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  1. Article: Computational methods for biofabrication in tissue engineering and regenerative medicine - a literature review.

    Bardini, Roberta / Di Carlo, Stefano

    Computational and structural biotechnology journal

    2024  Volume 23, Page(s) 601–616

    Abstract: This literature review rigorously examines the growing scientific interest in computational methods for Tissue Engineering and Regenerative Medicine biofabrication, a leading-edge area in biomedical innovation, emphasizing the need for accurate, multi- ... ...

    Abstract This literature review rigorously examines the growing scientific interest in computational methods for Tissue Engineering and Regenerative Medicine biofabrication, a leading-edge area in biomedical innovation, emphasizing the need for accurate, multi-stage, and multi-component biofabrication process models. The paper presents a comprehensive bibliometric and contextual analysis, followed by a literature review, to shed light on the vast potential of computational methods in this domain. It reveals that most existing methods focus on single biofabrication process stages and components, and there is a significant gap in approaches that utilize accurate models encompassing both biological and technological aspects. This analysis underscores the indispensable role of these methods in understanding and effectively manipulating complex biological systems and the necessity for developing computational methods that span multiple stages and components. The review concludes that such comprehensive computational methods are essential for developing innovative and efficient Tissue Engineering and Regenerative Medicine biofabrication solutions, driving forward advancements in this dynamic and evolving field.
    Language English
    Publishing date 2024-01-02
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.12.035
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cross-Omic Transcription Factor Analysis: An Insight on Transcription Factor Accessibility and Expression Correlation.

    Martini, Lorenzo / Bardini, Roberta / Savino, Alessandro / Di Carlo, Stefano

    Genes

    2024  Volume 15, Issue 3

    Abstract: It is well known how sequencing technologies propelled cellular biology research in recent years, providing incredible insight into the basic mechanisms of cells. Single-cell RNA sequencing is at the front in this field, with single-cell ATAC sequencing ... ...

    Abstract It is well known how sequencing technologies propelled cellular biology research in recent years, providing incredible insight into the basic mechanisms of cells. Single-cell RNA sequencing is at the front in this field, with single-cell ATAC sequencing supporting it and becoming more popular. In this regard, multi-modal technologies play a crucial role, allowing the possibility to simultaneously perform the mentioned sequencing modalities on the same cells. Yet, there still needs to be a clear and dedicated way to analyze these multi-modal data. One of the current methods is to calculate the Gene Activity Matrix (GAM), which summarizes the accessibility of the genes at the genomic level, to have a more direct link with the transcriptomic data. However, this concept is not well defined, and it is unclear how various accessible regions impact the expression of the genes. Moreover, the transcription process is highly regulated by the transcription factors that bind to the different DNA regions. Therefore, this work presents a continuation of the meta-analysis of Genomic-Annotated Gene Activity Matrix (GAGAM) contributions, aiming to investigate the correlation between the TF expression and motif information in the different functional genomic regions to understand the different Transcription Factors (TFs) dynamics involved in different cell types.
    MeSH term(s) Transcription Factors/genetics ; Transcription Factors/metabolism ; Gene Expression Regulation/genetics ; DNA/metabolism ; Genomics ; Genome
    Chemical Substances Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2024-02-21
    Publishing country Switzerland
    Document type Meta-Analysis ; Journal Article
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes15030268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.

    Giannantoni, Leonardo / Bardini, Roberta / Savino, Alessandro / Di Carlo, Stefano

    BMC bioinformatics

    2024  Volume 25, Issue 1, Page(s) 166

    Abstract: Background: The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to ... ...

    Abstract Background: The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems.
    Results: BiSDL's effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers.
    Conclusions: BiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.
    MeSH term(s) Synthetic Biology/methods ; Models, Biological ; Programming Languages ; Systems Biology/methods ; Software
    Language English
    Publishing date 2024-04-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-024-05782-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Spiker+

    Carpegna, Alessio / Savino, Alessandro / Di Carlo, Stefano

    a framework for the generation of efficient Spiking Neural Networks FPGA accelerators for inference at the edge

    2024  

    Abstract: Including Artificial Neural Networks in embedded systems at the edge allows applications to exploit Artificial Intelligence capabilities directly within devices operating at the network periphery. This paper introduces Spiker+, a comprehensive framework ... ...

