3,065 results on '"Ciorba A"'
Search Results
2. Autonomy Loops for Monitoring, Operational Data Analytics, Feedback, and Response in HPC Operations
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Boito, Francieli, Brandt, Jim, Cardellini, Valeria, Carns, Philip, Ciorba, Florina M., Egan, Hilary, Eleliemy, Ahmed, Gentile, Ann, Gruber, Thomas, Hanson, Jeff, Haus, Utz-Uwe, Huck, Kevin, Ilsche, Thomas, Jakobsche, Thomas, Jones, Terry, Karlsson, Sven, Mueen, Abdullah, Ott, Michael, Patki, Tapasya, Peng, Ivy, Raghavan, Krishnan, Simms, Stephen, Shoga, Kathleen, Showerman, Michael, Tiwari, Devesh, Wilde, Torsten, and Yamamoto, Keiji
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Many High Performance Computing (HPC) facilities have developed and deployed frameworks in support of continuous monitoring and operational data analytics (MODA) to help improve efficiency and throughput. Because of the complexity and scale of systems and workflows and the need for low-latency response to address dynamic circumstances, automated feedback and response have the potential to be more effective than current human-in-the-loop approaches which are laborious and error prone. Progress has been limited, however, by factors such as the lack of infrastructure and feedback hooks, and successful deployment is often site- and case-specific. In this position paper we report on the outcomes and plans from a recent Dagstuhl Seminar, seeking to carve a path for community progress in the development of autonomous feedback loops for MODA, based on the established formalism of similar (MAPE-K) loops in autonomous computing and self-adaptive systems. By defining and developing such loops for significant cases experienced across HPC sites, we seek to extract commonalities and develop conventions that will facilitate interoperability and interchangeability with system hardware, software, and applications across different sites, and will motivate vendors and others to provide telemetry interfaces and feedback hooks to enable community development and pervasive deployment of MODA autonomy loops.
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- 2024
3. Accurate Measurement of Application-level Energy Consumption for Energy-Aware Large-Scale Simulations
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Simsek, Osman Seckin, Piccinali, Jean-Guillaume, and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Sustainability in high performance computing (HPC) is a major challenge not only for HPC centers and their users, but also for society as the climate goals become stricter. A lot of effort went into reducing the energy consumption of systems in general. Even though certain efforts to optimize the energy-efficiency of HPC workloads exist, most such efforts propose solutions targeting CPUs. As HPC systems shift more and more to GPU-centric architectures, simulation codes increasingly adopt GPU-programming models. This leads to an urgent need to increase the energy-efficiency of GPU-enabled codes. However, studies for reducing the energy consumption of large-scale simulations executing on CPUs and GPUs have received insufficient attention. In this work, we enable accurate power and energy measurements using an open-source toolkit across a range of CPU+GPU node architectures. We use this approach in SPH-EXA, an open-source GPU-centric astrophysical and cosmological simulation framework. We show that with simple code instrumentation, users can accurately measure power and energy related data about their application, beyond data provided by HPC systems alone. The accurate power and energy data provide significant insight to users for conducting energy-aware computational experiments and future energy-aware code development., Comment: Appeared in Proceedings of the SC 23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis November 2023
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- 2023
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4. Promoting Adult Education for a Sustainable Future: Fostering Healthy Lifestyles
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Ana Darie and Ciorba Constantin
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As an integral part of the concept of lifelong learning, non formal learning enables adults to acquire the necessary skills to adapt more easily to the ever-changing social life. Concerned with these values, through the lens of the ODD, with reference to Health and well-being, which indicates "ensuring a healthy life and promoting well-being for all ages", we wanted to investigate a group of teachers who followed a training program aimed at the healthy lifestyle of the educable. Healthy lifestyle education can play a significant role in changing health behaviors and attitudes towards our own health, as well as those we educate. Teachers become not only mentors for children, but also role models. Starting from this concept, we want to find out if the learners are able to include health-promoting behaviors in their daily routine and if they implement strategies that promote health, well-being, for themselves, including the learners. A number of N=63 teaching staff from Ia?i county, located in the north-eastern part of Romania, participated in this study. Of these, a number of N=35 respondents teach at the preschool education level and a number of N=28 at the primary education level. All respondents are female, of whom N=49 teach in urban areas, and N=14 in rural areas. The research tools were applied in electronic version, using Google forms. The obtained data were statistically analyzed using IBM SPSS software. Findings indicate significant effects of the training program on all target variables. The results of this research will be used to add to our knowledge of behavioral change and learning in adulthood.
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- 2023
5. Late-onset, progressive sensorineural hearing loss in the paediatric population: a systematic review
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Corazzi, Virginia, Fordington, Surina, Brown, Tamsin Holland, Donnelly, Neil, Bewick, Jessica, Ehsani, Diana, Pelucchi, Stefano, Bianchini, Chiara, Ciorba, Andrea, and Borsetto, Daniele
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- 2024
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6. SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
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Munteanu, Viorel, Saldana, Michael, Ciorba, Dumitru, Bostan, Viorel, Su, Justin Maine, Kasianchuk, Nadiia, Sharma, Nitesh Kumar, Knyazev, Sergey, Gordeev, Victor, Aßmann, Eva, Lobiuc, Andrei, Covasa, Mihai, Crandall, Keith A., Ouyang, Wenhao O., Wu, Nicholas C., Mason, Christopher, Tierney, Braden T, Lucaci, Alexander G, Zelikovsky, Alex, Mohebbi, Fatemeh, Skums, Pavel, Gibas, Cynthia, Schlueter, Jessica, Rzymski, Piotr, Solo-Gabriele, Helena, Hölzer, Martin, Smith, Adam, and Mangul, Serghei
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Quantitative Biology - Genomics - Abstract
During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods., Comment: V Munteanu and M Saldana contributed equally to this work. M H\"olzer, A Smith and S Mangul jointly supervised this work. For correspondence: serghei.mangul@gmail.com
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- 2023
7. DaphneSched: A Scheduler for Integrated Data Analysis Pipelines
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Eleliemy, Ahmed and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
DAPHNE is a new open-source software infrastructure designed to address the increasing demands of integrated data analysis (IDA) pipelines, comprising data management (DM), high performance computing (HPC), and machine learning (ML) systems. Efficiently executing IDA pipelines is challenging due to their diverse computing characteristics and demands. Therefore, IDA pipelines executed with the DAPHNE infrastructure require an efficient and versatile scheduler to support these demands. This work introduces DaphneSched, the task-based scheduler at the core of DAPHNE. DaphneSched is versatile by incorporating eleven task partitioning and three task assignment techniques, bringing the state-of-the-art closer to the state-of-the-practice task scheduling. To showcase DaphneSched's effectiveness in scheduling IDA pipelines, we evaluate its performance on two applications: a product recommendation system and a linear regression model training. We conduct performance experiments on multicore platforms with 20 and 56 cores. The results show that the versatility of DaphneSched enabled combinations of scheduling strategies that outperform commonly used scheduling techniques by up to 13%. This work confirms the benefits of employing DaphneSched for the efficient execution of applications with IDA pipelines.
