bench Pyelolithotomy procedures on renal graft, demonstrating that ex vivo Bench Surgery is safe, less time-consuming, and equally effective for stone-bearing renal donor kidneys without compromising renal allograft function.
INDIAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Transplantation
Nripesh Sadasukhi, Ketul Patel, T. C. Sadasukhi, Manish Gupta, H. L. Gupta, Ashish Sharma, Sandeep Malik
Summary: This study demonstrates a high incidence of erectile dysfunction in patients with chronic kidney disease and kidney transplantation recipients. IIEF-5 is proven to be an effective tool in diagnosing erectile dysfunction. Advanced age, prolonged dialysis, diabetes mellitus, and smoking are significant risk factors for erectile dysfunction.
INDIAN JOURNAL OF TRANSPLANTATION
(2021)
Article
Urology & Nephrology
Suraj Godara, Karan Kumar Saraf, T. C. Sadasukhi, H. L. Gupta, Manish Gupta, Nripesh Sadasukhi, Ashish Sharma
Summary: COVID-19 poses a significant risk to kidney transplant recipients, who may experience similar initial symptoms to the general population but have a higher mortality rate. Management typically involves reducing immunosuppressants and using antiviral treatments like remdesivir, with a focus on monitoring and treating severe cases in intensive care units.
INDIAN JOURNAL OF NEPHROLOGY
(2021)
Article
Transplantation
Nripesh Sadasukhi, Ketul Patel, T. C. Sadasukhi, Manish Gupta, H. L. Gupta, Ashish Sharma, Sandeep Malik
Summary: This study reviewed published literature and compared it with 115 kidney transplant procedures conducted at the hospital from July 2020 to February 2021 to explore protocols for selecting uninfected donors and recipients during the COVID-19 pandemic. The results showed that strict screening measures can help ensure the safety of transplant recipients and reduce the risk of COVID-19 transmission.
INDIAN JOURNAL OF TRANSPLANTATION
(2021)
Article
Urology & Nephrology
Ashish Sharma, Gaurav Garg, Nripesh Sadasukhi, Trilok Chand Sadasukhi, Hoti Lal Gupta, Manish Gupta, Sandeep Malik, Ketul Patel, Rj Sinha
Summary: This study evaluated bone health in prostate cancer patients and found that ADT worsened FRAX and FACT-P scores, while BDT improved FRAX. The FRAX tool is advantageous in identifying high-risk patients for early intervention or therapy to prevent skeletal-related events.
AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY
(2021)
Article
Oncology
Anita Sharma, Apurva Agrawal, Girish Sindhwani, Ashish Sharma, Sojit Tomo, Jaykaran Charan, Dharmveer Yadav, Praveen Sharma
Summary: The study aimed to evaluate the predictive accuracy of PCT and PTX-3 in the differential diagnosis of pleural effusions compared to other biochemical markers, and found that PCT and PTX-3 have favorable discrimination ability in predicting different types of pleural effusions.
PLEURA AND PERITONEUM
(2021)
Article
Computer Science, Information Systems
Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Proceedings Paper
Computer Science, Artificial Intelligence
Daniel Garijo, Deborah Khider, Varun Ratnakar, Yolanda Gil, Ewa Deelman, Rafael Ferreira da Silva, Craig Knoblock, Yao-Yi Chiang, Minh Pham, Jay Pujara, Binh Vu, Dan Feldman, Rajiv Mayani, Kelly Cobourn, Chris Duffy, Armen Kemanian, Lele Shu, Vipin Kumar, Ankush Khandelwal, Kshitij Tayal, Scott Peckham, Maria Stoica, Anna Dabrowski, Daniel Hardesty-Lewis, Suzanne Pierce
PROCEEDINGS OF THE 24TH INTERNATIONAL CONFERENCE ON INTELLIGENT USER INTERFACES: COMPANION (IUI 2019)
(2019)
Proceedings Paper
Computer Science, Software Engineering
Yolanda Gil, James Honaker, Shikhar Gupta, Yibo Ma, Vito D'Orazio, Daniel Garijo, Shruti Gadewar, Qifan Yang, Neda Jahanshad
PROCEEDINGS OF IUI 2019
(2019)
Proceedings Paper
Mathematical & Computational Biology
Arunima Srivastava, Ravali Adusumilli, Hunter Boyce, Daniel Garijo, Varun Ratnakar, Rajiv Mayani, Thomas Yu, Raghu Machiraju, Yolanda Gil, Parag Mallick
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019
(2019)