    Abstract Including Artificial Neural Networks in embedded systems at the edge allows applications to exploit Artificial Intelligence capabilities directly within devices operating at the network periphery. This paper introduces Spiker+, a comprehensive framework for generating efficient, low-power, and low-area customized Spiking Neural Networks (SNN) accelerators on FPGA for inference at the edge. Spiker+ presents a configurable multi-layer hardware SNN, a library of highly efficient neuron architectures, and a design framework, enabling the development of complex neural network accelerators with few lines of Python code. Spiker+ is tested on two benchmark datasets, the MNIST and the Spiking Heidelberg Digits (SHD). On the MNIST, it demonstrates competitive performance compared to state-of-the-art SNN accelerators. It outperforms them in terms of resource allocation, with a requirement of 7,612 logic cells and 18 Block RAMs (BRAMs), which makes it fit in very small FPGA, and power consumption, draining only 180mW for a complete inference on an input image. The latency is comparable to the ones observed in the state-of-the-art, with 780us/img. To the authors' knowledge, Spiker+ is the first SNN accelerator tested on the SHD. In this case, the accelerator requires 18,268 logic cells and 51 BRAM, with an overall power consumption of 430mW and a latency of 54 us for a complete inference on input data. This underscores the significance of Spiker+ in the hardware-accelerated SNN landscape, making it an excellent solution to deploy configurable and tunable SNN architectures in resource and power-constrained edge applications.
    Keywords Computer Science - Neural and Evolutionary Computing ; Computer Science - Artificial Intelligence ; Computer Science - Hardware Architecture
    Subject code 006
    Publishing date 2024-01-02
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Current highlights on solid pseudopapillary neoplasm of the pancreas.

    Sibio, Simone / Di Carlo, Sara

    World journal of hepatology

    2021  Volume 14, Issue 1, Page(s) 300–303

    Abstract: Solid pseudopapillary neoplasm of the pancreas is a low-grade malignant tumor that predominantly affects young women in their third and fourth decade. Etiology and risk factors are unknown. Clinical symptoms are aspecific and most commonly due to mass ... ...

    Abstract Solid pseudopapillary neoplasm of the pancreas is a low-grade malignant tumor that predominantly affects young women in their third and fourth decade. Etiology and risk factors are unknown. Clinical symptoms are aspecific and most commonly due to mass effect. Diagnosis is made by computed tomography scan or magnetic resonance imaging and histological characterization is obtained by endoscopic ultrasound-guided fine needle biopsy. Microscopically, these lesions are composed by both solid and pseudopapillary structures with necrotic and hemorrhagic areas. Occasionally, the biological behavior is aggressive with tumor recurrence and distant metastasis. Usually, curative R0 surgical resection is the best option able to provide long term survival even in advanced disease. Unresectable disease is the main predictor of poor prognosis. Chemotherapy and radiotherapy regimens are not well standardized. However, they could be effective in reducing tumor size as neoadjuvant treatment or disease control in palliative setting. Although complete surgical resection provides a cure rate of > 95%, considering young age of the patients and morbidity associated to pancreatic surgery, further studies are needed to better investigate risk factors and responsiveness to hormones in order to allow early diagnosis and follow up strategies that could avoid unnecessary surgery in less aggressive disease.
    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2573703-X
    ISSN 1948-5182
    ISSN 1948-5182
    DOI 10.4254/wjh.v14.i1.300
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: Chapter Design Issues and Challenges of File Systems for Flash Memories

    Di Carlo, Stefano / Cramia, M. / Prinetto, Paolo / Fabiano, Michele

    2011  

    Keywords Biotechnology ; Technology, engineering, agriculture
    Size 1 Online-Ressource
    Publisher InTechOpen
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021047713
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  7. Article: Pregnancy in Glomerular Disease: From Risk Identification to Counseling and Management.

    Maressa, Veronica / Longhitano, Elisa / Casuscelli, Chiara / Di Carlo, Silvia / Peritore, Luigi / Santoro, Domenico

    Journal of clinical medicine

    2024  Volume 13, Issue 6

    Abstract: ... ...

    Abstract Background
    Language English
    Publishing date 2024-03-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm13061693
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  8. Article ; Online: Pediatric growth hormone deficiency: Understanding the patient and caregiver perspectives.

    Miller, Bradley S / Kelepouris, Nicky / Tenenbaum, Harlan / Di Carlo, Sonia / Backeljauw, Philippe

    Growth hormone & IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society

    2024  Volume 76, Page(s) 101592

    Abstract: Childhood growth hormone deficiency (GHD) is a rare disorder associated with significant burden on both patients and caregivers. Although previous reports have detailed aspects of the burden experienced by patients and their caregivers, there is a ... ...