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- 2023
8. Cornerstone: Octree Construction Algorithms for Scalable Particle Simulations
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Keller, Sebastian, Cavelan, Aurélien, Cabezon, Rubén, Mayer, Lucio, and Ciorba, Florina M.
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Cosmology and Nongalactic Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Computer Science - Data Structures and Algorithms ,J.2 - Abstract
This paper presents an octree construction method, called Cornerstone, that facilitates global domain decomposition and interactions between particles in mesh-free numerical simulations. Our method is based on algorithms developed for 3D computer graphics, which we extend to distributed high performance computing (HPC) systems. Cornerstone yields global and locally essential octrees and is able to operate on all levels of tree hierarchies in parallel. The resulting octrees are suitable for supporting the computation of various kinds of short and long range interactions in N-body methods, such as Barnes-Hut and the Fast Multipole Method (FMM). While we provide a CPU implementation, Cornerstone may run entirely on GPUs. This results in significantly faster tree construction compared to execution on CPUs and serves as a powerful building block for the design of simulation codes that move beyond an offloading approach, where only numerically intensive tasks are dispatched to GPUs. With data residing exclusively in GPU memory, Cornerstone eliminates data movements between CPUs and GPUs. As an example, we employ Cornerstone to generate locally essential octrees for a Barnes-Hut treecode running on almost the full LUMI-G system with up to 8 trillion particles.
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- 2023
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9. Starting with 24-h levodopa carbidopa intestinal gel at initiation in a large cohort of advanced Parkinson’s disease patients
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Szatmári, Szabolcs, Szász, József Attila, Orbán-Kis, Károly, Bataga, Simona, Ciorba, Marius, Nagy, Előd, Neagoe, Radu, Mihály, István, Szász, Péter Zsombor, Kelemen, Krisztina, Frigy, Attila, Csipor-Fodor, Andrea, and Constantin, Viorelia Adelina
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- 2024
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10. The impact of hearing loss on the quality of life of elderly adults
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Ciorba A, Bianchini C, Pelucchi S, and Pastore A
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hearing loss ,presbycusis ,cochlea ,quality of life ,elderly ,Geriatrics ,RC952-954.6 - Abstract
Andrea Ciorba, Chiara Bianchini, Stefano Pelucchi, Antonio PastoreENT and Audiology Department, University Hospital of Ferrara, Ferrara, ItalyAbstract: Hearing loss is the most common sensory deficit in the elderly, and it is becoming a severe social and health problem. Especially in the elderly, hearing loss can impair the exchange of information, thus significantly impacting everyday life, causing loneliness, isolation, dependence, and frustration, as well as communication disorders. Due to the aging of the population in the developed world, presbycusis is a growing problem that has been reported to reduce quality of life (QoL). Progression of presbycusis cannot be remediated; therefore, optimal management of this condition not only requires early recognition and rehabilitation, but it also should include an evaluation of QoL status and its assessment.Keywords: hearing loss, presbycusis, quality of life, elderly
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- 2012
11. DAPHNE Runtime: Harnessing Parallelism for Integrated Data Analysis Pipelines
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Vontzalidis, Aristotelis, Psomadakis, Stratos, Bitsakos, Constantinos, Dokter, Mark, Innerebner, Kevin, Damme, Patrick, Boehm, Matthias, Ciorba, Florina, Eleliemy, Ahmed, Karakostas, Vasileios, Zamuda, Aleš, Tsoumakos, Dimitrios, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Zeinalipour, Demetris, editor, Blanco Heras, Dora, editor, Pallis, George, editor, Herodotou, Herodotos, editor, Trihinas, Demetris, editor, Balouek, Daniel, editor, Diehl, Patrick, editor, Cojean, Terry, editor, Fürlinger, Karl, editor, Kirkeby, Maja Hanne, editor, Nardelli, Matteo, editor, and Di Sanzo, Pierangelo, editor
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- 2024
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12. Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
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Elwasif, Wael, Godoy, William, Hagerty, Nick, Harris, J. Austin, Hernandez, Oscar, Joo, Balint, Kent, Paul, Lebrun-Grandie, Damien, Maccarthy, Elijah, Vergara, Veronica G. Melesse, Messer, Bronson, Miller, Ross, Opal, Sarp, Bastrakov, Sergei, Bussmann, Michael, Debus, Alexander, Steinger, Klaus, Stephan, Jan, Widera, Rene, Bryngelson, Spencer H., Berre, Henry Le, Radhakrishnan, Anand, Young, Jefferey, Chandrasekaran, Sunita, Ciorba, Florina, Simsek, Osman, Spiga, Kate Clark Filippo, Hammond, Jeff, Hardy, John E. Stone. David, Keller, Sebastian, and Trott, Jean-Guillaume Piccinali. Christian
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Hardware Architecture - Abstract
This paper assesses and reports the experience of ten teams working to port,validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC Developer Kit systems built by GIGABYTE, each one equipped with a server-class Arm CPU from Ampere Computing and A100 data center GPU from NVIDIA Corp. The systems are connected together using Infiniband high-bandwidth low-latency interconnect. The selected applications and mini-apps are written using several programming languages and use multiple accelerator-based programming models for GPUs such as CUDA, OpenACC, and OpenMP offloading. Working on application porting requires a robust and easy-to-access programming environment, including a variety of compilers and optimized scientific libraries. The goal of this work is to evaluate platform readiness and assess the effort required from developers to deploy well-established scientific workloads on current and future generation Arm-based GPU-accelerated HPC systems. The reported case studies demonstrate that the current level of maturity and diversity of software and tools is already adequate for large-scale production deployments.
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- 2022
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13. Challenges and Opportunities of Machine Learning for Monitoring and Operational Data Analytics in Quantitative Codesign of Supercomputers
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Jakobsche, Thomas, Lachiche, Nicolas, and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
This work examines the challenges and opportunities of Machine Learning (ML) for Monitoring and Operational Data Analytics (MODA) in the context of Quantitative Codesign of Supercomputers (QCS). MODA is employed to gain insights into the behavior of current High Performance Computing (HPC) systems to improve system efficiency, performance, and reliability (e.g. through optimizing cooling infrastructure, job scheduling, and application parameter tuning). In this work, we take the position that QCS in general, and MODA in particular, require close exchange with the ML community to realize the full potential of data-driven analysis for the benefit of existing and future HPC systems. This exchange will facilitate identifying the appropriate ML methods to gain insights into current HPC systems and to go beyond expert-based knowledge and rules of thumb.
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- 2022
14. Multi-Magnet Cochlear Implant Technology and Magnetic Resonance Imaging: The Safety Issue
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Pietro Canzi, Elena Carlotto, Elisabetta Zanoletti, Johan H. M. Frijns, Daniele Borsetto, Antonio Caruso, Luisa Chiapparini, Andrea Ciorba, Giorgio Conte, Nathan Creber, Stefania Criscuolo, Filippo Di Lella, Sebastiano Franchella, Erik F. Hensen, Lorenzo Lauda, Stefano Malpede, Marco Mandalà, Liselotte J. C. Rotteveel, Anna Simoncelli, Anna Chiara Stellato, Diego Zanetti, and Marco Benazzo
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cochlear implants ,magnetic resonance imaging ,safety ,Ultra 3D ,magnet ,Otorhinolaryngology ,RF1-547 - Abstract
Despite the spread of novel-generation cochlear-implant (CI) magnetic systems, access to magnetic resonance imaging (MRI) for CI recipients is still limited due to safety concerns. The aim of this study is to assess and record the experiences of Hires Ultra 3D (Advanced Bionics) recipients who underwent an MRI examination. A multicentric European survey about this topic was conducted focusing on safety issues, and the results were compared with the current literature. We collected a total of 65 MRI scans performed in 9 otologic referral centers for a total of 47 Hires Ultra 3D recipients, including, for the first time, 2 children and 3 teenagers. Preventive measures were represented by scanning time and sedation for children. Head wrapping was used in eight cases, and six of the eight cases received local anesthesia, even if both measures were not needed. Only three patients complained of pain (3/65 examinations, 4.6%) due to the tight head bandage, and one of the three cases required MRI scan interruption. No other adverse events were reported. We believe that these results should encourage MRI execution in accordance with manufacturer recommendations for Ultra 3D recipients.
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- 2024
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15. Memory-like differentiation enhances NK cell responses against colorectal cancer
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Nancy D. Marin, Michelle Becker-Hapak, Wilbur M. Song, Quazim A. Alayo, Lynne Marsala, Naomi Sonnek, Melissa M. Berrien-Elliott, Mark Foster, Jennifer A. Foltz, Jennifer Tran, Pamela Wong, Celia C. Cubitt, Patrick Pence, Kimberly Hwang, Alice Y. Zhou, Miriam T. Jacobs, Timothy Schappe, David A. Russler-Germain, Ryan C. Fields, Matthew A. Ciorba, and Todd A. Fehniger
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Cetuximab ,colorectal cancer ,cytokines ,immunotherapy ,NK cells ,Immunologic diseases. Allergy ,RC581-607 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
ABSTRACTMetastatic (m) colorectal cancer (CRC) is an incurable disease with a poor prognosis and thus remains an unmet clinical need. Immune checkpoint blockade (ICB)-based immunotherapy is effective for mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) mCRC patients, but it does not benefit the majority of mCRC patients. NK cells are innate lymphoid cells with potent effector responses against a variety of tumor cells but are frequently dysfunctional in cancer patients. Memory-like (ML) NK cells differentiated after IL-12/IL-15/IL-18 activation overcome many challenges to effective NK cell anti-tumor responses, exhibiting enhanced recognition, function, and in vivo persistence. We hypothesized that ML differentiation enhances the NK cell responses to CRC. Compared to conventional (c) NK cells, ML NK cells displayed increased IFN-γ production against both CRC cell lines and primary patient-derived CRC spheroids. ML NK cells also exhibited improved killing of CRC target cells in vitro in short-term and sustained cytotoxicity assays, as well as in vivo in NSG mice. Mechanistically, enhanced ML NK cell responses were dependent on the activating receptor NKG2D as its blockade significantly decreased ML NK cell functions. Compared to cNK cells, ML NK cells exhibited greater antibody-dependent cytotoxicity when targeted against CRC by cetuximab. ML NK cells from healthy donors and mCRC patients exhibited increased anti-CRC responses. Collectively, our findings demonstrate that ML NK cells exhibit enhanced responses against CRC targets, warranting further investigation in clinical trials for mCRC patients, including those who have failed ICB.
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- 2024
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16. The IRE1[alpha]/XBP1 pathway sustains cytokine responses of group 3 innate lymphoid cells in inflammatory bowel disease
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Cao, Siyan, Fachi, Jose L., Ma, Kaiming, Antonova, Alina Ulezko, Wang, Qianli, Cai, Zhangying, Kaufman, Randal J., Ciorba, Matthew A., Deepak, Parakkal, and Colonna, Marco
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Cytokines -- Analysis ,Inflammatory bowel diseases -- Diagnosis -- Care and treatment ,Inositol -- Dosage and administration ,Disease susceptibility -- Analysis ,Health care industry ,Diagnosis ,Care and treatment ,Analysis ,Dosage and administration - Abstract
Group 3 innate lymphoid cells (ILC3s) are key players in intestinal homeostasis. ER stress is linked to inflammatory bowel disease (IBD). Here, we used cell culture, mouse models, and human specimens to determine whether ER stress in ILC3s affects IBD pathophysiology. We show that mouse intestinal ILC3s exhibited a 24-hour rhythmic expression pattern of the master ER stress response regulator inositol-requiring kinase 1[alpha]/X-box-binding protein 1 (IRE1[alpha]/XBP1). Proinflammatory cytokine IL-23 selectively stimulated IRE1[alpha]/XBP1 in mouse ILC3s through mitochondrial ROS (mtROS). IRE1[alpha]/XBP1 was activated in ILC3s from mice exposed to experimental colitis and in inflamed human IBD specimens. Mice with Ire1[alpha] deletion in ILC3s ([Ire1[alpha].sup.[DELTA]Rorc]) showed reduced expression of the ER stress response and cytokine genes including Il22 in ILC3s and were highly vulnerable to infections and colitis. Administration of IL-22 counteracted their colitis susceptibility. In human ILC3s, IRE1 inhibitors suppressed cytokine production, which was upregulated by an IRE1 activator. Moreover, the frequencies of intestinal [XBP1s.sup.+] ILC3s in patients with Crohn's disease before administration of ustekinumab, an anti-IL-12/IL- 23 antibody, positively correlated with the response to treatment. We demonstrate that a noncanonical mtROS-IRE1[alpha]/XBP1 pathway augmented cytokine production by ILC3s and identify [XBP1s.sup.+] ILC3s as a potential biomarker for predicting the response to anti-IL-23 therapies in IBD., Introduction Innate lymphoid cells (ILCs) are a group of immune cells that exhibit lymphoid characteristics yet lack antigen-specific receptors found on T and B cells (1). Group 3 ILCs (ILC3s) [...]