    Abstract Childhood growth hormone deficiency (GHD) is a rare disorder associated with significant burden on both patients and caregivers. Although previous reports have detailed aspects of the burden experienced by patients and their caregivers, there is a paucity of first-hand information on the patient and caregiver journeys from their respective voices. To address this need, an advisory board meeting was conducted on September 30, 2022, with 4 pediatric patients with GHD and their caregivers to discuss their experiences prior to GHD diagnosis, during the diagnostic process, and during ongoing treatment with recombinant growth hormone. Feedback from patients and caregivers was reviewed by pediatric endocrinologists, who provided their own perspectives on the patient and caregiver journeys based on the information reported. Despite the small sample size, important insights were obtained: patients and caregivers reported remarkable growth benefits achieved with treatment, which provided strong motivation to remain adherent to daily injection regimens. Patient and caregiver accounts reflected wide variability between families in time from suspicion to diagnosis and in treatment challenges faced, ranging from practical issues such as handling and administration of medication to broader concerns about treatment access and continuity, as well as key knowledge gaps among patients, caregivers, and clinicians. Recommendations are provided to enhance the patient and caregiver journeys, including increasing development and availability of educational materials, providing opportunities for patient advocacy by clinicians and health care providers, and encouraging institutional improvements to ensure that patients continue to receive uninterrupted treatment during their critical period of growth.
    Language English
    Publishing date 2024-04-16
    Publishing country Scotland
    Document type Journal Article
    ZDB-ID 1436781-6
    ISSN 1532-2238 ; 1096-6374
    ISSN (online) 1532-2238
    ISSN 1096-6374
    DOI 10.1016/j.ghir.2024.101592
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    In stock of ZB MED Cologne/Königswinter

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  9. Book ; Online: A Micro Architectural Events Aware Real-Time Embedded System Fault Injector

    Magliano, Enrico / Carpegna, Alessio / Savino, Alessadro / Di Carlo, Stefano

    2024  

    Abstract: In contemporary times, the increasing complexity of the system poses significant challenges to the reliability, trustworthiness, and security of the SACRES. Key issues include the susceptibility to phenomena such as instantaneous voltage spikes, ... ...

    Abstract In contemporary times, the increasing complexity of the system poses significant challenges to the reliability, trustworthiness, and security of the SACRES. Key issues include the susceptibility to phenomena such as instantaneous voltage spikes, electromagnetic interference, neutron strikes, and out-of-range temperatures. These factors can induce switch state changes in transistors, resulting in bit-flipping, soft errors, and transient corruption of stored data in memory. The occurrence of soft errors, in turn, may lead to system faults that can propel the system into a hazardous state. Particularly in critical sectors like automotive, avionics, or aerospace, such malfunctions can have real-world implications, potentially causing harm to individuals. This paper introduces a novel fault injector designed to facilitate the monitoring, aggregation, and examination of micro-architectural events. This is achieved by harnessing the microprocessor's PMU and the debugging interface, specifically focusing on ensuring the repeatability of fault injections. The fault injection methodology targets bit-flipping within the memory system, affecting CPU registers and RAM. The outcomes of these fault injections enable a thorough analysis of the impact of soft errors and establish a robust correlation between the identified faults and the essential timing predictability demanded by SACRES.
    Keywords Computer Science - Hardware Architecture ; Computer Science - Artificial Intelligence
    Publishing date 2024-01-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: GM-CSF suppresses antioxidant signaling and drives IL-1β secretion through NRF2 downregulation.

    Di Carlo, Sara / Häcker, Georg / Gentle, Ian E

    EMBO reports

    2022  Volume 23, Issue 8, Page(s) e54226

    Abstract: GM-CSF is a potent inflammatory cytokine regulating myeloid cell differentiation, hematopoiesis, and various other functions. It is functionally associated with a number of inflammatory pathologies including rheumatoid arthritis and inflammatory bowel ... ...

    Abstract GM-CSF is a potent inflammatory cytokine regulating myeloid cell differentiation, hematopoiesis, and various other functions. It is functionally associated with a number of inflammatory pathologies including rheumatoid arthritis and inflammatory bowel disease. GM-CSF has been found to promote NLRP3-dependent IL-1β secretion, which may have a significant role in driving inflammatory pathologies. However, the molecular mechanisms remain unknown. Here, we show that GM-CSF induces IL-1β secretion through a ROS-dependent pathway. TNF is required for reactive oxygen species (ROS) generation that strikingly does not promote NLRP3 activation, but instead drives ubiquitylation of IL-1β, promoting its cleavage through basal NRLP3 activity. GM-CSF regulates this pathway through suppression of antioxidant responses via preventing upregulation of NRF2. Thus, the pro-inflammatory effect of GM-CSF on IL-1β is through suppression of antioxidant responses, which leads to ubiquitylation of IL-1β and enhanced processing. This study highlights the role of metabolic regulation of inflammatory signaling and reveals a novel mechanism for GM-CSF to promote inflammation.
    MeSH term(s) Antioxidants/pharmacology ; Cells, Cultured ; Down-Regulation ; Granulocyte-Macrophage Colony-Stimulating Factor/genetics ; Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Inflammasomes/metabolism ; Interleukin-1beta/genetics ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; Reactive Oxygen Species/metabolism
    Chemical Substances Antioxidants ; Inflammasomes ; Interleukin-1beta ; NF-E2-Related Factor 2 ; NLR Family, Pyrin Domain-Containing 3 Protein ; Reactive Oxygen Species ; Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1)
    Language English
    Publishing date 2022-06-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202154226
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5433: Show issues Location:
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