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- 2024
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17. The Role of HPV in Head and Neck Cancer
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Migliorelli, A., primary, Manuelli, M., additional, Ciorba, A., additional, Pelucchi, S., additional, and Bianchini, C., additional
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- 2024
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18. Analytical code sharing practices in biomedical research
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Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha Patel, Viorel Munteanu, Dumitru Ciorba, Viorel Bostan, Andrada Fiscutean, Mohammad Vahed, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Maher, Nicole Nogoy, Malak Abedalthagafi, and Serghei Mangul
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Code sharing ,Data sharing ,Accessibility ,Transparency ,Reproducibility ,Open-source ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016–2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.
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- 2024
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19. First Experiences in Performance Benchmarking with the New SPEChpc 2021 Suites
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Brunst, Holger, Chandrasekaran, Sunita, Ciorba, Florina, Hagerty, Nick, Henschel, Robert, Juckeland, Guido, Li, Junjie, Vergara, Veronica G. Melesse, Wienke, Sandra, and Zavala, Miguel
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Modern HPC systems are built with innovative system architectures and novel programming models to further push the speed limit of computing. The increased complexity poses challenges for performance portability and performance evaluation. The Standard Performance Evaluation Corporation -SPEC has a long history of producing industry standard benchmarks for modern computer systems. SPEC is a newly released SPEChpc 2021 benchmark suites, developed by the High Performance Group, are a bold attempt to provide a fair and objective benchmarking tool designed for state of the art HPC systems. With the support of multiple host and accelerator programming models, the suites are portable across both homogeneous and heterogeneous architectures. Different workloads are developed to fit system sizes ranging from a few compute nodes to a few hundred compute nodes. In this manuscript, we take a first glance at these benchmark suites and evaluate their portability and basic performance characteristics on various popular and emerging HPC architectures, including x86 CPU, NVIDIA GPU, and AMD GPU. This study provides a first-hand experience of executing the SPEChpc 2021 suites at scale on production HPC systems, discusses real-world use cases, and serves as an initial guideline for using the benchmark suites.
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- 2022
20. Starting with 24-h levodopa carbidopa intestinal gel at initiation in a large cohort of advanced Parkinson’s disease patients
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Szabolcs Szatmári, József Attila Szász, Károly Orbán-Kis, Simona Bataga, Marius Ciorba, Előd Nagy, Radu Neagoe, István Mihály, Péter Zsombor Szász, Krisztina Kelemen, Attila Frigy, Andrea Csipor-Fodor, and Viorelia Adelina Constantin
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Medicine ,Science - Abstract
Abstract Continuous intra-jejunal infusion of levodopa-carbidopa intestinal gel (LCIG) is a long-term proven and effective treatment in advanced Parkinson’s Disease (APD). Efficacy and safety of 16-h administration of LCIG has already been established. Additional benefits of 24-h LCIG administration have been reported in several case series and small clinical studies. The aim of this retrospective study was to compare the characteristics of patients who needed 24-h LCIG from the beginning of the DAT (device-aided treatment) with those who remained with the standard 16-h LCIG treatment and to identify particular motives if any. We initiated LCIG in 150 patients out of which in case of 62 patients (41,3%) due to unsatisfactory initial clinical benefits continuous 24-h LCIG was deemed necessary. Despite the subjective complaints and more severe clinical condition, at baseline evaluation we found statistically significant differences between 16-h LCIG cohort and 24-h LCIG cohort only in case of incidence of freezing (47% vs 65%, p = 0.03) and sudden off (32% vs 48%, p = 0.04). Wake hours/daytime LCIG does not always sufficiently improve the patient's quality of life in some patients due to persistent nighttime troublesome symptoms. Instead of labeling the patient as a non-responder, it is worth trying the 24-h LCIG dosage in a carefully selected group of patients, as there is currently no consensus on reliable criteria that serve the decision in these patients.
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- 2024
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21. Characteristics of specific training in elite handball players specialized in goalkeeper position
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Ion Mihaila, Mihai - Cătălin Popescu, Xavier Pascual - Fuertes, Daniela - Corina Popescu, Maura Stancu, Alexandru Acsinte, and Constantin Ciorba
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elite athletes ,tests ,physical fitness ,performances ,correlation analysis ,training strategies ,Special aspects of education ,LC8-6691 ,Sports ,GV557-1198.995 - Abstract
Background and Study Aim. Elite handball goalkeepers undergo intensive training for reflexes and advanced techniques. They develop mental toughness to handle the pressure and responsibility at key moments of the game. Thus, they protect the goal of the team. This study aims to investigate and highlight the specific training characteristics of elite handball players specialized in the goalkeeper position. Material and Methods. The best 4 goalkeepers specialized in elite handball in Romania, aged between 22 and 33 years, were selected. Specific motor tests were used: Test 1 - Jumps 15 seconds; Test 2 – Reaction speed to visual stimulus; Test 3 – Execution speed. Technical tests were used: Test specific to goalkeeper, Triangle moving, The Ten Jump, Ball throwing, Standing long jump, Passes to a fixed point; The Cooper test. To improve specific training, there were applied strategies for training optimization which include stretching for mobility, segmental muscle strength, goalkeeping specific exercises and plyometrics. The nonparametric Spearman’s correlation coefficient was used to evaluate the relationship between technical training and motor skills parameters. The statistical significance level was set at p
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- 2024
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22. First-in-Human Assessment of Gut Permeability in Crohn’s Disease Patients Using Fluorophore Technology
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Lori R. Holtz, B. Darren Nix, Sewuese E. Akuse, Carla Hall-Moore, Rodney D. Newberry, Matthew A. Ciorba, Parakkal Deepak, Maria Zulfiqar, Jeng-Jong Shieh, James R. Johnson, I. Rochelle Riley, and Richard B. Dorshow
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Crohn’s Disease ,Dual Sugar Absorption Test ,Fluorescence Tracer Agent ,Intestinal Permeability ,MB-102 ,Relmapirazin ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background and Aims: The dual sugar absorption test as a classic measure of human intestinal permeability has limited clinical utility due to lengthy and cumbersome urine collection, assay variability, and long turnaround. We aimed to determine if the orally administered fluorophore MB-102 (relmapirazin) (molecular weight [MW] = 372) compares to lactulose (L) (MW = 342) and rhamnose (R) (MW = 164)-based dual sugar absorption test as a measure of gut permeability in people with a spectrum of permeability including those with Crohn’s disease (CD). Methods: We performed a single-center, randomized, open-label, crossover study comparing orally administered MB-102 (1.5 or 3.0 mg/kg) to L (1000 mg) and R (200 mg). Adults with active small bowel CD on magnetic resonance enterography (cases) and healthy adults (controls) were randomized to receive either MB-102 or L and R on study day 1, and the other tracer 3 to 7 days later. Urine was collected at baseline and 1, 2, 4, 6, 8, 10, and 12 hours after tracer ingestion to calculate the cumulative urinary percent excretion of MB-102 and L and R. Results: Nine cases and 10 controls completed the study without serious adverse events. Urinary recovery of administered MB-102 correlated with recovery of lactulose (r-squared = 0.83) for all participants. MB-102 urine recovery was also tracked with the L:R ratio urine recovery (r-squared = 0.57). In controls, the percentages of L and MB-102 recovered were similar within a narrow range, unlike in CD patients. Conclusion: This first-in-human study of an orally administered fluorophore to quantify gastrointestinal permeability in adults with CD demonstrates that MB-102 is well tolerated, and its recovery in urine mirrors that of percent L and the L:R ratio.
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- 2024
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23. Cochlear Implantation in Children Affected by Single-Sided Deafness: A Comprehensive Review
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Giuseppe Santopietro, Virginia Fancello, Giuseppe Fancello, Chiara Bianchini, Stefano Pelucchi, and Andrea Ciorba
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children ,single-sided deafness ,cochlear implants ,Otorhinolaryngology ,RF1-547 - Abstract
Children with single-sided deafness (SSD) may experience delays in language and speech development. Reduced speech discrimination and poor sound localization abilities in young SSD patients may result in greater cognitive efforts required to focus and process auditory information, as well as increased listening-related fatigue. Consequently, these children can have a higher risk of academic failure and are often in need of extra help at school. Recently, cochlear implants (CIs) have been introduced as a rehabilitative option for these children, but their effectiveness is still a topic of debate. A literature review was performed according to PRISMA guidelines, searching the Medline database from inception to October 2023. The research identified nine papers that met the inclusion criteria. Data extracted from the selected studies included 311 children affected by SSD and cochlear implants. The reported audiological outcomes were further analyzed. Overall, a high level of satisfaction was described by parents of children with SSD and CI, and those who received a CI under the age of 3 presented better results. However, a proportion of patients did not use the device daily. Our review highlights the possible, and still controversial, role of CI for the hearing rehabilitation of children with unilateral deafness, underlining the need for further research in this field. To date, careful and comprehensive counseling with the child and the family is necessary before considering this option.
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- 2024
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24. LINE-1 global DNA methylation, iron homeostasis genes, sex and age in sudden sensorineural hearing loss (SSNHL)
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Veronica Tisato, Alessandro Castiglione, Andrea Ciorba, Claudia Aimoni, Juliana Araujo Silva, Ines Gallo, Elisabetta D’Aversa, Francesca Salvatori, Chiara Bianchini, Stefano Pelucchi, Paola Secchiero, Giorgio Zauli, Ajay Vikram Singh, and Donato Gemmati
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Epigenomics ,Epigenetics ,Epidrugs ,Iron ,LINE-1 methylation ,Oxidative stress ,Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background Sudden sensorineural hearing loss (SSNHL) is an abrupt loss of hearing, still idiopathic in most of cases. Several mechanisms have been proposed including genetic and epigenetic interrelationships also considering iron homeostasis genes, ferroptosis and cellular stressors such as iron excess and dysfunctional mitochondrial superoxide dismutase activity. Results We investigated 206 SSNHL patients and 420 healthy controls for the following genetic variants in the iron pathway: SLC40A1 − 8CG (ferroportin; FPN1), HAMP − 582AG (hepcidin; HEPC), HFE C282Y and H63D (homeostatic iron regulator), TF P570S (transferrin) and SOD2 A16V in the mitochondrial superoxide dismutase-2 gene. Among patients, SLC40A1 − 8GG homozygotes were overrepresented (8.25% vs 2.62%; P = 0.0015) as well SOD2 16VV genotype (32.0% vs 24.3%; P = 0.037) accounting for increased SSNHL risk (OR = 3.34; 1.54–7.29 and OR = 1.47; 1.02–2.12, respectively). Moreover, LINE-1 methylation was inversely related (r 2 = 0.042; P = 0.001) with hearing loss score assessed as pure tone average (PTA, dB HL), and the trend was maintained after SLC40A1 − 8CG and HAMP − 582AG genotype stratification (Δ SLC40A1 = + 8.99 dB HL and Δ HAMP = − 6.07 dB HL). In multivariate investigations, principal component analysis (PCA) yielded PC1 (PTA, age, LINE-1, HAMP, SLC40A1) and PC2 (sex, HFE C282Y , SOD2, HAMP) among the five generated PCs, and logistic regression analysis ascribed to PC1 an inverse association with moderate/severe/profound HL (OR = 0.60; 0.42–0.86; P = 0.0006) and with severe/profound HL (OR = 0.52; 0.35–0.76; P = 0.001). Conclusion Recognizing genetic and epigenetic biomarkers and their mutual interactions in SSNHL is of great value and can help pharmacy science to design by pharmacogenomic data classical or advanced molecules, such as epidrugs, to target new pathways for a better prognosis and treatment of SSNHL.
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- 2023
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25. Inflammatory bowel diseases 2024
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Ciorba, Matthew A.
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- 2024
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26. Phytochemical and Functional Properties of Fruit and Vegetable Processing By-Products
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Roberto Ciccoritti, Roberto Ciorba, Danilo Ceccarelli, Monica Amoriello, and Tiziana Amoriello
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nutritional composition ,bioactive compounds ,phenolics ,flavonoids ,pigments ,antioxidant capacity ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Processing sustainability and the concept of zero waste discharge are of great interest for many industries. Every year, fruit and vegetable processing industries generate huge amounts of by-products, which are often intended for animal feed or discarded as waste, posing a problem to both environmental and economic points of view. However, to minimize the waste burden, the valorization of these residues received increased interest. In fact, fruit and vegetable by-products are an excellent source of valuable compounds, such as proteins, dietary fibers, lipids, minerals, vitamins, phenolic acids, flavonoids, anthocyanins, carotenoids, and pigments, which can be recovered and reused, creating new business prospects from a circular economy perspective. Understanding the chemical characteristics of these materials is a key concern for their valorization and the identification of their most appropriate intended use. In this study, the phytochemical and functional properties of fruit and vegetable processing by-products (peel and pomace) were investigated. Samples of different plants (i.e., apple, black and orange carrot, cucumber, kumquat, mango, parsnip, peach, black plum) were analyzed using chemical analytical methods and characterized using Fourier Transform Mid-Infrared spectroscopy (FT-MIR). The results highlighted their high nutritional composition in terms of protein, lipids, fiber, and ash, as well as bioactive and antioxidant profiles. These characteristics make these residues suitable as natural ingredients for the development of high-added-value products in food, cosmetic, and pharmaceutical industries.
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- 2024
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27. Longevity of Artifacts in Leading Parallel and Distributed Systems Conferences: a Review of the State of the Practice in 2023.
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Quentin Guilloteau, Florina M. Ciorba, Millian Poquet, Dorian Goepp, and Olivier Richard
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- 2024
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28. An Execution Fingerprint Dictionary for HPC Application Recognition
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Jakobsche, Thomas, Lachiche, Nicolas, Cavelan, Aurélien, and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Applications running on HPC systems waste time and energy if they: (a) use resources inefficiently, (b) deviate from allocation purpose (e.g. cryptocurrency mining), or (c) encounter errors and failures. It is important to know which applications are running on the system, how they use the system, and whether they have been executed before. To recognize known applications during execution on a noisy system, we draw inspiration from the way Shazam recognizes known songs playing in a crowded bar. Our contribution is an Execution Fingerprint Dictionary (EFD) that stores execution fingerprints of system metrics (keys) linked to application and input size information (values) as key-value pairs for application recognition. Related work often relies on extensive system monitoring (many system metrics collected over large time windows) and employs machine learning methods to identify applications. Our solution only uses the first 2 minutes and a single system metric to achieve F-scores above 95 percent, providing comparable results to related work but with a fraction of the necessary data and a straightforward mechanism of recognition.
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- 2021
29. LINE-1 global DNA methylation, iron homeostasis genes, sex and age in sudden sensorineural hearing loss (SSNHL)
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Tisato, Veronica, Castiglione, Alessandro, Ciorba, Andrea, Aimoni, Claudia, Silva, Juliana Araujo, Gallo, Ines, D’Aversa, Elisabetta, Salvatori, Francesca, Bianchini, Chiara, Pelucchi, Stefano, Secchiero, Paola, Zauli, Giorgio, Singh, Ajay Vikram, and Gemmati, Donato
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- 2023
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30. Calpain-2 mediates SARS-CoV-2 entry via regulating ACE2 levels
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Qiru Zeng, Avan Antia, Luis Alberto Casorla-Perez, Maritza Puray-Chavez, Sebla B. Kutluay, Matthew A. Ciorba, and Siyuan Ding
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SARS-CoV-2 ,viral entry ,antivirals ,Microbiology ,QR1-502 - Abstract
ABSTRACT Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, much effort has been dedicated to identifying effective antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A number of calpain inhibitors show excellent antiviral activities against SARS-CoV-2 by targeting the viral main protease (Mpro), which plays an essential role in processing viral polyproteins. In this study, we found that calpain inhibitors potently inhibited the infection of a chimeric vesicular stomatitis virus (VSV) encoding the SARS-CoV-2 spike protein but not Mpro. In contrast, calpain inhibitors did not exhibit antiviral activities toward the wild-type VSV with its native glycoprotein. Genetic knockout of calpain-2 by CRISPR/Cas9 conferred resistance of the host cells to the chimeric VSV-SARS-CoV-2 virus and a clinical isolate of wild-type SARS-CoV-2. Mechanistically, calpain-2 facilitates SARS-CoV-2 spike protein-mediated cell attachment by positively regulating the cell surface levels of ACE2. These results highlight an Mpro-independent pathway targeted by calpain inhibitors for efficient viral inhibition. We also identify calpain-2 as a novel host factor and a potential therapeutic target responsible for SARS-CoV-2 infection at the entry step.IMPORTANCEMany efforts in small-molecule screens have been made to counter SARS-CoV-2 infection by targeting the viral main protease, the major element that processes viral proteins after translation. Here, we discovered that calpain inhibitors further block SARS-CoV-2 infection in a main protease-independent manner. We identified the host cysteine protease calpain-2 as an important positive regulator of the cell surface levels of SARS-CoV-2 cellular receptor ACE2 and, thus, a facilitator of viral infection. By either pharmacological inhibition or genetic knockout of calpain-2, the SARS-CoV-2 binding to host cells is blocked and viral infection is decreased. Our findings highlight a novel mechanism of ACE2 regulation, which presents a potential new therapeutic target. Since calpain inhibitors also potently interfere with the viral main protease, our data also provide a mechanistic understanding of the potential use of calpain inhibitors as dual inhibitors (entry and replication) in the clinical setting of COVID-19 diseases. Our findings bring mechanistic insights into the cellular process of SARS-CoV-2 entry and offer a novel explanation to the mechanism of activities of calpain inhibitors.
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- 2024
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31. Introductory Chapter: A Short Excursus into the Realm of Cochlear Implants Today
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Ciorba, Andrea, primary, H. Skarzynski, Piotr, additional, and Hatzopoulos, Stavros, additional
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- 2023
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32. LB4OMP: A Dynamic Load Balancing Library for Multithreaded Applications
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Korndörfer, Jonas H. Müller, Eleliemy, Ahmed, Mohammed, Ali, and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Exascale computing systems will exhibit high degrees of hierarchical parallelism, with thousands of computing nodes and hundreds of cores per node. Efficiently exploiting hierarchical parallelism is challenging due to load imbalance that arises at multiple levels. OpenMP is the most widely-used standard for expressing and exploiting the ever-increasing node-level parallelism. The scheduling options in OpenMP are insufficient to address the load imbalance that arises during the execution of multithreaded applications. The limited scheduling options in OpenMP hinder research on novel scheduling techniques which require comparison with others from the literature. This work introduces LB4OMP, an open-source dynamic load balancing library that implements successful scheduling algorithms from the literature. LB4OMP is a research infrastructure designed to spur and support present and future scheduling research, for the benefit of multithreaded applications performance. Through an extensive performance analysis campaign, we assess the effectiveness and demystify the performance of all loop scheduling techniques in the library. We show that, for numerous applications-systems pairs, the scheduling techniques in LB4OMP outperform the scheduling options in OpenMP. Node-level load balancing using LB4OMP leads to reduced cross-node load imbalance and to improved MPI+OpenMP applications performance, which is critical for Exascale computing.
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- 2021
33. Oversewing and Gastropexy in Laparoscopic Sleeve Gastrectomy – Two Futile Steps of the Procedure? An Observational Case-Control Study
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Sala, Daniela T., Fodor, Stefania R., Voidăzan, Septimiu, Tilinca, Mariana C., Gomotîrceanu, Adriana M., Puiac, Ion C., Ciorba, Marius I., Moriczi, Renata, Kiss, Botond I., Ion, Razvan M., Calin, Constantin, and Neagoe, Radu Mircea
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- 2023
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34. Risk of Major Adverse Cardiovascular Events in Immune-Mediated Inflammatory Disorders on Biologics and Small Molecules: Network Meta-Analysis
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Mattay, Shivani Shah, Zamani, Mohammad, Saturno, Dany, Loftus, Edward V., Jr., Ciorba, Matthew A., Yarur, Andres, Singh, Siddharth, and Deepak, Parakkal
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- 2024
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35. A Resourceful Coordination Approach for Multilevel Scheduling
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Eleliemy, Ahmed and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
HPC users aim to improve their execution times without particular regard for increasing system utilization. On the contrary, HPC operators favor increasing the number of executed applications per time unit and increasing system utilization. This difference in the preferences promotes the following operational model. Applications execute on exclusively-allocated computing resources for a specific time and applications are assumed to utilize the allocated resources efficiently. In many cases, this operational model is inefficient, i.e., applications may not fully utilize their allocated resources. This inefficiency results in increasing application execution time and decreasing system utilization. In this work, we propose a resourceful coordination approach (RCA) that enables the cooperation between, currently independent, batch- and application-level schedulers. RCA enables application schedulers to share their allocated but idle computing resources with other applications through the batch system. The effective system performance (ESP) benchmark is used to assess the proposed approach. The results show that RCA increased system utilization up to 12.6% and decreased system makespan by the same percent without affecting applications' performance.
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- 2021
36. A Distributed Chunk Calculation Approach for Self-scheduling of Parallel Applications on Distributed-memory Systems
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Eleliemy, Ahmed and Ciorba, Florina M.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Loop scheduling techniques aim to achieve load-balanced executions of scientific applications. Dynamic loop self-scheduling (DLS) libraries for distributed-memory systems are typically MPI-based and employ a centralized chunk calculation approach (CCA) to assign variably-sized chunks of loop iterations. We present a distributed chunk calculation approach (DCA) that supports various types of DLS techniques. Using both CCA and DCA, twelve DLS techniques are implemented and evaluated in different CPU slowdown scenarios. The results show that the DLS techniques implemented using DCA outperform their corresponding ones implemented with CCA, especially in extreme system slowdown scenarios.
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- 2021
37. Particularities of Cataract Surgery in Elderly Patients: Corneal Structure and Endothelial Morphological Changes after Phacoemulsification
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Adela Laura Ciorba, Alin Teusdea, George Roiu, and Daniela Simona Cavalu
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phacoemulsification ,specular microscopy ,cell density ,corneal endothelial morphology ,central corneal thickness ,cataract ,Geriatrics ,RC952-954.6 - Abstract
The aim of this study was to evaluate the influence of ultrasounds used in phacoemulsification during cataract surgery on the corneal structure and morphology in patients over 65 years. We compared the outcomes of phacoemulsification techniques in terms of corneal cell morphology in 77 patients over 65 years old and 43 patients under 65 years old. Corneal cell density, central corneal thickness and hexagonality were measured preoperatively and post-surgery (at 1 and 4 weeks) by specular microscopy. The effect of gender, axial length and anterior chamber depth on the parameters of corneal endothelium were evaluated. In both groups, a progressive decrease in endothelial cells was observed, starting from the first week post-surgery until the fourth postoperative week. The central corneal thickness increased in both groups with maximum values at the first week postoperatively, while their initial values were restored in the fourth week post-surgery, with no statistical difference between groups. Statistically significant differences were noticed in terms of cell hexagonality in the group over 65, showing smaller hexagonality at all preoperative and postoperative time points compared to group under 65. Our result highlights the importance of routine specular microscopy performed before surgery, regardless the age of the patients, with caution and careful attention to the phaco power intensity, ultrasound energy consumption and intraoperative manipulation of instruments, as well as proper use of viscoelastic substances to reduce corneal endothelium damage, especially in elderly patients.
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- 2024
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38. Autonomy Loops for Monitoring, Operational Data Analytics, Feedback, and Response in HPC Operations.
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Francieli Boito, Jim M. Brandt, Valeria Cardellini, Philip H. Carns, Florina M. Ciorba, Hilary Egan, Ahmed Eleliemy, Ann C. Gentile, Thomas Gruber, Jeff Hanson, Utz-Uwe Haus, Kevin A. Huck, Thomas Ilsche, Thomas Jakobsche, Terry R. Jones, Sven Karlsson, Abdullah Mueen, Michael Ott 0001, Tapasya Patki, Ivy Peng, Krishnan Raghavan, Stephen Simms, Kathleen Shoga, Michael T. Showerman, Devesh Tiwari, Torsten Wilde, and Keiji Yamamoto
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- 2023
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39. Cornerstone: Octree Construction Algorithms for Scalable Particle Simulations.
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Sebastian Keller, Aurélien Cavelan, Rubén M. Cabezón, Lucio Mayer, and Florina M. Ciorba
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- 2023
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40. Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.
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Wael R. Elwasif, William F. Godoy, Nick Hagerty, James Austin Harris, Oscar R. Hernandez, Bálint Joó, Paul R. C. Kent, Damien Lebrun-Grandié, Elijah A. MacCarthy, Verónica G. Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei I. Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan, René Widera, Spencer H. Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey Young 0001, Sunita Chandrasekaran, Florina M. Ciorba, Osman Simsek, Kate Clark, Filippo Spiga, Jeff R. Hammond, John E. Stone, David J. Hardy, Sebastian Keller, Jean-Guillaume Piccinali, and Christian Trott
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- 2023
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41. How Do OS and Application Schedulers Interact? An Investigation with Multithreaded Applications.
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Jonas H. Müller Korndörfer, Ahmed Eleliemy, Osman Seckin Simsek, Thomas Ilsche, Robert Schöne, and Florina M. Ciorba
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- 2023
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42. DAPHNE Runtime: Harnessing Parallelism for Integrated Data Analysis Pipelines.
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Aristotelis Vontzalidis, Stratos Psomadakis, Constantinos Bitsakos, Mark Dokter, Kevin Innerebner, Patrick Damme, Matthias Boehm 0001, Florina M. Ciorba, Ahmed Eleliemy, Vasileios Karakostas, Ales Zamuda, and Dimitrios Tsoumakos
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- 2023
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43. Accurate Measurement of Application-level Energy Consumption for Energy-Aware Large-Scale Simulations.
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Osman Seckin Simsek, Jean-Guillaume Piccinali, and Florina M. Ciorba
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- 2023
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44. Hot-n-Cold: Mapping the Syscall Attack Surface Using Thermal Side Channels.
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Teodora Vasilas, Thomas Jakobsche, and Florina M. Ciorba
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- 2023
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45. Investigating HPC Job Resource Requests and Job Efficiency Reporting.
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Thomas Jakobsche, Nicolas Lachiche, and Florina M. Ciorba
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- 2023
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46. DaphneSched: A Scheduler for Integrated Data Analysis Pipelines.
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Ahmed Eleliemy and Florina M. Ciorba
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- 2023
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47. Automated Scheduling Algorithm Selection in OpenMP.
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Florina M. Ciorba, Ali Mohammed, Jonas H. Müller Korndörfer, and Ahmed Eleliemy
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- 2023
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48. How Do OS and Application Schedulers Interact? An Investigation with Multithreaded Applications
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Korndörfer, Jonas H. Müller, Eleliemy, Ahmed, Simsek, Osman Seckin, Ilsche, Thomas, Schöne, Robert, Ciorba, Florina M., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cano, José, editor, Dikaiakos, Marios D., editor, Papadopoulos, George A., editor, Pericàs, Miquel, editor, and Sakellariou, Rizos, editor
- Published
- 2023
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49. Effect of Immunosuppression on the Immunogenicity of mRNA Vaccines to SARS-CoV-2
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Deepak, Parakkal, Kim, Wooseob, Paley, Michael A, Yang, Monica, Carvidi, Alexander B, Demissie, Emanuel G, El-Qunni, Alia A, Haile, Alem, Huang, Katherine, Kinnett, Baylee, Liebeskind, Mariel J, Liu, Zhuoming, McMorrow, Lily E, Paez, Diana, Pawar, Niti, Perantie, Dana C, Schriefer, Rebecca E, Sides, Shannon E, Thapa, Mahima, Gergely, Maté, Abushamma, Suha, Akuse, Sewuese, Klebert, Michael, Mitchell, Lynne, Nix, Darren, Graf, Jonathan, Taylor, Kimberly E, Chahin, Salim, Ciorba, Matthew A, Katz, Patricia, Matloubian, Mehrdad, O'Halloran, Jane A, Presti, Rachel M, Wu, Gregory F, Whelan, Sean PJ, Buchser, William J, Gensler, Lianne S, Nakamura, Mary C, Ellebedy, Ali H, and Kim, Alfred HJ
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Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Research ,Prevention ,Rare Diseases ,Emerging Infectious Diseases ,Immunization ,Vaccine Related ,3.4 Vaccines ,Prevention of disease and conditions ,and promotion of well-being ,Good Health and Well Being ,Public Health and Health Services - Abstract
BackgroundPatients with chronic inflammatory disease (CID) treated with immunosuppressive medications have increased risk for severe COVID-19. Although mRNA-based SARS-CoV-2 vaccination provides protection in immunocompetent persons, immunogenicity in immunosuppressed patients with CID is unclear.ObjectiveTo determine the immunogenicity of mRNA-based SARS-CoV-2 vaccines in patients with CID.DesignProspective observational cohort study.SettingTwo U.S. CID referral centers.ParticipantsVolunteer sample of adults with confirmed CID eligible for early COVID-19 vaccination, including hospital employees of any age and patients older than 65 years. Immunocompetent participants were recruited separately from hospital employees. All participants received 2 doses of mRNA vaccine against SARS-CoV-2 between 10 December 2020 and 20 March 2021. Participants were assessed within 2 weeks before vaccination and 20 days after final vaccination.MeasurementsAnti-SARS-CoV-2 spike (S) IgG+ binding in all participants, and neutralizing antibody titers and circulating S-specific plasmablasts in a subset to assess humoral response after vaccination.ResultsMost of the 133 participants with CID (88.7%) and all 53 immunocompetent participants developed antibodies in response to mRNA-based SARS-CoV-2 vaccination, although some with CID developed numerically lower titers of anti-S IgG. Anti-S IgG antibody titers after vaccination were lower in participants with CID receiving glucocorticoids (n = 17) than in those not receiving them; the geometric mean of anti-S IgG antibodies was 357 (95% CI, 96 to 1324) for participants receiving prednisone versus 2190 (CI, 1598 to 3002) for those not receiving it. Anti-S IgG antibody titers were also lower in those receiving B-cell depletion therapy (BCDT) (n = 10). Measures of immunogenicity differed numerically between those who were and those who were not receiving antimetabolites (n = 48), tumor necrosis factor inhibitors (n = 39), and Janus kinase inhibitors (n = 11); however, 95% CIs were wide and overlapped. Neutralization titers seemed generally consistent with anti-S IgG results. Results were not adjusted for differences in baseline clinical factors, including other immunosuppressant therapies.LimitationsSmall sample that lacked demographic diversity, and residual confounding.ConclusionCompared with nonusers, patients with CID treated with glucocorticoids and BCDT seem to have lower SARS-CoV-2 vaccine-induced antibody responses. These preliminary findings require confirmation in a larger study.Primary funding sourceThe Leona M. and Harry B. Helmsley Charitable Trust, Marcus Program in Precision Medicine Innovation, National Center for Advancing Translational Sciences, and National Institute of Arthritis and Musculoskeletal and Skin Diseases.
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- 2021
50. Yield of Serial Testing for Tuberculosis Exposure in Patients With Inflammatory Bowel Diseases: One Test is Not Enough
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Kaur, Manreet, Dassopoulos, Themistocles, Snapper, Scott B., Korzenik, Joshua R., Bohm, Matthew, Raffals, Laura, Poonam, Beniwal-Patel, Hudesman, David, Russ, Kirk, Brook, Loren, Pekow, Joel, Cross, Raymond, Wong, Uni, Bishu, Shrinivas, Bewtra, Meenakshi, Lewis, James D., Duerr, Richard, Saha, Sumona, Caldera, Freddy, Scoville, Elizabeth, Deepak, Parakkal, Ciorba, Matthew, and Lapp, Sean L.
- Published
- 2024
- Full Text
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